Saliva diagnostics – Current views and directions

PubMed Central

Kaczor-Urbanowicz, Karolina Elżbieta; Martin Carreras-Presas, Carmen; Aro, Katri; Tu, Michael; Wong, David TW

2016-01-01

In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a “mirror of the body,” can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term “Salivaomics” aimed to highlight the rapid development of knowledge about various “omics” constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome. In the last few years, researchers have developed new technologies and validated a wide range of salivary biomarkers that will soon make the use of saliva a clinical reality. However, a great need still exists for convenient and accurate point-of-care devices that can serve as a non-invasive diagnostic tool. In addition, there is an urgent need to decipher the scientific rationale and mechanisms that convey systemic diseases to saliva. Another promising technology called liquid biopsy enables detection of circulating tumor cells (CTCs) and fragments of tumor DNA in saliva, thus enabling non-invasive early detection of various cancers. The newly developed technology—electric field-induced release and measurement (EFIRM) provides near perfect detection of actionable mutations in lung cancer patients. These recent advances widened the salivary diagnostic approach from the oral cavity to the whole physiological system, and thus point towards a promising future of salivary diagnostics for personalized individual medicine applications including clinical decisions and post-treatment outcome predictions. Impact statement The purpose of this mini-review is to make an update about the present and future applications of saliva as a diagnostic biofluid in many fields of science such

Serum Metabolomic Profiling in Acute Alcoholic Hepatitis Identifies Multiple Dysregulated Pathways

PubMed Central

Rachakonda, Vikrant; Gabbert, Charles; Raina, Amit; Bell, Lauren N.; Cooper, Sara; Malik, Shahid; Behari, Jaideep

2014-01-01

Background and Objectives While animal studies have implicated derangements of global energy homeostasis in the pathogenesis of acute alcoholic hepatitis (AAH), the relevance of these findings to the development of human AAH remains unclear. Using global, unbiased serum metabolomics analysis, we sought to characterize alterations in metabolic pathways associated with severe AAH and identify potential biomarkers for disease prognosis. Methods This prospective, case-control study design included 25 patients with severe AAH and 25 ambulatory patients with alcoholic cirrhosis. Serum samples were collected within 24 hours of the index clinical encounter. Global, unbiased metabolomics profiling was performed. Patients were followed for 180 days after enrollment to determine survival. Results Levels of 234 biochemicals were altered in subjects with severe AAH. Random-forest analysis, principal component analysis, and integrated hierarchical clustering methods demonstrated that metabolomics profiles separated the two cohorts with 100% accuracy. Severe AAH was associated with enhanced triglyceride lipolysis, impaired mitochondrial fatty acid beta oxidation, and upregulated omega oxidation. Low levels of multiple lysolipids and related metabolites suggested decreased plasma membrane remodeling in severe AAH. While most measured bile acids were increased in severe AAH, low deoxycholate and glycodeoxycholate levels indicated intestinal dysbiosis. Several changes in substrate utilization for energy homeostasis were identified in severe AAH, including increased glucose consumption by the pentose phosphate pathway, altered tricarboxylic acid (TCA) cycle activity, and enhanced peptide catabolism. Finally, altered levels of small molecules related to glutathione metabolism and antioxidant vitamin depletion were observed in patients with severe AAH. Univariable logistic regression revealed 15 metabolites associated with 180-day survival in severe AAH. Conclusion Severe AAH is

Identifying biomarkers for asthma diagnosis using targeted metabolomics approaches.

PubMed

Checkley, William; Deza, Maria P; Klawitter, Jost; Romero, Karina M; Klawitter, Jelena; Pollard, Suzanne L; Wise, Robert A; Christians, Uwe; Hansel, Nadia N

2016-12-01

The diagnosis of asthma in children is challenging and relies on a combination of clinical factors and biomarkers including methacholine challenge, lung function, bronchodilator responsiveness, and presence of airway inflammation. No single test is diagnostic. We sought to identify a pattern of inflammatory biomarkers that was unique to asthma using a targeted metabolomics approach combined with data science methods. We conducted a nested case-control study of 100 children living in a peri-urban community in Lima, Peru. We defined cases as children with current asthma, and controls as children with no prior history of asthma and normal lung function. We further categorized enrollment following a factorial design to enroll equal numbers of children as either overweight or not. We obtained a fasting venous blood sample to characterize a comprehensive panel of targeted markers using a metabolomics approach based on high performance liquid chromatography-mass spectrometry. A statistical comparison of targeted metabolites between children with asthma (n = 50) and healthy controls (n = 49) revealed distinct patterns in relative concentrations of several metabolites: children with asthma had approximately 40-50% lower relative concentrations of ascorbic acid, 2-isopropylmalic acid, shikimate-3-phosphate, and 6-phospho-d-gluconate when compared to children without asthma, and 70% lower relative concentrations of reduced glutathione (all p < 0.001 after Bonferroni correction). Moreover, a combination of 2-isopropylmalic acid and betaine strongly discriminated between children with asthma (2-isopropylmalic acid ≤ 13 077 normalized counts/second) and controls (2-isopropylmalic acid > 13 077 normalized counts/second and betaine ≤ 16 47 121 normalized counts/second). By using a metabolomics approach applied to serum, we were able to discriminate between children with and without asthma by revealing different metabolic patterns. These results suggest that

Livestock metabolomics and the livestock metabolome: A systematic review

PubMed Central

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

Livestock metabolomics and the livestock metabolome: A systematic review.

PubMed

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.

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

PubMed

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.

Behavioral metabolomics analysis identifies novel neurochemical signatures in methamphetamine sensitization

PubMed Central

Adkins, Daniel E.; McClay, Joseph L.; Vunck, Sarah A.; Batman, Angela M.; Vann, Robert E.; Clark, Shaunna L.; Souza, Renan P.; Crowley, James J.; Sullivan, Patrick F.; van den Oord, Edwin J.C.G.; Beardsley, Patrick M.

2014-01-01

Behavioral sensitization has been widely studied in animal models and is theorized to reflect neural modifications associated with human psychostimulant addiction. While the mesolimbic dopaminergic pathway is known to play a role, the neurochemical mechanisms underlying behavioral sensitization remain incompletely understood. In the present study, we conducted the first metabolomics analysis to globally characterize neurochemical differences associated with behavioral sensitization. Methamphetamine-induced sensitization measures were generated by statistically modeling longitudinal activity data for eight inbred strains of mice. Subsequent to behavioral testing, nontargeted liquid and gas chromatography-mass spectrometry profiling was performed on 48 brain samples, yielding 301 metabolite levels per sample after quality control. Association testing between metabolite levels and three primary dimensions of behavioral sensitization (total distance, stereotypy and margin time) showed four robust, significant associations at a stringent metabolome-wide significance threshold (false discovery rate < 0.05). Results implicated homocarnosine, a dipeptide of GABA and histidine, in total distance sensitization, GABA metabolite 4-guanidinobutanoate and pantothenate in stereotypy sensitization, and myo-inositol in margin time sensitization. Secondary analyses indicated that these associations were independent of concurrent methamphetamine levels and, with the exception of the myo-inositol association, suggest a mechanism whereby strain-based genetic variation produces specific baseline neurochemical differences that substantially influence the magnitude of MA-induced sensitization. These findings demonstrate the utility of mouse metabolomics for identifying novel biomarkers, and developing more comprehensive neurochemical models, of psychostimulant sensitization. PMID:24034544

Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans.

PubMed

Walsh, Marianne C; Brennan, Lorraine; Malthouse, J Paul G; Roche, Helen M; Gibney, Michael J

2006-09-01

Metabolomics in human nutrition research is faced with the challenge that changes in metabolic profiles resulting from diet may be difficult to differentiate from normal physiologic variation. We assessed the extent of intra- and interindividual variation in normal human metabolic profiles and investigated the effect of standardizing diet on reducing variation. Urine, plasma, and saliva were collected from 30 healthy volunteers (23 females, 7 males) on 4 separate mornings. For visits 1 and 2, free food choice was permitted on the day before biofluid collection. Food choice on the day before visit 3 was intended to mimic that for visit 2, and all foods were standardized on the day before visit 4. Samples were analyzed by using 1H nuclear magnetic resonance spectroscopy followed by multivariate data analysis. Intra- and interindividual variations were considerable for each biofluid. Visual inspection of the principal components analysis scores plots indicated a reduction in interindividual variation in urine, but not in plasma or saliva, after the standard diet. Partial least-squares discriminant analysis indicated time-dependent changes in urinary and salivary samples, mainly resulting from creatinine in urine and acetate in saliva. The predictive power of each model to classify the samples as either night or morning was 85% for urine and 75% for saliva. Urine represented a sensitive metabolic profile that reflected acute dietary intake, whereas plasma and saliva did not. Future metabolomics studies should consider recent dietary intake and time of sample collection as a means of reducing normal physiologic variation.

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

NASA Astrophysics Data System (ADS)

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.

Analysis of salivary phenotypes of generalized aggressive and chronic periodontitis through nuclear magnetic resonance-based metabolomics.

PubMed

Romano, Federica; Meoni, Gaia; Manavella, Valeria; Baima, Giacomo; Tenori, Leonardo; Cacciatore, Stefano; Aimetti, Mario

2018-06-07

Recent findings about the differential gene expression signature of periodontal lesions have raised the hypothesis of distinctive biological phenotypes expressed by generalized chronic periodontitis (GCP) and generalized aggressive periodontitis (GAgP) patients. Therefore, this cross-sectional investigation was planned, primarily, to determine the ability of nuclear magnetic resonance (NMR) spectroscopic analysis of unstimulated whole saliva to discriminate GCP and GAgP disease-specific metabolomic fingerprint and, secondarily, to assess potential metabolites discriminating periodontitis patients from periodontally healthy individuals (HI). NMR-metabolomics spectra were acquired from salivary samples of patients with a clinical diagnosis of GCP (n = 33) or GAgP (n = 28) and from HI (n = 39). The clustering of HI, GCP and GAgP patients was achieved by using a combination of the Principal Component Analysis and Canonical Correlation Analysis on the NMR profiles. These analyses revealed a significant predictive accuracy discriminating HI from GCP, and discriminating HI from GAgP patients (both 81%). In contrast, the GAgP and GCP saliva samples seem to belong to the same metabolic space (60% predictive accuracy). Significantly lower levels (P < 0.05) of pyruvate, N-acetyl groups and lactate and higher levels (P < 0.05) of proline, phenylalanine, and tyrosine were found in GCP and GAgP patients compared with HI. Within the limitations of this study, CGP and GAgP metabolomic profiles were not unequivocally discriminated through a NMR-based spectroscopic analysis of saliva. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Salivary microbiota and metabolome associated with celiac disease.

PubMed

Francavilla, Ruggiero; Ercolini, Danilo; Piccolo, Maria; Vannini, Lucia; Siragusa, Sonya; De Filippis, Francesca; De Pasquale, Ilaria; Di Cagno, Raffaella; Di Toma, Michele; Gozzi, Giorgia; Serrazanetti, Diana I; De Angelis, Maria; Gobbetti, Marco

2014-06-01

This study aimed to investigate the salivary microbiota and metabolome of 13 children with celiac disease (CD) under a gluten-free diet (treated celiac disease [T-CD]). The same number of healthy children (HC) was used as controls. The salivary microbiota was analyzed by an integrated approach using culture-dependent and -independent methods. Metabolome analysis was carried out by gas chromatography-mass spectrometry-solid-phase microextraction. Compared to HC, the number of some cultivable bacterial groups (e.g., total anaerobes) significantly (P < 0.05) differed in the saliva samples of the T-CD children. As shown by community-level catabolic profiles, the highest Shannon's diversity and substrate richness were found in HC. Pyrosequencing data showed the highest richness estimator and diversity index values for HC. Levels of Lachnospiraceae, Gemellaceae, and Streptococcus sanguinis were highest for the T-CD children. Streptococcus thermophilus levels were markedly decreased in T-CD children. The saliva of T-CD children showed the largest amount of Bacteroidetes (e.g., Porphyromonas sp., Porphyromonas endodontalis, and Prevotella nanceiensis), together with the smallest amount of Actinobacteria. T-CD children were also characterized by decreased levels of some Actinomyces species, Atopobium species, and Corynebacterium durum. Rothia mucilaginosa was the only Actinobacteria species found at the highest level in T-CD children. As shown by multivariate statistical analyses, the levels of organic volatile compounds markedly differentiated T-CD children. Some compounds (e.g., ethyl-acetate, nonanal, and 2-hexanone) were found to be associated with T-CD children. Correlations (false discovery rate [FDR], <0.05) were found between the relative abundances of bacteria and some volatile organic compounds (VOCs). The findings of this study indicated that CD is associated with oral dysbiosis that could affect the oral metabolome.

Salivary Microbiota and Metabolome Associated with Celiac Disease

PubMed Central

Francavilla, Ruggiero; Ercolini, Danilo; Piccolo, Maria; Vannini, Lucia; Siragusa, Sonya; De Filippis, Francesca; De Pasquale, Ilaria; Di Cagno, Raffaella; Di Toma, Michele; Gozzi, Giorgia; Serrazanetti, Diana I.; Gobbetti, Marco

2014-01-01

This study aimed to investigate the salivary microbiota and metabolome of 13 children with celiac disease (CD) under a gluten-free diet (treated celiac disease [T-CD]). The same number of healthy children (HC) was used as controls. The salivary microbiota was analyzed by an integrated approach using culture-dependent and -independent methods. Metabolome analysis was carried out by gas chromatography-mass spectrometry–solid-phase microextraction. Compared to HC, the number of some cultivable bacterial groups (e.g., total anaerobes) significantly (P < 0.05) differed in the saliva samples of the T-CD children. As shown by community-level catabolic profiles, the highest Shannon's diversity and substrate richness were found in HC. Pyrosequencing data showed the highest richness estimator and diversity index values for HC. Levels of Lachnospiraceae, Gemellaceae, and Streptococcus sanguinis were highest for the T-CD children. Streptococcus thermophilus levels were markedly decreased in T-CD children. The saliva of T-CD children showed the largest amount of Bacteroidetes (e.g., Porphyromonas sp., Porphyromonas endodontalis, and Prevotella nanceiensis), together with the smallest amount of Actinobacteria. T-CD children were also characterized by decreased levels of some Actinomyces species, Atopobium species, and Corynebacterium durum. Rothia mucilaginosa was the only Actinobacteria species found at the highest level in T-CD children. As shown by multivariate statistical analyses, the levels of organic volatile compounds markedly differentiated T-CD children. Some compounds (e.g., ethyl-acetate, nonanal, and 2-hexanone) were found to be associated with T-CD children. Correlations (false discovery rate [FDR], <0.05) were found between the relative abundances of bacteria and some volatile organic compounds (VOCs). The findings of this study indicated that CD is associated with oral dysbiosis that could affect the oral metabolome. PMID:24657864

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

PubMed

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.

On the ecosystemic network of saliva in healthy young adults

PubMed Central

Zaura, Egija; Brandt, Bernd W; Prodan, Andrei; Teixeira de Mattos, Maarten Joost; Imangaliyev, Sultan; Kool, Jolanda; Buijs, Mark J; Jagers, Ferry LPW; Hennequin-Hoenderdos, Nienke L; Slot, Dagmar E; Nicu, Elena A; Lagerweij, Maxim D; Janus, Marleen M; Fernandez-Gutierrez, Marcela M; Levin, Evgeni; Krom, Bastiaan P; Brand, Henk S; Veerman, Enno CI; Kleerebezem, Michiel; Loos, Bruno G; van der Weijden, G A; Crielaard, Wim; Keijser, Bart JF

2017-01-01

A dysbiotic state is believed to be a key factor in the onset of oral disease. Although oral diseases have been studied for decades, our understanding of oral health, the boundaries of a healthy oral ecosystem and ecological shift toward dysbiosis is still limited. Here, we present the ecobiological heterogeneity of the salivary ecosystem and relations between the salivary microbiome, salivary metabolome and host-related biochemical salivary parameters in 268 healthy adults after overnight fasting. Gender-specific differences in the microbiome and metabolome were observed and were associated with salivary pH and dietary protein intake. Our analysis grouped the individuals into five microbiome and four metabolome-based clusters that significantly related to biochemical parameters of saliva. Low salivary pH and high lysozyme activity were associated with high proportions of streptococcal phylotypes and increased membrane-lipid degradation products. Samples with high salivary pH displayed increased chitinase activity, higher abundance of Veillonella and Prevotella species and higher levels of amino acid fermentation products, suggesting proteolytic adaptation. An over-specialization toward either a proteolytic or a saccharolytic ecotype may indicate a shift toward a dysbiotic state. Their prognostic value and the degree to which these ecotypes are related to increased disease risk remains to be determined. PMID:28072421

Metabolomics: A Primer.

PubMed

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.

Sticky Saliva

NASA Astrophysics Data System (ADS)

McCarroll, Louise; Solomon, Michael; Schultz, William

2016-11-01

Oral and even systemic health begins with healthy saliva by maintaining antibacterial activity, lubricating hard and soft oral tissues, healing, tasting, chewing, and swallowing. Saliva functionality is intimately linked to its rheology. Alterations in saliva rheology may indicate or cause unhealthy biological function. One imprecise pathological designation is "sticky saliva", usually self-reported or qualitatively described by health professionals. Saliva is 99% water and therefore behaves like water in shear. Saliva also contains mucins, electrolytes, enzymes, hormones, and antibodies. These additional constituents enable saliva to form a long-lasting filament with a "beads-on-a-string" morphology in extension. Therefore, the main kinematic feature that distinguishes the coupling between the oral cavity and saliva elongational mechanics. We investigate the effect of pH and salinity on saliva filament formation with preliminary experiments and compare to 1D unsteady viscoelastic models. We discuss the results in the context of saliva functionality and in generating more satisfactory saliva substitutes for those suffering from xerostomia. We will discuss when beads-on-a-string are likely to occur.

Metabolomic profiling to identify potential serum biomarkers for schizophrenia and risperidone action.

PubMed

Xuan, Jiekun; Pan, Guihua; Qiu, Yunping; Yang, Lun; Su, Mingming; Liu, Yumin; Chen, Jian; Feng, Guoyin; Fang, Yiru; Jia, Wei; Xing, Qinghe; He, Lin

2011-12-02

Despite recent advances in understanding the pathophysiology of schizophrenia and the mechanisms of antipsychotic drug action, the development of biomarkers for diagnosis and therapeutic monitoring in schizophrenia remains challenging. Metabolomics provides a powerful approach to discover diagnostic and therapeutic biomarkers by analyzing global changes in an individual's metabolic profile in response to pathophysiological stimuli or drug intervention. In this study, we performed gas chromatography-mass spectrometry based metabolomic profiling in serum of unmedicated schizophrenic patients before and after an 8-week risperidone monotherapy, to detect potential biomarkers associated with schizophrenia and risperidone treatment. Twenty-two marker metabolites contributing to the complete separation of schizophrenic patients from matched healthy controls were identified, with citrate, palmitic acid, myo-inositol, and allantoin exhibiting the best combined classification performance. Twenty marker metabolites contributing to the complete separation between posttreatment and pretreatment patients were identified, with myo-inositol, uric acid, and tryptophan showing the maximum combined classification performance. Metabolic pathways including energy metabolism, antioxidant defense systems, neurotransmitter metabolism, fatty acid biosynthesis, and phospholipid metabolism were found to be disturbed in schizophrenic patients and partially normalized following risperidone therapy. Further study of these metabolites may facilitate the development of noninvasive biomarkers and more efficient therapeutic strategies for schizophrenia.

Fatty acids and small organic compounds bind to mineralo-organic nanoparticles derived from human body fluids as revealed by metabolomic analysis

NASA Astrophysics Data System (ADS)

Martel, Jan; Wu, Cheng-Yeu; Hung, Cheng-Yu; Wong, Tsui-Yin; Cheng, Ann-Joy; Cheng, Mei-Ling; Shiao, Ming-Shi; Young, John D.

2016-03-01

Nanoparticles entering the human body instantly become coated with a ``protein corona'' that influences the effects and distribution of the particles in vivo. Yet, whether nanoparticles may bind to other organic compounds remains unclear. Here we use an untargeted metabolomic approach based on ultra-performance liquid chromatography and quadruple time-of-flight mass spectrometry to identify the organic compounds that bind to mineral nanoparticles formed in human body fluids (serum, plasma, saliva, and urine). A wide range of organic compounds is identified, including fatty acids, glycerophospholipids, amino acids, sugars, and amides. Our results reveal that, in addition to the proteins identified previously, nanoparticles harbor an ``organic corona'' containing several fatty acids which may affect particle-cell interactions in vivo. This study provides a platform to study the organic corona of biological and synthetic nanoparticles found in the human body.Nanoparticles entering the human body instantly become coated with a ``protein corona'' that influences the effects and distribution of the particles in vivo. Yet, whether nanoparticles may bind to other organic compounds remains unclear. Here we use an untargeted metabolomic approach based on ultra-performance liquid chromatography and quadruple time-of-flight mass spectrometry to identify the organic compounds that bind to mineral nanoparticles formed in human body fluids (serum, plasma, saliva, and urine). A wide range of organic compounds is identified, including fatty acids, glycerophospholipids, amino acids, sugars, and amides. Our results reveal that, in addition to the proteins identified previously, nanoparticles harbor an ``organic corona'' containing several fatty acids which may affect particle-cell interactions in vivo. This study provides a platform to study the organic corona of biological and synthetic nanoparticles found in the human body. Electronic supplementary information (ESI) available. See

Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples.

PubMed

Mastrokolias, Anastasios; Pool, Rene; Mina, Eleni; Hettne, Kristina M; van Duijn, Erik; van der Mast, Roos C; van Ommen, GertJan; 't Hoen, Peter A C; Prehn, Cornelia; Adamski, Jerzy; van Roon-Mom, Willeke

Metabolic changes have been frequently associated with Huntington's disease (HD). At the same time peripheral blood represents a minimally invasive sampling avenue with little distress to Huntington's disease patients especially when brain or other tissue samples are difficult to collect. We investigated the levels of 163 metabolites in HD patient and control serum samples in order to identify disease related changes. Additionally, we integrated the metabolomics data with our previously published next generation sequencing-based gene expression data from the same patients in order to interconnect the metabolomics changes with transcriptional alterations. This analysis was performed using targeted metabolomics and flow injection electrospray ionization tandem mass spectrometry in 133 serum samples from 97 Huntington's disease patients (29 pre-symptomatic and 68 symptomatic) and 36 controls. By comparing HD mutation carriers with controls we identified 3 metabolites significantly changed in HD (serine and threonine and one phosphatidylcholine-PC ae C36:0) and an additional 8 phosphatidylcholines (PC aa C38:6, PC aa C36:0, PC ae C38:0, PC aa C38:0, PC ae C38:6, PC ae C42:0, PC aa C36:5 and PC ae C36:0) that exhibited a significant association with disease severity. Using workflow based exploitation of pathway databases and by integrating our metabolomics data with our gene expression data from the same patients we identified 4 deregulated phosphatidylcholine metabolism related genes ( ALDH1B1 , MBOAT1 , MTRR and PLB1 ) that showed significant association with the changes in metabolite concentrations. Our results support the notion that phosphatidylcholine metabolism is deregulated in HD blood and that these metabolite alterations are associated with specific gene expression changes.

Combining a nontargeted and targeted metabolomics approach to identify metabolic pathways significantly altered in polycystic ovary syndrome.

PubMed

Chang, Alice Y; Lalia, Antigoni Z; Jenkins, Gregory D; Dutta, Tumpa; Carter, Rickey E; Singh, Ravinder J; Nair, K Sreekumaran

2017-06-01

Polycystic ovary syndrome (PCOS) is a condition of androgen excess and chronic anovulation frequently associated with insulin resistance. We combined a nontargeted and targeted metabolomics approach to identify pathways and metabolites that distinguished PCOS from metabolic syndrome (MetS). Twenty obese women with PCOS were compared with 18 obese women without PCOS. Both groups met criteria for MetS but could not have diabetes mellitus or take medications that treat PCOS or affect lipids or insulin sensitivity. Insulin sensitivity was derived from the frequently sampled intravenous glucose tolerance test. A nontargeted metabolomics approach was performed on fasting plasma samples to identify differentially expressed metabolites, which were further evaluated by principal component and pathway enrichment analysis. Quantitative targeted metabolomics was then applied on candidate metabolites. Measured metabolites were tested for associations with PCOS and clinical variables by logistic and linear regression analyses. This multiethnic, obese sample was matched by age (PCOS, 37±6; MetS, 40±6years) and body mass index (BMI) (PCOS, 34.6±5.1; MetS, 33.7±5.2kg/m 2 ). Principal component analysis of the nontargeted metabolomics data showed distinct group separation of PCOS from MetS controls. From the subset of 385 differentially expressed metabolites, 22% were identified by accurate mass, resulting in 19 canonical pathways significantly altered in PCOS, including amino acid, lipid, steroid, carbohydrate, and vitamin D metabolism. Targeted metabolomics identified many essential amino acids, including branched-chain amino acids (BCAA) that were elevated in PCOS compared with MetS. PCOS was most associated with BCAA (P=.02), essential amino acids (P=.03), the essential amino acid lysine (P=.02), and the lysine metabolite α-aminoadipic acid (P=.02) in models adjusted for surrogate variables representing technical variation in metabolites. No significant differences between

Combining a Nontargeted and Targeted Metabolomics Approach to Identify Metabolic Pathways Significantly Altered in Polycystic Ovary Syndrome

PubMed Central

Chang, Alice Y.; Lalia, Antigoni Z.; Jenkins, Gregory D.; Dutta, Tumpa; Carter, Rickey E.; Singh, Ravinder J.; Sreekumaran Nair, K.

2017-01-01

Objective Polycystic ovary syndrome (PCOS) is a condition of androgen excess and chronic anovulation frequently associated with insulin resistance. We combined a nontargeted and targeted metabolomics approach to identify pathways and metabolites that distinguished PCOS from metabolic syndrome (MetS). Methods Twenty obese women with PCOS were compared with 18 obese women without PCOS. Both groups met criteria for MetS but could not have diabetes mellitus or take medications that treat PCOS or affect lipids or insulin sensitivity. Insulin sensitivity was derived from the frequently sampled intravenous glucose tolerance test. A nontargeted metabolomics approach was performed on fasting plasma samples to identify differentially expressed metabolites, which were further evaluated by principal component and pathway enrichment analysis. Quantitative targeted metabolomics was then applied on candidate metabolites. Measured metabolites were tested for associations with PCOS and clinical variables by logistic and linear regression analyses. Results This multiethnic, obese sample was matched by age (PCOS, 37 ± 6; MetS, 40 ± 6 years) and body mass index (BMI) (PCOS, 34.6 ± 5.1; MetS, 33.7 ± 5.2 kg/m2). Principal component analysis of the nontargeted metabolomics data showed distinct group separation of PCOS from MetS controls. From the subset of 385 differentially expressed metabolites, 22% were identified by accurate mass, resulting in 19 canonical pathways significantly altered in PCOS, including amino acid, lipid, steroid, carbohydrate, and vitamin D metabolism. Targeted metabolomics identified many essential amino acids, including branched-chain amino acids (BCAA) that were elevated in PCOS compared with MetS. PCOS was most associated with BCAA (P = .02), essential amino acids (P = .03), the essential amino acid lysine (P = .02), and the lysine metabolite α-aminoadipic acid (P = .02) in models adjusted for surrogate variables representing technical variation in

Targeted Metabolomics Identifies Pharmacodynamic Biomarkers for BIO 300 Mitigation of Radiation-Induced Lung Injury.

PubMed

Jones, Jace W; Jackson, Isabel L; Vujaskovic, Zeljko; Kaytor, Michael D; Kane, Maureen A

2017-12-01

Biomarkers serve a number of purposes during drug development including defining the natural history of injury/disease, serving as a secondary endpoint or trigger for intervention, and/or aiding in the selection of an effective dose in humans. BIO 300 is a patent-protected pharmaceutical formulation of nanoparticles of synthetic genistein being developed by Humanetics Corporation. The primary goal of this metabolomic discovery experiment was to identify biomarkers that correlate with radiation-induced lung injury and BIO 300 efficacy for mitigating tissue damage based upon the primary endpoint of survival. High-throughput targeted metabolomics of lung tissue from male C57L/J mice exposed to 12.5 Gy whole thorax lung irradiation, treated daily with 400 mg/kg BIO 300 for either 2 weeks or 6 weeks starting 24 h post radiation exposure, were assayed at 180 d post-radiation to identify potential biomarkers. A panel of lung metabolites that are responsive to radiation and able to distinguish an efficacious treatment schedule of BIO 300 from a non-efficacious treatment schedule in terms of 180 d survival were identified. These metabolites represent potential biomarkers that could be further validated for use in drug development of BIO 300 and in the translation of dose from animal to human.

The Human Serum Metabolome

PubMed Central

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

Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing

PubMed Central

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 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 GENIUSand 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. PMID:24846174

Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls.

PubMed

Belstrøm, Daniel; Jersie-Christensen, Rosa R; Lyon, David; Damgaard, Christian; Jensen, Lars J; Holmstrup, Palle; Olsen, Jesper V

2016-01-01

The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.

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

PubMed

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

2018-08-27

Mass spectral data sets often contain experimental artefacts, and data filtering prior to statistical analysis is crucial to extract reliable information. This is particularly true in untargeted metabolomics analyses, where the analyte(s) of interest are not known a priori. It is often assumed that chemical interferents (i.e. solvent contaminants such as plasticizers) are consistent across samples, and can be removed by background subtraction from blank injections. On the contrary, it is shown here that chemical contaminants may vary in abundance across each injection, potentially leading to their misidentification as relevant sample components. With this metabolomics study, we demonstrate the effectiveness of hierarchical cluster analysis (HCA) of replicate injections (technical replicates) as a methodology to identify chemical interferents and reduce their contaminating contribution to metabolomics models. Pools of metabolites with varying complexity were prepared from the botanical Angelica keiskei Koidzumi and spiked with known metabolites. Each set of pools was analyzed in triplicate and at multiple concentrations using ultraperformance liquid chromatography coupled to mass spectrometry (UPLC-MS). Before filtering, HCA failed to cluster replicates in the data sets. To identify contaminant peaks, we developed a filtering process that evaluated the relative peak area variance of each variable within triplicate injections. These interferent peaks were found across all samples, but did not show consistent peak area from injection to injection, even when evaluating the same chemical sample. This filtering process identified 128 ions that appear to originate from the UPLC-MS system. Data sets collected for a high number of pools with comparatively simple chemical composition were highly influenced by these chemical interferents, as were samples that were analyzed at a low concentration. When chemical interferent masses were removed, technical replicates clustered in

Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing.

PubMed

Kamodyová, Natália; Durdiaková, Jaroslava; Celec, Peter; Sedláčková, Tatiana; Repiská, Gabriela; Sviežená, Barbara; Minárik, Gabriel

2013-01-01

Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Large-scale neurochemical metabolomics analysis identifies multiple compounds associated with methamphetamine exposure.

PubMed

McClay, Joseph L; Adkins, Daniel E; Vunck, Sarah A; Batman, Angela M; Vann, Robert E; Clark, Shaunna L; Beardsley, Patrick M; van den Oord, Edwin J C G

2013-04-01

Methamphetamine (MA) is an illegal stimulant drug of abuse with serious negative health consequences. The neurochemical effects of MA have been partially characterized, with a traditional focus on classical neurotransmitter systems. However, these directions have not yet led to novel drug treatments for MA abuse or toxicity. As an alternative approach, we describe here the first application of metabolomics to investigate the neurochemical consequences of MA exposure in the rodent brain. We examined single exposures at 3 mg/kg and repeated exposures at 3 mg/kg over 5 days in eight common inbred mouse strains. Brain tissue samples were assayed using high-throughput gas and liquid chromatography mass spectrometry, yielding quantitative data on >300 unique metabolites. Association testing and false discovery rate control yielded several metabolome-wide significant associations with acute MA exposure, including compounds such as lactate ( p = 4.4 × 10 -5 , q = 0.013), tryptophan ( p = 7.0 × 10 -4 , q = 0.035) and 2-hydroxyglutarate ( p = 1.1 × 10 -4 , q = 0.022). Secondary analyses of MA-induced increase in locomotor activity showed associations with energy metabolites such as succinate ( p = 3.8 × 10 -7 ). Associations specific to repeated (5 day) MA exposure included phosphocholine ( p = 4.0 × 10 -4 , q = 0.087) and ergothioneine ( p = 3.0 × 10 -4 , q = 0.087). Our data appear to confirm and extend existing models of MA action in the brain, whereby an initial increase in energy metabolism, coupled with an increase in behavioral locomotion, gives way to disruption of mitochondria and phospholipid pathways and increased endogenous antioxidant response. Our study demonstrates the power of comprehensive MS-based metabolomics to identify drug-induced changes to brain metabolism and to develop neurochemical models of drug effects.

Large-scale neurochemical metabolomics analysis identifies multiple compounds associated with methamphetamine exposure

PubMed Central

Adkins, Daniel E.; Vunck, Sarah A.; Batman, Angela M.; Vann, Robert E.; Clark, Shaunna L.; Beardsley, Patrick M.; van den Oord, Edwin J. C. G.

2012-01-01

Methamphetamine (MA) is an illegal stimulant drug of abuse with serious negative health consequences. The neurochemical effects of MA have been partially characterized, with a traditional focus on classical neurotransmitter systems. However, these directions have not yet led to novel drug treatments for MA abuse or toxicity. As an alternative approach, we describe here the first application of metabolomics to investigate the neurochemical consequences of MA exposure in the rodent brain. We examined single exposures at 3 mg/kg and repeated exposures at 3 mg/kg over 5 days in eight common inbred mouse strains. Brain tissue samples were assayed using high-throughput gas and liquid chromatography mass spectrometry, yielding quantitative data on >300 unique metabolites. Association testing and false discovery rate control yielded several metabolome-wide significant associations with acute MA exposure, including compounds such as lactate (p = 4.4 × 10−5, q = 0.013), tryptophan (p = 7.0 × 10−4, q = 0.035) and 2-hydroxyglutarate (p = 1.1 × 10−4, q = 0.022). Secondary analyses of MA-induced increase in locomotor activity showed associations with energy metabolites such as succinate (p = 3.8 × 10−7). Associations specific to repeated (5 day) MA exposure included phosphocholine (p = 4.0 × 10−4, q = 0.087) and ergothioneine (p = 3.0 × 10−4, q = 0.087). Our data appear to confirm and extend existing models of MA action in the brain, whereby an initial increase in energy metabolism, coupled with an increase in behavioral locomotion, gives way to disruption of mitochondria and phospholipid pathways and increased endogenous antioxidant response. Our study demonstrates the power of comprehensive MS-based metabolomics to identify drug-induced changes to brain metabolism and to develop neurochemical models of drug effects. PMID:23554582

Disruption of TCA Cycle and Glutamate Metabolism Identified by Metabolomics in an In Vitro Model of Amyotrophic Lateral Sclerosis.

PubMed

Veyrat-Durebex, Charlotte; Corcia, Philippe; Piver, Eric; Devos, David; Dangoumau, Audrey; Gouel, Flore; Vourc'h, Patrick; Emond, Patrick; Laumonnier, Frédéric; Nadal-Desbarats, Lydie; Gordon, Paul H; Andres, Christian R; Blasco, Hélène

2016-12-01

This study aims to develop a cellular metabolomics model that reproduces the pathophysiological conditions found in amyotrophic lateral sclerosis in order to improve knowledge of disease physiology. We used a co-culture model combining the motor neuron-like cell line NSC-34 and the astrocyte clone C8-D1A, with each over-expressing wild-type or G93C mutant human SOD1, to examine amyotrophic lateral sclerosis (ALS) physiology. We focused on the effects of mutant human SOD1 as well as oxidative stress induced by menadione on intracellular metabolism using a metabolomics approach through gas chromatography coupled with mass spectrometry (GC-MS) analysis. Preliminary non-supervised analysis by Principal Component Analysis (PCA) revealed that cell type, genetic environment, and time of culture influenced the metabolomics profiles. Supervised analysis using orthogonal partial least squares discriminant analysis (OPLS-DA) on data from intracellular metabolomics profiles of SOD1 G93C co-cultures produced metabolites involved in glutamate metabolism and the tricarboxylic acid cycle (TCA) cycle. This study revealed the feasibility of using a metabolomics approach in a cellular model of ALS. We identified potential disruption of the TCA cycle and glutamate metabolism under oxidative stress, which is consistent with prior research in the disease. Analysis of metabolic alterations in an in vitro model is a novel approach to investigation of disease physiology.

Integrated redox proteomics and metabolomics of mitochondria to identify mechanisms of cd toxicity.

PubMed

Go, Young-Mi; Roede, James R; Orr, Michael; Liang, Yongliang; Jones, Dean P

2014-05-01

Cadmium (Cd) exposure contributes to human diseases affecting liver, kidney, lung, and other organ systems, but mechanisms underlying the pleotropic nature of these toxicities are poorly understood. Cd accumulates in humans from dietary, environmental (including cigarette smoke), and occupational sources, and has a twenty-year biologic half-life. Our previous mouse and cell studies showed that environmental low-dose Cd exposure altered protein redox states resulting in stimulation of inflammatory signaling and disruption of the actin cytoskeleton system, suggesting that Cd could impact multiple mechanisms of disease. In the current study, we investigated the effects of acute Cd exposure on the redox proteome and metabolome of mouse liver mitochondria to gain insight into associated toxicological mechanisms and functions. We analyzed redox states of liver mitochondrial proteins by redox proteomics using isotope coded affinity tag (ICAT) combined mass spectrometry. Redox ICAT identified 2687 cysteine-containing peptides (peptidyl Cys) of which 1667 peptidyl Cys (657 proteins) were detected in both control and Cd-exposed samples. Of these, 46% (1247 peptidyl Cys, 547 proteins) were oxidized by Cd more than 1.5-fold relative to controls. Bioinformatics analysis using MetaCore software showed that Cd affected 86 pathways, including 24 Cys in proteins functioning in branched chain amino acid (BCAA) and 14 Cys in proteins functioning in fatty acid (acylcarnitine/carnitine) metabolism. Consistently, high-resolution metabolomics data showed that Cd treatment altered levels of BCAA and carnitine metabolites. Together, these results show that mitochondrial protein redox and metabolites are targets in Cd-induced hepatotoxicity. The results further indicate that redox proteomics and metabolomics can be used in an integrated systems approach to investigate complex disease mechanisms.

Reprogramming the metabolome rescues retinal degeneration.

PubMed

Park, Karen Sophia; Xu, Christine L; Cui, Xuan; Tsang, Stephen H

2018-05-01

Metabolomics studies in the context of ophthalmology have largely focused on identifying metabolite concentrations that characterize specific retinal diseases. Studies involving mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have shown that individuals suffering from retinal diseases exhibit metabolic profiles that markedly differ from those of control individuals, supporting the notion that metabolites may serve as easily identifiable biomarkers for specific conditions. An emerging branch of metabolomics resulting from biomarker studies, however, involves the study of retinal metabolic dysfunction as causes of degeneration. Recent publications have identified a number of metabolic processes-including but not limited to glucose and oxygen metabolism-that, when perturbed, play a role in the degeneration of photoreceptor cells. As a result, such studies have led to further research elucidating methods for prolonging photoreceptor survival in an effort to halt degeneration in its early stages. This review will explore the ways in which metabolomics has deepened our understanding of the causes of retinal degeneration and discuss how metabolomics can be used to prevent retinal degeneration from progressing to its later disease stages.

Identification of aquaporin-5 and lipid rafts in human resting saliva and their release into cevimeline-stimulated saliva.

PubMed

Pan, Yan; Iwata, Fusako; Wang, Di; Muraguchi, Masahiro; Ooga, Keiko; Ohmoto, Yasukazu; Takai, Masaaki; Cho, Gota; Kang, Jinsen; Shono, Masayuki; Li, Xue-jun; Okamura, Ko; Mori, Toyoki; Ishikawa, Yasuko

2009-01-01

It is unknown whether AQP5 and lipid rafts are released into human unstimulated (resting) saliva and saliva in response to secretagogues. In order to quantitate the salivary concentration of AQP5, we produced a polyclonal antibody for human AQP5 and developed an enzyme-like immunosorbent assay (ELISA). AQP5 and lipid rafts were identified in human resting saliva. The amount of AQP5 in resting saliva showed a diurnal variation with high levels during waking hours, and an age-related decrease in AQP5 was coincident with the volume of resting saliva. Cevimeline, a muscarinic acetylcholine receptor (mAChR) agonist, induced the release of AQP5 with lipid rafts, amylase, mucin, and lysozyme. Changes in saliva AQP5 levels after cevimeline administration occurred simultaneously with changes in saliva flow rates. Confocal microscopy revealed that AQP5 was located in the apical plasma membrane and showed a diffuse pattern in parotid glands under resting conditions. Following cevimeline administration, AQP5 was predominantly associated with the APM and was localized in the lumen. AQP5 and lipid rafts were released with salivary proteins from human salivary glands by the stimulation of M3 mAChRs, and that changes in saliva AQP5 levels can be used as an indicator of salivary flow rate and also as a useful index of M3 mAChR agonist's action on human salivary glands.

Metabolomic profiling and genomic analysis of wheat aneuploid lines to identify genes controlling biochemical pathways in mature grain.

PubMed

Francki, Michael G; Hayton, Sarah; Gummer, Joel P A; Rawlinson, Catherine; Trengove, Robert D

2016-02-01

Metabolomics is becoming an increasingly important tool in plant genomics to decipher the function of genes controlling biochemical pathways responsible for trait variation. Although theoretical models can integrate genes and metabolites for trait variation, biological networks require validation using appropriate experimental genetic systems. In this study, we applied an untargeted metabolite analysis to mature grain of wheat homoeologous group 3 ditelosomic lines, selected compounds that showed significant variation between wheat lines Chinese Spring and at least one ditelosomic line, tracked the genes encoding enzymes of their biochemical pathway using the wheat genome survey sequence and determined the genetic components underlying metabolite variation. A total of 412 analytes were resolved in the wheat grain metabolome, and principal component analysis indicated significant differences in metabolite profiles between Chinese Spring and each ditelosomic lines. The grain metabolome identified 55 compounds positively matched against a mass spectral library where the majority showed significant differences between Chinese Spring and at least one ditelosomic line. Trehalose and branched-chain amino acids were selected for detailed investigation, and it was expected that if genes encoding enzymes directly related to their biochemical pathways were located on homoeologous group 3 chromosomes, then corresponding ditelosomic lines would have a significant reduction in metabolites compared with Chinese Spring. Although a proportion showed a reduction, some lines showed significant increases in metabolites, indicating that genes directly and indirectly involved in biosynthetic pathways likely regulate the metabolome. Therefore, this study demonstrated that wheat aneuploid lines are suitable experimental genetic system to validate metabolomics-genomics networks. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Human breath metabolomics using an optimized noninvasive exhaled breath condensate sampler

PubMed Central

Zamuruyev, Konstantin O.; Aksenov, Alexander A.; Pasamontes, Alberto; Brown, Joshua F.; Pettit, Dayna R.; Foutouhi, Soraya; Weimer, Bart C.; Schivo, Michael; Kenyon, Nicholas J.; Delplanque, Jean-Pierre; Davis, Cristina E.

2017-01-01

Exhaled breath condensate (EBC) analysis is a developing field with tremendous promise to advance personalized, non-invasive health diagnostics as new analytical instrumentation platforms and detection methods are developed. Multiple commercially-available and researcher-built experimental samplers are reported in the literature. However, there is very limited information available to determine an effective breath sampling approach, especially regarding the dependence of breath sample metabolomic content on the collection device design and sampling methodology. This lack of an optimal standard procedure results in a range of reported results that are sometimes contradictory. Here, we present a design of a portable human EBC sampler optimized for collection and preservation of the rich metabolomic content of breath. The performance of the engineered device is compared to two commercially available breath collection devices: the RTube™ and TurboDECCS. A number of design and performance parameters are considered, including: condenser temperature stability during sampling, collection efficiency, condenser material choice, and saliva contamination in the collected breath samples. The significance of the biological content of breath samples, collected with each device, is evaluated with a set of mass spectrometry methods and was the primary factor for evaluating device performance. The design includes an adjustable mass-size threshold for aerodynamic filtering of saliva droplets from the breath flow. Engineering an inexpensive device that allows efficient collection of metalomic-rich breath samples is intended to aid further advancement in the field of breath analysis for non-invasive health diagnostic. EBC sampling from human volunteers was performed under UC Davis IRB protocol 63701-3 (09/30/2014-07/07/2017). PMID:28004639

Fatty acids and small organic compounds bind to mineralo-organic nanoparticles derived from human body fluids as revealed by metabolomic analysis.

PubMed

Martel, Jan; Wu, Cheng-Yeu; Hung, Cheng-Yu; Wong, Tsui-Yin; Cheng, Ann-Joy; Cheng, Mei-Ling; Shiao, Ming-Shi; Young, John D

2016-03-14

Nanoparticles entering the human body instantly become coated with a "protein corona" that influences the effects and distribution of the particles in vivo. Yet, whether nanoparticles may bind to other organic compounds remains unclear. Here we use an untargeted metabolomic approach based on ultra-performance liquid chromatography and quadruple time-of-flight mass spectrometry to identify the organic compounds that bind to mineral nanoparticles formed in human body fluids (serum, plasma, saliva, and urine). A wide range of organic compounds is identified, including fatty acids, glycerophospholipids, amino acids, sugars, and amides. Our results reveal that, in addition to the proteins identified previously, nanoparticles harbor an "organic corona" containing several fatty acids which may affect particle-cell interactions in vivo. This study provides a platform to study the organic corona of biological and synthetic nanoparticles found in the human body.

Can Untargeted Metabolomics Be Utilized in Drug Discovery/Development?

PubMed

Caldwell, Gary W; Leo, Gregory C

2017-01-01

Untargeted metabolomics is a promising approach for reducing the significant attrition rate for discovering and developing drugs in the pharmaceutical industry. This review aims to highlight the practical decision-making value of untargeted metabolomics for the advancement of drug candidates in drug discovery/development including potentially identifying and validating novel therapeutic targets, creating alternative screening paradigms, facilitating the selection of specific and translational metabolite biomarkers, identifying metabolite signatures for the drug efficacy mechanism of action, and understanding potential drug-induced toxicity. The review provides an overview of the pharmaceutical process workflow to discover and develop new small molecule drugs followed by the metabolomics process workflow that is involved in conducting metabolomics studies. The pros and cons of the major components of the pharmaceutical and metabolomics workflows are reviewed and discussed. Finally, selected untargeted metabolomics literature examples, from primarily 2010 to 2016, are used to illustrate why, how, and where untargeted metabolomics can be integrated into the drug discovery/preclinical drug development process. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

PubMed

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations.

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

NASA Astrophysics Data System (ADS)

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.

Clinical Metabolomics and Glaucoma.

PubMed

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.

The metabolomic approach identifies a biological signature of low-dose chronic exposure to cesium 137.

PubMed

Grison, Stéphane; Martin, Jean-Charles; Grandcolas, Line; Banzet, Nathalie; Blanchardon, Eric; Tourlonias, Elie; Defoort, Catherine; Favé, Gaëlle; Bott, Romain; Dublineau, Isabelle; Gourmelon, Patrick; Souidi, Maâmar

2012-01-01

Reports have described apparent biological effects of (137)Cs (the most persistent dispersed radionuclide) irradiation in people living in Chernobyl-contaminated territory. The sensitive analytical technology described here should now help assess the relation of this contamination to the observed effects. A rat model chronically exposed to (137)Cs through drinking water was developed to identify biomarkers of radiation-induced metabolic disorders, and the biological impact was evaluated by a metabolomic approach that allowed us to detect several hundred metabolites in biofluids and assess their association with disease states. After collection of plasma and urine from contaminated and non-contaminated rats at the end of the 9-months contamination period, analysis with a LC-MS system detected 742 features in urine and 1309 in plasma. Biostatistical discriminant analysis extracted a subset of 26 metabolite signals (2 urinary, 4 plasma non-polar, and 19 plasma polar metabolites) that in combination were able to predict from 68 up to 94% of the contaminated rats, depending on the prediction method used, with a misclassification rate as low as 5.3%. The difference in this metabolic score between the contaminated and non-contaminated rats was highly significant (P = 0.019 after ANOVA cross-validation). In conclusion, our proof-of-principle study demonstrated for the first time the usefulness of a metabolomic approach for addressing biological effects of chronic low-dose contamination. We can conclude that a metabolomic signature discriminated (137)Cs-contaminated from control animals in our model. Further validation is nevertheless required together with full annotation of the metabolic indicators.

Human breath metabolomics using an optimized non-invasive exhaled breath condensate sampler.

PubMed

Zamuruyev, Konstantin O; Aksenov, Alexander A; Pasamontes, Alberto; Brown, Joshua F; Pettit, Dayna R; Foutouhi, Soraya; Weimer, Bart C; Schivo, Michael; Kenyon, Nicholas J; Delplanque, Jean-Pierre; Davis, Cristina E

2016-12-22

Exhaled breath condensate (EBC) analysis is a developing field with tremendous promise to advance personalized, non-invasive health diagnostics as new analytical instrumentation platforms and detection methods are developed. Multiple commercially-available and researcher-built experimental samplers are reported in the literature. However, there is very limited information available to determine an effective breath sampling approach, especially regarding the dependence of breath sample metabolomic content on the collection device design and sampling methodology. This lack of an optimal standard procedure results in a range of reported results that are sometimes contradictory. Here, we present a design of a portable human EBC sampler optimized for collection and preservation of the rich metabolomic content of breath. The performance of the engineered device is compared to two commercially available breath collection devices: the RTube ™ and TurboDECCS. A number of design and performance parameters are considered, including: condenser temperature stability during sampling, collection efficiency, condenser material choice, and saliva contamination in the collected breath samples. The significance of the biological content of breath samples, collected with each device, is evaluated with a set of mass spectrometry methods and was the primary factor for evaluating device performance. The design includes an adjustable mass-size threshold for aerodynamic filtering of saliva droplets from the breath flow. Engineering an inexpensive device that allows efficient collection of metalomic-rich breath samples is intended to aid further advancement in the field of breath analysis for non-invasive health diagnostic. EBC sampling from human volunteers was performed under UC Davis IRB protocol 63701-3 (09/30/2014-07/07/2017).

Metabolomics identifies a biological response to chronic low-dose natural uranium contamination in urine samples.

PubMed

Grison, Stéphane; Favé, Gaëlle; Maillot, Matthieu; Manens, Line; Delissen, Olivia; Blanchardon, Eric; Banzet, Nathalie; Defoort, Catherine; Bott, Romain; Dublineau, Isabelle; Aigueperse, Jocelyne; Gourmelon, Patrick; Martin, Jean-Charles; Souidi, Maâmar

2013-01-01

Because uranium is a natural element present in the earth's crust, the population may be chronically exposed to low doses of it through drinking water. Additionally, the military and civil uses of uranium can also lead to environmental dispersion that can result in high or low doses of acute or chronic exposure. Recent experimental data suggest this might lead to relatively innocuous biological reactions. The aim of this study was to assess the biological changes in rats caused by ingestion of natural uranium in drinking water with a mean daily intake of 2.7 mg/kg for 9 months and to identify potential biomarkers related to such a contamination. Subsequently, we observed no pathology and standard clinical tests were unable to distinguish between treated and untreated animals. Conversely, LC-MS metabolomics identified urine as an appropriate biofluid for discriminating the experimental groups. Of the 1,376 features detected in urine, the most discriminant were metabolites involved in tryptophan, nicotinate, and nicotinamide metabolic pathways. In particular, N -methylnicotinamide, which was found at a level seven times higher in untreated than in contaminated rats, had the greatest discriminating power. These novel results establish a proof of principle for using metabolomics to address chronic low-dose uranium contamination. They open interesting perspectives for understanding the underlying biological mechanisms and designing a diagnostic test of exposure.

The Human Urine Metabolome

PubMed Central

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

Metabolomics as a tool to identify biomarkers to predict and improve outcomes in reproductive medicine: a systematic review.

PubMed

Bracewell-Milnes, Timothy; Saso, Srdjan; Abdalla, Hossam; Nikolau, Dimitrios; Norman-Taylor, Julian; Johnson, Mark; Holmes, Elaine; Thum, Meen-Yau

2017-11-01

Infertility is a complex disorder with significant medical, psychological and financial consequences for patients. With live-birth rates per cycle below 30% and a drive from the Human Fertilisation and Embryology Authority (HFEA) to encourage single embryo transfer, there is significant research in different areas aiming to improve success rates of fertility treatments. One such area is investigating the causes of infertility at a molecular level, and metabolomics techniques provide a platform for studying relevant biofluids in the reproductive tract. The aim of this systematic review is to examine the recent findings for the potential application of metabolomics to female reproduction, specifically to the metabolomics of follicular fluid (FF), embryo culture medium (ECM) and endometrial fluid. To our knowledge no other systematic review has investigated this topic. English peer-reviewed journals on PubMed, Science Direct, SciFinder, were systematically searched for studies investigating metabolomics and the female reproductive tract with no time restriction set for publications. Studies were assessed for quality using the risk of bias assessment and ROBIN-I. There were 21 studies that met the inclusion criteria and were included in the systematic review. Metabolomic studies have been employed for the compositional analysis of various biofluids in the female reproductive tract, including FF, ECM, blastocoele fluid and endometrial fluid. There is some weak evidence that metabolomics technologies studying ECM might be able to predict the viability of individual embryos and implantation rate better than standard embryo morphology, However these data were not supported by randomized the controlled trials (RCTs) which showed no evidence that using metabolomics is able to improve the most important reproductive outcomes, such as clinical pregnancy and live-birth rates. This systematic review provides guidance for future metabolomic studies on biofluids of the female

Metabolomics in Newborns.

PubMed

Noto, Antonio; Fanos, Vassilios; Dessì, Angelica

2016-01-01

Metabolomics is the quantitative analysis of a large number of low molecular weight metabolites that are intermediate or final products of all the metabolic pathways in a living organism. Any metabolic profiles detectable in a human biological fluid are caused by the interaction between gene expression and the environment. The metabolomics approach offers the possibility to identify variations in metabolite profile that can be used to discriminate disease. This is particularly important for neonatal and pediatric studies especially for severe ill patient diagnosis and early identification. This property is of a great clinical importance in view of the newer definitions of health and disease. This review emphasizes the workflow of a typical metabolomics study and summarizes the latest results obtained in neonatal studies with particular interest in prematurity, intrauterine growth retardation, inborn errors of metabolism, perinatal asphyxia, sepsis, necrotizing enterocolitis, kidney disease, bronchopulmonary dysplasia, and cardiac malformation and dysfunction. © 2016 Elsevier Inc. All rights reserved.

Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics.

PubMed

Mosier, Annika C; Justice, Nicholas B; Bowen, Benjamin P; Baran, Richard; Thomas, Brian C; Northen, Trent R; Banfield, Jillian F

2013-03-12

Microorganisms grow under a remarkable range of extreme conditions. Environmental transcriptomic and proteomic studies have highlighted metabolic pathways active in extremophilic communities. However, metabolites directly linked to their physiology are less well defined because metabolomics methods lag behind other omics technologies due to a wide range of experimental complexities often associated with the environmental matrix. We identified key metabolites associated with acidophilic and metal-tolerant microorganisms using stable isotope labeling coupled with untargeted, high-resolution mass spectrometry. We observed >3,500 metabolic features in biofilms growing in pH ~0.9 acid mine drainage solutions containing millimolar concentrations of iron, sulfate, zinc, copper, and arsenic. Stable isotope labeling improved chemical formula prediction by >50% for larger metabolites (>250 atomic mass units), many of which were unrepresented in metabolic databases and may represent novel compounds. Taurine and hydroxyectoine were identified and likely provide protection from osmotic stress in the biofilms. Community genomic, transcriptomic, and proteomic data implicate fungi in taurine metabolism. Leptospirillum group II bacteria decrease production of ectoine and hydroxyectoine as biofilms mature, suggesting that biofilm structure provides some resistance to high metal and proton concentrations. The combination of taurine, ectoine, and hydroxyectoine may also constitute a sulfur, nitrogen, and carbon currency in the communities. Microbial communities are central to many critical global processes and yet remain enigmatic largely due to their complex and distributed metabolic interactions. Metabolomics has the possibility of providing mechanistic insights into the function and ecology of microbial communities. However, our limited knowledge of microbial metabolites, the difficulty of identifying metabolites from complex samples, and the inability to link metabolites directly

Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva

USDA-ARS?s Scientific Manuscript database

Dermacentor andersoni, known as the Rocky Mountain wood tick, is found in the western United States and transmits diseases of veterinary and public health importance including Rocky Mountain spotted fever, tularemia, Colarado tick fever and bovine anaplasmosis. Tick saliva is known to modulate both ...

Informatics for Metabolomics.

PubMed

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.

Chemical and metabolomic screens identify novel biomarkers and antidotes for cyanide exposure

PubMed Central

Nath, Anjali K.; Roberts, Lee D.; Liu, Yan; Mahon, Sari B.; Kim, Sonia; Ryu, Justine H.; Werdich, Andreas; Januzzi, James L.; Boss, Gerry R.; Rockwood, Gary A.; MacRae, Calum A.; Brenner, Matthew; Gerszten, Robert E.; Peterson, Randall T.

2013-01-01

Exposure to cyanide causes a spectrum of cardiac, neurological, and metabolic dysfunctions that can be fatal. Improved cyanide antidotes are needed, but the ideal biological pathways to target are not known. To understand better the metabolic effects of cyanide and to discover novel cyanide antidotes, we developed a zebrafish model of cyanide exposure and scaled it for high-throughput chemical screening. In a screen of 3120 small molecules, we discovered 4 novel antidotes that block cyanide toxicity. The most potent antidote was riboflavin. Metabolomic profiling of cyanide-treated zebrafish revealed changes in bile acid and purine metabolism, most notably by an increase in inosine levels. Riboflavin normalizes many of the cyanide-induced neurological and metabolic perturbations in zebrafish. The metabolic effects of cyanide observed in zebrafish were conserved in a rabbit model of cyanide toxicity. Further, humans treated with nitroprusside, a drug that releases nitric oxide and cyanide ions, display increased circulating bile acids and inosine. In summary, riboflavin may be a novel treatment for cyanide toxicity and prophylactic measure during nitroprusside treatment, inosine may serve as a biomarker of cyanide exposure, and metabolites in the bile acid and purine metabolism pathways may shed light on the pathways critical to reversing cyanide toxicity.—Nath, A. K., Roberts, L. D., Liu, Y., Mahon, S. B., Kim, S., Ryu, J. H., Werdich, A., Januzzi, J. L., Boss, G. R., Rockwood, G. A., MacRae, C. A., Brenner, M., Gerszten, R. E., Peterson, R. T. Chemical and metabolomic screens identify novel biomarkers and antidotes for cyanide exposure. PMID:23345455

Profiling the metabolome changes caused by cranberry procyanidins in plasma of female rats using (1) H NMR and UHPLC-Q-Orbitrap-HRMS global metabolomics approaches.

PubMed

Liu, Haiyan; Garrett, Timothy J; Tayyari, Fariba; Gu, Liwei

2015-11-01

The objective was to investigate the metabolome changes in female rats gavaged with partially purified cranberry procyanidins (PPCP) using (1) H NMR and UHPLC-Q-Orbitrap-HRMS metabolomics approaches, and to identify the contributing metabolites. Twenty-four female Sprague-Dawley rats were randomly separated into two groups and administered PPCP or partially purified apple procyanidins (PPAP) for three times using a 250 mg extracts/kg body weight dose. Plasma was collected 6 h after the last gavage and analyzed using (1) H NMR and UHPLC-Q-Orbitrap-HRMS. No metabolome difference was observed using (1) H NMR metabolomics approach. However, LC-HRMS metabolomics data show that metabolome in the plasma of female rats administered PPCP differed from those gavaged with PPAP. Eleven metabolites were tentatively identified from a total of 36 discriminant metabolic features based on accurate masses and/or product ion spectra. PPCP caused a greater increase of exogenous metabolites including p-hydroxybenzoic acid, phenol, phenol-sulphate, catechol sulphate, 3, 4-dihydroxyphenylvaleric acid, and 4'-O-methyl-(-)-epicatechin-3'-O-beta-glucuronide in rat plasma. Furthermore, the plasma level of O-methyl-(-)-epicatechin-O-glucuronide, 4-hydroxy-5-(hydroxyphenyl)-valeric acid-O-sulphate, 5-(hydroxyphenyl)-ϒ-valerolactone-O-sulphate, 4-hydroxydiphenylamine, and peonidin-3-O-hexose were higher in female rats administered with PPAP. The metabolome changes caused by cranberry procyanidins were revealed using an UHPLC-Q-Orbitrap-HRMS global metabolomics approach. Exogenous and microbial metabolites were the major identified discriminate biomarkers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metabolomics in amyotrophic lateral sclerosis: how far can it take us?

PubMed

Blasco, H; Patin, F; Madji Hounoum, B; Gordon, P H; Vourc'h, P; Andres, C R; Corcia, P

2016-03-01

Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease. Alongside identification of aetiologies, development of biomarkers is a foremost research priority. Metabolomics is one promising approach that is being utilized in the search for diagnosis and prognosis markers. Our aim is to provide an overview of the principal research in metabolomics applied to ALS. References were identified using PubMed with the terms 'metabolomics' or 'metabolomic' and 'ALS' or 'amyotrophic lateral sclerosis' or 'MND' or 'motor neuron disorders'. To date, nine articles have reported metabolomics research in patients and a few additional studies examined disease physiology and drug effects in patients or models. Metabolomics contribute to a better understanding of ALS pathophysiology but, to date, no biomarker has been validated for diagnosis, principally due to the heterogeneity of the disease and the absence of applied standardized methodology for biomarker discovery. A consensus on best metabolomics methodology as well as systematic independent validation will be an important accomplishment on the path to identifying the long-awaited biomarkers for ALS and to improve clinical trial designs. © 2016 EAN.

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

PubMed

Salek, Reza M; Neumann, Steffen; Schober, Daniel; Hummel, Jan; Billiau, Kenny; Kopka, Joachim; Correa, Elon; Reijmers, Theo; Rosato, Antonio; Tenori, Leonardo; Turano, Paola; Marin, Silvia; Deborde, Catherine; Jacob, Daniel; Rolin, Dominique; Dartigues, Benjamin; Conesa, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; O'Hagan, Steve; Hao, Jie; van Vliet, Michael; Sysi-Aho, Marko; Ludwig, Christian; Bouwman, Jildau; Cascante, Marta; Ebbels, Timothy; Griffin, Julian L; Moing, Annick; Nikolski, Macha; Oresic, Matej; Sansone, Susanna-Assunta; Viant, Mark R; Goodacre, Royston; Günther, Ulrich L; Hankemeier, Thomas; Luchinat, Claudio; Walther, Dirk; Steinbeck, Christoph

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 funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative 'coordination of standards in metabolomics' (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities' participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

Estimating Cotinine Associations and a Saliva Cotinine Level to Identify Active Cigarette Smoking in Alaska Native Pregnant Women

PubMed Central

Robinson, Renee F.; Khan, Burhan A.; Sosnoff, Connie S.; Dillard, Denise A.

2017-01-01

Studies indicate nicotine metabolism varies by race and can change during pregnancy. Given high rates of tobacco use and limited studies among Alaska Native (AN) women, we estimated associations of saliva cotinine levels with cigarette use and second-hand smoke (SHS) exposure and estimated a saliva cotinine cutoff to distinguish smoking from non-smoking pregnant AN women. Using questionnaire data and saliva cotinine, we utilized multivariable linear regression (n = 370) to estimate cotinine associations with tobacco use, SHS exposure, demographic, and pregnancy-related factors. Additionally, we estimated an optimal saliva cotinine cutoff for indication of active cigarette use in AN pregnant women using receiver operating characteristic (ROC) curve analysis (n = 377). Saliva cotinine significantly decreased with maternal age and significantly increased with cigarettes smoked per day, SHS exposure, and number of previous full term pregnancies. Using self-reported cigarette use in the past 7 days as indication of active smoking, the area under the ROC curve was 0.975 (95 % CI: 0.960–0.990). The point closest to 100 % specificity and sensitivity occurred with a cotinine concentration of 1.07 ng/mL, which corresponded to sensitivity of 94 % and specificity of 94 %. We recommend using a saliva cotinine cutoff of 1 ng/mL to distinguish active smoking in pregnant AN women. This cutoff is lower than used in other studies with pregnant women, most likely due to high prevalence of light or intermittent smoking in the AN population. Continued study of cotinine levels in diverse populations is needed. PMID:23423858

Rapid Identification of Buprenorphine in Patient Saliva

PubMed Central

Farquharson, Stuart; Dana, Kathryn; Shende, Chetan; Gladding, Zachary; Newcomb, Jenelle; Dascher, Jessica; Petrakis, Ismene L; Arias, Albert J

2017-01-01

Buprenorphine is becoming the medication of choice to help patients withdraw from opioid addiction. However, treatment is compromised by the inability of physicians to assess patient usage during scheduled examinations. Here we describe the development of a point-of-care (POC) analyzer that can rapidly measure both illicit and treatment drugs in patient saliva, ideally in the physician’s office, and with a degree of accuracy similar to chromatography. The analyzer employs a relatively simple supported liquid extraction to isolate the drugs from the saliva and surface-enhanced Raman spectroscopy (SERS) to detect the drugs. The SERS-based POC analyzer was used to identify buprenorphine and opioids in saliva samples by matching library spectra to samples collected from 7 veterans. The total analysis time, including sample preparation, was ~25 minutes. Buprenorphine concentration was estimated between 0 and 3 μg/mL. While no other prescription opioids were detected in any samples, heroin was identified in one sample; Δ-9 tetrahydrocannabinol (THC) was detected in 3 samples; and acetaminophen, caffeine, and nicotine were detected in several samples, none of which interfered with the measurements. The analysis was in very good agreement with urinalysis, correctly identifying the presence or absence of buprenorphine and THC in 13 of 14 measurements. PMID:28944090

An in vitro metabolomics approach to identify hepatotoxicity biomarkers in human L02 liver cells treated with pekinenal, a natural compound.

PubMed

Shi, Jiexia; Zhou, Jing; Ma, Hongyue; Guo, Hongbo; Ni, Zuyao; Duan, Jin'ao; Tao, Weiwei; Qian, Dawei

2016-02-01

An in vitro cell metabolomics study was performed on human L02 liver cells to investigate the toxic biomarkers of pekinenal from the herb Euphorbia pekinensis Rupr. Pekinenal significantly induced L02 cell damage, which was characterised by necrosis and apoptosis. Metabolomics combined with data pattern recognition showed that pekinenal significantly altered the profiles of more than 1299 endogenous metabolites with variable importance in the projection (VIP) > 1. Further, screening correlation coefficients between the intensities of all metabolites and the extent of L02 cell damage (MTT) identified 12 biomarker hits: ten were downregulated and two were upregulated. Among these hits, LysoPC(18:1(9Z)/(11Z)), PC(22:0/15:0) and PC(20:1(11Z)/14:1(9Z)) were disordered, implying the initiation of inflammation and cell damage. Several fatty acids (FAs) (3-hydroxytetradecanedioic acid, pivaloylcarnitine and eicosapentaenoyl ethanolamide) decreased due to fatty acid oxidation. Dihydroceramide and Cer(d18:0/14:0) were also altered and are associated with apoptosis. Additional examination of the levels of intracellular reactive oxygen species (ROS) and two eicosanoids (PGE2, PGF2α) in the cell supernatant confirmed the fatty acid oxidation and arachidonic acid metabolism pathways, respectively. In summary, cell metabolomics is a highly efficient approach for identifying toxic biomarkers and helping understand toxicity mechanisms and predict herb-induced liver injury.

Saliva Preservative for Diagnostic Purposes

NASA Technical Reports Server (NTRS)

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.

Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry

PubMed Central

Miyamoto, Suzanne; Taylor, Sandra L.; Barupal, Dinesh K.; Taguchi, Ayumu; Wohlgemuth, Gert; Wikoff, William R.; Yoneda, Ken Y.; Gandara, David R.; Hanash, Samir M.; Kim, Kyoungmi; Fiehn, Oliver

2015-01-01

Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection. PMID:25859693

An overview of renal metabolomics.

PubMed

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.

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A.; Caron, Christophe

2015-01-01

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org PMID:25527831

Saliva and wound healing.

PubMed

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.

Proteome and metabolome profiling of cytokinin action in Arabidopsis identifying both distinct and similar responses to cytokinin down- and up-regulation.

PubMed

Černý, Martin; Kuklová, Alena; Hoehenwarter, Wolfgang; Fragner, Lena; Novák, Ondrej; Rotková, Gabriela; Jedelsky, Petr L; Žáková, Katerina; Šmehilová, Mária; Strnad, Miroslav; Weckwerth, Wolfram; Brzobohaty, Bretislav

2013-11-01

In plants, numerous developmental processes are controlled by cytokinin (CK) levels and their ratios to levels of other hormones. While molecular mechanisms underlying the regulatory roles of CKs have been intensely researched, proteomic and metabolomic responses to CK deficiency are unknown. Transgenic Arabidopsis seedlings carrying inducible barley cytokinin oxidase/dehydrogenase (CaMV35S>GR>HvCKX2) and agrobacterial isopentenyl transferase (CaMV35S>GR>ipt) constructs were profiled to elucidate proteome- and metabolome-wide responses to down- and up-regulation of CK levels, respectively. Proteome profiling identified >1100 proteins, 155 of which responded to HvCKX2 and/or ipt activation, mostly involved in growth, development, and/or hormone and light signalling. The metabolome profiling covered 79 metabolites, 33 of which responded to HvCKX2 and/or ipt activation, mostly amino acids, carbohydrates, and organic acids. Comparison of the data sets obtained from activated CaMV35S>GR>HvCKX2 and CaMV35S>GR>ipt plants revealed unexpectedly extensive overlaps. Integration of the proteomic and metabolomic data sets revealed: (i) novel components of molecular circuits involved in CK action (e.g. ribosomal proteins); (ii) previously unrecognized links to redox regulation and stress hormone signalling networks; and (iii) CK content markers. The striking overlaps in profiles observed in CK-deficient and CK-overproducing seedlings might explain surprising previously reported similarities between plants with down- and up-regulated CK levels.

Think Tank on Metabolomics and Prospective Cohorts: How to Leverage Resources

Cancer.gov

This Think Tank identified resources that can be used collaboratively across prospective cohorts; developed strategies to leverage resources for advancing the use of metabolomics in prospective cohort studies; identified the best strategies for performing analyses using metabolomics data across multiple studies; and, established a collaborative group that will identify and tackle research projects that cannot be effectively investigated by one independent group.

Saliva and dental erosion

PubMed Central

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. 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. PMID:23138733

Saliva and dental erosion.

PubMed

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.

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A; Caron, Christophe

2015-05-01

The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). contact@workflow4metabolomics.org. © The Author 2014. Published by Oxford University Press.

Metabolomic Fingerprint of Heart Failure with Preserved Ejection Fraction

PubMed Central

Zordoky, Beshay N.; Sung, Miranda M.; Ezekowitz, Justin; Mandal, Rupasri; Han, Beomsoo; Bjorndahl, Trent C.; Bouatra, Souhaila; Anderson, Todd; Oudit, Gavin Y.; Wishart, David S.; Dyck, Jason R. B.

2015-01-01

Background Heart failure (HF) with preserved ejection fraction (HFpEF) is increasingly recognized as an important clinical entity. Preclinical studies have shown differences in the pathophysiology between HFpEF and HF with reduced ejection fraction (HFrEF). Therefore, we hypothesized that a systematic metabolomic analysis would reveal a novel metabolomic fingerprint of HFpEF that will help understand its pathophysiology and assist in establishing new biomarkers for its diagnosis. Methods and Results Ambulatory patients with clinical diagnosis of HFpEF (n = 24), HFrEF (n = 20), and age-matched non-HF controls (n = 38) were selected for metabolomic analysis as part of the Alberta HEART (Heart Failure Etiology and Analysis Research Team) project. 181 serum metabolites were quantified by LC-MS/MS and 1H-NMR spectroscopy. Compared to non-HF control, HFpEF patients demonstrated higher serum concentrations of acylcarnitines, carnitine, creatinine, betaine, and amino acids; and lower levels of phosphatidylcholines, lysophosphatidylcholines, and sphingomyelins. Medium and long-chain acylcarnitines and ketone bodies were higher in HFpEF than HFrEF patients. Using logistic regression, two panels of metabolites were identified that can separate HFpEF patients from both non-HF controls and HFrEF patients with area under the receiver operating characteristic (ROC) curves of 0.942 and 0.981, respectively. Conclusions The metabolomics approach employed in this study identified a unique metabolomic fingerprint of HFpEF that is distinct from that of HFrEF. This metabolomic fingerprint has been utilized to identify two novel panels of metabolites that can separate HFpEF patients from both non-HF controls and HFrEF patients. Clinical Trial Registration ClinicalTrials.gov NCT02052804 PMID:26010610

Metabolomics and Personalized Medicine.

PubMed

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.

Proteome Analysis of Watery Saliva Secreted by Green Rice Leafhopper, Nephotettix cincticeps

PubMed Central

Hattori, Makoto; Komatsu, Setsuko; Noda, Hiroaki; Matsumoto, Yukiko

2015-01-01

The green rice leafhopper, Nephotettix cincticeps, is a vascular bundle feeder that discharges watery and gelling saliva during the feeding process. To understand the potential functions of saliva for successful and safe feeding on host plants, we analyzed the complexity of proteinaceous components in the watery saliva of N. cincticeps. Salivary proteins were collected from a sucrose diet that adult leafhoppers had fed on through a membrane of stretched parafilm. Protein concentrates were separated using SDS-PAGE under reducing and non-reducing conditions. Six proteins were identified by a gas-phase protein sequencer and two proteins were identified using LC-MS/MS analysis with reference to expressed sequence tag (EST) databases of this species. Full -length cDNAs encoding these major proteins were obtained by rapid amplification of cDNA ends-PCR (RACE-PCR) and degenerate PCR. Furthermore, gel-free proteome analysis that was performed to cover the broad range of salivary proteins with reference to the latest RNA-sequencing data from the salivary gland of N. cincticeps, yielded 63 additional protein species. Out of 71 novel proteins identified from the watery saliva, about 60 % of those were enzymes or other functional proteins, including GH5 cellulase, transferrin, carbonic anhydrases, aminopeptidase, regucalcin, and apolipoprotein. The remaining proteins appeared to be unique and species- specific. This is the first study to identify and characterize the proteins in watery saliva of Auchenorrhyncha species, especially sheath-producing, vascular bundle-feeders. PMID:25909947

Proteomic Analysis of Cattle Tick Rhipicephalus (Boophilus) microplus Saliva: A Comparison between Partially and Fully Engorged Females

PubMed Central

Terra, Renata Maria Soares; Martins, João Ricardo; Mulenga, Albert; Sherman, Nicholas E.; Fox, Jay W.; Yates, John R.; Termignoni, Carlos; Pinto, Antônio F. M.; da Silva Vaz, Itabajara

2014-01-01

The cattle tick Rhipicephalus (Boophilus) microplus is one of the most harmful parasites affecting bovines. Similarly to other hematophagous ectoparasites, R. microplus saliva contains a collection of bioactive compounds that inhibit host defenses against tick feeding activity. Thus, the study of tick salivary components offers opportunities for the development of immunological based tick control methods and medicinal applications. So far, only a few proteins have been identified in cattle tick saliva. The aim of this work was to identify proteins present in R. microplus female tick saliva at different feeding stages. Proteomic analysis of R. microplus saliva allowed identifying peptides corresponding to 187 and 68 tick and bovine proteins, respectively. Our data confirm that (i) R. microplus saliva is complex, and (ii) that there are remarkable differences in saliva composition between partially engorged and fully engorged female ticks. R. microplus saliva is rich mainly in (i) hemelipoproteins and other transporter proteins, (ii) secreted cross-tick species conserved proteins, (iii) lipocalins, (iv) peptidase inhibitors, (v) antimicrobial peptides, (vii) glycine-rich proteins, (viii) housekeeping proteins and (ix) host proteins. This investigation represents the first proteomic study about R. microplus saliva, and reports the most comprehensive Ixodidae tick saliva proteome published to date. Our results improve the understanding of tick salivary modulators of host defense to tick feeding, and provide novel information on the tick-host relationship. PMID:24762651

Brief Functional Analysis and Intervention Evaluation for Treatment of Saliva-Play

ERIC Educational Resources Information Center

Luiselli, James K.; Ricciardi, Joseph N.; Schmidt, Sarah; Tarr, Melissa

2004-01-01

We conducted a brief (8 days) functional analysis to identify sources of control over persistent saliva-play displayed by a 6-year old child with autism in a school setting. The functional analysis suggested that saliva-play was maintained by automatic reinforcement, leading to an intervention evaluation (3 days) that compared two methods of…

Identifying the metabolic perturbations in earthworm induced by cypermethrin using gas chromatography-mass spectrometry based metabolomics

PubMed Central

Ch, Ratnasekhar; Singh, Amit Kumar; Pandey, Pathya; Saxena, Prem Narain; Reddy Mudiam, Mohana Krishna

2015-01-01

Globally, cypermethrin is one of the most widely used synthetic pyrethroid for agricultural and domestic purposes. Most part of the pesticides used in the agriculture ends up as residues in the soil, making soil dwelling organisms, especially earthworms more susceptible to pesticide intoxication. Cypermethrin is known to be a neurotoxicant to many model organisms, including mammals and insects, but such type of toxicity evidence is not available for invertebrate systems like earthworms. In the present work, metabolomics based approach was utilized to identify the toxic mechanism of action of cypermethrin on earthworm (Metaphire posthuma) and these were exposed to sub-lethal concentrations of cypermethrin such as 2.5 mg/kg, 5 mg/kg, 10 mg/kg and 20 mg/kg (1/40th, 1/20th, 1/10th and 1/5th of LC50, respectively) for fourteen days. The results revealed that 22 metabolites (mainly fatty acids, sugars and amino acids) were shown significant responses in the exposed earthworms and these responses are dose dependent. It is proposed that mainly carbohydrate and fatty acids in neural system metabolism was disturbed. Overall, the results provided that metabolomics can be an effective tool to understand the effects of cypermethrin on the metabolic responses of earthworm Metaphire posthuma. PMID:26514086

[Nicotine and benz(alpha)piren concentration in saliva of inveterate tobacco-smokers].

PubMed

Zurabashvili, Z A; Chanturiaia, I L; Kapanadze, L R

2009-11-01

The aim of the work is study in saliva the nicotine and benz(alphapiren concentration dynamic in morning without cigarette, after light first cigarette and after one hour after lighting. All biochemical substances is analyzed and identified chromatographically on Bondo-Pac C(18) column (Liquid Chromatography Millipor-Waters, USA). The conducted quantitative and qualitative analyzes show that at all examinations benz(alpha)piren concentration dynamic in saliva is very differently in compare of nicotine concentration dynamic. The content of benz(alpha)piren in saliva at all analyzes transfer very slowly. Our data show that with the increase of the time the concentration of nicotine in saliva in beginning increase, add then diminish. The studies are necessary to be held in different directions. First, the medical consequences of using the tobacco and the ways of their curing should be identified. The second direction should mean elaboration of preventive measures and programs, or measures of intervention.

Untargeted Plasma Metabolomics Identifies Endogenous Metabolite with Drug-like Properties in Chronic Animal Model of Multiple Sclerosis*

PubMed Central

Poisson, Laila M.; Suhail, Hamid; Singh, Jaspreet; Datta, Indrani; Denic, Aleksandar; Labuzek, Krzysztof; Hoda, Md Nasrul; Shankar, Ashray; Kumar, Ashok; Cerghet, Mirela; Elias, Stanton; Mohney, Robert P.; Rodriguez, Moses; Rattan, Ramandeep; Mangalam, Ashutosh K.; Giri, Shailendra

2015-01-01

We performed untargeted metabolomics in plasma of B6 mice with experimental autoimmune encephalitis (EAE) at the chronic phase of the disease in search of an altered metabolic pathway(s). Of 324 metabolites measured, 100 metabolites that mapped to various pathways (mainly lipids) linked to mitochondrial function, inflammation, and membrane stability were observed to be significantly altered between EAE and control (p < 0.05, false discovery rate <0.10). Bioinformatics analysis revealed six metabolic pathways being impacted and altered in EAE, including α-linolenic acid and linoleic acid metabolism (PUFA). The metabolites of PUFAs, including ω-3 and ω-6 fatty acids, are commonly decreased in mouse models of multiple sclerosis (MS) and in patients with MS. Daily oral administration of resolvin D1, a downstream metabolite of ω-3, decreased disease progression by suppressing autoreactive T cells and inducing an M2 phenotype of monocytes/macrophages and resident brain microglial cells. This study provides a proof of principle for the application of metabolomics to identify an endogenous metabolite(s) possessing drug-like properties, which is assessed for therapy in preclinical mouse models of MS. PMID:26546682

Metabolomics of Small Numbers of Cells: Metabolomic Profiling of 100, 1000, and 10000 Human Breast Cancer Cells.

PubMed

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.

Metabolomics for laboratory diagnostics.

PubMed

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.

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.

PubMed

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

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

PubMed Central

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

Causal Genetic Variation Underlying Metabolome Differences.

PubMed

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.

The Importance of Experimental Design, Quality Assurance, and Control in Plant Metabolomics Experiments.

PubMed

Martins, Marina C M; Caldana, Camila; Wolf, Lucia Daniela; de Abreu, Luis Guilherme Furlan

2018-01-01

The output of metabolomics relies to a great extent upon the methods and instrumentation to identify, quantify, and access spatial information on as many metabolites as possible. However, the most modern machines and sophisticated tools for data analysis cannot compensate for inappropriate harvesting and/or sample preparation procedures that modify metabolic composition and can lead to erroneous interpretation of results. In addition, plant metabolism has a remarkable degree of complexity, and the number of identified compounds easily surpasses the number of samples in metabolomics analyses, increasing false discovery risk. These aspects pose a large challenge when carrying out plant metabolomics experiments. In this chapter, we address the importance of a proper experimental design taking into consideration preventable complications and unavoidable factors to achieve success in metabolomics analysis. We also focus on quality control and standardized procedures during the metabolomics workflow.

A device for the collection of submandibular saliva.

PubMed

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.

Antimicrobial defense systems in saliva.

PubMed

van 't Hof, Wim; Veerman, Enno C I; Nieuw Amerongen, Arie V; Ligtenberg, Antoon J M

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 growth of bacteria. In this paper, we discuss the various mechanisms by which the composition of the oral microflora is modulated by saliva. Saliva covers the oral hard and soft tissues with a conditioning film which governs the initial attachment of microorganisms, a crucial step in the setup of the oral microflora. It furthermore contains proteins which in the soluble phase bind to bacteria, blocking their adherence to surfaces. When the supply of nutrients is diminished, bacteria use salivary glycoproteins, especially high-molecular-weight mucins, as a source of complex carbohydrates, requiring a consortium of microorganisms for breakdown. In this way saliva promotes the complexity of the oral microflora, which in itself protects against overgrowth by few pathogenic species. Finally, saliva harbors a large panel of antimicrobial proteins which directly and indirectly inhibit uncontrolled outgrowth of bacteria. These include lactoferrin, lactoperoxidase, lysozyme and antimicrobial peptides. Under pathological conditions serum leakage occurs, and saliva mobilizes the humoral and cellular defense mechanisms in the blood. In sum, saliva favors the establishment of a highly diverse microflora, rather than a semisterile environment.

Novel Genes Required for the Fitness of Streptococcus pyogenes in Human Saliva

PubMed Central

Zhu, Luchang; Charbonneau, Amelia R. L.; Waller, Andrew S.; Olsen, Randall J.; Beres, Stephen B.

2017-01-01

ABSTRACT Streptococcus pyogenes (group A streptococcus [GAS]) causes 600 million cases of pharyngitis each year. Despite this considerable disease burden, the molecular mechanisms used by GAS to infect, cause clinical pharyngitis, and persist in the human oropharynx are poorly understood. Saliva is ubiquitous in the human oropharynx and is the first material GAS encounters in the upper respiratory tract. Thus, a fuller understanding of how GAS survives and proliferates in saliva may provide valuable insights into the molecular mechanisms at work in the human oropharynx. We generated a highly saturated transposon insertion mutant library in serotype M1 strain MGAS2221, a strain genetically representative of a pandemic clone that arose in the 1980s and spread globally. The transposon mutant library was exposed to human saliva to screen for GAS genes required for wild-type fitness in this clinically relevant fluid. Using transposon-directed insertion site sequencing (TraDIS), we identified 92 genes required for GAS fitness in saliva. The more prevalent categories represented were genes involved in carbohydrate transport/metabolism, amino acid transport/metabolism, and inorganic ion transport/metabolism. Using six isogenic mutant strains, we confirmed that each of the mutants was significantly impaired for growth or persistence in human saliva ex vivo. Mutants with an inactivated Spy0644 (sptA) or Spy0646 (sptC) gene had especially severe persistence defects. This study is the first to use of TraDIS to study bacterial fitness in human saliva. The new information we obtained will be valuable for future translational maneuvers designed to prevent or treat human GAS infections. IMPORTANCE The human bacterial pathogen Streptococcus pyogenes (group A streptococcus [GAS]) causes more than 600 million cases of pharyngitis annually worldwide, 15 million of which occur in the United States. The human oropharynx is the primary anatomic site for GAS colonization and infection

Development of an Integrated Metabolomic Profiling Approach for Infectious Diseases Research

PubMed Central

Lv, Haitao; Hung, Chia S.; Chaturvedi, Kaveri S.; Hooton, Thomas M.; Henderson, Jeffrey P.

2013-01-01

Metabolomic profiling offers direct insights into the chemical environment and metabolic pathway activities at sites of human disease. During infection, this environment may receive important contributions from both host and pathogen. Here we apply untargeted metabolomics approach to identify compounds associated with an E. coli urinary tract infection population. Correlative and structural data from minimally processed samples were obtained using an optimized LC-MS platform capable of resolving ∼2300 molecular features. Principal components analysis readily distinguished patient groups and multiple supervised chemometric analyses resolved robust metabolomic shifts between groups. These analyses revealed nine compounds whose provisional structures suggest candidate infection-associated endocrine, catabolic, and lipid pathways. Several of these metabolite signatures may derive from microbial processing of host metabolites. Overall, this study highlights the ability of metabolomic approaches to directly identify compounds encountered by, and produced from, bacterial pathogens within human hosts. PMID:21922104

The food metabolome: a window over dietary exposure.

PubMed

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.

ARSENIC SPECIATION ANALYSIS IN HUMAN SALIVA

EPA Science Inventory

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 ...

Tongue-mandible coupling movements during saliva swallowing.

PubMed

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.

Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites.

PubMed

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 approach to identify all the metabolites in a given biological system is called metabolic fingerprinting. Using high-resolution and high-mass accuracy mass spectrometry, large metabolome coverage, sensitivity, and specificity can be attained. Although the theoretical concepts of this methodology are usually provided in life-science programs, hands-on laboratory experiments are not usually accessible to undergraduate students. Even if the instruments are available, there are not simple laboratory protocols created specifically for teaching metabolomics. We designed a straightforward hands-on laboratory experiment to introduce students to this methodology, relating it to biochemical knowledge through metabolic pathway mapping of the identified metabolites. This study focuses on mitochondrial metabolomics since mitochondria have a well-known, medium-sized cellular sub-metabolome. These features facilitate both data processing and pathway mapping. In this experiment, students isolate mitochondria from potatoes, extract the metabolites, and analyze them by high-resolution mass spectrometry (using an FT-ICR mass spectrometer). The resulting mass list is submitted to an online program for metabolite identification, and compounds associated with mitochondrial pathways can be highlighted in a metabolic network map. © 2015 The International Union of Biochemistry and Molecular Biology.

MetaboLights: An Open-Access Database Repository for Metabolomics Data.

PubMed

Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

2016-03-24

MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. Copyright © 2016 John Wiley & Sons, Inc.

Observations on saliva osmolality during progressive dehydration and partial rehydration.

PubMed

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.

Saliva as a diagnostic fluid. Literature review

PubMed Central

Mancheño-Franch, Aisha; Marzal-Gamarra, Cristina; Carlos-Fabuel, Laura

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 amount of desquamated epithelial cells, microorganisms and remnants of food and drink; it is essential to cleanse and refine the saliva samples to remove any external elements. Immediate processing of the sample is recommended in order to avoid decomposition, where this is not possible, the sample may be stored at -80ºC. Salivary analysis – much the same as blood analysis – aims to identify diverse medication or indications of certain diseases while providing a relatively simple tool for both early diagnosis and monitoring various irregularities. The practicalities of salivary analysis have been studied in fields such as: viral and bacterial infections, autoimmune diseases (like Sjögren’s syndrome and cɶliac disease), endocrinopathies (such as Cushing’s syndrome), oncology (early diagnosis of breast, lung and stomach carcinoma and oral squamous cell carcinoma), stress assessment, medication detection and forensic science among others. It is hoped that salivary analysis, with the help of current technological advances, will be valued much more highly in the near future. There still remain contradictory results with respect to analytic markers, which is why further studies into wider-ranging samples are fundamental to prove its viability. Key words:Saliva, biomarkers, early diagnosis. PMID:24558562

Exosome-like vesicles with dipeptidyl peptidase IV in human saliva.

PubMed

Ogawa, Yuko; Kanai-Azuma, Masami; Akimoto, Yoshihiro; Kawakami, Hayato; Yanoshita, Ryohei

2008-06-01

Saliva contains a large number of proteins that participate in the protection of oral tissue. We found, for the first time, small vesicles (30-130 nm in diameter) in human whole saliva. Vesicles from saliva were identified by electron microscopy after isolation by gel-filtration on Sepharose CL-4B. They resemble exosomes, which are vesicles with an endosome-derived limiting membrane that are secreted by a diverse range of cell types. We performed a biochemical characterization of these vesicles by amino acid sequence analysis and Western blot analysis. We found that they contain dipeptidyl peptidase IV (DPP IV), galectin-3 and immunoglobulin A, which have potential to influence immune response. The DPP IV in the vesicles was metabolically active in cleaving substance P and glucose-dependent insulinotropic polypeptide to release N-terminal dipeptides. Our results demonstrate that human whole saliva contains exosome-like vesicles; they might participate in the catabolism of bioactive peptides and play a regulatory role in local immune defense in the oral cavity.

Recent advances in the application of metabolomics to Alzheimer's Disease.

PubMed

Trushina, Eugenia; Mielke, Michelle M

2014-08-01

The pathophysiological changes associated with Alzheimer's Disease (AD) begin decades before the emergence of clinical symptoms. Understanding the early mechanisms associated with AD pathology is, therefore, especially important for identifying disease-modifying therapeutic targets. While the majority of AD clinical trials to date have focused on anti-amyloid-beta (Aβ) treatments, other therapeutic approaches may be necessary. The ability to monitor changes in cellular networks that include both Aβ and non-Aβ pathways is essential to advance our understanding of the etiopathogenesis of AD and subsequent development of cognitive symptoms and dementia. Metabolomics is a powerful tool that detects perturbations in the metabolome, a pool of metabolites that reflects changes downstream of genomic, transcriptomic and proteomic fluctuations, and represents an accurate biochemical profile of the organism in health and disease. The application of metabolomics could help to identify biomarkers for early AD diagnosis, to discover novel therapeutic targets, and to monitor therapeutic response and disease progression. Moreover, given the considerable parallel between mouse and human metabolism, the use of metabolomics provides ready translation of animal research into human studies for accelerated drug design. In this review, we will summarize current progress in the application of metabolomics in both animal models and in humans to further understanding of the mechanisms involved in AD pathogenesis. © 2013.

Metabolomics and Diabetes: Analytical and Computational Approaches

PubMed Central

Sas, Kelli M.; Karnovsky, Alla; Michailidis, George

2015-01-01

Diabetes is characterized by altered metabolism of key molecules and regulatory pathways. The phenotypic expression of diabetes and associated complications encompasses complex interactions between genetic, environmental, and tissue-specific factors that require an integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate small molecule metabolites from biological systems. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled identification of complex metabolic phenotypes. Continued development of bioinformatics and analytical strategies has facilitated the discovery of causal links in understanding the pathophysiology of diabetes and its complications. Here, we summarize the metabolomics workflow, including analytical, statistical, and computational tools, highlight recent applications of metabolomics in diabetes research, and discuss the challenges in the field. PMID:25713200

Distinct urine metabolome after Asian ginseng and American ginseng intervention based on GC-MS metabolomics approach

PubMed Central

Yang, Liu; Yu, Qing-Tao; Ge, Ya-Zhong; Zhang, Wen-Song; Fan, Yong; Ma, Chung-Wah; Liu, Qun; Qi, Lian-Wen

2016-01-01

Ginseng occupies a prominent position in the list of best-selling natural products worldwide. Asian ginseng (Panax ginseng) and American ginseng (Panax quinquefolius) show different properties and medicinal applications in pharmacology, even though the main active constituents of them are both thought to be ginsenosides. Metabolomics is a promising method to profile entire endogenous metabolites and monitor their fluctuations related to exogenous stimulus. Herein, an untargeted metabolomics approach was applied to study the overall urine metabolic differences between Asian ginseng and American ginseng in mice. Metabolomics analyses were performed using gas chromatography-mass spectrometry (GC-MS) together with multivariate statistical data analysis. A total of 21 metabolites related to D-glutamine and D-glutamate metabolism, glutathione metabolism, TCA cycle and glyoxylate and dicarboxylate metabolism, differed significantly under the Asian ginseng treatment; 34 metabolites mainly associated with glyoxylate and dicarboxylate metabolism, TCA cycle and taurine and hypotaurine metabolism, were significantly altered after American ginseng treatment. Urinary metabolomics reveal that Asian ginseng and American ginseng can benefit organism physiological and biological functions via regulating multiple metabolic pathways. The important pathways identified from Asian ginseng and American ginseng can also help to explore new therapeutic effects or action targets so as to broad application of these two ginsengs. PMID:27991533

[The physicochemical and microbiological characteristics of saliva during and after pregnancy].

PubMed

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.

Clinical aspects of Candida species carriage in saliva of xerotomic subjects.

PubMed

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.

Metabolomics in chemical ecology.

PubMed

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.

MEASURING CHOLINESTERASE ACTIVITY IN HUMAN SALIVA

EPA Science Inventory

To assess the potential for using saliva in pesticide biomonitoring, the consistency of cholinesterase activity in human saliva collected over time was examined. In this pilot study, saliva was collected from 20 healthy adults once per week for 5 consecutive weeks using 2 differe...

MEASURING CHOLINESTERASE ACTIVITY IN HUMAN SALIVA.

EPA Science Inventory

To assess the potential for using saliva in pesticide biomonitoring, the consistency of cholinesterase activity in human saliva collected over time was examined. In this pilot study, saliva was collected from 20 healthy adults once per week for 5 consecutive weeks using 2 differe...

Impact of Intestinal Microbiota on Intestinal Luminal Metabolome

PubMed Central

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 < 0.05), 77 metabolites were present in significantly lower concentrations and/or incidence in the GF mice than in the Ex-GF mice (p < 0.05), and 56 metabolites showed no differences in the concentration or incidence between GF and Ex-GF mice. These indicate that intestinal microbiota highly influenced the colonic luminal metabolome and a comprehensive understanding of intestinal luminal metabolome is critical for clarifying host-intestinal bacterial interactions. PMID:22724057

Metabolomic markers of fertility in bull seminal plasma

PubMed Central

Dinh, Thu; Kaya, Abdullah; Topper, Einko; Moura, Arlindo Alencar

2018-01-01

Metabolites play essential roles in biological systems, but detailed identities and significance of the seminal plasma metabolome related to bull fertility are still unknown. The objectives of this study were to determine the comprehensive metabolome of seminal plasma from Holstein bulls and to ascertain the potential of metabolites as biomarkers of bull fertility. The seminal plasma metabolome from 16 Holstein bulls with two fertility rates were determined by gas chromatography-mass spectrometry (GC-MS). Multivariate and univariate analyses of the data were performed, and the pathways associated with the seminal plasma metabolome were identified using bioinformatics approaches. Sixty-three metabolites were identified in the seminal plasma of all bulls. Fructose was the most abundant metabolite in the seminal fluid, followed for citric acid, lactic acid, urea and phosphoric acid. Androstenedione, 4-ketoglucose, D-xylofuranose, 2-oxoglutaric acid and erythronic acid represented the least predominant metabolites. Partial-Least Squares Discriminant Analysis (PLSDA) revealed a distinct separation between high and low fertility bulls. The metabolites with the greatest Variable Importance in Projection score (VIP > 2) were 2-oxoglutaric acid and fructose. Heat-map analysis, based on VIP score, and univariate analysis indicated that 2-oxoglutaric acid was less (P = 0.02); whereas fructose was greater (P = 0.02) in high fertility than in low fertility bulls. The current study is the first to describe the metabolome of bull seminal plasma using GC-MS and presented metabolites such as 2-oxoglutaric acid and fructose as potential biomarkers of bull fertility. PMID:29634739

Metabolomics window into diabetic complications.

PubMed

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.

Metabolomics and Its Application to Acute Lung Diseases

PubMed Central

Stringer, Kathleen A.; McKay, Ryan T.; Karnovsky, Alla; Quémerais, Bernadette; Lacy, Paige

2016-01-01

Metabolomics is a rapidly expanding field of systems biology that is gaining significant attention in many areas of biomedical research. Also known as metabonomics, it comprises the analysis of all small molecules or metabolites that are present within an organism or a specific compartment of the body. Metabolite detection and quantification provide a valuable addition to genomics and proteomics and give unique insights into metabolic changes that occur in tangent to alterations in gene and protein activity that are associated with disease. As a novel approach to understanding disease, metabolomics provides a “snapshot” in time of all metabolites present in a biological sample such as whole blood, plasma, serum, urine, and many other specimens that may be obtained from either patients or experimental models. In this article, we review the burgeoning field of metabolomics in its application to acute lung diseases, specifically pneumonia and acute respiratory disease syndrome (ARDS). We also discuss the potential applications of metabolomics for monitoring exposure to aerosolized environmental toxins. Recent reports have suggested that metabolomics analysis using nuclear magnetic resonance (NMR) and mass spectrometry (MS) approaches may provide clinicians with the opportunity to identify new biomarkers that may predict progression to more severe disease, such as sepsis, which kills many patients each year. In addition, metabolomics may provide more detailed phenotyping of patient heterogeneity, which is needed to achieve the goal of precision medicine. However, although several experimental and clinical metabolomics studies have been conducted assessing the application of the science to acute lung diseases, only incremental progress has been made. Specifically, little is known about the metabolic phenotypes of these illnesses. These data are needed to substantiate metabolomics biomarker credentials so that clinicians can employ them for clinical decision

Metabolomic Modularity Analysis (MMA) to Quantify Human Liver Perfusion Dynamics.

PubMed

Sridharan, Gautham Vivek; Bruinsma, Bote Gosse; Bale, Shyam Sundhar; Swaminathan, Anandh; Saeidi, Nima; Yarmush, Martin L; Uygun, Korkut

2017-11-13

Large-scale -omics data are now ubiquitously utilized to capture and interpret global responses to perturbations in biological systems, such as the impact of disease states on cells, tissues, and whole organs. Metabolomics data, in particular, are difficult to interpret for providing physiological insight because predefined biochemical pathways used for analysis are inherently biased and fail to capture more complex network interactions that span multiple canonical pathways. In this study, we introduce a nov-el approach coined Metabolomic Modularity Analysis (MMA) as a graph-based algorithm to systematically identify metabolic modules of reactions enriched with metabolites flagged to be statistically significant. A defining feature of the algorithm is its ability to determine modularity that highlights interactions between reactions mediated by the production and consumption of cofactors and other hub metabolites. As a case study, we evaluated the metabolic dynamics of discarded human livers using time-course metabolomics data and MMA to identify modules that explain the observed physiological changes leading to liver recovery during subnormothermic machine perfusion (SNMP). MMA was performed on a large scale liver-specific human metabolic network that was weighted based on metabolomics data and identified cofactor-mediated modules that would not have been discovered by traditional metabolic pathway analyses.

Metabolomics identifies an inflammatory cascade involved in dioxin- and diet-induced steatohepatitis

PubMed Central

Matsubara, Tsutomu; Tanaka, Naoki; Krausz, Kristopher W.; Manna, Soumen K.; Kang, Dong Wook; Anderson, Erik R.; Luecke, Hans; Patterson, Andrew D.; Shah, Yatrik M.; Gonzalez, Frank J.

2012-01-01

Summary 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is among the most potent environmentally toxic compounds. Serum metabolomics identified azelaic acid-mono esters as significantly increased metabolites after TCDD treatment, due to down-regulation of hepatic carboxylesterase 3 (CES3, also known as triglyceride hydrolase) expression in an arylhydrocarbon receptor (AhR)-dependent manner in mice. The decreased CES3 expression was accomplished by TCDD-stimulated TGFβ-SMAD3 and IL6-STAT3 signaling, but not by direct AhR signaling. Methionine- and choline-deficient (MCD) diet-treated mice also showed enhanced serum azelaic acid-mono ester levels following attenuation of hepatic CES3 expression, while db/db mice did not, thus suggesting an association with steatohepatitis. Forced expression of CES3 reversed serum azelaic acid-mono ester/azelaic acid ratios and hepatic TGFβ mRNA levels in TCDD- and MCD diet-treated mice and ameliorated steatohepatitis induced by MCD diet. These results support the view that azelaic acid-mono esters are possible indicators of TCDD exposure and steatohepatitis, and suggest a link between CES3, TGFβ, and steatohepatitis. PMID:23140643

Fluoride bioavailability in saliva and plaque

PubMed Central

2012-01-01

Background Different fluoride formulations may have different effects on caries prevention. It was the aim of this clinical study to assess the fluoride content, provided by NaF compared to amine fluoride, in saliva and plaque. Methods Eight trained volunteers brushed their teeth in the morning for 3 minutes with either NaF or amine fluoride, and saliva and 3-day-plaque-regrowth was collected at 5 time intervals during 6 hours after tooth brushing. The amount of collected saliva and plaque was measured, and the fluoride content was analysed using a fluoride sensitive electrode. All subjects repeated all study cycles 5 times, and 3 cycles per subject underwent statistical analysis using the Wilcoxon-Mann-Whitney test. Results Immediately after brushing the fluoride concentration in saliva increased rapidly and dropped to the baseline level after 360 minutes. No difference was found between NaF and amine fluoride. All plaque fluoride levels were elevated after 30 minutes until 120 minutes after tooth brushing, and decreasing after 360 minutes to baseline. According to the highly individual profile of fluoride in saliva and plaque, both levels of bioavailability correlated for the first 30 minutes, and the fluoride content of saliva and plaque was back to baseline after 6 hours. Conclusions Fluoride levels in saliva and plaque are interindividually highly variable. However, no significant difference in bioavailability between NaF and amine fluoride, in saliva, or in plaque was found. PMID:22230722

Metabolomic Profiles of Current Cigarette Smokers

PubMed Central

Hsu, Ping-Ching; Lan, Renny S.; Brasky, Theodore M.; Marian, Catalin; Cheema, Amrita K.; Ressom, Habtom W.; Loffredo, Christopher A.; Pickworth, Wallace B.; Shields, Peter G.

2017-01-01

Smoking-related biomarkers for lung cancer and other diseases are needed to enhance early detection strategies and to provide a science base for tobacco product regulation. An untargeted metabolomics approach by ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UHPLC-Q-TOF MS) totaling 957 assays was used in a novel experimental design where 105 current smokers smoked 2 cigarettes one hour apart. Blood was collected immediately before and after each cigarette allowing for within-subject replication. Dynamic changes of the metabolomic profiles from smokers’ four blood samples were observed and biomarkers affected by cigarette smoking were identified. Thirty-one metabolites were definitively shown to be affected by acute effect of cigarette smoking, uniquely including menthol-glucuronide, the reduction of glutamate, oleamide, and 13 glycerophospholipids. This first time identification of a menthol metabolite in smokers’ blood serves as proof-of-principle for using metabolomics to identify new tobacco-exposure biomarkers, and also provides new opportunities in studying menthol-containing tobacco products in humans. Gender and race differences also were observed. Network analysis revealed 12 molecules involved in cancer, notably inhibition of cAMP. These novel tobacco-related biomarkers provide new insights to the effects of smoking which may be important in carcinogenesis but not previously linked with tobacco-related diseases. PMID:27341184

Changes in the metabolome may serve as peripheral biomarkers of CNS toxicity.

EPA Science Inventory

Since our observation that an acute exposure to different classes of pesticides resulted in different changes in plasma metabolomics markers, a study of the metabolome has become of high interest for identifying markers of neurotoxicity. A Biocrates AbsoluteIDQTM p180 platform wa...

Metabolomics and Epidemiology Working Group

Cancer.gov

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.

Investigation of mixed saliva by optoelectronic methods

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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.

Enhancement of Cellulose Degradation by Cattle Saliva

PubMed Central

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

1H NMR-metabolomics: can they be a useful tool in our understanding of cardiac arrest?

PubMed

Chalkias, Athanasios; Fanos, Vassilios; Noto, Antonio; Castrén, Maaret; Gulati, Anil; Svavarsdóttir, Hildigunnur; Iacovidou, Nicoletta; Xanthos, Theodoros

2014-05-01

This review focuses on the presentation of the emerging technology of metabolomics, a promising tool for the detection of identifying the unrevealed biological pathways that lead to cardiac arrest. The electronic bases of PubMed, Scopus, and EMBASE were searched. Research terms were identified using the MESH database and were combined thereafter. Initial search terms were "cardiac arrest", "cardiopulmonary resuscitation", "post-cardiac arrest syndrome" combined with "metabolomics". Metabolomics allow the monitoring of hundreds of metabolites from tissues or body fluids and already influence research in the field of cardiac metabolism. This approach has elucidated several pathophysiological mechanisms and identified profiles of metabolic changes that can be used to follow the disease processes occurring in the peri-arrest period. This can be achieved through leveraging the strengths of unbiased metabolome-wide scans, which include thousands of final downstream products of gene transcription, enzyme activity and metabolic products of extraneously administered substances, in order to identify a metabolomic fingerprint associated with an increased risk of cardiac arrest. Although this technology is still under development, metabolomics is a promising tool for elucidating biological pathways and discovering clinical biomarkers, strengthening the efforts for optimizing both the prevention and treatment of cardiac arrest. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

SECIMTools: a suite of metabolomics data analysis tools.

PubMed

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.

Pattern recognition of estradiol, testosterone and dihydrotestosterone in children's saliva samples using stochastic microsensors

NASA Astrophysics Data System (ADS)

Staden, Raluca-Ioana Stefan-Van; Gugoaşă, Livia Alexandra; Calenic, Bogdan; Legler, Juliette

2014-07-01

Stochastic microsensors based on diamond paste and three types of electroactive materials (maltodextrin (MD), α-cyclodextrin (α-CD) and 5,10,15,20-tetraphenyl-21H,23H porphyrin (P)) were developed for the assay of estradiol (E2), testosterone (T2) and dihydrotestosterone (DHT) in children's saliva. The main advantage of utilization of such tools is the possibility to identify and quantify all three hormones within minutes in small volumes of childen's saliva. The limits of quantification obtained for DHT, T2, and E2 (1 fmol/L for DHT, 1 pmol/L for T2, and 66 fmol/L for E2) determined using the proposed tools allows the utilization of these new methods with high reliability for the screening of saliva samples from children. This new method proposed for the assay of the three hormones overcomes the limitations (regarding limits of determination) of ELISA method which is the standard method used in clinical laboratories for the assay of DHT, T2, and E2 in saliva samples. The main feature of its utilization for children's saliva is to identify earlier problems related to early puberty and obesity.

Metabolomic analysis of 92 pulmonary embolism patients from a nested case-control study identifies metabolites associated with adverse clinical outcomes.

PubMed

Zeleznik, O A; Poole, E M; Lindstrom, S; Kraft, P; Van Hylckama Vlieg, A; Lasky-Su, J A; Harrington, L B; Hagan, K; Kim, J; Parry, B A; Giordano, N; Kabrhel, C

2018-03-01

Essentials Risk-stratification often fails to predict clinical deterioration in pulmonary embolism (PE). First-ever high-throughput metabolomics analysis of risk-stratified PE patients. Changes in circulating metabolites reflect a compromised energy metabolism in PE. Metabolites play a key role in the pathophysiology and risk stratification of PE. Background Patients with acute pulmonary embolism (PE) exhibit wide variation in clinical presentation and outcomes. Our understanding of the pathophysiologic mechanisms differentiating low-risk and high-risk PE is limited, so current risk-stratification efforts often fail to predict clinical deterioration and are insufficient to guide management. Objectives To improve our understanding of the physiology differentiating low-risk from high-risk PE, we conducted the first-ever high-throughput metabolomics analysis (843 named metabolites) comparing PE patients across risk strata within a nested case-control study. Patients/methods We enrolled 92 patients diagnosed with acute PE and collected plasma within 24 h of PE diagnosis. We used linear regression and pathway analysis to identify metabolites and pathways associated with PE risk-strata. Results When we compared 46 low-risk with 46 intermediate/high-risk PEs, 50 metabolites were significantly different after multiple testing correction. These metabolites were enriched in the following pathways: tricarboxylic acid (TCA) cycle, fatty acid metabolism (acyl carnitine) and purine metabolism, (hypo)xanthine/inosine containing. Additionally, energy, nucleotide and amino acid pathways were downregulated in intermediate/high-risk PE patients. When we compared 28 intermediate-risk with 18 high-risk PE patients, 41 metabolites differed at a nominal P-value level. These metabolites were enriched in fatty acid metabolism (acyl cholines), and hemoglobin and porphyrin metabolism. Conclusion Our results suggest that high-throughput metabolomics can provide insight into the

High Resolution Separations and Improved Ion Production and Transmission in Metabolomics

PubMed Central

Metz, Thomas O.; Page, Jason S.; Baker, Erin S.; Tang, Keqi; Ding, Jie; Shen, Yufeng; Smith, Richard D.

2008-01-01

The goal of metabolomics analyses is the detection and quantitation of as many sample components as reasonably possible in order to identify compounds or “features” that can be used to characterize the samples under study. When utilizing electrospray ionization to produce ions for analysis by mass spectrometry (MS), it is important that metabolome sample constituents be efficiently separated prior to ion production, in order to minimize ionization suppression and thereby extend the dynamic range of the measurement, as well as the coverage of the metabolome. Similarly, optimization of the MS inlet and interface can lead to increased measurement sensitivity. This perspective review will focus on the role of high resolution liquid chromatography (LC) separations in conjunction with improved ion production and transmission for LC-MS-based metabolomics. Additional emphasis will be placed on the compromise between metabolome coverage and sample analysis throughput. PMID:19255623

Metabolomics for Biomarker Discovery: Moving to the Clinic

PubMed Central

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

2015-01-01

To improve the clinical course of diseases, more accurate diagnostic and assessment methods are required as early as possible. In order to achieve this, metabolomics offers new opportunities for biomarker discovery in complex diseases and may provide pathological understanding of diseases beyond traditional technologies. It is the systematic analysis of low-molecular-weight metabolites in biological samples and has become an important tool in clinical research and the diagnosis of human disease and has been applied to discovery and identification of the perturbed pathways. It provides a powerful approach to discover biomarkers in biological systems and offers a holistic approach with the promise to clinically enhance diagnostics. When carried out properly, it could provide insight into the understanding of the underlying mechanisms of diseases, help to identify patients at risk of disease, and predict the response to specific treatments. Currently, metabolomics has become an important tool in clinical research and the diagnosis of human disease and becomes a hot topic. This review will highlight the importance and benefit of metabolomics for identifying biomarkers that accurately screen potential biomarkers of diseases. PMID:26090402

Clinical metabolomics paves the way towards future healthcare strategies

PubMed Central

Collino, Sebastiano; Martin, François‐Pierre J.; Rezzi, Serge

2013-01-01

Metabolomics is recognized as a powerful top‐down system biological approach to understand genetic‐environment‐health paradigms paving new avenues to identify clinically relevant biomarkers. It is nowadays commonly used in clinical applications shedding new light on physiological regulatory processes of complex mammalian systems with regard to disease aetiology, diagnostic stratification and, potentially, mechanism of action of therapeutic solutions. A key feature of metabolomics lies in its ability to underpin the complex metabolic interactions of the host with its commensal microbial partners providing a new way to define individual and population phenotypes. This review aims at describing recent applications of metabolomics in clinical fields with insight into diseases, diagnostics/monitoring and improvement of homeostatic metabolic regulation. PMID:22348240

Detection of hepatitis E virus RNA in saliva for diagnosis of acute infection.

PubMed

Rivero-Juarez, A; Frias, M; Lopez-Lopez, P; Martinez-Peinado, A; Risalde, M Á; Brieva, T; Machuca, I; Camacho, Á; García-Bocanegra, I; Gomez-Villamandos, J C; Rivero, A

2018-04-16

Diagnosis of acute hepatitis E virus (HEV) infection is established by detection of anti-HEV IgM antibodies by ELISA or by amplification of serum viral RNA. Here, we evaluate the diagnostic value of testing HEV RNA in saliva to identify patients with acute HEV infection. Prospective proof-of-concept study including patients with acute hepatitis. Whole blood and neat saliva samples were obtained from all patients. Saliva samples were processed and analysed for HEV RNA by RT-PCR within 2 hr after collection. A total of 34 patients with acute hepatitis and 12 healthy donors were included in the study. HEV RNA in serum was confirmed by RT-PCR in eight of these patients (23.5%; 95% CI: 12.2%-40.2%). HEV was isolated in the saliva of eight of 34 patients (23.5%; 95% CI: 12.2%-40.2%). All patients with HEV RNA amplified in saliva had detectable HEV RNA in serum. HEV was isolated neither in the saliva of any of the 26 patients without detectable HEV RNA in serum nor in healthy donors. Our study suggests that acute HEV infection could be diagnosed by assessing viral load in saliva. © 2018 Blackwell Verlag GmbH.

Metabolomics to Explore Impact of Dairy Intake

PubMed Central

Zheng, Hong; Clausen, Morten R.; Dalsgaard, Trine K.; Bertram, Hanne C.

2015-01-01

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. PMID:26091233

Metabolomics: Definitions and Significance in Systems Biology.

PubMed

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.

Proteomic Profiling of Cereal Aphid Saliva Reveals Both Ubiquitous and Adaptive Secreted Proteins

PubMed Central

Wilkinson, Tom L.

2013-01-01

The secreted salivary proteins from two cereal aphid species, Sitobion avenae and Metopolophium dirhodum, were collected from artificial diets and analysed by tandem mass spectrometry. Protein identification was performed by searching MS data against the official protein set from the current pea aphid (Acyrthosiphon pisum) genome assembly and revealed 12 and 7 proteins in the saliva of S. avenae and M. dirhodum, respectively. When combined with a comparable dataset from A. pisum, only three individual proteins were common to all the aphid species; two paralogues of the GMC oxidoreductase family (glucose dehydrogenase; GLD) and ACYPI009881, an aphid specific protein previously identified as a putative component of the salivary sheath. Antibodies were designed from translated protein sequences obtained from partial cDNA sequences for ACYPI009881 and both saliva associated GLDs. The antibodies detected all parent proteins in secreted saliva from the three aphid species, but could only detect ACYPI009881, and not saliva associated GLDs, in protein extractions from the salivary glands. This result was confirmed by immunohistochemistry using whole and sectioned salivary glands, and in addition, localised ACYPI009881 to specific cell types within the principal salivary gland. The implications of these findings for the origin of salivary components and the putative role of the proteins identified are discussed in the context of our limited understanding of the functional relationship between aphid saliva and the plants they feed on. The mass spectrometry data have been deposited to the ProteomeXchange and can be accessed under the identifier PXD000113. PMID:23460852

Proteomic profiling of cereal aphid saliva reveals both ubiquitous and adaptive secreted proteins.

PubMed

Rao, Sohail A K; Carolan, James C; Wilkinson, Tom L

2013-01-01

The secreted salivary proteins from two cereal aphid species, Sitobion avenae and Metopolophium dirhodum, were collected from artificial diets and analysed by tandem mass spectrometry. Protein identification was performed by searching MS data against the official protein set from the current pea aphid (Acyrthosiphon pisum) genome assembly and revealed 12 and 7 proteins in the saliva of S. avenae and M. dirhodum, respectively. When combined with a comparable dataset from A. pisum, only three individual proteins were common to all the aphid species; two paralogues of the GMC oxidoreductase family (glucose dehydrogenase; GLD) and ACYPI009881, an aphid specific protein previously identified as a putative component of the salivary sheath. Antibodies were designed from translated protein sequences obtained from partial cDNA sequences for ACYPI009881 and both saliva associated GLDs. The antibodies detected all parent proteins in secreted saliva from the three aphid species, but could only detect ACYPI009881, and not saliva associated GLDs, in protein extractions from the salivary glands. This result was confirmed by immunohistochemistry using whole and sectioned salivary glands, and in addition, localised ACYPI009881 to specific cell types within the principal salivary gland. The implications of these findings for the origin of salivary components and the putative role of the proteins identified are discussed in the context of our limited understanding of the functional relationship between aphid saliva and the plants they feed on. The mass spectrometry data have been deposited to the ProteomeXchange and can be accessed under the identifier PXD000113.

Saliva and Serum Protein Exchange at the Tooth Enamel Surface

PubMed Central

Heller, D.; Helmerhorst, E.J.; Oppenheim, F.G.

2016-01-01

The acquired enamel pellicle is an oral, fluid-derived protein layer that forms on the tooth surface. It is a biologically and clinically important integument that protects teeth against enamel demineralization, and abrasion. Tooth surfaces are exposed to different proteinaceous microenvironments depending on the enamel location. For instance, tooth surfaces close to the gingival sulcus contact serum proteins that emanate via this sulcus, which may impact pellicle composition locally. The aims of this study were to define the major salivary and serum components that adsorb to hydroxyapatite, to study competition among them, and to obtain preliminary evidence in an in vivo saliva/serum pellicle model. Hydroxyapatite powder was incubated with saliva and serum, and the proteins that adsorbed were identified by mass spectrometry. To study competition, saliva and serum proteins were labeled with CyDyes, mixed in various proportions, and incubated with hydroxyapatite. In vivo competition was assessed using a split-mouth design, with half the buccal tooth surfaces coated with serum and the other half with saliva. After exposure to the oral environment for 0 min, 30 min and 2 h, the pellicles were analyzed by SDS-PAGE. In pure saliva- or serum-derived pellicles, 82 and 84 proteins were identified, respectively. When present concomitantly, salivary protein adsorbers effectively competed with serum protein adsorbers for the hydroxyapatite surface. Specifically, acidic proline-rich protein, cystatin, statherin and protein S100-A9 proteins competed off apolipoproteins, complement C4-A, haptoglobin, transthyretin and serotransferrin. In vivo evidence further supported the replacement of serum proteins by salivary proteins. In conclusion, although significant numbers of serum proteins emanate from the gingival sulcus, their ability to participate in dental pellicle formation is likely reduced in the presence of strong salivary protein adsorbers. The functional properties of the

The saliva microbiome of Pan and Homo

PubMed Central

2013-01-01

Background It is increasingly recognized that the bacteria that live in and on the human body (the microbiome) can play an important role in health and disease. The composition of the microbiome is potentially influenced by both internal factors (such as phylogeny and host physiology) and external factors (such as diet and local environment), and interspecific comparisons can aid in understanding the importance of these factors. Results To gain insights into the relative importance of these factors on saliva microbiome diversity, we here analyze the saliva microbiomes of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) from two sanctuaries in Africa, and from human workers at each sanctuary. The saliva microbiomes of the two Pan species are more similar to one another, and the saliva microbiomes of the two human groups are more similar to one another, than are the saliva microbiomes of human workers and apes from the same sanctuary. We also looked for the existence of a core microbiome and find no evidence for a taxon-based core saliva microbiome for Homo or Pan. In addition, we studied the saliva microbiome from apes from the Leipzig Zoo, and found an extraordinary diversity in the zoo ape saliva microbiomes that is not found in the saliva microbiomes of the sanctuary animals. Conclusions The greater similarity of the saliva microbiomes of the two Pan species to one another, and of the two human groups to one another, are in accordance with both the phylogenetic relationships of the hosts as well as with host physiology. Moreover, the results from the zoo animals suggest that novel environments can have a large impact on the microbiome, and that microbiome analyses based on captive animals should be viewed with caution as they may not reflect the microbiome of animals in the wild. PMID:24025115

Application of a Smartphone Metabolomics Platform to the Authentication of Schisandra sinensis.

PubMed

Kwon, Hyuk Nam; Phan, Hong-Duc; Xu, Wen Jun; Ko, Yoon-Joo; Park, Sunghyouk

2016-05-01

Herbal medicines have been used for a long time all around the world. Since the quality of herbal preparations depends on the source of herbal materials, there has been a strong need to develop methods to correctly identify the origin of materials. To develop a smartphone metabolomics platform as a simpler and low-cost alternative for the identification of herbal material source. Schisandra sinensis extracts from Korea and China were prepared. The visible spectra of all samples were measured by a smartphone spectrometer platform. This platform included all the necessary measures built-in for the metabolomics research: data acquisition, processing, chemometric analysis and visualisation of the results. The result of the smartphone metabolomics platform was compared to that of NMR-based metabolomics, suggesting the feasibility of smartphone platform in metabolomics research. The smartphone metabolomics platform gave similar results to the NMR method, showing good separation between Korean and Chinese materials and correct predictability for all test samples. With its accuracy and advantages of affordability, user-friendliness, and portability, the smartphone metabolomics platform could be applied to the authentication of other medicinal plants. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

MASS SPECTROMETRY-BASED METABOLOMICS

PubMed Central

Dettmer, Katja; Aronov, Pavel A.; Hammock, Bruce D.

2007-01-01

This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics. Metabolomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. These numerous analytes have very diverse physico-chemical properties and occur at different abundance levels. Consequently, comprehensive metabolomics investigations are primarily a challenge for analytical chemistry and specifically mass spectrometry has vast potential as a tool for this type of investigation. Metabolomics require special approaches for sample preparation, separation, and mass spectrometric analysis. Current examples of those approaches are described in this review. It primarily focuses on metabolic fingerprinting, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes. To perform this complex task, data analysis tools, metabolite libraries, and databases are required. Therefore, recent advances in metabolomics bioinformatics are also discussed. PMID:16921475

Investigation of Fe and Ca in non-stimulated human saliva using NAA

NASA Astrophysics Data System (ADS)

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.

Genomic and Metabolomic Profile Associated to Microalbuminuria

PubMed Central

Marrachelli, Vannina G.; Monleon, Daniel; Rentero, Pilar; Mansego, María L.; Morales, Jose Manuel; Galan, Inma; Segura, Remedios; Martinez, Fernando; Martin-Escudero, Juan Carlos; Briongos, Laisa; Marin, Pablo; Lliso, Gloria; Chaves, Felipe Javier; Redon, Josep

2014-01-01

To identify factors related with the risk to develop microalbuminuria using combined genomic and metabolomic values from a general population study. One thousand five hundred and two subjects, Caucasian, more than 18 years, representative of the general population, were included. Blood pressure measurement and albumin/creatinine ratio were measured in a urine sample. Using SNPlex, 1251 SNPs potentially associated to urinary albumin excretion (UAE) were analyzed. Serum metabolomic profile was assessed by 1H NMR spectra using a Brucker Advance DRX 600 spectrometer. From the total population, 1217 (mean age 54±19, 50.6% men, ACR>30 mg/g in 81 subjects) with high genotyping call rate were analysed. A characteristic metabolomic profile, which included products from mitochondrial and extra mitochondrial metabolism as well as branched amino acids and their derivative signals, were observed in microalbuminuric as compare to normoalbuminuric subjects. The comparison of the metabolomic profile between subjects with different UAE status for each of the genotypes associated to microalbuminuria revealed two SNPs, the rs10492025_TT of RPH3A gene and the rs4359_CC of ACE gene, with minimal or no statistically significant differences. Subjects with and without microalbuminuria, who shared the same genotype and metabolomic profile, differed in age. Microalbuminurics with the CC genotype of the rs4359 polymorphism and with the TT genotype of the rs10492025 polymorphism were seven years older and seventeen years younger, respectively as compared to the whole microalbuminuric subjects. With the same metabolomic environment, characteristic of subjects with microalbuminuria, the TT genotype of the rs10492025 polymorphism seems to increase and the CC genotype of the rs4359 polymorphism seems to reduce risk to develop microalbuminuria. PMID:24918908

Metabolomic Studies in Drosophila.

PubMed

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.

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection.

PubMed

Antharam, Vijay C; McEwen, Daniel C; Garrett, Timothy J; Dossey, Aaron T; Li, Eric C; Kozlov, Andrew N; Mesbah, Zhubene; Wang, Gary P

2016-01-01

Clostridium difficile infection (CDI) is characterized by dysbiosis of the intestinal microbiota and a profound derangement in the fecal metabolome. However, the contribution of specific gut microbes to fecal metabolites in C. difficile-associated gut microbiome remains poorly understood. Using gas-chromatography mass spectrometry (GC-MS) and 16S rRNA deep sequencing, we analyzed the metabolome and microbiome of fecal samples obtained longitudinally from subjects with Clostridium difficile infection (n = 7) and healthy controls (n = 6). From 155 fecal metabolites, we identified two sterol metabolites at >95% match to cholesterol and coprostanol that significantly discriminated C. difficile-associated gut microbiome from healthy microbiota. By correlating the levels of cholesterol and coprostanol in fecal extracts with 2,395 bacterial operational taxonomic units (OTUs) determined by 16S rRNA sequencing, we identified 63 OTUs associated with high levels of coprostanol and 2 OTUs correlated with low coprostanol levels. Using indicator species analysis (ISA), 31 of the 63 coprostanol-associated bacteria correlated with health, and two Veillonella species were associated with low coprostanol levels that correlated strongly with CDI. These 65 bacterial taxa could be clustered into 12 sub-communities, with each community containing a consortium of organisms that co-occurred with one another. Our studies identified 63 human gut microbes associated with cholesterol-reducing activities. Given the importance of gut bacteria in reducing and eliminating cholesterol from the GI tract, these results support the recent finding that gut microbiome may play an important role in host lipid metabolism.

The future of metabolomics in ELIXIR

PubMed Central

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

The future of metabolomics in ELIXIR.

PubMed

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.

Discriminant biomarkers of acute respiratory distress syndrome associated to H1N1 influenza identified by metabolomics HPLC-QTOF-MS/MS platform.

PubMed

Ferrarini, Alessia; Righetti, Laura; Martínez, Ma Paz; Fernández-López, Mariano; Mastrangelo, Annalaura; Horcajada, Juan P; Betbesé, Antoni; Esteban, Andrés; Ordóñez, Jordi; Gea, Joaquín; Cabello, Jesús Ruiz; Pellati, Federica; Lorente, José A; Nin, Nicolás; Rupérez, Francisco J

2017-09-01

Acute respiratory distress syndrome (ARDS) is a serious complication of influenza A (H1N1) virus infection. Its pathogenesis is unknown and biomarkers are lacking. Untargeted metabolomics allows the analysis of the whole metabolome in a biological compartment, identifying patterns associated with specific conditions. We hypothesized that LC-MS could help identify discriminant metabolites able to define the metabolic alterations occurring in patients with influenza A (H1N1) virus infection that developed ARDS. Serum samples from patients diagnosed with 2009 influenza A (H1N1) virus infection with (n = 25) or without (n = 32) ARDS were obtained on the day of hospital admission and analyzed by LC-MS/MS. Metabolite identification was determined by MS/MS analysis and analysis of standards. The specificity of the patterns identified was confirmed in patients without 2009 influenza A(H1N1) virus pneumonia (15 without and 17 with ARDS). Twenty-three candidate biomarkers were found to be significantly different between the two groups, including lysophospholipids and sphingolipids related to inflammation; bile acids, tryptophan metabolites, and thyroxine, related to the metabolism of the gut microflora. Confirmation results demonstrated the specificity of major alterations occurring in ARDS patients with influenza A (H1N1) virus infection. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.

PubMed

Yu, Tao; Wang, Yongtao; Zhang, Huizhen; Johnson, Caroline H; Jiang, Yiming; Li, Xiangjun; Wu, Zeming; Liu, Tian; Krausz, Kristopher W; Yu, Aiming; Gonzalez, Frank J; Huang, Min; Bi, Huichang

2016-06-01

Mycoplasma contamination is a common problem in cell culture and can alter cellular functions. Since cell metabolism is either directly or indirectly involved in every aspect of cell function, it is important to detect changes to the cellular metabolome after mycoplasma infection. In this study, liquid chromatography mass spectrometry (LC/MS)-based metabolomics was used to investigate the effect of mycoplasma contamination on the cellular metabolism of human pancreatic carcinoma cells (PANC-1). Multivariate analysis demonstrated that mycoplasma contamination induced significant metabolic changes in PANC-1 cells. Twenty-three metabolites were identified and found to be involved in arginine and purine metabolism and energy supply. This study demonstrates that mycoplasma contamination significantly alters cellular metabolite levels, confirming the compelling need for routine checking of cell cultures for mycoplasma contamination, particularly when used for metabolomics studies. Graphical abstract Metabolomics reveals mycoplasma contamination changes the metabolome of PANC-1 cells.

Introducing Undergraduate Students to Metabolomics Using a NMR-Based Analysis of Coffee Beans

ERIC Educational Resources Information Center

Sandusky, Peter Olaf

2017-01-01

Metabolomics applies multivariate statistical analysis to sets of high-resolution spectra taken over a population of biologically derived samples. The objective is to distinguish subpopulations within the overall sample population, and possibly also to identify biomarkers. While metabolomics has become part of the standard analytical toolbox in…

Women with preterm birth have a distinct cervicovaginal metabolome.

PubMed

Ghartey, Jeny; Bastek, Jamie A; Brown, Amy G; Anglim, Laura; Elovitz, Michal A

2015-06-01

Metabolomics has the potential to reveal novel pathways involved in the pathogenesis of preterm birth (PTB). The objective of this study was to investigate whether the cervicovaginal (CV) metabolome was different in asymptomatic women destined to have a PTB compared with term birth. A nested case-control study was performed using CV fluid collected from a larger prospective cohort. The CV fluid was collected between 20-24 weeks (V1) and 24-28 weeks (V2). The metabolome was compared between women with a spontaneous PTB (n = 10) to women who delivered at term (n = 10). Samples were extracted and prepared for analysis using a standard extraction solvent method. Global biochemical profiles were determined using gas chromatography/mass spectrometry and ultra-performance liquid chromatography/tandem mass spectrometry. An ANOVA was used to detect differences in biochemical compounds between the groups. A false discovery rate was estimated to account for multiple comparisons. A total of 313 biochemicals were identified in CV fluid. Eighty-two biochemicals were different in the CV fluid at V1 in those destined to have a PTB compared with term birth, whereas 48 were different at V2. Amino acid, carbohydrate, and peptide metabolites were distinct between women with and without PTB. These data suggest that the CV space is metabolically active during pregnancy. Changes in the CV metabolome may be observed weeks, if not months, prior to any clinical symptoms. Understanding the CV metabolome may hold promise for unraveling the pathogenesis of PTB and may provide novel biomarkers to identify women most at risk. Copyright © 2015 Elsevier Inc. All rights reserved.

[Clinical significance of analysis of immunoglobulin A levels in saliva].

PubMed

Bokor-Bratić, M

2000-01-01

plasma cells locally in the salivary glands. There is still little convincing evidence for the origin of predominantly immunoglobulin A secreting plasma cells in salivary glands. DETECTION OF IMMUNOGLOBULIN A IN SALIVA: Radial immunodiffusion (RID) was the most applicable method for detecting salivary immunoglobulin A. However, there are more sensitive and automatic methods such as nephelometry and ELISA. A standard level of immunoglobulin in saliva is still in question since the concentration varies in relation to origin of saliva, method of collection and stimulation of secretion (Table 1). PERIODONTAL DISEASE: Studies of the salivary immunoglobulin A in patients with periodontal disease and healthy persons showed that there are differences which can be used in detection of high-risk groups and individuals. If the bacterial adherence to the mucosa is a prerequisite for bacterial evolution in subgingival or any other region of the oral cavity respectively introduction in periodontitis development, than it is to be presumed that the basic function of salivary immunoglobulin A is inhibition of bacterial adherence rather than antigens destruction. Several bacterial species frequently isolated from the oral cavity of patients with periodontitis have been identified as producers of IgA protease. These enzymes cleave serum IgA and secretory IgA equally well. Additionally, most of the IgA proteases studied have cleaved the A1 and A2 subclass. Several studies have demonstrated that cleavage of human IgA occurs in vivo, resulting in generation of intact Fab alpha and (Fc alpha)2 fragment. Moreover, when bacteria are exposed to Fab alpha fragments released from IgA after cleavage by IgA protease, their surface antigens are likely to be occupied by Fab alpha fragments. These Fab alpha fragments left on the bacterial surface may mediate adhesion. Together, these results indicate that IgA proteases, by promoting adherence, contribute the pathogenic potential of bacteria in the oral

Increasing rigor in NMR-based metabolomics through validated and open source tools

PubMed Central

Eghbalnia, Hamid R; Romero, Pedro R; Westler, William M; Baskaran, Kumaran; Ulrich, Eldon L; Markley, John L

2016-01-01

The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism’s phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies. PMID:27643760

White Light Generation in Human Saliva

NASA Astrophysics Data System (ADS)

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.

Development of isotope labeling liquid chromatography mass spectrometry for mouse urine metabolomics: quantitative metabolomic study of transgenic mice related to Alzheimer's disease.

PubMed

Peng, Jun; Guo, Kevin; Xia, Jianguo; Zhou, Jianjun; Yang, Jing; Westaway, David; Wishart, David S; Li, Liang

2014-10-03

Because of a limited volume of urine that can be collected from a mouse, it is very difficult to apply the common strategy of using multiple analytical techniques to analyze the metabolites to increase the metabolome coverage for mouse urine metabolomics. We report an enabling method based on differential isotope labeling liquid chromatography mass spectrometry (LC-MS) for relative quantification of over 950 putative metabolites using 20 μL of urine as the starting material. The workflow involves aliquoting 10 μL of an individual urine sample for ¹²C-dansylation labeling that target amines and phenols. Another 10 μL of aliquot was taken from each sample to generate a pooled sample that was subjected to ¹³C-dansylation labeling. The ¹²C-labeled individual sample was mixed with an equal volume of the ¹³C-labeled pooled sample. The mixture was then analyzed by LC-MS to generate information on metabolite concentration differences among different individual samples. The interday repeatability for the LC-MS runs was assessed, and the median relative standard deviation over 4 days was 5.0%. This workflow was then applied to a metabolomic biomarker discovery study using urine samples obtained from the TgCRND8 mouse model of early onset familial Alzheimer's disease (FAD) throughout the course of their pathological deposition of beta amyloid (Aβ). It was showed that there was a distinct metabolomic separation between the AD prone mice and the wild type (control) group. As early as 15-17 weeks of age (presymptomatic), metabolomic differences were observed between the two groups, and after the age of 25 weeks the metabolomic alterations became more pronounced. The metabolomic changes at different ages corroborated well with the phenotype changes in this transgenic mice model. Several useful candidate biomarkers including methionine, desaminotyrosine, taurine, N1-acetylspermidine, and 5-hydroxyindoleacetic acid were identified. Some of them were found in previous

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

NASA Astrophysics Data System (ADS)

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.

Metabolomic Technologies for Improving the Quality of Food: Practice and Promise.

PubMed

Johanningsmeier, Suzanne D; Harris, G Keith; Klevorn, Claire M

2016-01-01

It is now well documented that the diet has a significant impact on human health and well-being. However, the complete set of small molecule metabolites present in foods that make up the human diet and the role of food production systems in altering this food metabolome are still largely unknown. Metabolomic platforms that rely on nuclear magnetic resonance (NMR) and mass spectrometry (MS) analytical technologies are being employed to study the impact of agricultural practices, processing, and storage on the global chemical composition of food; to identify novel bioactive compounds; and for authentication and region-of-origin classifications. This review provides an overview of the current terminology, analytical methods, and compounds associated with metabolomic studies, and provides insight into the application of metabolomics to generate new knowledge that enables us to produce, preserve, and distribute high-quality foods for health promotion.

Role of metabolomics in TBI research

PubMed Central

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

Applications of Metabolomics in Cancer Studies.

PubMed

Armitage, Emily Grace; Ciborowski, Michal

2017-01-01

Since the start of metabolomics as a field of research, the number of studies related to cancer has grown to such an extent that cancer metabolomics now represents its own discipline. In this chapter, the applications of metabolomics in cancer studies are explored. Different approaches and analytical platforms can be employed for the analysis of samples depending on the goal of the study and the aspects of the cancer metabolome being investigated. Analyses have concerned a range of cancers including lung, colorectal, bladder, breast, gastric, oesophageal and thyroid, amongst others. Developments in these strategies and methodologies that have been applied are discussed, in addition to exemplifying the use of cancer metabolomics in the discovery of biomarkers and in the assessment of therapy (both pharmaceutical and nutraceutical). Finally, the application of cancer metabolomics in personalised medicine is presented.

Comparative analysis of blood and saliva expression profiles in chronic and refractory periodontitis patients.

PubMed

Zhang, Bin; Lin, Ting; He, Hong

2015-12-24

This study aimed to identify characteristic representative genes through a comparative analysis of gene expression profiles in the blood and saliva of chronic periodontitis (CP) and refractory periodontitis (RP) patients to provide new treatment strategies that may be helpful in the treatment of different forms of periodontitis. GSE43525 was downloaded from Gene Expression Omnibus. In the dataset, thirteen samples were from blood including 4 controls, 4 CP and 5 RP samples, and ten samples were from saliva including 3 controls, 4 CP and 3 RP samples. After comparing the CP and RP samples, differentially expressed genes (DEGs) between these two types of periodontitis in the blood and saliva samples were identified by an LIMMA package. Then, functional and pathway enrichment analyses were performed by DAVID and KOBAS, respectively. The significantly associated miRNAs in CP and RP were searched by WebGestalt. In total, 213 DEGs in CP and 45 DEGs in RP were identified. Functional enrichment showed that the DEGs of CP were mainly enriched in ribosome and regulation of apoptosis-related pathways in blood as well as saliva, while the DEGs of RP were significantly enriched in immune responses and response to organic substance-related pathways. Several miRNAs, such as miR-381 and miR-494, were identified as being closely associated with CP. In addition, CD24, EST1, MTSS1, ING3, CCND2 and SYNE2 might be potential targets for diagnosis and treatment of CP. The identified DEGs and miRNAs might be potential targets for the treatment of chronic and refractory periodontitis.

Increasing rigor in NMR-based metabolomics through validated and open source tools.

PubMed

Eghbalnia, Hamid R; Romero, Pedro R; Westler, William M; Baskaran, Kumaran; Ulrich, Eldon L; Markley, John L

2017-02-01

The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker discovery, and the broader characterization of small molecules in mixtures. Owing to their close proximity to the functional endpoints that govern an organism's phenotype, metabolites are highly informative about functional states. The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. Information acquired from nuclear magnetic spectroscopy (NMR), mass spectrometry (MS), and the published literature, as processed by statistical approaches, are driving increasingly wider applications of metabolomics. This review focuses on the role of databases and software tools in advancing the rigor, robustness, reproducibility, and validation of metabolomics studies. Copyright © 2016. Published by Elsevier Ltd.

Quantitative detection of PfHRP2 in saliva of malaria patients in the Philippines

PubMed Central

2012-01-01

Background Malaria is a global health priority with a heavy burden of fatality and morbidity. Improvements in field diagnostics are needed to support the agenda for malaria elimination. Saliva has shown significant potential for use in non-invasive diagnostics, but the development of off-the-shelf saliva diagnostic kits requires best practices for sample preparation and quantitative insight on the availability of biomarkers and the dynamics of immunoassay in saliva. This pilot study measured the levels of the PfHRP2 in patient saliva to inform the development of salivary diagnostic tests for malaria. Methods Matched samples of blood and saliva were collected between January and May, 2011 from eight patients at Palawan Baptist Hospital in Roxas, Palawan, Philippines. Parasite density was determined from thick-film blood smears. Concentrations of PfHRP2 in saliva of malaria-positive patients were measured using a custom chemiluminescent ELISA in microtitre plates. Sixteen negative-control patients were enrolled at UCLA. A substantive difference between this protocol and previous related studies was that saliva samples were stabilized with protease inhibitors. Results Of the eight patients with microscopically confirmed P. falciparum malaria, seven tested positive for PfHRP2 in the blood using rapid diagnostic test kits, and all tested positive for PfHRP2 in saliva. All negative-control samples tested negative for salivary PfHRP2. On a binary-decision basis, the ELISA agreed with microscopy with 100 % sensitivity and 100 % specificity. Salivary levels of PfHRP2 ranged from 17 to 1,167 pg/mL in the malaria-positive group. Conclusion Saliva is a promising diagnostic fluid for malaria when protein degradation and matrix effects are mitigated. Systematic quantitation of other malaria biomarkers in saliva would identify those with the best clinical relevance and suitability for off-the-shelf diagnostic kits. PMID:22631858

Metabolomics for Assessment of Nutritional Status

PubMed Central

Zivkovic, Angela M.; German, J. Bruce

2010-01-01

Purpose of review The current rise in diet-related diseases continues to be one of the most significant health problems facing both the developed and the developing world. The use of metabolomics – the accurate and comprehensive measurement of a significant fraction of important metabolites in accessible biological fluids – for the assessment of nutritional status, is a promising way forward. The basic toolset, targets, and knowledge are all being developed in the emerging field of metabolomics, yet important knowledge and technology gaps will need to be addressed in order to bring such assessment to practice. Recent findings Dysregulation within the principal metabolic organs (e.g. intestine, adipose, skeletal muscle, liver) are at the center of a diet-disease paradigm that includes metabolic syndrome, type 2 diabetes, and obesity. The assessment of both essential nutrient status, and the more comprehensive systemic metabolic response to dietary, lifestyle, and environmental influences (e.g. metabolic phenotype) are necessary for the evaluation of status in individuals that can identify the multiple targets of intervention needed to address metabolic disease. Summary The first proofs of principle building the knowledge to bring actionable metabolic diagnostics to practice through metabolomics are now appearing. PMID:19584717

Identification of 24h Ixodes scapularis immunogenic tick saliva proteins.

PubMed

Lewis, Lauren A; Radulović, Željko M; Kim, Tae K; Porter, Lindsay M; Mulenga, Albert

2015-04-01

Ixodes scapularis is arguably the most medically important tick species in the United States. This tick transmits 5 of the 14 human tick-borne disease (TBD) agents in the USA: Borrelia burgdorferi, Anaplasma phagocytophilum, B. miyamotoi, Babesia microti, and Powassan virus disease. Except for the Powassan virus disease, I. scapularis-vectored TBD agents require more than 24h post attachment to be transmitted. This study describes identification of 24h immunogenic I. scapularis tick saliva proteins, which could provide opportunities to develop strategies to stop tick feeding before transmission of the majority of pathogens. A 24h fed female I. scapularis phage display cDNA expression library was biopanned using rabbit antibodies to 24h fed I. scapularis female tick saliva proteins, subjected to next generation sequencing, de novo assembly, and bioinformatic analyses. A total of 182 contigs were assembled, of which ∼19% (35/182) are novel and did not show identity to any known proteins in GenBank. The remaining ∼81% (147/182) of contigs were provisionally identified based on matches in GenBank including ∼18% (27/147) that matched protein sequences previously annotated as hypothetical and putative tick saliva proteins. Others include proteases and protease inhibitors (∼3%, 5/147), transporters and/or ligand binding proteins (∼6%, 9/147), immunogenic tick saliva housekeeping enzyme-like (17%, 25/147), ribosomal protein-like (∼31%, 46/147), and those classified as miscellaneous (∼24%, 35/147). Notable among the miscellaneous class include antimicrobial peptides (microplusin and ricinusin), myosin-like proteins that have been previously found in tick saliva, and heat shock tick saliva protein. Data in this study provides the foundation for in-depth analysis of I. scapularis feeding during the first 24h, before the majority of TBD agents can be transmitted. Copyright © 2015 Elsevier GmbH. All rights reserved.

Targeted metabolomics and medication classification data from participants in the ADNI1 cohort.

PubMed

St John-Williams, Lisa; Blach, Colette; Toledo, Jon B; Rotroff, Daniel M; Kim, Sungeun; Klavins, Kristaps; Baillie, Rebecca; Han, Xianlin; Mahmoudiandehkordi, Siamak; Jack, John; Massaro, Tyler J; Lucas, Joseph E; Louie, Gregory; Motsinger-Reif, Alison A; Risacher, Shannon L; Saykin, Andrew J; Kastenmüller, Gabi; Arnold, Matthias; Koal, Therese; Moseley, M Arthur; Mangravite, Lara M; Peters, Mette A; Tenenbaum, Jessica D; Thompson, J Will; Kaddurah-Daouk, Rima

2017-10-17

Alzheimer's disease (AD) is the most common neurodegenerative disease presenting major health and economic challenges that continue to grow. Mechanisms of disease are poorly understood but significant data point to metabolic defects that might contribute to disease pathogenesis. The Alzheimer Disease Metabolomics Consortium (ADMC) in partnership with Alzheimer Disease Neuroimaging Initiative (ADNI) is creating a comprehensive biochemical database for AD. Using targeted and non- targeted metabolomics and lipidomics platforms we are mapping metabolic pathway and network failures across the trajectory of disease. In this report we present quantitative metabolomics data generated on serum from 199 control, 356 mild cognitive impairment and 175 AD subjects enrolled in ADNI1 using AbsoluteIDQ-p180 platform, along with the pipeline for data preprocessing and medication classification for confound correction. The dataset presented here is the first of eight metabolomics datasets being generated for broad biochemical investigation of the AD metabolome. We expect that these collective metabolomics datasets will provide valuable resources for researchers to identify novel molecular mechanisms contributing to AD pathogenesis and disease phenotypes.

Targeted metabolomics and medication classification data from participants in the ADNI1 cohort

PubMed Central

St John-Williams, Lisa; Blach, Colette; Toledo, Jon B.; Rotroff, Daniel M.; Kim, Sungeun; Klavins, Kristaps; Baillie, Rebecca; Han, Xianlin; Mahmoudiandehkordi, Siamak; Jack, John; Massaro, Tyler J.; Lucas, Joseph E.; Louie, Gregory; Motsinger-Reif, Alison A.; Risacher, Shannon L.; Saykin, Andrew J.; Kastenmüller, Gabi; Arnold, Matthias; Koal, Therese; Moseley, M. Arthur; Mangravite, Lara M.; Peters, Mette A.; Tenenbaum, Jessica D.; Thompson, J. Will; Kaddurah-Daouk, Rima

2017-01-01

Alzheimer’s disease (AD) is the most common neurodegenerative disease presenting major health and economic challenges that continue to grow. Mechanisms of disease are poorly understood but significant data point to metabolic defects that might contribute to disease pathogenesis. The Alzheimer Disease Metabolomics Consortium (ADMC) in partnership with Alzheimer Disease Neuroimaging Initiative (ADNI) is creating a comprehensive biochemical database for AD. Using targeted and non- targeted metabolomics and lipidomics platforms we are mapping metabolic pathway and network failures across the trajectory of disease. In this report we present quantitative metabolomics data generated on serum from 199 control, 356 mild cognitive impairment and 175 AD subjects enrolled in ADNI1 using AbsoluteIDQ-p180 platform, along with the pipeline for data preprocessing and medication classification for confound correction. The dataset presented here is the first of eight metabolomics datasets being generated for broad biochemical investigation of the AD metabolome. We expect that these collective metabolomics datasets will provide valuable resources for researchers to identify novel molecular mechanisms contributing to AD pathogenesis and disease phenotypes. PMID:29039849

Influential Parameters for the Analysis of Intracellular Parasite Metabolomics.

PubMed

Carey, Maureen A; Covelli, Vincent; Brown, Audrey; Medlock, Gregory L; Haaren, Mareike; Cooper, Jessica G; Papin, Jason A; Guler, Jennifer L

2018-04-25

Metabolomics is increasingly popular for the study of pathogens. For the malaria parasite Plasmodium falciparum , both targeted and untargeted metabolomics have improved our understanding of pathogenesis, host-parasite interactions, and antimalarial drug treatment and resistance. However, purification and analysis procedures for performing metabolomics on intracellular pathogens have not been explored. Here, we purified in vitro -grown ring-stage intraerythrocytic P. falciparum parasites for untargeted metabolomics studies; the small size of this developmental stage amplifies the challenges associated with metabolomics studies as the ratio between host and parasite biomass is maximized. Following metabolite identification and data preprocessing, we explored multiple confounding factors that influence data interpretation, including host contamination and normalization approaches (including double-stranded DNA, total protein, and parasite numbers). We conclude that normalization parameters have large effects on differential abundance analysis and recommend the thoughtful selection of these parameters. However, normalization does not remove the contribution from the parasite's extracellular environment (culture media and host erythrocyte). In fact, we found that extraparasite material is as influential on the metabolome as treatment with a potent antimalarial drug with known metabolic effects (artemisinin). Because of this influence, we could not detect significant changes associated with drug treatment. Instead, we identified metabolites predictive of host and medium contamination that could be used to assess sample purification. Our analysis provides the first quantitative exploration of the effects of these factors on metabolomics data analysis; these findings provide a basis for development of improved experimental and analytical methods for future metabolomics studies of intracellular organisms. IMPORTANCE Molecular characterization of pathogens such as the

What computational non-targeted mass spectrometry-based metabolomics can gain from shotgun proteomics.

PubMed

Hamzeiy, Hamid; Cox, Jürgen

2017-02-01

Computational workflows for mass spectrometry-based shotgun proteomics and untargeted metabolomics share many steps. Despite the similarities, untargeted metabolomics is lagging behind in terms of reliable fully automated quantitative data analysis. We argue that metabolomics will strongly benefit from the adaptation of successful automated proteomics workflows to metabolomics. MaxQuant is a popular platform for proteomics data analysis and is widely considered to be superior in achieving high precursor mass accuracies through advanced nonlinear recalibration, usually leading to five to ten-fold better accuracy in complex LC-MS/MS runs. This translates to a sharp decrease in the number of peptide candidates per measured feature, thereby strongly improving the coverage of identified peptides. We argue that similar strategies can be applied to untargeted metabolomics, leading to equivalent improvements in metabolite identification. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

What Have Metabolomics Approaches Taught Us About Type 2 Diabetes?

PubMed

Gonzalez-Franquesa, Alba; Burkart, Alison M; Isganaitis, Elvira; Patti, Mary-Elizabeth

2016-08-01

Type 2 diabetes (T2D) is increasing worldwide, making identification of biomarkers for detection, staging, and effective prevention strategies an especially critical scientific and medical goal. Fortunately, advances in metabolomics techniques, together with improvements in bioinformatics and mathematical modeling approaches, have provided the scientific community with new tools to describe the T2D metabolome. The metabolomics signatures associated with T2D and obesity include increased levels of lactate, glycolytic intermediates, branched-chain and aromatic amino acids, and long-chain fatty acids. Conversely, tricarboxylic acid cycle intermediates, betaine, and other metabolites decrease. Future studies will be required to fully integrate these and other findings into our understanding of diabetes pathophysiology and to identify biomarkers of disease risk, stage, and responsiveness to specific treatments.

[Metabolomics research of medicinal plants].

PubMed

Duan, Li-Xin; Dai, Yun-Tao; Sun, Chao; Chen, Shi-Lin

2016-11-01

Metabolomics is the comprehensively study of chemical processes involving small molecule metabolites. It is an important part of systems biology, and is widely applied in complex traditional Chinese medicine（TCM）system. Metabolites biosynthesized by medicinal plants are the effective basis for TCM. Metabolomics studies of medicinal plants will usher in a new period of vigorous development with the implementation of Herb Genome Program and the development of TCM synthetic biology. This manuscript introduces the recent research progresses of metabolomics technology and the main research contents of metabolomics studies for medicinal plants, including identification and quality evaluation for medicinal plants, cultivars breeding, stress resistance, metabolic pathways, metabolic network, metabolic engineering and synthetic biology researches. The integration of genomics, transcriptomics and metabolomics approaches will finally lay foundation for breeding of medicinal plants, R&D, quality and safety evaluation of innovative drug. Copyright© by the Chinese Pharmaceutical Association.

Metabolomic markers of fatigue: Association between circulating metabolome and fatigue in women with chronic widespread pain.

PubMed

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.

Metabolomics and malaria biology

PubMed Central

Lakshmanan, Viswanathan; Rhee, Kyu Y.; Daily, Johanna P.

2010-01-01

Metabolomics has ushered in a novel and multi-disciplinary realm in biological research. It has provided researchers with a platform to combine powerful biochemical, statistical, computational, and bioinformatics techniques to delve into the mysteries of biology and disease. The application of metabolomics to study malaria parasites represents a major advance in our approach towards gaining a more comprehensive perspective on parasite biology and disease etiology. This review attempts to highlight some of the important aspects of the field of metabolomics, and its ongoing and potential future applications to malaria research. PMID:20970461

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

PubMed Central

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

2016-01-01

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. PMID:26467476

Metabolomics in Toxicology and Preclinical Research

PubMed Central

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

The human plasma-metabolome: Reference values in 800 French healthy volunteers; impact of cholesterol, gender and age

PubMed Central

Al-Salameh, Abdallah; Croixmarie, Vincent; Masson, Perrine; Corruble, Emmanuelle; Fève, Bruno; Colle, Romain; Ripoll, Laurent; Walther, Bernard; Boursier-Neyret, Claire; Werner, Erwan; Becquemont, Laurent; Chanson, Philippe

2017-01-01

Metabolomic approaches are increasingly used to identify new disease biomarkers, yet normal values of many plasma metabolites remain poorly defined. The aim of this study was to define the “normal” metabolome in healthy volunteers. We included 800 French volunteers aged between 18 and 86, equally distributed according to sex, free of any medication and considered healthy on the basis of their medical history, clinical examination and standard laboratory tests. We quantified 185 plasma metabolites, including amino acids, biogenic amines, acylcarnitines, phosphatidylcholines, sphingomyelins and hexose, using tandem mass spectrometry with the Biocrates AbsoluteIDQ p180 kit. Principal components analysis was applied to identify the main factors responsible for metabolome variability and orthogonal projection to latent structures analysis was employed to confirm the observed patterns and identify pattern-related metabolites. We established a plasma metabolite reference dataset for 144/185 metabolites. Total blood cholesterol, gender and age were identified as the principal factors explaining metabolome variability. High total blood cholesterol levels were associated with higher plasma sphingomyelins and phosphatidylcholines concentrations. Compared to women, men had higher concentrations of creatinine, branched-chain amino acids and lysophosphatidylcholines, and lower concentrations of sphingomyelins and phosphatidylcholines. Elderly healthy subjects had higher sphingomyelins and phosphatidylcholines plasma levels than young subjects. We established reference human metabolome values in a large and well-defined population of French healthy volunteers. This study provides an essential baseline for defining the “normal” metabolome and its main sources of variation. PMID:28278231

The human plasma-metabolome: Reference values in 800 French healthy volunteers; impact of cholesterol, gender and age.

PubMed

Trabado, Séverine; Al-Salameh, Abdallah; Croixmarie, Vincent; Masson, Perrine; Corruble, Emmanuelle; Fève, Bruno; Colle, Romain; Ripoll, Laurent; Walther, Bernard; Boursier-Neyret, Claire; Werner, Erwan; Becquemont, Laurent; Chanson, Philippe

2017-01-01

Metabolomic approaches are increasingly used to identify new disease biomarkers, yet normal values of many plasma metabolites remain poorly defined. The aim of this study was to define the "normal" metabolome in healthy volunteers. We included 800 French volunteers aged between 18 and 86, equally distributed according to sex, free of any medication and considered healthy on the basis of their medical history, clinical examination and standard laboratory tests. We quantified 185 plasma metabolites, including amino acids, biogenic amines, acylcarnitines, phosphatidylcholines, sphingomyelins and hexose, using tandem mass spectrometry with the Biocrates AbsoluteIDQ p180 kit. Principal components analysis was applied to identify the main factors responsible for metabolome variability and orthogonal projection to latent structures analysis was employed to confirm the observed patterns and identify pattern-related metabolites. We established a plasma metabolite reference dataset for 144/185 metabolites. Total blood cholesterol, gender and age were identified as the principal factors explaining metabolome variability. High total blood cholesterol levels were associated with higher plasma sphingomyelins and phosphatidylcholines concentrations. Compared to women, men had higher concentrations of creatinine, branched-chain amino acids and lysophosphatidylcholines, and lower concentrations of sphingomyelins and phosphatidylcholines. Elderly healthy subjects had higher sphingomyelins and phosphatidylcholines plasma levels than young subjects. We established reference human metabolome values in a large and well-defined population of French healthy volunteers. This study provides an essential baseline for defining the "normal" metabolome and its main sources of variation.

Food metabolomics: from farm to human.

PubMed

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.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

PubMed Central

Barnes, Stephen; Benton, H. Paul; Casazza, Krista; Cooper, Sara; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H.; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K.; Renfrow, Matthew B.; Tiwari, Hemant K.

2017-01-01

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites, and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. PMID:28239968

Comparison of Plasma, Saliva, and Hair Levetiracetam Concentrations.

PubMed

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.

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

PubMed

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.

Investigation of saliva of patients with periodontal disease using NAA

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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.

Metabolomics as a Functional Tool in Screening Gastro Intestinal Diseases: Where are we in High Throughput Screening?

PubMed

Gundamaraju, Rohit; Vemuri, Ravichandra; Eri, Rajaraman; Ishiki, Hamilton M; Coy-Barrera, Ericsson; Yarla, Nagendra Sastry; Dos Santos, Sócrates Golzio; Alves, Mateus Feitosa; Barbosa Filho, José Maria; Diniz, Margareth F F M; Scotti, Marcus T; Scotti, Luciana

2017-01-01

Identifying novel bio markers in gastro intestinal disease is a promising method where a comprehensive analysis of the metabolome is performed. Metabolomics has evolved enormously in the past decade, paving a path in gastro intestinal disease research, especially diseases which lead to high morbidity and mortality. Metabolomics involves identifying metabolites such as anti-oxidants, and amino acids etc., which are screened in the urine, feces and tissue samples. Certain cases employ advanced tools like GC-MS, 1HNMR and GC-MS/SPME which reveal valuable information concerning disease severity and differentiation. In light of escalating health care costs and risky invasive procedures, metabolomics can be chosen as a safe yet precise method for screening diseases like ulcerative colitis, Crohns' disease, celiac disease, and gastro intestinal cancers. The present review focuses on major advancements in gastro intestinal metabolomics, giving attention to which parameters are assessed, and to recent changes in metabolite analysis. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

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

PubMed

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.

Can NMR solve some significant challenges in metabolomics?

PubMed Central

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

Can NMR solve some significant challenges in metabolomics?

PubMed

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. Copyright © 2015 Elsevier Inc. All rights reserved.

Can NMR solve some significant challenges in metabolomics?

NASA Astrophysics Data System (ADS)

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.

Detection of Plasmodium falciparum DNA in saliva samples stored at room temperature: potential for a non-invasive saliva-based diagnostic test for malaria.

PubMed

Mfuh, Kenji O; Tassi Yunga, Samuel; Esemu, Livo F; Bekindaka, Obase Ngemani; Yonga, Jessica; Djontu, Jean Claude; Mbakop, Calixt D; Taylor, Diane W; Nerurkar, Vivek R; Leke, Rose G F

2017-10-27

Current malaria diagnostic methods require blood collection, that may be associated with pain and the risk of transmitting blood-borne pathogens, and often create poor compliance when repeated sampling is needed. On the other hand, the collection of saliva is minimally invasive; but saliva has not been widely used for the diagnosis of malaria. The aim of this study was to evaluate the diagnostic performance of saliva collected and stored at room temperature using the OMNIgene ® •ORAL kit for diagnosing Plasmodium falciparum malaria. Paired blood and saliva samples were collected from 222 febrile patients in Cameroon. Saliva samples were collected using the OMNIgene ® •ORAL (OM-501) kit and stored at room temperature for up to 13 months. Thick blood film microscopy (TFM) was used to detect P. falciparum blood-stage parasites in blood. Detection of P. falciparum DNA in blood and saliva was based on amplification of the multi-copy 18 s rRNA gene using the nested-polymerase chain reaction (nPCR). Prevalence of malaria detected by TFM, nPCR-saliva and nPCR-blood was 22, 29, and 35%, respectively. Using TFM as the gold standard, the sensitivity of nPCR-saliva and nPCR-blood in detecting P. falciparum was 95 and 100%, respectively; with corresponding specificities of 93 and 87%. When nPCR-blood was used as gold standard, the sensitivity of nPCR-saliva and microscopy was 82 and 68%, respectively; whereas, the specificity was 99 and 100%, respectively. Nested PCR-saliva had a very good agreement with both TFM (kappa value 0.8) and blood PCR (kappa value 0.8). At parasitaemia > 10,000 parasites/µl of blood, the sensitivity of nPCR-saliva was 100%. Nested PCR-saliva detected 16 sub-microscopic malaria infections. One year after sample collection, P. falciparum DNA was detected in 80% of saliva samples stored at room temperature. Saliva can potentially be used as an alternative non-invasive sample for the diagnosis of malaria and the OMNIgene ® •ORAL kit is

Metabolomic characterization of laborers exposed to welding fumes.

PubMed

Wang, Kuo-Ching; Kuo, Ching-Hua; Tian, Tze-Feng; Tsai, Mong-Hsun; Chiung, Yin-Mei; Hsiech, Chun-Ming; Tsai, Sung-Jeng; Wang, San-Yuan; Tsai, Dong-Ming; Huang, Chiang-Ching; Tseng, Y Jane

2012-03-19

The complex composition of welding fumes, multiplicity of molecular targets, diverse cellular effects, and lifestyles associated with laborers vastly complicate the assessment of welding fume exposure. The urinary metabolomic profiles of 35 male welders and 16 male office workers at a Taiwanese shipyard were characterized via (1)H NMR spectroscopy and pattern recognition methods. Blood samples for the same 51 individuals were also collected, and the expression levels of the cytokines and other inflammatory markers were examined. This study dichotomized the welding exposure variable into high (welders) versus low (office workers) exposures to examine the differences of continuous outcome markers-metabolites and inflammatory markers-between the two groups. Fume particle assessments showed that welders were exposed to different concentrations of chromium, nickel, and manganese particles. Multivariate statistical analysis of urinary metabolomic patterns showed higher levels of glycine, taurine, betaine/TMAO, serine, S-sulfocysteine, hippurate, gluconate, creatinine, and acetone and lower levels of creatine among welders, while only TNF-α was significantly associated with welding fume exposure among all cytokines and other inflammatory markers measured. Of the identified metabolites, the higher levels of glycine, taurine, and betaine among welders were suspected to play some roles in modulating inflammatory and oxidative tissue injury processes. In this metabolomics experiment, we also discovered that the association of the identified metabolites with welding exposure was confounded by smoking, but not with drinking, which is a finding consistent with known modified response of inflammatory markers among smokers. Our results correspond with prior studies that utilized nonmetabolomic analytical techniques and suggest that the metabolomic profiling is an efficient method to characterize the overall effect of welding fume exposure and other confounders. © 2012 American

Application of global metabolomic profiling of synovial fluid for osteoarthritis biomarkers.

PubMed

Carlson, Alyssa K; Rawle, Rachel A; Adams, Erik; Greenwood, Mark C; Bothner, Brian; June, Ronald K

2018-05-05

Osteoarthritis affects over 250 million individuals worldwide. Currently, there are no options for early diagnosis of osteoarthritis, demonstrating the need for biomarker discovery. To find biomarkers of osteoarthritis in human synovial fluid, we used high performance liquid-chromatography mass spectrometry for global metabolomic profiling. Metabolites were extracted from human osteoarthritic (n = 5), rheumatoid arthritic (n = 3), and healthy (n = 5) synovial fluid, and a total of 1233 metabolites were detected. Principal components analysis clearly distinguished the metabolomic profiles of diseased from healthy synovial fluid. Synovial fluid from rheumatoid arthritis patients contained expected metabolites consistent with the inflammatory nature of the disease. Similarly, unsupervised clustering analysis found that each disease state was associated with distinct metabolomic profiles and clusters of co-regulated metabolites. For osteoarthritis, co-regulated metabolites that were upregulated compared to healthy synovial fluid mapped to known disease processes including chondroitin sulfate degradation, arginine and proline metabolism, and nitric oxide metabolism. We utilized receiver operating characteristic analysis to determine the diagnostic value of each metabolite and identified 35 metabolites as potential biomarkers of osteoarthritis, with an area under the receiver operating characteristic curve >0.9. These metabolites included phosphatidylcholine, lysophosphatidylcholine, ceramides, myristate derivatives, and carnitine derivatives. This pilot study provides strong justification for a larger cohort-based study of human osteoarthritic synovial fluid using global metabolomics. The significance of these data is the demonstration that metabolomic profiling of synovial fluid can identify relevant biomarkers of joint disease. Copyright © 2018 Elsevier Inc. All rights reserved.

Plant metabolomics: from holistic hope, to hype, to hot topic.

PubMed

Hall, Robert D

2006-01-01

In a short time, plant metabolomics has gone from being just an ambitious concept to being a rapidly growing, valuable technology applied in the stride to gain a more global picture of the molecular organization of multicellular organisms. The combination of improved analytical capabilities with newly designed, dedicated statistical, bioinformatics and data mining strategies, is beginning to broaden the horizons of our understanding of how plants are organized and how metabolism is both controlled but highly flexible. Metabolomics is predicted to play a significant, if not indispensable role in bridging the phenotype-genotype gap and thus in assisting us in our desire for full genome sequence annotation as part of the quest to link gene to function. Plants are a fabulously rich source of diverse functional biochemicals and metabolomics is also already proving valuable in an applied context. By creating unique opportunities for us to interrogate plant systems and characterize their biochemical composition, metabolomics will greatly assist in identifying and defining much of the still unexploited biodiversity available today.

Canine leishmaniasis: Genome-wide analysis and antibody response to Lutzomyia longipalpis saliva.

PubMed

Batista, Luís F S; Utsunomiya, Yuri T; Silva, Thaís B F; Carneiro, Mariana M; Paiva, Joyr S F; Silva, Rafaela B; Tomokane, Thaíse Y; Rossi, Claudio N; Pacheco, Acácio D; Torrecilha, Rafaela B P; Silveira, Fernando T; Marcondes, Mary; Nunes, Cáris M; Laurenti, Márcia D

2018-01-01

The anti-inflammatory properties of sand fly saliva favor the establishment of the Leishmania infantum infection. In contrast, an antibody response against Lutzomyia longipalpis saliva is often associated with a protective cell-mediated response against canine visceral leishmaniasis. Genetic studies may demonstrate to what extent the ability to secrete anti-saliva antibodies depends on genetic or environmental factors. However, the genetic basis of canine antibody response against sand fly saliva has not been assessed. The aim of this study was to identify chromosomal regions associated with the anti-Lu. longipalpis salivary IgG response in 189 dogs resident in endemic areas in order to provide information for prophylactic strategies. Dogs were classified into five groups based on serological and parasitological diagnosis and clinical evaluation. Anti-salivary gland homogenate (SGH) IgG levels were assessed by Enzyme-Linked Immunosorbent Assay (ELISA). Genomic DNA was isolated from blood samples and genotyped using a SNP chip with 173,662 single nucleotide polymorphism (SNP) markers. The following linear regression model was fitted: IgG level = mean + origin + sex + age + use of a repellent collar, and the residuals were assumed as pseudo-phenotypes for the association test between phenotypes and genotypes (GWA). A component of variance model that takes into account polygenic and sample structure effects (EMMAX) was employed for GWA. Phenotypic findings indicated that anti-SGH IgG levels remained higher in exposed and subclinically infected dogs than in severely diseased dogs even in regression model residuals. Five associated markers were identified on chromosomes 2, 20 and 31. The mapped genes included CD180 (RP105) and MITF related to the rapid activation of B lymphocytes and differentiation into antibody-secreting plasma cells. The findings pointed to chromosomal segments useful for functional confirmation studies and a search for adjuvant molecules of the anti-saliva

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics.

PubMed

Guitton, Yann; Tremblay-Franco, Marie; Le Corguillé, Gildas; Martin, Jean-François; Pétéra, Mélanie; Roger-Mele, Pierrick; Delabrière, Alexis; Goulitquer, Sophie; Monsoor, Misharl; Duperier, Christophe; Canlet, Cécile; Servien, Rémi; Tardivel, Patrick; Caron, Christophe; Giacomoni, Franck; Thévenot, Etienne A

2017-12-01

Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the multiplicity of bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics (W4M; http://workflow4metabolomics.org) online infrastructure for metabolomics built on the Galaxy environment, which offers user-friendly features to build and run data analysis workflows including preprocessing, statistical analysis, and annotation steps. Here we present the new W4M 3.0 release, which contains twice as many tools as the first version, and provides two features which are, to our knowledge, unique among online resources. First, data from the four major metabolomics technologies (i.e., LC-MS, FIA-MS, GC-MS, and NMR) can be analyzed on a single platform. By using three studies in human physiology, alga evolution, and animal toxicology, we demonstrate how the 40 available tools can be easily combined to address biological issues. Second, the full analysis (including the workflow, the parameter values, the input data and output results) can be referenced with a permanent digital object identifier (DOI). Publication of data analyses is of major importance for robust and reproducible science. Furthermore, the publicly shared workflows are of high-value for e-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thus not only offers a unique online environment for analysis of data from the main metabolomics technologies, but it is also the first reference repository for metabolomics workflows. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Metabolomic Perspective on Coeliac Disease

PubMed Central

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

Characterization of the human submandibular/sublingual saliva glycoproteome using lectin affinity chromatography coupled to Multidimensional Protein Identification Technology

PubMed Central

Gonzalez-Begne, Mireya; Lu, Bingwen; Liao, Lujian; Xu, Tao; Bedi, Gurrinder; Melvin, James E.; Yates, John R.

2011-01-01

In-depth analysis of the salivary proteome is fundamental to understanding the functions of salivary proteins in the oral cavity and to reveal disease biomarkers involved in different pathophysiological conditions, with the ultimate goal of improving patient diagnosis and prognosis. Submandibular and sublingual glands contribute saliva rich in glycoproteins to the total saliva output, making them valuable sources for glycoproteomic analysis. Lectin-affinity chromatography coupled to mass spectrometry-based shotgun proteomics was used to explore the submandibular/sublingual (SM/SL) saliva glycoproteome. A total of 262 N- and O-linked glycoproteins were identified by multidimensional protein identification technology (MudPIT). Only 38 were previously described in SM and SL salivas from the human salivary N-linked glycoproteome, while 224 were unique. Further comparison analysis with SM/SL saliva of the human saliva proteome, revealed 125 glycoproteins not formerly reported in this secretion. KEGG pathway analyses demonstrated that many of these glycoproteins are involved in processes such as complement and coagulation cascades, cell communication, glycosphingolipid biosynthesis neo-lactoseries, O-glycan biosynthesis, glycan structures-biosynthesis 2, starch and sucrose metabolism, peptidoglycan biosynthesis or others pathways. In summary, lectin-affinity chromatography coupled to MudPIT mass spectrometry identified many novel glycoproteins in SM/SL saliva. These new additions to the salivary proteome may prove to be a critical step for providing reliable biomarkers in the diagnosis of a myriad of oral and systemic diseases. PMID:21936497

The scientific exploration of saliva in the post-proteomic era: from database back to basic function

PubMed Central

Ruhl, Stefan

2012-01-01

The proteome of human saliva can be considered as being essentially completed. Diagnostic markers for a number of diseases have been identified among salivary proteins and peptides, taking advantage of saliva as an easy-to-obtain biological fluid. Yet, the majority of disease markers identified so far are serum components and not intrinsic proteins produced by the salivary glands. Furthermore, despite the fact that saliva is essential for protecting the oral integuments and dentition, little progress has been made in finding risk predictors in the salivary proteome for dental caries or periodontal disease. Since salivary proteins, and in particular the attached glycans, play an important role in interactions with the microbial world, the salivary glycoproteome and other post-translational modifications of salivary proteins need to be studied. Risk markers for microbial diseases, including dental caries, are likely to be discovered among the highly glycosylated major protein species in saliva. This review will attempt to raise new ideas and also point to under-researched areas that may hold promise for future applicability in oral diagnostics and prediction of oral disease. PMID:22292826

Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome

PubMed Central

MacMillan, Heath A.; Knee, Jose M.; Dennis, Alice B.; Udaka, Hiroko; Marshall, Katie E.; Merritt, Thomas J. S.; Sinclair, Brent J.

2016-01-01

Cold tolerance is a key determinant of insect distribution and abundance, and thermal acclimation can strongly influence organismal stress tolerance phenotypes, particularly in small ectotherms like Drosophila. However, there is limited understanding of the molecular and biochemical mechanisms that confer such impressive plasticity. Here, we use high-throughput mRNA sequencing (RNA-seq) and liquid chromatography – mass spectrometry (LC-MS) to compare the transcriptomes and metabolomes of D. melanogaster acclimated as adults to warm (rearing) (21.5 °C) or cold conditions (6 °C). Cold acclimation improved cold tolerance and led to extensive biological reorganization: almost one third of the transcriptome and nearly half of the metabolome were differentially regulated. There was overlap in the metabolic pathways identified via transcriptomics and metabolomics, with proline and glutathione metabolism being the most strongly-supported metabolic pathways associated with increased cold tolerance. We discuss several new targets in the study of insect cold tolerance (e.g. dopamine signaling and Na+-driven transport), but many previously identified candidate genes and pathways (e.g. heat shock proteins, Ca2+ signaling, and ROS detoxification) were also identified in the present study, and our results are thus consistent with and extend the current understanding of the mechanisms of insect chilling tolerance. PMID:27357258

Whole-Genome Saliva and Blood DNA Methylation Profiling in Individuals with a Respiratory Allergy

PubMed Central

Declerck, Ken; Traen, Sophie; Koppen, Gudrun; Van Camp, Guy; Schoeters, Greet; Vanden Berghe, Wim; De Boever, Patrick

2016-01-01

The etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n = 5) compared to healthy controls (n = 5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437 (P<0.05 and |Δβ|>0.1), respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. The absolute levels of methylation in blood and saliva were confirmed for 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes using pyrosequencing analysis. The differential methylation could only be confirmed for DMS in PM20D1 and STK32C genes in saliva. We show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS when comparing RA cases and healthy controls. The results were replicated in blood cells of the same individuals and confirmed by pyrosequencing analysis. This study provides proof-of-concept for the applicability of saliva-based whole-genome methylation analysis in the field

COnsortium of METabolomics Studies (COMETS)

Cancer.gov

The COnsortium of METabolomics Studies (COMETS) is an extramural-intramural partnership that promotes collaboration among prospective cohort studies that follow participants for a range of outcomes and perform metabolomic profiling of individuals.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future.

PubMed

Barnes, Stephen; Benton, H Paul; Casazza, Krista; Cooper, Sara J; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K; Renfrow, Matthew B; Tiwari, Hemant K

2016-08-01

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

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

PubMed

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.

Siderophore biosynthesis coordinately modulated the virulence-associated interactive metabolome of uropathogenic Escherichia coli and human urine.

PubMed

Su, Qiao; Guan, Tianbing; Lv, Haitao

2016-04-14

Uropathogenic Escherichia coli (UPEC) growth in women's bladders during urinary tract infection (UTI) incurs substantial chemical exchange, termed the "interactive metabolome", which primarily accounts for the metabolic costs (utilized metabolome) and metabolic donations (excreted metabolome) between UPEC and human urine. Here, we attempted to identify the individualized interactive metabolome between UPEC and human urine. We were able to distinguish UPEC from non-UPEC by employing a combination of metabolomics and genetics. Our results revealed that the interactive metabolome between UPEC and human urine was markedly different from that between non-UPEC and human urine, and that UPEC triggered much stronger perturbations in the interactive metabolome in human urine. Furthermore, siderophore biosynthesis coordinately modulated the individualized interactive metabolome, which we found to be a critical component of UPEC virulence. The individualized virulence-associated interactive metabolome contained 31 different metabolites and 17 central metabolic pathways that were annotated to host these different metabolites, including energetic metabolism, amino acid metabolism, and gut microbe metabolism. Changes in the activities of these pathways mechanistically pinpointed the virulent capability of siderophore biosynthesis. Together, our findings provide novel insights into UPEC virulence, and we propose that siderophores are potential targets for further discovery of drugs to treat UPEC-induced UTI.

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets.

PubMed

Carroll, Adam J; Badger, Murray R; Harvey Millar, A

2010-07-14

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. 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. 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 assess data quality and draw their own insights from published

Effects of sucking acidic candy on whole-mouth saliva composition.

PubMed

Jensdottir, T; Nauntofte, B; Buchwald, C; Bardow, A

2005-01-01

Limited information is available on the effects of sucking acidic candies on saliva composition and the protective role of saliva in this relation. Therefore the aim of this study was to determine salivary effects of sucking acidic candies in vivo in relation to individual variations in whole-saliva flow rate (WSFR) and buffer capacity (WSbeta). Ten healthy young males (24 +/- 2 years) sucked a rhubarb-flavoured acidic hard-boiled candy with tartaric acid available on the Danish market. The whole saliva was collected into a closed system, regarding CO2, at different times as follows: firstly, unstimulated saliva for 5 min (baseline), secondly stimulated saliva for 4 min upon sucking the candy, and finally post-stimulated saliva for 10 min. Saliva pH was determined on a blood gas analyser and WSbeta was estimated from the saliva bicarbonate concentration obtained by the analyser and by ionic balance calculation. The erosive potential of the candy in saliva was estimated from the saliva pH values and degree of saturation with respect to hydroxyapatite (DS(HAp)). The results showed that saliva pH dropped from 6.5 (baseline) down to 4.5 at the fourth minute of sucking the candy, and returned to pH 6.5 five minutes after stimulation (post-stimulated). DS(HAp) decreased upon sucking the candy and saliva from all subjects became undersaturated with respect to HAp. Significant positive correlations were obtained between pH and WSFR (r(s) = 0.47; p < 0.05) and between pH and WSbeta (r(s) = 0.65; p < 0.01). In relation to WSbeta we found that 70% of the buffer capacity originating from the bicarbonate buffer system upon sucking the candy was exerted as phase buffering. We conclude that sucking this type of acidic candies changes whole-mouth saliva composition so that it may have erosive potential and that high WSFR and WSbeta have protective effects against these salivary changes. Copyright 2005 S. Karger AG, Basel.

Cerebrospinal fluid metabolomic profiling in tuberculous and viral meningitis: Screening potential markers for differential diagnosis.

PubMed

Li, Zihui; Du, Boping; Li, Jing; Zhang, Jinli; Zheng, Xiaojing; Jia, Hongyan; Xing, Aiying; Sun, Qi; Liu, Fei; Zhang, Zongde

2017-03-01

Tuberculous meningitis (TBM) is the most severe and frequent form of central nervous system tuberculosis. The current lack of efficient diagnostic tests makes it difficult to differentiate TBM from other common types of meningitis, especially viral meningitis (VM). Metabolomics is an important tool to identify disease-specific biomarkers. However, little metabolomic information is available on adult TBM. We used 1 H nuclear magnetic resonance-based metabolomics to investigate the metabolic features of the CSF from 18 TBM and 20 VM patients. Principal component analysis and orthogonal signal correction-partial least squares-discriminant analysis (OSC-PLS-DA) were applied to analyze profiling data. Metabolites were identified using the Human Metabolome Database and pathway analysis was performed with MetaboAnalyst 3.0. The OSC-PLS-DA model could distinguish TBM from VM with high reliability. A total of 25 key metabolites that contributed to their discrimination were identified, including some, such as betaine and cyclohexane, rarely reported before in TBM. Pathway analysis indicated that amino acid and energy metabolism was significantly different in the CSF of TBM compared with VM. Twenty-five key metabolites identified in our study may be potential biomarkers for TBM differential diagnosis and are worthy of further investigation. Copyright © 2017 Elsevier B.V. All rights reserved.

New Biomarkers of Coffee Consumption Identified by the Non-Targeted Metabolomic Profiling of Cohort Study Subjects

PubMed Central

Martin, Jean-François; Lyan, Bernard; Pujos-Guillot, Estelle; Fezeu, Leopold; Hercberg, Serge; Comte, Blandine; Galan, Pilar; Touvier, Mathilde; Manach, Claudine

2014-01-01

Coffee contains various bioactives implicated with human health and disease risk. To accurately assess the effects of overall consumption upon health and disease, individual intake must be measured in large epidemiological studies. Metabolomics has emerged as a powerful approach to discover biomarkers of intake for a large range of foods. Here we report the profiling of the urinary metabolome of cohort study subjects to search for new biomarkers of coffee intake. Using repeated 24-hour dietary records and a food frequency questionnaire, 20 high coffee consumers (183–540 mL/d) and 19 low consumers were selected from the French SU.VI.MAX2 cohort. Morning spot urine samples from each subject were profiled by high-resolution mass spectrometry. Partial least-square discriminant analysis of multidimensional liquid chromatography-mass spectrometry data clearly distinguished high consumers from low via 132 significant (p-value<0.05) discriminating features. Ion clusters whose intensities were most elevated in the high consumers were annotated using online and in-house databases and their identities checked using commercial standards and MS-MS fragmentation. The best discriminants, and thus potential markers of coffee consumption, were the glucuronide of the diterpenoid atractyligenin, the diketopiperazine cyclo(isoleucyl-prolyl), and the alkaloid trigonelline. Some caffeine metabolites, such as 1-methylxanthine, were also among the discriminants, however caffeine may be consumed from other sources and its metabolism is subject to inter-individual variation. Receiver operating characteristics curve analysis showed that the biomarkers identified could be used effectively in combination for increased sensitivity and specificity. Once validated in other cohorts or intervention studies, these specific single or combined biomarkers will become a valuable alternative to assessment of coffee intake by dietary survey and finally lead to a better understanding of the health

The saliva proteome of the blood-feeding insect Triatoma infestans is rich in platelet-aggregation inhibitors

NASA Astrophysics Data System (ADS)

Charneau, Sébastien; Junqueira, Magno; Costa, Camila M.; Pires, Daniele L.; Fernandes, Ellen S.; Bussacos, Ana C.; Sousa, Marcelo V.; Ricart, Carlos André O.; Shevchenko, Andrej; Teixeira, Antonio R. L.

2007-12-01

The saliva of the bloodsucking bug Triatoma infestans vector of Chagas disease contains an anti-hemostatic molecular cocktail that prevents coagulation, vasoconstriction and platelet aggregation in a vertebrate prey. In order to characterize T. infestans saliva proteome, we separated the secreted saliva by two-dimensional gel electrophoresis (2-DE). More than 200 salivary proteins were detected on the 2-DE map, mainly in the alkaline region. By nanoLC-MS/MS analysis using a LTQ-Orbitrap equipment followed by a combination of conventional and sequence-similarity searches, we identified 58 main protein spots. Most of such proteins possess potential blood-feeding associated functions, particularly anti-platelet aggregation proteins belonging to lipocalin and apyrase families. The saliva protein composition indicates a highly specific molecular mechanism of early response to platelet aggregation. This first proteome analysis of the T. infestans secreted saliva provides a basis for a better understanding of this fluid protein composition highly directed to counterpart hemostasis of the prey, thus promoting the bug's blood-feeding.

Metabolomics for Biomarker Discovery in Gastroenterological Cancer

PubMed Central

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

2014-01-01

The study of the omics cascade, which involves comprehensive investigations based on genomics, transcriptomics, proteomics, metabolomics, etc., has developed rapidly and now plays an important role in life science research. Among such analyses, metabolome analysis, in which the concentrations of low molecular weight metabolites are comprehensively analyzed, has rapidly developed along with improvements in analytical technology, and hence, has been applied to a variety of research fields including the clinical, cell biology, and plant/food science fields. The metabolome represents the endpoint of the omics cascade and is also the closest point in the cascade to the phenotype. Moreover, it is affected by variations in not only the expression but also the enzymatic activity of several proteins. Therefore, metabolome analysis can be a useful approach for finding effective diagnostic markers and examining unknown pathological conditions. The number of studies involving metabolome analysis has recently been increasing year-on-year. Here, we describe the findings of studies that used metabolome analysis to attempt to discover biomarker candidates for gastroenterological cancer and discuss metabolome analysis-based disease diagnosis. PMID:25003943

Metabolomic approach for improving ethanol stress tolerance in Saccharomyces cerevisiae.

PubMed

Ohta, Erika; Nakayama, Yasumune; Mukai, Yukio; Bamba, Takeshi; Fukusaki, Eiichiro

2016-04-01

The budding yeast Saccharomyces cerevisiae is widely used for brewing and ethanol production. The ethanol sensitivity of yeast cells is still a serious problem during ethanol fermentation, and a variety of genetic approaches (e.g., random mutant screening under selective pressure of ethanol) have been developed to improve ethanol tolerance. In this study, we developed a strategy for improving ethanol tolerance of yeast cells based on metabolomics as a high-resolution quantitative phenotypic analysis. We performed gas chromatography-mass spectrometry analysis to identify and quantify 36 compounds on 14 mutant strains including knockout strains for transcription factor and metabolic enzyme genes. A strong relation between metabolome of these mutants and their ethanol tolerance was observed. Data mining of the metabolomic analysis showed that several compounds (such as trehalose, valine, inositol and proline) contributed highly to ethanol tolerance. Our approach successfully detected well-known ethanol stress related metabolites such as trehalose and proline thus, to further prove our strategy, we focused on valine and inositol as the most promising target metabolites in our study. Our results show that simultaneous deletion of LEU4 and LEU9 (leading to accumulation of valine) or INM1 and INM2 (leading to reduction of inositol) significantly enhanced ethanol tolerance. This study shows the potential of the metabolomic approach to identify target genes for strain improvement of S. cerevisiae with higher ethanol tolerance. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Saliva and dental plaque.

PubMed

Rudney, J D

2000-12-01

Dental plaque is being redefined as oral biofilm. Diverse overlapping microbial consortia are present on all oral tissues. Biofilms are structured, displaying features like channels and projections. Constituent species switch back and forth between sessile and planktonic phases. Saliva is the medium for planktonic suspension. Several major functions can be defined for saliva in relation to oral biofilm. It serves as a medium for transporting planktonic bacteria within and between mouths. Bacteria in transit may be vulnerable to negative selection. Salivary agglutinins may prevent reattachment to surfaces. Killing by antimicrobial proteins may lead to attachment of dead cells. Salivary proteins form conditioning films on all oral surfaces. This contributes to positive selection for microbial adherence. Saliva carries chemical messengers which allow live adherent cells to sense a critical density of conspecifics. Growth begins, and thick biofilms may become resistant to antimicrobial substances. Salivary macromolecules may be catabolized, but salivary flow also may clear dietary substrates. Salivary proteins act in ways that benefit both host and microbe. All have multiple functions, and many do the same job. They form heterotypic complexes, which may exist in large micelle-like structures. These issues make it useful to compare subjects whose saliva functions differently. We have developed a simultaneous assay for aggregation, killing, live adherence, and dead adherence of oral species. Screening of 149 subjects has defined high killing/low adherence, low killing/high adherence, high killing/high adherence, and low killing/low adherence groups. These will be evaluated for differences in their flora.

Investigation of saliva of patients with periodontal disease using NAA

NASA Astrophysics Data System (ADS)

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.

Metabolic Mechanism for l-Leucine-Induced Metabolome To Eliminate Streptococcus iniae.

PubMed

Du, Chao-Chao; Yang, Man-Jun; Li, Min-Yi; Yang, Jun; Peng, Bo; Li, Hui; Peng, Xuan-Xian

2017-05-05

Crucial metabolites that modulate hosts' metabolome to eliminate bacterial pathogens have been documented, but the metabolic mechanisms are largely unknown. The present study explores the metabolic mechanism for l-leucine-induced metabolome to eliminate Streptococcus iniae in tilapia. GC-MS-based metabolomics was used to investigate the tilapia liver metabolic profile in the presence of exogenous l-leucine. Thirty-seven metabolites of differential abundance were determined, and 11 metabolic pathways were enriched. Pattern recognition analysis identified serine and proline as crucial metabolites, which are the two metabolites identified in survived tilapias during S. iniae infection, suggesting that the two metabolites play crucial roles in l-leucine-induced elimination of the pathogen by the host. Exogenous l-serine reduces the mortality of tilapias infected by S. iniae, providing a robust proof supporting the conclusion. Furthermore, exogenous l-serine elevates expression of genes IL-1β and IL-8 in tilapia spleen, but not TNFα, CXCR4 and Mx, suggesting that the metabolite promotes a phagocytosis role of macrophages, which is consistent with the finding that l-leucine promotes macrophages to kill both Gram-positive and Gram-negative bacterial pathogens. Therefore, the ability of phagocytosis enhanced by exogenous l-leucine is partly attributed to elevation of l-serine. These results demonstrate a metabolic mechanism by which exogenous l-leucine modulates tilapias' metabolome to enhance innate immunity and eliminate pathogens.

NMR Techniques in Metabolomic Studies: A Quick Overview on Examples of Utilization.

PubMed

Kruk, Joanna; Doskocz, Marek; Jodłowska, Elżbieta; Zacharzewska, Anna; Łakomiec, Joanna; Czaja, Kornelia; Kujawski, Jacek

2017-01-01

Metabolomics is a rapidly developing branch of science that concentrates on identifying biologically active molecules with potential biomarker properties. To define the best biomarkers for diseases, metabolomics uses both models (in vitro, animals) and human, as well as, various techniques such as mass spectroscopy, gas chromatography, liquid chromatography, infrared and UV-VIS spectroscopy and nuclear magnetic resonance. The last one takes advantage of the magnetic properties of certain nuclei, such as 1 H, 13 C, 31 P, 19 F, especially their ability to absorb and emit energy, what is crucial for analyzing samples. Among many spectroscopic NMR techniques not only one-dimensional (1D) techniques are known, but for many years two-dimensional (2D, for example, COSY, DOSY, JRES, HETCORE, HMQS), three-dimensional (3D, DART-MS, HRMAS, HSQC, HMBC) and solid-state NMR have been used. In this paper, authors taking apart fundamental division of nuclear magnetic resonance techniques intend to shown their wide application in metabolomic studies, especially in identifying biomarkers.

Comparative whole genome transcriptome and metabolome analyses of five Klebsiella pneumonia strains.

PubMed

Lee, Soojin; Kim, Borim; Yang, Jeongmo; Jeong, Daun; Park, Soohyun; Shin, Sang Heum; Kook, Jun Ho; Yang, Kap-Seok; Lee, Jinwon

2015-11-01

The integration of transcriptomics and metabolomics can provide precise information on gene-to-metabolite networks for identifying the function of novel genes. The goal of this study was to identify novel gene functions involved in 2,3-butanediol (2,3-BDO) biosynthesis by a comprehensive analysis of the transcriptome and metabolome of five mutated Klebsiella pneumonia strains (∆wabG = SGSB100, ∆wabG∆budA = SGSB106, ∆wabG∆budB = SGSB107, ∆wabG∆budC = SGSB108, ∆wabG∆budABC = SGSB109). First, the transcriptomes of all five mutants were analyzed and the genes exhibiting reproducible changes in expression were determined. The transcriptome was well conserved among the five strains, and differences in gene expression occurred mainly in genes coding for 2,3-BDO biosynthesis (budA, budB, and budC) and the genes involved in the degradation of reactive oxygen, biosynthesis and transport of arginine, cysteine biosynthesis, sulfur metabolism, oxidoreductase reaction, and formate dehydrogenase reaction. Second, differences in the metabolome (estimated by carbon distribution, CO2 emission, and redox balance) among the five mutant strains due to gene alteration of the 2,3-BDO operon were detected. The functional genomics approach integrating metabolomics and transcriptomics in K. Pneumonia presented here provides an innovative means of identifying novel gene functions involved in 2,3-BDO biosynthesis metabolism and whole cell metabolism.

Emerging Applications of Metabolomic and Genomic Profiling in Diabetic Clinical Medicine

PubMed Central

McKillop, Aine M.; Flatt, Peter R.

2011-01-01

Clinical and epidemiological metabolomics provides a unique opportunity to look at genotype-phenotype relationships as well as the body\\x{2019}s responses to environmental and lifestyle factors. Fundamentally, it provides information on the universal outcome of influencing factors on disease states and has great potential in the early diagnosis, therapy monitoring, and understanding of the pathogenesis of disease. Diseases, such as diabetes, with a complex set of interactions between genetic and environmental factors, produce changes in the body\\x{2019}s biochemical profile, thereby providing potential markers for diagnosis and initiation of therapies. There is clearly a need to discover new ways to aid diagnosis and assessment of glycemic status to help reduce diabetes complications and improve the quality of life. Many factors, including peptides, proteins, metabolites, nucleic acids, and polymorphisms, have been proposed as putative biomarkers for diabetes. Metabolomics is an approach used to identify and assess metabolic characteristics, changes, and phenotypes in response to influencing factors, such as environment, diet, lifestyle, and pathophysiological states. The specificity and sensitivity using metabolomics to identify biomarkers of disease have become increasingly feasible because of advances in analytical and information technologies. Likewise, the emergence of high-throughput genotyping technologies and genome-wide association studies has prompted the search for genetic markers of diabetes predisposition or susceptibility. In this review, we consider the application of key metabolomic and genomic methodologies in diabetes and summarize the established, new, and emerging metabolomic and genomic biomarkers for the disease. We conclude by summarizing future insights into the search for improved biomarkers for diabetes research and human diagnostics. PMID:22110171

Detection of chikungunya virus in saliva and urine.

PubMed

Musso, Didier; Teissier, Anita; Rouault, Eline; Teururai, Sylviane; de Pina, Jean-Jacques; Nhan, Tu-Xuan

2016-06-16

Saliva and urine have been used for arthropod-borne viruses molecular detection but not yet for chikungunya virus (CHIKV). We investigated the use of saliva and urine for molecular detection of CHIKV during the French Polynesian outbreak. During the French Polynesian chikungunya outbreak (2014-2015), we collected the same day blood and saliva samples from 60 patients with probable chikungunya (47 during the 1st week post symptoms onset and 13 after), urine was available for 39 of them. All samples were tested using a CHIKV reverse-transcription PCR. Forty eight patients had confirmed chikungunya. For confirmed chikungunya presenting during the 1st week post symptoms onset, CHIKV RNA was detected from 86.1 % (31/36) of blood, 58.3 % (21/36) of saliva and 8.3 % (2/24) of urine. Detection rate of CHIKV RNA was significantly higher in blood compared to saliva. For confirmed chikungunya presenting after the 1st week post symptoms onset, CHIKV RNA was detected from 8.3 % (1/12) of blood, 8.3 % (1/12) of saliva and 0 % (0/8) of urine. In contrast to Zika virus (ZIKV), saliva did not increased the detection rate of CHIKV RNA during the 1st week post symptoms onset. In contrast to ZIKV, dengue virus and West Nile virus, urine did not enlarged the window of detection of CHIKV RNA after the 1st week post symptoms onset. Saliva can be used for molecular detection of CHIKV during the 1st week post symptoms onset only if blood is impossible to collect but with a lower sensitivity compared to blood.

Saliva Liquid Biopsy for Point-of-Care Applications

PubMed Central

Aro, Katri; Wei, Fang; Wong, David T.; Tu, Michael

2017-01-01

Saliva is a non-invasive biofluid, which is easy to collect, transport, and store. Because of its accessibility and connection to systemic diseases, saliva is one of the best candidates for the advancement of point-of-care medicine, where individuals are able to easily monitor their health status by using portable convenient tools such as smartphones. There are a variety of scenarios with which saliva can be used: studies have been conducted on using saliva to measure stress hormones, enzyme levels, developmental disease biomarkers, and even cancer mutations. If validated biomarkers were combined with high-quality detection tools, saliva would open up a new frontier in high-quality healthcare, allowing physicians and patients to work together for real-time health monitoring and high-impact personalized preventative medicine. One of the most exciting emerging frontiers of saliva is liquid biopsy, which is a non-invasive means to assess the presence and characteristics of cancer in a patient. This article will review current basic knowledge of biomarkers, review their relation to different diseases and conditions, and explore liquid biopsy for point-of-care applications. PMID:28443278

Validation of a novel saliva-based ELISA test for diagnosing tapeworm burden in horses.

PubMed

Lightbody, Kirsty L; Davis, Paul J; Austin, Corrine J

2016-06-01

Tapeworm infections pose a significant threat to equine health as they are associated with clinical cases of colic. Diagnosis of tapeworm burden using fecal egg counts (FECs) is unreliable, and, although a commercial serologic ELISA for anti-tapeworm antibodies is available, it requires a veterinarian to collect the blood sample. A reliable diagnostic test using an owner-accessible sample such as saliva could provide a cost-effective alternative for tapeworm testing in horses, and allow targeted deworming strategies. The purpose of the study was to statistically validate a saliva tapeworm ELISA test and compare to a tapeworm-specific IgG(T) serologic ELISA. Serum samples (139) and matched saliva samples (104) were collected from horses at a UK abattoir. The ileocecal junction and cecum were visually examined for tapeworms and any present were counted. Samples were analyzed using a serologic ELISA and the saliva tapeworm test. The test results were compared to tapeworm numbers and the various data sets were statistically analyzed. Saliva scores had strong positive correlations with both infection intensity (0.74) and serologic results (Spearman's rank coefficients; 0.74 and 0.86, respectively). The saliva tapeworm test was capable of identifying the presence of one or more tapeworms with 83% sensitivity and 85% specificity. Importantly, no high-burden (more than 20 tapeworms) horses were misdiagnosed. The saliva tapeworm test has statistical accuracy for detecting tapeworm burdens in horses with 83% sensitivity and 85% specificity, similar to those of the serologic ELISA (85% and 78%, respectively). © 2016 American Society for Veterinary Clinical Pathology.

Conservation of streptococcal CRISPRs on human skin and saliva.

PubMed

Robles-Sikisaka, Refugio; Naidu, Mayuri; Ly, Melissa; Salzman, Julia; Abeles, Shira R; Boehm, Tobias K; Pride, David T

2014-06-06

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their content can provide clues as to the types and features of viruses they may have encountered. We investigated the conservation of CRISPR content from streptococci on skin and saliva of human subjects over 8-weeks to determine whether similarities existed in the CRISPR spacer profiles and whether CRISPR spacers were a stable component of each biogeographic site. Most of the CRISPR sequences identified were unique, but a small proportion of spacers from the skin and saliva of each subject matched spacers derived from previously sequenced loci of S. thermophilus and other streptococci. There were significant proportions of CRISPR spacers conserved over the entire 8-week study period for all subjects, and salivary CRISPR spacers sampled in the mornings showed significantly higher levels of conservation than any other time of day. We also found substantial similarities in the spacer repertoires of the skin and saliva of each subject. Many skin-derived spacers matched salivary viruses, supporting that bacteria of the skin may encounter viruses with similar sequences to those found in the mouth. Despite the similarities between skin and salivary spacer repertoires, the variation present was distinct based on each subject and body site. The conservation of CRISPR spacers in the saliva and the skin of human subjects over the time period studied suggests a relative conservation of the bacteria harboring them.

Conservation of streptococcal CRISPRs on human skin and saliva

PubMed Central

2014-01-01

Background Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their content can provide clues as to the types and features of viruses they may have encountered. Results We investigated the conservation of CRISPR content from streptococci on skin and saliva of human subjects over 8-weeks to determine whether similarities existed in the CRISPR spacer profiles and whether CRISPR spacers were a stable component of each biogeographic site. Most of the CRISPR sequences identified were unique, but a small proportion of spacers from the skin and saliva of each subject matched spacers derived from previously sequenced loci of S. thermophilus and other streptococci. There were significant proportions of CRISPR spacers conserved over the entire 8-week study period for all subjects, and salivary CRISPR spacers sampled in the mornings showed significantly higher levels of conservation than any other time of day. We also found substantial similarities in the spacer repertoires of the skin and saliva of each subject. Many skin-derived spacers matched salivary viruses, supporting that bacteria of the skin may encounter viruses with similar sequences to those found in the mouth. Despite the similarities between skin and salivary spacer repertoires, the variation present was distinct based on each subject and body site. Conclusions The conservation of CRISPR spacers in the saliva and the skin of human subjects over the time period studied suggests a relative conservation of the bacteria harboring them. PMID:24903519

Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data

PubMed Central

Barnes, Stephen; Benton, H. Paul; Casazza, Krista; Cooper, Sara J.; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H.; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K.; Renfrow, Matthew B.; Tiwari, Hemant K.

2016-01-01

The study of metabolism has had a long history. Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. The National Institutes of Health Common Fund Metabolomics Program was established in 2012 to stimulate interest in the approaches and technologies of metabolomics. To deliver one of the program’s goals, the University of Alabama at Birmingham has hosted an annual 4-day short course in metabolomics for faculty, postdoctoral fellows and graduate students from national and international institutions. This paper is the first part of a summary of the training materials presented in the course to be used as a resource for all those embarking on metabolomics research. PMID:27434804

Wine pH Prevails over Buffering Capacity of Human Saliva.

PubMed

Obreque-Slier, Elías; Espínola-Espínola, Valeria; López-Solís, Remigio

2016-11-02

Wine is an acidic beverage; its pH (2.9-3.8) is critically important to its organoleptic properties. During degustation, wine interacts with <1 mL of mouth saliva, the pH of which is near 7.0. This is buffered predominantly by the carbonate/bicarbonate pair (pK a = 6.1). Few data are available on whether the buffering capacity of saliva may alter the pH of wine and thus its sensorial properties. In this study both in vitro and in vivo approaches were conducted to measure pH in mixtures of representative red and white wines with human saliva. Continuous additions of microvolumes of either wine to a definite volume (3 mL) of saliva in vitro resulted in a progressive and steep decline in the pH of the wine/saliva mixture. Thus, a few microliters of either wine (<0.27 mL) was sufficient to reduce the pH of saliva by 1 pH unit. Further additions of wine to saliva lowered the pH to that of the corresponding wine. In the in vivo assay, definite volumes (1.5-18 mL) of either wine were mixed for 15 s with the mouth saliva of individual healthy subjects before pH determination in the expectorated wine/saliva mixtures. Compared to saliva, pronounced decreases in pH were observed, thus approaching the pH of wine even with the smallest volume of wine in the assay. Altogether, these results demonstrate that the buffering capacity of wine prevails over that of saliva and that during degustation the pH of the wine/saliva mixture in the mouth is, at least temporarily, that of the corresponding wine.

Improved artificial saliva for studying the cariogenic effect of carbohydrates.

PubMed

Björklund, Marika; Ouwehand, Arthur C; Forssten, Sofia D

2011-07-01

Saliva is a complex fluid that possesses many important functions regarding oral health. Many in vitro studies require relatively large quantities of saliva. While natural saliva would be the material of choice, it is difficult to obtain in sufficient quantities and varies in composition. Substitutes mimicking the physicochemical properties of saliva have been developed, but these are not appropriate to study the growth of mutans streptococci. Brain Heart Infusion (BHI) has been commonly used for this, but this medium is richer in nutrients than saliva. We therefore developed artificial saliva (AS) with nutrient levels resembling those in natural saliva as a substitute for natural human saliva (HS) to study the influence of different carbon sources on mutans streptococci growth. Growth of a wild-type Streptococcus mutans strain and S. mutans ATCC 15175 in BHI, HS, and AS was monitored anaerobically. Growth of S. mutans in the modified AS was very similar to the growth in HS, both in the absence and presence of different carbon sources. We therefore conclude that the developed AS is suitable for in vitro tests on S. mutans growth.

METABOLOMICS IN MEDICAL SCIENCES--TRENDS, CHALLENGES AND PERSPECTIVES.

PubMed

Klupczyńska, Agnieszka; Dereziński, Paweł; Kokot, Zenon J

2015-01-01

Metabolomics is the latest of the "omic" technologies that involves comprehensive analysis of small molecule metabolites of an organism or a specific biological sample. Metabolomics provides an insight into the cell status and describes an actual health condition of organisms. Analysis of metabolome offers a unique opportunity to study the influence of genetic variation, disease, applied treatment or diet on endogenous metabolic state of organisms. There are many areas that might benefit from metabolomic research. In the article some applications of this novel "omic" technology in the field of medical sciences are presented. One of the most popular aims of metabolomic studies is biomarker discovery. Despite using the state-of-art analytical techniques along with advanced bioinformatic tools, metabolomic experiments encounter numerous difficulties and pitfalls. Challenges that researchers in the field of analysis of metabolome have to face include i.a., technical limitations, bioinformatic challenges and integration with other "omic" sciences. One of the grand challenges for studies in the field of metabolomics is to tackle the problem of data analysis, which is probably the most time consuming stage of metabolomic workflow and requires close collaboration between analysts, clinicians and experts in chemometric analysis. Implementation of metabolomics into clinical practice will be dependent on establishment of standardized protocols in analytical performance and data analysis and development of fit-for-purpose biomarker method validation. Metabolomics allows to achieve a sophisticated level of information about biological systems and opens up new perspectives in many fields of medicine, especially in oncology. Apart from its extensive cognitive significance, metabolomics manifests also a practical importance as it may lead to design of new non-invasive, sensitive and specific diagnostic techniques and development of new therapies.

Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

PubMed Central

Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

2016-01-01

The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

Metabolomic signatures of aggressive prostate cancer.

PubMed

McDunn, Jonathan E; Li, Zhen; Adam, Klaus-Peter; Neri, Bruce P; Wolfert, Robert L; Milburn, Michael V; Lotan, Yair; Wheeler, Thomas M

2013-10-01

Current diagnostic techniques have increased the detection of prostate cancer; however, these tools inadequately stratify patients to minimize mortality. Recent studies have identified a biochemical signature of prostate cancer metastasis, including increased sarcosine abundance. This study examined the association of tissue metabolites with other clinically significant findings. A state of the art metabolomics platform analyzed prostatectomy tissues (331 prostate tumor, 178 cancer-free prostate tissues) from two independent sites. Biochemicals were analyzed by gas chromatography-mass spectrometry and ultrahigh performance liquid chromatography-tandem mass spectrometry. Statistical analyses identified metabolites associated with cancer aggressiveness: Gleason score, extracapsular extension, and seminal vesicle and lymph node involvement. Prostate tumors had significantly altered metabolite profiles compared to cancer-free prostate tissues, including biochemicals associated with cell growth, energetics, stress, and loss of prostate-specific biochemistry. Many metabolites were further associated with clinical findings of aggressive disease. Aggressiveness-associated metabolites stratified prostate tumor tissues with high abundances of compounds associated with normal prostate function (e.g., citrate and polyamines) from more clinically advanced prostate tumors. These aggressive prostate tumors were further subdivided by abundance profiles of metabolites including NAD+ and kynurenine. When added to multiparametric nomograms, metabolites improved prediction of organ confinement (AUROC from 0.53 to 0.62) and 5-year recurrence (AUROC from 0.53 to 0.64). These findings support and extend earlier metabolomic studies in prostate cancer and studies where metabolic enzymes have been associated with carcinogenesis and/or outcome. Furthermore, these data suggest that panels of analytes may be valuable to translate metabolomic findings to clinically useful diagnostic tests

Evaluation of HBsAg and anti-HBc assays in saliva and dried blood spot samples according HIV status.

PubMed

Flores, Geane Lopes; Cruz, Helena Medina; Potsch, Denise Vigo; May, Silvia Beatriz; Brandão-Mello, Carlos Eduardo; Pires, Marcia Maria Amendola; Pilotto, Jose Henrique; Lewis-Ximenez, Lia Laura; Lampe, Elisabeth; Villar, Livia Melo

2017-09-01

Influence of HIV status in HBV markers detection in saliva and dried blood spots (DBS) was not well established. This study aims to evaluate the performance of optimized commercial immunoassay for identifying HBsAg and anti-HBc in saliva and DBS according HIV status. A sum of 535 individuals grouped as HIV + , HBV + , HIV/HBV + and HIV/HBV- were recruited where 347 and 188 were included for HBsAg and anti-HBc evaluation, respectively. Serum, DBS collected in Whatman 903 paper and saliva obtained using salivette device were analyzed using EIA. Increased sample volume and ROC curve analysis for cut off determination were used for DBS and saliva testing. HBsAg detection in saliva and DBS exhibited sensitivities of 80.9% and 85.6% and specificities of 86.8% and 96.3%. Sensitivity of anti-HBc in saliva and DBS were 82.4% and 76.9% and specificities in saliva and DBS were 96.9% and 91.7%. Low sensitivities were observed for HBsAg (62%) and anti-HBc (47%) detection in saliva of HIV/HBV+ individuals. OD values were also lower for HBsAg detection in DBS and saliva of HIV/HBV+ individuals compared to their serum samples. Statistical significance was found for sensitivities in HBsAg detection between saliva and DBS demonstrating high sensitivity for DBS specimens. In conclusion, HIV status or antiretroviral treatment appears to interfere in the performance of HBsAg and anti-HBc detection in DBS and saliva samples using the adapted commercial EIA. Copyright © 2017 Elsevier B.V. All rights reserved.

Applied metabolomics in drug discovery.

PubMed

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.

Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery.

PubMed

Saigusa, Daisuke; Okamura, Yasunobu; Motoike, Ikuko N; Katoh, Yasutake; Kurosawa, Yasuhiro; Saijyo, Reina; Koshiba, Seizo; Yasuda, Jun; Motohashi, Hozumi; Sugawara, Junichi; Tanabe, Osamu; Kinoshita, Kengo; Yamamoto, Masayuki

2016-01-01

Metabolomics is a promising avenue for biomarker discovery. Although the quality of metabolomic analyses, especially global metabolomics (G-Met) using mass spectrometry (MS), largely depends on the instrumentation, potential bottlenecks still exist at several basic levels in the metabolomics workflow. Therefore, we established a precise protocol initially for the G-Met analyses of human blood plasma to overcome some these difficulties. In our protocol, samples are deproteinized in a 96-well plate using an automated liquid-handling system, and conducted either using a UHPLC-QTOF/MS system equipped with a reverse phase column or a LC-FTMS system equipped with a normal phase column. A normalization protocol of G-Met data was also developed to compensate for intra- and inter-batch differences, and the variations were significantly reduced along with our normalization, especially for the UHPLC-QTOF/MS data with a C18 reverse-phase column for positive ions. Secondly, we examined the changes in metabolomic profiles caused by the storage of EDTA-blood specimens to identify quality markers for the evaluation of the specimens' pre-analytical conditions. Forty quality markers, including lysophospholipids, dipeptides, fatty acids, succinic acid, amino acids, glucose, and uric acid were identified by G-Met for the evaluation of plasma sample quality and established the equation of calculating the quality score. We applied our quality markers to a small-scale study to evaluate the quality of clinical samples. The G-Met protocols and quality markers established here should prove useful for the discovery and development of biomarkers for a wider range of diseases.

Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data.

PubMed

Barnes, Stephen; Benton, H Paul; Casazza, Krista; Cooper, Sara J; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K; Renfrow, Matthew B; Tiwari, Hemant K

2016-07-01

The study of metabolism has had a long history. Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. The National Institutes of Health Common Fund Metabolomics Program was established in 2012 to stimulate interest in the approaches and technologies of metabolomics. To deliver one of the program's goals, the University of Alabama at Birmingham has hosted an annual 4-day short course in metabolomics for faculty, postdoctoral fellows and graduate students from national and international institutions. This paper is the first part of a summary of the training materials presented in the course to be used as a resource for all those embarking on metabolomics research. The complete set of training materials including slide sets and videos can be viewed at http://www.uab.edu/proteomics/metabolomics/workshop/workshop_june_2015.php. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Metabolomics of Genetically Modified Crops

PubMed Central

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

Linking gene regulation and the exo-metabolome: A comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast

PubMed Central

Rossouw, Debra; Næs, Tormod; Bauer, Florian F

2008-01-01

Background 'Omics' tools provide novel opportunities for system-wide analysis of complex cellular functions. Secondary metabolism is an example of a complex network of biochemical pathways, which, although well mapped from a biochemical point of view, is not well understood with regards to its physiological roles and genetic and biochemical regulation. Many of the metabolites produced by this network such as higher alcohols and esters are significant aroma impact compounds in fermentation products, and different yeast strains are known to produce highly divergent aroma profiles. Here, we investigated whether we can predict the impact of specific genes of known or unknown function on this metabolic network by combining whole transcriptome and partial exo-metabolome analysis. Results For this purpose, the gene expression levels of five different industrial wine yeast strains that produce divergent aroma profiles were established at three different time points of alcoholic fermentation in synthetic wine must. A matrix of gene expression data was generated and integrated with the concentrations of volatile aroma compounds measured at the same time points. This relatively unbiased approach to the study of volatile aroma compounds enabled us to identify candidate genes for aroma profile modification. Five of these genes, namely YMR210W, BAT1, AAD10, AAD14 and ACS1 were selected for overexpression in commercial wine yeast, VIN13. Analysis of the data show a statistically significant correlation between the changes in the exo-metabome of the overexpressing strains and the changes that were predicted based on the unbiased alignment of transcriptomic and exo-metabolomic data. Conclusion The data suggest that a comparative transcriptomics and metabolomics approach can be used to identify the metabolic impacts of the expression of individual genes in complex systems, and the amenability of transcriptomic data to direct applications of biotechnological relevance. PMID:18990252

Metabolomics discloses donor liver biomarkers associated with early allograft dysfunction.

PubMed

Cortes, Miriam; Pareja, Eugenia; García-Cañaveras, Juan C; Donato, M Teresa; Montero, Sandra; Mir, Jose; Castell, José V; Lahoz, Agustín

2014-09-01

Early allograft dysfunction (EAD) dramatically influences graft and patient outcome after orthotopic liver transplantation and its incidence is strongly determined by donor liver quality. Nevertheless, objective biomarkers, which can assess graft quality and anticipate organ function, are still lacking. This study aims to investigate whether there is a preoperative donor liver metabolomic biosignature associated with EAD. A comprehensive metabolomic profiling of 124 donor liver biopsies collected before transplantation was performed by mass spectrometry coupled to liquid chromatography. Donor liver grafts were classified into two groups: showing EAD and immediate graft function (IGF). Multivariate data analysis was used to search for the relationship between the metabolomic profiles present in donor livers before transplantation and their function in recipients. A set of liver graft dysfunction-associated biomarkers was identified. Key changes include significantly increased levels of bile acids, lysophospholipids, phospholipids, sphingomyelins and histidine metabolism products, all suggestive of disrupted lipid homeostasis and altered histidine pathway. Based on these biomarkers, a predictive EAD model was built and further evaluated by assessing 24 independent donor livers, yielding 91% sensitivity and 82% specificity. The model was also successfully challenged by evaluating donor livers showing primary non-function (n=4). A metabolomic biosignature that accurately differentiates donor livers, which later showed EAD or IGF, has been deciphered. The remarkable metabolomic differences between donor livers before transplant can relate to their different quality. The proposed metabolomic approach may become a clinical tool for donor liver quality assessment and for anticipating graft function before transplant. Copyright © 2014 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Menthol smokers: metabolomic profiling and smoking behavior

PubMed Central

Hsu, Ping-Ching; Lan, Renny S.; Brasky, Theodore M.; Marian, Catalin; Cheema, Amrita K.; Ressom, Habtom W.; Loffredo, Christopher A.; Pickworth, Wallace B.; Shields, Peter G.

2016-01-01

Background The use of menthol in cigarettes and marketing is under consideration for regulation by the FDA. However, the effects of menthol on smoking behavior and carcinogen exposure have been inconclusive. We previously reported metabolomic profiling for cigarette smokers, and novelly identified a menthol-glucuronide (MG) as the most significant metabolite directly related to smoking. Here, MG is studied in relation to smoking behavior and metabolomic profiles. Methods A cross-sectional study of 105 smokers who smoked two cigarettes in the laboratory one hour apart. Blood nicotine, MG and exhaled carbon monoxide (CO) boosts were determined (the difference before and after smoking). Spearman's correlation, Chi-Square and ANCOVA adjusted for gender, race and cotinine levels for menthol smokers assessed the relationship of MG boost, smoking behavior, and metabolic profiles. Multivariate metabolite characterization using supervised Partial Least Squares-Discriminant Analysis (PLS-DA) was carried out for the classification of metabolomics profiles. Results MG boost was positively correlated with CO boost, nicotine boost, average puff volume, puff duration, and total smoke exposure. Classification using PLS-DA, MG was the top metabolite discriminating metabolome of menthol vs. non-menthol smokers. Among menthol smokers, forty-two metabolites were significantly correlated with MG boost, which linked to cellular functions such as of cell death, survival, and movement. Conclusion Plasma MG boost is a new smoking behavior biomarker that may provides novel information over self-reported use of menthol cigarettes by integrating different smoking measures for understanding smoking behavior and harm of menthol cigarettes. Impacts These results provide insight into the biological effect of menthol smoking. PMID:27628308

In vitro assessment of artificial saliva formulations on initial enamel erosion remineralization.

PubMed

Ionta, Franciny Querobim; Mendonça, Fernanda Lyrio; de Oliveira, Gabriela Cristina; de Alencar, Catarina Ribeiro Barros; Honório, Heitor Marques; Magalhães, Ana Carolina; Rios, Daniela

2014-02-01

Various formulations of artificial saliva are present in the literature and little guidance is available on the standardization of type of saliva for use in in vitro protocols for erosive studies. The aim of this study was to evaluate the remineralizing capacity of different formulations of artificial saliva on initial enamel erosive lesion. Bovine enamel blocks were subjected to short-term acidic exposure by immersion in citric acid 0.05 M (pH 2.5) for 15s, resulting in surface softening without tissue loss. Then 90 selected eroded enamel blocks were randomly and equally divided into 6 groups according to saliva formulation (n=15): Saliva 1 (contain mucin); Saliva 2 (Saliva 1 without mucin); Saliva 3; Saliva 4; Saliva 5 (contain sodium carboxymethyl cellulose) and control (C) (deionized water). After demineralization enamel blocks were subjected to remineralization by immersion in the saliva's formulations for 2h. Enamel remineralization was measured by superficial hardness test (% superficial hardness change). The data were tested using ANOVA and Tukey's test (p<0.05). All the tested formulations of artificial saliva resulted in significantly higher enamel remineralization compared to control (p<0.001). Saliva 3 showed higher percentage of enamel remineralization than Saliva 5 (p<0.05). Besides the variety of artificial saliva for erosion in vitro protocols, all the formulations tested were able to partially remineralize initial erosive lesions. Copyright © 2013. Published by Elsevier Ltd.

NMR and MS Methods for Metabolomics.

PubMed

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.

Siderophore biosynthesis coordinately modulated the virulence-associated interactive metabolome of uropathogenic Escherichia coli and human urine

PubMed Central

Su, Qiao; Guan, Tianbing; Lv, Haitao

2016-01-01

Uropathogenic Escherichia coli (UPEC) growth in women’s bladders during urinary tract infection (UTI) incurs substantial chemical exchange, termed the “interactive metabolome”, which primarily accounts for the metabolic costs (utilized metabolome) and metabolic donations (excreted metabolome) between UPEC and human urine. Here, we attempted to identify the individualized interactive metabolome between UPEC and human urine. We were able to distinguish UPEC from non-UPEC by employing a combination of metabolomics and genetics. Our results revealed that the interactive metabolome between UPEC and human urine was markedly different from that between non-UPEC and human urine, and that UPEC triggered much stronger perturbations in the interactive metabolome in human urine. Furthermore, siderophore biosynthesis coordinately modulated the individualized interactive metabolome, which we found to be a critical component of UPEC virulence. The individualized virulence-associated interactive metabolome contained 31 different metabolites and 17 central metabolic pathways that were annotated to host these different metabolites, including energetic metabolism, amino acid metabolism, and gut microbe metabolism. Changes in the activities of these pathways mechanistically pinpointed the virulent capability of siderophore biosynthesis. Together, our findings provide novel insights into UPEC virulence, and we propose that siderophores are potential targets for further discovery of drugs to treat UPEC-induced UTI. PMID:27076285

Metabolomics study of human urinary metabolome modifications after intake of almond (Prunus dulcis (Mill.) D.A. Webb) skin polyphenols.

PubMed

Llorach, Rafael; Garrido, Ignacio; Monagas, Maria; Urpi-Sarda, Mireia; Tulipani, Sara; Bartolome, Begona; Andres-Lacueva, Cristina

2010-11-05

Almond, as a part of the nut family, is an important source of biological compounds, and specifically, almond skins have been considered an important source of polyphenols, including flavan-3-ols and flavonols. Polyphenol metabolism may produce several classes of metabolites that could often be more biologically active than their dietary precursor and could also become a robust new biomarker of almond polyphenol intake. In order to study urinary metabolome modifications during the 24 h after a single dose of almond skin extract, 24 volunteers (n = 24), who followed a polyphenol-free diet for 48 h before and during the study, ingested a dietary supplement of almond skin phenolic compounds (n = 12) or a placebo (n = 12). Urine samples were collected before ((-2)-0 h) and after (0-2 h, 2-6 h, 6-10 h, and 10-24 h) the intake and were analyzed by liquid chromatography-mass spectrometry (LC-q-TOF) and multivariate statistical analysis (principal component analysis (PCA) and orthogonal projection to latent structures (OPLS)). Putative identification of relevant biomarkers revealed a total of 34 metabolites associated with the single dose of almond extract, including host and, in particular, microbiota metabolites. As far as we know, this is the first time that conjugates of hydroxyphenylvaleric, hydroxyphenylpropionic, and hydroxyphenylacetic acids have been identified in human samples after the consumption of flavan-3-ols through a metabolomic approach. The results showed that this non-targeted approach could provide new intake biomarkers, contributing to the development of the food metabolome as an important part of the human urinary metabolome.

Dynamic changes in saliva after acute mental stress

PubMed Central

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

Realising the Potential of Urine and Saliva as Diagnostic Tools in Sport and Exercise Medicine.

PubMed

Lindsay, Angus; Costello, Joseph T

2017-01-01

Accurate monitoring of homeostatic perturbations following various psychophysiological stressors is essential in sports and exercise medicine. Various biomarkers are routinely used as monitoring tools in both clinical and elite sport settings. Blood collection and muscle biopsies, both invasive in nature, are considered the gold standard for the analysis of these biomarkers in exercise science. Exploring non-invasive methods of collecting and analysing biomarkers that are capable of providing accurate information regarding exercise-induced physiological and psychological stress is of obvious practical importance. This review describes the potential benefits, and the limitations, of using saliva and urine to ascertain biomarkers capable of identifying important stressors that are routinely encountered before, during, or after intense or unaccustomed exercise, competition, over-training, and inappropriate recovery. In particular, we focus on urinary and saliva biomarkers that have previously been used to monitor muscle damage, inflammation, cardiovascular stress, oxidative stress, hydration status, and brain distress. Evidence is provided from a range of empirical studies suggesting that urine and saliva are both capable of identifying various stressors. Although additional research regarding the efficacy of using urine and/or saliva to indicate the severity of exercise-induced psychophysiological stress is required, it is likely that these non-invasive biomarkers will represent "the future" in sports and exercise medicine.

Acid phosphatase test on Phadebas® sheets - An optimized method for presumptive saliva and semen detection.

PubMed

Herman, Yael; Feine, Ilan; Gafny, Ron

2018-04-30

The precise and efficient detection of semen and saliva in sexual assault case-work items is a critical step in the forensic pipeline. The outcome of this stage may have a profound impact on identifying perpetrators as well as on the investigation process and the final outcome in court. Semen detection is usually based on the activity of acid phosphatase (AP), an enzyme found in high concentration in the seminal plasma. Amylase, an enzyme catalyzing starch hydrolysis is found in high concentrations in saliva and therefore is a useful target for its detection. To screen case-work items, both presumptive tests require transfer of biological material from the item to paper in a moisturized environment. Since semen and saliva may appear in the same item, it is required in some cases to perform the tests one after the other. This may reduce the chances of identifying all stains on the item and obtaining a DNA profile. In the present study, we applied the AP biochemical test on a Phadebas ® sheet, a commercial starch containing paper used to detect saliva. This approach was found to be sensitive enough to detect diluted semen (1:50) after performing the Phadebas ® press test. In addition, it enabled detection of adjacent saliva and semen stains and stains containing a semen-saliva mixture. Finally, a DNA profile was successfully obtained from the Phadebas ® sheets after semen detection, a useful feature if the original item is lost or damaged. Taken together, this method provides a practical, reliable and convenient tool for screening sexual assault items of evidence. Copyright © 2018 Elsevier B.V. All rights reserved.

Review: Metabolomics in the developmental origins of obesity and its cardiometabolic consequences

PubMed Central

Hivert, MF; Perng, W; Watkins, S; Newgard, CB; Kenny, LC; Kristal, BS; Patti, ME; Isganaitis, E; DeMeo, DL; Oken, E; Gillman, MW

2015-01-01

In this review, we discuss the potential role of metabolomics to enhance understanding of obesity-related developmental origins of health and disease (DOHaD). We first provide an overview of common techniques and analytical approaches to help interested investigators dive into this relatively novel field. Next, we describe how metabolomics may capture exposures that are notoriously difficult to quantify, and help to further refine phenotypes associated with excess adiposity and related metabolic sequelae over the life course. Together, these data can ultimately help to elucidate mechanisms that underlie fetal metabolic programming. Finally, we review current gaps in knowledge and identify areas where the field of metabolomics is likely to provide insights into mechanisms linked to DOHaD in human populations. PMID:25631626

Evaluation of saliva collection devices for the analysis of proteins.

PubMed

Topkas, Eleni; Keith, Patricia; Dimeski, Goce; Cooper-White, Justin; Punyadeera, Chamindie

2012-07-11

Human saliva mirrors the body's health and can be collected non-invasively, does not require specialized skills and is suitable for large population based screening programs. The aims were twofold: to evaluate the suitability of commercially available saliva collection devices for quantifying proteins present in saliva and to provide levels for C-reactive protein (CRP), myoglobin, and immunoglobin E (IgE) in saliva of healthy individuals as a baseline for future studies. Saliva was collected from healthy volunteers (n=17, ages 18-33years). The following collection methods were evaluated: drool; Salimetrics® Oral Swab (SOS); Salivette® Cotton and Synthetic (Sarstedt) and Greiner Bio-One Saliva Collection System (GBO SCS®). We used AlphaLISA® assays to measure CRP, IgE and myoglobin levels in human saliva. Significant (p<0.05) differences in the salivary flow rates were observed based on the method of collection, i.e. salivary flow rates were significantly lower (p<0.05) in unstimulated saliva (i.e. drool and SOS), when compared with mechanically stimulated methods (p<0.05) (Salivette® Cotton and Synthetic) and acid stimulated method (p<0.05) (SCS®). Saliva collected using SOS yielded significantly (p<0.05) lower concentrations of myoglobin and CRP, whilst, saliva collected using the Salivette® Cotton and Synthetic swab yielded significantly (p<0.05) lower myoglobin and IgE concentrations respectively. The results demonstrated significantly relevant differences in analyte levels based on the collection method. Significant differences in the salivary flow rates were also observed depending on the saliva collection method. The data provide preliminary baseline values for salivary CRP, myoglobin, and IgE levels in healthy participants and based on the collection method. Copyright © 2012 Elsevier B.V. All rights reserved.

Candida in saliva of Brazilian hemophilic patients.

PubMed

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.

Comparative evaluation of saliva collection methods for proteome analysis.

PubMed

Golatowski, Claas; Salazar, Manuela Gesell; Dhople, Vishnu Mukund; Hammer, Elke; Kocher, Thomas; Jehmlich, Nico; Völker, Uwe

2013-04-18

Saliva collection devices are widely used for large-scale screening approaches. This study was designed to compare the suitability of three different whole-saliva collection approaches for subsequent proteome analyses. From 9 young healthy volunteers (4 women and 5 men) saliva samples were collected either unstimulated by passive drooling or stimulated using a paraffin gum or Salivette® (cotton swab). Saliva volume, protein concentration and salivary protein patterns were analyzed comparatively. Samples collected using paraffin gum showed the highest saliva volume (4.1±1.5 ml) followed by Salivette® collection (1.8±0.4 ml) and drooling (1.0±0.4 ml). Saliva protein concentrations (average 1145 μg/ml) showed no significant differences between the three sampling schemes. Each collection approach facilitated the identification of about 160 proteins (≥2 distinct peptides) per subject, but collection-method dependent variations in protein composition were observed. Passive drooling, paraffin gum and Salivette® each allows similar coverage of the whole saliva proteome, but the specific proteins observed depended on the collection approach. Thus, only one type of collection device should be used for quantitative proteome analysis in one experiment, especially when performing large-scale cross-sectional or multi-centric studies. Copyright © 2013 Elsevier B.V. All rights reserved.

Liver metabolomics analysis associated with feed efficiency on steers

USDA-ARS?s Scientific Manuscript database

The liver represents a metabolic crossroad regulating and modulating nutrients available from digestive tract absorption to the peripheral tissues. To identify potential differences in liver function that lead to differences in feed efficiency, liver metabolomic analysis was conducted using ultra-pe...

Urinary metabolomics analysis identifies key biomarkers of different stages of nonalcoholic fatty liver disease

PubMed Central

Dong, Shu; Zhan, Zong-Ying; Cao, Hong-Yan; Wu, Chao; Bian, Yan-Qin; Li, Jian-Yuan; Cheng, Gen-Hong; Liu, Ping; Sun, Ming-Yu

2017-01-01

AIM To identify a panel of biomarkers that can distinguish between non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), and explore molecular mechanism involved in the process of developing NASH from NAFLD. METHODS Biomarkers may differ during stages of NAFLD. Urine and blood were obtained from non-diabetic subjects with NAFLD and steatosis, with normal liver function (n = 33), from patients with NASH, with abnormal liver function (n = 45), and from healthy age and sex-matched controls (n = 30). Samples were subjected to metabolomic analysis to identify potential non-invasive biomarkers. Differences in urinary metabolic profiles were analyzed using liquid chromatography tandem mass spectrometry with principal component analysis and partial least squares-discriminate analysis. RESULTS Compared with NAFLD patients, patients with NASH had abnormal liver function and high serum lipid concentrations. Urinary metabonomics found differences in 31 metabolites between these two groups, including differences in nucleic acids and amino acids. Pathway analysis based on overlapping metabolites showed that pathways of energy and amino acid metabolism, as well as the pentose phosphate pathway, were closely associated with pathological processes in NAFLD and NASH. CONCLUSION These findings suggested that a panel of biomarkers could distinguish between NAFLD and NASH, and could help to determine the molecular mechanism involved in the process of developing NASH from NAFLD. Urinary biomarkers may be diagnostic in these patients and could be used to assess responses to therapeutic interventions. PMID:28487615

Impact of a western diet on the ovarian and serum metabolome.

PubMed

Dhungana, Suraj; Carlson, James E; Pathmasiri, Wimal; McRitchie, Susan; Davis, Matt; Sumner, Susan; Appt, Susan E

2016-10-01

The objective of this investigation was to determine differences in the profiles of endogenous metabolites (metabolomics) among ovaries and serum derived from Old World nonhuman primates fed prudent or Western diets. A retrospective, observational study was done using archived ovarian tissue and serum from midlife cynomolgus monkeys (Macaca fasicularis). Targeted and broad spectrum metabolomics analysis was used to compare ovarian tissue and serum from monkeys that had been exposed to a prudent diet or a Western diet. Monkeys in the prudent diet group (n=13) were research naïve and had been exposed only to a commercial monkey chow diet (low in cholesterol and saturated fats, high in complex carbohydrates). Western diet monkeys (n=8) had consumed a diet that was high in cholesterol, saturated animal fats and soluble carbohydrates for 2 years prior to ovarian tissue and serum collection. Metabolomic analyses were done on extracts of homogenized ovary tissue samples, and extracts of serum. Targeted analysis was conducted using the Biocrates p180 kit and broad spectrum analysis was conducted using UPLC-TOF-MS, resulting in the detection of 3500 compound ions. Using metabolomics methods, which capture thousands of signals for metabolites, 64 metabolites were identified in serum and 47 metabolites were identified in ovarian tissue that differed by diet. Quantitative targeted analysis revealed 13 amino acids, 6 acrylcarnitines, and 2 biogenic amines that were significantly (p<0.05) different between the two diet groups for serum extracts, and similar results were observed for the ovary extracts. These data demonstrate that dietary exposure had a significant impact on the serum and ovarian metabolome, and demonstrated perturbation in carnitine, lipids/fatty acid, and amino acid metabolic pathways. Published by Elsevier Ireland Ltd.

Saliva Proteomics Analysis Offers Insights on Type 1 Diabetes Pathology in a Pediatric Population

PubMed Central

Pappa, Eftychia; Vastardis, Heleni; Mermelekas, George; Gerasimidi-Vazeou, Andriani; Zoidakis, Jerome; Vougas, Konstantinos

2018-01-01

The composition of the salivary proteome is affected by pathological conditions. We analyzed by high resolution mass spectrometry approaches saliva samples collected from children and adolescents with type 1 diabetes and healthy controls. The list of more than 2000 high confidence protein identifications constitutes a comprehensive characterization of the salivary proteome. Patients with good glycemic regulation and healthy individuals have comparable proteomic profiles. In contrast, a significant number of differentially expressed proteins were identified in the saliva of patients with poor glycemic regulation compared to patients with good glycemic control and healthy children. These proteins are involved in biological processes relevant to diabetic pathology such as endothelial damage and inflammation. Moreover, a putative preventive therapeutic approach was identified based on bioinformatic analysis of the deregulated salivary proteins. Thus, thorough characterization of saliva proteins in diabetic pediatric patients established a connection between molecular changes and disease pathology. This proteomic and bioinformatic approach highlights the potential of salivary diagnostics in diabetes pathology and opens the way for preventive treatment of the disease. PMID:29755368

DNA methylation analysis from saliva samples for epidemiological studies.

PubMed

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.

An Ultrahigh-Performance Liquid Chromatography-Time-of-Flight Mass Spectrometry Metabolomic Approach to Studying the Impact of Moderate Red-Wine Consumption on Urinary Metabolome.

PubMed

Esteban-Fernández, Adelaida; Ibañez, Clara; Simó, Carolina; Bartolomé, Begoña; Moreno-Arribas, M Victoria

2018-04-06

Moderate red-wine consumption has been widely described to exert several benefits in human health. This is mainly due to its unique content of bioactive polyphenols, which suffer several modifications along their pass through the digestive system, including microbial transformation in the colon and phase-II metabolism, until they are finally excreted in urine and feces. To determine the impact of moderate wine consumption in the overall urinary metabolome of healthy volunteers ( n = 41), samples from a red-wine interventional study (250 mL/day, 28 days) were investigated. Urine (24 h) was collected before and after intervention and analyzed by an untargeted ultrahigh-performance liquid chromatography-time-of-flight mass spectrometry metabolomics approach. 94 compounds linked to wine consumption, including specific wine components (tartaric acid), microbial-derived phenolic metabolites (5-(dihydroxyphenyl)-γ-valerolactones and 4-hydroxyl-5-(phenyl)-valeric acids), and endogenous compounds were identified. Also, some relationships between parallel fecal and urinary metabolomes are discussed.

Comparative analysis of targeted metabolomics: dominance-based rough set approach versus orthogonal partial least square-discriminant analysis.

PubMed

Blasco, H; Błaszczyński, J; Billaut, J C; Nadal-Desbarats, L; Pradat, P F; Devos, D; Moreau, C; Andres, C R; Emond, P; Corcia, P; Słowiński, R

2015-02-01

Metabolomics is an emerging field that includes ascertaining a metabolic profile from a combination of small molecules, and which has health applications. Metabolomic methods are currently applied to discover diagnostic biomarkers and to identify pathophysiological pathways involved in pathology. However, metabolomic data are complex and are usually analyzed by statistical methods. Although the methods have been widely described, most have not been either standardized or validated. Data analysis is the foundation of a robust methodology, so new mathematical methods need to be developed to assess and complement current methods. We therefore applied, for the first time, the dominance-based rough set approach (DRSA) to metabolomics data; we also assessed the complementarity of this method with standard statistical methods. Some attributes were transformed in a way allowing us to discover global and local monotonic relationships between condition and decision attributes. We used previously published metabolomics data (18 variables) for amyotrophic lateral sclerosis (ALS) and non-ALS patients. Principal Component Analysis (PCA) and Orthogonal Partial Least Square-Discriminant Analysis (OPLS-DA) allowed satisfactory discrimination (72.7%) between ALS and non-ALS patients. Some discriminant metabolites were identified: acetate, acetone, pyruvate and glutamine. The concentrations of acetate and pyruvate were also identified by univariate analysis as significantly different between ALS and non-ALS patients. DRSA correctly classified 68.7% of the cases and established rules involving some of the metabolites highlighted by OPLS-DA (acetate and acetone). Some rules identified potential biomarkers not revealed by OPLS-DA (beta-hydroxybutyrate). We also found a large number of common discriminating metabolites after Bayesian confirmation measures, particularly acetate, pyruvate, acetone and ascorbate, consistent with the pathophysiological pathways involved in ALS. DRSA provides

Metabolomics-Based Discovery of Small Molecule Biomarkers in Serum Associated with Dengue Virus Infections and Disease Outcomes

PubMed Central

Voge, Natalia V.; Perera, Rushika; Mahapatra, Sebabrata; Gresh, Lionel; Balmaseda, Angel; Loroño-Pino, María A.; Hopf-Jannasch, Amber S.; Belisle, John T.; Harris, Eva; Blair, Carol D.; Beaty, Barry J.

2016-01-01

Background Epidemic dengue fever (DF) and dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS) are overwhelming public health capacity for diagnosis and clinical care of dengue patients throughout the tropical and subtropical world. The ability to predict severe dengue disease outcomes (DHF/DSS) using acute phase clinical specimens would be of enormous value to physicians and health care workers for appropriate triaging of patients for clinical management. Advances in the field of metabolomics and analytic software provide new opportunities to identify host small molecule biomarkers (SMBs) in acute phase clinical specimens that differentiate dengue disease outcomes. Methodology/Principal Findings Exploratory metabolomic studies were conducted to characterize the serum metabolome of patients who experienced different dengue disease outcomes. Serum samples from dengue patients from Nicaragua and Mexico were retrospectively obtained, and hydrophilic interaction liquid chromatography (HILIC)-mass spectrometry (MS) identified small molecule metabolites that were associated with and statistically differentiated DHF/DSS, DF, and non-dengue (ND) diagnosis groups. In the Nicaraguan samples, 191 metabolites differentiated DF from ND outcomes and 83 differentiated DHF/DSS and DF outcomes. In the Mexican samples, 306 metabolites differentiated DF from ND and 37 differentiated DHF/DSS and DF outcomes. The structural identities of 13 metabolites were confirmed using tandem mass spectrometry (MS/MS). Metabolomic analysis of serum samples from patients diagnosed as DF who progressed to DHF/DSS identified 65 metabolites that predicted dengue disease outcomes. Differential perturbation of the serum metabolome was demonstrated following infection with different DENV serotypes and following primary and secondary DENV infections. Conclusions/Significance These results provide proof-of-concept that a metabolomics approach can be used to identify metabolites or SMBs in serum

Metabolomic Strategies Involving Mass Spectrometry Combined with Liquid and Gas Chromatography.

PubMed

Lopes, Aline Soriano; Cruz, Elisa Castañeda Santa; Sussulini, Alessandra; Klassen, Aline

2017-01-01

Amongst all omics sciences, there is no doubt that metabolomics is undergoing the most important growth in the last decade. The advances in analytical techniques and data analysis tools are the main factors that make possible the development and establishment of metabolomics as a significant research field in systems biology. As metabolomic analysis demands high sensitivity for detecting metabolites present in low concentrations in biological samples, high-resolution power for identifying the metabolites and wide dynamic range to detect metabolites with variable concentrations in complex matrices, mass spectrometry is being the most extensively used analytical technique for fulfilling these requirements. Mass spectrometry alone can be used in a metabolomic analysis; however, some issues such as ion suppression may difficultate the quantification/identification of metabolites with lower concentrations or some metabolite classes that do not ionise as well as others. The best choice is coupling separation techniques, such as gas or liquid chromatography, to mass spectrometry, in order to improve the sensitivity and resolution power of the analysis, besides obtaining extra information (retention time) that facilitates the identification of the metabolites, especially when considering untargeted metabolomic strategies. In this chapter, the main aspects of mass spectrometry (MS), liquid chromatography (LC) and gas chromatography (GC) are discussed, and recent clinical applications of LC-MS and GC-MS are also presented.

Metabolomics by Gas Chromatography-Mass Spectrometry: the combination of targeted and untargeted profiling

PubMed Central

Fiehn, Oliver

2016-01-01

Gas chromatography-mass spectrometry (GC-MS)-based metabolomics is ideal for identifying and quantitating small molecular metabolites (<650 daltons), including small acids, alcohols, hydroxyl acids, amino acids, sugars, fatty acids, sterols, catecholamines, drugs, and toxins, often using chemical derivatization to make these compounds volatile enough for gas chromatography. This unit shows that on GC-MS- based metabolomics easily allows integrating targeted assays for absolute quantification of specific metabolites with untargeted metabolomics to discover novel compounds. Complemented by database annotations using large spectral libraries and validated, standardized standard operating procedures, GC-MS can identify and semi-quantify over 200 compounds per study in human body fluids (e.g., plasma, urine or stool) samples. Deconvolution software enables detection of more than 300 additional unidentified signals that can be annotated through accurate mass instruments with appropriate data processing workflows, similar to liquid chromatography-MS untargeted profiling (LC-MS). Hence, GC-MS is a mature technology that not only uses classic detectors (‘quadrupole’) but also target mass spectrometers (‘triple quadrupole’) and accurate mass instruments (‘quadrupole-time of flight’). This unit covers the following aspects of GC-MS-based metabolomics: (i) sample preparation from mammalian samples, (ii) acquisition of data, (iii) quality control, and (iv) data processing. PMID:27038389

Binding of corroded ions to human saliva.

PubMed

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.

The Role of Plasma and Urine Metabolomics in Identifying New Biomarkers in Severe Newborn Asphyxia: A Study of Asphyxiated Newborn Pigs following Cardiopulmonary Resuscitation.

PubMed

Sachse, Daniel; Solevåg, Anne Lee; Berg, Jens Petter; Nakstad, Britt

2016-01-01

Optimizing resuscitation is important to prevent morbidity and mortality from perinatal asphyxia. The metabolism of cells and tissues is severely disturbed during asphyxia and resuscitation, and metabolomic analyses provide a snapshot of many small molecular weight metabolites in body fluids or tissues. In this study metabolomics profiles were studied in newborn pigs that were asphyxiated and resuscitated using different protocols to identify biomarkers for subject characterization, intervention effects and possibly prognosis. A total of 125 newborn Noroc pigs were anesthetized, mechanically ventilated and inflicted progressive asphyxia until asystole. Pigs were randomized to resuscitation with a FiO2 0.21 or 1.0, different duration of ventilation before initiation of chest compressions (CC), and different CC to ventilation ratios. Plasma and urine samples were obtained at baseline, and 2 h and 4 h after return of spontaneous circulation (ROSC, heart rate > = 100 bpm). Metabolomics profiles of the samples were analyzed by nuclear magnetic resonance spectroscopy. Plasma and urine showed severe metabolic alterations consistent with hypoxia and acidosis 2 h and 4 h after ROSC. Baseline plasma hypoxanthine and lipoprotein concentrations were inversely correlated to the duration of hypoxia sustained before asystole occurred, but there was no evidence for a differential metabolic response to the different resuscitation protocols or in terms of survival. Metabolic profiles of asphyxiated newborn pigs showed severe metabolic alterations. Consistent with previously published reports, we found no evidence of differences between established and alternative resuscitation protocols. Lactate and pyruvate may have a prognostic value, but have to be independently confirmed.

The Role of Plasma and Urine Metabolomics in Identifying New Biomarkers in Severe Newborn Asphyxia: A Study of Asphyxiated Newborn Pigs following Cardiopulmonary Resuscitation

PubMed Central

Sachse, Daniel; Solevåg, Anne Lee; Berg, Jens Petter; Nakstad, Britt

2016-01-01

Background Optimizing resuscitation is important to prevent morbidity and mortality from perinatal asphyxia. The metabolism of cells and tissues is severely disturbed during asphyxia and resuscitation, and metabolomic analyses provide a snapshot of many small molecular weight metabolites in body fluids or tissues. In this study metabolomics profiles were studied in newborn pigs that were asphyxiated and resuscitated using different protocols to identify biomarkers for subject characterization, intervention effects and possibly prognosis. Methods A total of 125 newborn Noroc pigs were anesthetized, mechanically ventilated and inflicted progressive asphyxia until asystole. Pigs were randomized to resuscitation with a FiO2 0.21 or 1.0, different duration of ventilation before initiation of chest compressions (CC), and different CC to ventilation ratios. Plasma and urine samples were obtained at baseline, and 2 h and 4 h after return of spontaneous circulation (ROSC, heart rate > = 100 bpm). Metabolomics profiles of the samples were analyzed by nuclear magnetic resonance spectroscopy. Results Plasma and urine showed severe metabolic alterations consistent with hypoxia and acidosis 2 h and 4 h after ROSC. Baseline plasma hypoxanthine and lipoprotein concentrations were inversely correlated to the duration of hypoxia sustained before asystole occurred, but there was no evidence for a differential metabolic response to the different resuscitation protocols or in terms of survival. Conclusions Metabolic profiles of asphyxiated newborn pigs showed severe metabolic alterations. Consistent with previously published reports, we found no evidence of differences between established and alternative resuscitation protocols. Lactate and pyruvate may have a prognostic value, but have to be independently confirmed. PMID:27529347

Characterizing Alzheimer's disease through metabolomics and investigating anti-Alzheimer's disease effects of natural products.

PubMed

Yi, Lunzhao; Liu, Wenbin; Wang, Zhe; Ren, Dabing; Peng, Weijun

2017-06-01

Alzheimer's disease (AD) is the most common cause of dementia in elderly people and is among the greatest healthcare challenges of the 21st century. However, the etiology and pathogenesis of AD remain poorly understood, and no curative treatments are available to slow down or stop the degenerative effects of AD. As a high-throughput approach, metabolomics is gaining significant attention in AD research, because it has a powerful potential to discover novel biomarkers, unravel new therapeutic targets for AD, and identify perturbed metabolic pathways involved in AD progression. Here, we systematically review metabolomics with regard to its recent advances and applications in the identification of potential biomarkers for early AD diagnosis and pathogenesis research. In addition, we illustrate the developments in metabolomics as an effective tool for understanding the anti-AD mechanisms of natural products. We believe that the insights from these advances can narrow the gap between metabolomics research and clinical applications of laboratory findings. Moreover, we discuss some limitations and perspectives of biomarker identification in metabolomics. © 2017 New York Academy of Sciences.

Saliva Microbiota Carry Caries-Specific Functional Gene Signatures

PubMed Central

Chang, Xingzhi; Yuan, Xiao; Tu, Qichao; Yuan, Tong; Deng, Ye; Hemme, Christopher L.; Van Nostrand, Joy; Cui, Xinping; He, Zhili; Chen, Zhenggang; Guo, Dawei; Yu, Jiangbo; Zhang, Yue; Zhou, Jizhong; Xu, Jian

2014-01-01

Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. PMID:24533043

Saliva microbiota carry caries-specific functional gene signatures.

PubMed

Yang, Fang; Ning, Kang; Chang, Xingzhi; Yuan, Xiao; Tu, Qichao; Yuan, Tong; Deng, Ye; Hemme, Christopher L; Van Nostrand, Joy; Cui, Xinping; He, Zhili; Chen, Zhenggang; Guo, Dawei; Yu, Jiangbo; Zhang, Yue; Zhou, Jizhong; Xu, Jian

2014-01-01

Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis.

Urine metabolomics.

PubMed

Zhang, Aihua; Sun, Hui; Wu, Xiuhong; Wang, Xijun

2012-12-24

Metabolomics is a powerful technique for the discovery of novel biomarkers and elucidation of biochemical pathways to improve diagnosis, prognosis and therapy. An advantage of this approach is its ability to assess global metabolic profiles to enhance pathologic characterization. Urine is an ideal bio-medium for disease study because it is readily available, easily obtained and less complex than other body fluids. Ease of collection allows for serial sampling to monitor disease and therapeutic response. Because of this potential, this paper will review urine metabolomic analysis, discuss its significance in the post-genomic era and highlight the specific roles of endogenous small molecule metabolites in this emerging field. Copyright © 2012 Elsevier B.V. All rights reserved.

Advances in metabolomic applications in plant genetics and breeding

USDA-ARS?s Scientific Manuscript database

Metabolomics is a systems biology discipline wherein abundances of endogenous metabolites from biological samples are identified and quantitatively measured across a large range of metabolites and/or a large number of samples. Since all developmental, physiological and response to the environment ph...

Biomarkers of Fatigue: Metabolomics Profiles Predictive of Cognitive Performance

DTIC Science & Technology

2013-05-01

metabolites. The latest version of the Human Metabolome Database (v. 2.5; released August , 2009) includes approximately 8,000 identified mammalian...monoamine oxidase; COMT , catechol-O-methyl transferase. (Modiefied from Rubí and Maechler, 2010). Ovals indicate metabolites found to be significantly

Urine Metabolomics Analysis for Biomarker Discovery and Detection of Jaundice Syndrome in Patients With Liver Disease*

PubMed Central

Wang, Xijun; Zhang, Aihua; Han, Ying; Wang, Ping; Sun, Hui; Song, Gaochen; Dong, Tianwei; Yuan, Ye; Yuan, Xiaoxia; Zhang, Miao; Xie, Ning; Zhang, He; Dong, Hui; Dong, Wei

2012-01-01

Metabolomics is a powerful new technology that allows for the assessment of global metabolic profiles in easily accessible biofluids and biomarker discovery in order to distinguish between diseased and nondiseased status information. Deciphering the molecular networks that distinguish diseases may lead to the identification of critical biomarkers for disease aggressiveness. However, current diagnostic methods cannot predict typical Jaundice syndrome (JS) in patients with liver disease and little is known about the global metabolomic alterations that characterize JS progression. Emerging metabolomics provides a powerful platform for discovering novel biomarkers and biochemical pathways to improve diagnostic, prognostication, and therapy. Therefore, the aim of this study is to find the potential biomarkers from JS disease by using a nontarget metabolomics method, and test their usefulness in human JS diagnosis. Multivariate data analysis methods were utilized to identify the potential biomarkers. Interestingly, 44 marker metabolites contributing to the complete separation of JS from matched healthy controls were identified. Metabolic pathways (Impact-value≥0.10) including alanine, aspartate, and glutamate metabolism and synthesis and degradation of ketone bodies were found to be disturbed in JS patients. This study demonstrates the possibilities of metabolomics as a diagnostic tool in diseases and provides new insight into pathophysiologic mechanisms. PMID:22505723

Metabolomic biomarkers identify differences in milk produced by Holstein cows and other minor dairy animals.

PubMed

Yang, Yongxin; Zheng, Nan; Zhao, Xiaowei; Zhang, Yangdong; Han, Rongwei; Yang, Jinhui; Zhao, Shengguo; Li, Songli; Guo, Tongjun; Zang, Changjiang; Wang, Jiaqi

2016-03-16

Several milk metabolites are associated with breeds or species of dairy animals. A better understanding of milk metabolites from different dairy animals would advance their use in evaluating milk traits and detecting milk adulteration. The objective of this study was to characterize the milk metabolite profiles of Chinese Holstein, Jersey, yak, buffalo, goat, camel, and horse and identify any differences using non-targeted metabolomic approaches. Milk samples were tested using nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-tandem mass spectrometry (LC-MS). Data were analyzed using a multivariate analysis of variance and differences in milk metabolites between Holstein and the other dairy animals were assessed using orthogonal partial least-squares discriminant analysis. Differential metabolites were identified and some metabolites, such as choline and succinic acid, were used to distinguish Holstein milk from that of the other studied animals. Metabolic pathway analysis of different metabolites revealed that glycerophospholipid metabolism as well as valine, leucine, and isoleucine biosynthesis were shared in the other ruminant animals (Jersey, buffalo, yak, and goat), and biosynthesis of unsaturated fatty acids was shared in the non-ruminant animals (camel and horse). These results can be useful for gaining a better understanding of the differences in milk synthesis between Holstein and the other dairy animals. Copyright © 2016. Published by Elsevier B.V.

UHPLC-Q-Orbitrap-HRMS-based global metabolomics reveal metabolome modifications in plasma of young women after cranberry juice consumption.

PubMed

Liu, Haiyan; Garrett, Timothy J; Su, Zhihua; Khoo, Christina; Gu, Liwei

2017-07-01

Plasma metabolome in young women following cranberry juice consumption were investigated using a global UHPLC-Q-Orbitrap-HRMS approach. Seventeen female college students, between 21 and 29 years old, were given either cranberry juice or apple juice for three days using a cross-over design. Plasma samples were collected before and after juice consumption. Plasma metabolomes were analyzed using UHPLC-Q-Orbitrap-HRMS followed by orthogonal partial least squares-discriminant analyses (OPLS-DA). S-plot was used to identify discriminant metabolites. Validated OPLS-DA analyses showed that the plasma metabolome in young women, including both exogenous and endogenous metabolites, were altered following cranberry juice consumption. Cranberry juice caused increases of exogenous metabolites including quinic acid, vanilloloside, catechol sulfate, 3,4-dihydroxyphenyl ethanol sulfate, coumaric acid sulfate, ferulic acid sulfate, 5-(trihydroxphenyl)-gamma-valerolactone, 3-(hydroxyphenyl)proponic acid, hydroxyphenylacetic acid and trihydroxybenzoic acid. In addition, the plasma levels of endogenous metabolites including citramalic acid, aconitic acid, hydroxyoctadecanoic acid, hippuric acid, 2-hydroxyhippuric acid, vanilloylglycine, 4-acetamido-2-aminobutanoic acid, dihydroxyquinoline, and glycerol 3-phosphate were increased in women following cranberry juice consumption. The metabolic differences and discriminant metabolites observed in this study may serve as biomarkers of cranberry juice consumption and explain its health promoting properties in human. Copyright © 2017 Elsevier Inc. All rights reserved.

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

PubMed Central

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

Metabolome progression during early gut microbial colonization of gnotobiotic mice

PubMed Central

Marcobal, Angela; Yusufaly, Tahir; Higginbottom, Steven; Snyder, Michael; Sonnenburg, Justin L.; Mias, George I.

2015-01-01

The microbiome has been implicated directly in host health, especially host metabolic processes and development of immune responses. These are particularly important in infants where the gut first begins being colonized, and such processes may be modeled in mice. In this investigation we follow longitudinally the urine metabolome of ex-germ-free mice, which are colonized with two bacterial species, Bacteroides thetaiotaomicron and Bifidobacterium longum. High-throughput mass spectrometry profiling of urine samples revealed dynamic changes in the metabolome makeup, associated with the gut bacterial colonization, enabled by our adaptation of non-linear time-series analysis to urine metabolomics data. Results demonstrate both gradual and punctuated changes in metabolite production and that early colonization events profoundly impact the nature of small molecules circulating in the host. The identified small molecules are implicated in amino acid and carbohydrate metabolic processes, and offer insights into the dynamic changes occurring during the colonization process, using high-throughput longitudinal methodology. PMID:26118551

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science.

PubMed

Hong, Jun; Yang, Litao; Zhang, Dabing; Shi, Jianxin

2016-06-01

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.

Proteomic and N-glycoproteomic quantification reveal aberrant changes in the human saliva of oral ulcer patients.

PubMed

Zhang, Ying; Wang, Xi; Cui, Dan; Zhu, Jun

2016-12-01

Human whole saliva is a vital body fluid for studying the physiology and pathology of the oral cavity. As a powerful technique for biomarker discovery, MS-based proteomic strategies have been introduced for saliva analysis and identified hundreds of proteins and N-glycosylation sites. However, there is still a lack of quantitative analysis, which is necessary for biomarker screening and biological research. In this study, we establish an integrated workflow by the combination of stable isotope dimethyl labeling, HILIC enrichment, and high resolution MS for both quantification of the global proteome and N-glycoproteome of human saliva from oral ulcer patients. With the help of advanced bioinformatics, we comprehensively studied oral ulcers at both protein and glycoprotein scales. Bioinformatics analyses revealed that starch digestion and protein degradation activities are inhibited while the immune response is promoted in oral ulcer saliva. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclear magnetic resonance (NMR)-based metabolomics for cancer research.

PubMed

Ranjan, Renuka; Sinha, Neeraj

2018-05-07

Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research. Copyright © 2018 John Wiley & Sons, Ltd.

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

PubMed Central

Ramalingam, Abirami; Kudapa, Himabindu; Pazhamala, Lekha T.; Weckwerth, Wolfram; Varshney, Rajeev K.

2015-01-01

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

PubMed Central

Kümmel, Anne; Panke, Sven; Heinemann, Matthias

2006-01-01

As one of the most recent members of the omics family, large-scale quantitative metabolomics data are currently complementing our systems biology data pool and offer the chance to integrate the metabolite level into the functional analysis of cellular networks. Network-embedded thermodynamic analysis (NET analysis) is presented as a framework for mechanistic and model-based analysis of these data. By coupling the data to an operating metabolic network via the second law of thermodynamics and the metabolites' Gibbs energies of formation, NET analysis allows inferring functional principles from quantitative metabolite data; for example it identifies reactions that are subject to active allosteric or genetic regulation as exemplified with quantitative metabolite data from Escherichia coli and Saccharomyces cerevisiae. Moreover, the optimization framework of NET analysis was demonstrated to be a valuable tool to systematically investigate data sets for consistency, for the extension of sub-omic metabolome data sets and for resolving intracompartmental concentrations from cell-averaged metabolome data. Without requiring any kind of kinetic modeling, NET analysis represents a perfectly scalable and unbiased approach to uncover insights from quantitative metabolome data. PMID:16788595

Rumen fluid metabolomics analysis associated with feed efficiency on crossbred steers

USDA-ARS?s Scientific Manuscript database

The rumen has a central role in the efficiency of digestion in ruminants. To identify potential differences in rumen function that lead to differences in feed efficiency, rumen fluid metabolomic analysis by LC-MS and multivariate/univariate statistical analysis were used to identify differences in r...

Metabolomics for secondary metabolite research.

PubMed

Breitling, Rainer; Ceniceros, Ana; Jankevics, Andris; Takano, Eriko

2013-11-11

Metabolomics, the global characterization of metabolite profiles, is becoming an increasingly powerful tool for research on secondary metabolite discovery and production. In this review we discuss examples of recent technological advances and biological applications of metabolomics in the search for chemical novelty and the engineered production of bioactive secondary metabolites.

Disposable collection kit for rapid and reliable collection of saliva.

PubMed

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.

Disposable Collection Kit for Rapid and Reliable Collection of Saliva

PubMed Central

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 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. Results 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 (R2 > 0.96). Conclusions 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. Am. J. Hum. Biol. 27:720–723, 2015. © 2015 The Authors American Journal of Human Biology Published by Wiley Periodicals, Inc. PMID:25754371

Saliva viscosity as a potential risk factor for oral malodor.

PubMed

Ueno, Masayuki; Takeuchi, Susumu; Takehara, Sachiko; Kawaguchi, Yoko

2014-11-01

The objective of this study was to assess whether saliva viscosity, measured by a viscometer, was a predictor of oral malodor. The subjects were 617 patients who visited an oral malodor clinic. The organoleptic test (OT) was used for diagnosis of oral malodor. An oral examination assessed the numbers of teeth present and decayed teeth as well as the presence or absence of dentures. Further, periodontal pocket depths (PD), gingival bleeding, dental plaque and tongue coating were investigated. Unstimulated saliva were collected for 5 min. Saliva viscosity was measured with a viscometer. Logistic regression analysis with oral malodor status by OT as a dependent variable was performed. Possible confounders including age, gender, number of teeth present, number of decayed teeth, number of teeth with PD ≥ 4 mm, number of teeth with bleeding on probing, presence or absence of dentures, plaque index, area of tongue coating, saliva flow rate, saliva pH and saliva viscosity were used as independent variables. Saliva viscosity (p = 0.047) along with the number of teeth with PD ≥4 mm (p = 0.001), plaque index (p = 0.037) and area of tongue coating (p < 0.001) were significant variables for oral malodor. Subjects with a higher number of teeth with PD ≥ 4 mm (OR = 1.32), plaque index (OR = 2.13), area of tongue coating (OR = 3.17) and saliva viscosity (OR = 1.10) were more likely to have oral malodor compared to those with lower values. The results suggested that high saliva viscosity could be a potential risk factor for oral malodor.

Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of “Unknown Function”

PubMed Central

Quanbeck, Stephanie M.; Brachova, Libuse; Campbell, Alexis A.; Guan, Xin; Perera, Ann; He, Kun; Rhee, Seung Y.; Bais, Preeti; Dickerson, Julie A.; Dixon, Philip; Wohlgemuth, Gert; Fiehn, Oliver; Barkan, Lenore; Lange, Iris; Lange, B. Markus; Lee, Insuk; Cortes, Diego; Salazar, Carolina; Shuman, Joel; Shulaev, Vladimir; Huhman, David V.; Sumner, Lloyd W.; Roth, Mary R.; Welti, Ruth; Ilarslan, Hilal; Wurtele, Eve S.; Nikolau, Basil J.

2012-01-01

Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is determining the metabolomes of Arabidopsis T-DNA mutant stocks, grown in standardized controlled environment optimized to minimize environmental impacts on the metabolomes. Metabolomics data were generated with seven analytical platforms, and the combined data is being provided to the research community to formulate initial hypotheses about genes of unknown function (GUFs). A public database (www.PlantMetabolomics.org) has been developed to provide the scientific community with access to the data along with tools to allow for its interactive analysis. Exemplary datasets are discussed to validate the approach, which illustrate how initial hypotheses can be generated from the consortium-produced metabolomics data, integrated with prior knowledge to provide a testable hypothesis concerning the functionality of GUFs. PMID:22645570

Detection of Leishmania DNA in saliva among patients with HIV/AIDS in Trang Province, southern Thailand.

PubMed

Pandey, Netranapha; Siripattanapipong, Suradej; Leelayoova, Saovanee; Manomat, Jipada; Mungthin, Mathirut; Tan-Ariya, Peerapan; Bualert, Lertwut; Naaglor, Tawee; Siriyasatien, Padet; Phumee, Atchara; Piyaraj, Phunlerd

2018-06-08

Leishmaniasis is a neglected tropical disease causing opportunistic infection among patients with HIV/AIDS. The fatal form of this disease is visceral leishmaniasis (VL). DNA of Leishmania can be detected in saliva, for which the collection is noninvasive and requires little expertise. This study aimed to evaluate the sensitivity and specificity of a nested-PCR to amplify the Internal Transcribed Spacer 1 (ITS1) to detect Leishmania DNA in paired saliva and buffy coat samples of 305 Thai patients with HIV/AIDS in Trang Hospital, Trang Province, southern Thailand. For asymptomatic Leishmania infection among Thai patients with HIV/AIDS, the sensitivity and specificity of the nested-PCR-ITS1 in buffy coat were 73.9 and 100%, respectively. However, the sensitivity in saliva was 26.1% and specificity was 100%. Using the nested-PCR-ITS1, saliva and buffy coat samples showed positive agreement in only 52.0% of patients. Saliva tested results with the nested-PCR-ITS1 showed positive agreement with the Direct Agglutination Test (DAT) in 46.5% of patients. Only 12.1% of the samples showed positive agreement for Leishmania infection among all the three tests: saliva, buffy coat and DAT results. Using nucleotide sequencing, at least three species of Leishmania infection were identified in saliva, i.e., L. siamensis (n = 28), L. martiniquensis (n = 9), and L. donovani complex (n = 1). As a result, buffy coat still appears to be a better specimen to diagnose asymptomatic VL infection among individuals with HIV. However, the use of both buffy coat and saliva together as clinical specimens would increase the sensitivity of Leishmania detection. Copyright © 2018 Elsevier B.V. All rights reserved.

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report.

PubMed

Bowler, Russell P; Wendt, Chris H; Fessler, Michael B; Foster, Matthew W; Kelly, Rachel S; Lasky-Su, Jessica; Rogers, Angela J; Stringer, Kathleen A; Winston, Brent W

2017-12-01

This document presents the proceedings from the workshop entitled, "New Strategies and Challenges in Lung Proteomics and Metabolomics" held February 4th-5th, 2016, in Denver, Colorado. It was sponsored by the National Heart Lung Blood Institute, the American Thoracic Society, the Colorado Biological Mass Spectrometry Society, and National Jewish Health. The goal of this workshop was to convene, for the first time, relevant experts in lung proteomics and metabolomics to discuss and overcome specific challenges in these fields that are unique to the lung. The main objectives of this workshop were to identify, review, and/or understand: (1) emerging technologies in metabolomics and proteomics as applied to the study of the lung; (2) the unique composition and challenges of lung-specific biological specimens for metabolomic and proteomic analysis; (3) the diverse informatics approaches and databases unique to metabolomics and proteomics, with special emphasis on the lung; (4) integrative platforms across genetic and genomic databases that can be applied to lung-related metabolomic and proteomic studies; and (5) the clinical applications of proteomics and metabolomics. The major findings and conclusions of this workshop are summarized at the end of the report, and outline the progress and challenges that face these rapidly advancing fields.

Metabolomics: beyond biomarkers and towards mechanisms

PubMed Central

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

Endocrinology Meets Metabolomics: Achievements, Pitfalls, and Challenges.

PubMed

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.

Integrated and global pseudotargeted metabolomics strategy applied to screening for quality control markers of Citrus TCMs.

PubMed

Shu, Yisong; Liu, Zhenli; Zhao, Siyu; Song, Zhiqian; He, Dan; Wang, Menglei; Zeng, Honglian; Lu, Cheng; Lu, Aiping; Liu, Yuanyan

2017-08-01

Traditional Chinese medicine (TCM) exerts its therapeutic effect in a holistic fashion with the synergistic function of multiple characteristic constituents. The holism philosophy of TCM is coincident with global and systematic theories of metabolomics. The proposed pseudotargeted metabolomics methodologies were employed for the establishment of reliable quality control markers for use in the screening strategy of TCMs. Pseudotargeted metabolomics integrates the advantages of both targeted and untargeted methods. In the present study, targeted metabolomics equipped with the gold standard RRLC-QqQ-MS method was employed for in vivo quantitative plasma pharmacochemistry study of characteristic prototypic constituents. Meanwhile, untargeted metabolomics using UHPLC-QE Orbitrap HRMS with better specificity and selectivity was employed for identification of untargeted metabolites in the complex plasma matrix. In all, 32 prototypic metabolites were quantitatively determined, and 66 biotransformed metabolites were convincingly identified after being orally administered with standard extracts of four labeled Citrus TCMs. The global absorption and metabolism process of complex TCMs was depicted in a systematic manner.

Aphid watery saliva counteracts sieve-tube occlusion: a universal phenomenon?

PubMed

Will, Torsten; Kornemann, Sarah R; Furch, Alexandra C U; Tjallingii, W Fred; van Bel, Aart J E

2009-10-01

Ca2+-binding proteins in the watery saliva of Megoura viciae counteract Ca2+-dependent occlusion of sieve plates in Vicia faba and so prevent the shut-down of food supply in response to stylet penetration. The question arises whether this interaction between aphid saliva and sieve-element proteins is a universal phenomenon as inferred by the coincidence between sieve-tube occlusion and salivation. For this purpose, leaf tips were burnt in a number of plant species from four different families to induce remote sieve-plate occlusion. Resultant sieve-plate occlusion in these plant species was counteracted by an abrupt switch of aphid behaviour. Each of the seven aphid species tested interrupted its feeding behaviour and started secreting watery saliva. The protein composition of watery saliva appeared strikingly different between aphid species with less than 50% overlap. Secretion of watery saliva seems to be a universal means to suppress sieve-plate occlusion, although the protein composition of watery saliva seems to diverge between species.

Susceptibility of anthocyanins to ex vivo degradation in human saliva

PubMed Central

Kamonpatana, Kom; Giusti, M. Mónica; Chitchumroonchokchai, Chureeporn; MorenoCruz, Maria; Riedl, Ken M.; Kumar, Purnima; Failla, Mark L.

2013-01-01

Some fruits and their anthocyanin-rich extracts have been reported to exhibit chemopreventive activity in the oral cavity. Insights regarding oral metabolism of anthocyanins remain limited. Anthocyanin-rich extracts from blueberry, chokeberry, black raspberry, red grape, and strawberry were incubated ex vivo with human saliva from 14 healthy subjects. All anthocyanins were partially degraded in saliva. Degradation of chokeberry anthocyanins in saliva was temperature dependent and decreased by heating saliva to 80 °C and after removal of cells. Glycosides of delphinidin and petunidin were more susceptible to degradation than those of cyanidin, pelargonidin, peonidin and malvidin in both intact and artificial saliva. Stability of di- and tri-saccharide conjugates of anthocyanidins slightly, but significantly, exceeded that of monosaccharide compounds. Ex vivo degradation of anthocyanins in saliva was significantly decreased after oral rinsing with antibacterial chlorhexidine. These results suggest that anthocyanin degradation in the mouth is structure-dependent and largely mediated by oral microbiota. PMID:22868153

Detection of tumor cell-specific mRNA and protein in exosome-like microvesicles from blood and saliva.

PubMed

Yang, Jieping; Wei, Fang; Schafer, Christopher; Wong, David T W

2014-01-01

The discovery of disease-specific biomarkers in oral fluids has revealed a new dimension in molecular diagnostics. Recent studies have reported the mechanistic involvement of tumor cells derived mediators, such as exosomes, in the development of saliva-based mRNA biomarkers. To further our understanding of the origins of disease-induced salivary biomarkers, we here evaluated the hypothesis that tumor-shed secretory lipidic vesicles called exosome-like microvesicles (ELMs) that serve as protective carriers of tissue-specific information, mRNAs, and proteins, throughout the vasculature and bodily fluids. RNA content was analyzed in cell free-saliva and ELM-enriched fractions of saliva. Our data confirmed that the majority of extracellular RNAs (exRNAs) in saliva were encapsulated within ELMs. Nude mice implanted with human lung cancer H460 cells expressing hCD63-GFP were used to follow the circulation of tumor cell specific protein and mRNA in the form of ELMs in vivo. We were able to identify human GAPDH mRNA in ELMs of blood and saliva of tumor bearing mice using nested RT-qPCR. ELMs positive for hCD63-GFP were detected in the saliva and blood of tumor bearing mice as well as using electric field-induced release and measurement (EFIRM). Altogether, our results demonstrate that ELMs carry tumor cell-specific mRNA and protein from blood to saliva in a xenografted mouse model of human lung cancer. These results therefore strengthen the link between distal tumor progression and the biomarker discovery of saliva through the ELMs.

Sample normalization methods in quantitative metabolomics.

PubMed

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.

Global metabolomic profiling targeting childhood obesity in the Hispanic population

USDA-ARS?s Scientific Manuscript database

Metabolomics may unravel important biological pathways involved in the pathophysiology of childhood obesity. We aimed to 1) identify metabolites that differ significantly between nonobese and obese Hispanic children; 2) collapse metabolites into principal components (PCs) associated with obesity and...

Basics of mass spectrometry based metabolomics.

PubMed

Courant, Frédérique; Antignac, Jean-Philippe; Dervilly-Pinel, Gaud; Le Bizec, Bruno

2014-11-01

The emerging field of metabolomics, aiming to characterize small molecule metabolites present in biological systems, promises immense potential for different areas such as medicine, environmental sciences, agronomy, etc. The purpose of this article is to guide the reader through the history of the field, then through the main steps of the metabolomics workflow, from study design to structure elucidation, and help the reader to understand the key phases of a metabolomics investigation and the rationale underlying the protocols and techniques used. This article is not intended to give standard operating procedures as several papers related to this topic were already provided, but is designed as a tutorial aiming to help beginners understand the concept and challenges of MS-based metabolomics. A real case example is taken from the literature to illustrate the application of the metabolomics approach in the field of doping analysis. Challenges and limitations of the approach are then discussed along with future directions in research to cope with these limitations. This tutorial is part of the International Proteomics Tutorial Programme (IPTP18). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Translating Metabolomics to Cardiovascular Biomarkers

PubMed Central

Senn, Todd; Hazen, Stanley L.; Tang, W. H. Wilson

2012-01-01

Metabolomics is the systematic study of the unique chemical fingerprints of small-molecules, or metabolite profiles, that are related to a variety of cellular metabolic processes in a cell, organ, or organism. While mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling provides direct and indirect physiologic insights that can potentially be detectable in a wide range of biospecimens. Although not specific to cardiac conditions, translating metabolomics to cardiovascular biomarkers has followed the traditional path of biomarker discovery from identification and confirmation to clinical validation and bedside testing. With technological advances in metabolomic tools (such as nuclear magnetic resonance spectroscopy and mass spectrometry) and more sophisticated bioinformatics and analytical techniques, the ability to measure low-molecular-weight metabolites in biospecimens provides a unique insight into established and novel metabolic pathways. Systemic metabolomics may provide physiologic understanding of cardiovascular disease states beyond traditional profiling, and may involve descriptions of metabolic responses of an individual or population to therapeutic interventions or environmental exposures. PMID:22824112

Evaluation of metabolites extraction strategies for identifying different brain regions and their relationship with alcohol preference and gender difference using NMR metabolomics.

PubMed

Wang, Jie; Zeng, Hao-Long; Du, Hongying; Liu, Zeyuan; Cheng, Ji; Liu, Taotao; Hu, Ting; Kamal, Ghulam Mustafa; Li, Xihai; Liu, Huili; Xu, Fuqiang

2018-03-01

Metabolomics generate a profile of small molecules from cellular/tissue metabolism, which could directly reflect the mechanisms of complex networks of biochemical reactions. Traditional metabolomics methods, such as OPLS-DA, PLS-DA are mainly used for binary class discrimination. Multiple groups are always involved in the biological system, especially for brain research. Multiple brain regions are involved in the neuronal study of brain metabolic dysfunctions such as alcoholism, Alzheimer's disease, etc. In the current study, 10 different brain regions were utilized for comparative studies between alcohol preferring and non-preferring rats, male and female rats respectively. As many classes are involved (ten different regions and four types of animals), traditional metabolomics methods are no longer efficient for showing differentiation. Here, a novel strategy based on the decision tree algorithm was employed for successfully constructing different classification models to screen out the major characteristics of ten brain regions at the same time. Subsequently, this method was also utilized to select the major effective brain regions related to alcohol preference and gender difference. Compared with the traditional multivariate statistical methods, the decision tree could construct acceptable and understandable classification models for multi-class data analysis. Therefore, the current technology could also be applied to other general metabolomics studies involving multi class data. Copyright © 2017 Elsevier B.V. All rights reserved.

H-1 Nuclear Magnetic Resonance Metabolomics Analysis Identifies Novel Urinary Biomarkers for Lung Function

DOE Office of Scientific and Technical Information (OSTI.GOV)

MCClay, Joseph L.; Adkins, Daniel E.; Isern, Nancy G.

2010-06-04

Chronic obstructive pulmonary disease (COPD), characterized by chronic airflow limitation, is a serious and growing public health concern. The major environmental risk factor for COPD is tobacco smoking, but the biological mechanisms underlying COPD are not well understood. In this study, we used proton nuclear magnetic resonance (1H-NMR) spectroscopy to identify and quantify metabolites associated with lung function in COPD. Plasma and urine were collected from 197 adults with COPD and from 195 adults without COPD. Samples were assayed using a 600 MHz NMR spectrometer, and the resulting spectra were analyzed against quantitative spirometric measures of lung function. After correctingmore » for false discoveries and adjusting for covariates (sex, age, smoking) several spectral regions in urine were found to be significantly associated with baseline lung function. These regions correspond to the metabolites trigonelline, hippurate and formate. Concentrations of each metabolite, standardized to urinary creatinine, were associated with baseline lung function (minimum p-value = 0.0002 for trigonelline). No significant associations were found with plasma metabolites. Two of the three urinary metabolites positively associated with baseline lung function, i.e. hippurate and formate, are often related to gut microflora. This suggests that the microbiome composition is variable between individuals with different lung function. Alternatively, the nature and origins of all three associated metabolites may reflect lifestyle differences affecting overall health. Our results will require replication and validation, but demonstrate the utility of NMR metabolomics as a screening tool for identifying novel biomarkers of lung disease or disease risk.« less

Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome.

PubMed

Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

2018-05-01

Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed.

Metabolomic Characteristics of Arsenic-Associated Diabetes in a Prospective Cohort in Chihuahua, Mexico

PubMed Central

Martin, Elizabeth; González-Horta, Carmen; Rager, Julia; Bailey, Kathryn A.; Sánchez-Ramírez, Blanca; Ballinas-Casarrubias, Lourdes; Ishida, María C.; Gutiérrez-Torres, Daniela S.; Hernández Cerón, Roberto; Viniegra Morales, Damián; Baeza Terrazas, Francisco A.; Jesse Saunders, R.; Drobná, Zuzana; Mendez, Michelle A.; Buse, John B.; Loomis, Dana; Jia, Wei; García-Vargas, Gonzalo G.; Del Razo, Luz M.; Stýblo, Miroslav; Fry, Rebecca

2015-01-01

Chronic exposure to inorganic arsenic (iAs) has been linked to an increased risk of diabetes, yet the specific disease phenotype and underlying mechanisms are poorly understood. In the present study we set out to identify iAs exposure-associated metabolites with altered abundance in nondiabetic and diabetic individuals in an effort to understand the relationship between exposure, metabolomic response, and disease status. A nested study design was used to profile metabolomic shifts in urine and plasma collected from 90 diabetic and 86 nondiabetic individuals matched for varying iAs concentrations in drinking water, body mass index, age, and sex. Diabetes diagnosis was based on measures of fasting plasma glucose and 2-h blood glucose. Multivariable models were used to identify metabolites with altered abundance associated with iAs exposure among diabetic and nondiabetic individuals. A total of 132 metabolites were identified to shift in urine or plasma in response to iAs exposure characterized by the sum of iAs metabolites in urine (U-tAs). Although many metabolites were altered in both diabetic and nondiabetic 35 subjects, diabetic individuals displayed a unique response to iAs exposure with 59 altered metabolites including those that play a role in tricarboxylic acid cycle and amino acid metabolism. Taken together, these data highlight the broad impact of iAs exposure on the human metabolome, and demonstrate some specificity of the metabolomic response between diabetic and nondiabetic individuals. These data may provide novel insights into the mechanisms and phenotype of diabetes associated with iAs exposure. PMID:25577196

Mathematical Modeling Approaches in Plant Metabolomics.

PubMed

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.

Haystack, a web-based tool for metabolomics research.

PubMed

Grace, Stephen C; Embry, Stephen; Luo, Heng

2014-01-01

Liquid chromatography coupled to mass spectrometry (LCMS) has become a widely used technique in metabolomics research for differential profiling, the broad screening of biomolecular constituents across multiple samples to diagnose phenotypic differences and elucidate relevant features. However, a significant limitation in LCMS-based metabolomics is the high-throughput data processing required for robust statistical analysis and data modeling for large numbers of samples with hundreds of unique chemical species. To address this problem, we developed Haystack, a web-based tool designed to visualize, parse, filter, and extract significant features from LCMS datasets rapidly and efficiently. Haystack runs in a browser environment with an intuitive graphical user interface that provides both display and data processing options. Total ion chromatograms (TICs) and base peak chromatograms (BPCs) are automatically displayed, along with time-resolved mass spectra and extracted ion chromatograms (EICs) over any mass range. Output files in the common .csv format can be saved for further statistical analysis or customized graphing. Haystack's core function is a flexible binning procedure that converts the mass dimension of the chromatogram into a set of interval variables that can uniquely identify a sample. Binned mass data can be analyzed by exploratory methods such as principal component analysis (PCA) to model class assignment and identify discriminatory features. The validity of this approach is demonstrated by comparison of a dataset from plants grown at two light conditions with manual and automated peak detection methods. Haystack successfully predicted class assignment based on PCA and cluster analysis, and identified discriminatory features based on analysis of EICs of significant bins. Haystack, a new online tool for rapid processing and analysis of LCMS-based metabolomics data is described. It offers users a range of data visualization options and supports non

Metabolomics-Driven Nutraceutical Evaluation of Diverse Green Tea Cultivars

PubMed Central

Ida, Megumi; Kosaka, Reia; Miura, Daisuke; Wariishi, Hiroyuki; Maeda-Yamamoto, Mari; Nesumi, Atsushi; Saito, Takeshi; Kanda, Tomomasa; Yamada, Koji; Tachibana, Hirofumi

2011-01-01

Background Green tea has various health promotion effects. Although there are numerous tea cultivars, little is known about the differences in their nutraceutical properties. Metabolic profiling techniques can provide information on the relationship between the metabolome and factors such as phenotype or quality. Here, we performed metabolomic analyses to explore the relationship between the metabolome and health-promoting attributes (bioactivity) of diverse Japanese green tea cultivars. Methodology/Principal Findings We investigated the ability of leaf extracts from 43 Japanese green tea cultivars to inhibit thrombin-induced phosphorylation of myosin regulatory light chain (MRLC) in human umbilical vein endothelial cells (HUVECs). This thrombin-induced phosphorylation is a potential hallmark of vascular endothelial dysfunction. Among the tested cultivars, Cha Chuukanbohon Nou-6 (Nou-6) and Sunrouge (SR) strongly inhibited MRLC phosphorylation. To evaluate the bioactivity of green tea cultivars using a metabolomics approach, the metabolite profiles of all tea extracts were determined by high-performance liquid chromatography-mass spectrometry (LC-MS). Multivariate statistical analyses, principal component analysis (PCA) and orthogonal partial least-squares-discriminant analysis (OPLS-DA), revealed differences among green tea cultivars with respect to their ability to inhibit MRLC phosphorylation. In the SR cultivar, polyphenols were associated with its unique metabolic profile and its bioactivity. In addition, using partial least-squares (PLS) regression analysis, we succeeded in constructing a reliable bioactivity-prediction model to predict the inhibitory effect of tea cultivars based on their metabolome. This model was based on certain identified metabolites that were associated with bioactivity. When added to an extract from the non-bioactive cultivar Yabukita, several metabolites enriched in SR were able to transform the extract into a bioactive extract

Kinetics of fluoride bioavailability in supernatant saliva and salivary sediment.

PubMed

Naumova, E A; Sandulescu, T; Bochnig, C; Gaengler, P; Zimmer, S; Arnold, W H

2012-07-01

The assessment of the fluoride kinetics in whole saliva as well as in the different salivary phases (supernatant saliva and sediment) is essential for the understanding of fluoride bioavailability. To assess the fluoride content, provided by sodium fluoride and amine fluoride, in the supernatant saliva and in salivary sediment. Seven trained volunteers were randomly attributed to 2 groups in a cross-over design and brushed their teeth in the morning for 3 min with a product containing either sodium fluoride or amine fluoride. Saliva was collected before, immediately after tooth brushing and 30, 120, and 360 min later and measured. The samples were centrifuged 10 min at 3024 × g. Fluoride content of the supernatant saliva and of the sediment was analysed using a fluoride sensitive electrode. All subjects repeated the study cycles 2 times, and statistical analyses were made using the nonparametric sign test for related samples, the Wilcoxon-Mann-Whitney-test for independent samples. There was a significant increase in fluoride immediately after tooth brushing in both groups in saliva and sediment. The distribution of fluoride between salivary sediment and supernatant saliva (ratio) varied considerably at the different collection times: decreased from 17.87 in baseline samples of saliva to 0.07 immediately and to 0.86 half an hour after tooth brushing in the sodium fluoride group and from 14.33 to 2.85 and to 3.09 in the amine fluoride group. Furthermore after 120 min and after 360 min after tooth brushing the ratio increased from 17.6 to 31.6 in the sodium fluoride group and from 20.5 to 25.76 in the amine fluoride group. No difference was found in the sediment-supernatant saliva ratio between the sodium fluoride and the amine fluoride groups 360 min after tooth brushing. For the assessment of fluoride kinetics in whole saliva it is necessary to pay attention to at least four factors: fluoride formulation, time after fluoride application, fluoride concentration in

Dissemination of metabolomics results: role of MetaboLights and COSMOS.

PubMed

Salek, Reza M; Haug, Kenneth; Steinbeck, Christoph

2013-05-17

With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information.

Dissemination of metabolomics results: role of MetaboLights and COSMOS

PubMed Central

2013-01-01

With ever-increasing amounts of metabolomics data produced each year, there is an even greater need to disseminate data and knowledge produced in a standard and reproducible way. To assist with this a general purpose, open source metabolomics repository, MetaboLights, was launched in 2012. To promote a community standard, initially culminated as metabolomics standards initiative (MSI), COordination of Standards in MetabOlomicS (COSMOS) was introduced. COSMOS aims to link life science e-infrastructures within the worldwide metabolomics community as well as develop and maintain open source exchange formats for raw and processed data, ensuring better flow of metabolomics information. PMID:23683662

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

PubMed Central

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

Comprehensive metabolomic, lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis

DOE PAGES

Pomraning, Kyle R.; Wei, Siwei; Karagiosis, Sue A.; ...

2015-04-23

Yarrowia lipolytica is an oleaginous ascomycete yeast that accumulates large amounts of lipids and has potential as a biofuel producing organism. Despite a growing scientific literature focused on lipid production by Y. lipolytica, there remain significant knowledge gaps regarding the key biological processes involved. We applied a combination of metabolomic and lipidomic profiling approaches as well as microscopic techniques to identify and characterize the key pathways involved in de novo lipid accumulation from glucose in batch cultured, wild-type Y. lipolytica. We found that lipids accumulated rapidly and peaked at 48 hours during the five day experiment, concurrent with a shiftmore » in amino acid metabolism. We also report that Y. lipolytica secretes disaccharides early in batch culture and reabsorbs them when extracellular glucose is depleted. Exhaustion of extracellular sugars coincided with thickening of the cell wall, suggesting that genes involved in cell wall biogenesis may be a useful target for improving the efficiency of lipid producing yeast strains.« less

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

PubMed

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.

Updates in metabolomics tools and resources: 2014-2015.

PubMed

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.

Metabolomic does not predict response to cardiac resynchronization therapy in patients with heart failure.

PubMed

Padeletti, Luigi; Modesti, Pietro A; Cartei, Stella; Checchi, Luca; Ricciardi, Giuseppe; Pieragnolia, Paolo; Sacchi, Stefania; Padeletti, Margherita; Alterini, Brunetto; Pantaleo, Pietro; Hu, Xiaoyu; Tenori, Leonardo; Luchinat, Claudio

2014-04-01

Metabolomic, a systematic study of metabolites, may be a useful tool in understanding the pathological processes that underlie the occurrence and progression of a disease. We hypothesized that metabolomic would be helpful in assessing a specific pattern in heart failure patients, also according to the underlining causes and in defining, prior to device implantation, the responder and nonresponder patient to cardiac resynchronization therapy (CRT). In this prospective study, blood and urine samples were collected from 32 heart failure patients who underwent CRT. Clinical, electrocardiography and echocardiographic evaluation was performed in each patient before CRT and after 6 months of follow-up. Thirty-nine age and sex-matched healthy individuals were chosen as control group. For each sample, 1H-NMR spectra, Nuclear Overhauser Enhancement Spectroscopy, Carr-Purcell-Meiboom-Gill and diffusion edited spectra were measured. A different metabolomic fingerprint was demonstrated in heart failure patients compared to healthy controls with high accuracy level. Metabolomics fingerprint was similar between patients with ischemic and nonischemic dilated cardiomyopathy. At 6-month follow-up, metabolomic fingerprint was different from baseline. At follow-up, heart failure patients’ metabolomic fingerprint remained significantly different from that of healthy controls, and accuracy of cause discrimination remained low. Responders and nonresponders had a similar metabolic fingerprint at baseline and after 6 months of CRT. It is possible to identify a metabolomic fingerprint characterizing heart failure patients candidate to CRT, it is independent of the different causes of the disease and it is not predictive of the response to CRT.

Combined metabolomic and correlation networks analyses reveal fumarase insufficiency altered amino acid metabolism.

PubMed

Hou, Entai; Li, Xian; Liu, Zerong; Zhang, Fuchang; Tian, Zhongmin

2018-04-01

Fumarase catalyzes the interconversion of fumarate and l-malate in the tricarboxylic acid cycle. Fumarase insufficiencies were associated with increased levels of fumarate, decreased levels of malate and exacerbated salt-induced hypertension. To gain insights into the metabolism profiles induced by fumarase insufficiency and identify key regulatory metabolites, we applied a GC-MS based metabolomics platform coupled with a network approach to analyze fumarase insufficient human umbilical vein endothelial cells (HUVEC) and negative controls. A total of 24 altered metabolites involved in seven metabolic pathways were identified as significantly altered, and enriched for the biological module of amino acids metabolism. In addition, Pearson correlation network analysis revealed that fumaric acid, l-malic acid, l-aspartic acid, glycine and l-glutamic acid were hub metabolites according to Pagerank based on their three centrality indices. Alanine aminotransferase and glutamate dehydrogenase activities increased significantly in fumarase deficiency HUVEC. These results confirmed that fumarase insufficiency altered amino acid metabolism. The combination of metabolomics and network methods would provide another perspective on expounding the molecular mechanism at metabolomics level. Copyright © 2017 John Wiley & Sons, Ltd.

The Landscape of MicroRNA, Piwi-Interacting RNA, and Circular RNA in Human Saliva

PubMed Central

Bahn, Jae Hoon; Zhang, Qing; Li, Feng; Chan, Tak-Ming; Lin, Xianzhi; Kim, Yong; Wong, David T.W.; Xiao, Xinshu

2015-01-01

BACKGROUND Extracellular RNAs (exRNAs) in human body fluids are emerging as effective biomarkers for detection of diseases. Saliva, as the most accessible and noninvasive body fluid, has been shown to harbor exRNA biomarkers for several human diseases. However, the entire spectrum of exRNA from saliva has not been fully characterized. METHODS Using high-throughput RNA sequencing (RNA-Seq), we conducted an in-depth bioinformatic analysis of noncoding RNAs (ncRNAs) in human cell-free saliva (CFS) from healthy individuals, with a focus on microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and circular RNAs (circRNAs). RESULTS Our data demonstrated robust reproducibility of miRNA and piRNA profiles across individuals. Furthermore, individual variability of these salivary RNA species was highly similar to those in other body fluids or cellular samples, despite the direct exposure of saliva to environmental impacts. By comparative analysis of >90 RNA-Seq data sets of different origins, we observed that piRNAs were surprisingly abundant in CFS compared with other body fluid or intracellular samples, with expression levels in CFS comparable to those found in embryonic stem cells and skin cells. Conversely, miRNA expression profiles in CFS were highly similar to those in serum and cerebrospinal fluid. Using a customized bioinformatics method, we identified >400 circRNAs in CFS. These data represent the first global characterization and experimental validation of circRNAs in any type of extracellular body fluid. CONCLUSIONS Our study provides a comprehensive landscape of ncRNA species in human saliva that will facilitate further biomarker discoveries and lay a foundation for future studies related to ncRNAs in human saliva. PMID:25376581

Identifying developmental toxicity pathways for a subset of ToxCast chemicals using human embryonic stem cells and metabolomics

EPA Science Inventory

Metabolomics analysis was performed on the supernatant of human embryonic stem (hES) cell cultures exposed to a blinded subset of 11 chemicals selected from the chemical library of EPA's ToxCast™ chemical screening and prioritization research project. Metabolites from hES cultur...

Binary similarity measures for fingerprint analysis of qualitative metabolomic profiles.

PubMed

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.

Application of metabolomics to toxicology of drugs of abuse: A mini review of metabolomics approach to acute and chronic toxicity studies.

PubMed

Zaitsu, Kei; Hayashi, Yumi; Kusano, Maiko; Tsuchihashi, Hitoshi; Ishii, Akira

2016-02-01

Metabolomics has been widely applied to toxicological fields, especially to elucidate the mechanism of action of toxicity. In this review, metabolomics application with focus on the studies of chronic and acute toxicities of drugs of abuse like stimulants, opioids and the recently-distributed designer drugs will be presented in addition to an outline of basic analytical techniques used in metabolomics. Limitation of metabolomics studies and future perspectives will be also provided. Copyright © 2015 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

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

PubMed

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.

Periodontitis diagnostics using resonance Raman spectroscopy on saliva

NASA Astrophysics Data System (ADS)

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.

Chromosome-damaging activity of saliva of betel nut and tobacco chewers.

PubMed

Stich, H F; Stich, W

1982-01-01

Saliva of volunteers chewing betel quid, cured betel nut (Areca catechu), betel leaves (Piper betle), a mixture of quid ingredients (dried betel nut flakes, catechu, cardamon, lime, copra and menthol) and Indian tobacco was collected and examined for its genotoxic activity. Chromosome aberrations (chromatid breaks and chromatid exchanges) in Chinese hamster ovary (CHO) cells were used to estimate the genotoxic effect. No detectable levels of clastogenic activity were observed in the saliva of non-chewing individuals. After 5 min of chewing betel quid, betel nut, betel leaves, quid ingredients and Indian tobacco, the saliva samples showed relatively potent clastogenic activities. The addition of transition metals Mn2+ and Cu2+ to the saliva samples of betel nut and Indian tobacco chewers enhanced their clastogenic activities, whereas Fe3+ increased the clastogenicity of the betel nut saliva but decreased the genotoxic effect of the saliva of Indian tobacco chewers. After removal of the betel quid or its components from the mouth, the clastogenic activity disappeared within 5 min. The western-type chewing tobacco did not produce a genotoxic activity in the saliva of chewers. A possible association between the genotoxicity in the saliva of betel quid chewers and the development of oral, pharyngeal and esophageal carcinomas is discussed.

Computational strategy for quantifying human pesticide exposure based upon a saliva measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timchalk, Charles; Weber, Thomas J.; Smith, Jordan N.

The National Research Council of the National Academies report, Toxicity Testing in the 21st Century: A Vision and Strategy, highlighted the importance of quantitative exposure data for evaluating human toxicity risk and noted that biomonitoring is a critical tool for quantitatively evaluating exposure from both environmental and occupational settings. Direct measurement of chemical exposures using personal monitoring provides the most accurate estimation of a subject’s true exposure, and non-invasive methods have also been advocated for quantifying the pharmacokinetics and bioavailability of drugs and xenobiotics. In this regard, there is a need to identify chemicals that are readily cleared in salivamore » at concentrations that can be quantified to support the implementation of this approach.. The current manuscript describes the use of computational modeling approaches that are closely coupled to in vivo and in vitro experiments to predict salivary uptake and clearance of xenobiotics. The primary mechanism by which xenobiotics leave the blood and enter saliva is thought to involve paracellular transport, passive transcellular diffusion, or trancellular active transport with the majority of drugs and xenobiotics cleared from plasma into saliva by passive diffusion. The transcellular or paracellular diffusion of unbound chemicals in plasma to saliva has been computational modeled using a combination of compartmental and physiologically based approaches. Of key importance for determining the plasma:saliva partitioning was the utilization of a modified Schmitt algorithm that calculates partitioning based upon the tissue composition, pH, chemical pKa and plasma protein-binding. Sensitivity analysis of key model parameters specifically identified that both protein-binding and pKa (for weak acids and bases) had the most significant impact on the determination of partitioning and that there were clear species dependent differences based upon physiological variance

Metabolome strategy against Edwardsiella tarda infection through glucose-enhanced metabolic modulation in tilapias.

PubMed

Peng, Bo; Ma, Yan-Mei; Zhang, Jian-Ying; Li, Hui

2015-08-01

Edwardsiella tarda causes fish disease and great economic loss. However, metabolic strategy against the pathogen remains unexplored. In the present study, GC-MS based metabolomics was used to investigate the metabolic profile from tilapias infected by sublethal dose of E. tarda. The metabolic differences between the dying group and survival group allow the identification of key pathways and crucial metabolites during infections. More importantly, those metabolites may modulate the survival-related metabolome to enhance the anti-infective ability. Our data showed that tilapias generated two different strategies, survival-metabolome and death-metabolome, to encounter EIB202 infection, leading to differential outputs of the survival and dying. Glucose was the most crucial biomarker, which was upregulated and downregulated in the survival and dying groups, respectively. Exogenous glucose by injection or oral administration enhanced hosts' ability against EIB202 infection and increased the chances of survival. These findings highlight that host mounts the metabolic strategy to cope with bacterial infection, from which crucial biomarkers may be identified to enhance the metabolic strategy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Metabolomics through the lens of precision cardiovascular medicine.

PubMed

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.

Metabolomics in diabetes, a review.

PubMed

Pallares-Méndez, Rigoberto; Aguilar-Salinas, Carlos A; Cruz-Bautista, Ivette; Del Bosque-Plata, Laura

2016-01-01

Metabolomics is a promising approach for the identification of chemical compounds that serve for early detection, diagnosis, prediction of therapeutic response and prognosis of disease. Moreover, metabolomics has shown to increase the diagnostic threshold and prediction of type 2 diabetes. Evidence suggests that branched-chain amino acids, acylcarnitines and aromatic amino acids may play an early role on insulin resistance, exposing defects on amino acid metabolism, β-oxidation, and tricarboxylic acid cycle. This review aims to provide a panoramic view of the metabolic shifts that antecede or follow type 2 diabetes. Key messages BCAAs, AAAs and acylcarnitines are strongly associated with early insulin resistance. Diabetes risk prediction has been improved when adding metabolomic markers of dysglycemia to standard clinical and biochemical factors.

Assessment of data pre-processing methods for LC-MS/MS-based metabolomics of uterine cervix cancer.

PubMed

Chen, Yanhua; Xu, Jing; Zhang, Ruiping; Shen, Guoqing; Song, Yongmei; Sun, Jianghao; He, Jiuming; Zhan, Qimin; Abliz, Zeper

2013-05-07

A metabolomics strategy based on rapid resolution liquid chromatography/tandem mass spectrometry (RRLC-MS/MS) and multivariate statistics has been implemented to identify potential biomarkers in uterine cervix cancer. Due to the importance of the data pre-processing method, three popular software packages have been compared. Then they have been used to acquire respective data matrices from the same LC-MS/MS data. Multivariate statistics was subsequently used to identify significantly changed biomarkers for uterine cervix cancer from the resulting data matrices. The reliabilities of the identified discriminated metabolites have been further validated on the basis of manually extracted data and ROC curves. Nine potential biomarkers have been identified as having a close relationship with uterine cervix cancer. Considering these in combination as a biomarker group, the AUC amounted to 0.997, with a sensitivity of 92.9% and a specificity of 95.6%. The prediction accuracy was 96.6%. Among these potential biomarkers, the amounts of four purine derivatives were greatly decreased, which might be related to a P2 receptor that might lead to a decrease in cell number through apoptosis. Moreover, only two of them were identified simultaneously by all of the pre-processing tools. The results have demonstrated that the data pre-processing method could seriously bias the metabolomics results. Therefore, application of two or more data pre-processing methods would reveal a more comprehensive set of potential biomarkers in non-targeted metabolomics, before a further validation with LC-MS/MS based targeted metabolomics in MRM mode could be conducted.

Differentiation of oral bacteria in in vitro cultures and human saliva by secondary electrospray ionization - mass spectrometry

NASA Astrophysics Data System (ADS)

Bregy, Lukas; Müggler, Annick R.; Martinez-Lozano Sinues, Pablo; García-Gómez, Diego; Suter, Yannick; Belibasakis, Georgios N.; Kohler, Malcolm; Schmidlin, Patrick R.; Zenobi, Renato

2015-10-01

The detection of bacterial-specific volatile metabolites may be a valuable tool to predict infection. Here we applied a real-time mass spectrometric technique to investigate differences in volatile metabolic profiles of oral bacteria that cause periodontitis. We coupled a secondary electrospray ionization (SESI) source to a commercial high-resolution mass spectrometer to interrogate the headspace from bacterial cultures and human saliva. We identified 120 potential markers characteristic for periodontal pathogens Aggregatibacter actinomycetemcomitans (n = 13), Porphyromonas gingivalis (n = 70), Tanerella forsythia (n = 30) and Treponema denticola (n = 7) in in vitro cultures. In a second proof-of-principle phase, we found 18 (P. gingivalis, T. forsythia and T. denticola) of the 120 in vitro compounds in the saliva from a periodontitis patient with confirmed infection with P. gingivalis, T. forsythia and T. denticola with enhanced ion intensity compared to two healthy controls. In conclusion, this method has the ability to identify individual metabolites of microbial pathogens in a complex medium such as saliva.

GC-MS-Based Metabolome and Metabolite Regulation in Serum-Resistant Streptococcus agalactiae.

PubMed

Wang, Zhe; Li, Min-Yi; Peng, Bo; Cheng, Zhi-Xue; Li, Hui; Peng, Xuan-Xian

2016-07-01

Streptococcus agalactiae causes severe systemic infections in human and fish. In the present study, we established a pathogen-plasma interaction model by which we explored how S. agalactiae evaded serum-mediated killing. We found that S. agalactiae grew faster in the presence of yellow grouper plasma than in the absence of the plasma, indicating S. agalactiae evolved a way of evading the fish immune system. To determine the events underlying this phenotype, we applied GC-MS-based metabolomics approaches to identify differential metabolomes between S. agalactiae cultured with and without yellow grouper plasma. Through bioinformatics analysis, decreased malic acid and increased adenosine were identified as the most crucial metabolites that distinguish the two groups. Meanwhile, they presented with decreased TCA cycle and elevated purine metabolism, respectively. Finally, exogenous malic acid and adenosine were used to reprogram the plasma-resistant metabolome, leading to elevated and decreased susceptibility to the plasma, respectively. Therefore, our findings reveal for the first time that S. agalactiae utilizes a metabolic trick to respond to plasma killing as a result of serum resistance, which may be reverted or enhanced by exogenous malic acid and adenosine, respectively, suggesting that the metabolic trick can be regulated by metabolites.

Metabolomics applied to the pancreatic islet.

PubMed

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.

Discovery of Antimalarial Drugs from Streptomycetes Metabolites Using a Metabolomic Approach

PubMed Central

Baba, Mohd Shukri

2017-01-01

Natural products continue to play an important role as a source of biologically active substances for the development of new drug. Streptomyces, Gram-positive bacteria which are widely distributed in nature, are one of the most popular sources of natural antibiotics. Recently, by using a bioassay-guided fractionation, an antimalarial compound, Gancidin-W, has been discovered from these bacteria. However, this classical method in identifying potentially novel bioactive compounds from the natural products requires considerable effort and is a time-consuming process. Metabolomics is an emerging “omics” technology in systems biology study which integrated in process of discovering drug from natural products. Metabolomics approach in finding novel therapeutics agent for malaria offers dereplication step in screening phase to shorten the process. The highly sensitive instruments, such as Liquid Chromatography-Mass Spectrophotometry (LC-MS), Gas Chromatography-Mass Spectrophotometry (GC-MS), and Nuclear Magnetic Resonance (1H-NMR) spectroscopy, provide a wide range of information in the identification of potentially bioactive compounds. The current paper reviews concepts of metabolomics and its application in drug discovery of malaria treatment as well as assessing the antimalarial activity from natural products. Metabolomics approach in malaria drug discovery is still new and needs to be initiated, especially for drug research in Malaysia. PMID:29123551

Applying Metabolomics to differentiate amphibian responses ...

EPA Pesticide Factsheets

Introduction/Objectives/Methods One of the biggest challenges in ecological risk assessment is determining the impact of multiple stressors on individual organisms and populations in ‘real world’ scenarios. Emerging ‘omic technologies, notably, metabolomics, provides an opportunity to address the uncertainties surrounding ecological risk assessment of multiple stressors. The objective of this study was to use a metabolomics biomarker approach to investigate the effect of multiple stressors on amphibian metamorphs. To this end, metamorphs of Rana pipiens (northern leopard frogs) were exposed to the insecticide Carbaryl (0.32 μg/L), a conspecific predator alarm call (Lithobates catesbeianus), Carbaryl and the predator alarm call, and a control with no stressor. In addition to metabolomic fingerprinting, we measured corticosterone levels in each treatment to assess general stress response. We analyzed relative abundances of endogenous metabolites collected in liver tissue with gas chromatography coupled with mass spectrometry. Support vector machine (SVM) methods with recursive feature elimination (RFE) were applied to rank the metabolomic profiles produced. Results/Conclusions SVM-RFE of the acquired metabolomic spectra demonstrated 85-96% classification accuracy among control and all treatment groups when using the top 75 ranked retention time bins. Biochemical fluxes observed in the groups exposed to carbaryl, predation threat, and the combined treatmen

Clinical application of metabolomics in neonatology.

PubMed

Fanos, Vassilios; Antonucci, Roberto; Barberini, Luigi; Noto, Antonio; Atzori, Luigi

2012-04-01

The youngest and more rapidly increasing "omic" discipline, called metabolomics, is the process of describing the phenotype of a cell, tissue or organism through the full complement of metabolites present. Metabolomics measure global sets of low molecular weight metabolites (including amino acids, organic acids, sugars, fatty acids, lipids, steroids, small peptides, vitamins, etc.), thus providing a "snapshot" of the metabolic status of a cell, tissue or organism in relation to genetic variations or external stimuli. The use of metabolomics appears to be a promising tool in neonatology. The management of sick newborns might improve if more information on perinatal/neonatal maturational processes and their metabolic background were available. Urine ("a window on the organism") is a biofluid particularly suitable for metabolomic analysis in neonatology because it may be collected by using simple, noninvasive techniques and because it may provide valuable diagnostic information. In this review, the authors report the few literature data on neonatal metabolomics, including their personal experience, in the following fields: intrauterine growth restriction, perinatal transition, asphyxia, brain injury and hypothermia, maternal milk evaluation, postnatal maturation, bronchiolitis, sepsis, patent ductus arteriosus, respiratory distress syndrome, nephrouropathies, metabolic diseases, antibiotic treatment, perinatal programming and long-term outcome in extremely low birth-weight infants.

Global metabolomic profiling targeting childhood obesity in the Hispanic population.

PubMed

Butte, Nancy F; Liu, Yan; Zakeri, Issa F; Mohney, Robert P; Mehta, Nitesh; Voruganti, V Saroja; Göring, Harald; Cole, Shelley A; Comuzzie, Anthony G

2015-08-01

Metabolomics may unravel important biological pathways involved in the pathophysiology of childhood obesity. We aimed to 1) identify metabolites that differ significantly between nonobese and obese Hispanic children; 2) collapse metabolites into principal components (PCs) associated with obesity and metabolic risk, specifically hyperinsulinemia, hypertriglyceridemia, hyperleptinemia, and hyperuricemia; and 3) identify metabolites associated with energy expenditure and fat oxidation. This trial was a cross-sectional observational study of metabolomics by using gas chromatography-mass spectrometry and ultrahigh-performance liquid chromatography-tandem mass spectrometry analyses performed on fasting plasma samples from 353 nonobese and 450 obese Hispanic children. Branched-chained amino acids (BCAAs) (Leu, Ile, and Val) and their catabolites, propionylcarnitine and butyrylcarnitine, were significantly elevated in obese children. Strikingly lower lysolipids and dicarboxylated fatty acids were seen in obese children. Steroid derivatives were markedly higher in obese children as were markers of inflammation and oxidative stress. PC6 (BCAAs and aromatic AAs) and PC10 (asparagine, glycine, and serine) made the largest contributions to body mass index, and PC10 and PC12 (acylcarnitines) made the largest contributions to adiposity. Metabolic risk factors and total energy expenditure were associated with PC6, PC9 (AA and tricarboxylic acid cycle metabolites), and PC10. Fat oxidation was inversely related to PC8 (lysolipids) and positively related to PC16 (acylcarnitines). Global metabolomic profiling in nonobese and obese children replicates the increased BCAA and acylcarnitine catabolism and changes in nucleotides, lysolipids, and inflammation markers seen in obese adults; however, a strong signature of reduced fatty acid catabolism and increased steroid derivatives may be unique to obese children. Metabolic flexibility in fuel use observed in obese children may occur

Functional Evaluation of Proteins in Watery and Gel Saliva of Aphids

PubMed Central

van Bel, Aart J. E.; Will, Torsten

2016-01-01

Gel and watery saliva are regarded as key players in aphid–pIant interactions. The salivary composition seems to be influenced by the variable environment encountered by the stylet tip. Milieu sensing has been postulated to provide information needed for proper stylet navigation and for the required switches between gel and watery saliva secretion during stylet progress. Both the chemical and physical factors involved in sensing of the stylet’s environment are discussed. To investigate the salivary proteome, proteins were collected from dissected gland extracts or artificial diets in a range of studies. We discuss the advantages and disadvantages of either collection method. Several proteins were identified by functional assays or by use of proteomic tools, while most of their functions still remain unknown. These studies disclosed the presence of at least two proteins carrying numerous sulfhydryl groups that may act as the structural backbone of the salivary sheath. Furthermore, cell-wall degrading proteins such a pectinases, pectin methylesterases, polygalacturonases, and cellulases as well as diverse Ca2+-binding proteins (e.g., regucalcin, ARMET proteins) were detected. Suppression of the plant defense may be a common goal of salivary proteins. Salivary proteases are likely involved in the breakdown of sieve-element proteins to invalidate plant defense or to increase the availability of organic N compounds. Salivary polyphenoloxidases, peroxidases and oxidoreductases were suggested to detoxify, e.g., plant phenols. During the last years, an increasing number of salivary proteins have been categorized under the term ‘effector’. Effectors may act in the suppression (C002 or MIF cytokine) or the induction (e.g., Mp10 or Mp 42) of plant defense, respectively. A remarkable component of watery saliva seems the protein GroEL that originates from Buchnera aphidicola, the obligate symbiont of aphids and probably reflects an excretory product that induces plant

A targeted metabolomics approach for clinical diagnosis of inborn errors of metabolism.

PubMed

Jacob, Minnie; Malkawi, Abeer; Albast, Nour; Al Bougha, Salam; Lopata, Andreas; Dasouki, Majed; Abdel Rahman, Anas M

2018-09-26

Metabolome, the ultimate functional product of the genome, can be studied through identification and quantification of small molecules. The global metabolome influences the individual phenotype through clinical and environmental interventions. Metabolomics has become an integral part of clinical research and allowed for another dimension of better understanding of disease pathophysiology and mechanism. More than 95% of the clinical biochemistry laboratory routine workload is based on small molecular identification, which can potentially be analyzed through metabolomics. However, multiple challenges in clinical metabolomics impact the entire workflow and data quality, thus the biological interpretation needs to be standardized for a reproducible outcome. Herein, we introduce the establishment of a comprehensive targeted metabolomics method for a panel of 220 clinically relevant metabolites using Liquid chromatography-tandem mass spectrometry (LC-MS/MS) standardized for clinical research. The sensitivity, reproducibility and molecular stability of each targeted metabolite (amino acids, organic acids, acylcarnitines, sugars, bile acids, neurotransmitters, polyamines, and hormones) were assessed under multiple experimental conditions. The metabolic tissue distribution was determined in various rat organs. Furthermore, the method was validated in dry blood spot (DBS) samples collected from patients known to have various inborn errors of metabolism (IEMs). Using this approach, our panel appears to be sensitive and robust as it demonstrated differential and unique metabolic profiles in various rat tissues. Also, as a prospective screening method, this panel of diverse metabolites has the ability to identify patients with a wide range of IEMs who otherwise may need multiple, time-consuming and expensive biochemical assays causing a delay in clinical management. Copyright © 2018 Elsevier B.V. All rights reserved.

Subclinical Reactivation and Shed of Infectious Varicella Zoster Virus in Saliva of Astronauts

NASA Technical Reports Server (NTRS)

Cohrs, Randall J.; Mehta, Satish K.; Schmid, D. Scott; Gilden, Donald H.; Pierson, Duane L.

2007-01-01

We have previously detected VZV in healthy astronauts both during spaceflight and shortly after landing. Herein, we show that VZV shed in seropositive astronauts is infectious. A total of 40 saliva samples were obtained from each of the 3 astronauts. From each astronaut, 14 samples were taken 109 to 133 days before liftoff, 1 sample was taken every day during 12 days in space, and one sample was taken for 14 consecutive days beginning the second day after landing. Quantitative PCR was used to detect VZV DNA in saliva. None of 42 preflight saliva samples contained VZV DNA. VZV DNA was detected in saliva from 2 of 3 astronauts. In 1 astronaut, 6 of 12 samples obtained during space flight contained 120 to 2,500 copies of VZV DNA per ml; after landing, 1250 copies of VZV DNA were present on day 2, 45 copies on day 3, and 110 copies on day 5. All samples taken 6 to 15 days after touchdown were negative for VZV DNA. In the second astronaut, 5 of 12 samples obtained during space flight contained 18 to 650 copies of VZV DNA per ml; after landing, 560 copies of VZV DNA were present in saliva on day 2, 340 copies on day 4, 45 copies on day 5, and 23 copes on day 6. All samples taken 7 to 15 days after touchdown were negative for VZV DNA. Saliva taken 2 to 6 days after landing from all 3 astronauts was cultured on human fetal lung cells. After one subcultivation, a cytopathic effect developed in cultures inoculated with saliva from the two astronauts whose saliva contained VZV DNA. Both PCR and immunostaining identified the isolates to be VZV and not HSV-1. Importantly, the astronaut in whom no VZV was detected had a history of zoster 9 years earlier. It is possible that a boost in cell-mediated immunity to VZV which is known to develop after zoster protected him from subclinical reactivation. The genotype of the two VZV isolates was determined by VZV ORF22-based PCR/sequencing along with FRET-based PCR assays that target specific nucleotide polymorphisms. Both VZV isolates

Establishing Substantial Equivalence: Metabolomics

NASA Astrophysics Data System (ADS)

Beale, Michael H.; Ward, Jane L.; Baker, John M.

Modern ‘metabolomic’ methods allow us to compare levels of many structurally diverse compounds in an automated fashion across a large number of samples. This technology is ideally suited to screening of populations of plants, including trials where the aim is the determination of unintended effects introduced by GM. A number of metabolomic methods have been devised for the determination of substantial equivalence. We have developed a methodology, using [1H]-NMR fingerprinting, for metabolomic screening of plants and have applied it to the study of substantial equivalence of field-grown GM wheat. We describe here the principles and detail of that protocol as applied to the analysis of flour generated from field plots of wheat. Particular emphasis is given to the downstream data processing and comparison of spectra by multivariate analysis, from which conclusions regarding metabolome changes due to the GM can be assessed against the background of natural variation due to environment.

Assessment of extracellular dehydration using saliva osmolality.

PubMed

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 (<10 mmol/kg) and weakly correlated with changes in absolute or relative PV losses. Overall diagnostic accuracy was poor (AUC = 0.77-0.78) for all body fluids evaluated. Strong agreement was observed between Sosm methods (Expectoration: 61 ± 10 mmol/kg, Salivette: 61 ± 8 mmol/kg, p > 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.

Metabolomic analysis of pancreatic β-cell insulin release in response to glucose.

PubMed

Huang, Mei; Joseph, Jamie W

2012-01-01

Defining the key metabolic pathways that are important for fuel-regulated insulin secretion is critical to providing a complete picture of how nutrients regulate insulin secretion. We have performed a detailed metabolomics study of the clonal β-cell line 832/13 using a gas chromatography-mass spectrometer (GC-MS) to investigate potential coupling factors that link metabolic pathways to insulin secretion. Mid-polar and polar metabolites, extracted from the 832/13 β-cells, were derivatized and then run on a GC/MS to identify and quantify metabolite concentrations. Three hundred fifty-five out of 527 chromatographic peaks could be identified as metabolites by our metabolomic platform. These identified metabolites allowed us to perform a systematic analysis of key pathways involved in glucose-stimulated insulin secretion (GSIS). Of these metabolites, 41 were consistently identified as biomarker for GSIS by orthogonal partial least-squares (OPLS). Most of the identified metabolites are from common metabolic pathways including glycolytic, sorbitol-aldose reductase pathway, pentose phosphate pathway, and the TCA cycle suggesting these pathways play an important role in GSIS. Lipids and related products were also shown to contribute to the clustering of high glucose sample groups. Amino acids lysine, tyrosine, alanine and serine were upregulated by glucose whereas aspartic acid was downregulated by glucose suggesting these amino acids might play a key role in GSIS. In summary, a coordinated signaling cascade elicited by glucose metabolism in pancreatic β-cells is revealed by our metabolomics platform providing a new conceptual framework for future research and/or drug discovery.

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

PubMed

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.

Systematic Applications of Metabolomics in Metabolic Engineering

PubMed Central

Dromms, Robert A.; Styczynski, Mark P.

2012-01-01

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. PMID:24957776

Tools for the functional interpretation of metabolomic experiments.

PubMed

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.

Potential Impact and Study Considerations of Metabolomics in Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association.

PubMed

Cheng, Susan; Shah, Svati H; Corwin, Elizabeth J; Fiehn, Oliver; Fitzgerald, Robert L; Gerszten, Robert E; Illig, Thomas; Rhee, Eugene P; Srinivas, Pothur R; Wang, Thomas J; Jain, Mohit

2017-04-01

Through the measure of thousands of small-molecule metabolites in diverse biological systems, metabolomics now offers the potential for new insights into the factors that contribute to complex human diseases such as cardiovascular disease. Targeted metabolomics methods have already identified new molecular markers and metabolomic signatures of cardiovascular disease risk (including branched-chain amino acids, select unsaturated lipid species, and trimethylamine- N -oxide), thus in effect linking diverse exposures such as those from dietary intake and the microbiota with cardiometabolic traits. As technologies for metabolomics continue to evolve, the depth and breadth of small-molecule metabolite profiling in complex systems continue to advance rapidly, along with prospects for ongoing discovery. Current challenges facing the field of metabolomics include scaling throughput and technical capacity for metabolomics approaches, bioinformatic and chemoinformatic tools for handling large-scale metabolomics data, methods for elucidating the biochemical structure and function of novel metabolites, and strategies for determining the true clinical relevance of metabolites observed in association with cardiovascular disease outcomes. Progress made in addressing these challenges will allow metabolomics the potential to substantially affect diagnostics and therapeutics in cardiovascular medicine. © 2017 American Heart Association, Inc.

MetaboLights: towards a new COSMOS of metabolomics data management.

PubMed

Steinbeck, Christoph; Conesa, Pablo; Haug, Kenneth; Mahendraker, Tejasvi; Williams, Mark; Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Salek, Reza M; Griffin, Julian L

2012-10-01

Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6-8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

Plasma metabolomic profiles predict near-term death among individuals with lower extremity peripheral arterial disease.

PubMed

Huang, Chiang-Ching; McDermott, Mary M; Liu, Kiang; Kuo, Ching-Hua; Wang, San-Yuan; Tao, Huimin; Tseng, Yufeng Jane

2013-10-01

Individuals with peripheral arterial disease (PAD) have a nearly two-fold increased risk of all-cause and cardiovascular disease mortality compared to those without PAD. This pilot study determined whether metabolomic profiling can accurately identify patients with PAD who are at increased risk of near-term mortality. We completed a case-control study using (1)H NMR metabolomic profiling of plasma from 20 decedents with PAD, without critical limb ischemia, who had blood drawn within 8 months prior to death (index blood draw) and within 10 to 28 months prior to death (preindex blood draw). Twenty-one PAD participants who survived more than 30 months after their index blood draw served as a control population. Results showed distinct metabolomic patterns between preindex decedent, index decedent, and survivor samples. The major chemical signals contributing to the differential pattern (between survivors and decedents) arose from the fatty acyl chain protons of lipoproteins and the choline head group protons of phospholipids. Using the top 40 chemical signals for which the intensity was most distinct between survivor and preindex decedent samples, classification models predicted near-term all-cause death with overall accuracy of 78% (32/41), a sensitivity of 85% (17/20), and a specificity of 71% (15/21). When comparing survivor with index decedent samples, the overall classification accuracy was optimal at 83% (34/41) with a sensitivity of 80% (16/20) and a specificity of 86% (18/21), using as few as the top 10 to 20 chemical signals. Our results suggest that metabolomic profiling of plasma may be useful for identifying PAD patients at increased risk for near-term death. Larger studies using more sensitive metabolomic techniques are needed to identify specific metabolic pathways associated with increased risk of near-term all-cause mortality among PAD patients. Copyright © 2013 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

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

DTIC Science & Technology

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

Quantification of anti-Leishmania antibodies in saliva of dogs.

PubMed

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 (p<0.0001), whereas no significant differences for anti-Leishmania 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

Prevalence of Enterococcus faecalis in saliva and filled root canals of teeth associated with apical periodontitis

PubMed Central

Wang, Qian-Qian; Zhang, Cheng-Fei; Chu, Chun-Hung; Zhu, Xiao-Fei

2012-01-01

To investigate the prevalence of Enterococcus faecalis in saliva and filled root canals of patients requiring endodontic retreatment for apical periodontitis. Patients with apical periodontitis who were referred for endodontic retreatment were examined. The type and quality of the restoration, symptoms, quality of obturation were recorded. During retreatment, an oral rinse sample and root canal sample were cultured using brain-heart infusion agar and bile esculinazide agar to select for E. faecalis. The 16S rRNA technique was used to identify E. faecalis. A total of 32 women and 22 men (mean age: 38 years; s.d.: 11 years) and 58 teeth were studied. The prevalence of E. faecalis was 19% in the saliva and 38% in the root canals. The odds that root canals harbored E. faecalis were increased if the saliva habored this bacterium (odds ratio=9.7; 95% confidence interval=1.8–51.6; P<0.05). Teeth with unsatisfactory root obturation had more cultivable bacterial species in root canals than teeth with satisfactory root obturation (P<0.05). E. faecalis is more common in root canals of teeth with apical periodontitis than in saliva. The prevalence of E. faecalis in root canals is associated with the presence of E. faecalis in saliva. PMID:22422085

Antioxidant capacity of human saliva and periodontal screening assessment in healthy adults.

PubMed

Tartaglia, Gianluca Martino; Gagliano, Nicoletta; Zarbin, Luca; Tolomeo, Giorgia; Sforza, Chiarella

2017-06-01

Saliva plays a pivotal role as an antioxidant system, and saliva antioxidant levels are reduced in patients with periodontal disease. Recently, a biochemical test able to determine saliva antioxidant levels was proposed as predictive for oral cavity diseases, but it was not clinically tested. In this preliminary study, we evaluated the relationships between Periodontal Screening and Recordings characteristics of patients and saliva antioxidant levels measures. Thirty-nine patients (12 men, 27 women; mean age, 46 years, SD 17) attending the dental hygiene unit of a Private Clinic underwent a Periodontal Screening and Recordings examination and a saliva antioxidant levels measurement using a biochemical commercial test. The results of the clinical periodontal examination were compared to those obtained by the saliva test. Approximately 70% of patients showed a low saliva antioxidant levels value, while the other patients had Optimal/Normal values. Thirteen patients (33%) resulted positive to Periodontal Screening and Recordings test. Using Periodontal Screening and Recordings values as gold standard, the saliva antioxidant levels test correctly classified 52.6% of patients; sensitivity was 84.6%, specificity was 36%. The saliva antioxidant levels test had a good sensitivity when compared to the gold standard; this finding corroborates the hypothesis that alterations of the oral antioxidant levels are related to periodontal disease. The reduced specificity shows that saliva antioxidant levels test could detect alterations predisposing to periodontal disease before clinically evident aspects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Relationships between nicotine and cotinine concentrations in maternal milk and saliva.

PubMed

Jacob, Nelly; Golmard, Jean-Louis; Berlin, Ivan

2015-08-01

Breastfeeding may be impaired due to nicotine excreted into the milk of smoking mothers. We investigated the relationships between nicotine and cotinine concentrations in maternal milk and saliva among breastfeeding smokers. The 41 mothers reported their cigarette consumption between waking up and milk and saliva sampling. The median sampling time took place four days after delivery. Nicotine and cotinine concentrations were determined by liquid chromatography and UV detection, after a single-step saliva or three-step milk liquid-to-liquid extraction. The median (interquartile range) concentrations in milk and saliva were 7 (6-22) and 27 (4-207) μg/L for nicotine and 24 (5-111) and 22 (4-120) μg/L for cotinine, respectively. Milk cotinine was positively associated with saliva cotinine (p < 0.0001) and cigarette consumption (p = 0.039) and inversely associated with the time since the last cigarette (p = 0.0004, model R(2) = 0.90). Milk nicotine was associated with saliva nicotine concentration (p = 0.0017) and cigarette consumption (p = 0.0023, model R(2) = 0.63). Saliva nicotine concentration was not a very good estimate of milk nicotine concentration in breastfeeding mothers. Saliva cotinine concentration may be used instead of milk cotinine concentration to estimate tobacco or nicotine exposure among breastfed neonates or infants. ©2015 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

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

PubMed Central

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

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data.

PubMed

Reisetter, Anna C; Muehlbauer, Michael J; Bain, James R; Nodzenski, Michael; Stevens, Robert D; Ilkayeva, Olga; Metzger, Boyd E; Newgard, Christopher B; Lowe, William L; Scholtens, Denise M

2017-02-02

Metabolomics offers a unique integrative perspective for health research, reflecting genetic and environmental contributions to disease-related phenotypes. Identifying robust associations in population-based or large-scale clinical studies demands large numbers of subjects and therefore sample batching for gas-chromatography/mass spectrometry (GC/MS) non-targeted assays. When run over weeks or months, technical noise due to batch and run-order threatens data interpretability. Application of existing normalization methods to metabolomics is challenged by unsatisfied modeling assumptions and, notably, failure to address batch-specific truncation of low abundance compounds. To curtail technical noise and make GC/MS metabolomics data amenable to analyses describing biologically relevant variability, we propose mixture model normalization (mixnorm) that accommodates truncated data and estimates per-metabolite batch and run-order effects using quality control samples. Mixnorm outperforms other approaches across many metrics, including improved correlation of non-targeted and targeted measurements and superior performance when metabolite detectability varies according to batch. For some metrics, particularly when truncation is less frequent for a metabolite, mean centering and median scaling demonstrate comparable performance to mixnorm. When quality control samples are systematically included in batches, mixnorm is uniquely suited to normalizing non-targeted GC/MS metabolomics data due to explicit accommodation of batch effects, run order and varying thresholds of detectability. Especially in large-scale studies, normalization is crucial for drawing accurate conclusions from non-targeted GC/MS metabolomics data.

GC-TOF/MS-based metabolomic profiling of estrogen deficiency-induced obesity in ovariectomized rats

PubMed Central

Ma, Bo; Zhang, Qi; Wang, Guang-ji; A, Ji-ye; Wu, Di; Liu, Ying; Cao, Bei; Liu, Lin-sheng; Hu, Ying-ying; Wang, Yong-lu; Zheng, Ya-ya

2011-01-01

Aim: To explore the alteration of endogenous metabolites and identify potential biomarkers using metabolomic profiling with gas chromatography coupled a time-of-flight mass analyzer (GC/TOF-MS) in a rat model of estrogen-deficiency-induced obesity. Methods: Twelve female Sprague-Dawley rats six month of age were either sham-operated or ovariectomized (OVX). Rat blood was collected, and serum was analyzed for biomarkers using standard colorimetric methods with commercial assay kits and a metabolomic approach with GC/TOF-MS. The data were analyzed using multivariate statistical techniques. Results: A high body weight and body mass index inversely correlated with serum estradiol (E2) in the OVX rats compared to the sham rats. Estrogen deficiency also significantly increased serum total cholesterol, triglycerides, and low-density lipoprotein cholesterol. Utilizing GC/TOF-MS-based metabolomic analysis and the partial least-squares discriminant analysis, the OVX samples were discriminated from the shams. Elevated levels of cholesterol, glycerol, glucose, arachidonic acid, glutamic acid, glycine, and cystine and reduced alanine levels were observed. Serum glucose metabolism, energy metabolism, lipid metabolism, and amino acid metabolism were involved in estrogen-deficiency-induced obesity in OVX rats. Conclusion: The series of potential biomarkers identified in the present study provided fingerprints of rat metabolomic changes during obesity and an overview of multiple metabolic pathways during the progression of obesity involving glucose metabolism, lipid metabolism, and amino acid metabolism. PMID:21293480

Towards a scientific interpretation of the terroir concept: plasticity of the grape berry metabolome.

PubMed

Anesi, Andrea; Stocchero, Matteo; Dal Santo, Silvia; Commisso, Mauro; Zenoni, Sara; Ceoldo, Stefania; Tornielli, Giovanni Battista; Siebert, Tracey E; Herderich, Markus; Pezzotti, Mario; Guzzo, Flavia

2015-08-07

The definition of the terroir concept is one of the most debated issues in oenology and viticulture. The dynamic interaction among diverse factors including the environment, the grapevine plant and the imposed viticultural techniques means that the wine produced in a given terroir is unique. However, there is an increasing interest to define and quantify the contribution of individual factors to a specific terroir objectively. Here, we characterized the metabolome and transcriptome of berries from a single clone of the Corvina variety cultivated in seven different vineyards, located in three macrozones, over a 3-year trial period. To overcome the anticipated strong vintage effect, we developed statistical tools that allowed us to identify distinct terroir signatures in the metabolic composition of berries from each macrozone, and from different vineyards within each macrozone. We also identified non-volatile and volatile components of the metabolome which are more plastic and therefore respond differently to terroir diversity. We observed some relationships between the plasticity of the metabolome and transcriptome, allowing a multifaceted scientific interpretation of the terroir concept. Our experiments with a single Corvina clone in different vineyards have revealed the existence of a clear terroir-specific effect on the transcriptome and metabolome which persists over several vintages and allows each vineyard to be characterized by the unique profile of specific metabolites.

Metabolomic determinants of metabolic risk in Mexican adolescents

PubMed Central

Perng, Wei; Hector, Emily C.; Song, Peter X.K.; Rojo, Martha Maria Tellez; Raskind, Sasha; Kachman, Maureen; Cantoral, Alejandra; Burant, Charles F.; Peterson, Karen E.

2017-01-01

Objective To identify metabolites associated with metabolic risk, separately by sex, in Mexican adolescents. Methods We carried out untargeted metabolomic profiling on fasting serum of 238 youth age 8–14 years, and identified metabolites associated with a metabolic syndrome risk z-score (MetRisk z-score), separately for boys and girls using the simulation and extrapolation (SIMEX) algorithm. We examined associations of each metabolite with MetRisk z-score using linear regression models that accounted for maternal education, child’s age, and pubertal status. Results Of the 938 features identified in metabolomics analysis, 7 named compounds (of 27 identified metabolites) were associated with MetRisk z-score in girls, and 3 named compounds (of 14 identified) were associated with MetRisk z-score in boys. In girls, diacylglycerol (DG) 16:0/16:0, 1,3-dielaidin, myo-inositol, and urate corresponded with higher MetRisk z-score, whereas N-acetylglycine, thymine, and dodecenedioic acid were associated with lower MetRisk z-score. For example, each z-score increment in DG 16:0/16:0 corresponded with 0.60 (0.47, 0.74). In boys, we found positive associations of DG 16:0/16:0, tyrosine, and 5′-methylthioadenosine with MetRisk z-score. Conclusions Metabolites on lipid, amino acid, and carbohydrate metabolism pathways are associated with metabolic risk in girls. Compounds on lipid and DNA pathways correspond with metabolic risk in boys. PMID:28758362

Emerging field of metabolomics: big promise for cancer biomarker identification and drug discovery.

PubMed

Patel, Seema; Ahmed, Shadab

2015-03-25

Most cancers are lethal and metabolic alterations are considered a hallmark of this deadly disease. Genomics and proteomics have contributed vastly to understand cancer biology. Still there are missing links as downstream to them molecular divergence occurs. Metabolomics, the omic science that furnishes a dynamic portrait of metabolic profile is expected to bridge these gaps and boost cancer research. Metabolites being the end products are more stable than mRNAs or proteins. Previous studies have shown the efficacy of metabolomics in identifying biomarkers associated with diagnosis, prognosis and treatment of cancer. Metabolites are highly informative about the functional status of the biological system, owing to their proximity to organismal phenotypes. Scores of publications have reported about high-throughput data generation by cutting-edge analytic platforms (mass spectrometry and nuclear magnetic resonance). Further sophisticated statistical softwares (chemometrics) have enabled meaningful information extraction from the metabolomic data. Metabolomics studies have demonstrated the perturbation in glycolysis, tricarboxylic acid cycle, choline and fatty acid metabolism as traits of cancer cells. This review discusses the latest progress in this field, the future trends and the deficiencies to be surmounted for optimally implementation in oncology. The authors scoured through the most recent, high-impact papers archived in Pubmed, ScienceDirect, Wiley and Springer databases to compile this review to pique the interest of researchers towards cancer metabolomics. Copyright © 2014 Elsevier B.V. All rights reserved.

Untargeted metabolomics reveals specific withanolides and fatty acyl glycoside as tentative metabolites to differentiate organic and conventional Physalis peruviana fruits.

PubMed

Llano, Sandra M; Muñoz-Jiménez, Ana M; Jiménez-Cartagena, Claudio; Londoño-Londoño, Julián; Medina, Sonia

2018-04-01

The agronomic production systems may affect the levels of food metabolites. Metabolomics approaches have been applied as useful tool for the characterization of fruit metabolome. In this study, metabolomics techniques were used to assess the differences in phytochemical composition between goldenberry samples produced by organic and conventional systems. To verify that the organic samples were free of pesticides, individual pesticides were analyzed. Principal component analysis showed a clear separation of goldenberry samples from two different farming systems. Via targeted metabolomics assays, whereby carotenoids and ascorbic acid were analyzed, not statistical differences between both crops were found. Conversely, untargeted metabolomics allowed us to identify two withanolides and one fatty acyl glycoside as tentative metabolites to differentiate goldenberry fruits, recording organic fruits higher amounts of these compounds than conventional samples. Hence, untargeted metabolomics technology could be suitable to research differences on phytochemicals under different agricultural management practices and to authenticate organic products. Copyright © 2017 Elsevier Ltd. All rights reserved.

Present and foreseeable future of metabolomics in forensic analysis.

PubMed

Castillo-Peinado, L S; Luque de Castro, M D

2016-06-21

The revulsive publications during the last years on the precariousness of forensic sciences worldwide have promoted the move of major steps towards improvement of this science. One of the steps (viz. a higher involvement of metabolomics in the new era of forensic analysis) deserves to be discussed under different angles. Thus, the characteristics of metabolomics that make it a useful tool in forensic analysis, the aspects in which this omics is so far implicit, but not mentioned in forensic analyses, and how typical forensic parameters such as the post-mortem interval or fingerprints take benefits from metabolomics are critically discussed in this review. The way in which the metabolomics-forensic binomial succeeds when either conventional or less frequent samples are used is highlighted here. Finally, the pillars that should support future developments involving metabolomics and forensic analysis, and the research required for a fruitful in-depth involvement of metabolomics in forensic analysis are critically discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Does human saliva decrease the antimicrobial activity of chlorhexidine against oral bacteria?

PubMed

Abouassi, Thaer; Hannig, Christian; Mahncke, Katja; Karygianni, Lamprini; Wolkewitz, Martin; Hellwig, Elmar; Al-Ahmad, Ali

2014-10-10

Several studies have shown the antibacterial effectiveness of 0.2% chlorhexidine (CHX) in both in vitro and in vivo studies. In this way, CHX comes directly in contact with saliva. This in vitro study aimed at investigating the possible neutralizing effect of saliva on CHX. Saliva samples (12 ml) were collected from twenty healthy volunteers. The aerobic and anaerobic bacterial counts in saliva were determined on Colombia blood agar (CBA) and yeast cysteine agar (HCB), respectively. Saliva from each subject was divided among 4 experimental groups (3 ml/group). Samples were centrifuged at 4000 g for 10 min. The centrifuged salivary bacteria were incubated with the following solutions: 0.2% CHX in saliva, CHX in saliva with 7% ethanol, CHX in 0.9% NaCl, CHX in 0.9% NaCl with 7% ethanol. After exposure for 1 min or 3 min to these CHX solutions, the CHX was neutralized and the bacteria were cultivated, after which the number of colony forming units (aerobic and anaerobic) was determined. CHX reduced the CFU in all groups significantly (p = 0.0001). Therefore, CHX had a similar effect on both aerobic and anaerobic microorganisms. Significantly more bacteria survived the effect of CHX when kept in salivary solution. This effect from saliva could be compensated by the addition of ethanol. In the absence of saliva there was no significant difference observed in the effectiveness of CHX with respect to ethanol. Prolonging the exposure time to 3 min enhanced the effectiveness of CHX. The effect of saliva on the antimicrobial activity of CHX was weak albeit statistically significant. However, addition of 7% ethanol compensates this effect. The impact of saliva on the reduction of the antimicrobial efficacy of mouthrinses such as CHX needs to be taken into consideration with regard to improving their antibacterial properties.

Exploring natural variation of Pinus pinaster Aiton using metabolomics: Is it possible to identify the region of origin of a pine from its metabolites?

PubMed

Meijón, Mónica; Feito, Isabel; Oravec, Michal; Delatorre, Carolina; Weckwerth, Wolfram; Majada, Juan; Valledor, Luis

2016-02-01

Natural variation of the metabolome of Pinus pinaster was studied to improve understanding of its role in the adaptation process and phenotypic diversity. The metabolomes of needles and the apical and basal section of buds were analysed in ten provenances of P. pinaster, selected from France, Spain and Morocco, grown in a common garden for 5 years. The employment of complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) together with bioinformatics tools allowed the reliable quantification of 2403 molecular masses. The analysis of the metabolome showed that differences were maintained across provenances and that the metabolites characteristic of each organ are mainly related to amino acid metabolism, while provenances were distinguishable essentially through secondary metabolism when organs were analysed independently. Integrative analyses of metabolome, environmental and growth data provided a comprehensive picture of adaptation plasticity in conifers. These analyses defined two major groups of plants, distinguished by secondary metabolism: that is, either Atlantic or Mediterranean provenance. Needles were the most sensitive organ, where strong correlations were found between flavonoids and the water regime of the geographic origin of the provenance. The data obtained point to genome specialization aimed at maximizing the drought stress resistance of trees depending on their origin. © 2016 John Wiley & Sons Ltd.

Metabolomics analysis identifies sex-associated metabotypes of oxidative stress and the autotaxin–lysoPA axis in COPD

PubMed Central

Naz, Shama; Kolmert, Johan; Yang, Mingxing; Reinke, Stacey N.; Kamleh, Muhammad Anas; Snowden, Stuart; Heyder, Tina; Levänen, Bettina; Erle, David J.; Sköld, C. Magnus; Wheelock, Åsa M.; Wheelock, Craig E.

2017-01-01

Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease and a leading cause of mortality and morbidity worldwide. The aim of this study was to investigate the sex dependency of circulating metabolic profiles in COPD. Serum from healthy never-smokers (healthy), smokers with normal lung function (smokers), and smokers with COPD (COPD; Global Initiative for Chronic Obstructive Lung Disease stages I–II/A–B) from the Karolinska COSMIC cohort (n=116) was analysed using our nontargeted liquid chromatography–high resolution mass spectrometry metabolomics platform. Pathway analyses revealed that several altered metabolites are involved in oxidative stress. Supervised multivariate modelling showed significant classification of smokers from COPD (p=2.8×10−7). Sex stratification indicated that the separation was driven by females (p=2.4×10−7) relative to males (p=4.0×10−4). Significantly altered metabolites were confirmed quantitatively using targeted metabolomics. Multivariate modelling of targeted metabolomics data confirmed enhanced metabolic dysregulation in females with COPD (p=3.0×10−3) relative to males (p=0.10). The autotaxin products lysoPA (16:0) and lysoPA (18:2) correlated with lung function (forced expiratory volume in 1 s) in males with COPD (r=0.86; p<0.0001), but not females (r=0.44; p=0.15), potentially related to observed dysregulation of the miR-29 family in the lung. These findings highlight the role of oxidative stress in COPD, and suggest that sex-enhanced dysregulation in oxidative stress, and potentially the autotaxin–lysoPA axis, are associated with disease mechanisms and/or prevalence. PMID:28642310

Impact of a cafeteria diet and daily physical training on the rat serum metabolome

PubMed Central

Suárez-García, Susana; del Bas, Josep M.; Caimari, Antoni; Escorihuela, Rosa M.; Arola, Lluís; Suárez, Manuel

2017-01-01

Regular physical activity and healthy dietary patterns are commonly recommended for the prevention and treatment of metabolic syndrome (MetS), which is diagnosed at an alarmingly increasing rate, especially among adolescents. Nevertheless, little is known regarding the relevance of physical exercise on the modulation of the metabolome in healthy people and those with MetS. We have previously shown that treadmill exercise ameliorated different symptoms of MetS. The aim of this study was to investigate the impact of a MetS-inducing diet and different intensities of aerobic training on the overall serum metabolome of adolescent rats. For 8 weeks, young rats were fed either standard chow (ST) or cafeteria diet (CAF) and were subjected to a daily program of training on a treadmill at different speeds. Non-targeted metabolomics was used to identify changes in circulating metabolites, and a combination of multivariate analysis techniques was implemented to achieve a holistic understanding of the metabolome. Among all the identified circulating metabolites influenced by CAF, lysophosphatidylcholines were the most represented family. Serum sphingolipids, bile acids, acylcarnitines, unsaturated fatty acids and vitamin E and A derivatives also changed significantly in CAF-fed rats. These findings suggest that an enduring systemic inflammatory state is induced by CAF. The impact of physical training on the metabolome was less striking than the impact of diet and mainly altered circulating bile acids and glycerophospholipids. Furthermore, the serum levels of monocyte chemoattractant protein-1 were increased in CAF-fed rats, and C-reactive protein was decreased in trained groups. The leptin/adiponectin ratio, a useful marker of MetS, was increased in CAF groups, but decreased in proportion to training intensity. Multivariate analysis revealed that ST-fed animals were more susceptible to exercise-induced changes in metabolites than animals with MetS, in which moderate

Impact of a cafeteria diet and daily physical training on the rat serum metabolome.

PubMed

Suárez-García, Susana; Del Bas, Josep M; Caimari, Antoni; Escorihuela, Rosa M; Arola, Lluís; Suárez, Manuel

2017-01-01

Regular physical activity and healthy dietary patterns are commonly recommended for the prevention and treatment of metabolic syndrome (MetS), which is diagnosed at an alarmingly increasing rate, especially among adolescents. Nevertheless, little is known regarding the relevance of physical exercise on the modulation of the metabolome in healthy people and those with MetS. We have previously shown that treadmill exercise ameliorated different symptoms of MetS. The aim of this study was to investigate the impact of a MetS-inducing diet and different intensities of aerobic training on the overall serum metabolome of adolescent rats. For 8 weeks, young rats were fed either standard chow (ST) or cafeteria diet (CAF) and were subjected to a daily program of training on a treadmill at different speeds. Non-targeted metabolomics was used to identify changes in circulating metabolites, and a combination of multivariate analysis techniques was implemented to achieve a holistic understanding of the metabolome. Among all the identified circulating metabolites influenced by CAF, lysophosphatidylcholines were the most represented family. Serum sphingolipids, bile acids, acylcarnitines, unsaturated fatty acids and vitamin E and A derivatives also changed significantly in CAF-fed rats. These findings suggest that an enduring systemic inflammatory state is induced by CAF. The impact of physical training on the metabolome was less striking than the impact of diet and mainly altered circulating bile acids and glycerophospholipids. Furthermore, the serum levels of monocyte chemoattractant protein-1 were increased in CAF-fed rats, and C-reactive protein was decreased in trained groups. The leptin/adiponectin ratio, a useful marker of MetS, was increased in CAF groups, but decreased in proportion to training intensity. Multivariate analysis revealed that ST-fed animals were more susceptible to exercise-induced changes in metabolites than animals with MetS, in which moderate

Challenges of metabolomics in human gut microbiota research.

PubMed

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.

The Effect of Smoking on Mineral and Protein Compositionof Saliva.

PubMed

Fattahi Bafghi, Ali; Goljanian Tabrizi, Ali; Bakhshayi, Peyman

2015-07-01

To assess the salivary composition of proteins and minerals in smokers compared with non-smokers. In this study we compared the total protein and Ca, Na, K, Mg, Pb of whole saliva in two groups of men (28 smokers and 31nonsmokers) aged between 29-41years. Fifty-nine participants were evaluated. The mean age was 33.14±5.32 years among smokers and 32.15±5.12 years among non-smokers (P>0.05). The mean concentration of total protein, Ca, Pb, and Zn of whole saliva in smokers was lower than that in non-smokers, but the difference was not statistically significant (P>0.05). The mean concentration of Na, K, Mg in whole saliva was not significantly different between smokers and non-smokers (P>0.05). We specified that smoking reduced the value of total protein, Ca and Pb of saliva, however it did not have an impact on Na, K, and Mg of saliva.

Brain Injury Alters Volatile Metabolome

PubMed Central

Cohen, Akiva S.; Gordon, Amy R.; Opiekun, Maryanne; Martin, Talia; Elkind, Jaclynn; Lundström, Johan N.; Beauchamp, Gary K.

2016-01-01

Chemical signals arising from body secretions and excretions communicate information about health status as have been reported in a range of animal models of disease. A potential common pathway for diseases to alter chemical signals is via activation of immune function—which is known to be intimately involved in modulation of chemical signals in several species. Based on our prior findings that both immunization and inflammation alter volatile body odors, we hypothesized that injury accompanied by inflammation might correspondingly modify the volatile metabolome to create a signature endophenotype. In particular, we investigated alteration of the volatile metabolome as a result of traumatic brain injury. Here, we demonstrate that mice could be trained in a behavioral assay to discriminate mouse models subjected to lateral fluid percussion injury from appropriate surgical sham controls on the basis of volatile urinary metabolites. Chemical analyses of the urine samples similarly demonstrated that brain injury altered urine volatile profiles. Behavioral and chemical analyses further indicated that alteration of the volatile metabolome induced by brain injury and alteration resulting from lipopolysaccharide-associated inflammation were not synonymous. Monitoring of alterations in the volatile metabolome may be a useful tool for rapid brain trauma diagnosis and for monitoring recovery. PMID:26926034

Metabolomic analysis of insulin resistance across different mouse strains and diets.

PubMed

Stöckli, Jacqueline; Fisher-Wellman, Kelsey H; Chaudhuri, Rima; Zeng, Xiao-Yi; Fazakerley, Daniel J; Meoli, Christopher C; Thomas, Kristen C; Hoffman, Nolan J; Mangiafico, Salvatore P; Xirouchaki, Chrysovalantou E; Yang, Chieh-Hsin; Ilkayeva, Olga; Wong, Kari; Cooney, Gregory J; Andrikopoulos, Sofianos; Muoio, Deborah M; James, David E

2017-11-24

Insulin resistance is a major risk factor for many diseases. However, its underlying mechanism remains unclear in part because it is triggered by a complex relationship between multiple factors, including genes and the environment. Here, we used metabolomics combined with computational methods to identify factors that classified insulin resistance across individual mice derived from three different mouse strains fed two different diets. Three inbred ILSXISS strains were fed high-fat or chow diets and subjected to metabolic phenotyping and metabolomics analysis of skeletal muscle. There was significant metabolic heterogeneity between strains, diets, and individual animals. Distinct metabolites were changed with insulin resistance, diet, and between strains. Computational analysis revealed 113 metabolites that were correlated with metabolic phenotypes. Using these 113 metabolites, combined with machine learning to segregate mice based on insulin sensitivity, we identified C22:1-CoA, C2-carnitine, and C16-ceramide as the best classifiers. Strikingly, when these three metabolites were combined into one signature, they classified mice based on insulin sensitivity more accurately than each metabolite on its own or other published metabolic signatures. Furthermore, C22:1-CoA was 2.3-fold higher in insulin-resistant mice and correlated significantly with insulin resistance. We have identified a metabolomic signature composed of three functionally unrelated metabolites that accurately predicts whole-body insulin sensitivity across three mouse strains. These data indicate the power of simultaneous analysis of individual, genetic, and environmental variance in mice for identifying novel factors that accurately predict metabolic phenotypes like whole-body insulin sensitivity. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster

PubMed Central

Hoffman, Jessica M; Soltow, Quinlyn A; Li, Shuzhao; Sidik, Alfire; Jones, Dean P; Promislow, Daniel E L

2014-01-01

Researchers have used whole-genome sequencing and gene expression profiling to identify genes associated with age, in the hope of understanding the underlying mechanisms of senescence. But there is a substantial gap from variation in gene sequences and expression levels to variation in age or life expectancy. In an attempt to bridge this gap, here we describe the effects of age, sex, genotype, and their interactions on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Among the 6800 features analyzed, we found that over one-quarter of all metabolites were significantly associated with age, sex, genotype, or their interactions, and multivariate analysis shows that individual metabolomic profiles are highly predictive of these traits. Using a metabolomic equivalent of gene set enrichment analysis, we identified numerous metabolic pathways that were enriched among metabolites associated with age, sex, and genotype, including pathways involving sugar and glycerophospholipid metabolism, neurotransmitters, amino acids, and the carnitine shuttle. Our results suggest that high-sensitivity metabolomic studies have excellent potential not only to reveal mechanisms that lead to senescence, but also to help us understand differences in patterns of aging among genotypes and between males and females. PMID:24636523

Isolation of Infective Zika Virus from Urine and Saliva of Patients in Brazil

PubMed Central

da Silva, Kely A. B.; de Castro, Marcia G.; Gerber, Alexandra L.; de Almeida, Luiz G. P.; Lourenço-de-Oliveira, Ricardo; Vasconcelos, Ana Tereza R.

2016-01-01

Background Zika virus (ZIKV) is an emergent threat provoking a worldwide explosive outbreak. Since January 2015, 41 countries reported autochthonous cases. In Brazil, an increase in Guillain-Barré syndrome and microcephaly cases was linked to ZIKV infections. A recent report describing low experimental transmission efficiency of its main putative vector, Ae. aegypti, in conjunction with apparent sexual transmission notifications, prompted the investigation of other potential sources of viral dissemination. Urine and saliva have been previously established as useful tools in ZIKV diagnosis. Here, we described the presence and isolation of infectious ZIKV particles from saliva and urine of acute phase patients in the Rio de Janeiro state, Brazil. Methodology/Principal Findings Nine urine and five saliva samples from nine patients from Rio de Janeiro presenting rash and other typical Zika acute phase symptoms were inoculated in Vero cell culture and submitted to specific ZIKV RNA detection and quantification through, respectively, NAT-Zika, RT-PCR and RT-qPCR. Two ZIKV isolates were achieved, one from urine and one from saliva specimens. ZIKV nucleic acid was identified by all methods in four patients. Whenever both urine and saliva samples were available from the same patient, urine viral loads were higher, corroborating the general sense that it is a better source for ZIKV molecular diagnostic. In spite of this, from the two isolated strains, each from one patient, only one derived from urine, suggesting that other factors, like the acidic nature of this fluid, might interfere with virion infectivity. The complete genome of both ZIKV isolates was obtained. Phylogenetic analysis revealed similarity with strains previously isolated during the South America outbreak. Conclusions/Significance The detection of infectious ZIKV particles in urine and saliva of patients during the acute phase may represent a critical factor in the spread of virus. The epidemiological

[The biological and clinical relevance of estrogen metabolome].

PubMed

Kovács, Krisztián; Vásárhelyi, Barna; Mészáros, Katalin; Patócs, Attila; Karvaly, Gellért

2017-06-01

Considerable knowledge has been gathered on the physiological role of estrogens. However, fairly little information is available on the role of compounds produced in the breakdown process of estrone and estradiol wich may play a role in various diseases associated with estrogen impact. To date, approximately 15 extragonadal estrogen-related compounds have been identified. These metabolites may exert protective, or, instead, pro-inflammatory and/or pro-oncogenic activity in a tissue-specific manner. Systemic and local estrogen metabolite levels are not necesserily correlated, which may promote the diagnostic significance of the locally produced estrogen metabolites in the future. The aim of the present study is a bibliographic review of the extragonadal metabolome in peripheral tissues, and to highlight the role of the peripheral tissue homeostasis of estrogens as well as the non-hormonal biological activity and clinical significance of the estrogen metabolome. Orv Hetil. 2017; 158(24): 929-937.

The investigations of changes in mineral-organic and carbon-phosphate ratios in the mixed saliva by synchrotron infrared spectroscopy

NASA Astrophysics Data System (ADS)

Seredin, Pavel; Goloshchapov, Dmitry; Kashkarov, Vladimir; Ippolitov, Yuri; Bambery, Keith

The objective of this study was to investigate the efficiency of the saturation of mixed saliva by mineral complexes and groups necessary for the remineralisation of tooth enamel using exogenous and endogenous methods of caries prevention. Using IR spectroscopy and high-intensity synchrotron radiation, changes in the composition of the human mixed saliva were identified when exogenous and endogenous methods of caries prevention are employed. Based on the calculations of mineral/organic and carbon/phosphate ratios, changes in the composition of the human mixed saliva depending on a certain type of prevention were identified. It is shown that the use of a toothpaste (exogenous prevention) alone based on a multi-mineral complex including calcium glycerophosphate provides only a short-term effect of saturating the oral cavity with mineral complexes and groups. Rinsing of the oral cavity with water following the preventive use of a toothpaste completely removes the effect of the saturation of the mixed saliva with mineral groups and complexes. The use of tablets of a multi-mineral complex with calcium glycerophosphate (endogenous prevention) in combination with exogenous prevention causes an average increase of ∼10% in the content of mineral groups and complexes in the mixed saliva and allows long-term saturation of the oral fluid by them. This method outperforms the exogenous one owing to a long-term effect of optimal concentrations of endogenous and biologically available derivatives of phosphates on the enamel surface.

Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers.

PubMed

Puchades-Carrasco, Leonor; Palomino-Schätzlein, Martina; Pérez-Rambla, Clara; Pineda-Lucena, Antonio

2016-05-01

Metabolomics, a systems biology approach focused on the global study of the metabolome, offers a tremendous potential in the analysis of clinical samples. Among other applications, metabolomics enables mapping of biochemical alterations involved in the pathogenesis of diseases, and offers the opportunity to noninvasively identify diagnostic, prognostic and predictive biomarkers that could translate into early therapeutic interventions. Particularly, metabolomics by Nuclear Magnetic Resonance (NMR) has the ability to simultaneously detect and structurally characterize an abundance of metabolic components, even when their identities are unknown. Analysis of the data generated using this experimental approach requires the application of statistical and bioinformatics tools for the correct interpretation of the results. This review focuses on the different steps involved in the metabolomics characterization of biofluids for clinical applications, ranging from the design of the study to the biological interpretation of the results. Particular emphasis is devoted to the specific procedures required for the processing and interpretation of NMR data with a focus on the identification of clinically relevant biomarkers. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Influence of local radiotherapy on penetration of fluconazole into human saliva.

PubMed Central

Oliary, J; Tod, M; Louchahi, K; Petitjean, O; Frachet, B; Le Gros, V; Brion, N

1993-01-01

The pharmacokinetics of fluconazole (50 mg, single oral dose) in saliva and plasma were determined for five healthy subjects and five patients who underwent radiotherapy (dose, > 45 Gy over a 6-week period) in the salivary gland area and suffered from oropharyngeal candidiasis. Saliva was collected after electrical stimulation. Fluconazole was measured by liquid chromatography. From healthy volunteers and patients, saliva and plasma were sampled from 0 to 24 h. Although fluconazole penetration kinetics were significantly slowed down in irradiated patients, saliva concentrations of fluconazole were higher than those in the plasma, except at 1 h. In the postdistribution phase, the saliva/plasma concentration ratio was in the range of 1.2 to 1.4, and there was no significant difference between healthy subjects and patients. The saliva concentration of fluconazole was over 1 mg/liter throughout the entire interval 2 to 24 h after drug intake. From these results, the clinical efficacy of fluconazole for oropharyngeal candidiasis is not expected to be less than that in subjects with normal salivary glands, provided that salivary secretion remains. PMID:8109935

Metabolome Integrated Analysis of High-Temperature Response in Pinus radiata.

PubMed

Escandón, Mónica; Meijón, Mónica; Valledor, Luis; Pascual, Jesús; Pinto, Gloria; Cañal, María Jesús

2018-01-01

The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, Pinus radiata plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites. The analysis of identified metabolites and highlighter metabolic pathways across heat time exposure reveal the dynamism of the metabolome in relation to high-temperature response in P. radiata , identifying the existence of a turning point (on day 3) at which P. radiata plants changed from an initial stress response program (shorter-term response) to an acclimation one (longer-term response). Furthermore, the integration of metabolome and physiological measurements, which cover from the photosynthetic state to hormonal profile, suggests a complex metabolic pathway interaction network related to heat-stress response. Cytokinins (CKs), fatty acid metabolism and flavonoid and terpenoid biosynthesis were revealed as the most important pathways involved in heat-stress response in P. radiata , with zeatin riboside (ZR) and isopentenyl adenosine (iPA) as the key hormones coordinating these multiple and complex interactions. On the other hand, the integrative approach allowed elucidation of crucial metabolic mechanisms involved in heat response in P. radiata , as well as the identification of thermotolerance metabolic biomarkers (L-phenylalanine, hexadecanoic acid, and dihydromyricetin), crucial metabolites which can reschedule the metabolic strategy to adapt to high temperature.

Metabolome Integrated Analysis of High-Temperature Response in Pinus radiata

PubMed Central

Escandón, Mónica; Meijón, Mónica; Valledor, Luis; Pascual, Jesús; Pinto, Gloria; Cañal, María Jesús

2018-01-01

The integrative omics approach is crucial to identify the molecular mechanisms underlying high-temperature response in non-model species. Based on future scenarios of heat increase, Pinus radiata plants were exposed to a temperature of 40°C for a period of 5 days, including recovered plants (30 days after last exposure to 40°C) in the analysis. The analysis of the metabolome using complementary mass spectrometry techniques (GC-MS and LC-Orbitrap-MS) allowed the reliable quantification of 2,287 metabolites. The analysis of identified metabolites and highlighter metabolic pathways across heat time exposure reveal the dynamism of the metabolome in relation to high-temperature response in P. radiata, identifying the existence of a turning point (on day 3) at which P. radiata plants changed from an initial stress response program (shorter-term response) to an acclimation one (longer-term response). Furthermore, the integration of metabolome and physiological measurements, which cover from the photosynthetic state to hormonal profile, suggests a complex metabolic pathway interaction network related to heat-stress response. Cytokinins (CKs), fatty acid metabolism and flavonoid and terpenoid biosynthesis were revealed as the most important pathways involved in heat-stress response in P. radiata, with zeatin riboside (ZR) and isopentenyl adenosine (iPA) as the key hormones coordinating these multiple and complex interactions. On the other hand, the integrative approach allowed elucidation of crucial metabolic mechanisms involved in heat response in P. radiata, as well as the identification of thermotolerance metabolic biomarkers (L-phenylalanine, hexadecanoic acid, and dihydromyricetin), crucial metabolites which can reschedule the metabolic strategy to adapt to high temperature. PMID:29719546

Metabolomic responses to lumacaftor/ivacaftor in cystic fibrosis.

PubMed

Kopp, Benjamin T; McCulloch, Scott; Shrestha, Chandra L; Zhang, Shuzhong; Sarzynski, Lisa; Woodley, Frederick W; Hayes, Don

2018-05-01

Cystic fibrosis (CF) is a life-limiting disease caused by a defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Lumacaftor/Ivacaftor is a novel CFTR modulator approved for patients that are homozygous for Phe508del CFTR, but its clinical effectiveness varies amongst patients, making it difficult to determine clinical responders. Therefore, identifying biochemical biomarkers associated with drug response are clinically important for follow-up studies. Serum metabolomics was performed on twenty patients with CF pre- and 6-month post-Lumacaftor/Ivacaftor response via Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS). Correlation with clinical variables was performed. Metabolomics analysis demonstrated 188 differentially regulated metabolites between patients pre- and post-Lumacaftor/Ivacaftor initiation, with a predominance of lipid and amino acid alterations. The top 30 metabolites were able to differentiate pre- and post-Lumacaftor/Ivacaftor status in greater than 90% of patients via a random-forest confusion matrix. Alterations in bile acids, phospholipids, and bacteria-associated metabolites were the predominant changes associated with drug response. Importantly, changes in metabolic patterns were associated with clinical responders. Selected key lipid and amino acid metabolic pathways were significantly affected by Lumacaftor/Ivacaftor initiation and similar pathways were affected in clinical responders. Targeted metabolomics may provide useful and relevant biomarkers of CFTR modulator responses. © 2018 Wiley Periodicals, Inc.

Biomarkers for predicting type 2 diabetes development-Can metabolomics improve on existing biomarkers?

PubMed

Savolainen, Otto; Fagerberg, Björn; Vendelbo Lind, Mads; Sandberg, Ann-Sofie; Ross, Alastair B; Bergström, Göran

2017-01-01

The aim was to determine if metabolomics could be used to build a predictive model for type 2 diabetes (T2D) risk that would improve prediction of T2D over current risk markers. Gas chromatography-tandem mass spectrometry metabolomics was used in a nested case-control study based on a screening sample of 64-year-old Caucasian women (n = 629). Candidate metabolic markers of T2D were identified in plasma obtained at baseline and the power to predict diabetes was tested in 69 incident cases occurring during 5.5 years follow-up. The metabolomics results were used as a standalone prediction model and in combination with established T2D predictive biomarkers for building eight T2D prediction models that were compared with each other based on their sensitivity and selectivity for predicting T2D. Established markers of T2D (impaired fasting glucose, impaired glucose tolerance, insulin resistance (HOMA), smoking, serum adiponectin)) alone, and in combination with metabolomics had the largest areas under the curve (AUC) (0.794 (95% confidence interval [0.738-0.850]) and 0.808 [0.749-0.867] respectively), with the standalone metabolomics model based on nine fasting plasma markers having a lower predictive power (0.657 [0.577-0.736]). Prediction based on non-blood based measures was 0.638 [0.565-0.711]). Established measures of T2D risk remain the best predictor of T2D risk in this population. Additional markers detected using metabolomics are likely related to these measures as they did not enhance the overall prediction in a combined model.

Biomarkers for predicting type 2 diabetes development—Can metabolomics improve on existing biomarkers?

PubMed Central

Savolainen, Otto; Fagerberg, Björn; Vendelbo Lind, Mads; Sandberg, Ann-Sofie; Ross, Alastair B.; Bergström, Göran

2017-01-01

Aim The aim was to determine if metabolomics could be used to build a predictive model for type 2 diabetes (T2D) risk that would improve prediction of T2D over current risk markers. Methods Gas chromatography-tandem mass spectrometry metabolomics was used in a nested case-control study based on a screening sample of 64-year-old Caucasian women (n = 629). Candidate metabolic markers of T2D were identified in plasma obtained at baseline and the power to predict diabetes was tested in 69 incident cases occurring during 5.5 years follow-up. The metabolomics results were used as a standalone prediction model and in combination with established T2D predictive biomarkers for building eight T2D prediction models that were compared with each other based on their sensitivity and selectivity for predicting T2D. Results Established markers of T2D (impaired fasting glucose, impaired glucose tolerance, insulin resistance (HOMA), smoking, serum adiponectin)) alone, and in combination with metabolomics had the largest areas under the curve (AUC) (0.794 (95% confidence interval [0.738–0.850]) and 0.808 [0.749–0.867] respectively), with the standalone metabolomics model based on nine fasting plasma markers having a lower predictive power (0.657 [0.577–0.736]). Prediction based on non-blood based measures was 0.638 [0.565–0.711]). Conclusions Established measures of T2D risk remain the best predictor of T2D risk in this population. Additional markers detected using metabolomics are likely related to these measures as they did not enhance the overall prediction in a combined model. PMID:28692646

Compliance with minimum information guidelines in public metabolomics repositories

PubMed Central

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

2017-01-01

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. PMID:28949328

Compliance with minimum information guidelines in public metabolomics repositories.

PubMed

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.

Dynamic metabolome profiling reveals significant metabolic changes during grain development of bread wheat (Triticum aestivum L.).

PubMed

Zhen, Shoumin; Dong, Kun; Deng, Xiong; Zhou, Jiaxing; Xu, Xuexin; Han, Caixia; Zhang, Wenying; Xu, Yanhao; Wang, Zhimin; Yan, Yueming

2016-08-01

Metabolites in wheat grains greatly influence nutritional values. Wheat provides proteins, minerals, B-group vitamins and dietary fiber to humans. These metabolites are important to human health. However, the metabolome of the grain during the development of bread wheat has not been studied so far. In this work the first dynamic metabolome of the developing grain of the elite Chinese bread wheat cultivar Zhongmai 175 was analyzed, using non-targeted gas chromatography/mass spectrometry (GC/MS) for metabolite profiling. In total, 74 metabolites were identified over the grain developmental stages. Metabolite-metabolite correlation analysis revealed that the metabolism of amino acids, carbohydrates, organic acids, amines and lipids was interrelated. An integrated metabolic map revealed a distinct regulatory profile. The results provide information that can be used by metabolic engineers and molecular breeders to improve wheat grain quality. The present metabolome approach identified dynamic changes in metabolite levels, and correlations among such levels, in developing seeds. The comprehensive metabolic map may be useful when breeding programs seek to improve grain quality. The work highlights the utility of GC/MS-based metabolomics, in conjunction with univariate and multivariate data analysis, when it is sought to understand metabolic changes in developing seeds. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

MetaboLyzer: A Novel Statistical Workflow for Analyzing Post-Processed LC/MS Metabolomics Data

PubMed Central

Mak, Tytus D.; Laiakis, Evagelia C.; Goudarzi, Maryam; Fornace, Albert J.

2014-01-01

Metabolomics, the global study of small molecules in a particular system, has in the last few years risen to become a primary –omics platform for the study of metabolic processes. With the ever-increasing pool of quantitative data yielded from metabolomic research, specialized methods and tools with which to analyze and extract meaningful conclusions from these data are becoming more and more crucial. Furthermore, the depth of knowledge and expertise required to undertake a metabolomics oriented study is a daunting obstacle to investigators new to the field. As such, we have created a new statistical analysis workflow, MetaboLyzer, which aims to both simplify analysis for investigators new to metabolomics, as well as provide experienced investigators the flexibility to conduct sophisticated analysis. MetaboLyzer’s workflow is specifically tailored to the unique characteristics and idiosyncrasies of postprocessed liquid chromatography/mass spectrometry (LC/MS) based metabolomic datasets. It utilizes a wide gamut of statistical tests, procedures, and methodologies that belong to classical biostatistics, as well as several novel statistical techniques that we have developed specifically for metabolomics data. Furthermore, MetaboLyzer conducts rapid putative ion identification and putative biologically relevant analysis via incorporation of four major small molecule databases: KEGG, HMDB, Lipid Maps, and BioCyc. MetaboLyzer incorporates these aspects into a comprehensive workflow that outputs easy to understand statistically significant and potentially biologically relevant information in the form of heatmaps, volcano plots, 3D visualization plots, correlation maps, and metabolic pathway hit histograms. For demonstration purposes, a urine metabolomics data set from a previously reported radiobiology study in which samples were collected from mice exposed to gamma radiation was analyzed. MetaboLyzer was able to identify 243 statistically significant ions out of a

Metabolomic characteristics of arsenic-associated diabetes in a prospective cohort in Chihuahua, Mexico.

PubMed

Martin, Elizabeth; González-Horta, Carmen; Rager, Julia; Bailey, Kathryn A; Sánchez-Ramírez, Blanca; Ballinas-Casarrubias, Lourdes; Ishida, María C; Gutiérrez-Torres, Daniela S; Hernández Cerón, Roberto; Viniegra Morales, Damián; Baeza Terrazas, Francisco A; Saunders, R Jesse; Drobná, Zuzana; Mendez, Michelle A; Buse, John B; Loomis, Dana; Jia, Wei; García-Vargas, Gonzalo G; Del Razo, Luz M; Stýblo, Miroslav; Fry, Rebecca

2015-04-01

Chronic exposure to inorganic arsenic (iAs) has been linked to an increased risk of diabetes, yet the specific disease phenotype and underlying mechanisms are poorly understood. In the present study we set out to identify iAs exposure-associated metabolites with altered abundance in nondiabetic and diabetic individuals in an effort to understand the relationship between exposure, metabolomic response, and disease status. A nested study design was used to profile metabolomic shifts in urine and plasma collected from 90 diabetic and 86 nondiabetic individuals matched for varying iAs concentrations in drinking water, body mass index, age, and sex. Diabetes diagnosis was based on measures of fasting plasma glucose and 2-h blood glucose. Multivariable models were used to identify metabolites with altered abundance associated with iAs exposure among diabetic and nondiabetic individuals. A total of 132 metabolites were identified to shift in urine or plasma in response to iAs exposure characterized by the sum of iAs metabolites in urine (U-tAs). Although many metabolites were altered in both diabetic and nondiabetic 35 subjects, diabetic individuals displayed a unique response to iAs exposure with 59 altered metabolites including those that play a role in tricarboxylic acid cycle and amino acid metabolism. Taken together, these data highlight the broad impact of iAs exposure on the human metabolome, and demonstrate some specificity of the metabolomic response between diabetic and nondiabetic individuals. These data may provide novel insights into the mechanisms and phenotype of diabetes associated with iAs exposure. © The Author 2015. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Metabolomics in transfusion medicine.

PubMed

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.

Ultrasound: a subexploited tool for sample preparation in metabolomics.

PubMed

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.

Serum Metabolomics to Identify the Liver Disease-Specific Biomarkers for the Progression of Hepatitis to Hepatocellular Carcinoma

NASA Astrophysics Data System (ADS)

Gao, Rong; Cheng, Jianhua; Fan, Chunlei; Shi, Xiaofeng; Cao, Yuan; Sun, Bo; Ding, Huiguo; Hu, Chengjin; Dong, Fangting; Yan, Xianzhong

2015-12-01

Hepatocellular carcinoma (HCC) is a common malignancy that has region specific etiologies. Unfortunately, 85% of cases of HCC are diagnosed at an advanced stage. Reliable biomarkers for the early diagnosis of HCC are urgently required to reduced mortality and therapeutic expenditure. We established a non-targeted gas chromatography-time of flight-mass spectrometry (GC-TOFMS) metabolomics method in conjunction with Random Forests (RF) analysis based on 201 serum samples from healthy controls (NC), hepatitis B virus (HBV), liver cirrhosis (LC) and HCC patients to explore the metabolic characteristics in the progression of hepatocellular carcinogenesis. Ultimately, 15 metabolites were identified intimately associated with the process. Phenylalanine, malic acid and 5-methoxytryptamine for HBV vs. NC, palmitic acid for LC vs. HBV, and asparagine and β-glutamate for HCC vs. LC were screened as the liver disease-specific potential biomarkers with an excellent discriminant performance. All the metabolic perturbations in these liver diseases are associated with pathways for energy metabolism, macromolecular synthesis, and maintaining the redox balance to protect tumor cells from oxidative stress.

Estradiol in saliva for monitoring follicular stimulation in an in vitro fertilization program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belkien, L.D.; Bordt, J.; Moeller, P.

1985-09-01

A rapid and sensitive radioimmunoassay (RIA) was developed to compare serum and saliva estradiol (E/sub 2/) levels in patients undergoing ovulation induction in an in vitro fertilization and embryo transfer (IVF-ET) program. Serum and saliva E/sub 2/ were compared in 23 patients. The sensitivity of the saliva RIA standard curve was 11 fmol/tube (equal to 3.2 pg/tube). There was a highly significant correlation between serum and saliva E/sub 2/ throughout the stimulated cycles. The ratio of serum to saliva E/sub 2/ was constant throughout the stimulated cycles. The E/sub 2/ concentration per follicle was 1548 pmol/l in serum and 23more » pmol/l in saliva. Mean E/sub 2/ levels in saliva (+/- SD) were 74 +/- 21 pmol/l at midcycle and 46 +/- 12 pmol/l at midluteal phase. The findings indicate that measurement of saliva E/sub 2/ provides a reliable, noninvasive method and may replace serum measurements for monitoring stimulated cycles in an IVF-ET program.« less

Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bingol, Kerem; Brüschweiler, Rafael

Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexitymore » of these tasks.« less

The effects of age and dietary restriction on the tissue-specific metabolome of Drosophila

PubMed Central

Laye, Matthew J; Tran, ViLinh; Jones, Dean P; Kapahi, Pankaj; Promislow, Daniel E L

2015-01-01

Dietary restriction (DR) is a robust intervention that extends lifespan and slows the onset of age-related diseases in diverse organisms. While significant progress has been made in attempts to uncover the genetic mechanisms of DR, there are few studies on the effects of DR on the metabolome. In recent years, metabolomic profiling has emerged as a powerful technology to understand the molecular causes and consequences of natural aging and disease-associated phenotypes. Here, we use high-resolution mass spectroscopy and novel computational approaches to examine changes in the metabolome from the head, thorax, abdomen, and whole body at multiple ages in Drosophila fed either a nutrient-rich ad libitum (AL) or nutrient-restricted (DR) diet. Multivariate analysis clearly separates the metabolome by diet in different tissues and different ages. DR significantly altered the metabolome and, in particular, slowed age-related changes in the metabolome. Interestingly, we observed interacting metabolites whose correlation coefficients, but not mean levels, differed significantly between AL and DR. The number and magnitude of positively correlated metabolites was greater under a DR diet. Furthermore, there was a decrease in positive metabolite correlations as flies aged on an AL diet. Conversely, DR enhanced these correlations with age. Metabolic set enrichment analysis identified several known (e.g., amino acid and NAD metabolism) and novel metabolic pathways that may affect how DR effects aging. Our results suggest that network structure of metabolites is altered upon DR and may play an important role in preventing the decline of homeostasis with age. PMID:26085309

Haystack, a web-based tool for metabolomics research

PubMed Central

2014-01-01

Background Liquid chromatography coupled to mass spectrometry (LCMS) has become a widely used technique in metabolomics research for differential profiling, the broad screening of biomolecular constituents across multiple samples to diagnose phenotypic differences and elucidate relevant features. However, a significant limitation in LCMS-based metabolomics is the high-throughput data processing required for robust statistical analysis and data modeling for large numbers of samples with hundreds of unique chemical species. Results To address this problem, we developed Haystack, a web-based tool designed to visualize, parse, filter, and extract significant features from LCMS datasets rapidly and efficiently. Haystack runs in a browser environment with an intuitive graphical user interface that provides both display and data processing options. Total ion chromatograms (TICs) and base peak chromatograms (BPCs) are automatically displayed, along with time-resolved mass spectra and extracted ion chromatograms (EICs) over any mass range. Output files in the common .csv format can be saved for further statistical analysis or customized graphing. Haystack's core function is a flexible binning procedure that converts the mass dimension of the chromatogram into a set of interval variables that can uniquely identify a sample. Binned mass data can be analyzed by exploratory methods such as principal component analysis (PCA) to model class assignment and identify discriminatory features. The validity of this approach is demonstrated by comparison of a dataset from plants grown at two light conditions with manual and automated peak detection methods. Haystack successfully predicted class assignment based on PCA and cluster analysis, and identified discriminatory features based on analysis of EICs of significant bins. Conclusion Haystack, a new online tool for rapid processing and analysis of LCMS-based metabolomics data is described. It offers users a range of data visualization

Metabolomics as a tool in the identification of dietary biomarkers.

PubMed

Gibbons, Helena; Brennan, Lorraine

2017-02-01

Current dietary assessment methods including FFQ, 24-h recalls and weighed food diaries are associated with many measurement errors. In an attempt to overcome some of these errors, dietary biomarkers have emerged as a complementary approach to these traditional methods. Metabolomics has developed as a key technology for the identification of new dietary biomarkers and to date, metabolomic-based approaches have led to the identification of a number of putative biomarkers. The three approaches generally employed when using metabolomics in dietary biomarker discovery are: (i) acute interventions where participants consume specific amounts of a test food, (ii) cohort studies where metabolic profiles are compared between consumers and non-consumers of a specific food and (iii) the analysis of dietary patterns and metabolic profiles to identify nutritypes and biomarkers. The present review critiques the current literature in terms of the approaches used for dietary biomarker discovery and gives a detailed overview of the currently proposed biomarkers, highlighting steps needed for their full validation. Furthermore, the present review also evaluates areas such as current databases and software tools, which are needed to advance the interpretation of results and therefore enhance the utility of dietary biomarkers in nutrition research.

Aphid Gel Saliva: Sheath Structure, Protein Composition and Secretory Dependence on Stylet-Tip Milieu

PubMed Central

Will, Torsten; Steckbauer, Kathrin; Hardt, Martin; van Bel, Aart J. E.

2012-01-01

In order to separate and analyze saliva types secreted during stylet propagation and feeding, aphids were fed on artificial diets. Gel saliva was deposited as chains of droplets onto Parafilm membranes covering the diets into which watery saliva was secreted. Saliva compounds collected from the diet fluid were separated by SDS-PAGE, while non-soluble gel saliva deposits were processed in a novel manner prior to protein separation by SDS-PAGE. Soluble (watery saliva) and non-soluble (gel saliva) protein fractions were significantly different. To test the effect of the stylet milieu on saliva secretion, aphids were fed on various diets. Hardening of gel saliva is strongly oxygen-dependent, probably owing to formation of sulfide bridges by oxidation of sulphydryl groups. Surface texture of gel saliva deposits is less pronounced under low-oxygen conditions and disappears in dithiothreitol containing diet. Using diets mimicking sieve-element sap and cell-wall fluid respectively showed that the soluble protein fraction was almost exclusively secreted in sieve elements while non-soluble fraction was preferentially secreted at cell wall conditions. This indicates that aphids are able to adapt salivary secretion in dependence of the stylet milieu. PMID:23056521

Stable isotope-resolved metabolomics and applications for drug development

PubMed Central

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

Metabolic changes associated with papillary thyroid carcinoma: A nuclear magnetic resonance-based metabolomics study.

PubMed

Li, Yanyun; Chen, Minjian; Liu, Cuiping; Xia, Yankai; Xu, Bo; Hu, Yanhui; Chen, Ting; Shen, Meiping; Tang, Wei

2018-05-01

Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. Nuclear magnetic resonance (NMR)‑based metabolomic technique is the gold standard in metabolite structural elucidation, and can provide different coverage of information compared with other metabolomic techniques. Here, we firstly conducted NMR based metabolomics study regarding detailed metabolic changes especially metabolic pathway changes related to PTC pathogenesis. 1H NMR-based metabolomic technique was adopted in conju-nction with multivariate analysis to analyze matched tumor and normal thyroid tissues obtained from 16 patients. The results were further annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG), and Human Metabolome Database, and then were analyzed using modules of pathway analysis and enrichment analysis of MetaboAnalyst 3.0. Based on the analytical techniques, we established the models of principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least-squares discriminant analysis (OPLS‑DA) which could discriminate PTC from normal thyroid tissue, and found 15 robust differentiated metabolites from two OPLS-DA models. We identified 8 KEGG pathways and 3 pathways of small molecular pathway database which were significantly related to PTC by using pathway analysis and enrichment analysis, respectively, through which we identified metabolisms related to PTC including branched chain amino acid metabolism (leucine and valine), other amino acid metabolism (glycine and taurine), glycolysis (lactate), tricarboxylic acid cycle (citrate), choline metabolism (choline, ethanolamine and glycerolphosphocholine) and lipid metabolism (very-low‑density lipoprotein and low-density lipoprotein). In conclusion, the PTC was characterized with increased glycolysis and inhibited tricarboxylic acid cycle, increased oncogenic amino acids as well as abnormal choline and lipid metabolism. The findings in this study provide new

Tolerability, pharmacokinetics, and bioequivalence of the tablet and syrup formulations of lacosamide in plasma, saliva, and urine: saliva as a surrogate of pharmacokinetics in the central compartment.

PubMed

Cawello, Willi; Bökens, Hilmar; Nickel, Brunhild; Andreas, Jens-Otto; Halabi, Atef

2013-01-01

To test for bioequivalence of 200 mg lacosamide oral tablet and syrup formulations. Additional objectives were to compare the pharmacokinetic profile of lacosamide in saliva and plasma, and to evaluate its tolerability. This open-label, randomized, two-way crossover trial was conducted in 16 healthy Caucasian male participants in Germany. The bioequivalence of 200 mg lacosamide tablet and syrup was evaluated using plasma to determine maximum measured concentration (C(max)) and area under the curve from zero to the last time point (AUC)(0-tz). Plasma and saliva samples for evaluation of pharmacokinetic parameters of lacosamide and the major metabolite O-desmethyl lacosamide (SPM 12809) were taken over 15 time points (0.5-72 h) and used to statistically compare bioavailability of the two. Urine samples were collected predose and over five time points (0-48 h) to evaluate the cumulative amount of unchanged drug and metabolite. Lacosamide median time to reach C(max) (t(max)) was 1 h for tablet and 0.5 h for syrup in plasma and saliva. Mean terminal half life (t(½)) for tablet and syrup was 12.5 and 12.4 h in plasma, and 13.1 and 13.3 h in saliva, respectively. Tablet and syrup mean plasma AUC(0-tz) was 84.5 and 83.3 μg/mL*h, respectively. Mean AUC(0-tz) in saliva was 93.2 μg/mL*h for tablet and syrup. Mean C(max) for tablet was 5.26 μg/mL in plasma and 5.63 μg/mL in saliva. Syrup mean C(max) was 5.14 and 8.32 μg/mL in plasma and saliva, respectively. Within 2 h of syrup administration, elevated lacosamide concentration in saliva compared to plasma was observed. The ratio of lacosamide syrup to tablet was 0.98 for C(max) and 0.99 for AUC(0-tz) in plasma, and 1.00 for AUC((0-tz)) in saliva; the 90% confidence intervals (CIs) for these parameters were within the range of 0.80-1.25, which meets accepted bioequivalence criteria. The syrup-to-tablet ratio for C(max) in saliva was 1.48, and the 90% CIs exceeded the accepted upper boundary for bioequivalence (1

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine

PubMed Central

Piombino, Paola; Genovese, Alessandro; Esposito, Silvia; Moio, Luigi; Cutolo, Pier Paolo; Chambery, Angela; Severino, Valeria; Moneta, Elisabetta; Smith, Daniel P.; Owens, Sarah M.; Gilbert, Jack A.; Ercolini, Danilo

2014-01-01

Background Recent evidence suggests that a lower extent of the retronasal aroma release correspond to a higher amount of ad libitum food intake. This has been regarded as one of the bases of behavioral choices towards food consumption in obese people. In this pilot study we investigated the hypothesis that saliva from obese individuals could be responsible for an alteration of the retro-nasal aroma release. We tested this hypothesis in vitro, by comparing the release of volatiles from a liquid food matrix (wine) after its interaction with saliva from 28 obese (O) and 28 normal-weight (N) individuals. Methods and Findings Amplicon sequencing of the 16S rRNA V4 region indicated that Firmicutes and Actinobacteria were more abundant in O, while Proteobacteria and Fusobacteria dominated in N. Streptococcaceae were significantly more abundant in the O subjects and constituted 34% and 19% on average of the saliva microbiota of O and N subjects, respectively. The Total Antioxidant Capacity was higher in O vs N saliva samples. A model mouth system was used to test whether the in-mouth wine aroma release differs after the interaction with O or N saliva. In O samples, a 18% to 60% significant decrease in the mean concentration of wine volatiles was detected as a result of interaction with saliva, compared with N. This suppression was linked to biochemical differences in O and N saliva composition, which include protein content. Conclusion Microbiological and biochemical differences were found in O vs N saliva samples. An impaired retronasal aroma release from white wine was detected in vitro and linked to compositional differences between saliva from obese and normal-weight subjects. Additional in vivo investigations on diverse food matrices could contribute to understanding whether a lower olfactory stimulation due to saliva composition can be a co-factor in the development/maintenance of obesity. PMID:24465618

Cultural, behavioral, social, and psychological perceptions of saliva: relevance to clinical diagnostics.

PubMed

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.

Rumen fluid metabolomics analysis associated with feed efficiency on crossbred steers

USDA-ARS?s Scientific Manuscript database

The rumen plays a central role in the efficiency of digestion in ruminants. To identify potential differences in rumen function that lead to differences in feed efficiency, rumen metabolomic analysis by ultra-performance liquid chromatography/ time-of-flight mass spectrometry (MS) and multivariate/u...

Calcium kinetics with microgram stable isotope doses and saliva sampling

NASA Technical Reports Server (NTRS)

Smith, S. M.; Wastney, M. E.; Nyquist, L. E.; Shih, C. Y.; Wiesmann, H.; Nillen, J. L.; Lane, H. W.

1996-01-01

Studies of calcium kinetics require administration of tracer doses of calcium and subsequent repeated sampling of biological fluids. This study was designed to develop techniques that would allow estimation of calcium kinetics by using small (micrograms) doses of isotopes instead of the more common large (mg) doses to minimize tracer perturbation of the system and reduce cost, and to explore the use of saliva sampling as an alternative to blood sampling. Subjects received an oral dose (133 micrograms) of 43Ca and an i.v. dose (7.7 micrograms) of 46Ca. Isotopic enrichment in blood, urine, saliva and feces was well above thermal ionization mass spectrometry measurement precision up to 170 h after dosing. Fractional calcium absorptions determined from isotopic ratios in blood, urine and saliva were similar. Compartmental modeling revealed that kinetic parameters determined from serum or saliva data were similar, decreasing the necessity for blood samples. It is concluded from these results that calcium kinetics can be assessed with micrograms doses of stable isotopes, thereby reducing tracer costs and with saliva samples, thereby reducing the amount of blood needed.

Validation of an enzyme-linked immunosorbent assay developed for measuring cortisol concentration in human saliva and serum for its applicability to analyze cortisol in pig saliva.

PubMed

Thomsson, Ola; Ström-Holst, Bodil; Sjunnesson, Ylva; Bergqvist, Ann-Sofi

2014-09-06

The purpose of this study was to validate a commercially available enzyme-linked immunosorbent assay (ELISA) developed for measuring free cortisol in human saliva and total cortisol concentration in diluted human serum, for its applicability in measuring cortisol concentration in pig saliva. Collection of saliva is less stressful than e.g. blood sampling, and is a non-invasive method. Saliva was collected by allowing sows to chew on cotton swabs held by forceps. Thereafter, the swabs were centrifuged to retrieve the saliva. The ELISA was performed according to instructions provided by the manufacturer. To validate the ELISA, determination of the intra-assay coefficient of variation (CV), inter-assay CV, recovery, linearity and parallelism was performed. The intra-assay CV was below 10% and inter-assay CV below 15% for samples of high, medium and low cortisol concentrations. The mean recovery was 117% and the linearity and parallelism showed an r2-value of 0.994 and 0.993, respectively. For biological assessment of induced social stress, two saliva samples were collected in the morning from 6 primiparous and 21 multiparous sows. One sample was collected when the sows were individually housed in a farrowing pen and a second sample was collected when the sows were group housed. The primiparous sows had a significant higher cortisol concentration compared to the multiparous sows when group housed. The results obtained in this validation study indicate that the ELISA is suitable for measuring cortisol concentration in porcine saliva.

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients.

PubMed

Jacobs, Jonathan P; Goudarzi, Maryam; Singh, Namita; Tong, Maomeng; McHardy, Ian H; Ruegger, Paul; Asadourian, Miro; Moon, Bo-Hyun; Ayson, Allyson; Borneman, James; McGovern, Dermot P B; Fornace, Albert J; Braun, Jonathan; Dubinsky, Marla

2016-11-01

Microbes may increase susceptibility to inflammatory bowel disease (IBD) by producing bioactive metabolites that affect immune activity and epithelial function. We undertook a family based study to identify microbial and metabolic features of IBD that may represent a predisease risk state when found in healthy first-degree relatives. Twenty-one families with pediatric IBD were recruited, comprising 26 Crohn's disease patients in clinical remission, 10 ulcerative colitis patients in clinical remission, and 54 healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing, untargeted liquid chromatography-mass spectrometry metabolomics, and calprotectin measurement. Individuals were grouped into microbial and metabolomics states using Dirichlet multinomial models. Multivariate models were used to identify microbes and metabolites associated with these states. Individuals were classified into 2 microbial community types. One was associated with IBD but irrespective of disease status, had lower microbial diversity, and characteristic shifts in microbial composition including increased Enterobacteriaceae, consistent with dysbiosis. This microbial community type was associated similarly with IBD and reduced microbial diversity in an independent pediatric cohort. Individuals also clustered bioinformatically into 2 subsets with shared fecal metabolomics signatures. One metabotype was associated with IBD and was characterized by increased bile acids, taurine, and tryptophan. The IBD-associated microbial and metabolomics states were highly correlated, suggesting that they represented an integrated ecosystem. Healthy relatives with the IBD-associated microbial community type had an increased incidence of elevated fecal calprotectin. Healthy first-degree relatives can have dysbiosis associated with an altered intestinal metabolome that may signify a predisease microbial susceptibility state or subclinical inflammation. Longitudinal prospective

Identifying developmental toxicity pathways for a subset of ToxCast chemicals using human embryonic stem cells and metabolomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kleinstreuer, N.C., E-mail: kleinstreuer.nicole@epa.gov; Smith, A.M.; West, P.R.

2011-11-15

Metabolomics analysis was performed on the supernatant of human embryonic stem (hES) cell cultures exposed to a blinded subset of 11 chemicals selected from the chemical library of EPA's ToxCast Trade-Mark-Sign chemical screening and prioritization research project. Metabolites from hES cultures were evaluated for known and novel signatures that may be indicative of developmental toxicity. Significant fold changes in endogenous metabolites were detected for 83 putatively annotated mass features in response to the subset of ToxCast chemicals. The annotations were mapped to specific human metabolic pathways. This revealed strong effects on pathways for nicotinate and nicotinamide metabolism, pantothenate and CoAmore » biosynthesis, glutathione metabolism, and arginine and proline metabolism pathways. Predictivity for adverse outcomes in mammalian prenatal developmental toxicity studies used ToxRefDB and other sources of information, including Stemina Biomarker Discovery's predictive DevTox Registered-Sign model trained on 23 pharmaceutical agents of known developmental toxicity and differing potency. The model initially predicted developmental toxicity from the blinded ToxCast compounds in concordance with animal data with 73% accuracy. Retraining the model with data from the unblinded test compounds at one concentration level increased the predictive accuracy for the remaining concentrations to 83%. These preliminary results on a 11-chemical subset of the ToxCast chemical library indicate that metabolomics analysis of the hES secretome provides information valuable for predictive modeling and mechanistic understanding of mammalian developmental toxicity. -- Highlights: Black-Right-Pointing-Pointer We tested 11 environmental compounds in a hESC metabolomics platform. Black-Right-Pointing-Pointer Significant changes in secreted small molecule metabolites were observed. Black-Right-Pointing-Pointer Perturbed mass features map to pathways critical for normal

Arbuscular Mycorrhizal Fungi and Plant Chemical Defence: Effects of Colonisation on Aboveground and Belowground Metabolomes.

PubMed

Hill, Elizabeth M; Robinson, Lynne A; Abdul-Sada, Ali; Vanbergen, Adam J; Hodge, Angela; Hartley, Sue E

2018-02-01

Arbuscular mycorrhizal fungal (AMF) colonisation of plant roots is one of the most ancient and widespread interactions in ecology, yet the systemic consequences for plant secondary chemistry remain unclear. We performed the first metabolomic investigation into the impact of AMF colonisation by Rhizophagus irregularis on the chemical defences, spanning above- and below-ground tissues, in its host-plant ragwort (Senecio jacobaea). We used a non-targeted metabolomics approach to profile, and where possible identify, compounds induced by AMF colonisation in both roots and shoots. Metabolomics analyses revealed that 33 compounds were significantly increased in the root tissue of AMF colonised plants, including seven blumenols, plant-derived compounds known to be associated with AMF colonisation. One of these was a novel structure conjugated with a malonyl-sugar and uronic acid moiety, hitherto an unreported combination. Such structural modifications of blumenols could be significant for their previously reported functional roles associated with the establishment and maintenance of AM colonisation. Pyrrolizidine alkaloids (PAs), key anti-herbivore defence compounds in ragwort, dominated the metabolomic profiles of root and shoot extracts. Analyses of the metabolomic profiles revealed an increase in four PAs in roots (but not shoots) of AMF colonised plants, with the potential to protect colonised plants from below-ground organisms.

Metabolomics approach to reduce the Crabtree effect in continuous culture of Saccharomyces cerevisiae.

PubMed

Imura, Makoto; Iwakiri, Ryo; Bamba, Takeshi; Fukusaki, Eiichiro

2018-04-20

The budding yeast Saccharomyces cerevisiae is an important microorganism for fermentation and the food industry. However, during production, S. cerevisiae commonly uses the ethanol fermentation pathway for glucose utilization if excess sugar is present, even in the presence of sufficient oxygen levels. This aerobic ethanol fermentation, referred to as "the Crabtree effect" is one of the most significant reasons for low cell yield. To weaken the Crabtree effect in fed-batch and continuous culture, sugar flow should be limited. In addition, in continuous culture, the dilution rate must be reduced to avoid washing out cells. However, under such conditions, production speed might be sacrificed. It is difficult to solve this problem with the tradeoff between cell yield and production speed by using conventional tactics. However, a metabolomics approach may be an effective way to search for clues regarding metabolic modulation. Therefore, the purpose of this study was to reduce ethanol production in continuous culture of S. cerevisiae at a higher dilution rate through a metabolomics approach. We used a metabolomics analysis to identify metabolites that were drastically increased or decreased in continuous culture when the dilution rate shifted from biomass formation to ethanol fermentation. The individual addition of two of the selected metabolites, fumaric acid and malic acid, reduced ethanol production at a higher dilution rate. This result demonstrates the potential for using metabolomics approaches to identify metabolites that reduce ethanol production in continuous culture at high dilution rates. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A Plasma Metabolomic Signature of the Exfoliation Syndrome Involves Amino Acids, Acylcarnitines, and Polyamines.

PubMed

Leruez, Stéphanie; Bresson, Thomas; Chao de la Barca, Juan M; Marill, Alexandre; de Saint Martin, Grégoire; Buisset, Adrien; Muller, Jeanne; Tessier, Lydie; Gadras, Cédric; Verny, Christophe; Amati-Bonneau, Patrizia; Lenaers, Guy; Gohier, Philippe; Bonneau, Dominique; Simard, Gilles; Milea, Dan; Procaccio, Vincent; Reynier, Pascal

2018-02-01

To determine the plasma metabolomic signature of the exfoliative syndrome (XFS), the most common cause worldwide of secondary open-angle glaucoma. We performed a targeted metabolomic study, using the standardized p180 Biocrates Absolute IDQ p180 kit with a QTRAP 5500 mass spectrometer, to compare the metabolomic profiles of plasma from individuals with XFS (n = 16), and an age- and sex-matched control group with cataract (n = 18). A total of 151 metabolites were detected correctly, 16 of which allowed for construction of an OPLS-DA model with a good predictive capability (Q2cum = 0.51) associated with a low risk of over-fitting (permQ2 = -0.48, CV-ANOVA P-value <0.001). The metabolites contributing the most to the signature were octanoyl-carnitine (C8) and decanoyl-carnitine (C10), the branched-chain amino acids (i.e., isoleucine, leucine, and valine), and tyrosine, all of which were at higher concentrations in the XFS group, whereas spermine and spermidine, together with their precursor acetyl-ornithine, were at lower concentrations than in the control group. We identified a significant metabolomic signature in the plasma of individuals with XFS. Paradoxically, this signature, characterized by lower concentrations of the neuroprotective spermine and spermidine polyamines than in controls, partially overlaps the plasma metabolomic profile associated with insulin resistance, despite the absence of evidence of insulin resistance in XFS.

Insights into the Saliva of the Brown Marmorated Stink Bug Halyomorpha halys (Hemiptera: Pentatomidae)

PubMed Central

Peiffer, Michelle; Felton, Gary W.

2014-01-01

We examined the salivary gland structure of the brown marmorated stink bug (Pentatomidae: Halyomorpha halys) and developed methods for independent collection of watery saliva and sheath saliva. This stink bug has become a serious invasive pest of agriculture in the United States and its saliva is largely responsible for the damage it causes. We determined by protein gel analysis and shotgun proteomics that the suite of proteins comprising the sheath and watery saliva are very distinct. Our results indicate that a substantial amount of sheath proteins are derived from tomato when stink bugs feed on tomato fruit. Consequently, the sheath saliva is comprised of both insect and plant-derived proteins. Both sheath and watery saliva possessed amylase activities, but polyphenol oxidase and glucose oxidase activities were not detected in either saliva. Peroxidase activity was only detected in salivary sheaths, but only when stink bugs fed on tomato. Proteomic analysis indicated that the peroxidase was likely of plant origin. We also determined that sheath saliva, but not watery saliva elicited the jasmonate inducible defense gene proteinase inhibitor 2 (Pin2), but this induction was only observed when sheaths had been collected from tomato. This indicates that the eliciting factor of the saliva is likely of plant origin. Lastly, neither watery or sheath saliva affected the expression of the salicylate inducible gene pathogenesis related gene (Pr1a-P4). PMID:24586332

Varicella Zoster Virus in Saliva of Patients With Herpes Zoster

NASA Technical Reports Server (NTRS)

Mehta, Satish K.; Tyring, Stephen K.; Gilden, Donald H.; Cohrs, Randall J.; Leal, Melanie J.; Castro, Victoria A.; Feiveson, Alan H.; Ott, C. Mark; Pierson, Duane L.

2007-01-01

Background. VZV DNA is present in saliva of healthy astronauts and patients with Ramsay Hunt syndrome (geniculate zoster). We hypothesized that a prospective analysis of patients with zoster would detect VZV in saliva independent of zoster location. Methods. We treated 54 patients with valacyclovir. On the first treatment day, 7- and 14-days later, pain was scored and saliva examined for VZV DNA. Saliva from six subjects with chronic pain and 14 healthy subjects was similarly studied. Results. Follow-up data was available for 50/54 patients. Pain decreased in 43/50 (86 percent), disappeared in 37 (74 percent), recurred after disappearing in three (6 percent) and increased in four (8 percent). VZV DNA was found in every patient the day treatment was started, decreased in 47/50 (94 percent), transiently increased in three (6 percent) before decreasing, increased in two (4 percent) and disappeared in 41 (82 percent). There was a positive correlation between the presence of VZV DNA and pain, as well as between the VZV DNA copy number and pain (P<0.0005). Saliva of two patients was cultured, and infectious VZV was isolated from one. VZV DNA was present in one patient before rash and in four patients after pain resolved, and not in any control subjects. Conclusion. VZV DNA is present in saliva of zoster patients.

Fish mucus metabolome reveals fish life-history traits

NASA Astrophysics Data System (ADS)

Reverter, M.; Sasal, P.; Banaigs, B.; Lecchini, D.; Lecellier, G.; Tapissier-Bontemps, N.

2017-06-01

Fish mucus has important biological and ecological roles such as defense against fish pathogens and chemical mediation among several species. A non-targeted liquid chromatography-mass spectrometry metabolomic approach was developed to study gill mucus of eight butterflyfish species in Moorea (French Polynesia), and the influence of several fish traits (geographic site and reef habitat, species taxonomy, phylogeny, diet and parasitism levels) on the metabolic variability was investigated. A biphasic extraction yielding two fractions (polar and apolar) was used. Fish diet (obligate corallivorous, facultative corallivorous or omnivorous) arose as the main driver of the metabolic differences in the gill mucus in both fractions, accounting for 23% of the observed metabolic variability in the apolar fraction and 13% in the polar fraction. A partial least squares discriminant analysis allowed us to identify the metabolites (variable important in projection, VIP) driving the differences between fish with different diets (obligate corallivores, facultative corallivores and omnivorous). Using accurate mass data and fragmentation data, we identified some of these VIP as glycerophosphocholines, ceramides and fatty acids. Level of monogenean gill parasites was the second most important factor shaping the gill mucus metabolome, and it explained 10% of the metabolic variability in the polar fraction and 5% in the apolar fraction. A multiple regression tree revealed that the metabolic variability due to parasitism in the polar fraction was mainly due to differences between non-parasitized and parasitized fish. Phylogeny and butterflyfish species were factors contributing significantly to the metabolic variability of the apolar fraction (10 and 3%, respectively) but had a less pronounced effect in the polar fraction. Finally, geographic site and reef habitat of butterflyfish species did not influence the gill mucus metabolome of butterflyfishes.

Composition of betel specific chemicals in saliva during betel chewing for the identification of biomarkers

PubMed Central

Franke, Adrian A.; Mendez, Ana Joy; Lai, Jennifer F.; Arat-Cabading, Celine; Li, Xingnan; Custer, Laurie J.

2015-01-01

Betel nut chewing causes cancer in humans including strong associations with head and neck cancer in Guam. In the search for biomarkers of betel chewing we sought to identify chemicals specific for the 3 most commonly consumed betel preparations in Guam: nut (‘BN’), nut + Piper betle leaf (‘BL’), and betel quid (‘BQ’) consisting of nut+lime+tobacco+Piper betle leaf. Chemicals were extracted from the chewing material and saliva of subjects chewing these betel preparations. Saliva analysis involved protein precipitation with acetonitrile, dilution with formic acid followed by LCMS analysis. Baseline and chewing saliva levels were compared using t-tests and differences between groups were compared by ANOVA; p<0.05 indicated significance. Predominant compounds in chewing material were guvacine, arecoline, guvacoline, arecaidine, chavibetol, and nicotine. In chewing saliva we found significant increases from baseline for guvacine (BN, BQ), arecoline (all groups), guvacoline (BN), arecaidine (all groups), nicotine (BQ), and chavibetol (BL, BQ) and significant differences between all groups for total areca- specific alkaloids, total tobacco-specific alkaloids and chavibetol. From this pilot study, we propose the following chemical patterns as biomarkers: areca alkaloids for BN use, areca alkaloids and chavibetol for BL use, and areca alkaloids plus chavibetol and tobacco-specific alkaloids for BQ use. PMID:25797484

Aedes mosquito saliva modulates Rift Valley fever virus pathogenicity.

PubMed

Le Coupanec, Alain; Babin, Divya; Fiette, Laurence; Jouvion, Grégory; Ave, Patrick; Misse, Dorothee; Bouloy, Michèle; Choumet, Valerie

2013-01-01

Rift Valley fever (RVF) is a severe mosquito-borne disease affecting humans and domestic ruminants. Mosquito saliva contains compounds that counteract the hemostatic, inflammatory, and immune responses of the host. Modulation of these defensive responses may facilitate virus infection. Indeed, Aedes mosquito saliva played a crucial role in the vector's capacity to effectively transfer arboviruses such as the Cache Valley and West Nile viruses. The role of mosquito saliva in the transmission of Rift Valley fever virus (RVFV) has not been investigated. Using a murine model, we explored the potential for mosquitoes to impact the course of RVF disease by determining whether differences in pathogenesis occurred in the presence or absence of mosquito saliva and salivary gland extract. C57BL/6NRJ male mice were infected with the ZH548 strain of RVFV via intraperitoneal or intradermal route, or via bites from RVFV-exposed mosquitoes. The virus titers in mosquitoes and mouse organs were determined by plaque assays. After intraperitoneal injection, RVFV infection primarily resulted in liver damage. In contrast, RVFV infection via intradermal injection caused both liver and neurological symptoms and this route best mimicked the natural infection by mosquitoes. Co-injections of RVFV with salivary gland extract or saliva via intradermal route increased the mortality rates of mice, as well as the virus titers measured in several organs and in the blood. Furthermore, the blood cell counts of infected mice were altered compared to those of uninfected mice. Different routes of infection determine the pattern in which the virus spreads and the organs it targets. Aedes saliva significantly increases the pathogenicity of RVFV.

The Development of Metabolomic Sampling Procedures for Pichia pastoris, and Baseline Metabolome Data

PubMed Central

Tredwell, Gregory D.; Edwards-Jones, Bryn; Leak, David J.; Bundy, Jacob G.

2011-01-01

Metabolic profiling is increasingly being used to investigate a diverse range of biological questions. Due to the rapid turnover of intracellular metabolites it is important to have reliable, reproducible techniques for sampling and sample treatment. Through the use of non-targeted analytical techniques such as NMR and GC-MS we have performed a comprehensive quantitative investigation of sampling techniques for Pichia pastoris. It was clear that quenching metabolism using solutions based on the standard cold methanol protocol caused some metabolite losses from P. pastoris cells. However, these were at a low level, with the NMR results indicating metabolite increases in the quenching solution below 5% of their intracellular level for 75% of metabolites identified; while the GC-MS results suggest a slightly higher level with increases below 15% of their intracellular values. There were subtle differences between the four quenching solutions investigated but broadly, they all gave similar results. Total culture extraction of cells + broth using high cell density cultures typical of P. pastoris fermentations, was an efficient sampling technique for NMR analysis and provided a gold standard of intracellular metabolite levels; however, salts in the media affected the GC-MS analysis. Furthermore, there was no benefit in including an additional washing step in the quenching process, as the results were essentially identical to those obtained just by a single centrifugation step. We have identified the major high-concentration metabolites found in both the extra- and intracellular locations of P. pastoris cultures by NMR spectroscopy and GC-MS. This has provided us with a baseline metabolome for P. pastoris for future studies. The P. pastoris metabolome is significantly different from that of Saccharomyces cerevisiae, with the most notable difference being the production of high concentrations of arabitol by P. pastoris. PMID:21283710

Prevalence of Methicillin-Resistant and Methicillin-Susceptible S. Aureusin the Saliva of Health Professionals

PubMed Central

de Carvalho, Milton Jorge; Pimenta, Fabiana Cristina; Hayashida, Miyeko; Gir, Elucir; da Silva, Adriana Maria; Barbosa, Caio Parente; da Silva Canini, Silvia Rita Marin; Santiago, Silvana

2009-01-01

INTRODUCTION: S. aureus is one of the main agents of nosocomial infection and is sometimes difficult to treat with currently available active antimicrobials. PURPOSE: To analyze the prevalence of methicillin-susceptible S.aureus (MSSA) and methicillin-resistant S. aureus (MRSA) as well as the MRSA antimicrobial susceptibility profile isolated in the saliva of health professionals at a large public education hospital. MATERIALS AND METHODS: The project was approved by the research and ethics committee of the institution under study. Three samples of saliva from 340 health professionals were collected. The saliva analysis used to identify S. aureus was based on mannitol fermentation tests, catalase production, coagulase, DNAse, and lecithinase. In order to detect MRSA, samples were submitted to the disk diffusion test and the oxacillin agar screening test. In order to identify the minimum inhibitory concentration, the Etest® technique was used. RESULTS: The prevalence of MSSA was 43.5% (148/340), and MRSA was 4.1% (14/340). MRSA detected by the diffusion disk test, was 100% resistant to penicillin and oxacillin, 92.9% resistant to erythromycin, 57.1% resistant to clindamycin, 42.9% resistant to ciprofloxacin and 57.1% resistant to cefoxetin. CONCLUSION: This subject is important for both the education of health professionals and for preventative measures. Standard and contact-precautions should be employed in professional practice. PMID:19488585

Breastmilk-Saliva Interactions Boost Innate Immunity by Regulating the Oral Microbiome in Early Infancy

PubMed Central

Al-Shehri, Saad S.; Knox, Christine L.; Liley, Helen G.; Cowley, David M.; Wright, John R.; Henman, Michael G.; Hewavitharana, Amitha K.; Charles, Bruce G.; Shaw, Paul N.; Sweeney, Emma L.; Duley, John A.

2015-01-01

Introduction Xanthine oxidase (XO) is distributed in mammals largely in the liver and small intestine, but also is highly active in milk where it generates hydrogen peroxide (H2O2). Adult human saliva is low in hypoxanthine and xanthine, the substrates of XO, and high in the lactoperoxidase substrate thiocyanate, but saliva of neonates has not been examined. Results Median concentrations of hypoxanthine and xanthine in neonatal saliva (27 and 19 μM respectively) were ten-fold higher than in adult saliva (2.1 and 1.7 μM). Fresh breastmilk contained 27.3±12.2 μM H2O2 but mixing baby saliva with breastmilk additionally generated >40 μM H2O2, sufficient to inhibit growth of the opportunistic pathogens Staphylococcus aureus and Salmonella spp. Oral peroxidase activity in neonatal saliva was variable but low (median 7 U/L, range 2–449) compared to adults (620 U/L, 48–1348), while peroxidase substrate thiocyanate in neonatal saliva was surprisingly high. Baby but not adult saliva also contained nucleosides and nucleobases that encouraged growth of the commensal bacteria Lactobacillus, but inhibited opportunistic pathogens; these nucleosides/bases may also promote growth of immature gut cells. Transition from neonatal to adult saliva pattern occurred during the weaning period. A survey of saliva from domesticated mammals revealed wide variation in nucleoside/base patterns. Discussion and Conclusion During breast-feeding, baby saliva reacts with breastmilk to produce reactive oxygen species, while simultaneously providing growth-promoting nucleotide precursors. Milk thus plays more than a simply nutritional role in mammals, interacting with infant saliva to produce a potent combination of stimulatory and inhibitory metabolites that regulate early oral–and hence gut–microbiota. Consequently, milk-saliva mixing appears to represent unique biochemical synergism which boosts early innate immunity. PMID:26325665

Short communication: Ability of dogs to detect cows in estrus from sniffing saliva samples.

PubMed

Fischer-Tenhagen, C; Tenhagen, B-A; Heuwieser, W

2013-02-01

Efficient estrus detection in high-producing dairy cows is a permanent challenge for successful reproductive performance. In former studies, dogs have been trained to identify estrus-specific odor in vaginal fluid, milk, urine, and blood samples under laboratory conditions with an accuracy of more than 80%. For on-farm utilization of estrus-detection dogs it would be beneficial in terms of hygiene and safety if dogs could identify cows from the feed alley. The objective of this proof of concept study was to test if dogs can be trained to detect estrus-specific scent in saliva of cows. Saliva samples were collected from cows in estrus and diestrus. Thirteen dogs of various breeds and both sexes were trained in this study. Five dogs had no experience in scent detection, whereas 8 dogs had been formerly trained for detection of narcotics or cancer. In the training and test situation, dogs had to detect 1 positive out of 4 samples. Dog training was based on positive reinforcement and dogs were rewarded with a clicker and food for indicating saliva samples of cows in estrus. A false indication was ignored and documented in the test situation. Dogs with and without prior training were trained for 1 and 5 d, respectively. For determining the accuracy of detection, the position of the positive sample was unknown to the dog handler, to avoid hidden cues to the dog. The overall percentage of correct positive indications was 57.6% (175/304), with a range from 40 (1 dog) to 75% (3 dogs). To our knowledge, this is the first indication that dogs are able to detect estrus-specific scent in saliva of cows. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Autologous saliva transfusion: treatment for HIV?

PubMed

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.

Immunomodulatory Effects of Amblyomma variegatum Saliva on Bovine Cells: Characterization of Cellular Responses and Identification of Molecular Determinants

PubMed Central

Rodrigues, Valérie; Fernandez, Bernard; Vercoutere, Arthur; Chamayou, Léo; Andersen, Alexandre; Vigy, Oana; Demettre, Edith; Seveno, Martial; Aprelon, Rosalie; Giraud-Girard, Ken; Stachurski, Frédéric; Loire, Etienne; Vachiéry, Nathalie; Holzmuller, Philippe

2018-01-01

The tropical bont tick, Amblyomma variegatum, is a tick species of veterinary importance and is considered as one of major pest of ruminants in Africa and in the Caribbean. It causes direct skin lesions, transmits heartwater, and reactivates bovine dermatophilosis. Tick saliva is reported to affect overall host responses through immunomodulatory and anti-inflammatory molecules, among other bioactive molecules. The general objective of this study was to better understand the role of saliva in interaction between the Amblyomma tick and the host using cellular biology approaches and proteomics, and to discuss its impact on disease transmission and/or activation. We first focused on the immuno-modulating effects of semi-fed A. variegatum female saliva on bovine peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages in vitro. We analyzed its immuno-suppressive properties by measuring the effect of saliva on PBMC proliferation, and observed a significant decrease in ConA-stimulated PBMC lymphoproliferation. We then studied the effect of saliva on bovine macrophages using flow cytometry to analyze the expression of MHC-II and co-stimulation molecules (CD40, CD80, and CD86) and by measuring the production of nitric oxide (NO) and pro- or anti-inflammatory cytokines. We observed a significant decrease in the expression of MHC-II, CD40, and CD80 molecules, associated with decreased levels of IL-12-p40 and TNF-α and increased level of IL-10, which could explain the saliva-induced modulation of NO. To elucidate these immunomodulatory effects, crude saliva proteins were analyzed using proteomics with an Orbitrap Elite mass spectrometer. Among the 336 proteins identified in A. variegatum saliva, we evidenced bioactive molecules exhibiting anti-inflammatory, immuno-modulatory, and anti-oxidant properties (e.g., serpins, phospholipases A2, heme lipoprotein). We also characterized an intriguing ubiquitination complex that could be involved in saliva

Probing viscosity of nanoliter droplets of butterfly saliva by magnetic rotational spectroscopy

NASA Astrophysics Data System (ADS)

Tokarev, Alexander; Kaufman, Bethany; Gu, Yu; Andrukh, Taras; Adler, Peter H.; Kornev, Konstantin G.

2013-01-01

Magnetic rotational spectroscopy was employed for rheological analysis of nanoliter droplets of butterfly saliva. Saliva viscosity of butterflies is 4-5 times greater than that of water and similar to that of 30%-40% sucrose solutions at 25 °C. Hence, viscosity stratification would not be expected when butterflies feed on nectar with 30%-40% sugar concentrations. We did not observe any viscoelastic effects or non-Newtonian behavior of saliva droplets. Thus, butterfly saliva is significantly different rheologically from that of humans, which demonstrates a viscoelastic behavior.

High-Resolution Metabolomics: Review of the Field and Implications for Nursing Science and the Study of Preterm Birth.

PubMed

Li, Shuzhao; Dunlop, Anne L; Jones, Dean P; Corwin, Elizabeth J

2016-01-01

Most complex health conditions do not have a single etiology but rather develop from exposure to multiple risk factors that interact to influence individual susceptibility. In this review, we discuss the emerging field of metabolomics as a means by which metabolic pathways underlying a disease etiology can be exposed and specific metabolites can be identified and linked, ultimately providing biomarkers for early detection of disease onset and new strategies for intervention. We present the theoretical foundation of metabolomics research, the current methods employed in its conduct, and the overlap of metabolomics research with other "omic" approaches. As an exemplar, we discuss the potential of metabolomics research in the context of deciphering the complex interactions of the maternal-fetal exposures that underlie the risk of preterm birth, a condition that accounts for substantial portions of infant morbidity and mortality and whose etiology and pathophysiology remain incompletely defined. We conclude by providing strategies for including metabolomics research in future nursing studies for the advancement of nursing science. © The Author(s) 2015.

Time is ripe: maturation of metabolomics in chronobiology.

PubMed

Rhoades, Seth D; Sengupta, Arjun; Weljie, Aalim M

2017-02-01

Sleep and circadian rhythms studies have recently benefited from metabolomics analyses, uncovering new connections between chronobiology and metabolism. From untargeted mass spectrometry to quantitative nuclear magnetic resonance spectroscopy, a diversity of analytical approaches has been applied for biomarker discovery in the field. In this review we consider advances in the application of metabolomics technologies which have uncovered significant effects of sleep and circadian cycles on several metabolites, namely phosphatidylcholine species, medium-chain carnitines, and aromatic amino acids. Study design and data processing measures essential for detecting rhythmicity in metabolomics data are also discussed. Future developments in these technologies are anticipated vis-à-vis validating early findings, given metabolomics has only recently entered the ring with other systems biology assessments in chronometabolism studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

MVAPACK: A Complete Data Handling Package for NMR Metabolomics

PubMed Central

2015-01-01

Data handling in the field of NMR metabolomics has historically been reliant on either in-house mathematical routines or long chains of expensive commercial software. Thus, while the relatively simple biochemical protocols of metabolomics maintain a low barrier to entry, new practitioners of metabolomics experiments are forced to either purchase expensive software packages or craft their own data handling solutions from scratch. This inevitably complicates the standardization and communication of data handling protocols in the field. We report a newly developed open-source platform for complete NMR metabolomics data handling, MVAPACK, and describe its application on an example metabolic fingerprinting data set. PMID:24576144

Discovery of urine biomarkers for bladder cancer via global metabolomics.

PubMed

Shi, Hangchuan; Li, Xiang; Zhang, Qingyang; Yang, Hongmei; Zhang, Xiaoping

2016-11-01

Bladder cancer (BC) is latent in its early stage and lethal in its late stage. Therefore, early diagnosis and intervention are essential for successful BC treatment. Considering the limitations of current diagnostic tools, noninvasive biomarkers that are both highly sensitive and specific are needed to improve the overall survival and quality of life of patients. With the advent of systems biology, "-omics" technologies have been developed over the past few decades. As a promising member, global metabolomics has increasingly been found to have clear potential for biomarker discovery. However, urinary metabolomics studies related to BC have lagged behind those of other urinary cancers, and major findings have not been systematically reported. The objective of this review is to comprehensively list the currently identified potential urinary metabolite biomarkers for BC.

Rechargeable anticandidal denture material with sustained release in saliva.

PubMed

Malakhov, A; Wen, J; Zhang, B-X; Wang, H; Geng, H; Chen, X-D; Sun, Y; Yeh, C-K

2016-07-01

Candida-induced denture stomatitis is a common debilitating problem among denture wearers. Previously, we described the fabrication of a new denture material that released antifungal drugs when immersed in phosphate buffered saline. Here, we use more clinically relevant immersion conditions (human saliva; 37°C) and measure miconazole release and bioactivity. Disks were prepared by grafting PNVP [poly(N-vinyl-2-pyrrolidinone)] onto PMMA [poly(methylmethacrylate)] using plasma initiation (PMMA-g-PNVP) and then loaded with miconazole. Drug-loaded disks were immersed in 10-100% human saliva (1-30 days). Miconazole release was measured and then tested for bioactivity vs miconazole-sensitive and miconazole-resistant Candida isolates. HPLC was used to quantify miconazole levels in saliva. Miconazole-loaded disks released antifungal drug for up to 30 days. Higher drug release was found with higher concentrations of saliva, and, interestingly, miconazole solubility was increased with higher saliva concentrations. The released miconazole retained its anticandidal activity. After immersion, the residual miconazole could be quenched and the disks recharged. Freshly recharged disks displayed the same release kinetics and bioactivity as the original disks. Quenched disks could also be charged with chlorhexidine that displayed anticandidal activity. These results suggest that PMMA-g-PNVP is a promising new denture material for long-term management of denture stomatitis. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Rechargeable anticandidal denture material with sustained release in saliva

PubMed Central

Malakhov, Andrey; Wen, Jianchuan; Zhang, Bin-Xian; Wang, Hanzhou; Geng, Hui; Chen, Xiao-Dong; Sun, Yuyu; Yeh, Chih-Ko

2016-01-01

Objective Candida-induced denture stomatitis is a common debilitating problem among denture wearers. Previously, we described the fabrication of a new denture material that released antifungal drugs when immersed in phosphate buffered saline. Here, we use more clinically relevant immersion conditions (human saliva; 37°C) and measure miconazole release and bioactivity. Materials and Methods Disks were prepared by grafting PNVP [poly(N-vinyl-2-pyrrolidinone)] onto PMMA [poly(methylmethacrylate)] using plasma initiation (PMMA-g-PNVP) and then loaded with miconazole. Drug-loaded disks were immersed in 10–100% human saliva (1–30 days). Miconazole release was measured and then tested for bioactivity versus miconazole-sensitive and -resistant Candida isolates. Results HPLC was used to quantify miconazole levels in saliva. Miconazole-loaded disks released antifungal drug for up to 30 days. Higher drug release was found with higher concentrations of saliva and, interestingly, miconazole solubility was increased with higher saliva concentrations. The released miconazole retained its anticandidal activity. After immersion, the residual miconazole could be quenched and the disks recharged. Freshly recharged disks displayed the same release kinetics and bioactivity as the original disks. Quenched disks could also be charged with chlorhexidine that displayed anticandidal activity. Conclusions These results suggest that PMMA-g-PNVP is a promising new denture material for long-term management of denture stomatitis. PMID:26855200

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites.

PubMed

Covington, Brett C; McLean, John A; Bachmann, Brian O

2017-01-04

Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.

Comparison of subacute effects of two types of pyrethroid insecticides using metabolomics methods.

PubMed

Miao, Jiyan; Wang, Dezhen; Yan, Jin; Wang, Yao; Teng, Miaomiao; Zhou, Zhiqiang; Zhu, Wentao

2017-11-01

In this study, 1 H NMR based metabolomics analysis, LC-MS/MS based serum metabolomics and histopathology techniques were used to investigate the toxic effects of subacute exposure to two types of pyrethroid insecticides bifenthrin and lambda-cyhalothrin in mice. Metabolomic analysis of tissues extracts and serum showed that these two types of pyrethroid insecticides resulted in alterations of metabolites in the liver, kidney and serum of mice. Based on the altered metabolites, several significant pathways were identified, which are associated with gut microbial metabolism, lipid metabolism, nucleotide catabolism, tyrosine metabolism and energy metabolism. The results showed that bifenthrin and lambda-cyhalothrin have similarities in disruption of metabolic pathways in kidney, indicating that the toxicological mechanisms of these two types of insecticides have some likeness to each other. This study may provide novel insight into revealing differences of toxicological mechanisms between these two types of pyrethroid insecticides. Copyright © 2017 Elsevier Inc. All rights reserved.

Serial Metabolome Changes in a Prospective Cohort of Subjects with Influenza Viral Infection and Comparison with Dengue Fever.

PubMed

Cui, Liang; Fang, Jinling; Ooi, Eng Eong; Lee, Yie Hou

2017-07-07

Influenza virus infection (IVI) and dengue virus infection (DVI) are major public health threats. Between IVI and DVI, clinical symptoms can be overlapping yet infection-specific, but host metabolome changes are not well-described. Untargeted metabolomics and targeted oxylipinomic analyses were performed on sera serially collected at three phases of infection from a prospective cohort study of adult subjects with either H3N2 influenza infection or dengue fever. Untargeted metabolomics identified 26 differential metabolites, and major perturbed pathways included purine metabolism, fatty acid biosynthesis and β-oxidation, tryptophan metabolism, phospholipid catabolism, and steroid hormone pathway. Alterations in eight oxylipins were associated with the early symptomatic phase of H3N2 flu infection, were mostly arachidonic acid-derived, and were enriched in the lipoxygenase pathway. There was significant overlap in metabolome profiles in both infections. However, differences specific to IVI and DVI were observed. DVI specifically attenuated metabolites including serotonin, bile acids and biliverdin. Additionally, metabolome changes were more persistent in IVI in which metabolites such as hypoxanthine, inosine, and xanthine of the purine metabolism pathway remained significantly elevated at 21-27 days after fever onset. This study revealed the dynamic metabolome changes in IVI subjects and provided biochemical insights on host physiological similarities and differences between IVI and DVI.

Pharmacokinetic Modeling of Intranasal Scopolamine in Plasma Saliva and Urine

NASA Technical Reports Server (NTRS)

Wu, L.; Tam, V. H.; Chow, D. S. L.; Putcha, L.

2015-01-01

An intranasal gel dosage formulation of scopolamine (INSCOP) was developed for the treatment of Space Motion Sickness (SMS). The bioavailability and pharmacokinetics (PK) were evaluated under IND (Investigational New Drug) guidelines. The aim of the project was to develop a PK model that can predict the relationships among plasma, saliva and urinary scopolamine concentrations using data collected from the IND clinical trial protocol with INSCOP. Twelve healthy human subjects were administered at three dose levels (0.1, 0.2 and 0.4 mg) of INSCOP. Serial blood, saliva and urine samples were collected between 5 min to 24 h after dosing and scopolamine concentrations were measured by using a validated LC-MS-MS assay. PK compartmental models, using actual dosing and sampling time, were established using Phoenix (version 1.2). Model selection was based on a likelihood ratio test on the difference of criteria (-2LL (i.e. log-likelihood ratio test)) and comparison of the quality of fit plots. The results: Predictable correlations among scopolamine concentrations in compartments of plasma, saliva and urine were established, and for the first time the model satisfactorily predicted the population and individual PK of INSCOP in plasma, saliva and urine. The model can be utilized to predict the INSCOP plasma concentration by saliva and urine data, and it will be useful for monitoring the PK of scopolamine in space and other remote environments using non-invasive sampling of saliva and/or urine.

The effects of age and dietary restriction on the tissue-specific metabolome of Drosophila.

PubMed

Laye, Matthew J; Tran, ViLinh; Jones, Dean P; Kapahi, Pankaj; Promislow, Daniel E L

2015-10-01

Dietary restriction (DR) is a robust intervention that extends lifespan and slows the onset of age-related diseases in diverse organisms. While significant progress has been made in attempts to uncover the genetic mechanisms of DR, there are few studies on the effects of DR on the metabolome. In recent years, metabolomic profiling has emerged as a powerful technology to understand the molecular causes and consequences of natural aging and disease-associated phenotypes. Here, we use high-resolution mass spectroscopy and novel computational approaches to examine changes in the metabolome from the head, thorax, abdomen, and whole body at multiple ages in Drosophila fed either a nutrient-rich ad libitum (AL) or nutrient-restricted (DR) diet. Multivariate analysis clearly separates the metabolome by diet in different tissues and different ages. DR significantly altered the metabolome and, in particular, slowed age-related changes in the metabolome. Interestingly, we observed interacting metabolites whose correlation coefficients, but not mean levels, differed significantly between AL and DR. The number and magnitude of positively correlated metabolites was greater under a DR diet. Furthermore, there was a decrease in positive metabolite correlations as flies aged on an AL diet. Conversely, DR enhanced these correlations with age. Metabolic set enrichment analysis identified several known (e.g., amino acid and NAD metabolism) and novel metabolic pathways that may affect how DR effects aging. Our results suggest that network structure of metabolites is altered upon DR and may play an important role in preventing the decline of homeostasis with age. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Fluoride concentration in saliva after use of oral hygiene products.

PubMed

Campus, Guglielmo; Lallai, Maria Rosario; Carboni, Roberto

2003-01-01

The purpose of this in vivo, single-blind, randomized study was to compare fluoride concentrations in saliva of patients treated with oral hygiene products containing different fluoride salts. The study involved 104 students attending the University of Sassari. Participants were subdivided: group A used a sodium monofluorophosphate (NaMFP) toothpaste; groups B and C used an amine fluoride (AmF) toothpaste; group D used a toothpaste and a mouthwash both based on AmF, and group E used a toothpaste and a varnish both on an NaMFP base. Samples of unstimulated saliva were collected at baseline (t(0)), at the end of the 20 days' treatment phase (t(1)) and after 24 h, during which the volunteers refrained from any oral hygiene measure (t(2)). Saliva fluoride concentrations were measured using an ion-specific electrode. All measurements were made in triplicate and analysed statistically using ANOVA. In saliva, the mean fluoride concentration increased significantly in each treatment group. In conclusion, the fluoride concentration in saliva can be maintained to an optimal therapeutic level with the regular use of fluoridated products. Copyright 2003 S. Karger AG, Basel

Cortisol in saliva and plasma of cattle after ACTH administration and milking.

PubMed

Negrão, J A; Porcionato, M A; de Passillé, A M; Rushen, J

2004-06-01

Interest in the measurement of salivary cortisol has increased recently because saliva can be easily collected before and after an imposed stress. This study evaluated the relationship between plasma and salivary concentrations of cortisol following ACTH administration in calves (experiment 1) and machine milking of adult cows (experiment 2). A catheter was inserted into the jugular vein of all animals 72 h before the beginning of experiments. Blood and saliva samples were collected before and after ACTH administration (0.6 IU/kg BW) in calves or before and after machine milking of cows. Using a cotton swab, each saliva sample was taken immediately following the blood sample. In general, cortisol profiles were similar in plasma and saliva and correlated in both experiments; however, plasma concentrations were significantly higher than salivary concentrations. In addition, the differences between cortisol concentrations measured in saliva and plasma within each experiment varied substantially between animals and samples. Furthermore, in experiment 2, nearly 10% of salivary samples were below limits of detection. The sharp peaks in cortisol after ACTH administration in both the plasma and saliva were reflected adrenal stimulation. In addition, increases in cortisol in response to milking in both the plasma and saliva suggest that salivary sampling is a reliable option when studying cortisol responses to normal physiological events.

Saliva as a non-invasive diagnostic tool for inflammation and insulin-resistance

PubMed Central

Desai, Gauri S; Mathews, Suresh T

2014-01-01

Saliva has been progressively studied as a non-invasive and relatively stress-free diagnostic alternative to blood. Currently, saliva testing is used for clinical assessment of hormonal perturbations, detection of HIV antibodies, DNA analysis, alcohol screening, and drug testing. Recently, there has been increasing interest in evaluating the diagnostic potential of saliva in obesity, inflammation, and insulin-resistance. Current literature has demonstrated elevated levels of inflammatory biomarkers including C-reactive protein, tumor necrosis factor-α, interleukin-6, and interferon-γ in saliva of obese/overweight children and adults. Salivary antioxidant status has also been studied as a measure of oxidative stress in individuals with type 2 diabetes. Further, several studies have demonstrated correlations of salivary markers of stress and insulin resistance including cortisol, insulin, adiponectin, and resistin with serum concentrations. These findings suggest the potential diagnostic value of saliva in health screening and risk stratification studies, particularly in the pediatric population, with implications for inflammatory, metabolic and cardiovascular conditions. However, additional studies are required to standardize saliva collection and storage procedures, validate analytical techniques for biomarker detection, and establish reference ranges for routine clinical use. The purpose of this review is to summarize and evaluate recent advancements in using saliva as a diagnostic tool for inflammation and insulin-resistance. PMID:25512775

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine

DOE PAGES

Piombino, Paola; Genovese, Alessandro; Esposito, Silvia; ...

2014-01-22

Background: Recent evidence suggests that a lower extent of the retronasal aroma release correspond to a higher amount of ad libitum food intake. This has been regarded as one of the bases of behavioral choices towards food consumption in obese people. Here in this pilot study we investigated the hypothesis that saliva from obese individuals could be responsible for an alteration of the retro-nasal aroma release. We tested this hypothesis in vitro, by comparing the release of volatiles from a liquid food matrix (wine) after its interaction with saliva from 28 obese (O) and 28 normal-weight (N) individuals. Methods andmore » Findings: Amplicon sequencing of the 16S rRNA V4 region indicated that Firmicutes and Actinobacteria were more abundant in O, while Proteobacteria and Fusobacteria dominated in N. Streptococcaceae were significantly more abundant in the O subjects and constituted 34% and 19% on average of the saliva microbiota of O and N subjects, respectively. The Total Antioxidant Capacity was higher in O vs N saliva samples. A model mouth system was used to test whether the in-mouth wine aroma release differs after the interaction with O or N saliva. In O samples, a 18% to 60% significant decrease in the mean concentration of wine volatiles was detected as a result of interaction with saliva, compared with N. This suppression was linked to biochemical differences in O and N saliva composition, which include protein content. Conclusion: Microbiological and biochemical differences were found in O vs N saliva samples. An impaired retronasal aroma release from white wine was detected in vitro and linked to compositional differences between saliva from obese and normal-weight subjects. Additional in vivo investigations on diverse food matrices could contribute to understanding whether a lower olfactory stimulation due to saliva composition can be a co-factor in the development/maintenance of obesity.« less

NMR metabolomics of thrips (Frankliniella occidentalis) resistance in Senecio hybrids.

PubMed

Leiss, Kirsten A; Choi, Young H; Abdel-Farid, Ibrahim B; Verpoorte, Robert; Klinkhamer, Peter G L

2009-02-01

Western flower thrips (Frankliniella occidentalis) has become a key insect pest of agricultural and horticultural crops worldwide. Little is known about host plant resistance to thrips. In this study, we investigated thrips resistance in F (2) hybrids of Senecio jacobaea and Senecio aquaticus. We identified thrips-resistant hybrids applying three different bioassays. Subsequently, we compared the metabolomic profiles of these hybrids applying nuclear magnetic resonance spectroscopy (NMR). The new developments of NMR facilitate a wide range coverage of the metabolome. This makes NMR especially suitable if there is no a priori knowledge of the compounds related to herbivore resistance and allows a holistic approach analyzing different chemical compounds simultaneously. We show that the metabolomes of thrips-resistant and -susceptible hybrids differed considerably. Thrips-resistant hybrids contained higher amounts of the pyrrolizidine alkaloids (PA), jacobine, and jaconine, especially in younger leaves. Also, a flavanoid, kaempferol glucoside, accumulated in the resistant plants. Both PAs and kaempferol are known for their inhibitory effect on herbivores. In resistant and susceptible F (2) hybrids, young leaves showed less thrips damage than old leaves. Consistent with the optimal plant defense theory, young leaves contained increased levels of primary metabolites such as sucrose, raffinose, and stachyose, but also accumulated jacaranone as a secondary plant defense compound. Our results prove NMR as a promising tool to identify different metabolites involved in herbivore resistance. It constitutes a significant advance in the study of plant-insect relationships, providing key information on the implementation of herbivore resistance breeding strategies in plants.