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Sample records for acid biomarker analysis

  1. Strategies for comprehensive analysis of amino acid biomarkers of oxidative stress.

    PubMed

    Ptolemy, A S; Lee, R; Britz-McKibbin, P

    2007-07-01

    Despite the wide interest in using modified amino acids as putative biomarkers of oxidative stress, many issues remain as to their overall reliability for early detection and diagnosis of diseases. In contrast to conventional single biomarker studies, comprehensive analysis of biomarkers offers an unbiased strategy for global assessment of modified amino acid metabolism due to reactive oxygen and nitrogen species. This review examines recent analytical techniques amenable for analysis of modified amino acids in biological samples reported during 2003-2007. Particular attention is devoted to the need for validated methods applicable to high-throughput analysis of multiple amino acid biomarkers, as well as consideration of sample pretreatment protocols on artifact formation for improved clinical relevance.

  2. Development and evaluation of a microdevice for amino acid biomarker detection and analysis on Mars

    PubMed Central

    Skelley, Alison M.; Scherer, James R.; Aubrey, Andrew D.; Grover, William H.; Ivester, Robin H. C.; Ehrenfreund, Pascale; Grunthaner, Frank J.; Bada, Jeffrey L.; Mathies, Richard A.

    2005-01-01

    The Mars Organic Analyzer (MOA), a microfabricated capillary electrophoresis (CE) instrument for sensitive amino acid biomarker analysis, has been developed and evaluated. The microdevice consists of a four-wafer sandwich combining glass CE separation channels, microfabricated pneumatic membrane valves and pumps, and a nanoliter fluidic network. The portable MOA instrument integrates high voltage CE power supplies, pneumatic controls, and fluorescence detection optics necessary for field operation. The amino acid concentration sensitivities range from micromolar to 0.1 nM, corresponding to part-per-trillion sensitivity. The MOA was first used in the lab to analyze soil extracts from the Atacama Desert, Chile, detecting amino acids ranging from 10–600 parts per billion. Field tests of the MOA in the Panoche Valley, CA, successfully detected amino acids at 70 parts per trillion to 100 parts per billion in jarosite, a sulfate-rich mineral associated with liquid water that was recently detected on Mars. These results demonstrate the feasibility of using the MOA to perform sensitive in situ amino acid biomarker analysis on soil samples representative of a Mars-like environment. PMID:15657130

  3. Analysis of Potential Amino Acid Biomarkers in Brain Tissue and the Effect of Galangin on Cerebral Ischemia.

    PubMed

    Yang, Ruocong; Chen, Kun; Zhao, Yanyan; Tian, Pengpeng; Duan, Feipeng; Sun, Wenli; Liu, Yuxin; Yan, Zhiyong; Li, Shaojing

    2016-04-06

    Galangin, a potent scavenger of free radicals, has been used as an herbal medicine for various ailments for centuries in Asia. With complex pathophysiology, ischemic stroke is one of the most frequent causes of death and disability worldwide. We have reported that galangin provides direct protection against ischemic injury as a potential neuroprotective agent and has potential therapeutic effects on the changes of serum amino acids in ischemic stroke; however, the mechanism of the changes of amino acids in the ischemic brain tissue has not yet been clarified. In this paper, we explored brain tissue amino acid biomarkers in the acute phase of cerebral ischemia and the effect of galangin on those potential biomarkers. Finally, we identified that glutamic acid, alanine and aspartic acid showed significant changes (p < 0.05 or p < 0.01) in galangin-treated groups compared with vehicle-treated rats and the four enzymes associated with these three AAs' metabolic pathways; GLUD1, SLC16A10, SLC1A1 and GPT were identified by multiplex interactions with the three amino acids. By metabolite-protein network analysis and molecular docking, six of 28 proteins were identified and might become potential galangin biomarkers for acute ischemic stroke. The data in our study provides thoughts for exploring the mechanism of disease, discovering new targets for drug candidates and elucidating the related regulatory signal network.

  4. Immunochemical analysis of 3-phenoxybenzoic acid, a biomarker of forestry worker exposure to pyrethroid insecticides.

    PubMed

    Ahn, Ki Chang; Gee, Shirley J; Kim, Hee-Joo; Aronov, Pavel A; Vega, Helen; Krieger, Robert I; Hammock, Bruce D

    2011-09-01

    Pyrethroid insecticides widely used in forestry, agricultural, industrial, and residential applications have potential for human exposure. Short sample preparation time and sensitive, economical high-throughput assays are needed for biomonitoring studies that analyze a large number of samples. An enzyme-linked immunosorbent assay (ELISA) was used for determining 3-phenoxybenzoic acid (3-PBA), a general urinary biomarker of exposure to some pyrethroid insecticides. A mixed-mode solid-phase extraction reduced interferences from acid hydrolyzed urine and gave 110 ± 6% recoveries from spiked samples. The method limit of quantification was 2 μg/L. Urine samples were collected from forestry workers that harvest pine cone seeds where pyrethroid insecticides were applied at ten different orchards. At least four samples for each worker were collected in a 1-week period. The 3-PBA in workers classified as high, low, or no exposure based on job analysis over all sampling days was 6.40 ± 9.60 (n = 200), 5.27 ± 5.39 (n = 52), and 3.56 ± 2.64 ng/mL (n = 34), respectively. Pair-wise comparison of the differences in least squares means of 3-PBA concentrations among groups only showed a significant difference between high and no exposure. Although this difference was not significant when 3-PBA excretion was normalized by creatinine excretion, the general trend was still apparent. No significant differences were observed among days or orchards. This ELISA method using a 96-well plate was performed as a high-throughput tool for analyzing around 300 urine samples measured in triplicate to provide data for workers exposure assessment.

  5. Immunochemical analysis of 3-phenoxybenzoic acid, a biomarker of forestry worker exposure to pyrethroid insecticides

    PubMed Central

    Ahn, Ki Chang; Gee, Shirley J.; Kim, Hee-Joo; Aronov, Pavel A.; Vega, Helen; Krieger, Robert I.

    2013-01-01

    Pyrethroid insecticides widely used in forestry, agricultural, industrial, and residential applications have potential for human exposure. Short sample preparation time and sensitive, economical high-throughput assays are needed for biomonitoring studies that analyze a large number of samples. An enzyme-linked immunosorbent assay (ELISA) was used for determining 3-phenoxybenzoic acid (3-PBA), a general urinary biomarker of exposure to some pyrethroid insecticides. A mixed-mode solid-phase extraction reduced interferences from acid hydrolyzed urine and gave 110±6% recoveries from spiked samples. The method limit of quantification was 2 μg/L. Urine samples were collected from forestry workers that harvest pine cone seeds where pyrethroid insecticides were applied at ten different orchards. At least four samples for each worker were collected in a 1-week period. The 3-PBA in workers classified as high, low, or no exposure based on job analysis over all sampling days was 6.40± 9.60 (n=200), 5.27±5.39 (n=52), and 3.56±2.64 ng/mL (n=34), respectively. Pair-wise comparison of the differences in least squares means of 3-PBA concentrations among groups only showed a significant difference between high and no exposure. Although this difference was not significant when 3-PBA excretion was normalized by creatinine excretion, the general trend was still apparent. No significant differences were observed among days or orchards. This ELISA method using a 96-well plate was performed as a high-throughput tool for analyzing around 300 urine samples measured in triplicate to provide data for workers exposure assessment. PMID:21717113

  6. Analysis of serum metabolites for the discovery of amino acid biomarkers and the effect of galangin on cerebral ischemia.

    PubMed

    Gao, Jian; Yang, Hongjun; Chen, Jianxin; Fang, Jiansong; Chen, Chang; Liang, Rixin; Yang, Gengliang; Wu, Hongwei; Wu, Chuanhong; Li, Shaojing

    2013-09-01

    Ischemic stroke, a devastating disease with a complex pathophysiology, is a leading cause of death and disability worldwide. In our previous study, we reported that galangin provided direct protection against ischemic injury and acted as a potential neuroprotective agent. However, its associated neuroprotective mechanism has not yet been clarified. In this paper, we explored the potential AA biomarkers in the acute phase of cerebral ischemia and the effect of galangin on those potential biomarkers. In our study, 12 AAs were quantified in rat serum and found to be impaired by middle cerebral artery occlusion (MCAO)-induced focal cerebral ischemia. Using partial least squares discriminate analysis (PLS-DA), we identified the following amino acids as potential biomarkers of cerebral ischemia: glutamic acid (Glu), homocysteine (Hcy), methionine (Met), tryptophan (Trp), aspartic acid (Asp), alanine (Ala) and tyrosine (Tyr). Moreover, four amino acids (Hcy, Met, Glu and Trp) showed significant change in galangin-treated (100 and 50 mg kg(-1)) groups compared to vehicle groups. Furthermore, we identified three pathway-related enzymes tyrosine aminotransferase (TAT), glutamine synthetase (GLUL) and monocarboxylate transporter (SLC16A10) by multiplex interactions with Glu and Hcy, which have been previously reported to be closely related to cerebral ischemia. Through an analysis of the metabolite-protein network analysis, we identified 16 proteins that were associated with two amino acids by multiple interactions with three enzymes; five of them may become potential biomarkers of galangin for acute ischemic stroke as the result of molecule docking. Our results may help develop novel strategies to explore the mechanism of cerebral ischemia, discover potential targets for drug candidates and elucidate the related regulatory signal network.

  7. Characterizing estuarine plume discharge into the coastal ocean using fatty acid biomarkers and pigment analysis.

    PubMed

    Fischer, Andrew M; Ryan, John P; Levesque, Christian; Welschmeyer, Nicholas

    2014-08-01

    The transformation of estuaries by human activities continues to alter the biogeochemical balance of the coastal ocean. The disruption of this balance can negatively impact the provision of goods and services, including fisheries, commerce and transportation, recreation and esthetic enjoyment. Here we examine a link, between the Elkhorn Slough and the coastal ocean in Monterey Bay, California (USA) using a novel application of fatty acid and pigment analysis. Fatty acid analysis of filtered water samples showed biologically distinct water types between the Elkhorn Slough plume and the receiving waters of the coastal ocean. A remarkable feature of the biological content of the plume entering the coastal ocean was the abundance of bacteria-specific fatty acids, which correlated well with concentrations of colored dissolved organic matter (CDOM). Pigment analysis showed that plume waters contained higher concentrations of diatoms and cryptophytes, while the coastal ocean waters showed higher relative concentrations of dinoflagellates. Bacteria and cryptophytes can provide a source of labile, energy-rich organic matter that may be locally important as a source of food for pelagic and benthic communities. Surface and depth surveys of the plume show that the biogeochemical constituents of the slough waters are injected into the coastal waters and become entrained in the northward flowing, nearshore current of Monterey Bay. Transport of these materials to the northern portion of the bay can fuel a bloom incubator, which exists in this region. This study shows that fatty acid markers can reveal the biogeochemical interactions between estuaries and the coastal ocean and highlights how man-made changes have the potential to influence coastal ecological change.

  8. A SURVEY OF LIQUID CHROMATOGRAPHIC-MASS SPECTROMETRIC ANALYSIS OF MERCAPTURIC ACID BIOMARKERS IN OCCUPATIONAL AND ENVIRONMENTAL EXPOSURE MONITORING

    PubMed Central

    Mathias, Patricia I.; B’Hymer, Clayton

    2015-01-01

    High-performance liquid chromatography/mass spectrometry (HPLC/MS) is sensitive and specific for targeted quantitative analysis and is readily utilized for small molecules from biological matricies. This brief review describes recent selected HPLC/MS methods for the determination of urinary mercapturic acids (mercapturates) which are useful as biomarkers in characterizing human exposure to electrophilic industrial chemicals in occupational and environmental studies. Electrophilic compounds owing to their reactivity are used in chemical and industrial processes. They are present in industrial emissions, are combustion products of fossil fuels, and are components in tobacco smoke. Their presence in both the industrial and general environment are of concern for human and environmental health. Urinary mercapturates which are the products of metabolic detoxification of reactive chemicals provide a non-invasive tool to investigate human exposure to electrophilic toxicants. Selected recent mercapturate quantification methods are summarized and specific cases are presented. The biological formation of mercapturates is introduced and their use as biomarkers of metabolic processing of electrophilic compounds is discussed. Also, the use of liquid chromatography/tandem mass spectrometry in simultaneous determinations of the mercapturates of multiple parent compounds in a single determination is considered, as well as future trends and limitations in this area of research. PMID:24746702

  9. Application of Microchip for Biomarker Analysis

    NASA Astrophysics Data System (ADS)

    Kataoka, Masatoshi; Yatsushiro, Shouki; Yamamura, Shouhei; Abe, Hiroko

    Microchip technologies have received considerable attention, due to their competitive advantages, especially in regards to reduced sample and reagent consumption, analysis time, and easy operation. This approach has been successfully used to analyze DNA, amino acids, proteins, and carbohydrates. In the present study, we showed the potential of microchip technologies for the biomarker analysis, blood carbohydrate analysis on microchip electrophoresis, quantitative analysis of protein with antigen-antibody reaction on microchip, and the detection of malaria-infected erythrocyte with a cell microarray chip.

  10. Serum fatty acid profiles and potential biomarkers of ankylosing spondylitis determined by gas chromatography-mass spectrometry and multivariate statistical analysis.

    PubMed

    Chen, Rui; Han, Su; Dong, Daming; Wang, Yansong; Liu, Qingpeng; Xie, Wei; Li, Mi; Yao, Meng

    2015-04-01

    Ankylosing spondylitis (AS) is a common chronic inflammatory rheumatic disease. Early and accurate detection is essential for effective disease treatment. Recently, research has focused on genomics and proteomics. However, the associated metabolic variations, especially fatty acid profiles, have been poorly discussed. In this study, the gas chromatography-mass spectrometry (GC-MS) approach and multivariate statistical analysis were used to investigate the metabolic profiles of serum free fatty acids (FFAs) and esterified fatty acids (EFAs) in AS patients. The results showed that significant differences in most of the FFA (C12:0, C16:0, C16:1, C18:3, C20:4, C20:5, C22:5 and C22:6) and EFA (C12:0, C16:1, C18:0, C18:1, C18:2, C18:3, C20:4 and C22:6) concentrations were found between the AS patients and healthy controls (p < 0.05). Principal component analysis and partial least squares discriminant analysis were performed to classify the AS patients and controls. Additionally, FFAs C20:4, C12:0, C18:3 and EFAs C22:6, C12:0 were confirmed as potential biomarkers to identify AS patients and healthy controls. The present study highlights that differences in the serum FFA and EFA profiles of AS patients reflect the metabolic disorder. Moreover, FFA and EFA biomarkers appear to have clinical applications for the screening and diagnosis of AS.

  11. Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus) Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis.

    PubMed

    Neely, Benjamin A; Ferrante, Jason A; Chaves, J Mauro; Soper, Jennifer L; Almeida, Jonas S; Arthur, John M; Gulland, Frances M D; Janech, Michael G

    2014-01-01

    Domoic acid toxicosis (DAT) in California sea lions (Zalophus californianus) is caused by exposure to the marine biotoxin domoic acid and has been linked to massive stranding events and mortality. Diagnosis is based on clinical signs in addition to the presence of domoic acid in body fluids. Chronic DAT further is characterized by reoccurring seizures progressing to status epilepticus. Diagnosis of chronic DAT is often slow and problematic, and minimally invasive tests for DAT have been the focus of numerous recent biomarker studies. The goal of this study was to retrospectively profile plasma proteins in a population of sea lions with chronic DAT and those without DAT using two dimensional gel electrophoresis to discover whether individual, multiple, or combinations of protein and clinical data could be utilized to identify sea lions with DAT. Using a training set of 32 sea lion sera, 20 proteins and their isoforms were identified that were significantly different between the two groups (p<0.05). Interestingly, 11 apolipoprotein E (ApoE) charge forms were decreased in DAT samples, indicating that ApoE charge form distributions may be important in the progression of DAT. In order to develop a classifier of chronic DAT, an independent blinded test set of 20 sea lions, seven with chronic DAT, was used to validate models utilizing ApoE charge forms and eosinophil counts. The resulting support vector machine had high sensitivity (85.7% with 92.3% negative predictive value) and high specificity (92.3% with 85.7% positive predictive value). These results suggest that ApoE and eosinophil counts along with machine learning can perform as a robust and accurate tool to diagnose chronic DAT. Although this analysis is specifically focused on blood biomarkers and routine clinical data, the results demonstrate promise for future studies combining additional variables in multidimensional space to create robust classifiers.

  12. Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus) Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis

    PubMed Central

    Neely, Benjamin A.; Ferrante, Jason A.; Chaves, J. Mauro; Soper, Jennifer L.; Almeida, Jonas S.; Arthur, John M.; Gulland, Frances M. D.; Janech, Michael G.

    2015-01-01

    Domoic acid toxicosis (DAT) in California sea lions (Zalophus californianus) is caused by exposure to the marine biotoxin domoic acid and has been linked to massive stranding events and mortality. Diagnosis is based on clinical signs in addition to the presence of domoic acid in body fluids. Chronic DAT further is characterized by reoccurring seizures progressing to status epilepticus. Diagnosis of chronic DAT is often slow and problematic, and minimally invasive tests for DAT have been the focus of numerous recent biomarker studies. The goal of this study was to retrospectively profile plasma proteins in a population of sea lions with chronic DAT and those without DAT using two dimensional gel electrophoresis to discover whether individual, multiple, or combinations of protein and clinical data could be utilized to identify sea lions with DAT. Using a training set of 32 sea lion sera, 20 proteins and their isoforms were identified that were significantly different between the two groups (p<0.05). Interestingly, 11 apolipoprotein E (ApoE) charge forms were decreased in DAT samples, indicating that ApoE charge form distributions may be important in the progression of DAT. In order to develop a classifier of chronic DAT, an independent blinded test set of 20 sea lions, seven with chronic DAT, was used to validate models utilizing ApoE charge forms and eosinophil counts. The resulting support vector machine had high sensitivity (85.7% with 92.3% negative predictive value) and high specificity (92.3% with 85.7% positive predictive value). These results suggest that ApoE and eosinophil counts along with machine learning can perform as a robust and accurate tool to diagnose chronic DAT. Although this analysis is specifically focused on blood biomarkers and routine clinical data, the results demonstrate promise for future studies combining additional variables in multidimensional space to create robust classifiers. PMID:25919366

  13. Biomarker analysis of American toad (Anaxyrus americanus) ...

    EPA Pesticide Factsheets

    The objective of the current study was to use a biomarker-based approach to investigate the influence of atrazine exposure on American toad (Anaxyrus americanus) and grey tree frog (Hyla versicolor) tadpoles. Atrazine is one of the most frequently detected herbicides in environmental matrices throughout the United States. In surface waters, it has been found at concentrations from 0.04–2859 μg/L and thus presents a likely exposure scenario for non-target species such as amphibians. Studies have examined the effect of atrazine on the metamorphic parameters of amphibians, however, the data are often contradictory. Gosner stage 22–24 tadpoles were exposed to 0 (control), 10, 50, 250 or 1250 μg/L of atrazine for 48 h. Endogenous polar metabolites were extracted and analyzed using gas chromatography coupled with mass spectrometry. Statistical analyses of the acquired spectra with machine learning classification models demonstrated identifiable changes in the metabolomic profiles between exposed and control tadpoles. Support vector machine models with recursive feature elimination created a more efficient, non-parametric data analysis and increased interpretability of metabolomic profiles. Biochemical fluxes observed in the exposed groups of both A. americanus and H. versicolor displayed perturbations in a number of classes of biological macromolecules including fatty acids, amino acids, purine nucleosides, pyrimidines, and mono- and di-saccharides. Metabolomic

  14. Enantiomeric resolution of biomarkers in space analysis: Chemical derivatization and signal processing for gas chromatography-mass spectrometry analysis of chiral amino acids.

    PubMed

    Pietrogrande, M C; Basaglia, G

    2010-02-12

    The work compares two GC-MS methods for enantioselective separation of amino acids as suitable candidate for stereochemical analysis of chiral amino acids on board spacecrafts in space exploration missions of solar system body environments. Different derivatization reagents are used: a mixture of alkyl chloroformate-alcohol-pyridine to obtain the alkyl alkoxy carbonyl esters and a mixture of perfluorinated alcohols and anhydrides to form perfluoroacyl perfluoroalkyl esters. 20 proteinogenic amino acids were derivatized with the two procedures and submitted to GC-MS analysis on a Chirasil-l-Val stationary phase. The results were then compared in terms of the enantiomeric separation achieved and intensity of MS response. The combination of methyl chloroformate (MCF) and heptafluoro-1-butanol (HFB) allows separation of 14 enantiomeric pairs, five of which display a resolution (R(s)>or=1.2) supposed to be sufficient to quantify the enantiomeric excess. Three mixtures of trifluoroacetic (TFAA) and heptafluorobutyric (HFBA) anhydrides were combined with the corresponding perfluorinated alcohols - TFE (2,2,2-trifluoro-1-ethanol) and HFB (2,2,3,3,4,4,4-heptafluoro-1-butanol) - to give three different reagents (TFAA-TFE, TFAA-HFB, HFBA-HFB): the derivatives obtained show separation of the same number of proteinogenic amino acids (14 of 20) at a temperature lower than column bleeding limit (200 degrees C) and 8 of them give a separation with R(s)>or=1.2. Linearity study and limit of detection (X(LOD)) computation show that both methods are suitable for quantitative determination of several amino acid diastereomers at trace level (X(LOD) approximately 0.5nmol as derivatized quantity). Both the procedures were coupled with automatic data handling to increase their suitability for space analysis: the simplified data treatment is especially helpful to handle the low quality data recovered from space experiments and labor and time are saved, as imposed by the space experiments

  15. Fatty acid profile of the sea snail Gibbula umbilicalis as a biomarker for coastal metal pollution.

    PubMed

    Silva, Carla O; Simões, Tiago; Novais, Sara C; Pimparel, Inês; Granada, Luana; Soares, Amadeu M V M; Barata, Carlos; Lemos, Marco F L

    2017-05-15

    Metals are among the most common environmental pollutants with natural or anthropogenic origin that can be easily transferred through the food chain. Marine gastropods are known to accumulate high concentrations of these metals in their tissues. Gibbula umbilicalis ecological importance and abundant soft tissues, which enables extent biochemical assessments, makes this particular organism a potentially suitable species for marine ecotoxicological studies. Fatty acids are carbon-rich compounds that are ubiquitous in all organisms and easy to metabolize. Their biological specificity, relatively well-studied functions and importance, and the fact that they may alter when stress is induced, make fatty acids prospect biomarkers. This work aimed to assess fatty acid profile changes in the gastropod G. umbilicalis exposed to three metal contaminants. After a 168h exposure to cadmium, mercury, and nickel, the following lipid related endpoints were measured: total lipid content; lipid peroxidation; and fatty acid profile (FAP). The analysis of the FAP suggested an alteration in the fatty acid metabolism and indicated a link between metals exposure and homeoviscous adaptation and immune response. In particular, five fatty acids (palmitic, eicosatrienoic, arachidonic, eicosapentaenoic, and docosahexaenoic acids), demonstrated to be especially good indicators of G. umbilicalis responses to the array of metals used, having thus the potential to be used as biomarkers for metal contamination in this species. This work represents a first approach for the use of FAP signature as a sensitive and informative parameter and novel tool in environmental risk assessment (ERA) of coastal environments, using G. umbilicalis as model species.

  16. Polyunsaturated lysophosphatidic acid as a potential asthma biomarker

    PubMed Central

    Ackerman, Steven J; Park, Gye Young; Christman, John W; Nyenhuis, Sharmilee; Berdyshev, Evgeny; Natarajan, Viswanathan

    2016-01-01

    Lysophosphatidic acid (LPA), a lipid mediator in biological fluids and tissues, is generated mainly by autotaxin that hydrolyzes lysophosphatidylcholine to LPA and choline. Total LPA levels are increased in bronchoalveolar lavage fluid from asthmatic lung, and are strongly induced following subsegmental bronchoprovocation with allergen in subjects with allergic asthma. Polyunsaturated molecular species of LPA (C22:5 and C22:6) are selectively synthesized in the airways of asthma subjects following allergen challenge and in mouse models of allergic airway inflammation, having been identified and quantified by LC/MS/MS lipidomics. This review discusses current knowledge of LPA production in asthmatic lung and the potential utility of polyunsaturated LPA molecular species as novel biomarkers in bronchoalveolar lavage fluid and exhaled breath condensate of asthma subjects. PMID:26808693

  17. Amino Acid Profiles of Serum and Urine in Search for Prostate Cancer Biomarkers: a Pilot Study

    PubMed Central

    Dereziński, Paweł; Klupczynska, Agnieszka; Sawicki, Wojciech; Pałka, Jerzy A.; Kokot, Zenon J.

    2017-01-01

    There is a great interest in searching for diagnostic biomarkers in prostate cancer patients. The aim of the pilot study was to evaluate free amino acid profiles in their serum and urine. The presented paper shows the first comprehensive analysis of a wide panel of amino acids in two different physiological fluids obtained from the same groups of prostate cancer patients (n = 49) and healthy men (n = 40). The potential of free amino acids, both proteinogenic and non-proteinogenic, as prostate cancer biomarkers and their utility in classification of study participants have been assessed. Several metabolites, which deserve special attention in the further metabolomic investigations on searching for prostate cancer markers, were indicated. Moreover, free amino acid profiles enabled to classify samples to one of the studied groups with high sensitivity and specificity. The presented research provides a strong evidence that ethanolamine, arginine and branched-chain amino acids metabolic pathways can be a valuable source of markers for prostate cancer. The altered concentrations of the above-mentioned metabolites suggest their role in pathogenesis of prostate cancer and they should be further evaluated as clinically useful markers of prostate cancer. PMID:28138303

  18. Biomarker Validation: Common Data Analysis Concerns

    PubMed Central

    2014-01-01

    Biomarker validation, like any other confirmatory process based on statistical methodology, must discern associations that occur by chance from those reflecting true biological relationships. Validity of a biomarker is established by authenticating its correlation with clinical outcome. Validated biomarkers can lead to targeted therapy, improve clinical diagnosis, and serve as useful prognostic and predictive factors of clinical outcome. Statistical concerns such as confounding and multiplicity are common in biomarker validation studies. This article discusses four major areas of concern in the biomarker validation process and some of the proposed solutions. Because present-day statistical packages enable the researcher to address these common concerns, the purpose of this discussion is to raise awareness of these statistical issues in the hope of improving the reproducibility of validation study findings. PMID:25001264

  19. APPLICATIONS OF MICROFLUIDICS AND MICROCHIP ELECTROPHORESIS FOR POTENTIAL CLINICAL BIOMARKER ANALYSIS

    PubMed Central

    Pagaduan, Jayson V.; Sahore, Vishal; Woolley, Adam T.

    2015-01-01

    This article reviews advances over the last 5 years in microfluidics and microchip electrophoresis techniques for detection of clinical biomarkers. The various advantages of miniaturization compared with conventional benchtop methods for detecting biomarkers have resulted in increased interest in developing cheap, fast, and sensitive platforms. We discuss the development of applications of microfluidics and microchip electrophoresis for analysis of various clinical samples for pathogen identification, personalized medicine, and biomarker detection. We highlight the advantages of microfluidics platforms over conventional methods that make them an attractive future diagnostic tool. We also discuss the versatility and adaptability of this technology for analysis of various biomarkers, including lipids, small molecules, carbohydrates, nucleic acids, proteins and cells. Finally, we conclude with a discussion of areas that need to be improved upon to move this technology towards routine clinical and point-of-care applications. PMID:25855148

  20. Associations of erythrocyte ω-3 fatty acids with biomarkers of ω-3 fatty acids and inflammation in breast tissue.

    PubMed

    Roy, Shuvro; Brasky, Theodore M; Belury, Martha A; Krishnan, Shiva; Cole, Rachel M; Marian, Catalin; Yee, Lisa D; Llanos, Adana A; Freudenheim, Jo L; Shields, Peter G

    2015-12-15

    There is increasing evidence that chronic inflammation is associated with increased breast cancer risk. Long-chain omega-3 polyunsaturated fatty acids (LCω-3PUFA) may reduce circulating biomarkers of inflammation; however associations of blood LCω-3PUFA with breast tissue LCω-3PUFA and breast tissue biomarkers of inflammation are not well understood. We conducted a cross-sectional analysis of breast tissue and blood samples from n = 85 women with no history of breast cancer, who underwent breast reduction surgery. Fatty acids of erythrocytes and undissected breast tissues were analyzed by gas chromatography; C-reactive protein (CRP), interleukin (IL)-6 and IL-8 in plasma and tissue were measured by ELISA. Multivariable-adjusted regression models were used to estimate associations between erythrocyte LCω-3PUFA and breast tissue biomarkers. Women in the highest erythrocyte LCω-3PUFA tertile had LCω-3PUFA concentrations in the breast 73% (95% CI: 31-128%; p trend < 0.0001) higher than women in the lowest tertile. Associations for each individual LCω-3PUFA were similar in magnitude. No significant association was found for the shorter ω-3 PUFA, α-linolenic acid. Although compatible with no association, women in the highest tertile of erythrocyte eicosapentaenoic acid had a nonsignificant 32% (95% CI: -23 to 62%) reduced breast tissue CRP. No correlation was observed between erythrocyte ω-3 PUFA and tissue IL-6 or IL-8 concentrations. Our findings provide evidence that erythrocyte ω-3 fatty acids are valid measures of breast tissue concentrations, and limited evidence that inverse associations from prospective epidemiologic studies of blood LCω-3PUFA and breast cancer risk may be partly explained by reductions in breast tissue inflammation; however, these findings require replication.

  1. Exploration of amino acid biomarkers in polar ice with the Mars Organic Analyzer

    NASA Astrophysics Data System (ADS)

    Jayarajah, C.; Botta, O.; Aubrey, A.; Parker, E.; Bada, J.; Mathies, R.

    2009-05-01

    A portable microfabricated capillary electrophoresis (CE) system named the Mars Organic Analyzer (MOA) has been developed to analyze fluorescently-labeled biomarkers including amino acids, amines, nucleobases, and amino sugars with the goal of life detection on Mars (1,2). This technology has also been shown to be effective in screening the formation of biogenic amines during fermentation (3). The MOA is a part of the Urey instrument package that has been selected for the 2016 European ExoMars mission by ESA. The identification of recent gully erosion sites, observations of ice on and beneath the surface of Mars, and the discovery of large reservoirs of sub-surface ice on Mars point to water-ice as an important target for astrobiological analyses. In addition, the ice samples on the Moon, Mercury, Europa and Enceladus are of interest due to the possibility that they may contain information on biogenic material relevant to the evolution of life. We explore here the use of the MOA instrument for the analysis of amino acids in polar ice samples. The amino acids valine, alanine/serine, glycine, glutamic acid, and aspartic acid were found in the parts-per-billion range from Greenland ice-core samples. Chiral analysis of these samples yielded D/L ratios of 0.51/0.09 for alanine/serine and 0.14/0.06 for aspartic acid. Individual amino acids in the parts-per-trillion range were found in Antarctic ice samples collected from the surface of a meteorite collection area. The distinct amino acid and amine content of these samples indicates that further biomarker characterization of ice samples as a function of sampling location, depth, and structural features will be highly informative. The rapid sensitive analysis capabilities demonstrated here establish the feasibility of using the MOA to analyze the biomarker content of ice samples in planetary exploration. 1. Skelley, A. M.; Scherer, J. R.; Aubrey, A. D.; Grover, W. H.; Ivester, R. H. C., Ehrenfreund, P.; Grunthaner, F. J

  2. LIPID BIOMARKER ANALYSIS OF MARINE DINOFLAGELLATES

    EPA Science Inventory

    Many marine eukaryotic algae have been shown to possess characteristic chemotaxonomic lipid biomarkers. Dinoflagellates in particular are often characterized by the presence of sterols and pigments that are rarely found in other classes of algae. To evaluate the utility of chemic...

  3. Calcium-deficiency assessment and biomarker identification by an integrated urinary metabonomics analysis

    PubMed Central

    2013-01-01

    Background Calcium deficiency is a global public-health problem. Although the initial stage of calcium deficiency can lead to metabolic alterations or potential pathological changes, calcium deficiency is difficult to diagnose accurately. Moreover, the details of the molecular mechanism of calcium deficiency remain somewhat elusive. To accurately assess and provide appropriate nutritional intervention, we carried out a global analysis of metabolic alterations in response to calcium deficiency. Methods The metabolic alterations associated with calcium deficiency were first investigated in a rat model, using urinary metabonomics based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry and multivariate statistical analysis. Correlations between dietary calcium intake and the biomarkers identified from the rat model were further analyzed to confirm the potential application of these biomarkers in humans. Results Urinary metabolic-profiling analysis could preliminarily distinguish between calcium-deficient and non-deficient rats after a 2-week low-calcium diet. We established an integrated metabonomics strategy for identifying reliable biomarkers of calcium deficiency using a time-course analysis of discriminating metabolites in a low-calcium diet experiment, repeating the low-calcium diet experiment and performing a calcium-supplement experiment. In total, 27 biomarkers were identified, including glycine, oxoglutaric acid, pyrophosphoric acid, sebacic acid, pseudouridine, indoxyl sulfate, taurine, and phenylacetylglycine. The integrated urinary metabonomics analysis, which combined biomarkers with regular trends of change (types A, B, and C), could accurately assess calcium-deficient rats at different stages and clarify the dynamic pathophysiological changes and molecular mechanism of calcium deficiency in detail. Significant correlations between calcium intake and two biomarkers, pseudouridine (Pearson

  4. Innovation Analysis on Postgenomic Biomarkers: Glycomics for Chronic Diseases.

    PubMed

    Adua, Eric; Russell, Alyce; Roberts, Peter; Wang, Youxin; Song, Manshu; Wang, Wei

    2017-04-01

    Despite decades of investment in biomarker research, we still do not have robust and field-tested biomarkers for many chronic diseases so as to anticipate clinical outcomes and thus move toward personalized medicine. Biomarker innovations have tended to focus on genomics, but next-generation biomarkers from the nascent field of glycomics now offer fresh vistas for innovation in chronic disease biomarkers and systems diagnostics. Glycosylation, regarded as a complex enzymatic process where sugars (glycans) bind to proteins and lipids, affects many human biological functions, including cell signaling, adhesion, and motility. Notably, and contrary to proteins, glycan biosynthesis does not require a template; rather its final structure is catalyzed by a repertoire of enzymes that attach or detach monosaccharides in the glycosylation pathway, making glycomics research more challenging than proteomics or genomics. Yet, given glycans' biological significance, alterations in their processing may be detrimental to human health and also offer insights for preventive medicine and wellness interventions. Therefore, studying glycans' structure and understanding their function and molecular interactions in the emerging field of glycomics are key to unraveling the pathogenesis of various common chronic diseases. This review summarizes the major concepts in glycomics, including glycan release methods, techniques for large-scale glycan analysis, and glycoinformatic tools for data handling and storage. In all, this analysis on glycomics offers strategies to build a robust postgenomic innovation roadmap for glycan-driven biomarkers as the field is anticipated to mature further and gain greater prominence in the near future.

  5. Prediction of Bacillus weihenstephanensis acid resistance: the use of gene expression patterns to select potential biomarkers.

    PubMed

    Desriac, N; Postollec, F; Coroller, L; Sohier, D; Abee, T; den Besten, H M W

    2013-10-01

    Exposure to mild stress conditions can activate stress adaptation mechanisms and provide cross-resistance towards otherwise lethal stresses. In this study, an approach was followed to select molecular biomarkers (quantitative gene expressions) to predict induced acid resistance after exposure to various mild stresses, i.e. exposure to sublethal concentrations of salt, acid and hydrogen peroxide during 5 min to 60 min. Gene expression patterns of unstressed and mildly stressed cells of Bacillus weihenstephanensis were correlated to their acid resistance (3D value) which was estimated after exposure to lethal acid conditions. Among the twenty-nine candidate biomarkers, 12 genes showed expression patterns that were correlated either linearly or non-linearly to acid resistance, while for the 17 other genes the correlation remains to be determined. The selected genes represented two types of biomarkers, (i) four direct biomarker genes (lexA, spxA, narL, bkdR) for which expression patterns upon mild stress treatment were linearly correlated to induced acid resistance; and (ii) nine long-acting biomarker genes (spxA, BcerKBAB4_0325, katA, trxB, codY, lacI, BcerKBAB4_1716, BcerKBAB4_2108, relA) which were transiently up-regulated during mild stress exposure and correlated to increased acid resistance over time. Our results highlight that mild stress induced transcripts can be linearly or non-linearly correlated to induced acid resistance and both approaches can be used to find relevant biomarkers. This quantitative and systematic approach opens avenues to select cellular biomarkers that could be incremented in mathematical models to predict microbial behaviour.

  6. Biomarkers of fish oil omega-3 polyunsaturated fatty acids intake in humans.

    PubMed

    Silva, Veronica; Barazzoni, Rocco; Singer, Pierre

    2014-02-01

    A biomarker is a measured characteristic that may be used as an indicator of some biological state or condition. In health and disease, biomarkers have been used not only for clinical diagnosis purposes but also as tools to assess effectiveness of a nutrition or drug intervention. When considering nutrition studies, evaluating the appropriate biomarker is a useful tool to assess compliance and incidence of a particular dietary component in the biochemistry of the organism. Fish oil is rich in ω-3 fatty acids that have well-known beneficial effects on human health mainly through its anti-inflammatory properties. It has been widely use to improve health and as a nutrition supplement in different pathological conditions such as cardiovascular, neurological, and critically ill related diseases. Eicosapentaenoic acid and docosahexaenoic acid levels present in different biological moieties (plasma, cellular membranes, adipose tissue, etc) are the best biomarkers of fish oil intake. Each biological source of fatty acids has its own advantages and disadvantages, thus which biomarker to choose and where to measure it requires a comprehension of the objectives of the investigation. In this article we will review key facts about fish oil intake biomarkers to evaluate how components of a specific diet could be monitored and identified in biological samples. Having an accurate assessment of nutrition patterns could provide effective targets for intervention aimed at modifying eating habits and lifestyle towards the improvement of health.

  7. Serum Collagen Type II Cleavage Epitope and Serum Hyaluronic Acid as Biomarkers for Treatment Monitoring of Dogs with Hip Osteoarthritis

    PubMed Central

    Vilar, José M.; Rubio, Mónica; Spinella, Giuseppe; Cuervo, Belén; Sopena, Joaquín; Cugat, Ramón; Garcia-Balletbó, Montserrat; Dominguez, Juan M.; Granados, Maria; Tvarijonaviciute, Asta; Ceron, José J.; Carrillo, José M.

    2016-01-01

    The aim of this study was to evaluate the use of serum type II collagen cleavage epitope and serum hyaluronic acid as biomarkers for treatment monitoring in osteoarthritic dogs. For this purpose, a treatment model based on mesenchymal stem cells derived from adipose tissue combined with plasma rich in growth factors was used. This clinical study included 10 dogs with hip osteoarthritis. Both analytes were measured in serum at baseline, just before applying the treatment, and 1, 3, and 6 months after treatment. These results were compared with those obtained from force plate analysis using the same animals during the same study period. Levels of type II collagen cleavage epitope decreased and those of hyaluronic acid increased with clinical improvement objectively verified via force plate analysis, suggesting these two biomarkers could be effective as indicators of clinical development of joint disease in dogs. PMID:26886592

  8. Serum Collagen Type II Cleavage Epitope and Serum Hyaluronic Acid as Biomarkers for Treatment Monitoring of Dogs with Hip Osteoarthritis.

    PubMed

    Vilar, José M; Rubio, Mónica; Spinella, Giuseppe; Cuervo, Belén; Sopena, Joaquín; Cugat, Ramón; Garcia-Balletbó, Montserrat; Dominguez, Juan M; Granados, Maria; Tvarijonaviciute, Asta; Ceron, José J; Carrillo, José M

    2016-01-01

    The aim of this study was to evaluate the use of serum type II collagen cleavage epitope and serum hyaluronic acid as biomarkers for treatment monitoring in osteoarthritic dogs. For this purpose, a treatment model based on mesenchymal stem cells derived from adipose tissue combined with plasma rich in growth factors was used. This clinical study included 10 dogs with hip osteoarthritis. Both analytes were measured in serum at baseline, just before applying the treatment, and 1, 3, and 6 months after treatment. These results were compared with those obtained from force plate analysis using the same animals during the same study period. Levels of type II collagen cleavage epitope decreased and those of hyaluronic acid increased with clinical improvement objectively verified via force plate analysis, suggesting these two biomarkers could be effective as indicators of clinical development of joint disease in dogs.

  9. Identification of urine tauro-β-muricholic acid as a promising biomarker in Polygoni Multiflori Radix-induced hepatotoxicity by targeted metabolomics of bile acids.

    PubMed

    Zhao, Dong-Sheng; Jiang, Li-Long; Fan, Ya-Xi; Dong, Lei-Chi; Ma, Jiang; Dong, Xin; Xu, Xiao-Jun; Li, Ping; Li, Hui-Jun

    2017-02-24

    Polygoni Multiflori Radix (PMR) has been widely used as a tonic for centuries. However, hepatotoxicity cases linked to PMR have been frequently reported and appropriate biomarkers for clinical diagnosis are currently lacking. Here, an approach using UPLC-QqQ/MS-based targeted metabolomics of bile acids (BAs) complemented with biochemistry and histopathology was applied to characterize the development and recovery processes of PMR-induced hepatotoxicity in rats and to identify biomarkers. The expression of bile salt export pump (Bsep) and sodium taurocholate cotransporting polypeptide (Ntcp) were evaluated to investigate the underlying mechanism. Steatosis and inflammatory cell infiltration were observed in PMR-treated rats, which were accompanied by the elevation of serum biochemistry. The metabolic profiles of BAs were analyzed by Principal Component Analysis, hyodeoxycholic acid (HDCA) in serum and tauro-β-muricholic acid (TβMCA) in urine were identified as potential biomarkers for PMR-induced hepatotoxicity. The elevated expression of Bsep and decreased expression of Ntcp in the liver of PMRtreated rats indicated that hepatotoxicity was related to the disorders of BAs metabolism. Our study demonstrated that BAs may be used for clinical diagnosis of PMR-induced hepatotoxicity. Urine TβMCA was identified as a promising biomarker to facilitate the clinical monitoring of PMR-induced hepatotoxicity and may serve as potential therapeutic target.

  10. Detection of trace amino acid biomarkers in ice from extreme environments with the Mars Organic Analyzer

    NASA Astrophysics Data System (ADS)

    Jayarajah, Christine; Jayarajah, Christine; Botta, Oliver; Aubrey, Andrew; Parker, Eric; Bada, Jeffrey; Mathies, Richard

    A portable microfabricated capillary electrophoresis (CE) system named the Mars Organic Analyzer (MOA) has been developed to analyze fluorescently-labeled biomarkers including amino acids, amines, nucleobases, and amino sugars with the goal of life detection on Mars (1,2). This system consists of a multilayer microfabricated glass wafer containing electrophoresis channels as well as microfluidic valves and pumps for sample manipulation, a confocal laser excitation and fluorescence detection system, and integrated CE power supplies. The MOA has been successfully field tested in the Panoche Valley, CA and in the Atacama Desert, Chile, detecting amino acids at the ppb levels (3). In addition, this technology has been shown to be effective in screening the formation of biogenic amines during fermentation (4). The MOA is a part of the Urey instrument package that has been selected for the 2013 European ExoMars mission by ESA. The identification of recent gully erosion sites, observations of ice on and beneath the surface of Mars, and the discovery of large reservoirs of sub-surface ice on Mars point to water-ice as an important target for astrobiological analyses (5). In addition, the ice moons Europa and Enceladus are of astrobiological interest due to the possibility that they may contain liquid water under their ice crusts. Consequently, we explore here the use of the MOA instrument for the analysis of amino acids in polar ice samples. Soil extracts as well as concentrated icecore samples tend to be highly saline and inhomogeneous. Furthermore, brine pockets in ice form potential refugia for extant extra-terrestrial life, rendering near surface ice a key target for the search for a record of past life on the planet (6). Therefore, we have determined the effect of salinity on sample injection parameters in ice-core samples retrieved from Greenland. The amino acids valine, alanine/serine, glycine, glutamic acid, and aspartic acid were found in the parts

  11. Integrative analysis to select cancer candidate biomarkers to targeted validation.

    PubMed

    Kawahara, Rebeca; Meirelles, Gabriela V; Heberle, Henry; Domingues, Romênia R; Granato, Daniela C; Yokoo, Sami; Canevarolo, Rafael R; Winck, Flavia V; Ribeiro, Ana Carolina P; Brandão, Thaís Bianca; Filgueiras, Paulo R; Cruz, Karen S P; Barbuto, José Alexandre; Poppi, Ronei J; Minghim, Rosane; Telles, Guilherme P; Fonseca, Felipe Paiva; Fox, Jay W; Santos-Silva, Alan R; Coletta, Ricardo D; Sherman, Nicholas E; Paes Leme, Adriana F

    2015-12-22

    Targeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS.

  12. Integrative analysis to select cancer candidate biomarkers to targeted validation

    PubMed Central

    Heberle, Henry; Domingues, Romênia R.; Granato, Daniela C.; Yokoo, Sami; Canevarolo, Rafael R.; Winck, Flavia V.; Ribeiro, Ana Carolina P.; Brandão, Thaís Bianca; Filgueiras, Paulo R.; Cruz, Karen S. P.; Barbuto, José Alexandre; Poppi, Ronei J.; Minghim, Rosane; Telles, Guilherme P.; Fonseca, Felipe Paiva; Fox, Jay W.; Santos-Silva, Alan R.; Coletta, Ricardo D.; Sherman, Nicholas E.; Paes Leme, Adriana F.

    2015-01-01

    Targeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS. PMID:26540631

  13. Amino acid composition, including key derivatives of eccrine sweat: potential biomarkers of certain atopic skin conditions.

    PubMed

    Mark, Harker; Harding, Clive R

    2013-04-01

    The free amino acid (AA) composition of eccrine sweat is different from other biological fluids, for reasons which are not properly understood. We undertook the detailed analysis of the AA composition of freshly isolated pure human eccrine sweat, including some of the key derivatives of AA metabolism, to better understand the key biological mechanisms governing its composition. Eccrine sweat was collected from the axillae of 12 healthy subjects immediately upon formation. Free AA analysis was performed using an automatic AA analyser after ninhydrin derivatization. Pyrrolidine-5-carboxylic acid (PCA) and urocanic acid (UCA) levels were determined using GC/MS. The free AA composition of sweat was dominated by the presence of serine accounting for just over one-fifth of the total free AA composition. Glycine was the next most abundant followed by PCA, alanine, citrulline and threonine, respectively. The data obtained indicate that the AA content of sweat bears a remarkable similarity to the AA composition of the epidermal protein profilaggrin. This protein is the key source of free AAs and their derivatives that form a major part of the natural moisturizing factor (NMF) within the stratum corneum (SC) and plays a major role in maintaining the barrier integrity of human skin. As perturbations in the production of NMF can lead to abnormal barrier function and can arise as a consequence of filaggrin genotype, we propose the quantification of AAs in sweat may serve as a non-invasive diagnostic biomarker for certain atopic skin conditions, that is, atopic dermatitis (AD).

  14. The conifer biomarkers dehydroabietic and abietic acids are widespread in Cyanobacteria

    NASA Astrophysics Data System (ADS)

    Costa, Maria Sofia; Rego, Adriana; Ramos, Vitor; Afonso, Tiago B.; Freitas, Sara; Preto, Marco; Lopes, Viviana; Vasconcelos, Vitor; Magalhães, Catarina; Leão, Pedro N.

    2016-03-01

    Terpenes, a large family of natural products with important applications, are commonly associated with plants and fungi. The diterpenoids dehydroabietic and abietic acids are defense metabolites abundant in resin, and are used as biomarkers for conifer plants. We report here for the first time that the two diterpenoid acids are produced by members of several genera of cyanobacteria. Dehydroabietic acid was isolated from two cyanobacterial strains and its identity was confirmed spectroscopically. One or both of the diterpenoids were detected in the cells of phylogenetically diverse cyanobacteria belonging to four cyanobacterial ‘botanical orders’, from marine, estuarine and inland environments. Dehydroabietic acid was additionally found in culture supernatants. We investigated the natural role of the two resin acids in cyanobacteria using ecologically-relevant bioassays and found that the compounds inhibited the growth of a small coccoid cyanobacterium. The unexpected discovery of dehydroabietic and abietic acids in a wide range of cyanobacteria has implications for their use as plant biomarkers.

  15. The conifer biomarkers dehydroabietic and abietic acids are widespread in Cyanobacteria

    PubMed Central

    Costa, Maria Sofia; Rego, Adriana; Ramos, Vitor; Afonso, Tiago B.; Freitas, Sara; Preto, Marco; Lopes, Viviana; Vasconcelos, Vitor; Magalhães, Catarina; Leão, Pedro N.

    2016-01-01

    Terpenes, a large family of natural products with important applications, are commonly associated with plants and fungi. The diterpenoids dehydroabietic and abietic acids are defense metabolites abundant in resin, and are used as biomarkers for conifer plants. We report here for the first time that the two diterpenoid acids are produced by members of several genera of cyanobacteria. Dehydroabietic acid was isolated from two cyanobacterial strains and its identity was confirmed spectroscopically. One or both of the diterpenoids were detected in the cells of phylogenetically diverse cyanobacteria belonging to four cyanobacterial ‘botanical orders’, from marine, estuarine and inland environments. Dehydroabietic acid was additionally found in culture supernatants. We investigated the natural role of the two resin acids in cyanobacteria using ecologically-relevant bioassays and found that the compounds inhibited the growth of a small coccoid cyanobacterium. The unexpected discovery of dehydroabietic and abietic acids in a wide range of cyanobacteria has implications for their use as plant biomarkers. PMID:26996104

  16. The conifer biomarkers dehydroabietic and abietic acids are widespread in Cyanobacteria.

    PubMed

    Costa, Maria Sofia; Rego, Adriana; Ramos, Vitor; Afonso, Tiago B; Freitas, Sara; Preto, Marco; Lopes, Viviana; Vasconcelos, Vitor; Magalhães, Catarina; Leão, Pedro N

    2016-03-21

    Terpenes, a large family of natural products with important applications, are commonly associated with plants and fungi. The diterpenoids dehydroabietic and abietic acids are defense metabolites abundant in resin, and are used as biomarkers for conifer plants. We report here for the first time that the two diterpenoid acids are produced by members of several genera of cyanobacteria. Dehydroabietic acid was isolated from two cyanobacterial strains and its identity was confirmed spectroscopically. One or both of the diterpenoids were detected in the cells of phylogenetically diverse cyanobacteria belonging to four cyanobacterial 'botanical orders', from marine, estuarine and inland environments. Dehydroabietic acid was additionally found in culture supernatants. We investigated the natural role of the two resin acids in cyanobacteria using ecologically-relevant bioassays and found that the compounds inhibited the growth of a small coccoid cyanobacterium. The unexpected discovery of dehydroabietic and abietic acids in a wide range of cyanobacteria has implications for their use as plant biomarkers.

  17. Human saliva proteome analysis and disease biomarker discovery.

    PubMed

    Hu, Shen; Loo, Joseph A; Wong, David T

    2007-08-01

    Human saliva is an attractive body fluid for disease diagnosis and prognosis because saliva testing is simple, safe, low-cost and noninvasive. Comprehensive analysis and identification of the proteomic content in human whole and ductal saliva will not only contribute to the understanding of oral health and disease pathogenesis, but also form a foundation for the discovery of saliva protein biomarkers for human disease detection. In this article, we have summarized the proteomic technologies for comprehensive identification of proteins in human whole and ductal saliva. We have also discussed potential quantitative proteomic approaches to the discovery of saliva protein biomarkers for human oral and systemic diseases. With the fast development of mass spectrometry and proteomic technologies, we are enthusiastic that saliva protein biomarkers will be developed for clinical diagnosis and prognosis of human diseases in the future.

  18. RECONSTRUCTING EXPOSURE SCENARIOS USING DOSE BIOMARKERS - AN APPLICATION OF BAYESIAN UNCERTAINTY ANALYSIS

    EPA Science Inventory

    We use Bayesian uncertainty analysis to explore how to estimate pollutant exposures from biomarker concentrations. The growing number of national databases with exposure data makes such an analysis possible. They contain datasets of pharmacokinetic biomarkers for many polluta...

  19. Digital pathology and image analysis in tissue biomarker research.

    PubMed

    Hamilton, Peter W; Bankhead, Peter; Wang, Yinhai; Hutchinson, Ryan; Kieran, Declan; McArt, Darragh G; James, Jacqueline; Salto-Tellez, Manuel

    2014-11-01

    Digital pathology and the adoption of image analysis have grown rapidly in the last few years. This is largely due to the implementation of whole slide scanning, advances in software and computer processing capacity and the increasing importance of tissue-based research for biomarker discovery and stratified medicine. This review sets out the key application areas for digital pathology and image analysis, with a particular focus on research and biomarker discovery. A variety of image analysis applications are reviewed including nuclear morphometry and tissue architecture analysis, but with emphasis on immunohistochemistry and fluorescence analysis of tissue biomarkers. Digital pathology and image analysis have important roles across the drug/companion diagnostic development pipeline including biobanking, molecular pathology, tissue microarray analysis, molecular profiling of tissue and these important developments are reviewed. Underpinning all of these important developments is the need for high quality tissue samples and the impact of pre-analytical variables on tissue research is discussed. This requirement is combined with practical advice on setting up and running a digital pathology laboratory. Finally, we discuss the need to integrate digital image analysis data with epidemiological, clinical and genomic data in order to fully understand the relationship between genotype and phenotype and to drive discovery and the delivery of personalized medicine.

  20. Amino acid analysis

    NASA Technical Reports Server (NTRS)

    Winitz, M.; Graff, J. (Inventor)

    1974-01-01

    The process and apparatus for qualitative and quantitative analysis of the amino acid content of a biological sample are presented. The sample is deposited on a cation exchange resin and then is washed with suitable solvents. The amino acids and various cations and organic material with a basic function remain on the resin. The resin is eluted with an acid eluant, and the eluate containing the amino acids is transferred to a reaction vessel where the eluant is removed. Final analysis of the purified acylated amino acid esters is accomplished by gas-liquid chromatographic techniques.

  1. Urine metabolomics analysis for kidney cancer detection and biomarker discovery.

    PubMed

    Kim, Kyoungmi; Aronov, Pavel; Zakharkin, Stanislav O; Anderson, Danielle; Perroud, Bertrand; Thompson, Ian M; Weiss, Robert H

    2009-03-01

    Renal cell carcinoma (RCC) accounts for 11,000 deaths per year in the United States. When detected early, generally serendipitously by imaging conducted for other reasons, long term survival is generally excellent. When detected with symptoms, prognosis is poor. Under these circumstances, a screening biomarker has the potential for substantial public health benefit. The purpose of this study was to evaluate the utility of urine metabolomics analysis for metabolomic profiling, identification of biomarkers, and ultimately for devising a urine screening test for RCC. Fifty urine samples were obtained from RCC and control patients from two institutions, and in a separate study, urine samples were taken from 13 normal individuals. Hydrophilic interaction chromatography-mass spectrometry was performed to identify small molecule metabolites present in each sample. Cluster analysis, principal components analysis, linear discriminant analysis, differential analysis, and variance component analysis were used to analyze the data. Previous work is extended to confirm the effectiveness of urine metabolomics analysis using a larger and more diverse patient cohort. It is now shown that the utility of this technique is dependent on the site of urine collection and that there exist substantial sources of variation of the urinary metabolomic profile, although group variation is sufficient to yield viable biomarkers. Surprisingly there is a small degree of variation in the urinary metabolomic profile in normal patients due to time since the last meal, and there is little difference in the urinary metabolomic profile in a cohort of pre- and postnephrectomy (partial or radical) renal cell carcinoma patients, suggesting that metabolic changes associated with RCC persist after removal of the primary tumor. After further investigations relating to the discovery and identity of individual biomarkers and attenuation of residual sources of variation, our work shows that urine metabolomics

  2. Accumulated metabolites of hydroxybutyric acid serve as diagnostic and prognostic biomarkers of ovarian high-grade serous carcinomas

    PubMed Central

    Hilvo, Mika; de Santiago, Ines; Gopalacharyulu, Peddinti; Schmitt, Wolfgang D.; Budczies, Jan; Kuhberg, Marc; Dietel, Manfred; Aittokallio, Tero; Markowetz, Florian; Denkert, Carsten; Sehouli, Jalid; Frezza, Christian

    2016-01-01

    Ovarian cancer is a heterogeneous disease of low prevalence, but poor survival. Early diagnosis is critical for survival, but is often challenging because the symptoms of ovarian cancer are subtle and become apparent only during advanced stages of the disease. Therefore, the identification of robust biomarkers of early disease is a clinical priority. Metabolomic profiling is an emerging diagnostic tool enabling the detection of biomarkers reflecting alterations in tumor metabolism, a hallmark of cancer. In this study, we performed metabolomic profiling of serum and tumor tissue from 158 patients with high-grade serous ovarian cancer (HGSOC) and 100 control patients with benign or non-neoplastic lesions. We report metabolites of hydroxybutyric acid (HBA) as novel diagnostic and prognostic biomarkers associated with tumor burden and patient survival. The accumulation of HBA metabolites caused by HGSOC was also associated with reduced expression of succinic semialdehyde dehydrogenase (encoded by ALDH5A1), and with the presence of an epithelial-to-mesenchymal transition (EMT) gene signature, implying a role for these metabolic alterations in cancer cell migration and invasion. In conclusion, our findings represent the first comprehensive metabolomics analysis in HGSOC and propose a new set of metabolites as biomarkers of disease with diagnostic and prognostic capabilities. PMID:26685161

  3. Three aromatic amino acids in gastric juice as potential biomarkers for gastric malignancies.

    PubMed

    Deng, Kai; Lin, Sanren; Zhou, Liya; Geng, Qiuming; Li, Yuan; Xu, Ming; Na, Renhua

    2011-05-23

    For screening early-stage gastric malignancies, the existing serum biomarkers have limited sensitivity and specificity. Gastric juice biomarkers are scarce and require further investigation. We divided this study on searching potential biomarkers into four parts: (1) detection of differential fluorescence spectrum and peaks in the gastric juice from patients using fluorescence spectroscopy and HPLC, (2) identification and validation of differential peaks using LC/MS and NMR, (3) quantification of potential biomarkers, and (4) establishment of diagnostic detection. The fluorescence intensity (FI), tyrosine, phenylalanine, tryptophan and total protein content were significantly higher in the gastric juice of patients with gastric malignancies (all P<0.01). With all P<0.001, the areas under the receiver operating characteristic curves of the biomarkers were tyrosine, 0.838; phenylalanine, 0.856; and tryptophan, 0.816. At a specificity of 79.4%, the sensitivity for gastric malignancy detection with phenylalanine was 87.9% only. Aromatic amino acids in gastric juices could be used as potential diagnostic biomarkers to screen gastric malignancies. It is a less-invasive and economical method compared to gastric biopsy.

  4. Analysis of Biomarker Utility using a PBPK Model for Carbaryl

    EPA Science Inventory

    There are many types of biomarkers; the two common ones are biomarkers of exposure and biomarkers of effect. The utility of a biomarker for estimating exposures or predicting risks depends on the strength of the correlation between biomarker concentrations and exposure/effects. I...

  5. Analysis of gene expression profile identifies potential biomarkers for atherosclerosis

    PubMed Central

    Liu, Luran; Liu, Yan; Liu, Chang; Zhang, Zhuobo; Du, Yaojun; Zhao, Hao

    2016-01-01

    The present study aimed to identify potential biomarkers for atherosclerosis via analysis of gene expression profiles. The microarray dataset no. GSE20129 was downloaded from the Gene Expression Omnibus database. A total of 118 samples from the peripheral blood of female patients was used, including 47 atherosclerotic and 71 non-atherosclerotic patients. The differentially expressed genes (DEGs) in the atherosclerosis samples were identified using the Limma package. Gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses for DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery tool. The recursive feature elimination (RFE) algorithm was applied for feature selection via iterative classification, and support vector machine classifier was used for the validation of prediction accuracy. A total of 430 DEGs in the atherosclerosis samples were identified, including 149 up- and 281 downregulated genes. Subsequently, the RFE algorithm was used to identify 11 biomarkers, whose receiver operating characteristic curves had an area under curve of 0.92, indicating that the identified 11 biomarkers were representative. The present study indicated that APH1B, JAM3, FBLN2, CSAD and PSTPIP2 may have important roles in the progression of atherosclerosis in females and may be potential biomarkers for early diagnosis and prognosis as well as treatment targets for this disease. PMID:27573188

  6. Plasma concentrations of amino acid and nicotinamide metabolites in rheumatoid arthritis--potential biomarkers of disease activity and drug treatment.

    PubMed

    Smolenska, Zaneta; Smolenski, Ryszard T; Zdrojewski, Zbigniew

    2016-01-01

    This study aimed to evaluate changes in plasma amino acid and nicotinamide metabolites concentrations in rheumatoid arthritis (RA) in a search for potential biomarkers of the disease activity and the effect treatment. Analysis of plasma metabolite patterns with liquid chromatography/mass spectrometry revealed specific changes in RA as well as correlations with clinical parameters. Combined concentration parameter calculated as [aspartic acid] + [threonine] + [tryptophan] - [histidine] - [phenylalanine] offered the strongest correlation (p < 0.001) with pain joint count, swollen joint count and DAS 28. Such analysis of amino acid and related metabolite pattern offers potential for diagnosis as well as for monitoring disease progression and therapy in RA.

  7. Enantioselective separation of amino acids as biomarkers indicating life in extraterrestrial environments.

    PubMed

    Pietrogrande, Maria Chiara

    2013-10-01

    Traces of prebiotic amino acids, i.e., the building blocks of proteins, are excellent biomarkers that could provide evidence of extinct or extant life in extra-terrestrial environments. In particular, characterization of the enantiomeric excess of amino acids gives relevant information about the biotic or abiotic origin of molecules, because it is generally assumed that life elsewhere could be based on either L or D amino acids, but not both. The analytical procedures used in in-situ space missions for chiral discrimination of amino acids must meet severe requirements imposed by flight conditions: short analysis time, low energy consumption, robustness, storage for long periods under extreme conditions, high efficiency and sensitivity, automation, and remote-control operation. Such methods are based on gas chromatography, high-pressure liquid chromatography, and capillary electrophoresis, usually coupled with mass spectrometry; of these, gas chromatography-mass spectrometry (GC-MS) is the only such combination yet used in space missions. Preliminary in-situ sample derivatization is required before GC-MS analysis to convert amino acids into volatile and thermally stable compounds. The silylation reagent most commonly used, N-(tert-butyldimethylsilyl)-N-methyltrifluoroacetamide, is unsuitable for detection of homochirality, and alternative derivatization techniques have been developed that preserve the stereochemical configuration of the original compounds and are compatible with spaceflight conditions. These include the reagent N,N-dimethylformamide dimethylacetal, which has already been used in the Rosetta mission, a mixture of alkyl chloroformate, ethanol, and pyridine, a mixture of perfluorinated anhydrides and perfluoro alcohols, and hexafluoroacetone, the first gaseous derivatizing agent. In all the space instruments, solvent extraction of organic matter and chemical derivatization have been combined in a single automatic and remote-controlled procedure in a

  8. Biomarker discovery by CE-MS enables sequence analysis via MS/MS with platform-independent separation.

    PubMed

    Zürbig, Petra; Renfrow, Matthew B; Schiffer, Eric; Novak, Jan; Walden, Michael; Wittke, Stefan; Just, Ingo; Pelzing, Matthias; Neusüss, Christian; Theodorescu, Dan; Root, Karen E; Ross, Mark M; Mischak, Harald

    2006-06-01

    CE-MS is a successful proteomic platform for the definition of biomarkers in different body fluids. Besides the biomarker defining experimental parameters, CE migration time and molecular weight, especially biomarker's sequence identity is an indispensable cornerstone for deeper insights into the pathophysiological pathways of diseases or for made-to-measure therapeutic drug design. Therefore, this report presents a detailed discussion of different peptide sequencing platforms consisting of high performance separation method either coupled on-line or off-line to different MS/MS devices, such as MALDI-TOF-TOF, ESI-IT, ESI-QTOF and Fourier transform ion cyclotron resonance, for sequencing indicative peptides. This comparison demonstrates the unique feature of CE-MS technology to serve as a reliable basis for the assignment of peptide sequence data obtained using different separation MS/MS methods to the biomarker defining parameters, CE migration time and molecular weight. Discovery of potential biomarkers by CE-MS enables sequence analysis via MS/MS with platform-independent sample separation. This is due to the fact that the number of basic and neutral polar amino acids of biomarkers sequences distinctly correlates with their CE-MS migration time/molecular weight coordinates. This uniqueness facilitates the independent entry of different sequencing platforms for peptide sequencing of CE-MS-defined biomarkers from highly complex mixtures.

  9. Fatty Acids in Membranes as Homeostatic, Metabolic and Nutritional Biomarkers: Recent Advancements in Analytics and Diagnostics

    PubMed Central

    Ferreri, Carla; Masi, Annalisa; Sansone, Anna; Giacometti, Giorgia; Larocca, Anna Vita; Menounou, Georgia; Scanferlato, Roberta; Tortorella, Silvia; Rota, Domenico; Conti, Marco; Deplano, Simone; Louka, Maria; Maranini, Anna Rosaria; Salati, Arianna; Sunda, Valentina; Chatgilialoglu, Chryssostomos

    2016-01-01

    Fatty acids, as structural components of membranes and inflammation/anti-inflammatory mediators, have well-known protective and regulatory effects. They are studied as biomarkers of pathological conditions, as well as saturated and unsaturated hydrophobic moieties in membrane phospholipids that contribute to homeostasis and physiological functions. Lifestyle, nutrition, metabolism and stress—with an excess of radical and oxidative processes—cause fatty acid changes that are examined in the human body using blood lipids. Fatty acid-based membrane lipidomics represents a powerful diagnostic tool for assessing the quantity and quality of fatty acid constituents and also for the follow-up of the membrane fatty acid remodeling that is associated with different physiological and pathological conditions. This review focuses on fatty acid biomarkers with two examples of recent lipidomic research and health applications: (i) monounsaturated fatty acids and the analytical challenge offered by hexadecenoic fatty acids (C16:1); and (ii) the cohort of 10 fatty acids in phospholipids of red blood cell membranes and its connections to metabolic and nutritional status in healthy and diseased subjects. PMID:28025506

  10. Advanced Microfabricated Devices for Sensitive Biomarker Detection and Analysis on Mars

    NASA Astrophysics Data System (ADS)

    Skelley, A. M.; Scherer, J. R.; Aubrey, A. D.; Grover, W. H.; Ehrenfreund, P.; Grunthaner, F. J.; Bada, J. L.; Willis, P.; Mathies, R. A.

    2006-12-01

    Detection of life on Mars requires definition of a suitable biomarker and development of sensitive instrumentation capable of performing in situ chemical analyses [1]. Our studies have focused on amino acid analysis because amino acids are more resistant to decomposition than other biomolecules, and because amino acid chirality is a well-defined biomarker. We have developed the Mars Organic Analyzer (MOA), a portable amino acid analysis system that consists of a compact instrument and a novel multi-layer CE microchip, and we have performed extensive laboratory and field validation of this instrument [2]. The heart of the MOA is the 100-mm diameter, 4-mm thick microchip that contains the CE separation channels as well as microfabricated valves and pumps for automated integrated sample preparation and handling. The microfabricated device is operated by a portable instrument that performs CE separation and LIF detection. The limits of detection of fluorescamine-labeled amino acids are in the nM to pM range corresponding to part- per-trillion sensitivities. The MOA has been field tested on soil samples rich in jarosite from the Panoche Valley, CA. These results demonstrate that amines and amino acids can be extracted from sulfate-rich acidic soils such as jarosite and analyzed using the MOA. The MOA was also recently field tested in the Yungay region of the Atacama Desert in Chile. The instrument was successfully operated in this challenging environment and performed over 300 amino acid analyses in a two week period. The MOA has also been used to label and analyze two of the four nucleobases, and methods are being developed to detect PAH's [3]. This presentation will discuss the unique challenges of developing microdevices for sensitive analysis of biomarker compounds. We will also describe current efforts to develop multichannel analysis systems and microfluidic automated analysis systems that will be used to enable flight versions of this instrument. For more details

  11. Determination of methyl-, 2-hydroxyethyl- and 2-cyanoethylmercapturic acids as biomarkers of exposure to alkylating agents in cigarette smoke.

    PubMed

    Scherer, Gerhard; Urban, Michael; Hagedorn, Heinz-Werner; Serafin, Richard; Feng, Shixia; Kapur, Sunil; Muhammad, Raheema; Jin, Yan; Sarkar, Mohamadi; Roethig, Hans-Juergen

    2010-10-01

    Alkylating agents occur in the environment and are formed endogenously. Tobacco smoke contains a variety of alkylating agents or precursors including, among others, N-nitrosodimethylamine (NDMA), 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), acrylonitrile and ethylene oxide. We developed and validated a method for the simultaneous determination of methylmercapturic acid (MMA, biomarker for methylating agents such as NDMA and NNK), 2-hydroxyethylmercapturic acid (HEMA, biomarker for ethylene oxide) and 2-cyanoethylmercapturic acid (CEMA, biomarker for acrylonitrile) in human urine using deuterated internal standards of each compound. The method involves liquid/liquid extraction of the urine sample, solid phase extraction on anion exchange cartridges, derivatization with pentafluorobenzyl bromide (PFBBr), liquid/liquid extraction of the reaction mixture and LC-MS/MS analysis with positive electrospray ionization. The method was linear in the ranges of 5.00-600, 1.00-50.0 and 1.50-900 ng/ml for MMA, HEMA and CEMA, respectively. The method was applied to two clinical studies in adult smokers of conventional cigarettes who either continued smoking conventional cigarettes, were switched to test cigarettes consisting of either an electrically heated cigarette smoking system (EHCSS) or having a highly activated carbon granule filter that were shown to have reduced exposure to specific smoke constituents, or stopped smoking. Urinary excretion of MMA was found to be unaffected by switching to the test cigarettes or stop smoking. Urinary HEMA excretion decreased by 46 to 54% after switching to test cigarettes and by approximately 74% when stopping smoking. Urinary CEMA excretion decreased by 74-77% when switching to test cigarettes and by approximately 90% when stopping smoking. This validated method for urinary alkylmercapturic acids is suitable to distinguish differences in exposure not only between smokers and nonsmokers but also between smoking of conventional and

  12. Metabolic Disease Risk in Children by Salivary Biomarker Analysis

    PubMed Central

    Goodson, J. Max; Kantarci, Alpdogan; Hartman, Mor-Li; Denis, Gerald V.; Stephens, Danielle; Hasturk, Hatice; Yaskell, Tina; Vargas, Jorel; Wang, Xiaoshan; Cugini, Maryann; Barake, Roula; Alsmadi, Osama; Al-Mutawa, Sabiha; Ariga, Jitendra; Soparkar, Pramod; Behbehani, Jawad; Behbehani, Kazem; Welty, Francine

    2014-01-01

    Objective The study of obesity-related metabolic syndrome or Type 2 diabetes (T2D) in children is particularly difficult because of fear of needles. We tested a non-invasive approach to study inflammatory parameters in an at-risk population of children to provide proof-of-principle for future investigations of vulnerable subjects. Design and Methods We evaluated metabolic differences in 744, 11-year old children selected from underweight, normal healthy weight, overweight and obese categories by analyzing fasting saliva samples for 20 biomarkers. Saliva supernatants were obtained following centrifugation and used for analyses. Results Salivary C-reactive protein (CRP) was 6 times higher, salivary insulin and leptin were 3 times higher, and adiponectin was 30% lower in obese children compared to healthy normal weight children (all P<0.0001). Categorical analysis suggested that there might be three types of obesity in children. Distinctly inflammatory characteristics appeared in 76% of obese children while in 13%, salivary insulin was high but not associated with inflammatory mediators. The remaining 11% of obese children had high insulin and reduced adiponectin. Forty percent of the non-obese children were found in groups which, based on biomarker characteristics, may be at risk for becoming obese. Conclusions Significantly altered levels of salivary biomarkers in obese children from a high-risk population, suggest the potential for developing non-invasive screening procedures to identify T2D-vulnerable individuals and a means to test preventative strategies. PMID:24915044

  13. Stable-isotope dilution LC–MS for quantitative biomarker analysis

    PubMed Central

    Ciccimaro, Eugene; Blair, Ian A

    2010-01-01

    The ability to conduct validated analyses of biomarkers is critically important in order to establish the sensitivity and selectivity of the biomarker in identifying a particular disease. The use of stable-isotope dilution (SID) methodology in combination with LC–MS/MS provides the highest possible analytical specificity for quantitative determinations. This methodology is now widely used in the discovery and validation of putative exposure and disease biomarkers. This review will describe the application of SID LC–MS methodology for the analysis of small-molecule and protein biomarkers. It will also discuss potential future directions for the use of this methodology for rigorous biomarker analysis. PMID:20352077

  14. Identification of Palmitoleic Acid Controlled by mTOR Signaling as a Biomarker of Polymyositis.

    PubMed

    Yin, Geng; Wang, Ying; Cen, Xiao-Min; Yang, Yuan; Yang, Min; Xie, Qi-Bing

    2017-01-01

    Polymyositis (PM) is a chronic disease characterized by muscle pain, weakness, and increase in muscle-related enzymes, accompanied with inflammations in lymphocytes. However, it is not well understood how the molecular alternations in lymphocytes contribute to the development of polymyositis. The mechanistic target of rapamycin (mTOR) signaling is the central regulator of metabolism and inflammation in mammalian cells. Based on previous studies, we proposed that mTOR signaling may control inflammatory reactions via lipid metabolism. In this study, we aim to figure out the role of mTOR signaling in the development of polymyositis and identify novel biomarkers for the detection and therapy of polymyositis. After screening and validation, we found that palmitoleic acid, a monounsaturated fatty acid, is highly regulated by mTOR signaling. Inhibition of mTORC1 activity decreases palmitoleic acid level. Moreover, mTORC1 regulates the level of palmitoleic acid by controlling its de novo synthesis. Importantly, increased palmitoleic acid has been proven to be a marker of polymyositis. Our work identifies palmitoleic acid in peripheral blood mononuclear cells (PBMC) as a biomarker of polymyositis and offers new targets to the clinical therapy.

  15. Identification of Palmitoleic Acid Controlled by mTOR Signaling as a Biomarker of Polymyositis

    PubMed Central

    Wang, Ying; Cen, Xiao-min; Yang, Yuan; Yang, Min

    2017-01-01

    Polymyositis (PM) is a chronic disease characterized by muscle pain, weakness, and increase in muscle-related enzymes, accompanied with inflammations in lymphocytes. However, it is not well understood how the molecular alternations in lymphocytes contribute to the development of polymyositis. The mechanistic target of rapamycin (mTOR) signaling is the central regulator of metabolism and inflammation in mammalian cells. Based on previous studies, we proposed that mTOR signaling may control inflammatory reactions via lipid metabolism. In this study, we aim to figure out the role of mTOR signaling in the development of polymyositis and identify novel biomarkers for the detection and therapy of polymyositis. After screening and validation, we found that palmitoleic acid, a monounsaturated fatty acid, is highly regulated by mTOR signaling. Inhibition of mTORC1 activity decreases palmitoleic acid level. Moreover, mTORC1 regulates the level of palmitoleic acid by controlling its de novo synthesis. Importantly, increased palmitoleic acid has been proven to be a marker of polymyositis. Our work identifies palmitoleic acid in peripheral blood mononuclear cells (PBMC) as a biomarker of polymyositis and offers new targets to the clinical therapy. PMID:28194428

  16. Plasmatic retinol-binding protein 4 and glial fibrillary acidic protein as biomarkers to differentiate ischemic stroke and intracerebral hemorrhage.

    PubMed

    Llombart, Víctor; García-Berrocoso, Teresa; Bustamante, Alejandro; Giralt, Dolors; Rodriguez-Luna, David; Muchada, Marian; Penalba, Anna; Boada, Cristina; Hernández-Guillamon, Mar; Montaner, Joan

    2016-01-01

    A rapid differentiation of acute ischemic stroke and intracerebral hemorrhage (ICH) is essential for an adequate treatment and to promote a better outcome. Our aim was to identify new plasma biomarkers to differentiate stroke subtypes and to combine their diagnostic ability with other biomarkers already described for this clinical indication. Plasma samples of ischemic stroke patients (36) and ICH patients (10) were screened using a 177 antibodies library, and 11 showed different concentrations among stroke subtypes (p < 0.05), mainly chemokines, growth factors and angiogenic factors. Five proteins were selected for replication in 16 ischemic stroke patients and 16 ICH patients, and retinol-binding protein 4 (RPB4), apolipoprotein B100 and pigment epithelial-derived factor were replicated (p < 0.05). These proteins, together with glial fibrillary acidic protein (GFAP) and receptor for advanced glycation end product, were tested in 38 ischemic stroke and 28 ICH samples. Finally, RBP4 >61 μg/mL and GFAP <0.07 ng/mL showed a specificity of 100% for both subtypes. Moreover, after multivariate logistic regression analysis, RBP4 >48.75 μg/mL (ORadj : 6.09 (1.3-28.57), p = 0.02) and GFAP <0.07 ng/mL (ORadj : 0.03 (0.003-0.31), p = 0.003) resulted in independent predictors of stroke subtype, improving discrimination by 29% (p < 0.0001). Both biomarkers might be useful as diagnostic biomarkers to differentiate ischemic stroke and ICH. A rapid differentiation of ischemic stroke from intracerebral hemorrhage is essential to provide the appropriate treatment. We describe the discovery and subsequent replications of RBP4 and its combination with circulating GFAP as plasmatic biomarkers for hyperacute stroke subtype differentiation. The combination of these biomarkers and others might aid to speed up the discrimination of both stroke subtypes improving the outcome of patients.

  17. Fatty acid metabolism in fish species as a biomarker for environmental monitoring.

    PubMed

    Olivares-Rubio, Hugo F; Vega-López, Armando

    2016-11-01

    Pollution by Organic Contaminants (OC) in aquatic environments is a relevant issue at the global scale. Lipids comprised of Fatty Acids (FA) play many important roles in the physiology and life history of fishes. Toxic effects of OC are partly dependent on its bioaccumulation in the lipids of aquatic organisms due its physicochemical properties. Therefore, there is an increasing interest to investigate the gene expression as well as the presence and activity of proteins involved in FA metabolism. The attention on Peroxisome Proliferation Activate Receptors (PPARs) also prevails in fish species exposed to OC and in the transport, biosynthesis and β-oxidation of FA. Several studies have been conducted under controlled conditions to evaluate these biological aspects of fish species exposed to OC, as fibrates, endocrine disrupting compounds, perfluoroalkyl acids, flame retardants, metals and mixtures of organic compounds associated with a polluted area. However, only fibrates, which are agonists of PPARs, induce biological responses suitable to be considered as biomarkers of exposure to these pollutants. According to the documented findings on this topic, it is unlikely that these physiological aspects are suitable to be employed as biomarkers with some noticeable exceptions, which depend on experimental design. This emphasises the need to investigate the responses in fish treated with mixtures of OC and in wild fish species from polluted areas to validate or refute the suitability of these biomarkers for environmental or fish health monitoring.

  18. Sensitive Amino Acid Composition and Chirality Analysis with the Mars Organic Analyzer (MOA)

    NASA Technical Reports Server (NTRS)

    Skelley, Alison M.; Scherer, James R.; Aubrey, Andrew D.; Grover, William H.; Ivester, Robin H. C.; Ehrenfreund, Pascale; Grunthaner, Frank J.; Bada, Jeffrey L.; Mathies, Richard A.

    2005-01-01

    Detection of life on Mars requires definition of a suitable biomarker and development of sensitive yet compact instrumentation capable of performing in situ analyses. Our studies are focused on amino acid analysis because amino acids are more resistant to decomposition than other biomolecules, and because amino acid chirality is a well-defined biomarker. Amino acid composition and chirality analysis has been previously demonstrated in the lab using microfabricated capillary electrophoresis (CE) chips. To analyze amino acids in the field, we have developed the Mars Organic Analyzer (MOA), a portable analysis system that consists of a compact instrument and a novel multi-layer CE microchip.

  19. Sensitive quantitative detection/identification of infectious Cryptosporidium parvum oocysts by signature lipid biomarker analysis

    SciTech Connect

    White, D.C. |; Alugupalli, S.; Schrum, D.P.

    1997-08-01

    Unique signature lipid biomarkers were found in the acid-fast oocytes of Cryptosporidium parvum. This makes possible the rapid detection/identification and potential infectivity directly from drinking water membrane filtrates.

  20. The use of S-phenylmercapturic acid as a biomarker in molecular epidemiology studies of benzene.

    PubMed

    Farmer, Peter B; Kaur, Balvinder; Roach, Jonathan; Levy, Len; Consonni, Dario; Bertazzi, Pietro A; Pesatori, Angela; Fustinoni, Silvia; Buratti, Marina; Bonzini, Matteo; Colombi, Antonio; Popov, Todor; Cavallo, Domenico; Desideri, Arianna; Valerio, Federico; Pala, Mauro; Bolognesi, Claudia; Merlo, Franco

    2005-05-30

    S-Phenylmercapturic acid (S-PMA), is a urinary metabolite of benzene, thought to be derived from the condensation product of benzene oxide with glutathione. S-PMA may be determined by GC, HPLC (UV or fluorescence detection), GC-MS, LC-MS/MS or immunoassays. The limit of sensitivities of most of these techniques is 1 microg/l urine or below. It has been suggested that S-PMA may have value as a biomarker for low level human exposure to benzene, in view of the facts that urinary excretion of S-PMA has been found to be related to airborne benzene in occupationally exposed workers, and that only low background levels of S-PMA have been found in control subjects. We have evaluated the use of S-PMA as a biomarker, using a commercially available analytical service, in a multicentre European study of populations exposed to varying levels of benzene, in Italy (Milan, Genoa) and in Bulgaria (Sofia). These were filling station attendants, urban policemen, bus drivers, petrochemical workers and referents (a total of 623 subjects). S-PMA was measured at the end of the work shift by an immunoassay procedure. Urinary benzene (in Milan only) and the benzene metabolite trans,trans-muconic acid (t,t-MA) were measured before and after the work shift. Air-borne benzene was measured as a monitor of exposure. Urinary benzene was the most discriminatory biomarker and showed a relationship with airborne benzene at all levels of exposure studied (including groups exposed to <0.1 ppm benzene), whereas t,t-MA and S-PMA, as determined by immunoassay, were suitable only in the highest exposed workers (petrochemical industry, geometric mean 1765 microg/m3 (0.55 ppm) benzene). All three biomarkers were positively correlated with smoking as measured by urinary cotinine).

  1. Phospholipid fatty acid biomarkers in a freshwater periphyton community exposed to uranium: discovery by non-linear statistical learning

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Bunn, Amoret L.; Bailey, Vanessa L.

    2011-01-01

    Phospholipid fatty acids (PLFA) have been widely used to characterize environmental microbial communities, generating community profiles that can distinguish phylogenetic or functional groups within the community. The poor specificity of organism groups with fatty acid biomarkers in the classic PLFA-microorganism associations is a confounding factor in many of the statistical classification/clustering approaches traditionally used to interpret PLFA profiles. In this paper we demonstrate that non-linear statistical learning methods, such as a support vector machine (SVM), can more accurately find patterns related to uranyl nitrate exposure in a freshwater periphyton community than linear methods, such as partial least squares discriminant analysis. In addition, probabilistic models of exposure can be derived from the identified lipid biomarkers to demonstrate the potential model-based approach that could be used in remediation. The SVM probability model separates dose groups at accuracies of ~87.0%, ~71.4%, ~87.5%, and 100% for the four groups; Control (non-amended system), low-dose (amended at 10 µg U L-1), medium dose (amended at 100 µg U L-1), and high dose (500 µg U L-1). The SVM model achieved an overall cross-validated classification accuracy of ~87% in contrast to ~59% for the best linear classifier.

  2. Potential for proteomic approaches in determining efficacy biomarkers following administration of fish oils rich in omega-3 fatty acids: application in pancreatic cancers.

    PubMed

    Runau, Franscois; Arshad, Ali; Isherwood, John; Norris, Leonie; Howells, Lynne; Metcalfe, Matthew; Dennison, Ashley

    2015-06-01

    Pancreatic cancer is a disease with a significantly poor prognosis. Despite modern advances in other medical, surgical, and oncologic therapy, the outcome from pancreatic cancer has improved little over the last 40 years. To improve the management of this difficult disease, trials investigating the use of dietary and parenteral fish oils rich in omega-3 (ω-3) fatty acids, exhibiting proven anti-inflammatory and anticarcinogenic properties, have revealed favorable results in pancreatic cancers. Proteomics is the large-scale study of proteins that attempts to characterize the complete set of proteins encoded by the genome of an organism and that, with the use of sensitive mass spectrometric-based techniques, has allowed high-throughput analysis of the proteome to aid identification of putative biomarkers pertinent to given disease states. These biomarkers provide useful insight into potentially discovering new markers for early detection or elucidating the efficacy of treatment on pancreatic cancers. Here, our review identifies potential proteomic-based biomarkers in pancreatic cancer relating to apoptosis, cell proliferation, angiogenesis, and metabolic regulation in clinical studies. We also reviewed proteomic biomarkers from the administration of ω-3 fatty acids that act on similar anticarcinogenic pathways as above and reflect that proteomic studies on the effect of ω-3 fatty acids in pancreatic cancer will yield favorable results.

  3. Fatty Acid Synthesis Intermediates Represent Novel Noninvasive Biomarkers of Prostate Cancer Chemoprevention by Phenethyl Isothiocyanate.

    PubMed

    Singh, Krishna B; Singh, Shivendra V

    2017-03-14

    Increased de novo synthesis of fatty acids is a distinctive feature of prostate cancer, which continues to be a leading cause of cancer-related deaths among American men. Therefore, inhibition of de novo fatty acid synthesis represents an attractive strategy for chemoprevention of prostate cancer. We have shown previously that dietary feeding of phenethyl isothiocyanate (PEITC), a phytochemical derived from edible cruciferous vegetables such as watercress, inhibits incidence and burden of poorly-differentiated prostate cancer in Transgenic Adenocarcinoma of Mouse Prostate (TRAMP) model. The present study was designed to test the hypothesis of whether fatty acid intermediate(s) can serve as noninvasive biomarker(s) of prostate cancer chemoprevention by PEITC using archived plasma and tumor specimens from the TRAMP study as well as cellular models of prostate cancer. Exposure of prostate cancer cells (LNCaP and 22Rv1) to pharmacological concentrations of PEITC resulted in downregulation of key fatty acid metabolism proteins, including acetyl-CoA carboxylase 1 (ACC1), fatty acid synthase (FASN), and carnitine palmitoyltransferase 1A (CPT1A). The mRNA expression of FASN and CPT1A as well as acetyl-CoA levels were decreased by PEITC treatment in both cell lines. PEITC administration to TRAMP mice also resulted in a significant decrease in tumor expression of FASN protein. Consistent with these findings, the levels of total free fatty acids, total phospholipids, triglyceride, and ATP were significantly lower in the plasma and/or prostate tumors of PEITC-treated TRAMP mice compared with controls. The present study is the first to implicate inhibition of fatty acid synthesis in prostate cancer chemoprevention by PEITC.

  4. Bile acid aspiration associated with lung chemical profile linked to other biomarkers of injury after lung transplantation.

    PubMed

    Neujahr, D C; Uppal, K; Force, S D; Fernandez, F; Lawrence, C; Pickens, A; Bag, R; Lockard, C; Kirk, A D; Tran, V; Lee, K; Jones, D P; Park, Y

    2014-04-01

    Aspiration of gastrointestinal contents has been linked to worse outcomes following lung transplantation but uncertainty exists about underlying mechanisms. We applied high-resolution metabolomics of bronchoalveolar lavage fluid (BALF) in patients with episodic aspiration (defined by bile acids in the BALF) to identify potential metabolic changes associated with aspiration. Paired samples, one with bile acids and another without, from 29 stable lung transplant patients were studied. Liquid chromatography coupled to high-resolution mass spectroscopy was used to interrogate metabolomic contents of these samples. Data were obtained for 7068 ions representing intermediary metabolites, environmental agents and chemicals associated with microbial colonization. A substantial number (2302) differed between bile acid positive and negative samples when analyzed by false discovery rate at q = 0.01. These included pathways associated with microbial metabolism. Hierarchical cluster analysis defined clusters of chemicals associated with bile acid aspiration that were correlated to previously reported biomarkers of lung injury including T cell granzyme B level and the chemoattractants CXCL9 and CXCL10. These data specifically link bile acids presence in lung allografts to inflammatory pathways known to segregate with worsening allograft outcome, and provide additional mechanistic insight into the association between reflux and lung allograft injury.

  5. Sublineage structure analysis of Mycobacterium tuberculosis complex strains using multiple-biomarker tensors

    PubMed Central

    2011-01-01

    Background Strains of Mycobacterium tuberculosis complex (MTBC) can be classified into major lineages based on their genotype. Further subdivision of major lineages into sublineages requires multiple biomarkers along with methods to combine and analyze multiple sources of information in one unsupervised learning model. Typically, spacer oligonucleotide type (spoligotype) and mycobacterial interspersed repetitive units (MIRU) are used for TB genotyping and surveillance. Here, we examine the sublineage structure of MTBC strains with multiple biomarkers simultaneously, by employing a tensor clustering framework (TCF) on multiple-biomarker tensors. Results Simultaneous analysis of the spoligotype and MIRU type of strains using TCF on multiple-biomarker tensors leads to coherent sublineages of major lineages with clear and distinctive spoligotype and MIRU signatures. Comparison of tensor sublineages with SpolDB4 families either supports tensor sublineages, or suggests subdivision or merging of SpolDB4 families. High prediction accuracy of major lineage classification with supervised tensor learning on multiple-biomarker tensors validates our unsupervised analysis of sublineages on multiple-biomarker tensors. Conclusions TCF on multiple-biomarker tensors achieves simultaneous analysis of multiple biomarkers and suggest a new putative sublineage structure for each major lineage. Analysis of multiple-biomarker tensors gives insight into the sublineage structure of MTBC at the genomic level. PMID:21988942

  6. Glyphosate spray drift in Coffea arabica - sensitivity of coffee plants and possible use of shikimic acid as a biomarker for glyphosate exposure.

    PubMed

    Schrübbers, Lars C; Valverde, Bernal E; Sørensen, Jens C; Cedergreen, Nina

    2014-10-01

    Glyphosate is widely used in coffee plantations to control weeds. Lacking selectivity, glyphosate spray drift is suspected to cause adverse effects in coffee plants. Symptoms caused by glyphosate can be similar to those produced by other stress factors. However, shikimic acid accumulation should be a useful biomarker for glyphosate exposure as shown for other crops. The aim of this study was to assess the sensitivity of coffee plants towards glyphosate on different biological response variables and to evaluate the use of shikimic acid as biomarker. Dose-response experiments yielded ED50 values (50% effect dose) in the range of 38-550 ga.e.ha(-1) depending on the quantitative or qualitative variable monitored. The frequency of plants showing symptoms was the most sensitive variable. The best sampling time for shikimic acid accumulation was 1-2 weeks after glyphosate application, depending on experimental conditions. The highest shikimic acid accumulation was observed in young leaves. Shikimic acid is a suitable biomarker for a glyphosate exposure in coffee, using only young leaves for the analysis. Young coffee plants are susceptible to glyphosate damage. If symptoms are absent the risk of severe crop damage or yield loss is low.

  7. Intra-articular hyaluronic acid increases cartilage breakdown biomarker in patients with knee osteoarthritis.

    PubMed

    Gonzalez-Fuentes, Alexandra M; Green, David M; Rossen, Roger D; Ng, Bernard

    2010-06-01

    Intra-articular hyaluronic acid has been used in treatment of patients with knee osteoarthritis. Though its effect on pain has been well studied, it is not clear how it affects the articular cartilage. This is a preliminary study to evaluate the kinetics of urinary collagen type-II C-telopeptide (CTX-II) as a biomarker of collagen breakdown in response to intra-articular hyaluronic acid injection in patients with symptomatic knee osteoarthritis. Intra-articular injections of hyaluronan were administered to ten patients with symptomatic knee osteoarthritis. Urine collection for urinary CTX-II was obtained at baseline, before each injection and once every other week for a total of 6 months. Urine CTX-II was measured using a CartiLaps(c) ELISA kit. There was a statistically significant increase (p = 0.0136) in CTX-II a week after the third intra-articular injection of hyaluronic acid (6,216 ng/mmol +/- 4,428) compared with baseline (2,233 ng/mmol +/- 1,220). This increase in CTX-II was sustained throughout the entire 6 months follow-up period (repeated measures ANOVA, p < 0.015). This is the first study of changes in an osteoarthritis biomarker after intra-articular hyaluronic acid injections in patients with symptomatic knee osteoarthritis. Contrary to our initial hypothesis that CTX-II levels should decrease after intra-articular hyaluronic acid injections, we found a significant increase in urinary CTX-II levels that was sustained throughout the study. These observations suggest that intra-articular hyaluronic acid injections may accelerate cartilage breakdown in patients with symptomatic knee osteoarthritis. The responsible mechanisms are unknown and warrant further study.

  8. Extracellular Fatty Acid Synthase: A Possible Surrogate Biomarker of Insulin Resistance

    PubMed Central

    Fernandez-Real, Jose Manuel; Menendez, Javier A.; Moreno-Navarrete, Jose Maria; Blüher, Matthias; Vazquez-Martin, Alejandro; Vázquez, María Jesús; Ortega, Francisco; Diéguez, Carlos; Frühbeck, Gema; Ricart, Wifredo; Vidal-Puig, Antonio

    2010-01-01

    CONTEXT Circulating fatty acid synthase (FASN) is a biomarker of metabolically demanding human diseases. The aim of this study was to determine whether circulating FASN could be a biomarker of overnutrition-induced metabolic stress and insulin resistance in common metabolic disorders. RESEARCH DESIGN AND METHODS Circulating FASN was evaluated in two cross-sectional studies in association with insulin sensitivity and in four longitudinal studies investigating the effect of diet- and surgery-induced weight loss, physical training, and adipose tissue expansion using peroxisome proliferator–activated receptor agonist rosiglitazone on circulating FASN. RESULTS Age- and BMI-adjusted FASN concentrations were significantly increased in association with obesity-induced insulin resistance in two independent cohorts. Both visceral and subcutaneous FASN expression and protein levels correlated inversely with extracellular circulating FASN (P = −0.63; P < 0.0001), suggesting that circulating FASN is linked to depletion of intracellular FASN. Improved insulin sensitivity induced by therapeutic strategies that decreased fat mass (diet induced, surgery induced, or physical training) all led to decreased FASN levels in blood (P values between 0.02 and 0.04). To discriminate whether this was an effect related to insulin sensitization, we also investigated the effects of rosiglitazone. Rosiglitazone did not lead to significant changes in circulating FASN concentration. CONCLUSIONS Our results suggest that circulating FASN is a biomarker of overnutrition-induced insulin resistance that could provide diagnostic and prognostic advantages by providing insights on the individualized metabolic stress. PMID:20299470

  9. Nucleic acids within urinary exosomes/microvesicles are potential biomarkers for renal disease

    PubMed Central

    Miranda, Kevin C.; Bond, Daniel T.; McKee, Mary; Skog, Johan; Păunescu, Teodor G.; Da Silva, Nicolas; Brown, Dennis; Russo, Leileata M.

    2015-01-01

    Urinary exosomes or microvesicles are being studied intensively to identify potential new biomarkers for renal disease. We sought to identify whether these microvesicles contain nucleic acids. We isolated microvesicles from human urine in the same density range as that previously described for urinary exosomes and found them to have an RNA integrity profile similar to that of kidney tissue, including 18S and 28S rRNA. This profile was better preserved in urinary microvesicles compared with whole cells isolated from urine, suggesting that microvesicles may protect RNA during urine passage. We were able to detect mRNA in the human urinary microvesicles encoding proteins from all regions of the nephron and the collecting duct. Further, to provide a proof of principle, we found that microvesicles isolated from the urine of the V-ATPase B1 subunit knockout mice lacked mRNA of this subunit while containing a normal amount of the B2 subunit and aquaporin 2. The microvesicles were found to be contaminated with extraneous DNA potentially on their surface; therefore, we developed a rapid and reliable means to isolate nucleic acids from within urine microvesicles devoid of this extraneous contamination. Our study provides an experimental strategy for the routine isolation and use of urinary microvesicles as a novel and non-invasive source of nucleic acids to further renal disease biomarker discovery. PMID:20428099

  10. Aspartic acid in the hippocampus: a biomarker for postoperative cognitive dysfunction

    PubMed Central

    Hu, Rong; Huang, Dong; Tong, Jianbin; Liao, Qin; Hu, Zhonghua; Ouyang, Wen

    2014-01-01

    This study established an aged rat model of cognitive dysfunction using anesthesia with 2% isoflurane and 80% oxygen for 2 hours. Twenty-four hours later, Y-maze test results showed that isoflurane significantly impaired cognitive function in aged rats. Gas chromatography-mass spectrometry results showed that isoflurane also significantly increased the levels of N,N-diethylacetamide, n-ethylacetamide, aspartic acid, malic acid and arabinonic acid in the hippocampus of isoflurane-treated rats. Moreover, aspartic acid, N,N-diethylacetamide, n-ethylacetamide and malic acid concentration was positively correlated with the degree of cognitive dysfunction in the isoflurane-treated rats. It is evident that hippocampal metabolite changes are involved in the formation of cognitive dysfunction after isoflurane anesthesia. To further verify these results, this study cultured hippocampal neurons in vitro, which were then treated with aspartic acid (100 μmol/L). Results suggested that aspartic acid concentration in the hippocampus may be a biomarker for predicting the occurrence and disease progress of cognitive dysfunction. PMID:25206795

  11. Diagnostic capability of salivary biomarkers in the assessment of head and neck cancer: A systematic review and meta-analysis.

    PubMed

    Guerra, Eliete Neves Silva; Acevedo, Ana Carolina; Leite, André Ferreira; Gozal, David; Chardin, Hélène; De Luca Canto, Graziela

    2015-09-01

    The purpose of this systematic review and meta-analysis was to evaluate the diagnostic value of salivary biological markers in the diagnosis of head and neck carcinoma. Studies were gathered by searching Cochrane, EMBASE, LILACS, MEDLINE, and PubMed. The references were also crosschecked and a partial grey literature search was undertaken using Google Scholar. The methodology of selected studies was evaluated using the 14-item Quality Assessment Tool for Diagnostic Accuracy Studies. After a two-step selection process, 15 articles were identified and subjected to qualitative and quantitative analyses. The studies were homogeneous, and all had high methodological quality. Combined biomarkers demonstrated better accuracy with higher sensitivity and specificity than those tested individually. Furthermore, the salivary biomarkers reviewed predicted the early stages of head and neck carcinoma better than the advanced stages. A restricted set of five single biomarkers (interleukin-8, choline, pipecolinic acid, l-phenylalanine, and S-carboxymethyl-l-cysteine) as well as combined biomarkers demonstrated excellent diagnostic test accuracy. The present systematic review confirms the potential value of a selected set of salivary biomarkers as diagnostic tools for head and neck carcinoma.

  12. CSF xanthine, homovanillic acid, and their ratio as biomarkers of Parkinson's disease.

    PubMed

    LeWitt, Peter; Schultz, Lonni; Auinger, Peggy; Lu, Mei

    2011-08-23

    Diminished nigrostriatal dopaminergic neurotransmission is a biochemical hallmark of Parkinson's disease. Despite this, a reliable trait biomarker of sporadic Parkinson's disease has not emerged from measurements of cerebrospinal fluid dopamine metabolites. Previous studies have highlighted strong neurochemical relationships between dopamine and various purine compounds. In this study, we analyzed cerebrospinal fluid concentrations of homovanillic acid (the major catabolite of dopamine) and the purine compound xanthine for a comparison of 217 unmedicated Parkinson's disease subjects and 26 healthy controls. These compounds were highly correlated for both the Parkinson's disease subjects (r=0.68) and for controls (r=0.73; both groups, p<0.001). While neither homovanillic acid nor xanthine concentrations differentiated Parkinson's disease from controls, their ratio did. For controls, the mean [xanthine]/[homovanillic acid] quotient was 13.1±5.5 as compared to the Parkinson's disease value of 17.4±6.7 at an initial lumbar CSF collection (p=0.0017), and 19.7±8.7 (p<0.001) at a second CSF collection up to 24 months later. The [xanthine]/[homovanillic acid] ratio in the Parkinson's disease subjects differed as a function of disease severity, as measured by the sum of Unified Parkinson's Disease Rating Scale Activities of Daily Living and Motor Exam ratings. The [xanthine]/[homovanillic acid] ratio also increased between the first and second CSF collections, suggesting that this quotient provides both a state and trait biomarker of Parkinson's disease. These observations add to other neurochemical evidence that links purine metabolism to Parkinson's disease.

  13. Data mining for biomarker development: a review of tissue specificity analysis.

    PubMed

    Klee, Eric W

    2008-03-01

    Novel biomarker development requires a significant resource commitment to translate candidate markers into clinical assays. Consequently, it is imperative high quality candidates are selected early in a biomarker development program. High throughput gene expression data are routinely used to identify transcripts differentially expressed in diseased versus normal samples. Data-mining Expressed Sequence Tag, Serial Analysis of Gene Expression, Massively Parallel Signature Sequencing, and microarray expression databases can provide additional information on the expression of candidate biomarkers across multiple tissues, organs, and disease states. From this information, quantitative measures of tissue-specific gene specificity are computed and used to guide candidate biomarker selection.

  14. Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery

    PubMed Central

    Farrar, Jason E.; Considine, Michael; Wei, Yingying; Meshinchi, Soheil; Arceci, Robert J.

    2014-01-01

    Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, including gene mutation, epigenetic changes in gene promoters, overexpression, and gene amplifications or deletions. We demonstrate a novel approach that identifies pathways of interest by integrating outlier analysis within and across molecular data types with gene set analysis. We use the results to seed the top-scoring pair algorithm to identify robust biomarkers associated with pathway deregulation. We demonstrate this methodology on pediatric acute myeloid leukemia (AML) data. We develop a biomarker in primary AML tumors, demonstrate robustness with an independent primary tumor data set, and show that the identified biomarkers also function well in relapsed pediatric AML tumors. PMID:26356020

  15. Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery.

    PubMed

    Ochs, Michael F; Farrar, Jason E; Considine, Michael; Wei, Yingying; Meshinchi, Soheil; Arceci, Robert J

    2014-01-01

    Pathway deregulation has been identified as a key driver of carcinogenesis, with proteins in signaling pathways serving as primary targets for drug development. Deregulation can be driven by a number of molecular events, including gene mutation, epigenetic changes in gene promoters, overexpression, and gene amplifications or deletions. We demonstrate a novel approach that identifies pathways of interest by integrating outlier analysis within and across molecular data types with gene set analysis. We use the results to seed the top-scoring pair algorithm to identify robust biomarkers associated with pathway deregulation. We demonstrate this methodology on pediatric acute myeloid leukemia (AML) data. We develop a biomarker in primary AML tumors, demonstrate robustness with an independent primary tumor data set, and show that the identified biomarkers also function well in relapsed pediatric AML tumors.

  16. P4 radiology of hepatobiliary diseases with gadoxetic acid-enhanced MRI as a biomarker.

    PubMed

    Ba-Ssalamah, Ahmed; Qayyum, Aliya; Bastati, Nina; Fakhrai, Negar; Herold, Christian J; Caseiro Alves, Filipe

    2014-02-01

    A recent paradigm shift in radiology has focused on the globalization of so-called P4 radiology. P4 radiology represents delivery of imaging results that are predictive, personalized, pre-emptive and participatory. The combination of the P4 approach and biomarkers is particularly pertinent to MRI, especially with technological advances such as diffusion-weighted imaging. The development of new liver-specific MRI contrast media, particularly gadoxetic acid, demonstrate specific pharmacokinetic properties, which provide combined morphologic and functional information in the same setting. The evaluation of hepatobiliary pathology beyond morphology gives rise to the possibilty of using gadoxetic acid-enhanced MRI as an imaging biomarker of hepatobiliary diseases. The integration of functional imaging with an understanding of complex disease mechanisms forms the basis for P4 radiology, which may ultimately lead to individualized, cost-effective, targeted therapy for patients. This will enable radiologists to determine the prognosis of the disease and estimate early response to treatment, with the participation of all the required medical disciplines.

  17. Source identification analysis for the airborne bacteria and fungi using a biomarker approach

    NASA Astrophysics Data System (ADS)

    Lee, Alex K. Y.; Lau, Arthur P. S.; Cheng, Jessica Y. W.; Fang, Ming; Chan, Chak K.

    Our recent studies have reported the feasibility of employing the 3-hydoxy fatty acids (3-OH FAs) and ergosterol as biomarkers to determine the loading of the airborne endotoxin from the Gram-negative bacteria and fungal biomass in atmospheric aerosols, respectively [Lee, A.K.Y., Chan, C.K., Fang, K., Lau, A.P.S., 2004. The 3-hydroxy fatty acids as biomarkers for quantification and characterization of endotoxins and Gram-negative bacteria in atmospheric aerosols in Hong Kong. Atmospheric Environment 38, 6807-6317; Lau, A.P.S., Lee, A.K.Y., Chan, C.K., Fang, K., 2006. Ergosterol as a biomarker for the quantification of the fungal biomass in atmospheric aerosols. Atmospheric Environment 40, 249-259]. These quantified biomarkers do not, however, provide information on their sources. In this study, the year-long dataset of the endotoxin and ergosterol measured in Hong Kong was integrated with the common water-soluble inorganic ions for source identification through the principal component analysis (PCA) and backward air mass trajectory analysis. In the coarse particles (PM 2.5-10), the bacterial endotoxin is loaded in the same factor group with Ca 2+ and accounted for about 20% of the total variance of the PCA. This implies the crustal origin for the airborne bacterial assemblage. The fungal ergosterol in the coarse particles (PM 2.5-10) had by itself loaded in a factor group of 10.8% of the total variance in one of the sampling sites with large area of natural vegetative coverage. This suggests the single entity nature of the fungal spores and their independent emission to the ambient air upon maturation of their vegetative growth. In the fine particles (

  18. Lipid biomarker analysis for the quantitative analysis of airborne microorganisms

    SciTech Connect

    Macnaughton, S.J.; Jenkins, T.L.; Cormier, M.R.

    1997-08-01

    There is an ever increasing concern regarding the presence of airborne microbial contaminants within indoor air environments. Exposure to such biocontaminants can give rise to large numbers of different health effects including infectious diseases, allergenic responses and respiratory problems, Biocontaminants typically round in indoor air environments include bacteria, fungi, algae, protozoa and dust mites. Mycotoxins, endotoxins, pollens and residues of organisms are also known to cause adverse health effects. A quantitative detection/identification technique independent of culturability that assays both culturable and non culturable biomass including endotoxin is critical in defining risks from indoor air biocontamination. Traditionally, methods employed for the monitoring of microorganism numbers in indoor air environments involve classical culture based techniques and/or direct microscopic counting. It has been repeatedly documented that viable microorganism counts only account for between 0.1-10% of the total community detectable by direct counting. The classic viable microbiologic approach doe`s not provide accurate estimates of microbial fragments or other indoor air components that can act as antigens and induce or potentiate allergic responses. Although bioaerosol samplers are designed to damage the microbes as little as possible, microbial stress has been shown to result from air sampling, aerosolization and microbial collection. Higher collection efficiency results in greater cell damage while less cell damage often results in lower collection efficiency. Filtration can collect particulates at almost 100% efficiency, but captured microorganisms may become dehydrated and damaged resulting in non-culturability, however, the lipid biomarker assays described herein do not rely on cell culture. Lipids are components that are universally distributed throughout cells providing a means to assess independent of culturability.

  19. Identification of organic acids as potential biomarkers in the urine of autistic children using gas chromatography/mass spectrometry.

    PubMed

    Kałużna-Czaplińska, Joanna; Żurawicz, Ewa; Struck, Wiktoria; Markuszewski, Michał

    2014-09-01

    There is a need to identify metabolic phenotypes in autism as they might each require unique approaches to prevention. Biological markers can help define autism subtypes and reveal potential therapeutic targets. The aim of the study was to identify alterations of small molecular weight compounds and to find potential biomarkers. Gas chromatography/mass spectrometry was employed to evaluate major metabolic changes in low molecular weight urine metabolites of 14 children with autism spectrum disorders vs. 10 non-autistic subjects. The results prove the usefulness of an identified set of 21 endogenous compounds (including 14 organic acids), whose levels are changed in diseased children. Gas chromatography/mass spectrometry method combined with multivariate statistical analysis techniques provide an efficient way of depicting metabolic perturbations of diseases, and may potentially be applicable as a novel strategy for the noninvasive diagnosis and treatment of autism.

  20. Inflammation as a predictive biomarker for response to omega-3 fatty acids in major depressive disorder: a proof-of-concept study.

    PubMed

    Rapaport, M H; Nierenberg, A A; Schettler, P J; Kinkead, B; Cardoos, A; Walker, R; Mischoulon, D

    2016-01-01

    This study explores whether inflammatory biomarkers act as moderators of clinical response to omega-3 (n-3) fatty acids in subjects with major depressive disorder (MDD). One hundred fifty-five subjects with Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV) MDD, a baseline 17-item Hamilton Depression Rating Scale (HAM-D-17) score ⩾ 15 and baseline biomarker data (interleukin (IL)-1ra, IL-6, high-sensitivity C-reactive protein (hs-CRP), leptin and adiponectin) were randomized between 18 May 2006 and 30 June 2011 to 8 weeks of double-blind treatment with eicosapentaenoic acid (EPA)-enriched n-3 1060 mg day(-1), docosahexaenoic acid (DHA)-enriched n-3 900 mg day(-1) or placebo. Outcomes were determined using mixed model repeated measures analysis for 'high' and 'low' inflammation groups based on individual and combined biomarkers. Results are presented in terms of standardized treatment effect size (ES) for change in HAM-D-17 from baseline to treatment week 8. Although overall treatment group differences were negligible (ES=-0.13 to +0.04), subjects with any 'high' inflammation improved more on EPA than placebo (ES=-0.39) or DHA (ES=-0.60) and less on DHA than placebo (ES=+0.21); furthermore, EPA-placebo separation increased with increasing numbers of markers of high inflammation. Subjects randomized to EPA with 'high' IL-1ra or hs-CRP or low adiponectin ('high' inflammation) had medium ES decreases in HAM-D-17 scores vs subjects 'low' on these biomarkers. Subjects with 'high' hs-CRP, IL-6 or leptin were less placebo-responsive than subjects with low levels of these biomarkers (medium to large ES differences). Employing multiple markers of inflammation facilitated identification of a more homogeneous cohort of subjects with MDD responding to EPA vs placebo in our cohort. Studies are needed to replicate and extend this proof-of-concept work.

  1. Evaluation and identification of dioxin exposure biomarkers in human urine by high-resolution metabolomics, multivariate analysis and in vitro synthesis.

    PubMed

    Jeanneret, Fabienne; Tonoli, David; Hochstrasser, Denis; Saurat, Jean-Hilaire; Sorg, Olivier; Boccard, Julien; Rudaz, Serge

    2016-01-05

    A previous high-resolution metabolomic study pointed out a dysregulation of urinary steroids and bile acids in human cases of acute dioxin exposure. A subset of 24 compounds was highlighted as putative biomarkers. The aim of the current study was (i) to evaluate the 24 biomarkers in an independent human cohort exposed to dioxins released from the incineration fumes of a municipal waste incinerator and; (ii) to identify them by comparison with authentic chemical standards and biosynthesised products obtained with in vitro metabolic reactions. An orthogonal projection to latent structures discriminant analysis built on biomarker profiles measured in the intoxicated cohort and the controls separated both groups with reported values of 93.8%; 100% and 87.5% for global accuracy; sensitivity and specificity; respectively. These results corroborated the 24 compounds as exposure biomarkers; but a definite identification was necessary for a better understanding of dioxin toxicity. Dehydroepiandrosterone 3β-sulfate, androsterone 3α-glucuronide, androsterone 3α-sulfate, pregnanediol 3α-glucuronide and 11-ketoetiocholanolone 3α-glucuronide were identified by authentic standards. Metabolic reactions characterised four biomarkers: glucuronide conjugates of 11β-hydroxyandrosterone; glycochenodeoxycholic acid and glycocholic acid produced in human liver microsomes and glycoursodeoxycholic acid sulfate generated in cytosol fraction. The combination of metabolomics by high-resolution mass spectrometry with in vitro metabolic syntheses confirmed a perturbed profile of steroids and bile acids in human cases of dioxin exposure.

  2. Analysis of biomarker utility using a PBPK/PD model for carbaryl

    PubMed Central

    Phillips, Martin B.; Yoon, Miyoung; Young, Bruce; Tan, Yu-Mei

    2014-01-01

    There are many types of biomarkers; the two common ones are biomarkers of exposure and biomarkers of effect. The utility of a biomarker for estimating exposures or predicting risks depends on the strength of the correlation between biomarker concentrations and exposure/effects. In the current study, a combined exposure and physiologically-based pharmacokinetic/pharmacodynamic (PBPK/PD) model of carbaryl was used to demonstrate the use of computational modeling for providing insight into the selection of biomarkers for different purposes. The Cumulative and Aggregate Risk Evaluation System (CARES) was used to generate exposure profiles, including magnitude and timing, for use as inputs to the PBPK/PD model. The PBPK/PD model was then used to predict blood concentrations of carbaryl and urine concentrations of its principal metabolite, 1-naphthol (1-N), as biomarkers of exposure. The PBPK/PD model also predicted acetylcholinesterase (AChE) inhibition in red blood cells (RBC) as a biomarker of effect. The correlations of these simulated biomarker concentrations with intake doses or brain AChE inhibition (as a surrogate of effects) were analyzed using a linear regression model. Results showed that 1-N in urine is a better biomarker of exposure than carbaryl in blood, and that 1-N in urine is correlated with the dose averaged over the last 2 days of the simulation. They also showed that RBC AChE inhibition is an appropriate biomarker of effect. This computational approach can be applied to a wide variety of chemicals to facilitate quantitative analysis of biomarker utility. PMID:25477820

  3. Enzymatic analysis of α-ketoglutaramate—A biomarker for hyperammonemia

    PubMed Central

    Halámková, Lenka; Mailloux, Shay; Halámek, Jan; Cooper, Arthur J.L.; Katz, Evgeny

    2012-01-01

    Two enzymatic assays were developed for the analysis of α-ketoglutaramate (KGM)—an important biomarker of hepatic encephalopathy and other hyperammonemic diseases. In both procedures, KGM is first converted to α-ketoglutarate (KTG) via a reaction catalyzed by ω-amidase (AMD). In the first procedure, KTG generated in the AMD reaction initiates a biocatalytic cascade in which the concerted action of alanine transaminase and lactate dehydrogenase results in the oxidation of NADH. In the second procedure, KTG generated from KGM is reductively aminated, with the concomitant oxidation of NADH, in a reaction catalyzed by L-glutamic dehydrogenase. In both assays, the decrease in optical absorbance (λ=340 nm) corresponding to NADH oxidation is used to quantify concentrations of KGM. The two analytical procedures were applied to 50% (v/v) human serum diluted with aqueous solutions containing the assay components and spiked with concentrations of KGM estimated to be present in normal human plasma and in plasma from hyperammonemic patients. Since KTG is the product of AMD-catalyzed hydrolysis of KGM, in a separate study, this compound was used as a surrogate for KGM. Statistical analyses of samples mimicking the concentration of KGM assumed to be present in normal and pathological concentration ranges were performed. Both enzymatic assays for KGM were confirmed to discriminate between the predicted normal and pathophysiological concentrations of the analyte. The present study is the first step toward the development of a clinically useful probe for KGM analysis in biological fluids. PMID:23141304

  4. Fatty acid profiles as a potential lipidomic biomarker of exposure to brevetoxin for endangered Florida manatees (Trichechus manatus latirostris).

    PubMed

    Wetzel, Dana L; Reynolds, John E; Sprinkel, Jay M; Schwacke, Lori; Mercurio, Philip; Rommel, Sentiel A

    2010-11-15

    Fatty acid signature analysis (FASA) is an important tool by which marine mammal scientists gain insight into foraging ecology. Fatty acid profiles (resulting from FASA) represent a potential biomarker to assess exposure to natural and anthropogenic stressors. Florida manatees are well studied, and an excellent necropsy program provides a basis against which to assess this budding tool. Results using samples from 54 manatees assigned to four cause-of-death categories indicated that those animals exposed to or that died due to brevetoxin exposure (red tide, or RT samples) demonstrate a distinctive hepatic fatty acid profile. Discriminant function analysis indicated that hepatic fatty acids could be used to classify RT versus non-RT liver samples with reasonable certainty. A discriminant function was derived based on 8 fatty acids which correctly classified 100% of samples from a training dataset (10 RT and 25 non-RT) and 85% of samples in a cross-validation dataset (5 RT and 13 non-RT). Of the latter dataset, all RT samples were correctly classified, but two of thirteen non-RT samples were incorrectly classified. However, the "incorrect" samples came from manatees that died due to other causes during documented red tide outbreaks; thus although the proximal cause of death was due to watercraft collisions, exposure to brevetoxin may have affected these individuals in ways that increased their vulnerability. This use of FASA could: a) provide an additional forensic tool to help scientists and managers to understand cause of death or debilitation due to exposure to red tide in manatees; b) serve as a model that could be applied to studies to improve assessments of cause of death in other marine mammals; and c) be used, as in humans, to help diagnose metabolic disorders or disease states in manatees and other species.

  5. Bacillus cereus cell response upon exposure to acid environment: toward the identification of potential biomarkers

    PubMed Central

    Desriac, Noémie; Broussolle, Véronique; Postollec, Florence; Mathot, Anne-Gabrielle; Sohier, Danièle; Coroller, Louis; Leguerinel, Ivan

    2013-01-01

    Microorganisms are able to adapt to different environments and evolve rapidly, allowing them to cope with their new environments. Such adaptive response and associated protections toward other lethal stresses, is a crucial survival strategy for a wide spectrum of microorganisms, including food spoilage bacteria, pathogens, and organisms used in functional food applications. The growing demand for minimal processed food yields to an increasing use of combination of hurdles or mild preservation factors in the food industry. A commonly used hurdle is low pH which allows the decrease in bacterial growth rate but also the inactivation of pathogens or spoilage microorganisms. Bacillus cereus is a well-known food-borne pathogen leading to economical and safety issues in food industry. Because survival mechanisms implemented will allow bacteria to cope with environmental changes, it is important to provide understanding of B. cereus stress response. Thus this review deals with the adaptive traits of B. cereus cells facing to acid stress conditions. The acid stress response of B. cereus could be divided into four groups (i) general stress response (ii) pH homeostasis, (iii) metabolic modifications and alkali production and (iv) secondary oxidative stress response. This current knowledge may be useful to understand how B. cereus cells may cope to acid environment such as encountered in food products and thus to find some molecular biomarkers of the bacterial behavior. These biomarkers could be furthermore used to develop new microbial behavior prediction tools which can provide insights into underlying molecular physiological states which govern the behavior of microorganisms and thus opening the avenue toward the detection of stress adaptive behavior at an early stage and the control of stress-induced resistance throughout the food chain. PMID:24106490

  6. Hippuric acid in 24 h urine collections as a biomarker of fruits and vegetables intake in kidney stone formers.

    PubMed

    Guerra, Angela; Folesani, Giuseppina; Mena, Pedro; Ticinesi, Andrea; Allegri, Franca; Nouvenne, Antonio; Pinelli, Silvana; Del Rio, Daniele; Borghi, Loris; Meschi, Tiziana

    2014-12-01

    This work aimed to underline the prospects of hippuric acid, a product of the metabolism of polyphenols, as a new biomarker of fruits and vegetables intake associated with lithogenic risk. Biochemical parameters of lithogenic risk and hippuric acid were measured in the 24 h urine collections of a cohort of 696 Italian kidney stone formers divided into two subgroups according to their different dietary habits. The link between lithogenic risk parameters and hippuric acid was assessed and this compound was revealed as a valuable biomarker of fruits and vegetables intake in kidney stone formers. A cut-off value of urinary excretion of hippuric acid, 300 mg/24 h, was set as the threshold of discrimination between low and high intake of fruits and vegetables for these patients. These results highlight the importance of monitoring of the excretion hippuric acid in urine to address proper dietary guidelines for the management of stone former patients.

  7. Preliminary Use of Uric Acid as a Biomarker for Wading Birds on Everglades Tree Islands, Florida, United States

    USGS Publications Warehouse

    Bates, Anne L.; Orem, William H.; Newman, Susan; Gawlik, Dale E.; Lerch, Harry E.; Corum, Margo D.; Van Winkle, Monica

    2010-01-01

    Concentrations of organic biomarkers and concentrations of phosphorus in soil cores can potentially be used as proxies for historic population densities of wading birds on tree islands in the Florida Everglades. This report focuses on establishing a link between the organic biomarker uric acid found in wading bird guano and the high phosphorus concentrations in tree island soils in the Florida Everglades. Uric acid was determined in soil core sections, in surface samples, and in bird guano by using a method of high-performance liquid chromatography-mass spectrometry (HPLC-MS) developed for this purpose. Preliminary results show an overall correlation between uric acid and total phosphorus in three soil cores, with a general trend of decreasing concentrations of both uric acid and phosphorus with depth. However, we have also found no uric acid in a soil core having high concentrations of phosphorus. We believe that this result may be explained by different geochemical circumstances at that site.

  8. 3-hydroxykynurenine and other Parkinson's disease biomarkers discovered by metabolomic analysis.

    PubMed

    Lewitt, Peter A; Li, Jia; Lu, Mei; Beach, Thomas G; Adler, Charles H; Guo, Lining

    2013-10-01

    Parkinson's disease (PD) biomarkers are needed to enhance therapeutics research and to understand PD pathogenesis. Methods that simultaneously measure hundreds of small molecular-weight compounds-metabolomic analysis-"fingerprint" disease-specific alterations in individual compounds or metabolic pathways. Beyond a nontargeted search for PD biomarkers, we hypothesized that PD cerebrospinal fluid would show increased formation of the excitotoxin 3-hydroxykynurenine and diminished concentration of the antioxidant glutathione. Cerebrospinal fluid was collected at <4 hours postmortem from 48 pathologically-verified PD subjects and 57 comparably-aged controls. Assays involved ultra-high-performance liquid and gas chromatography linked to mass spectrometry. We used univariate techniques to determine fold-changes in concentrations of biochemicals; false-discovery rates were calculated to exclude spurious findings. Data was modeled using a Support Vector Machine for analyzing compounds selected by Welch's t test. Classification accuracy was determined by cross-validation. Of 243 structurally-identified biochemicals,19 compounds differentiated PD from controls at a 20% false-discovery level. In PD, mean 3-hydroxykynurenine concentration was increased by one-third, and mean oxidized glutathione was decreased by 40% (for each, P < .01). Four of the 19 compounds differentiating PD from controls were N-acetylated amino acids, suggesting a generalized alteration in N-acetylation activity. The Support Vector Machine classification model distinguished between groups at 83% sensitivity and 91% specificity for the learning data, and at 65% and 79% from cross-validation. In this study, the first for metabolomic profiling of PD cerebrospinal fluid, we found several novel biomarkers and offer new directions for recognizing disease-specific biochemical indicators. The findings support involvement of excitotoxicity and oxidative stress in the pathogenesis of PD.

  9. Microarray expression analysis and identification of serum biomarkers for Niemann–Pick disease, type C1

    PubMed Central

    Cluzeau, Celine V.M.; Watkins-Chow, Dawn E.; Fu, Rao; Borate, Bhavesh; Yanjanin, Nicole; Dail, Michelle K.; Davidson, Cristin D.; Walkley, Steven U.; Ory, Daniel S.; Wassif, Christopher A.; Pavan, William J.; Porter, Forbes D.

    2012-01-01

    Niemann–Pick disease type C (NPC) is a lysosomal storage disorder characterized by liver disease and progressive neurodegeneration. Deficiency of either NPC1 or NPC2 leads to the accumulation of cholesterol and glycosphingolipids in late endosomes and early lysosomes. In order to identify pathological mechanisms underlying NPC and uncover potential biomarkers, we characterized liver gene expression changes in an Npc1 mouse model at six ages spanning the pathological progression of the disease. We identified altered gene expression at all ages, including changes in asymptomatic, 1-week-old mice. Biological pathways showing early altered gene expression included: lipid metabolism, cytochrome P450 enzymes involved in arachidonic acid and drug metabolism, inflammation and immune responses, mitogen-activated protein kinase and G-protein signaling, cell cycle regulation, cell adhesion and cytoskeleton remodeling. In contrast, apoptosis and oxidative stress appeared to be late pathological processes. To identify potential biomarkers that could facilitate monitoring of disease progression, we focused on a subset of 103 differentially expressed genes that encode secreted proteins. Further analysis identified two secreted proteins with increased serum levels in NPC1 patients: galectin-3 (LGALS3), a pro-inflammatory molecule, and cathepsin D (CTSD), a lysosomal aspartic protease. Elevated serum levels of both proteins correlated with neurological disease severity and appeared to be specific for NPC1. Expression of Lgals3 and Ctsd was normalized following treatment with 2-hydroxypropyl-β-cyclodextrin, a therapy that reduces pathological findings and significantly increases Npc1−/− survival. Both LGALS3 and CTSD have the potential to aid in diagnosis and serve as biomarkers to monitor efficacy in therapeutic trials. PMID:22619379

  10. Hematological effect of benzene exposure with emphasis of muconic acid as a biomarker.

    PubMed

    Ibrahim, Khadiga S; Amer, Nagat M; El-dossuky, Elsaid A; Emara, Ahmed M; El-Fattah, Abd El-Samei M Abd; Shahy, Eman Mohamed

    2014-06-01

    Human exposure to benzene in work environment is a global occupational health problem. It is established that benzene requires to be metabolized to induce its effects. Benzene has been associated with various hematotoxins and carcinogens. The aim of this study was to investigate the effect of benzene on complete blood picture, with emphasis of trans, trans-muconic acid (t,t-MA) as a biomarker of benzene in urine, considering the influence of cigarette smoke. A total of 81 workers (61 males and 20 females) have been occupationally exposed to benzene. In addition, 83 workers (55males and 28 females) were also recruited as a control group. Complete blood picture was analyzed and urinary t,t-MA was determined by liquid chromatography. In addition, creatinine in the urine samples was determined. Levels of blood elements (white blood cells, red blood cells and platelets) were decreased among exposed workers compared with the controls. The urinary level of t,t-MA/creatinine of the exposed workers was elevated especially in the smoking group compared to the controls. This study recommends that complete blood picture and t,t-MA are helpful biomarker tests that should be done to detect the early effects of benzene exposure.

  11. Cell-free nucleic acids as noninvasive biomarkers for colorectal cancer detection

    PubMed Central

    Mansour, Hicham

    2014-01-01

    Cell-free nucleic acids (CFNA) have been reported by several authors in blood, stool, and urine of patients with colorectal cancer (CRC). These genetic biomarkers can be an indication of neoplastic colorectal epithelial cells, and can thus potentially be used as noninvasive tests for the detection of the disease in CRC patients and monitor their staging, without the need to use heavier and invasive tools. In a number of test-trials, these genetic tests have shown the advantage of non-invasiveness, making them well accepted by most of the patients, without major side effects. They have also shown a promising sensitivity and specificity in the detection of malignant and premalignant neoplasms. Moreover, costs for performing such tests are very low. Several studies reported and confirmed the proof of the principle for these genetic tests for screening, diagnosis, and prognosis; the main challenge of translating this approach from research to clinical laboratory is the validation from large and long-term randomized trials to prove sustainable high sensitivity and specificity. In this paper, we present a review on the noninvasive genetics biomarkers for CRC detection described in the literature and the challenges that can be encountered for validation processes. PMID:25221563

  12. Dietary polyunsaturated fatty acids and heme iron induce oxidative stress biomarkers and a cancer promoting environment in the colon of rats.

    PubMed

    Guéraud, Françoise; Taché, Sylviane; Steghens, Jean-Paul; Milkovic, Lidija; Borovic-Sunjic, Suzana; Zarkovic, Neven; Gaultier, Eric; Naud, Nathalie; Héliès-Toussaint, Cécile; Pierre, Fabrice; Priymenko, Nathalie

    2015-06-01

    The end products of polyunsaturated fatty acid (PUFA) peroxidation, such as malondialdehyde (MDA), 4-hydroxynonenal (HNE), and isoprostanes (8-iso-PGF2α), are widely used as systemic lipid oxidation/oxidative stress biomarkers. However, some of these compounds have also a dietary origin. Thus, replacing dietary saturated fat by PUFAs would improve health but could also increase the formation of such compounds, especially in the case of a pro-oxidant/antioxidant imbalanced diet. Hence, the possible impact of dietary fatty acids and pro-oxidant compounds was studied in rats given diets allowing comparison of the effects of heme iron vs. ferric citrate and of ω-6- vs. ω-3-rich oil on the level of lipid peroxidation/oxidative stress biomarkers. Rats given a heme iron-rich diet without PUFA were used as controls. The results obtained have shown that MDA and the major urinary metabolite of HNE (the mercapturic acid of dihydroxynonane, DHN-MA) were highly dependent on the dietary factors tested, while 8-iso-PGF2α was modestly but significantly affected. Intestinal inflammation and tissue fatty acid composition were checked in parallel and could only explain the differences we observed to a limited extent. Thus, the differences in biomarkers were attributed to the formation of lipid oxidation compounds in food or during digestion, their intestinal absorption, and their excretion into urine. Moreover, fecal extracts from the rats fed the heme iron or fish oil diets were highly toxic for immortalized mouse colon cells. Such toxicity can eventually lead to promotion of colorectal carcinogenesis, supporting the epidemiological findings between red meat intake and colorectal cancer risk. Therefore, the analysis of these biomarkers of lipid peroxidation/oxidative stress in urine should be used with caution when dietary factors are not well controlled, while control of their possible dietary intake is needed also because of their pro-inflammatory, toxic, and even

  13. Magnetic materials for the selective analysis of peptide and protein biomarkers.

    PubMed

    Capriotti, Anna Laura; Piovesana, Susy

    2016-08-05

    This mini-review article provides an overview on the use of magnetic materials for the analysis of protein biomarkers. In particular, the advantage provided by magnetic solid phase extraction will be discussed with selected examples, considering untargeted analysis for screening new biomarker proteins and targeted investigation on known and suggested new biomarkers. Aspects, such as enrichment efficiency over conventional techniques, ease of use, functionalization versatility and automation will be considered, together with quantification and deeper structure elucidation provided by coupling selective or specific enrichment to powerful characterization techniques, such as mass spectrometry.

  14. Kidney tumor biomarkers revealed by simultaneous multiple matrix metabolomics analysis.

    PubMed

    Ganti, Sheila; Taylor, Sandra L; Abu Aboud, Omran; Yang, Joy; Evans, Christopher; Osier, Michael V; Alexander, Danny C; Kim, Kyoungmi; Weiss, Robert H

    2012-07-15

    Metabolomics is increasingly being used in cancer biology for biomarker discovery and identification of potential novel therapeutic targets. However, a systematic metabolomics study of multiple biofluids to determine their interrelationships and to describe their use as tumor proxies is lacking. Using a mouse xenograft model of kidney cancer, characterized by subcapsular implantation of Caki-1 clear cell human kidney cancer cells, we examined tissue, serum, and urine all obtained simultaneously at baseline (urine) and at, or close to, animal sacrifice (urine, tissue, and plasma). Uniform metabolomics analysis of all three "matrices" was accomplished using gas chromatography- and liquid chromatography-mass spectrometry. Of all the metabolites identified (267 in tissue, 246 in serum, and 267 in urine), 89 were detected in all 3 matrices, and the majority was altered in the same direction. Heat maps of individual metabolites showed that alterations in serum were more closely related to tissue than was urine. Two metabolites, cinnamoylglycine and nicotinamide, were concordantly and significantly (when corrected for multiple testing) altered in tissue and serum, and cysteine-glutathione disulfide showed the highest change (232.4-fold in tissue) of any metabolite. On the basis of these and other considerations, three pathways were chosen for biologic validation of the metabolomic data, resulting in potential therapeutic target identification. These data show that serum metabolomics analysis is a more accurate proxy for tissue changes than urine and that tryptophan degradation (yielding anti-inflammatory metabolites) is highly represented in renal cell carcinoma, and support the concept that PPAR-α antagonism may be a potential therapeutic approach for this disease.

  15. Polymethylene-interrupted fatty acids: Biomarkers for native and exotic mussels in the Laurentian Great Lakes

    USGS Publications Warehouse

    Mezek, Tadej; Sverko, Ed; Ruddy, Martina D.; Zaruk, Donna; Capretta, Alfredo; Hebert, Craig E.; Fisk, Aaron T.; McGoldrick, Daryl J.; Newton, Teresa J.; Sutton, Trent M.; Koops, Marten A.; Muir, Andrew M.; Johnson, Timothy B.; Ebener, Mark P.; Arts, Michael T.

    2011-01-01

    Freshwater organisms synthesize a wide variety of fatty acids (FAs); however, the ability to synthesize and/or subsequently modify a particular FA is not universal, making it possible to use certain FAs as biomarkers. Herein we document the occurrence of unusual FAs (polymethylene-interrupted fatty acids; PMI-FAs) in select freshwater organisms in the Laurentian Great Lakes. We did not detect PMI-FAs in: (a) natural seston from Lake Erie and Hamilton Harbor (Lake Ontario), (b) various species of laboratory-cultured algae including a green alga (Scenedesmus obliquus), two cyanobacteria (Aphanizomenon flos-aquae and Synechococystis sp.), two diatoms (Asterionella formosa, Diatoma elongatum) and a chrysophyte (Dinobryon cylindricum) or, (c) zooplankton (Daphnia spp., calanoid or cyclopoid copepods) from Lake Ontario, suggesting that PMI-FAs are not substantively incorporated into consumers at the phytoplankton–zooplankton interface. However, these unusual FAs comprised 4-6% of total fatty acids (on a dry tissue weight basis) of native fat mucket (Lampsilis siliquoidea) and plain pocketbook (L. cardium) mussels and in invasive zebra (Dreissena polymorpha) and quagga (D. bugensis) mussels. We were able to clearly partition Great Lakes' mussels into three separate groups (zebra, quagga, and native mussels) based solely on their PMI-FA profiles. We also provide evidence for the trophic transfer of PMI-FAs from mussels to various fishes in Lakes Ontario and Michigan, further underlining the potential usefulness of PMI-FAs for tracking the dietary contribution of mollusks in food web and contaminant-fate studies.

  16. Development of a temperature gradient focusing method for in situ extraterrestrial biomarker analysis.

    PubMed

    Danger, Grégoire; Ross, David

    2008-08-01

    Scanning temperature gradient focusing (TGF) is a recently described technique for the simultaneous concentration and separation of charged analytes. It allows for high analyte peak capacities and low LODs in microcolumn electrophoretic separations. In this paper, we present the application of scanning TGF for chiral separations of amino acids. Using a mixture of seven carboxyfluorescein succinimidyl ester-labeled amino acids (including five chiral amino acids) which constitute the Mars7 standard, we show that scanning TGF is a very simple and efficient method for chiral separations. The modulation of TGF separation parameters (temperature window, pressure scan rate, temperature range, and chiral selector concentration) allows optimization of peak efficiencies and analyte resolutions. The use of hydroxypropyl-beta-CD at low concentration (1-5 mmol/L) as a chiral selector, with an appropriate pressure scan rate ( -0.25 Pa/s) and with a low temperature range (3-25 degrees C over 1 cm) provided high resolution between enantiomers (Rs >1.5 for each pair of enantiomers) using a short, 4 cm long capillary. With these new results, the scanning TGF method appears to be a viable method for in situ trace biomarker analysis for future missions to Mars or other solar system bodies.

  17. Automated analysis of immunohistochemistry images identifies candidate location biomarkers for cancers

    PubMed Central

    Kumar, Aparna; Rao, Arvind; Bhavani, Santosh; Newberg, Justin Y.; Murphy, Robert F.

    2014-01-01

    Molecular biomarkers are changes measured in biological samples that reflect disease states. Such markers can help clinicians identify types of cancer or stages of progression, and they can guide in tailoring specific therapies. Many efforts to identify biomarkers consider genes that mutate between normal and cancerous tissues or changes in protein or RNA expression levels. Here we define location biomarkers, proteins that undergo changes in subcellular location that are indicative of disease. To discover such biomarkers, we have developed an automated pipeline to compare the subcellular location of proteins between two sets of immunohistochemistry images. We used the pipeline to compare images of healthy and tumor tissue from the Human Protein Atlas, ranking hundreds of proteins in breast, liver, prostate, and bladder based on how much their location was estimated to have changed. The performance of the system was evaluated by determining whether proteins previously known to change location in tumors were ranked highly. We present a number of candidate location biomarkers for each tissue, and identify biochemical pathways that are enriched in proteins that change location. The analysis technology is anticipated to be useful not only for discovering new location biomarkers but also for enabling automated analysis of biomarker distributions as an aid to determining diagnosis. PMID:25489103

  18. Analysis of Organic Acids.

    ERIC Educational Resources Information Center

    Griswold, John R.; Rauner, Richard A.

    1990-01-01

    Presented are the procedures and a discussion of the results for an experiment in which students select unknown carboxylic acids, determine their melting points, and investigate their solubility behavior in water and ethanol. A table of selected carboxylic acids is included. (CW)

  19. Bioinformatics facilitating the use of microarrays to delineate potential miRNA biomarkers in aristolochic acid nephropathy

    PubMed Central

    Chen, Xi; Lu, Haitao

    2016-01-01

    Aristolochic acid nephropathy (AAN) is a rapidly progressive acute or chronic tubulointerstitial nephritis (TIN). The present study attempted to explore the molecular mechanisms underlying the miRNA-directed development of AAN. Our differentially expressed analysis identified 11 DE-miRNAs and retrieved the target genes of these DE-miRNAs; then, network analysis and functional analysis further identified 6 DE-miRNAs (has-miR-192, has-miR-194, has-miR-542-3p, has-miR-450a, has-miR-584, has-miR-33a) as phenotypic biomarkers of AAN. Surprisingly, of has-miR-192 has been reported to be associated with the pathogenesis of AAN, and has-miR-194, has-miR-542-3p and has-miR-450a was first-time identified to link to the development of AAN. In addition, the expressional changes of has-miR-584 and has-miR-33a may be associated with the development of AAN as well, which must be further confirmed by the associated experiments. Taken together, our work reveals for the first time the regulatory mechanisms of miRNAs in the development of AAN and this will contribute to miRNA-based diagnosis and treatment of AAN. PMID:27418141

  20. Development of fatty acid biomarkers for the identification of wild and aquacultured sea cucumber ( Apostichopus japonicus)

    NASA Astrophysics Data System (ADS)

    Zadorozhnyj, P. A.; Pivnenko, T. N.; Kovalev, N. N.

    2016-02-01

    In this study, the fatty acids (FAs) of the organs and tissues of sea cucumber ( Apostichopus japonicus) were profiled in order to compare the FA composition of sea cucumber collected from natural habitat (wild) and cages (cultured). The differences in FA contents in dermomuscular tube, peripharyngeal annulus, gonad and intestine (with or without content) between the wild and the cultured were determined. The main fatty acids in all organs and tissues were 20:5n-3, 16:1n-7, 20:4n-6, 22:6n-3, 18:0, and 18:1n-7. The basically different FAs of body wall and digestive tube were 16:1n-7, 18:1n-9 and 20:1n-11. The ratio of saturated to mono- and polyunsaturated FAs in digestive tube was independent on inside content while there was a redistribution of the total amount of n-3 and n-6 fatty acids. The comparison of FA composition of the wild and the cultured sea cucumber showed that 20:5n-3, 16:1n-7 and 18:1n-7 predominated the wild while 20:4n-6 predominated the cultured. The content of branched-chain fatty acids in the wild was 3%-4% and about 9% in the cultured. The possible FAs for identifying the wild and the cultured sea cucumbers were selected. It was suggested that the indexes such as the ratio of either (n-3:n-6) to (n-7:n-6) or (n-3) + (n-7) to (n-6) may serve as the biomarkers distinguishing the wild and the cultured sea cucumber.

  1. Urinary t,t-muconic acid, S-phenylmercapturic acid and benzene as biomarkers of low benzene exposure.

    PubMed

    Fustinoni, Silvia; Buratti, Marina; Campo, Laura; Colombi, Antonio; Consonni, Dario; Pesatori, Angela C; Bonzini, Matteo; Farmer, Peter; Garte, Seymour; Valerio, Federico; Merlo, Domenico F; Bertazzi, Pier A

    2005-05-30

    This research compared the capability of urinary trans,trans-muconic acid (t,t-MA), S-phenylmercapturic acid (S-PMA) and benzene excreted in urine (U-benzene) to monitor low benzene exposure and evaluated the influence of smoking habit on these indices. Gasoline attendants, urban policemen, bus drivers and two groups of referents working in two large Italian cities (415 people) were studied. Median benzene exposure was 61, 22, 21, 9 and 6 microg/m3, respectively, with higher levels in workers than in referents. U-benzene, but not t,t-MA and S-PMA, showed an exposure-related increase. All the biomarkers were strongly influenced by cigarette smoking, with values up to five-fold higher in smokers compared to non-smokers. In conclusion, in the range of investigated benzene exposure (<478 microg/m3 or <0.15 ppm), the smoking habit may be regarded as a major source of benzene intake; among the study indices, U-benzene is the marker of choice for the biological monitoring of occupational and environmental exposure.

  2. Computational Analysis of Specific MicroRNA Biomarkers for Noninvasive Early Cancer Detection

    PubMed Central

    Song, Tianci; Liang, Yanchun; Cao, Zhongbo

    2017-01-01

    Cancer is a complex disease residing in various tissues of human body, accompanied with many abnormalities and mutations in genomes, transcriptome, and epigenome. Early detection plays a crucial role in extending survival time of all major cancer types. Recent advances in microarray and sequencing techniques have given more support to identifying effective biomarkers for early detection of cancer. MicroRNAs (miRNAs) are more and more frequently used as candidates for biomarkers in cancer related studies due to their regulation of target gene expression. In this paper, the comparative analysis is used to discover miRNA expression patterns in cancer versus normal samples on early stage of eight prevalent cancer types. Our work focuses on the specific miRNAs biomarkers identification and function analysis. Several identified miRNA biomarkers in this paper are matched well with those reported in existing researches, and most of them could serve as potential candidate indicators for clinical early diagnosis applications. PMID:28357401

  3. Heterogeneous multimodal biomarkers analysis for Alzheimer's disease via Bayesian network.

    PubMed

    Jin, Yan; Su, Yi; Zhou, Xiao-Hua; Huang, Shuai

    2016-12-01

    By 2050, it is estimated that the number of worldwide Alzheimer's disease (AD) patients will quadruple from the current number of 36 million, while no proven disease-modifying treatments are available. At present, the underlying disease mechanisms remain under investigation, and recent studies suggest that the disease involves multiple etiological pathways. To better understand the disease and develop treatment strategies, a number of ongoing studies including the Alzheimer's Disease Neuroimaging Initiative (ADNI) enroll many study participants and acquire a large number of biomarkers from various modalities including demographic, genotyping, fluid biomarkers, neuroimaging, neuropsychometric test, and clinical assessments. However, a systematic approach that can integrate all the collected data is lacking. The overarching goal of our study is to use machine learning techniques to understand the relationships among different biomarkers and to establish a system-level model that can better describe the interactions among biomarkers and provide superior diagnostic and prognostic information. In this pilot study, we use Bayesian network (BN) to analyze multimodal data from ADNI, including demographics, volumetric MRI, PET, genotypes, and neuropsychometric measurements and demonstrate our approach to have superior prediction accuracy.

  4. An alternative analytical method based on ultrasound micro bath hydrolysis and GC-MS analysis for the characterization of organic biomarkers in archaeological ceramics.

    PubMed

    Blanco-Zubiaguirre, Laura; Olivares, Maitane; Castro, Kepa; Iñañez, Javier G; Madariaga, Juan Manuel

    2016-11-01

    The analysis of organic biomarkers in ancient and valuable archaeological remains provides a worthwhile source of information regarding their management. This work was focused on the development of an analytical procedure to characterize organic residues that have remained in archaeological ceramic samples. A novel analytical approach based on an alkaline hydrolysis by means of an ultrasound micro bath followed by liquid extraction was proposed to isolate saturated and unsaturated fatty acids, degradation products such as dihydroxy acids or dienoic fatty acids, isoprenoid fatty acids, and many other biomarkers from archaeological remains. This main goal has been achieved after the optimization of the main parameters affecting the hydrolysis step, the extraction procedure, and the derivatization step prior to the gas chromatography-mass spectrometry analysis. In this work, archaeological ceramic remains suspected to have been used by Basque Whalers to store whale oil in the period from the sixteenth to the seventeenth century were studied. Nevertheless, the proposed method is useful to determine the organic remains preserved in many other archaeological ceramic remains. Moreover, this methodology can be used to determine organic remains in any porous ceramic, archaeological or not. The preliminary results of the analysis of ceramic vessels led to the determination of some interesting unsaturated compounds such as 11-eicosenoic acid, an important biomarker of marine commodities, and several saturated fatty acids, which could be indicative of having used the vessels to store whale oil. Graphical abstract ᅟ.

  5. Novel biomarker analysis of pleural effusion enhances differentiation of tuberculous from malignant pleural effusion

    PubMed Central

    Chen, Kuan-Yuan; Feng, Po-Hao; Chang, Chih-Cheng; Chen, Tzu-Tao; Chuang, Hsiao-Chi; Lee, Chun-Nin; Su, Chien-Ling; Lin, Lian-Yu; Lee, Kang-Yun

    2016-01-01

    Lymphocytic pleurisy is commonly observed in tuberculosis and cancer. Noninvasive biomarkers are needed to distinguish tuberculous pleural effusion (TPE) from malignant pleural effusion (MPE) because current clinical diagnostic procedures are often invasive. We identified immune response biomarkers that can discriminate between TPE and MPE. Fourteen pleural effusion biomarkers were compared in 22 MPE patients and five TPE patients. Of the innate immunity biomarkers, the median levels of interleukin (IL)-1β and interferon-induced protein-10 (IP-10) were higher in TPE patients than in MPE patients (P<0.05 and P<0.01, respectively). Of the adaptive immunity biomarkers, the median levels of IL-13 and interferon-γ (IFN-γ) were higher in TPE patients than in MPE patients (P<0.05). In addition, the levels of basic fibroblast growth factor were higher in MPE patients than in TPE patients (P<0.05). Receiver operator characteristic analysis of these biomarkers was performed, resulting in the highest area under the curve (AUC) for IP-10 (AUC =0.95, 95% confidence interval, P<0.01), followed by IL-13 (AUC =0.86, 95% confidence interval, P<0.05). Our study shows that five biomarkers (IL-1β, IP-10, IFN-γ, IL-13, and basic fibroblast growth factor) have a potential diagnostic role in differentiating TPE from MPE, particularly in lung cancer-related MPE. PMID:27354819

  6. Analysis of plasma metabolic biomarkers in the development of 4-nitroquinoline-1-oxide-induced oral carcinogenesis in rats

    PubMed Central

    KONG, XIANGLI; YANG, XIAOQIN; ZHOU, JINGLIN; CHEN, SIXIU; LI, XIAOYU; JIAN, FAN; DENG, PENGCHI; LI, WEI

    2015-01-01

    The aim of the present study was to identify time-dependent changes in the expression of metabolic biomarkers during the various stages of oral carcinogenesis to provide an insight into the sequential mechanism of oral cancer development. An 1H nuclear magnetic resonance (NMR)-based metabolomics approach was used to analyze the blood plasma samples of Sprague-Dawley rats exhibiting various oral lesions induced by the administration of 4-nitroquinoline-1-oxide (4NQO) in drinking water. The 1H NMR spectra were processed by principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) to determine the metabolic differences between the three developmental stages of oral mucosa cancer (health, oral leukoplakia [OLK] and oral squamous cell carcinoma [OSCC]). The variable importance in projection (VIP) score derived from the PLS-DA model was used to screen for important metabolites, whose significance was further verified through analysis of variance (ANOVA). Data from the present study indicated that 4NQO-induced rat oral carcinogenesis produced oral pre-neoplastic and neoplastic lesions and provided an effective model for analyzing sequential changes in the 1H NMR spectra of rat blood plasma. The 1H NMR-based metabolomics approach clearly differentiates between healthy, OLK and OSSC rats in the PCA and PLS-DA models. Furthermore, lactic acid, choline, glucose, proline, valine, isoleucine, aspartic acid and 2-hydroxybutyric acid demonstrated VIP>1 in the PLS-D model and P<0.05 with ANOVA. It was also identified that increases in lactic acid, choline and glucose, and decreases in proline, valine, isoleucine, aspartic acid and 2-hydroxybutyric acid may be relative to the characteristic mechanisms of oral carcinogenesis. Therefore, these plasma metabolites may serve as metabolic biomarkers in oral carcinogenesis and assist in the early diagnosis and preventive treatment of oral cancer. PMID:25435976

  7. Suitability of Phytosterols Alongside Fatty Acids as Chemotaxonomic Biomarkers for Phytoplankton

    PubMed Central

    Taipale, Sami J.; Hiltunen, Minna; Vuorio, Kristiina; Peltomaa, Elina

    2016-01-01

    The composition and abundance of phytoplankton is an important factor defining ecological status of marine and freshwater ecosystems. Chemotaxonomic markers (e.g., pigments and fatty acids) are needed for monitoring changes in a phytoplankton community and to know the nutritional quality of seston for herbivorous zooplankton. Here we investigated the suitability of sterols along with fatty acids as chemotaxonomic markers using multivariate statistics, by analyzing the sterol and fatty acid composition of 10 different phytoplankton classes including altogether 37 strains isolated from freshwater lakes. We were able to detect a total of 47 fatty acids and 29 sterols in our phytoplankton samples, which both differed statistically significantly between phytoplankton classes. Due to the high variation of fatty acid composition among Cyanophyceae, taxonomical differentiation increased when Cyanophyceae were excluded from statistical analysis. Sterol composition was more heterogeneous within class than fatty acids and did not improve separation of phytoplankton classes when used alongside fatty acids. However, we conclude that sterols can provide additional information on the abundance of specific genera within a class which can be generated by using fatty acids. For example, whereas high C16 ω-3 PUFA (polyunsaturated fatty acid) indicates the presence of Chlorophyceae, a simultaneous high amount of ergosterol could specify the presence of Chlamydomonas spp. (Chlorophyceae). Additionally, we found specific 4α-methyl sterols for distinct Dinophyceae genera, suggesting that 4α-methyl sterols can potentially separate freshwater dinoflagellates from each other. PMID:26973664

  8. Alkyl protocatechuates as novel urinary biomarkers of exposure to p-hydroxybenzoic acid esters (parabens).

    PubMed

    Wang, Lei; Kannan, Kurunthachalam

    2013-09-01

    Human exposure to p-hydroxybenzoic acid esters (parabens) is a concern, owing to adverse health effects of these compounds. Parabens are metabolized and eliminated from the human bodies within a few hours of exposure. In this study, for the first time, methyl- and ethyl-protocatechuates (OH-MeP and OH-EtP) and their parent compounds, methyl- (MeP) and ethyl-parabens (EtP), were determined in urine samples collected from U.S. children and adults. Alkyl protocatechuates were found in almost all urine samples, with median concentrations of 11.8 (OH-MeP) and 2.90ng/mL (OH-EtP) in adults, and 5.43 (OH-MeP) and 0.85ng/mL (OH-EtP) in children. In adults, the concentrations of urinary OH-MeP and OH-EtP were higher than the corresponding concentrations of MeP and EtP. Significant correlation between OH-MeP/OH-EtP and MeP/EtP was observed. This is the first report to document hydroxylation of parabens in humans, and to propose hydroxylated metabolites (i.e., alkyl protocatechuates) as alternative biomarkers of exposure to parabens in human biomonitoring studies. The rates of transformation of parabens between children and adults appeared to be different, as evidenced from the slopes of regression between alkyl protocatechuates and parabens. In addition to alkyl protocatechuates, hydroxybenzoic acid (4-HB) and 3,4-dihydroxybenzoic acid (3,4-DHB) were found at considerable levels in the urine samples. The occurrence of a significant proportion of alkyl protocatechuates and 3,4-DHB suggests the need for inclusion of these derivatives in accurate estimation of human exposure to parabens and in epidemiological studies that associate paraben exposure to health outcomes in populations.

  9. Urinary tartaric acid as a potential biomarker for the dietary assessment of moderate wine consumption: a randomised controlled trial.

    PubMed

    Regueiro, Jorge; Vallverdú-Queralt, Anna; Simal-Gándara, Jesús; Estruch, Ramón; Lamuela-Raventós, Rosa María

    2014-05-01

    The availability of biomarkers that allow the estimation of the intake of specific foods and dietary components, as an alternative or addition to self-reported dietary questionnaires, could greatly enhance the effectiveness of nutritional research. The aim of the present study was to assess tartaric acid, one of the major components of red and white wines, as a potential biomarker of wine consumption. A total of twenty-one healthy men participated in a randomised cross-over feeding trial. They consumed a single dose of 100, 200 or 300 ml wine at dinner. Before each intervention, the participants followed a 7 d washout period during which they avoided consuming wine or grape-based products. Morning urine was collected and analysed by liquid chromatography coupled to electrospray ionisation tandem MS. A strong significant correlation was found between wine intake and urinary tartaric acid (r(s) = 0·9220; P <0·001). Using a cut-off value of 8·84 μg/mg creatinine, tartaric acid allowed wine consumers to be differentiated from non-wine consumers. The results suggest that urinary tartaric acid may be a sensitive and specific dietary biomarker of wine consumption.

  10. Identification of Methanotrophic Lipid Biomarkers in Cold-Seep Mussel Gills: Chemical and Isotopic Analysis

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Summons, Roger E.; Dowling, Lesley M.; Zahiralis, Karen D.

    1995-01-01

    A lipid analysis of the tissues of a cold-seep mytilid mussel collected from the Louisiana slope of the Gulf of Mexico was used in conjunction with a compound-specific isotope analysis to demonstrate the presence of methanotrophic symbionts in the mussel gill tissue and to demonstrate the host's dependence on bacterially synthesized metabolic intermediates. The gill tissue contained large amounts of group-specific methanotrophic biomarkers, bacteriohopanoids, 4-methylsterols, lipopolysaccharide-associated hydroxy fatty acids, and type I-specific 16:1 fatty acid isomers with bond positions at delta-8, delta-10, and delta-ll. Only small amounts of these compounds were detected in the mantle or other tissues of the host animal. A variety of cholesterol and 4-methylsterol isomers were identified as both free and steryl esters, and the sterol double bond positions suggested that the major bacterially derived gill sterol(11.0% 4(alpha)-methyl-cholesta-8(14), 24-dien-3(beta)-ol) was converted to host cholesterol (64.2% of the gill sterol was cholest-5-en-3(beta)-ol). The stable carbon isotope values for gill and mantle preparations were, respectively, -59.0 and -60.4 per thousand for total tissue, -60.6 and -62.4 per thousand for total lipids, -60.2 and -63.9 per thousand for phospholipid fatty acids, and -71.8 and -73.8 per thousand for sterols. These stable carbon isotope values revealed that the relative fractionation pattern was similar to the patterns obtained in pure culture experiments with methanotrophic bacteria further supporting the conversion of the bacterial methyl-sterol pool.

  11. Acid retention with reduced glomerular filtration rate increases urine biomarkers of kidney and bone injury.

    PubMed

    Wesson, Donald E; Pruszynski, Jessica; Cai, Wendy; Simoni, Jan

    2017-04-01

    Diets high in acid of developed societies that do not cause metabolic acidosis in patients with chronic kidney disease nevertheless appear to cause acid retention with associated morbidity, particularly in those with reduced glomerular filtration rate. Here we used a rat 2/3 nephrectomy model of chronic kidney disease to study induction and maintenance of acid retention and its consequences on indicators of kidney and bone injury. Dietary acid was increased in animals eating base-producing soy protein with acid-producing casein and in casein-eating animals with added ammonium chloride. Using microdialysis to measure the kidney cortical acid content, we found that nephrectomized animals had greater acid retention than sham-operated animals when both ate the soy diet. Each increment in dietary acid further increased acid retention more in nephrectomized than in sham rats. Nephrectomized and sham animals achieved similar steady-state daily urine net acid excretion in response to increments in dietary acid but nephrectomized animals took longer to do so, contributing to greater acid retention that was maintained until the increased dietary acid was stopped. Acid retention was associated with increased urine excretion of both N-acetyl-β-D-glucosaminidase and deoxypyridinoline, greater in nephrectomized than control rats, consistent with kidney tubulointerstitial and bone matrix injury, respectively. Greater acid retention in nephrectomized than control animals was induced by a slower increase in urinary net acid excretion rate in response to the increment in dietary acid and also maintained until the dietary acid increment was stopped. Thus, acid retention increased biomarkers of kidney and bone injury in the urine, supporting untoward consequences to these two tissues.

  12. Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data

    SciTech Connect

    McDermott, Jason E.; Wang, Jing; Mitchell, Hugh D.; Webb-Robertson, Bobbie-Jo M.; Hafen, Ryan P.; Ramey, John A.; Rodland, Karin D.

    2013-01-01

    The advent of high throughput technologies capable of comprehensive analysis of genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification of molecular markers of disease processes. However, it has simultaneously complicated the problem of extracting meaningful signatures of biological processes from these complex datasets. The process of biomarker discovery and characterization provides opportunities both for purely statistical and expert knowledge-based approaches and would benefit from improved integration of the two. Areas covered In this review we will present examples of current practices for biomarker discovery from complex omic datasets and the challenges that have been encountered. We will then present a high-level review of data-driven (statistical) and knowledge-based methods applied to biomarker discovery, highlighting some current efforts to combine the two distinct approaches. Expert opinion Effective, reproducible and objective tools for combining data-driven and knowledge-based approaches to biomarker discovery and characterization are key to future success in the biomarker field. We will describe our recommendations of possible approaches to this problem including metrics for the evaluation of biomarkers.

  13. Human urinary biomarkers of dioxin exposure: analysis by metabolomics and biologically driven data dimensionality reduction.

    PubMed

    Jeanneret, Fabienne; Boccard, Julien; Badoud, Flavia; Sorg, Olivier; Tonoli, David; Pelclova, Daniela; Vlckova, Stepanka; Rutledge, Douglas N; Samer, Caroline F; Hochstrasser, Denis; Saurat, Jean-Hilaire; Rudaz, Serge

    2014-10-15

    Untargeted metabolomic approaches offer new opportunities for a deeper understanding of the molecular events related to toxic exposure. This study proposes a metabolomic investigation of biochemical alterations occurring in urine as a result of dioxin toxicity. Urine samples were collected from Czech chemical workers submitted to severe dioxin occupational exposure in a herbicide production plant in the late 1960s. Experiments were carried out with ultra-high pressure liquid chromatography (UHPLC) coupled to high-resolution quadrupole time-of-flight (QTOF) mass spectrometry. A chemistry-driven feature selection was applied to focus on steroid-related metabolites. Supervised multivariate data analysis allowed biomarkers, mainly related to bile acids, to be highlighted. These results supported the hypothesis of liver damage and oxidative stress for long-term dioxin toxicity. As a second step of data analysis, the information gained from the urine analysis of Victor Yushchenko after his poisoning was examined. A subset of relevant urinary markers of acute dioxin toxicity from this extreme phenotype, including glucuro- and sulfo-conjugated endogenous steroid metabolites and bile acids, was assessed for its ability to detect long-term effects of exposure. The metabolomic strategy presented in this work allowed the determination of metabolic patterns related to dioxin effects in human and the discovery of highly predictive subsets of biologically meaningful and clinically relevant compounds. These results are expected to provide valuable information for a deeper understanding of the molecular events related to dioxin toxicity. Furthermore, it presents an original methodology of data dimensionality reduction by using extreme phenotype as a guide to select relevant features prior to data modeling (biologically driven data reduction).

  14. Defining Multiple Characteristic Raman Bands of α-Amino Acids as Biomarkers for Planetary Missions Using a Statistical Method.

    PubMed

    Rolfe, S M; Patel, M R; Gilmour, I; Olsson-Francis, K; Ringrose, T J

    2016-06-01

    Biomarker molecules, such as amino acids, are key to discovering whether life exists elsewhere in the Solar System. Raman spectroscopy, a technique capable of detecting biomarkers, will be on board future planetary missions including the ExoMars rover. Generally, the position of the strongest band in the spectra of amino acids is reported as the identifying band. However, for an unknown sample, it is desirable to define multiple characteristic bands for molecules to avoid any ambiguous identification. To date, there has been no definition of multiple characteristic bands for amino acids of interest to astrobiology. This study examined L-alanine, L-aspartic acid, L-cysteine, L-glutamine and glycine and defined several Raman bands per molecule for reference as characteristic identifiers. Per amino acid, 240 spectra were recorded and compared using established statistical tests including ANOVA. The number of characteristic bands defined were 10, 12, 12, 14 and 19 for L-alanine (strongest intensity band: 832 cm(-1)), L-aspartic acid (938 cm(-1)), L-cysteine (679 cm(-1)), L-glutamine (1090 cm(-1)) and glycine (875 cm(-1)), respectively. The intensity of bands differed by up to six times when several points on the crystal sample were rotated through 360 °; to reduce this effect when defining characteristic bands for other molecules, we find that spectra should be recorded at a statistically significant number of points per sample to remove the effect of sample rotation. It is crucial that sets of characteristic Raman bands are defined for biomarkers that are targets for future planetary missions to ensure a positive identification can be made.

  15. Defining Multiple Characteristic Raman Bands of α-Amino Acids as Biomarkers for Planetary Missions Using a Statistical Method

    NASA Astrophysics Data System (ADS)

    Rolfe, S. M.; Patel, M. R.; Gilmour, I.; Olsson-Francis, K.; Ringrose, T. J.

    2016-06-01

    Biomarker molecules, such as amino acids, are key to discovering whether life exists elsewhere in the Solar System. Raman spectroscopy, a technique capable of detecting biomarkers, will be on board future planetary missions including the ExoMars rover. Generally, the position of the strongest band in the spectra of amino acids is reported as the identifying band. However, for an unknown sample, it is desirable to define multiple characteristic bands for molecules to avoid any ambiguous identification. To date, there has been no definition of multiple characteristic bands for amino acids of interest to astrobiology. This study examined l-alanine, l-aspartic acid, l-cysteine, l-glutamine and glycine and defined several Raman bands per molecule for reference as characteristic identifiers. Per amino acid, 240 spectra were recorded and compared using established statistical tests including ANOVA. The number of characteristic bands defined were 10, 12, 12, 14 and 19 for l-alanine (strongest intensity band: 832 cm-1), l-aspartic acid (938 cm-1), l-cysteine (679 cm-1), l-glutamine (1090 cm-1) and glycine (875 cm-1), respectively. The intensity of bands differed by up to six times when several points on the crystal sample were rotated through 360 °; to reduce this effect when defining characteristic bands for other molecules, we find that spectra should be recorded at a statistically significant number of points per sample to remove the effect of sample rotation. It is crucial that sets of characteristic Raman bands are defined for biomarkers that are targets for future planetary missions to ensure a positive identification can be made.

  16. Red Blood Cell Fatty Acids and Biomarkers of Inflammation: A Cross-sectional Study in a Community-based Cohort

    PubMed Central

    Fontes, João D.; Rahman, Faisal; Lacey, Sean; Larson, Martin G.; Vasan, Ramachandran S.; Benjamin, Emelia J.; Harris, William S.; Robins, Sander J.

    2015-01-01

    Introduction Inflammation and inflammatory biomarkers have emerged as integral components and predictors of incident cardiovascular (CV) disease. Omega-3 fatty acids, particularly eicosapentaenoic and docosahexaenoic acids (EPA and DHA) have anti-inflammatory properties, and have been variably associated with lower blood pressure, favorable blood lipid changes, and reduced CV events. Methods and Results We examined the cross-sectional association of red blood cell (RBC) fatty acids, representative of body membrane fatty acid composition, with 10 biomarkers active in multiple inflammatory pathways in 2724 participants (mean age 66±9 years, 54% women, 8% minorities) from the Framingham Offspring and minority Omni Cohorts. . After multivariable adjustment, the RBC EPA and DHA content was inversely correlated (all P≤0.001) with 8 markers of inflammation, receptors, or pathways: urinary isoprostanes (r=−0.16); and soluble interleukin-6 (r=−0.10); C-reactive protein (r=−0.08); tumor necrosis factor receptor 2 (r=−0.08); intercellular adhesion molecule-1 (r=−0.08); P-selectin (r=−0.06); lipoprotein-associated phospholipase-A2 mass (r=−0.11) and activity (r=−0.08). The correlations for monocyte chemoattractant protein-1 was −0.05, P=0.006 and osteoprotegerin (r= −0.06, P=0.002) were only nominally significant. Conclusion In our large community-based study, we observed modest inverse associations between several types of inflammatory biomarkers with RBC omega-3 fatty acid levels. Our findings are consistent with the hypothesis that omega-3 fatty acids have anti-inflammatory properties. PMID:25897795

  17. Deoxyribonucleic acid damage-associated biomarkers of ionising radiation: current status and future relevance for radiology and radiotherapy

    PubMed Central

    Rothkamm, K

    2013-01-01

    Diagnostic and therapeutic radiation technology has developed dramatically in recent years, and its use has increased significantly, bringing clinical benefit. The use of diagnostic radiology has become widespread in modern society, particularly in paediatrics where the clinical benefit needs to be balanced with the risk of leukaemia and brain cancer increasing after exposure to low doses of radiation. With improving long-term survival rates of radiotherapy patients and the ever-increasing use of diagnostic and interventional radiology procedures, concern has risen over the long-term risks and side effects from such treatments. Biomarker development in radiology and radiotherapy has progressed significantly in recent years to investigate the effects of such use and optimise treatment. Recent biomarker development has focused on improving the limitations of established techniques by the use of automation, increasing sensitivity and developing novel biomarkers capable of quicker results. The effect of low-dose exposure (0–100 mGy) used in radiology, which is increasingly linked to cancer incidences, is being investigated, as some recent research challenges the linear-no-threshold model. Radiotherapy biomarkers are focused on identifying radiosensitive patients, determining the treatment-associated risk and allowing for a tailored and more successful treatment of cancer patients. For biomarkers in any of these areas to be successfully developed, stringent criteria must be applied in techniques and analysis of data to reduce variation among reports and allow data sets to be accurately compared. Newly developed biomarkers can then be used in combination with the established techniques to better understand and quantify the individual biological response to exposures associated with radiology tests and to personalise treatment plans for patients. PMID:23659923

  18. Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Gastric Ulcer and Intervention Effects of Corydalis yanhusuo Alkaloid

    PubMed Central

    Shuai, Wang; Yongrui, Bao; Shanshan, Guan; Bo, Liu; Lu, Chen; Lei, Wang; Xiaorong, Ran

    2014-01-01

    Metabolomics, the systematic analysis of potential metabolites in a biological specimen, has been increasingly applied to discovering biomarkers, identifying perturbed pathways, measuring therapeutic targets, and discovering new drugs. By analyzing and verifying the significant difference in metabolic profiles and changes of metabolite biomarkers, metabolomics enables us to better understand substance metabolic pathways which can clarify the mechanism of Traditional Chinese Medicines (TCM). Corydalis yanhusuo alkaloid (CA) is a major component of Qizhiweitong (QZWT) prescription which has been used for treating gastric ulcer for centuries and its mechanism remains unclear completely. Metabolite profiling was performed by high-performance liquid chromatography combined with time-of-flight mass spectrometry (HPLC/ESI-TOF-MS) and in conjunction with multivariate data analysis and pathway analysis. The statistic software Mass Profiller Prossional (MPP) and statistic method including ANOVA and principal component analysis (PCA) were used for discovering novel potential biomarkers to clarify mechanism of CA in treating acid injected rats with gastric ulcer. The changes in metabolic profiling were restored to their base-line values after CA treatment according to the PCA score plots. Ten different potential biomarkers and seven key metabolic pathways contributing to the treatment of gastric ulcer were discovered and identified. Among the pathways, sphingophospholipid metabolism and fatty acid metabolism related network were acutely perturbed. Quantitative real time polymerase chain reaction (RT-PCR) analysis were performed to evaluate the expression of genes related to the two pathways for verifying the above results. The results show that changed biomarkers and pathways may provide evidence to insight into drug action mechanisms and enable us to increase research productivity toward metabolomics drug discovery. PMID:24454691

  19. Feeding ecology of Ammothella longipes (Arthropoda: Pycnogonida) in the Mediterranean Sea: A fatty acid biomarker approach

    NASA Astrophysics Data System (ADS)

    Soler-Membrives, Anna; Rossi, Sergio; Munilla, Tomás

    2011-05-01

    Fatty acid analysis has proved valuable in determining seasonal trophic links and the feeding behavior in organisms in which these diet and trophic links cannot be inferred from stomach content analyses. Seasonal variations in total free fatty acid content (TFFA) and fatty acid composition of seston (<250 μm), the brown macroalgae Stypocaulon spp., polychaetes (Nereididae) and the pycnogonid Ammothella longipes have been used to establish their trophic links, with particular focus on seasonality and feeding ecology of A. longipes. Samples were collected in a coastal environment (NW Mediterranean Sea) at 7-10 m depth, in five different periods (August and October 2008, February, June and September 2009). Seston and Stypocaulon spp. samples did not show significant seasonal variations in TFFA content, while nereids showed a significant variation. Analysis of fatty acid profile showed high similarities of fatty acid composition between seston and Stypocaulon spp. Nereids were closer to seston and Stypocaulon spp. than A. longipes, which seemed to follow a seasonal trend. The results of this study reveal that A. longipes may change its feeding behavior depending on the season and available food. This pycnogonid species appears to be carnivore during spring and early summer but seems to feed on detritus when availability of prey diminishes during winter. Notable high amounts of odd-chain fatty acids are found in summer-autumn for this species, which may come from bacteria acquired from the detrital diet or from de novo biosynthesis from propionate. The results obtained provide new and valuable data on the understudied feeding biology of pycnogonids in general, and contribute to the understanding of their functioning of Mediterranean shallow oligotrophic systems and their trophic links.

  20. Urine metabolomic analysis identifies potential biomarkers and pathogenic pathways in kidney cancer.

    PubMed

    Kim, Kyoungmi; Taylor, Sandra L; Ganti, Sheila; Guo, Lining; Osier, Michael V; Weiss, Robert H

    2011-05-01

    Kidney cancer is the seventh most common cancer in the Western world, its incidence is increasing, and it is frequently metastatic at presentation, at which stage patient survival statistics are grim. In addition, there are no useful biofluid markers for this disease, such that diagnosis is dependent on imaging techniques that are not generally used for screening. In the present study, we use metabolomics techniques to identify metabolites in kidney cancer patients' urine, which appear at different levels (when normalized to account for urine volume and concentration) from the same metabolites in nonkidney cancer patients. We found that quinolinate, 4-hydroxybenzoate, and gentisate are differentially expressed at a false discovery rate of 0.26, and these metabolites are involved in common pathways of specific amino acid and energetic metabolism, consistent with high tumor protein breakdown and utilization, and the Warburg effect. When added to four different (three kidney cancer-derived and one "normal") cell lines, several of the significantly altered metabolites, quinolinate, α-ketoglutarate, and gentisate, showed increased or unchanged cell proliferation that was cell line-dependent. Further evaluation of the global metabolomics analysis, as well as confirmation of the specific potential biomarkers using a larger sample size, will lead to new avenues of kidney cancer diagnosis and therapy.

  1. Electrochemical, Electrochemiluminescence, and Photoelectrochemical Aptamer-Based Nanostructured Sensors for Biomarker Analysis

    PubMed Central

    Ravalli, Andrea; Voccia, Diego; Palchetti, Ilaria; Marrazza, Giovanna

    2016-01-01

    Aptamer-based sensors have been intensively investigated as potential analytical tools in clinical analysis providing the desired portability, fast response, sensitivity, and specificity, in addition to lower cost and simplicity versus conventional methods. The aim of this review, without pretending to be exhaustive, is to give the readers an overview of recent important achievements about electrochemical, electrochemiluminescence, and photoelectrochemical aptasensors for the protein biomarker determination, mainly cancer related biomarkers, by selected recent publications. Special emphasis is placed on nanostructured-based aptasensors, which show a substantial improvement of the analytical performances. PMID:27490578

  2. Electrochemical, Electrochemiluminescence, and Photoelectrochemical Aptamer-Based Nanostructured Sensors for Biomarker Analysis.

    PubMed

    Ravalli, Andrea; Voccia, Diego; Palchetti, Ilaria; Marrazza, Giovanna

    2016-08-02

    Aptamer-based sensors have been intensively investigated as potential analytical tools in clinical analysis providing the desired portability, fast response, sensitivity, and specificity, in addition to lower cost and simplicity versus conventional methods. The aim of this review, without pretending to be exhaustive, is to give the readers an overview of recent important achievements about electrochemical, electrochemiluminescence, and photoelectrochemical aptasensors for the protein biomarker determination, mainly cancer related biomarkers, by selected recent publications. Special emphasis is placed on nanostructured-based aptasensors, which show a substantial improvement of the analytical performances.

  3. Biomarker discovery by sparse canonical correlation analysis of complex clinical phenotypes of tuberculosis and malaria.

    PubMed

    Rousu, Juho; Agranoff, Daniel D; Sodeinde, Olugbemiro; Shawe-Taylor, John; Fernandez-Reyes, Delmiro

    2013-04-01

    Biomarker discovery aims to find small subsets of relevant variables in 'omics data that correlate with the clinical syndromes of interest. Despite the fact that clinical phenotypes are usually characterized by a complex set of clinical parameters, current computational approaches assume univariate targets, e.g. diagnostic classes, against which associations are sought for. We propose an approach based on asymmetrical sparse canonical correlation analysis (SCCA) that finds multivariate correlations between the 'omics measurements and the complex clinical phenotypes. We correlated plasma proteomics data to multivariate overlapping complex clinical phenotypes from tuberculosis and malaria datasets. We discovered relevant 'omic biomarkers that have a high correlation to profiles of clinical measurements and are remarkably sparse, containing 1.5-3% of all 'omic variables. We show that using clinical view projections we obtain remarkable improvements in diagnostic class prediction, up to 11% in tuberculosis and up to 5% in malaria. Our approach finds proteomic-biomarkers that correlate with complex combinations of clinical-biomarkers. Using the clinical-biomarkers improves the accuracy of diagnostic class prediction while not requiring the measurement plasma proteomic profiles of each subject. Our approach makes it feasible to use omics' data to build accurate diagnostic algorithms that can be deployed to community health centres lacking the expensive 'omics measurement capabilities.

  4. A Pilot Proteomic Analysis of Salivary Biomarkers in Autism Spectrum Disorder.

    PubMed

    Ngounou Wetie, Armand G; Wormwood, Kelly L; Russell, Stefanie; Ryan, Jeanne P; Darie, Costel C; Woods, Alisa G

    2015-06-01

    Autism spectrum disorder (ASD) prevalence is increasing, with current estimates at 1/68-1/50 individuals diagnosed with an ASD. Diagnosis is based on behavioral assessments. Early diagnosis and intervention is known to greatly improve functional outcomes in people with ASD. Diagnosis, treatment monitoring and prognosis of ASD symptoms could be facilitated with biomarkers to complement behavioral assessments. Mass spectrometry (MS) based proteomics may help reveal biomarkers for ASD. In this pilot study, we have analyzed the salivary proteome in individuals with ASD compared to neurotypical control subjects, using MS-based proteomics. Our goal is to optimize methods for salivary proteomic biomarker discovery and to identify initial putative biomarkers in people with ASDs. The salivary proteome is virtually unstudied in ASD, and saliva could provide an easily accessible biomaterial for analysis. Using nano liquid chromatography-tandem mass spectrometry, we found statistically significant differences in several salivary proteins, including elevated prolactin-inducible protein, lactotransferrin, Ig kappa chain C region, Ig gamma-1 chain C region, Ig lambda-2 chain C regions, neutrophil elastase, polymeric immunoglobulin receptor and deleted in malignant brain tumors 1. Our results indicate that this is an effective method for identification of salivary protein biomarkers, support the concept that immune system and gastrointestinal disturbances may be present in individuals with ASDs and point toward the need for larger studies in behaviorally-characterized individuals.

  5. Analysis of Scanning Electron Microscopy Images To Investigate Adsorption Processes Responsible for Detection of Cancer Biomarkers.

    PubMed

    Rodrigues, Valquiria da Cruz; Comin, Cesar H; Soares, Juliana Coatrini; Soares, Andrey Coatrini; Melendez, Matias Eliseo; Fregnani, José Humberto T G; Carvalho, André Lopes; Costa, Luciano da F; Oliveira, Osvaldo N

    2017-02-22

    Adsorption processes are responsible for detection of cancer biomarkers in biosensors (and immunosensors), which can be captured with various principles of detection. In this study, we used a biosensor made with nanostructured films of polypyrrole and p53 antibodies, and image analysis of scanning electron microscopy data made it possible to correlate morphological changes of the biosensor with the concentration of cells containing the cancer biomarker p53. The selectivity of the biosensor was proven by distinguishing images obtained with exposure of the biosensor to cells containing the biomarker from those acquired with cells that did not contain it. Detection was confirmed with cyclic voltammetry measurements, while the adsorption of the p53 biomarker was probed with polarization-modulated infrared reflection absorption (PM-IRRAS) and a quartz crystal microbalance (QCM). Adsorption is described using the Langmuir-Freundlich model, with saturation taking place at a concentration of 100 Ucells/mL. Taken together, our results point to novel ways to detect biomarkers or any type of analyte for which detection is based on adsorption as is the case of the majority of biosensors.

  6. Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data.

    PubMed

    McDermott, Jason E; Wang, Jing; Mitchell, Hugh; Webb-Robertson, Bobbie-Jo; Hafen, Ryan; Ramey, John; Rodland, Karin D

    2013-01-01

    INTRODUCTION: The advent of high throughput technologies capable of comprehensive analysis of genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification of molecular markers of disease processes. However, it has simultaneously complicated the problem of extracting meaningful molecular signatures of biological processes from these complex datasets. The process of biomarker discovery and characterization provides opportunities for more sophisticated approaches to integrating purely statistical and expert knowledge-based approaches. AREAS COVERED: In this review we will present examples of current practices for biomarker discovery from complex omic datasets and the challenges that have been encountered in deriving valid and useful signatures of disease. We will then present a high-level review of data-driven (statistical) and knowledge-based methods applied to biomarker discovery, highlighting some current efforts to combine the two distinct approaches. EXPERT OPINION: Effective, reproducible and objective tools for combining data-driven and knowledge-based approaches to identify predictive signatures of disease are key to future success in the biomarker field. We will describe our recommendations for possible approaches to this problem including metrics for the evaluation of biomarkers.

  7. Dietary pattern analysis and biomarkers of low-grade inflammation: a systematic literature review.

    PubMed

    Barbaresko, Janett; Koch, Manja; Schulze, Matthias B; Nöthlings, Ute

    2013-08-01

    The purpose of the present literature review was to investigate and summarize the current evidence on associations between dietary patterns and biomarkers of inflammation, as derived from epidemiological studies. A systematic literature search was conducted using PubMed, Web of Science, and EMBASE, and a total of 46 studies were included in the review. These studies predominantly applied principal component analysis, factor analysis, reduced rank regression analysis, the Healthy Eating Index, or the Mediterranean Diet Score. No prospective observational study was found. Patterns identified by reduced rank regression as being statistically significantly associated with biomarkers of inflammation were almost all meat-based or "Western" patterns. Studies using principal component analysis or a priori-defined diet scores found that meat-based or "Western-like" patterns tended to be positively associated with biomarkers of inflammation, predominantly C-reactive protein, while vegetable- and fruit-based or "healthy" patterns tended to be inversely associated. While results of the studies were inconsistent, interventions with presumed healthy diets resulted in reductions of almost all investigated inflammatory biomarkers. In conclusion, prospective studies are warranted to confirm the reported findings and further analyze associations, particularly by investigating dietary patterns as risk factors for changes in inflammatory markers over time.

  8. ANALYSIS OR THE POTENTIAL SPERM BIOMARKER, SP22, IN HUMAN SEMEN

    EPA Science Inventory

    ANALYSIS OF THE POTENTIAL SPERM BIOMARKER SP22 IN HUMAN SEMEN
    Rebecca A. Morris Ph.D.1, Gary R. Klinefelter Ph.D.1, Naomi L. Roberts 1, Juan D. Suarez 1,
    Lillian F. Strader 1, Susan C. Jeffay 1 and Sally D. Perreault Ph.D.1

    1 U.S. EPA / ORD / National Health a...

  9. Automated Protein Biomarker Analysis: on-line extraction of clinical samples by Molecularly Imprinted Polymers

    NASA Astrophysics Data System (ADS)

    Rossetti, Cecilia; Świtnicka-Plak, Magdalena A.; Grønhaug Halvorsen, Trine; Cormack, Peter A. G.; Sellergren, Börje; Reubsaet, Léon

    2017-03-01

    Robust biomarker quantification is essential for the accurate diagnosis of diseases and is of great value in cancer management. In this paper, an innovative diagnostic platform is presented which provides automated molecularly imprinted solid-phase extraction (MISPE) followed by liquid chromatography-mass spectrometry (LC-MS) for biomarker determination using ProGastrin Releasing Peptide (ProGRP), a highly sensitive biomarker for Small Cell Lung Cancer, as a model. Molecularly imprinted polymer microspheres were synthesized by precipitation polymerization and analytical optimization of the most promising material led to the development of an automated quantification method for ProGRP. The method enabled analysis of patient serum samples with elevated ProGRP levels. Particularly low sample volumes were permitted using the automated extraction within a method which was time-efficient, thereby demonstrating the potential of such a strategy in a clinical setting.

  10. Automated Protein Biomarker Analysis: on-line extraction of clinical samples by Molecularly Imprinted Polymers

    PubMed Central

    Rossetti, Cecilia; Świtnicka-Plak, Magdalena A.; Grønhaug Halvorsen, Trine; Cormack, Peter A.G.; Sellergren, Börje; Reubsaet, Léon

    2017-01-01

    Robust biomarker quantification is essential for the accurate diagnosis of diseases and is of great value in cancer management. In this paper, an innovative diagnostic platform is presented which provides automated molecularly imprinted solid-phase extraction (MISPE) followed by liquid chromatography-mass spectrometry (LC-MS) for biomarker determination using ProGastrin Releasing Peptide (ProGRP), a highly sensitive biomarker for Small Cell Lung Cancer, as a model. Molecularly imprinted polymer microspheres were synthesized by precipitation polymerization and analytical optimization of the most promising material led to the development of an automated quantification method for ProGRP. The method enabled analysis of patient serum samples with elevated ProGRP levels. Particularly low sample volumes were permitted using the automated extraction within a method which was time-efficient, thereby demonstrating the potential of such a strategy in a clinical setting. PMID:28303910

  11. Identification of MicroRNAs as Potential Biomarker for Gastric Cancer by System Biological Analysis

    PubMed Central

    Yan, Wenying; Wang, Shouli; Sun, Zhandong; Lin, Yuxin; Sun, Shengwei; Chen, Jiajia; Chen, Weichang

    2014-01-01

    Gastric cancers (GC) have the high morbidity and mortality rates worldwide and there is a need to identify sufficiently sensitive biomarkers for GC. MicroRNAs (miRNAs) could be promising potential biomarkers for GC diagnosis. We employed a systematic and integrative bioinformatics framework to identify GC-related microRNAs from the public microRNA and mRNA expression dataset generated by RNA-seq technology. The performance of the 17 candidate miRNAs was evaluated by hierarchal clustering, ROC analysis, and literature mining. Fourteen have been found to be associated with GC and three microRNAs (miR-211, let-7b, and miR-708) were for the first time reported to associate with GC and may be used for diagnostic biomarkers for GC. PMID:24982912

  12. Comparison of two reference systems for biomarker data analysis in a freshwater biomonitoring context.

    PubMed

    Sanchez, Wilfried; Piccini, Benjamin; Maillot-Maréchal, Emmanuelle; Porcher, Jean-Marc

    2010-05-01

    The usefulness of fish biomarkers for freshwater biomonitoring is now well recognized, but they still pose several questions to ecotoxicology researchers. The present study, designed to assess the effects of a small city located in an agricultural river basin watershed on sticklebacks living in an adjacent river, underlines the importance of reference selection. Two reference systems were used to analyse responses of a set of biomarkers, including biotransformation enzymes, oxidative stress parameters, neurotoxicity and endocrine disruption end-points, measured in wild sticklebacks electrofished in a contaminated stream. The results showed that the investigated urban pressure disturbed CYP3A activity but also induced hepatic lipoperoxidation and circulating vitellogenine but this result is strongly influenced by the selected reference system. This work therefore demonstrates the need for further research to identify a robust reference system for stickleback biomarker analysis.

  13. Fatty acids as biomarkers for food web structure in the eastern North Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Behrens, J.; Aluwihare, L.; Stephens, B. M.

    2015-12-01

    Resulting from a NSF funded REU program at Scripps Institution of Oceanography in 2015, this research utilized gas chromatography-mass spectrometry (GC-MS) to analyze the fatty acid composition of suspended particulate organic matter (POM) and zooplankton (ZP; primarily copepods). Samples analyzed for this study were collected simultaneously from surface waters approximately 9 miles off the coast of San Diego in June 2015. I was testing the hypothesis that essential fatty acids in ZP should reflect their diet, in particular, distinguishing contributions from a microbial versus traditional food web. Food web structure in this region of the ocean has been shown to be sensitive to climate change on inter-annual and longer timescales. Thus, a proxy that identifies restructuring of food webs would be useful for examining the response of ocean ecosystems to future climate change. Lipids were extracted from ZP and POM using a modified Bligh and Dyer method with sonication. Following saponification free fatty acids and other lipids were further purified using column chromatography. Polar functional groups in lipids were then methylated prior to GC-MS analysis. In addition, 2-dimensional GCxGC with time of flight MS was used to distinguish polyunsaturated fatty acid isomers. My poster will present initial findings of shared fatty acids of zooplankton and POM suspended material from the Northern Pacific collection site. Further research will be focused on analyzing the hydrogen isotope composition of fatty acids in zooplankton and suspended DOM obtained at the collection site to further characterize and increase certainty on the role of microbes and phytoplankton in the region's food-web to distinguish prokaryotic and eukaryotic sources.

  14. Identification and Quantitation of Malonic Acid Biomarkers of In-Born Error Metabolism by Targeted Metabolomics

    NASA Astrophysics Data System (ADS)

    Ambati, Chandra Shekar R.; Yuan, Furong; Abu-Elheiga, Lutfi A.; Zhang, Yiqing; Shetty, Vivekananda

    2017-03-01

    Malonic acid (MA), methylmalonic acid (MMA), and ethylmalonic acid (EMA) metabolites are implicated in various non-cancer disorders that are associated with inborn-error metabolism. In this study, we have slightly modified the published 3-nitrophenylhydrazine (3NPH) derivatization method and applied it to derivatize MA, MMA, and EMA to their hydrazone derivatives, which were amenable for liquid chromatography- mass spectrometry (LC-MS) quantitation. 3NPH was used to derivatize MA, MMA, and EMA, and multiple reaction monitoring (MRM) transitions of the corresponding derivatives were determined by product-ion experiments. Data normalization and absolute quantitation were achieved by using 3NPH derivatized isotopic labeled compounds 13C2-MA, MMA-D3, and EMA-D3. The detection limits were found to be at nanomolar concentrations and a good linearity was achieved from nanomolar to millimolar concentrations. As a proof of concept study, we have investigated the levels of malonic acids in mouse plasma with malonyl-CoA decarboxylase deficiency (MCD-D), and we have successfully applied 3NPH method to identify and quantitate all three malonic acids in wild type (WT) and MCD-D plasma with high accuracy. The results of this method were compared with that of underivatized malonic acid standards experiments that were performed using hydrophilic interaction liquid chromatography (HILIC)-MRM. Compared with HILIC method, 3NPH derivatization strategy was found to be very efficient to identify these molecules as it greatly improved the sensitivity, quantitation accuracy, as well as peak shape and resolution. Furthermore, there was no matrix effect in LC-MS analysis and the derivatized metabolites were found to be very stable for longer time.

  15. Identification and Quantitation of Malonic Acid Biomarkers of In-Born Error Metabolism by Targeted Metabolomics.

    PubMed

    Ambati, Chandra Shekar R; Yuan, Furong; Abu-Elheiga, Lutfi A; Zhang, Yiqing; Shetty, Vivekananda

    2017-03-17

    Malonic acid (MA), methylmalonic acid (MMA), and ethylmalonic acid (EMA) metabolites are implicated in various non-cancer disorders that are associated with inborn-error metabolism. In this study, we have slightly modified the published 3-nitrophenylhydrazine (3NPH) derivatization method and applied it to derivatize MA, MMA, and EMA to their hydrazone derivatives, which were amenable for liquid chromatography- mass spectrometry (LC-MS) quantitation. 3NPH was used to derivatize MA, MMA, and EMA, and multiple reaction monitoring (MRM) transitions of the corresponding derivatives were determined by product-ion experiments. Data normalization and absolute quantitation were achieved by using 3NPH derivatized isotopic labeled compounds (13)C2-MA, MMA-D3, and EMA-D3. The detection limits were found to be at nanomolar concentrations and a good linearity was achieved from nanomolar to millimolar concentrations. As a proof of concept study, we have investigated the levels of malonic acids in mouse plasma with malonyl-CoA decarboxylase deficiency (MCD-D), and we have successfully applied 3NPH method to identify and quantitate all three malonic acids in wild type (WT) and MCD-D plasma with high accuracy. The results of this method were compared with that of underivatized malonic acid standards experiments that were performed using hydrophilic interaction liquid chromatography (HILIC)-MRM. Compared with HILIC method, 3NPH derivatization strategy was found to be very efficient to identify these molecules as it greatly improved the sensitivity, quantitation accuracy, as well as peak shape and resolution. Furthermore, there was no matrix effect in LC-MS analysis and the derivatized metabolites were found to be very stable for longer time. Graphical Abstract ᅟ.

  16. Identification of Novel Biomarkers in Seasonal Allergic Rhinitis by Combining Proteomic, Multivariate and Pathway Analysis

    PubMed Central

    Wang, Hui; Gottfries, Johan; Barrenäs, Fredrik; Benson, Mikael

    2011-01-01

    Background Glucocorticoids (GCs) play a key role in the treatment of seasonal allergic rhinitis (SAR). However, some patients show a low response to GC treatment. We hypothesized that proteins that correlated to discrimination between symptomatic high and low responders (HR and LR) to GC treatment might be regulated by GCs and therefore suitable as biomarkers for GC treatment. Methodology/Principal Findings We identified 953 nasal fluid proteins in symptomatic HR and LR with a LC MS/MS based-quantitative proteomics analysis and performed multivariate analysis to identify a combination of proteins that best separated symptomatic HR and LR. Pathway analysis showed that those proteins were most enriched in the acute phase response pathway. We prioritized candidate biomarkers for GC treatment based on the multivariate and pathway analysis. Next, we tested if those candidate biomarkers differed before and after GC treatment in nasal fluids from 40 patients with SAR using ELISA. Several proteins including ORM (P<0.0001), APOH (P<0.0001), FGA (P<0.01), CTSD (P<0.05) and SERPINB3 (P<0.05) differed significantly before and after GC treatment. Particularly, ORM (P<0.01), FGA (P<0.05) and APOH (P<0.01) that belonged to the acute phase response pathway decreased significantly in HR but not LR before and after GC treatment. Conclusions/Significance We identified several novel biomarkers for GC treatment response in SAR with combined proteomics, multivariate and pathway analysis. The analytical principles may be generally applicable to identify biomarkers in clinical studies of complex diseases. PMID:21887273

  17. Potential Biomarkers of Fatigue Identified by Plasma Metabolome Analysis in Rats

    PubMed Central

    Kume, Satoshi; Yamato, Masanori; Tamura, Yasuhisa; Jin, Guanghua; Nakano, Masayuki; Miyashige, Yukiharu; Eguchi, Asami; Ogata, Yoshiyuki; Goda, Nobuhito; Iwai, Kazuhiro; Yamano, Emi; Watanabe, Yasuyoshi; Soga, Tomoyoshi; Kataoka, Yosky

    2015-01-01

    In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capillary electrophoresis-mass spectrometry (CE-MS). In order to obtain a fatigued animal group, rats were placed in a cage filled with water to a height of 2.2 cm for 5 days. A food-restricted group, in which rats were limited to 10 g/d of food (around 50% of the control group), was also assessed. The food-restricted group exhibited weight reduction similar to that of the fatigued group. CE-MS measurements were performed to evaluate the profile of food intake-dependent metabolic changes, as well as the profile in fatigue loading, resulting in the identification of 48 metabolites in plasma. Multivariate analyses using hierarchical clustering and principal component analysis revealed that the plasma metabolome in the fatigued group showed clear differences from those in the control and food-restricted groups. In the fatigued group, we found distinctive changes in metabolites related to branched-chain amino acid metabolism, urea cycle, and proline metabolism. Specifically, the fatigued group exhibited significant increases in valine, leucine, isoleucine, and 2-oxoisopentanoate, and significant decreases in citrulline and hydroxyproline compared with the control and food-restricted groups. Plasma levels of total nitric oxide were increased in the fatigued group, indicating systemic oxidative stress. Further, plasma metabolites involved in the citrate cycle, such as cis-aconitate and isocitrate, were reduced in the fatigued group. The levels of ATP were significantly decreased in the liver and skeletal muscle, indicative of a deterioration in energy metabolism in these organs. Thus, this comprehensive metabolic analysis furthered our understanding of the pathophysiology of fatigue, and identified potential diagnostic biomarkers based on fatigue pathophysiology. PMID

  18. [Development of microchips for the analysis of biomarkers in blood].

    PubMed

    Kataoka, Masatoshi; Abe, Kaori; Hashimoto, Yoshiko; Yamamura, Shohei; Yatsushiro, Shouki

    2012-11-01

    Several types of microchips have been developed for application in clinical diagnosis. A microchip made of cyclic olefin copolymer with straight microchannels (300 microm width and 100 microm depth) was employed for sandwich ELISA for the determination of serum type I C-peptide (PICP), a biomarker of osteoporosis. This assay enabled us to determine PICP with accuracy and high sensitivity, reducing the time for the immunoassay to 1/6, and the consumption of samples and reagents to 1/50 compared with the conventional method. Furthermore, cell microarray chips with 20,944 microchambers (105 microm width and 50 microm depth), made of polystyrene, were employed for malaria diagnosis and the detection of carcinoma cells among the leukocytes. Around 100 erythrocytes or leukocytes were accommodated in each microchamber with the formation of a monolayer. For malaria diagnosis, it offered 10-100 times higher sensitivity in the detection of malaria infected erythrocytes than conventional light microscopy, and easy operation within 15 min. By double staining for epithelial cells on the cell microarray chip, one carcinoma cell could be detected among 1,800,000 leukocytes. These results indicate the potential of microchips for clinic diagnosis.

  19. Dietary anhydrous milk fat naturally enriched with conjugated linoleic acid and vaccenic acid modify cardiovascular risk biomarkers in spontaneously hypertensive rats.

    PubMed

    Herrera-Meza, M S; Mendoza-López, M R; García-Barradas, O; Sanchez-Otero, M G; Silva-Hernández, E R; Angulo, J O; Oliart-Ros, R M

    2013-08-01

    Saturated and trans fatty acids have been associated with the risk to develop cardiovascular diseases. However, health-promoting effects are associated with consumption of anhydrous milk fat (AMF) and ruminant trans fatty acids, such as conjugated linoleic acid (CLA) and vaccenic acid (VA) contained in the lipid fraction of milk and dairy products. The purpose of this study was to evaluate the effect of AMF naturally enriched with CLA and VA in spontaneously hypertensive rats (SHR), using sterculic oil to inhibit the conversion of VA into CLA. The administration of AMF to SHR during 7 weeks exerted beneficial effects on cardiovascular risk biomarkers (reduction of insulin, blood lipids, increase of adiponectin). When sterculic oil was included, some parameters were further ameliorated (reduction of insulin, increase of adiponectin). Sterculic oil alone reduced body weight and adiposity, and improved blood pressure, adiponectin and triglyceride levels.

  20. Validation of urinary trichloroacetic acid as a biomarker of exposure to drinking water disinfection by-products.

    PubMed

    Zhang, Weiping; Gabos, Stephan; Schopflocher, Donald; Li, Xing-Fang; Gati, Wendy P; Hrudey, Steve E

    2009-09-01

    Disinfection by-products (DBPs) in drinking water represent a public health issue and a challenge for epidemiology to provide evidence towards the causation of various hypothesized health effects. Validation of a biomarker of exposure to DBPs is a strategy to achieve progress which has been advocated. The objective of this study was to validate urinary trichloroacetic acid (TCAA) excretion as a biomarker of exposure to DBPs in an experimental exposure cohort. A total of 52 healthy women participated in the study. Participants consumed supplied tap water for 15 d and provided urine and blood samples for TCAA measurements. The findings revealed that (1) background levels of TCAA in urine and blood were readily detectable, (2) TCAA levels in blood and urine increased with increased amounts of TCAA ingested, (3) the correlations between measurements of TCAA ingestion and urinary excretion were modest (r=0.66, p<0.001) based on one days' sampling and high (r=0.77-0.83, p<0.001) based on two to four days' sampling, (4) the correlations between measurements of TCAA ingestion and blood TCAA concentration were high (r=0.80, p<0.001) and (5) multiple days' urinary TCAA measures improved the prediction of TCAA ingestion through urinary TCAA excretion. TCAA can be a valid biomarker of exposure for DBPs in drinking water.

  1. Network Analysis-Based Approach for Exploring the Potential Diagnostic Biomarkers of Acute Myocardial Infarction

    PubMed Central

    Chen, Jiaqi; Yu, Ling; Zhang, Siwei; Chen, Xia

    2016-01-01

    Acute myocardial infarction (AMI) is a severe cardiovascular disease that is a serious threat to human life. However, the specific diagnostic biomarkers have not been fully clarified and candidate regulatory targets for AMI have not been identified. In order to explore the potential diagnostic biomarkers and possible regulatory targets of AMI, we used a network analysis-based approach to analyze microarray expression profiling of peripheral blood in patients with AMI. The significant differentially-expressed genes (DEGs) were screened by Limma and constructed a gene function regulatory network (GO-Tree) to obtain the inherent affiliation of significant function terms. The pathway action network was constructed, and the signal transfer relationship between pathway terms was mined in order to investigate the impact of core pathway terms in AMI. Subsequently, constructed the transcription regulatory network of DEGs. Weighted gene co-expression network analysis (WGCNA) was employed to identify significantly altered gene modules and hub genes in two groups. Subsequently, the transcription regulation network of DEGs was constructed. We found that specific gene modules may provide a better insight into the potential diagnostic biomarkers of AMI. Our findings revealed and verified that NCF4, AQP9, NFIL3, DYSF, GZMA, TBX21, PRF1 and PTGDR genes by RT-qPCR. TBX21 and PRF1 may be potential candidates for diagnostic biomarker and possible regulatory targets in AMI. PMID:28018242

  2. Variable importance analysis based on rank aggregation with applications in metabolomics for biomarker discovery.

    PubMed

    Yun, Yong-Huan; Deng, Bai-Chuan; Cao, Dong-Sheng; Wang, Wei-Ting; Liang, Yi-Zeng

    2016-03-10

    Biomarker discovery is one important goal in metabolomics, which is typically modeled as selecting the most discriminating metabolites for classification and often referred to as variable importance analysis or variable selection. Until now, a number of variable importance analysis methods to discover biomarkers in the metabolomics studies have been proposed. However, different methods are mostly likely to generate different variable ranking results due to their different principles. Each method generates a variable ranking list just as an expert presents an opinion. The problem of inconsistency between different variable ranking methods is often ignored. To address this problem, a simple and ideal solution is that every ranking should be taken into account. In this study, a strategy, called rank aggregation, was employed. It is an indispensable tool for merging individual ranking lists into a single "super"-list reflective of the overall preference or importance within the population. This "super"-list is regarded as the final ranking for biomarker discovery. Finally, it was used for biomarkers discovery and selecting the best variable subset with the highest predictive classification accuracy. Nine methods were used, including three univariate filtering and six multivariate methods. When applied to two metabolic datasets (Childhood overweight dataset and Tubulointerstitial lesions dataset), the results show that the performance of rank aggregation has improved greatly with higher prediction accuracy compared with using all variables. Moreover, it is also better than penalized method, least absolute shrinkage and selectionator operator (LASSO), with higher prediction accuracy or less number of selected variables which are more interpretable.

  3. Peri-Implant Crevicular Fluid Analysis, Enzymes and Biomarkers: a Systemetic Review

    PubMed Central

    Dursun, Erhan

    2016-01-01

    ABSTRACT Objectives To review the current understanding of the biomarkers and enzymes associated with different forms peri-implant diseases and how their level changes influence the pathogenesis of the inflammatory diseases around dental implants. Material and Methods An electronic search in two different databases was performed including MEDLINE (PubMed) and EMBASE between 1996 to 2016. Human studies analyse peri-implant crevicular fluid (PICF) biomarker and enzyme levels of implants having peri-implant mucositis and peri-implantitis published in English language, were evaluated. A systematic review was performed to assess which biomarkers and enzymes in PICF were used to identify the inflammatory conditions around dental implants. Results Fifty-one articles were identified of which 41 were further evaluated and included in the analysis. Due to significant heterogeneity between included studies, a meta-analysis could not be performed. Instead, a systematic descriptive review was performed. Conclusions Biomarkers and enzymes in peri-implant crevicular fluid have shown promising results in differentiating from peri-implant disease condition to health. However, due to inconsistent results and acquiring much evidence from cross-sectional studies, additional evidence supported by randomized-controlled trials is needed to validate the links reported. PMID:27833734

  4. Fatty acids from lipids of marine organisms: molecular biodiversity, roles as biomarkers, biologically active compounds, and economical aspects.

    PubMed

    Bergé, Jean-Pascal; Barnathan, Gilles

    2005-01-01

    Because of their characteristic living environments, marine organisms produce a variety of lipids. Fatty acids constitute the essential part of triglycerides and wax esters, which are the major components of fats and oils. Nevertheless, phospholipids and glycolipids have considerable importance and will be taken into account, especially the latter compounds that excite increasing interest regarding their promising biological activities. Thus, in addition to the major polyunsaturated fatty acids (PUFA) such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, a great number of various fatty acids occur in marine organisms, e.g. saturated, mono- and diunsaturated, branched, halogenated, hydroxylated, methoxylated, non-methylene-interrupted. Various unprecedented chemical structures of fatty acids, and lipid-containing fatty acids, have recently been discovered, especially from the most primitive animals such as sponges and gorgonians. This review of marine lipidology deals with recent advances in the field of fatty acids since the end of the 1990s. Different approaches will be followed, mainly developing biomarkers of trophic chains in marine ecosystems and of chemotaxonomic interest, reporting new structures, especially those with biological activities or biosynthetic interest. An important part of this review will be devoted to the major PUFA, their relevance to health and nutrition, their biosynthesis, their sources (usual and promising) and market.

  5. Urinary excretion of the acrylonitrile metabolite 2-cyanoethylmercapturic acid is correlated with a variety of biomarkers of tobacco smoke exposure and consumption.

    PubMed

    Minet, Emmanuel; Cheung, Francis; Errington, Graham; Sterz, Katharina; Scherer, Gerhard

    2011-02-01

    Acrylonitrile is an IARC class 2B carcinogen present in cigarette smoke. Urinary 2-cyanoethylmercapturic acid (CEMA) is an acrylonitrile metabolite and a potential biomarker for acrylonitrile exposure. The objective of this work was to study the dose response of CEMA in urine of non-smokers and smokers of different ISO tar yield cigarettes. We observed that smokers excreted >100-fold higher amounts of urinary CEMA than non-smokers. The CEMA levels in smokers were significantly correlated with ISO tar yield, daily cigarette consumption, and urinary biomarkers of smoke exposure. In conclusion, urinary CEMA is a suitable biomarker for assessing smoking-related exposure to acrylonitrile.

  6. Urinary excretion of the acrylonitrile metabolite 2-cyanoethylmercapturic acid is correlated with a variety of biomarkers of tobacco smoke exposure and consumption

    PubMed Central

    Minet, Emmanuel; Cheung, Francis; Errington, Graham; Sterz, Katharina; Scherer, Gerhard

    2011-01-01

    Acrylonitrile is an IARC class 2B carcinogen present in cigarette smoke. Urinary 2-cyanoethylmercapturic acid (CEMA) is an acrylonitrile metabolite and a potential biomarker for acrylonitrile exposure. The objective of this work was to study the dose response of CEMA in urine of non-smokers and smokers of different ISO tar yield cigarettes. We observed that smokers excreted >100-fold higher amounts of urinary CEMA than non-smokers. The CEMA levels in smokers were significantly correlated with ISO tar yield, daily cigarette consumption, and urinary biomarkers of smoke exposure. In conclusion, urinary CEMA is a suitable biomarker for assessing smoking-related exposure to acrylonitrile. PMID:21108560

  7. Feeding ecology of mesopelagic zooplankton of the subtropical and subarctic North Pacific Ocean determined with fatty acid biomarkers

    NASA Astrophysics Data System (ADS)

    Wilson, S. E.; Steinberg, D. K.; Chu, F.-L. E.; Bishop, J. K. B.

    2010-10-01

    Mesopelagic zooplankton may meet their nutritional and metabolic requirements in a number of ways including consumption of sinking particles, carnivory, and vertical migration. How these feeding modes change with depth or location, however, is poorly known. We analyzed fatty acid (FA) profiles to characterize zooplankton diet and large particle (>51 μm) composition in the mesopelagic zone (base of euphotic zone -1000 m) at two contrasting time-series sites in the subarctic (station K2) and subtropical (station ALOHA) Pacific Ocean. Total FA concentration was 15.5 times higher in zooplankton tissue at K2, largely due to FA storage by seasonal vertical migrators such as Neocalanus and Eucalanus. FA biomarkers specific to herbivory implied a higher plant-derived food source at mesotrophic K2 than at oligotrophic ALOHA. Zooplankton FA biomarkers specific to dinoflagellates and diatoms indicated that diatoms, and to a lesser extent, dinoflagellates were important food sources at K2. At ALOHA, dinoflagellate FAs were more prominent. Bacteria-specific FA biomarkers in zooplankton tissue were used as an indicator of particle feeding, and peaks were recorded at depths where known particle feeders were present at ALOHA (e.g., ostracods at 100-300 m). In contrast, depth profiles of bacterial FA were relatively constant with depth at K2. Diatom, dinoflagellate, and bacterial biomarkers were found in similar proportions in both zooplankton and particles with depth at both locations, providing additional evidence that mesopelagic zooplankton consume sinking particles. Carnivory indices were higher and increased significantly with depth at ALOHA, and exhibited distinct peaks at K2, representing an increase in dependence on other zooplankton for food in deep waters. Our results indicate that feeding ecology changes with depth as well as by location. These changes in zooplankton feeding ecology from the surface through the mesopelagic zone, and between contrasting environments

  8. Correlation analysis between four serum biomarkers of liver fibrosis and liver function in infants with cholestasis

    PubMed Central

    TANG, NING; ZHANG, YAPING; LIU, ZEYU; FU, TAO; LIANG, QINGHONG; AI, XUEMEI

    2016-01-01

    The aim of the present study was to investigate the correlation between four serum biomarkers of liver fibrosis and liver function in infants with cholestasis. A total of 30 infants with cholestasis and 20 healthy infants were included in the study. Biochemical assays based on the initial rate method and colorimetric assays were conducted to determine the levels of liver function markers in the serum [such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), direct bilirubin (DBIL), indirect bilirubin (IBIL), γ-glutamyl transferase (γ-GT), cholinesterase (CHE) and total bile acids (TBA)] and four serum biomarkers of liver fibrosis were measured using radioimmunoassays [hyaluronic acid (HA), procollagen type III (PCIII), laminin (LN) and collagen type IV (cIV)]. The serum levels of ALT, AST, TBIL, DBIL, IBIL, γ-GT and TBA in the infants with cholestasis were significantly higher compared to the healthy infants (P<0.01); the serum levels of CHE in the infants with cholestasis were significantly lower compared to the healthy infants (P<0.01). The serum levels of HA, PCIII, and cIV in the infants with cholestasis were significantly higher compared to the healthy infants (P<0.01). Correlation analyses between liver function and the four biomarkers of liver fibrosis showed that HA was positively correlated with AST and γ-GT (P<0.05) and negatively correlated with ALT, CHE and TBA (P<0.05). cIV was positively correlated with γ-GT (P<0.05) and negatively correlated with CHE (P<0.05). In conclusion, statistically significant differences were identified for the liver function markers (ALT, AST, TBIL, DBIL, IBIL, γ-GT and TBA) and the biomarkers HA, PCIII and cIV of liver fibrosis between infants with cholestasis and healthy infants. Thus, the serum levels of HA, cIV, γ-GT and CHE are sensitive markers for cholestatic liver fibrosis in infants. PMID:27347413

  9. Applications of pathology-assisted image analysis of immunohistochemistry-based biomarkers in oncology.

    PubMed

    Shinde, V; Burke, K E; Chakravarty, A; Fleming, M; McDonald, A A; Berger, A; Ecsedy, J; Blakemore, S J; Tirrell, S M; Bowman, D

    2014-01-01

    Immunohistochemistry-based biomarkers are commonly used to understand target inhibition in key cancer pathways in preclinical models and clinical studies. Automated slide-scanning and advanced high-throughput image analysis software technologies have evolved into a routine methodology for quantitative analysis of immunohistochemistry-based biomarkers. Alongside the traditional pathology H-score based on physical slides, the pathology world is welcoming digital pathology and advanced quantitative image analysis, which have enabled tissue- and cellular-level analysis. An automated workflow was implemented that includes automated staining, slide-scanning, and image analysis methodologies to explore biomarkers involved in 2 cancer targets: Aurora A and NEDD8-activating enzyme (NAE). The 2 workflows highlight the evolution of our immunohistochemistry laboratory and the different needs and requirements of each biological assay. Skin biopsies obtained from MLN8237 (Aurora A inhibitor) phase 1 clinical trials were evaluated for mitotic and apoptotic index, while mitotic index and defects in chromosome alignment and spindles were assessed in tumor biopsies to demonstrate Aurora A inhibition. Additionally, in both preclinical xenograft models and an acute myeloid leukemia phase 1 trial of the NAE inhibitor MLN4924, development of a novel image algorithm enabled measurement of downstream pathway modulation upon NAE inhibition. In the highlighted studies, developing a biomarker strategy based on automated image analysis solutions enabled project teams to confirm target and pathway inhibition and understand downstream outcomes of target inhibition with increased throughput and quantitative accuracy. These case studies demonstrate a strategy that combines a pathologist's expertise with automated image analysis to support oncology drug discovery and development programs.

  10. Quantitative Plasma Biomarker Analysis in HDI Exposure Assessment

    PubMed Central

    Flack, Sheila L.; Fent, Kenneth W.; Trelles Gaines, Linda G.; Thomasen, Jennifer M.; Whittaker, Steve; Ball, Louise M.; Nylander-French, Leena A.

    2010-01-01

    Quantification of amines in biological samples is important for evaluating occupational exposure to diisocyanates. In this study, we describe the quantification of 1,6-hexamethylene diamine (HDA) levels in hydrolyzed plasma of 46 spray painters applying 1,6-hexamethylene diisocyanate (HDI)-containing paint in vehicle repair shops collected during repeated visits to their workplace and their relationship with dermal and inhalation exposure to HDI monomer. HDA was detected in 76% of plasma samples, as heptafluorobutyryl derivatives, and the range of HDA concentrations was ≤0.02–0.92 μg l−1. After log-transformation of the data, the correlation between plasma HDA levels and HDI inhalation exposure measured on the same workday was low (N = 108, r = 0.22, P = 0.026) compared with the correlation between plasma HDA levels and inhalation exposure occurring ∼20 to 60 days before blood collection (N = 29, r = 0.57, P = 0.0014). The correlation between plasma HDA levels and HDI dermal exposure measured on the same workday, although statistically significant, was low (N = 108, r = 0.22, P = 0.040) while the correlation between HDA and dermal exposure occurring ∼20 to 60 days before blood collection was slightly improved (N = 29, r = 0.36, P = 0.053). We evaluated various workplace factors and controls (i.e. location, personal protective equipment use and paint booth type) as modifiers of plasma HDA levels. Workers using a downdraft-ventilated booth had significantly lower plasma HDA levels relative to semi-downdraft and crossdraft booth types (P = 0.0108); this trend was comparable to HDI inhalation and dermal exposure levels stratified by booth type. These findings indicate that HDA concentration in hydrolyzed plasma may be used as a biomarker of cumulative inhalation and dermal exposure to HDI and for investigating the effectiveness of exposure controls in the workplace. PMID:19805392

  11. Urinary trans-trans muconic acid (exposure biomarker to benzene) and hippuric acid (exposure biomarker to toluene) concentrations in Mexican women living in high-risk scenarios of air pollution.

    PubMed

    Pruneda-Alvarez, Lucía G; Ruíz-Vera, Tania; Ochoa-Martínez, Angeles C; Pérez-Maldonado, Iván N

    2016-12-16

    This study aimed to determine t,t-muconic acid (t,t-MA; exposure biomarker for benzene) and hippuric acid (HA; exposure biomarker for toluene) concentrations in the urine of women living in Mexico. In a cross-sectional study, apparently healthy women (n = 104) were voluntarily recruited from localities with a high risk of air pollution; t,t-MA and HA in urine were quantified using a high-performance liquid chromatography (HPLC) technique. Mean urinary levels of t,t-MA ranged from 680 to 1,310 μg/g creatinine. Mean values of HA ranged from 0.38 to 0.87 g/g creatinine. In conclusion, compared to data recently reported in literature, we found high urinary levels of t,t-MA and HA in assessed women participating in this study. We therefore deem the implementation of a strategy aimed at the reduction of exposure as a necessary measure for the evaluated communities.

  12. Milk fatty acids as possible biomarkers to early diagnose elevated concentrations of blood plasma nonesterified fatty acids in dairy cows.

    PubMed

    Jorjong, S; van Knegsel, A T M; Verwaeren, J; Lahoz, M Val; Bruckmaier, R M; De Baets, B; Kemp, B; Fievez, V

    2014-11-01

    Most cows encounter a state of negative energy balance during the periparturient period, which may lead to metabolic disorders and impaired fertility. The aim of this study was to assess the potential of milk fatty acids as diagnostic tools of detrimental levels of blood plasma nonesterified fatty acids (NEFA), defined as NEFA concentrations beyond 0.6 mmol/L, in a data set of 92 early lactating cows fed a glucogenic or lipogenic diet and subjected to 0-, 30-, or 60-d dry period before parturition. Milk was collected in wk 2, 3, 4, and 8 (n = 368) and blood was sampled weekly from wk 2 to 8 after parturition. Milk was analyzed for milk fatty acids and blood plasma for NEFA. Data were classified as "at risk of detrimental blood plasma NEFA" (NEFA ≥ 0.6 mmol/L) and "not at risk of detrimental blood plasma NEFA" (NEFA <0.6 mmol/L). Concentrations of 45 milk fatty acids and milk fat C18:1 cis-9-to-C15:0 ratio were subjected to a discriminant analysis. Milk fat C18:1 cis-9 revealed the most discriminating variable to identify detrimental blood plasma NEFA. A false positive rate of 10% allowed us to diagnose 46% of the detrimental blood plasma NEFA cases based on a milk fat C18:1 cis-9 concentration of at least 230 g/kg of milk fatty acids. Additionally, it was assessed whether the milk fat C18:1 cis-9 concentrations of wk 2 could be used as an early warning for detrimental blood plasma NEFA risk during the first 8 wk in lactation. Cows with at least 240 g/kg of C18:1 cis-9 in milk fat had about 50% chance to encounter blood plasma NEFA values of 0.6 mmol/L or more during the first 8 wk of lactation, with a false positive rate of 11.4%. Profit simulations were based on costs for cows suffering from detrimental blood plasma NEFA, and costs for preventive treatment based on daily dosing of propylene glycol for 3 wk. Given the relatively low incidence rate (8% of all observations), continuous monitoring of milk fatty acids during the first 8 wk of lactation to diagnose

  13. Intact-Protein Analysis System for Discovery of Serum-Based Disease Biomarkers

    PubMed Central

    Wang, Hong; Hanash, Samir

    2015-01-01

    Profiling of serum and plasma proteins has substantial relevance to the discovery of circulating disease biomarkers. However, the extreme complexity and vast dynamic range of protein abundance in serum and plasma present a formidable challenge for protein analysis. Thus, integration of multiple technologies is required to achieve high-resolution and high-sensitivity proteomic analysis of serum or plasma. In this chapter, we describe an orthogonal multidimensional intact-protein analysis system (IPAS) (Wang et al., Mol Cell Proteomics 4:618–625, 2005) coupled with protein tagging (Faca et al., J Proteome Res 5:2009–2018, 2006) to profile the serum and plasma proteomes quantitatively, which we have applied in our biomarker discovery studies (Katayama et al., Genome Med 1:47, 2009; Faca et al., PLoS Med 5:e123, 2008; Zhang et al. Genome Biol 9:R93, 2008). PMID:21468941

  14. Intact-protein analysis system for discovery of serum-based disease biomarkers.

    PubMed

    Wang, Hong; Hanash, Samir

    2011-01-01

    Profiling of serum and plasma proteins has substantial relevance to the discovery of circulating disease biomarkers. However, the extreme complexity and vast dynamic range of protein abundance in serum and plasma present a formidable challenge for protein analysis. Thus, integration of multiple technologies is required to achieve high-resolution and high-sensitivity proteomic analysis of serum or plasma. In this chapter, we describe an orthogonal multidimensional intact-protein analysis system (IPAS) (Wang et al., Mol Cell Proteomics 4:618-625, 2005) coupled with protein tagging (Faca et al., J Proteome Res 5:2009-2018, 2006) to profile the serum and plasma proteomes quantitatively, which we have applied in our biomarker discovery studies (Katayama et al., Genome Med 1:47, 2009; Faca et al., PLoS Med 5:e123, 2008; Zhang et al. Genome Biol 9:R93, 2008).

  15. Optimization of a histopathological biomarker for sphingomyelin accumulation in acid sphingomyelinase deficiency.

    PubMed

    Taksir, Tatyana V; Johnson, Jennifer; Maloney, Colleen L; Yandl, Emily; Griffiths, Denise; Thurberg, Beth L; Ryan, Susan

    2012-08-01

    Niemann-Pick disease (types A and B), or acid sphingomyelinase deficiency, is an inherited deficiency of acid sphingomyelinase, resulting in intralysosomal accumulation of sphingomyelin in cells throughout the body, particularly within those of the reticuloendothelial system. These cellular changes result in hepatosplenomegaly and pulmonary infiltrates in humans. A knockout mouse model mimics many elements of human ASMD and is useful for studying disease histopathology. However, traditional formalin-fixation and paraffin embedding of ASMD tissues dissolves sphingomyelin, resulting in tissues with a foamy cell appearance, making quantitative analysis of the substrate difficult. To optimize substrate fixation and staining, a modified osmium tetroxide and potassium dichromate postfixation method was developed to preserve sphingomyelin in epon-araldite embedded tissue and pulmonary cytology specimens. After processing, semi-thin sections were incubated with tannic acid solution followed by staining with toluidine blue/borax. This modified method provides excellent preservation and staining contrast of sphingomyelin with other cell structures. The resulting high-resolution light microscopy sections permit digital quantification of sphingomyelin in light microscopic fields. A lysenin affinity stain for sphingomyelin was also developed for use on these semi-thin epon sections. Finally, ultrathin serial sections can be cut from these same tissue blocks and stained for ultrastructural examination by electron microscopy.

  16. Use of urinary renal biomarkers to evaluate the nephrotoxic effects of melamine or cyanuric acid in non-pregnant and pregnant rats.

    PubMed

    Bandele, O J; Stine, C B; Ferguson, M; Black, T; Olejnik, N; Keltner, Z; Evans, E R; Crosby, T C; Reimschuessel, R; Sprando, R L

    2014-12-01

    Although traditional assessments of renal damage detect loss of kidney function, urinary renal biomarkers are proposed to indicate early changes in renal integrity. The recent adulteration of infant formula and other milk-based foods with melamine revealed a link between melamine ingestion and nephropathy. Thus, the effects of melamine and related analogs (e.g., cyanuric acid) should be assessed in other potentially sensitive groups. We evaluated whether urinary Kim-1, clusterin, and osteopontin could detect the effects of high doses of melamine or cyanuric acid in pregnant and non-pregnant female rats gavaged with 1000 mg/kg bw/day for 10 days. We demonstrate that these biomarkers can differentiate the severity of effects induced by melamine or cyanuric acid. All melamine-treated animals experienced adverse effects; however, pregnant rats were most sensitive as indicated by increased SCr, BUN, and kidney weights, decreased body weight, and presence of renal crystals. These effects coincided with elevated urinary biomarker levels as early as day 2 of exposure. One cyanuric acid-treated rat displayed effects similar to melamine, including increased urinary biomarker levels. This work illustrates that these biomarkers can detect early effects of melamine or cyanuric acid crystal-induced nephropathy and further supports the use of urinary protein immunoassays as a powerful, non-invasive method to assess nephrotoxicity.

  17. Identification of trophic interactions within an estuarine food web (northern New Zealand) using fatty acid biomarkers and stable isotopes

    NASA Astrophysics Data System (ADS)

    Alfaro, Andrea C.; Thomas, François; Sergent, Luce; Duxbury, Mark

    2006-10-01

    Fatty acid biomarkers and stable isotope signatures were used to identify the trophic dynamics of a mangrove/seagrass estuarine food web at Matapouri, northern New Zealand. Specific fatty acids were used to identify the preferred food sources (i.e., mangroves, seagrass, phytoplankton, macroalgae, bacteria, and zooplankton) of dominant fauna (i.e., filter feeders, grazing snails, scavenger/predatory snails, shrimp, crabs, and fish), and their presence in water and sediment samples throughout the estuary. The diets of filter feeders were found to be dominated by dinoflagellates, whereas grazers showed a higher diatom contribution. Bacteria associated with organic debris on surface sediments and brown algal ( Hormosira banksii) material in the form of suspended organic matter also accounted for a high proportion of most animal diets. Animals within higher trophic levels had diverse fatty acid profiles, revealing their varied feeding strategies and carbon sources. The stable isotope (δ 13C and δ 15N) analyses of major primary producers and consumers/predators revealed a trend of 15N enrichment with increasing trophic level, while δ 13C values provided a generally good description of carbon flow through the food web. Overall results from both fatty acid profiles and stable isotopes indicate that a variety of carbon sources with a range of trophic pathways typify this food web. Moreover, none of the animals studied was dependent on a single food source. This study is the first to use a comprehensive fatty acid biomarker and stable isotope approach to investigate the food web dynamics within a New Zealand temperate mangrove/seagrass estuary. This quantitative research may contribute to the currently developing management strategies for estuaries in northern New Zealand, especially for those perceived to have expanding mangrove fringes.

  18. Covalently deposited dyes: a new chromogen paradigm that facilitates analysis of multiple biomarkers in situ.

    PubMed

    Day, William A; Lefever, Mark R; Ochs, Robert L; Pedata, Anne; Behman, Lauren J; Ashworth-Sharpe, Julia; Johnson, Donald D; May, Eric J; Grille, James G; Roberts, Esteban A; Kosmeder, Jerry W; Morrison, Larry E

    2017-01-01

    Multiplexed analysis of multiple biomarkers in a tissue sample requires use of reporter dyes with specific spectral properties that enable discrimination of signals. Conventional chromogens with broad absorbance spectra, widely used in immunohistochemistry (IHC), offer limited utility for multiplexed detection. Many dyes with narrow absorbance spectra, eg rhodamines, fluoresceins, and cyanines, potentially useful for multiplexed detection are well-characterized; however, generation of a chromogenic reagent useful for IHC analysis has not been demonstrated. Studies reported herein demonstrate utility of tyramine-chemistry for synthesis of a wide variety of new chromogenic dye conjugates useful for multiplexed in situ analysis using conventional light microscopes. The dyes, useful individually or in blends to generate new colors, provide signal sensitivity and dynamic range similar to conventional DAB chromogen, while enabling analysis of co-localized biomarkers. It is anticipated that this new paradigm will enable generation of a wide variety of new chromogens, useful for both research and clinical biomarker analysis that will benefit clinicians and patients.

  19. Quantitative proteomic analysis of microdissected oral epithelium for cancer biomarker discovery.

    PubMed

    Xiao, Hua; Langerman, Alexander; Zhang, Yan; Khalid, Omar; Hu, Shen; Cao, Cheng-Xi; Lingen, Mark W; Wong, David T W

    2015-11-01

    Specific biomarkers are urgently needed for the detection and progression of oral cancer. The objective of this study was to discover cancer biomarkers from oral epithelium through utilizing high throughput quantitative proteomics approaches. Morphologically malignant, epithelial dysplasia, and adjacent normal epithelial tissues were laser capture microdissected (LCM) from 19 patients and used for proteomics analysis. Total proteins from each group were extracted, digested and then labelled with corresponding isobaric tags for relative and absolute quantitation (iTRAQ). Labelled peptides from each sample were combined and analyzed by liquid chromatography-mass spectrometry (LC-MS/MS) for protein identification and quantification. In total, 500 proteins were identified and 425 of them were quantified. When compared with adjacent normal oral epithelium, 17 and 15 proteins were consistently up-regulated or down-regulated in malignant and epithelial dysplasia, respectively. Half of these candidate biomarkers were discovered for oral cancer for the first time. Cornulin was initially confirmed in tissue protein extracts and was further validated in tissue microarray. Its presence in the saliva of oral cancer patients was also explored. Myoglobin and S100A8 were pre-validated by tissue microarray. These data demonstrated that the proteomic biomarkers discovered through this strategy are potential targets for oral cancer detection and salivary diagnostics.

  20. Predicting MicroRNA Biomarkers for Cancer Using Phylogenetic Tree and Microarray Analysis

    PubMed Central

    Wang, Hsiuying

    2016-01-01

    MicroRNAs (miRNAs) are shown to be involved in the initiation and progression of cancers in the literature, and the expression of miRNAs is used as an important cancer prognostic tool. The aim of this study is to predict high-confidence miRNA biomarkers for cancer. We adopt a method that combines miRNA phylogenetic structure and miRNA microarray data analysis to discover high-confidence miRNA biomarkers for colon, prostate, pancreatic, lung, breast, bladder and kidney cancers. There are 53 miRNAs selected through this method that either have potential to involve a single cancer’s development or to involve several cancers’ development. These miRNAs can be used as high-confidence miRNA biomarkers of these seven investigated cancers for further experiment validation. miR-17, miR-20, miR-106a, miR-106b, miR-92, miR-25, miR-16, miR-195 and miR-143 are selected to involve a single cancer’s development in these seven cancers. They have the potential to be useful miRNA biomarkers when the result can be confirmed by experiments. PMID:27213352

  1. Multiplex Serum Protein Analysis Identifies Novel Biomarkers of Advanced Fibrosis in Patients with Chronic Liver Disease with the Potential to Improve Diagnostic Accuracy of Established Biomarkers

    PubMed Central

    Irvine, Katharine M.; Wockner, Leesa F.; Hoffmann, Isabell; Horsfall, Leigh U.; Fagan, Kevin J.; Bijin, Veonice; Lee, Bernett; Clouston, Andrew D.; Lampe, Guy; Connolly, John E.; Powell, Elizabeth E.

    2016-01-01

    Background and Aims Non-invasive markers of liver fibrosis are urgently required, especially for use in non-specialist settings. The aim of this study was to identify novel serum biomarkers of advanced fibrosis. Methods We performed an unbiased screen of 120 serum analytes including cytokines, chemokines and proteases in 70 patients (35 without fibrosis, 35 with cirrhosis on biopsy), and selected a panel of 44 candidate biomarkers, which were subsequently measured in a mixed-etiology cohort of 432 patients with known serum HA, PIIINP and TIMP1 (which comprise the validated Enhanced Liver Fibrosis (ELF) test). Multivariate logistic regression modelling was used to generate models for the prediction of advanced or significant fibrosis (METAVIR ≥F3 and ≥F2, respectively); in addition to identifying biomarkers of disease activity and steatohepatitis. Results Seventeen analytes were significantly differentially expressed between patients with no advanced fibrosis and patients with advanced fibrosis, the most significant being hyaluronic acid (HA) and matrix metalloproteinase (MMP) 7 (p = 2.9E-41 and p = 1.0E-26, respectively). The optimal model for the prediction of advanced fibrosis comprised HA, MMP7, MMP1, alphafetoprotein (AFP) and the AST to platelet ratio index (APRI). We demonstrate enhanced diagnostic accuracy (AUROC = 0.938) compared to a model comprising HA, PIIINP and TIMP1 alone (ELF) (AUROC = 0.898, p<0.0001, De Long’s test). Conclusions We have identified novel serum biomarkers of advanced liver fibrosis, which have the potential to enhance the diagnostic accuracy of established biomarkers. Our data suggest MMP7 is a valuable indicator of advanced fibrosis and may play a role in liver fibrogenesis. PMID:27861569

  2. Impact of clinical context on acute kidney injury biomarker performances: differences between neutrophil gelatinase-associated lipocalin and L-type fatty acid-binding protein

    PubMed Central

    Asada, Toshifumi; Isshiki, Rei; Hayase, Naoki; Sumida, Maki; Inokuchi, Ryota; Noiri, Eisei; Nangaku, Masaomi; Yahagi, Naoki; Doi, Kent

    2016-01-01

    Application of acute kidney injury (AKI) biomarkers with consideration of nonrenal conditions and systemic severity has not been sufficiently determined. Herein, urinary neutrophil gelatinase-associated lipocalin (NGAL), L-type fatty acid-binding protein (L-FABP) and nonrenal disorders, including inflammation, hypoperfusion and liver dysfunction, were evaluated in 249 critically ill patients treated at our intensive care unit. Distinct characteristics of NGAL and L-FABP were revealed using principal component analysis: NGAL showed linear correlations with inflammatory markers (white blood cell count and C-reactive protein), whereas L-FABP showed linear correlations with hypoperfusion and hepatic injury markers (lactate, liver transaminases and bilirubin). We thus developed a new algorithm by combining urinary NGAL and L-FABP with stratification by the Acute Physiology and Chronic Health Evaluation score, presence of sepsis and blood lactate levels to improve their AKI predictive performance, which showed a significantly better area under the receiver operating characteristic curve [AUC-ROC 0.940; 95% confidential interval (CI) 0.793–0.985] than that under NGAL alone (AUC-ROC 0.858, 95% CI 0.741–0.927, P = 0.03) or L-FABP alone (AUC-ROC 0.837, 95% CI 0.697–0.920, P = 0.007) and indicated that nonrenal conditions and systemic severity should be considered for improved AKI prediction by NGAL and L-FABP as biomarkers. PMID:27605390

  3. Search for Chemical Biomarkers on Mars Using the Sample Analysis at Mars Instrument Suite on the Mars Science Laboratory

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Conrad, P.; Dworkin, J. P.; Eigenbrode, J.; Mahaffy, P. R.

    2011-01-01

    One key goal for the future exploration of Mars is the search for chemical biomarkers including complex organic compounds important in life on Earth. The Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) will provide the most sensitive measurements of the organic composition of rocks and regolith samples ever carried out in situ on Mars. SAM consists of a gas chromatograph (GC), quadrupole mass spectrometer (QMS), and tunable laser spectrometer to measure volatiles in the atmosphere and released from rock powders heated up to 1000 C. The measurement of organics in solid samples will be accomplished by three experiments: (1) pyrolysis QMS to identify alkane fragments and simple aromatic compounds; pyrolysis GCMS to separate and identify complex mixtures of larger hydrocarbons; and (3) chemical derivatization and GCMS extract less volatile compounds including amino and carboxylic acids that are not detectable by the other two experiments.

  4. Comparative analysis of selected exhaled breath biomarkers obtained with two different temperature-controlled devices

    PubMed Central

    2009-01-01

    Background The collection of exhaled breath condensate (EBC) is a suitable and non-invasive method for evaluation of airway inflammation. Several studies indicate that the composition of the condensate and the recovery of biomarkers are affected by physical characteristics of the condensing device and collecting circumstances. Additionally, there is an apparent influence of the condensing temperature, and often the level of detection of the assay is a limiting factor. The ECoScreen2 device is a new, partly single-use disposable system designed for studying different lung compartments. Methods EBC samples were collected from 16 healthy non-smokers by using the two commercially available devices ECoScreen2 and ECoScreen at a controlled temperature of -20°C. EBC volume, pH, NOx, LTB4, PGE2, 8-isoprostane and cys-LTs were determined. Results EBC collected with ECoScreen2 was less acidic compared to ECoScreen. ECoScreen2 was superior concerning condensate volume and detection of biomarkers, as more samples were above the detection limit (LTB4 and PGE2) or showed higher concentrations (8-isoprostane). However, NOx was detected only in EBC sampled by ECoScreen. Conclusion ECoScreen2 in combination with mediator specific enzyme immunoassays may be suitable for measurement of different biomarkers. Using this equipment, patterns of markers can be assessed that are likely to reflect the complex pathophysiological processes in inflammatory respiratory disease. PMID:19948050

  5. The added value of biomarker analysis to the genesis of Plaggic Anthrosols.

    NASA Astrophysics Data System (ADS)

    van Mourik, Jan; Jansen, Boris

    2015-04-01

    Coversands (chemical poor Late-glacial aeolian sand deposits) dominate the surface geology of an extensive area in northwestern Europe. Plaggic Anthrosols occur in cultural landscapes, developed on coversands. They are the characteristic soils that developed on ancient fertilized arable fields. Plaggic Anthrosols have a complex genesis. They are records of aspects environmental and agricultural history. In previous studies information of the soil records was unlocked by application of pollen analysis, 14C and OSL dating. In this study we applied biomarker analysis to unlock additional information about the applied organic sources in the production of plaggic manure. Radiocarbon dating suggested the start of sedentary agriculture (after a period, characterized by shifting cultivation and Celtic fields) between 3000 and 2000 BP. In previous studies is assumed that farmers applied organic sods, dug on forest soils and heath to produce organic stable manure to fertilize the fields. The mineral fraction of the sods was supposed to be responsible for the development of the plaggic horizon and the raise of the land surface. Optically stimulated Luminescence dating however suggested that plaggic deposition on the fields started relatively late, in the 18th century. The use of ectorganic matter from the forest soils must have been ended in the 10th-12th century, due to commercial forest clear cuttings as recorded in archived documents. These deforestations resulted in the first extension of sand drifting and famers had to protect the valuable heath against this ' environmental catastrophe' . The use of heath for sheep grazing and other purposes as honey production could continue till the 18th century, as recorded in archived documents. In the course of the 18th century, the population growth resulted in increasing demand for food. The deep stable economy was introduced and the booming demand for manure resulted in intensive sod digging on the heath. This caused heath

  6. Evaluation of biomarkers of environmental exposures: urinary haloacetic acids associated with ingestion of chlorinated drinking water.

    PubMed

    Kim, H; Haltmeier, P; Klotz, J B; Weisel, C P

    1999-02-01

    A study was conducted to determine if DCAA and TCAA urinary excretion rates are valid biomarkers of chronic ingestion exposure to these disinfection by-products of chlorination of drinking water. Entire first morning urine voids, time-of-visit urine samples, and tap water samples were collected from 47 female subjects. In addition, a 48-h recall questionnaire was administered to determine the amounts and types of liquids ingested by each subject as well as other exposures that could lead to DCAA and TCAA urinary excretion. The TCAA excretion rate for the first morning urine samples was significantly correlated with the estimated 48-h TCAA ingestion exposure for 25 subjects whose ingestion exposures primarily occurred at home, while the DCAA excretion rate was not correlated with the DCAA ingestion exposure. Thus, urinary TCAA appears to be a valid biomarker of chronic ingestion exposure to TCAA from chlorinated water, while urinary DCAA is not. It is proposed that the difference in the biological half-lives between these two compounds is the rationale for this finding. The biological half-life of TCAA is longer than successive exposure intervals; thus TCAA accumulates until it reaches a steady state. The half-life of DCAA is shorter than successive exposure intervals; thus DCAA is almost completely metabolized following an exposure and is eliminated from the body. This study suggests that biological half-life, exposure interval, and sample collection interval should be considered in selecting biomarkers and designing studies to validate them.

  7. Diagnostic biomarkers for renal cell carcinoma: selection using novel bioinformatics systems for microarray data analysis

    PubMed Central

    Osunkoya, Adeboye O; Yin-Goen, Qiqin; Phan, John H; Moffitt, Richard A; Stokes, Todd H; Wang, May D; Young, Andrew N

    2009-01-01

    Summary The differential diagnosis of clear cell, papillary and chromophobe renal cell carcinoma is clinically important, because these tumor subtypes are associated with different pathobiology and clinical behavior. For cases in which histopathology is equivocal, immunohistochemistry and quantitative RT-PCR can assist in the differential diagnosis by measuring expression of subtype-specific biomarkers. Several renal tumor biomarkers have been discovered in expression microarray studies. However, due to heterogeneity of gene and protein expression, additional biomarkers are needed for reliable diagnostic classification. We developed novel bioinformatics systems to identify candidate renal tumor biomarkers from the microarray profiles of 45 clear cell, 16 papillary and 10 chromophobe renal cell carcinoma; the microarray data was derived from two independent published studies. The ArrayWiki biocomputing system merged the microarray datasets into a single file, so gene expression could be analyzed from a larger number of tumors. The caCORRECT system removed non-random sources of error from the microarray data, and the omniBioMarker system analyzed data with several gene-ranking algorithms, in order to identify algorithms effective at recognizing previously described renal tumor biomarkers. We predicted these algorithms would also be effective at identifying unknown biomarkers that could be verified by independent methods. We selected six novel candidate biomakers from the omniBioMarker analysis, and verified their differential expression in formalin-fixed paraffin-embedded tissues by quantitative RT-PCR and immunohistochemistry. The candidate biomarkers were carbonic anhydrase IX, ceruloplasmin, schwannomin-interacting protein 1, E74-like factor 3, cytochrome c oxidase subunit 5a and acetyl-CoA acetyltransferase 1. Quantitative RT-PCR was performed on 17 clear cell, 13 papillary and 7 chromophobe renal cell carcinoma. Carbonic anhydrase IX and ceruloplasmin were

  8. Plasma Acylcarnitines and Amino Acid Levels As an Early Complex Biomarker of Propensity to High-Fat Diet-Induced Obesity in Mice

    PubMed Central

    Bardova, Kristina; Gardlo, Alzbeta; Rombaldova, Martina; Kuda, Ondrej; Rossmeisl, Martin; Kopecky, Jan

    2016-01-01

    Obesity is associated with insulin resistance and impaired glucose tolerance, which represent characteristic features of the metabolic syndrome. Development of obesity is also linked to changes in fatty acid and amino acid metabolism observed in animal models of obesity as well as in humans. The aim of this study was to explore whether plasma metabolome, namely the levels of various acylcarnitines and amino acids, could serve as a biomarker of propensity to obesity and impaired glucose metabolism. Taking advantage of a high phenotypic variation in diet-induced obesity in C57BL/6J mice, 12-week-old male and female mice (n = 155) were fed a high-fat diet (lipids ~32 wt%) for a period of 10 weeks, while body weight gain (BWG) and changes in insulin sensitivity (ΔHOMA-IR) were assessed. Plasma samples were collected before (week 4) and after (week 22) high-fat feeding. Both univariate and multivariate statistical analyses were then used to examine the relationships between plasma metabolome and selected phenotypes including BWG and ΔHOMA-IR. Partial least squares-discrimination analysis was able to distinguish between animals selected either for their low or high BWG (or ΔHOMA-IR) in male but not female mice. Among the metabolites that differentiated male mice with low and high BWG, and which also belonged to the major discriminating metabolites when analyzed in plasma collected before and after high-fat feeding, were amino acids Tyr and Orn, as well as acylcarnitines C16-DC and C18:1-OH. In general, the separation of groups selected for their low or high ΔHOMA-IR was less evident and the outcomes of a corresponding multivariate analysis were much weaker than in case of BWG. Thus, our results document that plasma acylcarnitines and amino acids could serve as a gender-specific complex biomarker of propensity to obesity, however with a limited predictive value in case of the associated impairment of insulin sensitivity. PMID:27183228

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

    PubMed

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

    2016-02-05

    NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.

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

    PubMed Central

    2016-01-01

    NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment. PMID:26745651

  11. Breath Analysis Using Laser Spectroscopic Techniques: Breath Biomarkers, Spectral Fingerprints, and Detection Limits

    PubMed Central

    Wang, Chuji; Sahay, Peeyush

    2009-01-01

    Breath analysis, a promising new field of medicine and medical instrumentation, potentially offers noninvasive, real-time, and point-of-care (POC) disease diagnostics and metabolic status monitoring. Numerous breath biomarkers have been detected and quantified so far by using the GC-MS technique. Recent advances in laser spectroscopic techniques and laser sources have driven breath analysis to new heights, moving from laboratory research to commercial reality. Laser spectroscopic detection techniques not only have high-sensitivity and high-selectivity, as equivalently offered by the MS-based techniques, but also have the advantageous features of near real-time response, low instrument costs, and POC function. Of the approximately 35 established breath biomarkers, such as acetone, ammonia, carbon dioxide, ethane, methane, and nitric oxide, 14 species in exhaled human breath have been analyzed by high-sensitivity laser spectroscopic techniques, namely, tunable diode laser absorption spectroscopy (TDLAS), cavity ringdown spectroscopy (CRDS), integrated cavity output spectroscopy (ICOS), cavity enhanced absorption spectroscopy (CEAS), cavity leak-out spectroscopy (CALOS), photoacoustic spectroscopy (PAS), quartz-enhanced photoacoustic spectroscopy (QEPAS), and optical frequency comb cavity-enhanced absorption spectroscopy (OFC-CEAS). Spectral fingerprints of the measured biomarkers span from the UV to the mid-IR spectral regions and the detection limits achieved by the laser techniques range from parts per million to parts per billion levels. Sensors using the laser spectroscopic techniques for a few breath biomarkers, e.g., carbon dioxide, nitric oxide, etc. are commercially available. This review presents an update on the latest developments in laser-based breath analysis. PMID:22408503

  12. Human Xeno-autoantibodies Against a Non-human Sialic acid Serve As Novel Serum Biomarkers and Immunotherapeutics in Cancer

    PubMed Central

    Padler-Karavani, Vered; Hurtado-Ziola, Nancy; Pu, Minya; Yu, Hai; Huang, Shengshu; Muthana, Saddam; Chokhawala, Harshal A.; Cao, Hongzhi; Secrest, Patrick; Friedmann-Morvinski, Dinorah; Singer, Oded; Ghaderi, Darius; Verma, Inder M.; Liu, Yu-Tsueng; Messer, Karen; Chen, Xi; Varki, Ajit; Schwab, Richard

    2011-01-01

    Human carcinomas can metabolically incorporate and present the dietary non-human sialic acid Neu5Gc, which differs from the human sialic acid N-acetylneuraminic acid (Neu5Ac) by one oxygen atom. Tumor-associated Neu5Gc can interact with low levels of circulating anti-Neu5Gc antibodies, thereby facilitating tumor progression via chronic inflammation in a human-like Neu5Gc-deficient mouse model. Here we show that human anti-Neu5Gc antibodies can be affinity-purified in substantial amounts from clinically-approved intravenous IgG (IVIG) and used at higher concentrations to suppress growth of the same Neu5Gc-expressing tumors. Hypothesizing that this polyclonal spectrum of human anti-Neu5Gc antibodies also includes potential cancer biomarkers, we then characterize them in cancer and non-cancer patients’ sera, using a novel sialoglycan-microarray presenting multiple Neu5Gc-glycans and control Neu5Ac-glycans. Antibodies against Neu5Gcα2–6GalNAcα1-O-Ser/Thr (GcSTn) were found to be more prominent in patients with carcinomas than with other diseases. This unusual epitope arises from dietary Neu5Gc incorporation into the carcinoma marker Sialyl-Tn, and is the first example of such a novel mechanism for biomarker generation. Finally, human serum or purified antibodies rich in anti-GcSTn-reactivity kill GcSTn-expressing human tumors via complement-dependent-cytotoxicity or antibody-dependent-cellular-cytotoxicity. Such xeno-autoantibodies and xenoautoantigens have potential for novel diagnostics, prognostics and therapeutics in human carcinomas. PMID:21505105

  13. Identification of candidate diagnostic serum biomarkers for Kawasaki disease using proteomic analysis

    PubMed Central

    Kimura, Yayoi; Yanagimachi, Masakatsu; Ino, Yoko; Aketagawa, Mao; Matsuo, Michie; Okayama, Akiko; Shimizu, Hiroyuki; Oba, Kunihiro; Morioka, Ichiro; Imagawa, Tomoyuki; Kaneko, Tetsuji; Yokota, Shumpei; Hirano, Hisashi; Mori, Masaaki

    2017-01-01

    Kawasaki disease (KD) is a systemic vasculitis and childhood febrile disease that can lead to cardiovascular complications. The diagnosis of KD depends on its clinical features, and thus it is sometimes difficult to make a definitive diagnosis. In order to identify diagnostic serum biomarkers for KD, we explored serum KD-related proteins, which differentially expressed during the acute and recovery phases of two patients by mass spectrometry (MS). We identified a total of 1,879 proteins by MS-based proteomic analysis. The levels of three of these proteins, namely lipopolysaccharide-binding protein (LBP), leucine-rich alpha-2-glycoprotein (LRG1), and angiotensinogen (AGT), were higher in acute phase patients. In contrast, the level of retinol-binding protein 4 (RBP4) was decreased. To confirm the usefulness of these proteins as biomarkers, we analyzed a total of 270 samples, including those collected from 55 patients with acute phase KD, by using western blot analysis and microarray enzyme-linked immunosorbent assays (ELISAs). Over the course of this experiment, we determined that the expression level of these proteins changes specifically in the acute phase of KD, rather than the recovery phase of KD or other febrile illness. Thus, LRG1 could be used as biomarkers to facilitate KD diagnosis based on clinical features. PMID:28262744

  14. Novel Biomarker Candidates for Colorectal Cancer Metastasis: A Meta-analysis of In Vitro Studies

    PubMed Central

    Long, Nguyen Phuoc; Lee, Wun Jun; Huy, Nguyen Truong; Lee, Seul Ji; Park, Jeong Hill; Kwon, Sung Won

    2016-01-01

    Colorectal cancer (CRC) is one of the most common and lethal cancers. Although numerous studies have evaluated potential biomarkers for early diagnosis, current biomarkers have failed to reach an acceptable level of accuracy for distant metastasis. In this paper, we performed a gene set meta-analysis of in vitro microarray studies and combined the results from this study with previously published proteomic data to validate and suggest prognostic candidates for CRC metastasis. Two microarray data sets included found 21 significant genes. Of these significant genes, ALDOA, IL8 (CXCL8), and PARP4 had strong potential as prognostic candidates. LAMB2, MCM7, CXCL23A, SERPINA3, ABCA3, ALDH3A2, and POLR2I also have potential. Other candidates were more controversial, possibly because of the biologic heterogeneity of tumor cells, which is a major obstacle to predicting metastasis. In conclusion, we demonstrated a meta-analysis approach and successfully suggested ten biomarker candidates for future investigation. PMID:27688707

  15. Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers.

    PubMed

    Labaj, Wojciech; Papiez, Anna; Polanski, Andrzej; Polanska, Joanna

    2017-03-01

    Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study. Here, the basic knowledge on molecular mechanisms is confirmed quantitatively and by literature references. Second, pairwise comparison testing is performed for juxtaposing the main leukaemia types among each other. In this case by means of the Dice coefficient similarity measure the general relations are pointed out. Moreover, lists of candidate main leukaemia group biomarkers are proposed. Finally, with this approach being successful, the third analysis provides insight into all of the studied subtypes, followed by the emergence of four leukaemia subtype biomarkers. In addition, the class enhanced DEG signature obtained on the basis of novel pipeline processing leads to significantly better classification power of multi-class data classifiers. The developed methodology consisting of batch effect adjustment, adaptive noise and feature filtration coupled with adequate statistical testing and biomarker definition proves to be an effective approach towards knowledge discovery in high-throughput molecular biology experiments.

  16. Solvent interaction analysis as a proteomic approach to structure-based biomarker discovery and clinical diagnostics.

    PubMed

    Zaslavsky, Boris Y; Uversky, Vladimir N; Chait, Arnon

    2016-01-01

    Proteins have several measurable features in biological fluids that may change under pathological conditions. The current disease biomarker discovery is mostly based on protein concentration in the sample as the measurable feature. Changes in protein structures, such as post-translational modifications and in protein-partner interactions are known to accompany pathological processes. Changes in glycosylation profiles are well-established for many plasma proteins in various types of cancer and other diseases. The solvent interaction analysis method is based on protein partitioning in aqueous two-phase systems and is highly sensitive to changes in protein structure and protein-protein- and protein-partner interactions while independent of the protein concentration in the biological sample. It provides quantitative index: partition coefficient representing changes in protein structure and interactions with partners. The fundamentals of the method are presented with multiple examples of applications of the method to discover and monitor structural protein biomarkers as disease-specific diagnostic indicators.

  17. Microarray Meta-Analysis and Cross-Platform Normalization: Integrative Genomics for Robust Biomarker Discovery

    PubMed Central

    Walsh, Christopher J.; Hu, Pingzhao; Batt, Jane; Dos Santos, Claudia C.

    2015-01-01

    The diagnostic and prognostic potential of the vast quantity of publicly-available microarray data has driven the development of methods for integrating the data from different microarray platforms. Cross-platform integration, when appropriately implemented, has been shown to improve reproducibility and robustness of gene signature biomarkers. Microarray platform integration can be conceptually divided into approaches that perform early stage integration (cross-platform normalization) versus late stage data integration (meta-analysis). A growing number of statistical methods and associated software for platform integration are available to the user, however an understanding of their comparative performance and potential pitfalls is critical for best implementation. In this review we provide evidence-based, practical guidance to researchers performing cross-platform integration, particularly with an objective to discover biomarkers. PMID:27600230

  18. The Kirki episode: Detailed biomarker analysis provides some surprises

    SciTech Connect

    Currie, T.J.; Alexander, R.; Kagi, R.I.

    1996-12-31

    On Sunday 21st July 1991 the oil tanker Kirki caught fire when its bow broke off in heavy seas just 40 km off the Western Australian coastline near Jurien, approximately 200 km north of Perth. The tanker was carrying 80,000 tonnes of Murban light crude oil from the Middle East. Over the next three days approximately 10,000 tonnes of this oil was released into the marine environment, the heavy seas rapidly spreading the oil slick to a thin sheen. There was extensive media coverage of this event and it was widely considered that the spill posed a serious environmental threat to reef systems, recreational beaches and the local rock lobster fishery. This report describes results of analysis performed on several of the samples.

  19. Uric Acid as a potential biomarker of pulmonary arterial hypertension in patients with sickle cell disease.

    PubMed

    Joshi, Keval; Anjum, Fatima; Gowda, Satish; Damania, Dushyant; Graham-Hill, Suzette; Gillette, Peter; Zein, Joe; Jamaleddine, Ghassan; Demetis, Spiro; Wadgaonkar, Raj

    2011-06-01

    Serum uric acid (UA) is emerging as a strong and independent marker for pulmonary arterial hypertension (PAH). PAH is well recognized as a life threatening complication of sickle cell disease (SCD). However, the association between UA and PAH in SCD is unknown. We reviewed electronic medical records (EMR) of 559 consecutive adult SCD patients from Kings County Hospital Center (KCHC) between January 2005 and February 2010. Patients (n = 96) with measurement of UA in close temporal proximity to the transthoracic echocardiography (TTE) were identified. PAH was defined as pulmonary artery systolic pressure (PASP) ≥30 mm Hg. Patients (n = 16) with other risk factors which may cause PAH and chronic renal insufficiency were excluded. In 18 patients, TTE could not measure PASP. Finally, 62 patients were selected. Statistical analysis was performed using Student t tests, Pearson correlation coefficient and multivariate regression analysis. Out of 62 patients, 30 had PAH. Patients with PAH had a higher UA level (8.67 ± 4.8 vs. 5.35 ± 2.1, P = 0.001). We found strong positive correlation between the UA level and PASP (r = 0.71; P < 0.0001). This correlation was independent of diuretic use. UA could be a potential marker for PAH in SCD. However, its' prognostic and pathophysiologic role in SCD patients with PAH needs to be further investigated.

  20. Plasma Elaidic Acid Level as Biomarker of Industrial Trans Fatty Acids and Risk of Weight Change: Report from the EPIC Study

    PubMed Central

    Chajès, Véronique; Biessy, Carine; Ferrari, Pietro; Romieu, Isabelle; Freisling, Heinz; Huybrechts, Inge; Scalbert, Augustin; Bueno de Mesquita, Bas; Romaguera, Dora; Gunter, Marc J.; Vineis, Paolo; Hansen, Camilla Plambeck; Jakobsen, Marianne Uhre; Clavel-Chapelon, Françoise; Fagherazzi, Guy; Boutron-Ruault, Marie-Christine; Katzke, Verana; Neamat-Allah, Jasmine; Boeing, Heiner; Bachlechner, Ursula; Trichopoulou, Antonia; Naska, Androniki; Orfanos, Philippos; Pala, Valeria; Masala, Giovanna; Mattiello, Amalia; Skeie, Guri; Weiderpass, Elisabete; Agudo, Antonio; Huerta, Jose Maria; Ardanaz, Eva; Sánchez, Maria Jose; Dorronsoro, Miren; Quirós, Jose Ramon; Johansson, Ingegerd; Winkvist, Anna; Sonested, Emily; Key, Tim; Khaw, Kay-Tee; Wareham, Nicolas J.; Peeters, Petra H.M.; Slimani, Nadia

    2015-01-01

    Background Few epidemiological studies have examined the association between dietary trans fatty acids and weight gain, and the evidence remains inconsistent. The main objective of the study was to investigate the prospective association between biomarker of industrial trans fatty acids and change in weight within the large study European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Methods Baseline plasma fatty acid concentrations were determined in a representative EPIC sample from the 23 participating EPIC centers. A total of 1,945 individuals were followed for a median of 4.9 years to monitor weight change. The association between elaidic acid level and percent change of weight was investigated using a multinomial logistic regression model, adjusted by length of follow-up, age, energy, alcohol, smoking status, physical activity, and region. Results In women, doubling elaidic acid was associated with a decreased risk of weight loss (odds ratio (OR) = 0.69, 95% confidence interval (CI) = 0.55-0.88, p = 0.002) and a trend was observed with an increased risk of weight gain during the 5-year follow-up (OR = 1.23, 95% CI = 0.97-1.56, p = 0.082) (p-trend<.0001). In men, a trend was observed for doubling elaidic acid level and risk of weight loss (OR = 0.82, 95% CI = 0.66-1.01, p = 0.062) while no significant association was found with risk of weight gain during the 5-year follow-up (OR = 1.08, 95% CI = 0.88-1.33, p = 0.454). No association was found for saturated and cis-monounsaturated fatty acids. Conclusions These data suggest that a high intake of industrial trans fatty acids may decrease the risk of weight loss, particularly in women. Prevention of obesity should consider limiting the consumption of highly processed foods, the main source of industrially-produced trans fatty acids. PMID:25675445

  1. Dietary exposure biomarker-lead discovery based on metabolomics analysis of urine samples.

    PubMed

    Beckmann, Manfred; Lloyd, Amanda J; Haldar, Sumanto; Favé, Gaëlle; Seal, Chris J; Brandt, Kirsten; Mathers, John C; Draper, John

    2013-08-01

    Although robust associations between dietary intake and population health are evident from conventional observational epidemiology, the outcomes of large-scale intervention studies testing the causality of those links have often proved inconclusive or have failed to demonstrate causality. This apparent conflict may be due to the well-recognised difficulty in measuring habitual food intake which may lead to confounding in observational epidemiology. Urine biomarkers indicative of exposure to specific foods offer information supplementary to the reliance on dietary intake self-assessment tools, such as FFQ, which are subject to individual bias. Biomarker discovery strategies using non-targeted metabolomics have been used recently to analyse urine from either short-term food intervention studies or from cohort studies in which participants consumed a freely-chosen diet. In the latter, the analysis of diet diary or FFQ information allowed classification of individuals in terms of the frequency of consumption of specific diet constituents. We review these approaches for biomarker discovery and illustrate both with particular reference to two studies carried out by the authors using approaches combining metabolite fingerprinting by MS with supervised multivariate data analysis. In both approaches, urine signals responsible for distinguishing between specific foods were identified and could be related to the chemical composition of the original foods. When using dietary data, both food distinctiveness and consumption frequency influenced whether differential dietary exposure could be discriminated adequately. We conclude that metabolomics methods for fingerprinting or profiling of overnight void urine, in particular, provide a robust strategy for dietary exposure biomarker-lead discovery.

  2. Metallothionein – Immunohistochemical Cancer Biomarker: A Meta-Analysis

    PubMed Central

    Gumulec, Jaromir; Raudenska, Martina; Adam, Vojtech; Kizek, Rene; Masarik, Michal

    2014-01-01

    Metallothionein (MT) has been extensively investigated as a molecular marker of various types of cancer. In spite of the fact that numerous reviews have been published in this field, no meta-analytical approach has been performed. Therefore, results of to-date immunohistochemistry-based studies were summarized using meta-analysis in this review. Web of science, PubMed, Embase and CENTRAL databases were searched (up to April 30, 2013) and the eligibility of individual studies and heterogeneity among the studies was assessed. Random and fixed effects model meta-analysis was employed depending on the heterogeneity, and publication bias was evaluated using funnel plots and Egger's tests. A total of 77 studies were included with 8,015 tissue samples (4,631 cases and 3,384 controls). A significantly positive association between MT staining and tumors (vs. healthy tissues) was observed in head and neck (odds ratio, OR 9.95; 95% CI 5.82–17.03) and ovarian tumors (OR 7.83; 1.09–56.29), and a negative association was ascertained in liver tumors (OR 0.10; 0.03–0.30). No significant associations were identified in breast, colorectal, prostate, thyroid, stomach, bladder, kidney, gallbladder, and uterine cancers and in melanoma. While no associations were identified between MT and tumor staging, a positive association was identified with the tumor grade (OR 1.58; 1.08–2.30). In particular, strong associations were observed in breast, ovarian, uterine and prostate cancers. Borderline significant association of metastatic status and MT staining were determined (OR 1.59; 1.03–2.46), particularly in esophageal cancer. Additionally, a significant association between the patient prognosis and MT staining was also demonstrated (hazard ratio 2.04; 1.47–2.81). However, a high degree of inconsistence was observed in several tumor types, including colorectal, kidney and prostate cancer. Despite the ambiguity in some tumor types, conclusive results are provided in the tumors of

  3. Extended Survival of Several Microorganisms and Relevant Amino Acid Biomarkers under Simulated Martian Surface Conditions as a Function of Burial Depth

    SciTech Connect

    Johnson, Adam; Pratt, L.M.; Vishnivetskaya, Tatiana A; Pfiffner, S. M.; Bryan, R. A.; Dadachova, E.; Whyte, L G; Radtke, K.; Chan, E.; Tronick, S.; Borgonie, G.; Mancinelli, R.; Rothschild, L.; Rogoff, D.; Horikawa, D. D.; Onstott, T. C.

    2011-01-01

    Recent orbital and landed missions have provided substantial evidence for ancient liquid water on the martian surface as well as evidence of more recent sedimentary deposits formed by water and/or ice. These observations raise serious questions regarding an independent origin and evolution of life on Mars. Future missions seek to identify signs of extinct martian biota in the form of biomarkers or morphological characteristics, but the inherent danger of spacecraft-borne terrestrial life makes the possibility of forward contamination a serious threat not only to the life detection experiments, but also to any extant martian ecosystem. A variety of cold and desiccation-tolerant organisms were exposed to 40 days of simulated martian surface conditions while embedded within several centimeters of regolith simulant in order to ascertain the plausibility of such organisms survival as a function of environmental parameters and burial depth. Relevant amino acid biomarkers associated with terrestrial life were also analyzed in order to understand the feasibility of detecting chemical evidence for previous biological activity. Results indicate that stresses due to desiccation and oxidation were the primary deterrent to organism survival, and that the effects of UV-associated damage, diurnal temperature variations, and reactive atmospheric species were minimal. Organisms with resistance to desiccation and radiation environments showed increased levels of survival after the experiment compared to organisms characterized as psychrotolerant. Amino acid analysis indicated the presence of an oxidation mechanism that migrated downward through the samples during the course of the experiment and likely represents the formation of various oxidizing species at mineral surfaces as water vapor diffused through the regolith. Current sterilization protocols may specifically select for organisms best adapted to survival at the martian surface, namely species that show tolerance to radical

  4. Biomarker analysis of American toad (Anaxyrus americanus) and grey tree frog (Hyla versicolor) tadpoles following exposure to atrazine.

    PubMed

    Snyder, Marcía N; Henderson, W Matthew; Glinski, Donna A; Purucker, S Thomas

    2017-01-01

    The objective of the current study was to use a biomarker-based approach to investigate the influence of atrazine exposure on American toad (Anaxyrus americanus) and grey tree frog (Hyla versicolor) tadpoles. Atrazine is one of the most frequently detected herbicides in environmental matrices throughout the United States. In surface waters, it has been found at concentrations from 0.04-2859μg/L and thus presents a likely exposure scenario for non-target species such as amphibians. Studies have examined the effect of atrazine on the metamorphic parameters of amphibians, however, the data are often contradictory. Gosner stage 22-24 tadpoles were exposed to 0 (control), 10, 50, 250 or 1250μg/L of atrazine for 48h. Endogenous polar metabolites were extracted and analyzed using gas chromatography coupled with mass spectrometry. Statistical analyses of the acquired spectra with machine learning classification models demonstrated identifiable changes in the metabolomic profiles between exposed and control tadpoles. Support vector machine models with recursive feature elimination created a more efficient, non-parametric data analysis and increased interpretability of metabolomic profiles. Biochemical fluxes observed in the exposed groups of both A. americanus and H. versicolor displayed perturbations in a number of classes of biological macromolecules including fatty acids, amino acids, purine nucleosides, pyrimidines, and mono- and di-saccharides. Metabolomic pathway analyses are consistent with findings of other studies demonstrating disruption of amino acid and energy metabolism from atrazine exposure to non-target species.

  5. Circulating glioma biomarkers

    PubMed Central

    Kros, Johan M.; Mustafa, Dana M.; Dekker, Lennard J.M.; Sillevis Smitt, Peter A.E.; Luider, Theo M.; Zheng, Ping-Pin

    2015-01-01

    Validated biomarkers for patients suffering from gliomas are urgently needed for standardizing measurements of the effects of treatment in daily clinical practice and trials. Circulating body fluids offer easily accessible sources for such markers. This review highlights various categories of tumor-associated circulating biomarkers identified in blood and cerebrospinal fluid of glioma patients, including circulating tumor cells, exosomes, nucleic acids, proteins, and oncometabolites. The validation and potential clinical utility of these biomarkers is briefly discussed. Although many candidate circulating protein biomarkers were reported, none of these have reached the required validation to be introduced for clinical practice. Recent developments in tracing circulating tumor cells and their derivatives as exosomes and circulating nuclear acids may become more successful in providing useful biomarkers. It is to be expected that current technical developments will contribute to the finding and validation of circulating biomarkers. PMID:25253418

  6. Serological proteome analysis of dogs with breast cancer unveils common serum biomarkers with human counterparts.

    PubMed

    Zamani-Ahmadmahmudi, Mohamad; Nassiri, Seyed Mahdi; Rahbarghazi, Reza

    2014-03-01

    Canine mammary tumor is being touted as a model for investigating the human breast cancer. Breast cancer of the both species has similar biological behavior, histopathologic characteristics, and metastatic pattern. In this study, we used the serological proteome analysis to detect autoantigens that elicit a humoral response in dogs with mammary tumor in order to identify serum biomarkers with potential usefulness as diagnostic markers and to better understand molecular mechanisms underlying canine breast cancer development. Protein extract from a cell line was subject to 2DE followed by Western blotting using sera from 15 dogs with mammary tumor and sera from 15 healthy control dogs. Immunoreactive autoantigens were subsequently identified by the MALDI-TOF MS. Four autoantigens, including manganese-superoxide dismutase, triose phosphate isomerase, alpha-enolase, and phosphoglycerate mutase1, with significantly higher immunoreactivity in the tumor samples than in the normal samples were identified as biomarker candidates. Immunohistochemistry and Western blotting revealed higher expression of these biomarkers in the malignant tumors than in the normal or benign tumors. The autoantigens found in this study have been reported to elicit autoantibody response in the human breast cancer, indicating the similarity of breast cancer proteome profile in dogs with that in human beings.

  7. Current Challenges in Volatile Organic Compounds Analysis as Potential Biomarkers of Cancer

    PubMed Central

    Schmidt, Kamila; Podmore, Ian

    2015-01-01

    An early diagnosis and appropriate treatment are crucial in reducing mortality among people suffering from cancer. There is a lack of characteristic early clinical symptoms in most forms of cancer, which highlights the importance of investigating new methods for its early detection. One of the most promising methods is the analysis of volatile organic compounds (VOCs). VOCs are a diverse group of carbon-based chemicals that are present in exhaled breath and biofluids and may be collected from the headspace of these matrices. Different patterns of VOCs have been correlated with various diseases, cancer among them. Studies have also shown that cancer cells in vitro produce or consume specific VOCs that can serve as potential biomarkers that differentiate them from noncancerous cells. This review identifies the current challenges in the investigation of VOCs as potential cancer biomarkers, by the critical evaluation of available matrices for the in vivo and in vitro approaches in this field and by comparison of the main extraction and detection techniques that have been applied to date in this area of study. It also summarises complementary in vivo, ex vivo, and in vitro studies conducted to date in order to try to identify volatile biomarkers of cancer. PMID:26317039

  8. [Histopathological findings and biomarker analysis in cutaneous graft-versus-host disease ].

    PubMed

    García Gutiérrez, J V; González García, C; Fleta, B; Sánchez-Ortega, I; Herrera, P; Chinea, A; López, J; Ramos, L; Ramos, R P; Duarte, R; Odriozola, J

    2010-12-01

    Graft-versus-host disease (GVHD) remains the greatest source of morbidity-mortality in allogenic transplant patients. Although in most cases the more easily obtainable clinical and laboratory test parameters suffice to confirm the diagnosis and establish the stage of the disease biopsies of the affected organ are sometimes needed. At present there is great Interest in the study of factors allowing a prognosis of the course and type of response to treatment in patients with CVHD. In this sense, It would be necessary to objectively Identify and validate biomarkers capable of predicting biological or pathological processes in patients with cVHD. To this effect we have performed serial analyses of skin tissue using peripheral blood and tissue biomarkers in a prospective observational study conducted in three transplant centers. The still preliminary results Indicate that certain histopathological findings classically attributed to CVHD ore also seen in patients not clinically affected by the disease--this probably being related to other physiopathological phenomena occurring during transplantation. The study of these findings, combined with biomarker analysis, will allow improved understanding of the underlying etiopathogenesis, as well as the definition of new diagnostic, prognostic and response-evaluating criteria.

  9. Parkinson's disease plasma biomarkers: an automated literature analysis followed by experimental validation.

    PubMed

    Alberio, Tiziana; Bucci, Enrico M; Natale, Massimo; Bonino, Dario; Di Giovanni, Marco; Bottacchi, Edo; Fasano, Mauro

    2013-09-02

    Diagnosis of Parkinson's disease (PD) is currently assessed by the clinical evaluation of extrapyramidal signs. The identification of specific biomarkers would be advisable, however most studies stop at the discovery phase, with no biomarkers reaching clinical exploitation. To this purpose, we developed an automated literature analysis procedure to retrieve all the background knowledge available in public databases. The bioinformatic platform allowed us to analyze more than 51,000 scientific papers dealing with PD, containing information on 4121 proteins. Out of these, we could track back 35 PD-related proteins as present in at least two published 2-DE maps of human plasma. Then, 9 different proteins (haptoglobin, transthyretin, apolipoprotein A-1, serum amyloid P component, apolipoprotein E, complement factor H, fibrinogen γ, thrombin, complement C3) split into 32 spots were identified as a potential diagnostic pattern. Eventually, we compared the collected literature data to experimental gels from 90 subjects (45 PD patients, 45 non-neurodegenerative control subjects) to experimentally verify their potential as plasma biomarkers of PD.

  10. Cartilage oligomeric matrix protein and hyaluronic acid are sensitive serum biomarkers for early cartilage lesions in the knee joint.

    PubMed

    Jiao, Qiang; Wei, Lei; Chen, Chongwei; Li, Pengcui; Wang, Xiaohu; Li, Yongping; Guo, Li; Zhang, Congming; Wei, Xiaochun

    2016-01-01

    The purpose of this study was to evaluate the relationship between five previously established serum osteoarthritis biomarkers and the severity of cartilage lesions in the knee. Cartilage damage (classified according to the Outerbridge scoring system) and serum concentrations of cartilage oligomeric matrix protein (COMP), collagen type II C-telopeptide (CTX-II), matrix metalloproteinase-3 (MMP-3), collagen type III N-propeptide, (PIIINP), and hyaluronic acid (HA) were determined in 79 patients who underwent knee arthroscopy or total knee replacement. HA and COMP concentrations were significantly higher in the Outerbridge score 1 and 2 groups, respectively. These results suggest that serum COMP and HA concentrations can be used to predict early cartilage lesions in the knee.

  11. Urinary Phthalate Metabolites and Biomarkers of Oxidative Stress in Pregnant Women: A Repeated Measures Analysis

    PubMed Central

    Ferguson, Kelly K.; McElrath, Thomas F.; Chen, Yin-Hsiu; Mukherjee, Bhramar

    2014-01-01

    Background Phthalate exposure occurs readily in the environment and has been associated with an array of health end points, including adverse birth outcomes. Some of these may be mediated by oxidative stress, a proposed mechanism for phthalate action. Objectives In the present study, we explored the associations between phthalate metabolites and biomarkers of oxidative stress measured in urine samples from multiple time points during pregnancy. Methods Women were participants in a nested case–control study of preterm birth (n = 130 cases, n = 352 controls). Each was recruited early in pregnancy and followed until delivery, providing urine samples at up to four visits. Nine phthalate metabolites were measured to assess exposure, and 8-hydroxydeoxyguanosine and 8-isoprostane were also measured in urine as markers of oxidative stress. Associations were assessed using linear mixed models to account for intraindividual correlation, with inverse selection probability weightings based on case status to allow for greater generalizability. Results Interquartile range increases in phthalate metabolites were associated with significantly higher concentrations of both biomarkers. Estimated differences were greater in association with monobenzyl phthalate (MBzP), mono-n-butyl phthalate (MBP), and monoisobutyl phthalate (MiBP), compared with di(2-ethylhexyl) phthalate (DEHP) metabolites. Conclusions Urinary phthalate metabolites were associated with increased oxidative stress biomarkers in our study population of pregnant women. These relationships may be particularly relevant to the study of birth outcomes linked to phthalate exposure. Although replication is necessary in other populations, these results may also be of great importance for a range of other health outcomes associated with phthalates. Citation Ferguson KK, McElrath TF, Chen YH, Mukherjee B, Meeker JD. 2015. Urinary phthalate metabolites and biomarkers of oxidative stress in pregnant women: a repeated measures

  12. Identification of Epigenetic Biomarkers of Lung Adenocarcinoma through Multi-Omics Data Analysis.

    PubMed

    Kikutake, Chie; Yahara, Koji

    2016-01-01

    Epigenetic mechanisms such as DNA methylation or histone modifications are essential for the regulation of gene expression and development of tissues. Alteration of epigenetic modifications can be used as an epigenetic biomarker for diagnosis and as promising targets for epigenetic therapy. A recent study explored cancer-cell specific epigenetic biomarkers by examining different types of epigenetic modifications simultaneously. However, it was based on microarrays and reported biomarkers that were also present in normal cells at a low frequency. Here, we first analyzed multi-omics data (including ChIP-Seq data of six types of histone modifications: H3K27ac, H3K4me1, H3K9me3, H3K36me3, H3K27me3, and H3K4me3) obtained from 26 lung adenocarcinoma cell lines and a normal cell line. We identified six genes with both H3K27ac and H3K4me3 histone modifications in their promoter regions, which were not present in the normal cell line, but present in ≥85% (22 out of 26) and ≤96% (25 out of 26) of the lung adenocarcinoma cell lines. Of these genes, NUP210 (encoding a main component of the nuclear pore complex) was the only gene in which the two modifications were not detected in another normal cell line. RNA-Seq analysis revealed that NUP210 was aberrantly overexpressed among the 26 lung adenocarcinoma cell lines, although the frequency of NUP210 overexpression was lower (19.3%) in 57 lung adenocarcinoma tissue samples studied and stored in another database. This study provides a basis to discover epigenetic biomarkers highly specific to a certain cancer, based on multi-omics data at the cell population level.

  13. Uncovering precision phenotype-biomarker associations in traumatic brain injury using topological data analysis

    PubMed Central

    Nielson, Jessica L.; Cooper, Shelly R.; Sorani, Marco D.; Inoue, Tomoo; Yuh, Esther L.; Mukherjee, Pratik; Petrossian, Tanya C.; Lum, Pek Y.; Lingsma, Hester F.; Gordon, Wayne A.; Okonkwo, David O.; Manley, Geoffrey T.

    2017-01-01

    Background Traumatic brain injury (TBI) is a complex disorder that is traditionally stratified based on clinical signs and symptoms. Recent imaging and molecular biomarker innovations provide unprecedented opportunities for improved TBI precision medicine, incorporating patho-anatomical and molecular mechanisms. Complete integration of these diverse data for TBI diagnosis and patient stratification remains an unmet challenge. Methods and findings The Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot multicenter study enrolled 586 acute TBI patients and collected diverse common data elements (TBI-CDEs) across the study population, including imaging, genetics, and clinical outcomes. We then applied topology-based data-driven discovery to identify natural subgroups of patients, based on the TBI-CDEs collected. Our hypothesis was two-fold: 1) A machine learning tool known as topological data analysis (TDA) would reveal data-driven patterns in patient outcomes to identify candidate biomarkers of recovery, and 2) TDA-identified biomarkers would significantly predict patient outcome recovery after TBI using more traditional methods of univariate statistical tests. TDA algorithms organized and mapped the data of TBI patients in multidimensional space, identifying a subset of mild TBI patients with a specific multivariate phenotype associated with unfavorable outcome at 3 and 6 months after injury. Further analyses revealed that this patient subset had high rates of post-traumatic stress disorder (PTSD), and enrichment in several distinct genetic polymorphisms associated with cellular responses to stress and DNA damage (PARP1), and in striatal dopamine processing (ANKK1, COMT, DRD2). Conclusions TDA identified a unique diagnostic subgroup of patients with unfavorable outcome after mild TBI that were significantly predicted by the presence of specific genetic polymorphisms. Machine learning methods such as TDA may provide a robust

  14. LASER BIOLOGY AND MEDICINE: Application of tunable diode lasers for a highly sensitive analysis of gaseous biomarkers in exhaled air

    NASA Astrophysics Data System (ADS)

    Stepanov, E. V.; Milyaev, Varerii A.

    2002-11-01

    The application of tunable diode lasers for a highly sensitive analysis of gaseous biomarkers in exhaled air in biomedical diagnostics is discussed. The principle of operation and the design of a laser analyser for studying the composition of exhaled air are described. The results of detection of gaseous biomarkers in exhaled air, including clinical studies, which demonstrate the diagnostic possibilities of the method, are presented.

  15. BROMOCHLOROACETIC ACID EXERTS QUALITATIVE EFFECTS ON RAT SPERM: IMPLICATIONS FOR A NOVEL BIOMARKER

    EPA Science Inventory

    ABSTRACT
    Disubstituted haloacid by-products of drinking water disinfection such as dibromoacetic acid and dichloroacetic acid have been shown to perturb spermatogenesis and fertility in adult male rats. In the present study we sought to establish whether equimolar exposur...

  16. Lipid biomarker production and preservation in acidic ecosystems: Relevance to early Earth and Mars

    NASA Astrophysics Data System (ADS)

    Jahnke, L. L.; Parenteau, M. N.; Harris, R.; Bristow, T.; Farmer, J. D.; Des Marais, D. J.

    2013-12-01

    Compared to relatively benign carbonate buffered marine environments, terrestrial Archean and Paleoproterozoic life was forced to cope with a broader range of pH values. In particular, acidic terrestrial ecosystems arose from the oxidation of reduced species in hydrothermal settings and crustal reservoirs of metal sulfides, creating acid sulfate conditions. While oxidation of reduced species is facilitated by reactions with molecular oxygen, acidic conditions also arose in Archean hydrothermal systems before the rise of oxygen (Van Kranendonk, 2006), expanding the range of time over which acidophiles could have existed on the early Earth. Acidic terrestrial habitats would have included acidic hydrothermal springs, acid sulfate soils, and possibly lakes and streams lacking substantial buffering capacity with sources of acidity in their catchments. Although acidic hot springs are considered extreme environments on Earth, robust and diverse microbial communities thrive in these habitats. Such acidophiles are found across all three domains of life and include both phototrophic and chemotrophic members. In this presentation, we examine hopanes and sterols that are characteristic of microbial communities living in acidic hydrothermal environments. Moreover we discuss taphonomic processes governing the capture and preservation of these biosignatures in acid environments. In particular, we discuss the production and early preservation of hopanoids and sterols in the following geological/mineralogical settings: 1) rapid entombment of microbes and organic matter by predominantly fine-grained silica; 2) rapid burial of organic matter by clay-rich, silica poor sediments; 3) and the survival of organics in iron oxide and sulfate rich sediments. We discovered and isolated an acid-tolerant purple non-sulfur anoxygenic phototroph from Lassen Volcanic National Park that synthesizes 3methyl-bacteriohopanepolyols. These compounds were previously thought to be exclusively made by

  17. Detection of the dipicolinic acid biomarker in Bacillus spores using Curie-point pyrolysis mass spectrometry and Fourier transform infrared spectroscopy.

    PubMed

    Goodacre, R; Shann, B; Gilbert, R J; Timmins, E M; McGovern, A C; Alsberg, B K; Kell, D B; Logan, N A

    2000-01-01

    Thirty-six strains of aerobic endospore-forming bacteria confirmed by polyphasic taxonomic methods to belong to Bacillus amyloliquefaciens, Bacillus cereus, Bacillus licheniformis, Bacillus megaterium, Bacillus subtilis (including Bacillus niger and Bacillus globigii), Bacillus sphaericus, and Brevi laterosporus were grown axenically on nutrient agar, and vegetative and sporulated biomasses were analyzed by Curie-point pyrolysis mass spectrometry (PyMS) and diffuse reflectance-absorbance Fourier-transform infrared spectroscopy (FT-IR). Chemometric methods based on rule induction and genetic programming were used to determine the physiological state (vegetative cells or spores) correctly, and these methods produced mathematical rules which could be simply interpreted in biochemical terms. For PyMS it was found that m/z 105 was characteristic and is a pyridine ketonium ion (C6H3ON+) obtained from the pyrolysis of dipicolinic acid (pyridine-2,6-dicarboxylic acid; DPA), a substance found in spores but not in vegetative cells; this was confirmed using pyrolysis-gas chromatography/mass spectrometry. In addition, a pyridine ring vibration at 1447-1439 cm-1 from DPA was found to be highly characteristic of spores in FT-IR analysis. Thus, although the original data sets recorded hundreds of spectral variables from whole cells simultaneously, a simple biomarker can be used for the rapid and unequivocal detection of spores of these organisms.

  18. In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

    PubMed Central

    Ozerov, Ivan V.; Lezhnina, Ksenia V.; Izumchenko, Evgeny; Artemov, Artem V.; Medintsev, Sergey; Vanhaelen, Quentin; Aliper, Alexander; Vijg, Jan; Osipov, Andreyan N.; Labat, Ivan; West, Michael D.; Buzdin, Anton; Cantor, Charles R.; Nikolsky, Yuri; Borisov, Nikolay; Irincheeva, Irina; Khokhlovich, Edward; Sidransky, David; Camargo, Miguel Luiz; Zhavoronkov, Alex

    2016-01-01

    Signalling pathway activation analysis is a powerful approach for extracting biologically relevant features from large-scale transcriptomic and proteomic data. However, modern pathway-based methods often fail to provide stable pathway signatures of a specific phenotype or reliable disease biomarkers. In the present study, we introduce the in silico Pathway Activation Network Decomposition Analysis (iPANDA) as a scalable robust method for biomarker identification using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and pathway topology decomposition for obtaining pathway activation scores. Using Microarray Analysis Quality Control (MAQC) data sets and pretreatment data on Taxol-based neoadjuvant breast cancer therapy from multiple sources, we demonstrate that iPANDA provides significant noise reduction in transcriptomic data and identifies highly robust sets of biologically relevant pathway signatures. We successfully apply iPANDA for stratifying breast cancer patients according to their sensitivity to neoadjuvant therapy. PMID:27848968

  19. Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery

    PubMed Central

    Wachter, Astrid; Bernhardt, Stephan; Beissbarth, Tim; Korf, Ulrike

    2015-01-01

    Mastering the systematic analysis of tumor tissues on a large scale has long been a technical challenge for proteomics. In 2001, reverse phase protein arrays (RPPA) were added to the repertoire of existing immunoassays, which, for the first time, allowed a profiling of minute amounts of tumor lysates even after microdissection. A characteristic feature of RPPA is its outstanding sample capacity permitting the analysis of thousands of samples in parallel as a routine task. Until today, the RPPA approach has matured to a robust and highly sensitive high-throughput platform, which is ideally suited for biomarker discovery. Concomitant with technical advancements, new bioinformatic tools were developed for data normalization and data analysis as outlined in detail in this review. Furthermore, biomarker signatures obtained by different RPPA screens were compared with another or with that obtained by other proteomic formats, if possible. Options for overcoming the downside of RPPA, which is the need to steadily validate new antibody batches, will be discussed. Finally, a debate on using RPPA to advance personalized medicine will conclude this article. PMID:27600238

  20. Proteomic analysis of temporally stimulated ovarian cancer cells for biomarker discovery.

    PubMed

    Marzinke, Mark A; Choi, Caitlin H; Chen, Li; Shih, Ie-Ming; Chan, Daniel W; Zhang, Hui

    2013-02-01

    While ovarian cancer remains the most lethal gynecological malignancy in the United States, there are no biomarkers available that are able to predict therapeutic responses to ovarian malignancies. One major hurdle in the identification of useful biomarkers has been the ability to obtain enough ovarian cancer cells from primary tissues diagnosed in the early stages of serous carcinomas, the most deadly subtype of ovarian tumor. In order to detect ovarian cancer in a state of hyperproliferation, we analyzed the implications of molecular signaling cascades in the ovarian cancer cell line OVCAR3 in a temporal manner, using a mass-spectrometry-based proteomics approach. OVCAR3 cells were treated with EGF(1), and the time course of cell progression was monitored based on Akt phosphorylation and growth dynamics. EGF-stimulated Akt phosphorylation was detected at 12 h post-treatment, but an effect on proliferation was not observed until 48 h post-exposure. Growth-stimulated cellular lysates were analyzed for protein profiles between treatment groups and across time points using iTRAQ labeling and mass spectrometry. The protein response to EGF treatment was identified via iTRAQ analysis in EGF-stimulated lysates relative to vehicle-treated specimens across the treatment time course. Validation studies were performed on one of the differentially regulated proteins, lysosomal-associated membrane protein 1 (LAMP-1), in human tissue lysates and ovarian tumor tissue sections. Further, tissue microarray analysis was performed to demarcate LAMP-1 expression across different stages of epithelial ovarian cancers. These data support the use of this approach for the efficient identification of tissue-based markers in tumor development related to specific signaling pathways. LAMP-1 is a promising biomarker for studies of the progression of EGF-stimulated ovarian cancers and might be useful in predicting treatment responses involving tyrosine kinase inhibitors or EGF receptor

  1. Single Gene Prognostic Biomarkers in Ovarian Cancer: A Meta-Analysis

    PubMed Central

    Willis, Scooter; Villalobos, Victor M.; Gevaert, Olivier; Abramovitz, Mark; Williams, Casey; Sikic, Branimir I.; Leyland-Jones, Brian

    2016-01-01

    Purpose To discover novel prognostic biomarkers in ovarian serous carcinomas. Methods A meta-analysis of all single genes probes in the TCGA and HAS ovarian cohorts was performed to identify possible biomarkers using Cox regression as a continuous variable for overall survival. Genes were ranked by p-value using Stouffer’s method and selected for statistical significance with a false discovery rate (FDR) <.05 using the Benjamini-Hochberg method. Results Twelve genes with high mRNA expression were prognostic of poor outcome with an FDR <.05 (AXL, APC, RAB11FIP5, C19orf2, CYBRD1, PINK1, LRRN3, AQP1, DES, XRCC4, BCHE, and ASAP3). Twenty genes with low mRNA expression were prognostic of poor outcome with an FDR <.05 (LRIG1, SLC33A1, NUCB2, POLD3, ESR2, GOLPH3, XBP1, PAXIP1, CYB561, POLA2, CDH1, GMNN, SLC37A4, FAM174B, AGR2, SDR39U1, MAGT1, GJB1, SDF2L1, and C9orf82). Conclusion A meta-analysis of all single genes identified thirty-two candidate biomarkers for their possible role in ovarian serous carcinoma. These genes can provide insight into the drivers or regulators of ovarian cancer and should be evaluated in future studies. Genes with high expression indicating poor outcome are possible therapeutic targets with known antagonists or inhibitors. Additionally, the genes could be combined into a prognostic multi-gene signature and tested in future ovarian cohorts. PMID:26886260

  2. Detecting neuroimaging biomarkers for schizophrenia: a meta-analysis of multivariate pattern recognition studies.

    PubMed

    Kambeitz, Joseph; Kambeitz-Ilankovic, Lana; Leucht, Stefan; Wood, Stephen; Davatzikos, Christos; Malchow, Berend; Falkai, Peter; Koutsouleris, Nikolaos

    2015-06-01

    Multivariate pattern recognition approaches have recently facilitated the search for reliable neuroimaging-based biomarkers in psychiatric disorders such as schizophrenia. By taking into account the multivariate nature of brain functional and structural changes as well as their distributed localization across the whole brain, they overcome drawbacks of traditional univariate approaches. To evaluate the overall reliability of neuroimaging-based biomarkers, we conducted a comprehensive literature search to identify all studies that used multivariate pattern recognition to identify patterns of brain alterations that differentiate patients with schizophrenia from healthy controls. A bivariate random-effects meta-analytic model was implemented to investigate the sensitivity and specificity across studies as well as to assess the robustness to potentially confounding variables. In the total sample of n=38 studies (1602 patients and 1637 healthy controls), patients were differentiated from controls with a sensitivity of 80.3% (95% CI: 76.7-83.5%) and a specificity of 80.3% (95% CI: 76.9-83.3%). Analysis of neuroimaging modality indicated higher sensitivity (84.46%, 95% CI: 79.9-88.2%) and similar specificity (76.9%, 95% CI: 71.3-81.6%) of rsfMRI studies as compared with structural MRI studies (sensitivity: 76.4%, 95% CI: 71.9-80.4%, specificity of 79.0%, 95% CI: 74.6-82.8%). Moderator analysis identified significant effects of age (p=0.029), imaging modality (p=0.019), and disease stage (p=0.025) on sensitivity as well as of positive-to-negative symptom ratio (p=0.022) and antipsychotic medication (p=0.016) on specificity. Our results underline the utility of multivariate pattern recognition approaches for the identification of reliable neuroimaging-based biomarkers. Despite the clinical heterogeneity of the schizophrenia phenotype, brain functional and structural alterations differentiate schizophrenic patients from healthy controls with 80% sensitivity and specificity.

  3. Branched-Chain Amino Acids as New Biomarkers of Major Depression - A Novel Neurobiology of Mood Disorder

    PubMed Central

    Baranyi, Andreas; Amouzadeh-Ghadikolai, Omid; von Lewinski, Dirk; Rothenhäusler, Hans-Bernd; Theokas, Simon; Robier, Christoph; Mangge, Harald; Reicht, Gerhard; Hlade, Peter; Meinitzer, Andreas

    2016-01-01

    Background The proteinogenic branched-chain amino acids (BCAAs) valine, leucine and isoleucine might play an unrecognised crucial role in the development of depression through their activation of the mammalian target of rapamycin (mTor) pathway. The aim of this research project is to evaluate whether BCAAs are altered in patients with major depression and might thus be appropriate biomarkers for major depression. Methods The concentrations of valine, leucine and isoleucine were determined in 71 in-patients with major depression and 48 healthy controls by high-pressure liquid chromatography. Psychiatric and laboratory assessments were obtained at the time of in-patient admittance. Results The BCAAs are significantly decreased in patients with major depression in comparison with healthy subjects (valine: Mann-Whitney-U: 968.0; p <0.0001, leucine: Mann-Whitney-U: 1246.5; p = 0.013, isoleucine: Mann-Whitney-U: 1252.5; p = 0.014). Furthermore, as shown by Spearman's rank correlation coefficients, there is a significant negative correlation between valine, leucine and isoleucine concentrations and the Hamilton Depression Rating Scale (HAMD-17) as well as Beck Depression Inventory (BDI-II) scores. Conclusions Our study results are strong evidence that in patients with major depression, BCAAs might be appropriate biomarkers for depression. Reduced activation of the mammalian target of rapamycin (mTor) due to a reduction of BCAAs might play a crucial unrecognised factor in the etiology of depression and may evoke depressive symptomatology and lower energy metabolism in patients with major depression. In the future, mTor and its up- and downstream signalling partners might be important targets for the development of novel antidepressants. PMID:27490818

  4. Meta-analysis method for discovering reliable biomarkers by integrating statistical and biological approaches: An application to liver toxicity.

    PubMed

    Cho, Hyeyoung; Kim, Hyosil; Na, Dokyun; Kim, So Youn; Jo, Deokyeon; Lee, Doheon

    2016-03-04

    Biomarkers that are identified from a single study often appear to be biologically irrelevant or false positives. Meta-analysis techniques allow integrating data from multiple studies that are related but independent in order to identify biomarkers across multiple conditions. However, existing biomarker meta-analysis methods tend to be sensitive to the dataset being analyzed. Here, we propose a meta-analysis method, iMeta, which integrates t-statistic and fold change ratio for improved robustness. For evaluation of predictive performance of the biomarkers identified by iMeta, we compare our method with other meta-analysis methods. As a result, iMeta outperforms the other methods in terms of sensitivity and specificity, and especially shows robustness to study variance increase; it consistently shows higher classification accuracy on diverse datasets, while the performance of the others is highly affected by the dataset being analyzed. Application of iMeta to 59 drug-induced liver injury studies identified three key biomarker genes: Zwint, Abcc3, and Ppp1r3b. Experimental evaluation using RT-PCR and qRT-PCR shows that their expressional changes in response to drug toxicity are concordant with the result of our method. iMeta is available at http://imeta.kaist.ac.kr/index.html.

  5. Biomarkers of Eating Disorders Using Support Vector Machine Analysis of Structural Neuroimaging Data: Preliminary Results

    PubMed Central

    Cerasa, Antonio; Castiglioni, Isabella; Salvatore, Christian; Funaro, Angela; Martino, Iolanda; Alfano, Stefania; Donzuso, Giulia; Perrotta, Paolo; Gioia, Maria Cecilia; Gilardi, Maria Carla; Quattrone, Aldo

    2015-01-01

    Presently, there are no valid biomarkers to identify individuals with eating disorders (ED). The aim of this work was to assess the feasibility of a machine learning method for extracting reliable neuroimaging features allowing individual categorization of patients with ED. Support Vector Machine (SVM) technique, combined with a pattern recognition method, was employed utilizing structural magnetic resonance images. Seventeen females with ED (six with diagnosis of anorexia nervosa and 11 with bulimia nervosa) were compared against 17 body mass index-matched healthy controls (HC). Machine learning allowed individual diagnosis of ED versus HC with an Accuracy ≥ 0.80. Voxel-based pattern recognition analysis demonstrated that voxels influencing the classification Accuracy involved the occipital cortex, the posterior cerebellar lobule, precuneus, sensorimotor/premotor cortices, and the medial prefrontal cortex, all critical regions known to be strongly involved in the pathophysiological mechanisms of ED. Although these findings should be considered preliminary given the small size investigated, SVM analysis highlights the role of well-known brain regions as possible biomarkers to distinguish ED from HC at an individual level, thus encouraging the translational implementation of this new multivariate approach in the clinical practice. PMID:26648660

  6. Genomic reprograming analysis of the Mesothelial to Mesenchymal Transition identifies biomarkers in peritoneal dialysis patients

    PubMed Central

    Ruiz-Carpio, Vicente; Sandoval, Pilar; Aguilera, Abelardo; Albar-Vizcaíno, Patricia; Perez-Lozano, María Luisa; González-Mateo, Guadalupe T.; Acuña-Ruiz, Adrián; García-Cantalejo, Jesús; Botías, Pedro; Bajo, María Auxiliadora; Selgas, Rafael; Sánchez-Tomero, José Antonio; Passlick-Deetjen, Jutta; Piecha, Dorothea; Büchel, Janine; Steppan, Sonja; López-Cabrera, Manuel

    2017-01-01

    Peritoneal dialysis (PD) is an effective renal replacement therapy, but a significant proportion of patients suffer PD-related complications, which limit the treatment duration. Mesothelial-to-mesenchymal transition (MMT) contributes to the PD-related peritoneal dysfunction. We analyzed the genetic reprograming of MMT to identify new biomarkers that may be tested in PD-patients. Microarray analysis revealed a partial overlapping between MMT induced in vitro and ex vivo in effluent-derived mesothelial cells, and that MMT is mainly a repression process being higher the number of genes that are down-regulated than those that are induced. Cellular morphology and number of altered genes showed that MMT ex vivo could be subdivided into two stages: early/epithelioid and advanced/non-epithelioid. RT-PCR array analysis demonstrated that a number of genes differentially expressed in effluent-derived non-epithelioid cells also showed significant differential expression when comparing standard versus low-GDP PD fluids. Thrombospondin-1 (TSP1), collagen-13 (COL13), vascular endothelial growth factor A (VEGFA), and gremlin-1 (GREM1) were measured in PD effluents, and except GREM1, showed significant differences between early and advanced stages of MMT, and their expression was associated with a high peritoneal transport status. The results establish a proof of concept about the feasibility of measuring MMT-associated secreted protein levels as potential biomarkers in PD. PMID:28327551

  7. Migraine biomarkers in cerebrospinal fluid: A systematic review and meta-analysis.

    PubMed

    van Dongen, Robin M; Zielman, Ronald; Noga, Marek; Dekkers, Olaf M; Hankemeier, Thomas; van den Maagdenberg, Arn Mjm; Terwindt, Gisela M; Ferrari, Michel D

    2017-01-01

    Objective To perform a meta-analysis of migraine biomarkers in cerebrospinal fluid (CSF) and of corresponding blood concentrations. Methods We conducted a systematic search for studies that measured biochemical compounds in CSF of chronic or episodic migraineurs and non-headache controls. Subsequent searches retrieved studies with blood measurements of selected CSF biomarkers. If a compound was assessed in three or more studies, results were pooled in a meta-analysis with standardised mean differences (SMD) as effect measures. Results Sixty-two compounds were measured in 40 CSF studies. Most important results include: increased glutamate (five studies, SMD 2.22, 95% CI: 1.30, 3.13), calcitonin gene-related peptide (CGRP) (three studies, SMD: 3.80, 95% CI: 3.19, 4.41) and nerve growth factor (NGF) (three studies, SMD: 6.47, 95% CI: 5.55, 7.39) in chronic migraine patients and decreased β-endorphin (β-EP) in both chronic (four studies, SMD: -1.37, 95% CI: -1.80, -0.94) and interictal episodic migraine patients (three studies, SMD: -1.12, 95% CI: -1.65, -0.58). In blood, glutamate (interictal) and CGRP (chronic, interictal and ictal) were increased and β-EP (chronic, interictal and ictal) was decreased. Conclusions Glutamate, β-EP, CGRP and NGF concentrations are altered in CSF and, except for NGF, also in blood of migraineurs. Future research should focus on the pathophysiological roles of these compounds in migraine.

  8. An optimized procedure for exosome isolation and analysis using serum samples: Application to cancer biomarker discovery.

    PubMed

    Li, Mu; Rai, Alex J; DeCastro, G Joel; Zeringer, Emily; Barta, Timothy; Magdaleno, Susan; Setterquist, Robert; Vlassov, Alexander V

    2015-10-01

    Exosomes are RNA and protein-containing nanovesicles secreted by all cell types and found in abundance in body fluids, including blood, urine and cerebrospinal fluid. These vesicles seem to be a perfect source of biomarkers, as their cargo largely reflects the content of parental cells, and exosomes originating from all organs can be obtained from circulation through minimally invasive or non-invasive means. Here we describe an optimized procedure for exosome isolation and analysis using clinical samples, starting from quick and robust extraction of exosomes with Total exosome isolation reagent, then isolation of RNA followed by qRT-PCR. Effectiveness of this workflow is exemplified by analysis of the miRNA content of exosomes derived from serum samples - obtained from the patients with metastatic prostate cancer, treated prostate cancer patients who have undergone prostatectomy, and control patients without prostate cancer. Three promising exosomal microRNA biomarkers were identified, discriminating these groups: hsa-miR375, hsa-miR21, hsa-miR574.

  9. Mass spectrum analysis of serum biomarker proteins from patients with schizophrenia.

    PubMed

    Zhou, Na; Wang, Jie; Yu, Yaqin; Shi, Jieping; Li, Xiaokun; Xu, Bin; Yu, Qiong

    2014-05-01

    Diagnosis of schizophrenia does not have a clear objective test at present, so we aimed to identify the potential biomarkers for the diagnosis of schizophrenia by comparison of serum protein profiling between first-episode schizophrenia patients and healthy controls. The combination of a magnetic bead separation system with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF-MS) was used to analyze the serum protein spectra of 286 first-episode patients with schizophrenia, 41 chronic disease patients and 304 healthy controls. FlexAnlysis 3.0 and ClinProTools(TM) 2.1 software was used to establish a diagnostic model for schizophrenia. The results demonstrated that 10 fragmented peptides demonstrated an optimal discriminatory performance. Among these fragmented peptides, the peptide with m/z 1206.58 was identified as a fragment of fibrinopeptide A. Receiver operating characteristic analysis for m/z 1206.58 showed that the area under the curve was 0.981 for schizophrenia vs healthy controls, and 0.999 for schizophrenia vs other chronic disease controls. From our result, we consider that the analysis of serum protein spectrum using the magnetic bead separation system and MALDI-TOF/TOF-MS is an objective diagnostic tool. We conclude that fibrinopeptide A has the potential to be a biomarker for diagnosis of schizophrenia. This protein may also help to elucidate schizophrenia disease pathogenesis.

  10. Genomic reprograming analysis of the Mesothelial to Mesenchymal Transition identifies biomarkers in peritoneal dialysis patients.

    PubMed

    Ruiz-Carpio, Vicente; Sandoval, Pilar; Aguilera, Abelardo; Albar-Vizcaíno, Patricia; Perez-Lozano, María Luisa; González-Mateo, Guadalupe T; Acuña-Ruiz, Adrián; García-Cantalejo, Jesús; Botías, Pedro; Bajo, María Auxiliadora; Selgas, Rafael; Sánchez-Tomero, José Antonio; Passlick-Deetjen, Jutta; Piecha, Dorothea; Büchel, Janine; Steppan, Sonja; López-Cabrera, Manuel

    2017-03-22

    Peritoneal dialysis (PD) is an effective renal replacement therapy, but a significant proportion of patients suffer PD-related complications, which limit the treatment duration. Mesothelial-to-mesenchymal transition (MMT) contributes to the PD-related peritoneal dysfunction. We analyzed the genetic reprograming of MMT to identify new biomarkers that may be tested in PD-patients. Microarray analysis revealed a partial overlapping between MMT induced in vitro and ex vivo in effluent-derived mesothelial cells, and that MMT is mainly a repression process being higher the number of genes that are down-regulated than those that are induced. Cellular morphology and number of altered genes showed that MMT ex vivo could be subdivided into two stages: early/epithelioid and advanced/non-epithelioid. RT-PCR array analysis demonstrated that a number of genes differentially expressed in effluent-derived non-epithelioid cells also showed significant differential expression when comparing standard versus low-GDP PD fluids. Thrombospondin-1 (TSP1), collagen-13 (COL13), vascular endothelial growth factor A (VEGFA), and gremlin-1 (GREM1) were measured in PD effluents, and except GREM1, showed significant differences between early and advanced stages of MMT, and their expression was associated with a high peritoneal transport status. The results establish a proof of concept about the feasibility of measuring MMT-associated secreted protein levels as potential biomarkers in PD.

  11. Isoprostanes-Biomarkers of Lipid Peroxidation: Their Utility in Evaluating Oxidative Stress and Analysis

    PubMed Central

    Janicka, Monika; Kot-Wasik, Agata; Kot, Jacek; Namieśnik, Jacek

    2010-01-01

    Isoprostanes (IsoPs) are key biomarkers for investigating the role of free radical generation in the pathogenesis of human disorders. To solve IsoPs-related problems with regard to isoprostanes, analytical tools are required. This paper reviews the problems and trends in this field focusing on the methodology for assaying biomarkers in exhaled breath condensate (EBC) samples. A large amount of work has been done in the qualitative and quantitative analysis of IsoPs, but a standardized method has yet to emerge. The methodologies described differ, either in the sample preparation steps or in the detection techniques, or both. Requiring a number of chromatographic steps, the relevant extraction and purification procedures are often critical and time-consuming, and they lead to a substantial loss of target compounds. Recent data show that EBC is a promising non-invasive tool for the evaluation of different diseases. Two main analytical approaches have been adopted for IsoPs measurement: immunological methods and mass spectrometry. The methodologies for the extraction, purification and analysis of IsoPs in EBC samples are presented. PMID:21151461

  12. Biomarkers in nonalcoholic fatty liver disease

    PubMed Central

    Neuman, Manuela G; Cohen, Lawrence B; Nanau, Radu M

    2014-01-01

    BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a chronic liver condition characterized by insulin resistance, type 2 diabetes and fat accumulation in the liver that may cause hepatic inflammation and progressive scarring leading to nonalcoholic steatohepatitis (NASH) and irreversible liver damage (cirrhosis). As a result, there has been increased recognition of the need to assess and closely monitor individuals for risk factors of components of NAFLD and NASH, as well as the severity of these conditions using biomarkers. AIM: To review the biomarkers used to diagnose and define the severity of NAFLD and NASH. METHODS: A comprehensive PubMed and Google Scholar literature search was performed using the terms “non-alcoholic fatty liver disease”, “non-alcoholic steatohepatitis”, as well as the name of each biomarker known to be used. Articles indexed between 2004 and 2014 were used. Each author read the publications separately and the results were discussed. RESULTS: Biomarkers offer a potential prognostic or diagnostic indicator for disease manifestation, progression or both. Serum biomarkers, including total cholesterol, triglycerides, insulin resistance and C-peptide, have been used for many years. Emerging biomarkers, such as apolipoprotein A1, apolipoprotein B, leptin, adiponectin, free fatty acids, ghrelin and tumour necrosis factor-alpha, have been proposed as tools that could provide valuable complementary information to that obtained from traditional biomarkers. Moreover, markers of cell death and mitochondrial dysfunction (cytokeratins) represent powerful predictors of risk. For biomarkers to be clinically useful in accurately diagnosing and treating disorders, age-specific reference intervals that account for differences in sex and ethnic origin are a necessity. CONCLUSIONS: The present review attempts to provide a comprehensive analysis of the emerging risk biomarkers of NAFLD and NASH, and to use the clinical significance and analytical

  13. Biomarker Utility Analysis Using an Exposure-PBPK/PD Model: A Carbaryl Case Study

    EPA Science Inventory

    There are two common biomarkers: markers of exposure and markers of health effects. The strength of the correlation between exposure or effect and a biomarker measurement determines the utility of a biomarker for assessing exposures or risks. In the current study, a linked expo...

  14. Warehousing re-annotated cancer genes for biomarker meta-analysis.

    PubMed

    Orsini, M; Travaglione, A; Capobianco, E

    2013-07-01

    Translational research in cancer genomics assigns a fundamental role to bioinformatics in support of candidate gene prioritization with regard to both biomarker discovery and target identification for drug development. Efforts in both such directions rely on the existence and constant update of large repositories of gene expression data and omics records obtained from a variety of experiments. Users who interactively interrogate such repositories may have problems in retrieving sample fields that present limited associated information, due for instance to incomplete entries or sometimes unusable files. Cancer-specific data sources present similar problems. Given that source integration usually improves data quality, one of the objectives is keeping the computational complexity sufficiently low to allow an optimal assimilation and mining of all the information. In particular, the scope of integrating intraomics data can be to improve the exploration of gene co-expression landscapes, while the scope of integrating interomics sources can be that of establishing genotype-phenotype associations. Both integrations are relevant to cancer biomarker meta-analysis, as the proposed study demonstrates. Our approach is based on re-annotating cancer-specific data available at the EBI's ArrayExpress repository and building a data warehouse aimed to biomarker discovery and validation studies. Cancer genes are organized by tissue with biomedical and clinical evidences combined to increase reproducibility and consistency of results. For better comparative evaluation, multiple queries have been designed to efficiently address all types of experiments and platforms, and allow for retrieval of sample-related information, such as cell line, disease state and clinical aspects.

  15. Neurofilaments as Biomarkers for Amyotrophic Lateral Sclerosis: A Systematic Review and Meta-Analysis

    PubMed Central

    Henderson, Robert David; David, Michael; McCombe, Pamela Ann

    2016-01-01

    Background To allow early diagnosis and monitoring of disease progression, there is a need for biomarkers in amyotrophic lateral sclerosis (ALS). Neurofilaments (NF) are emerging protein biomarkers in other neurological diseases, and are of possible use in ALS. Objective The aim of this study is to evaluate the utility of NF levels as blood or cerebrospinal fluid (CSF) biomarker in patients with ALS. Methods A systematic search of Pubmed, Embase and Scopus was performed. Methodological quality assessment was applied to refine the final search results. Meta-analysis of the data was performed. Results Level of NF heavy chain and light chains were significantly elevated in the CSF of ALS patients compared to healthy controls/controls without parenchymal central nervous system (CNS) involvement and ALS mimic disease patients. NF light chain level in CSF was higher in ALS patients than in neurological patients with CNS involvement (SMD = 1.352, P = 0.01). NF light chain concentration in blood was higher in ALS patients than healthy controls/controls without CNS involvement (SMD = 1.448, P<0.0001). NF heavy chain levels in CSF were negatively correlated disease duration and ALSFRS-R ((r = -0.447, P<0.0001; r = -0.486, P<0.0001). NF light chain levels in CSF were negatively correlated with disease duration (r = -0.273, P = 0.011). Conclusion NF heavy and light chain levels have potential use as a marker of neural degeneration in ALS, but are not specific for the disease, and are more likely to be used as measures of disease progression. PMID:27732645

  16. Nutritional biomarkers in Alzheimer's disease: the association between carotenoids, n-3 fatty acids, and dementia severity.

    PubMed

    Wang, Wei; Shinto, Lynne; Connor, William E; Quinn, Joseph F

    2008-02-01

    Carotenoids are fat-soluble antioxidants that may protect polyunsaturated fatty acids, such as n-3 fatty acids from oxidation, and are potentially important for Alzheimer's disease (AD) prevention and treatment. Fasting plasma carotenoids were measured in 36 AD subjects and 10 control subjects by HPLC. Correlations between plasma carotenoid levels, red blood cell (RBC) n-3 fatty acids, and dementia severity were examined in AD patients. Moderately severe AD patients (MMSE=16-19) had much lower plasma levels of two major carotenoids: lutein and beta-carotene, compared to mild AD patients (MMSE=24-27) or controls. Among AD patients, variables (lutein, beta-carotene, RBC docosahexaenoic acid (DHA) and LDL-cholesterol) were significantly correlated with MMSE. A lower MMSE score was associated with lower lutein, beta-carotene and RBC DHA levels, and a higher LDL-cholesterol level. These variables explained the majority of variation in dementia severity (55% of variance in MMSE). Lutein, beta-carotene and beta-cryptoxanthin were positively correlated with RBC DHA in AD patients. The association between higher carotenoids levels and DHA and higher MMSE scores, supports a protective role of both types of nutrients in AD. These findings suggest targeting multiple specific nutrients, lutein, beta-carotene, and DHA in strategies to slow the rate of cognitive decline.

  17. Application in pesticide analysis: Liquid chromatography - A review of the state of science for biomarker discovery and identification

    EPA Science Inventory

    Book Chapter 18, titled Application in pesticide analysis: Liquid chromatography - A review of the state of science for biomarker discovery and identification, will be published in the book titled High Performance Liquid Chromatography in Pesticide Residue Analysis (Part of the C...

  18. Urinary Tetrabromobenzoic Acid (TBBA) as a Biomarker of Exposure to the Flame Retardant Mixture Firemaster® 550

    PubMed Central

    Hoffman, Kate; Fang, Mingliang; Horman, Brian; Patisaul, Heather B.; Garantziotis, Stavros; Birnbaum, Linda S.

    2014-01-01

    Background: Firemaster® 550 (FM550) is commonly added to residential furniture to reduce its flammability. Recent toxicological evidence suggests that FM550 may be endocrine disrupting and obesogenic. Objectives: Our objectives were to develop methods to assess exposure to FM550 in human populations and to identify potential routes of exposure. Methods: Using mass spectrometry methods, we developed a method to measure 2,3,4,5-tetrabromobenzoic acid (TBBA), a urinary metabolite of the major brominated FM550 component 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (TBB). The method was applied to a cohort of adult volunteers (n = 64). Participants completed questionnaires, provided urine and handwipe samples, and collected dust samples from their homes. We measured TBB and the other major brominated FM550 component, bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate (TBPH), in paired dust and handwipe samples. Results: TBBA was detected in 72.4% of urine samples. Although TBBA is a rapidly formed metabolite, analyses indicated moderate temporal reliability (interclass correlation coefficient = 0.56; 95% confidence interval: 0.46, 0.66). TBB and TBPH were detected frequently in dust samples [geometric mean (GM) = 315.1 and 364.7 ng/g, respectively] and in handwipes (GM = 31.4 and 23.4 ng, respectively). Levels of TBB and TBPH in dust were positively correlated with levels in handwipes. In addition, levels of TBB in handwipes were positively correlated with urinary TBBA. Results suggest frequent hand washing may reduce the mass of TBB on participants’ hands and reduce urinary TBBA levels. Conclusions: Cumulatively, our data indicate that exposures to FM550 are widespread and that the home environment may be an important source of exposure. Urinary TBBA provides a potentially useful biomarker of FM550 exposure for epidemiologic studies. Citation: Hoffman K, Fang M, Horman B, Patisaul HB, Garantziotis S, Birnbaum LS, Stapleton HM. 2014. Urinary tetrabromobenzoic acid (TBBA) as a

  19. Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets.

    PubMed

    Amar, David; Hait, Tom; Izraeli, Shai; Shamir, Ron

    2015-09-18

    Genome-wide expression profiling has revolutionized biomedical research; vast amounts of expression data from numerous studies of many diseases are now available. Making the best use of this resource in order to better understand disease processes and treatment remains an open challenge. In particular, disease biomarkers detected in case-control studies suffer from low reliability and are only weakly reproducible. Here, we present a systematic integrative analysis methodology to overcome these shortcomings. We assembled and manually curated more than 14,000 expression profiles spanning 48 diseases and 18 expression platforms. We show that when studying a particular disease, judicious utilization of profiles from other diseases and information on disease hierarchy improves classification quality, avoids overoptimistic evaluation of that quality, and enhances disease-specific biomarker discovery. This approach yielded specific biomarkers for 24 of the analyzed diseases. We demonstrate how to combine these biomarkers with large-scale interaction, mutation and drug target data, forming a highly valuable disease summary that suggests novel directions in disease understanding and drug repurposing. Our analysis also estimates the number of samples required to reach a desired level of biomarker stability. This methodology can greatly improve the exploitation of the mountain of expression profiles for better disease analysis.

  20. Metabolic Biomarkers and Neurodegeneration: A Pathway Enrichment Analysis of Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis.

    PubMed

    Kori, Medi; Aydın, Busra; Unal, Semra; Arga, Kazim Yalcin; Kazan, Dilek

    2016-11-01

    Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) lack robust diagnostics and prognostic biomarkers. Metabolomics is a postgenomics field that offers fresh insights for biomarkers of common complex as well as rare diseases. Using data on metabolite-disease associations published in the previous decade (2006-2016) in PubMed, ScienceDirect, Scopus, and Web of Science, we identified 101 metabolites as putative biomarkers for these three neurodegenerative diseases. Notably, uric acid, choline, creatine, L-glutamine, alanine, creatinine, and N-acetyl-L-aspartate were the shared metabolite signatures among the three diseases. The disease-metabolite-pathway associations pointed out the importance of membrane transport (through ATP binding cassette transporters), particularly of arginine and proline amino acids in all three neurodegenerative diseases. When disease-specific and common metabolic pathways were queried by using the pathway enrichment analyses, we found that alanine, aspartate, glutamate, and purine metabolism might act as alternative pathways to overcome inadequate glucose supply and energy crisis in neurodegeneration. These observations underscore the importance of metabolite-based biomarker research in deciphering the elusive pathophysiology of neurodegenerative diseases. Future research investments in metabolomics of complex diseases might provide new insights on AD, PD, and ALS that continue to place a significant burden on global health.

  1. Salivary Thiocyanate, Uric Acid and pH as Biomarkers of Periodontal Disease in Tobacco Users and Non-Users- An In-Vitro Study

    PubMed Central

    Panchmal, Ganesh Shenoy; Siddique, Sabin

    2015-01-01

    Introduction: Biomarkers of tobacco exposure are used to confirm the absorption of specific smoke constituents in a quantitative manner. Materials and Methods: Periodontal status was measured by Community periodontal Index (WHO). Salivary thiocyanate was determined using spectrophotometric analysis, Salivary uric acid concentration was determined using the enzymatic uric acid assay reagent. pH was measured using pH strips. Results: Proportion of participants with periodontal pockets of 4-5mm was highest among tobacco smokers (80.0%) and periodontal pockets of 6mm or more were observed to be higher among tobacco chewers (26.67%). When LOA scores among tobacco chewers were recorded 26.7% of them presented with attachment loss of 0-3mm. 46.7% of them were affected with loss of attachment of 4-5mm and loss of attachment 6-8mm was found in 16.7%. 6.7% of them were found to be having loss of attachment of 9-11mm. 3.3% of them were found to be having loss of attachment of 12mm or more. The LOA scores in non- tobacco users showed 46.7% of 0-3mm, 50.0% of 4-5mm and 3.33% of 6-8mm attachment loss. The mean level of thiocyanate level detected in saliva of tobacco smokers was 172 ± 54.7 μg/ml and 203.70± 45.7 μg/ml in tobacco chewers. The mean uric acid levels was found to be 2.54 ±0.63 (μg/dl) in smokers and 2.65 ± 0.37(μg/dl) in chewers and in non tobacco users it was 2.33 ± 0.47 μg/dl. Conclusion: Tobacco users had significantly higher concentration of SCN levels than non-users. PMID:26393205

  2. Effect of docosahexaenoic acid and furan fatty acids on cytokinesis block micronucleus cytome assay biomarkers in astrocytoma cell lines under conditions of oxidative stress.

    PubMed

    Chua, Ann; Thomas, Philip; Wijesundera, Chakra; Clifton, Peter; Fenech, Michael

    2014-08-01

    Fatty acids from fish such as docosahexaenoic acid (DHA) are associated with improved brain function, whereas furan fatty acids (FFAs) also found in fish oil at low levels (1%) are thought to have antioxidant properties. Understanding their effects in astrocytes is important as these cells are responsible for maintaining healthy neurons via lipid homeostasis and distribution within the brain, and their decline with aging is a possible cause of dementia. We investigated the cytotoxic and genotoxic effects of DHA and FFA using the cytokinesis-block micronucleus cytome assay in in vitro cultures of U87MG (APOE ɛ3/ɛ3) and U118MG (APOE ɛ2/ɛ4) astrocytoma cell lines with and without a hydrogen peroxide (H2O2, 100 µM) challenge. U118MG was found to be more sensitive to the cytostatic, cytotoxic (i.e., apoptosis), and DNA damaging effects [micronuclei (MNi), nucleoplasmic bridges (NPBs), and nuclear buds (NBUDs)] of H2O2 (P < 0.01 and P < 0.001) when compared with U87MG. DHA at 100 µg/mL significantly affected cytostasis (P < 0.05) and increased DNA damage in the form of NPBs and MNi (P < 0.05) in both cell lines, whereas it decreased necrosis (P = 0.0251) in U87MG. Significant DHA-H2O2 interactions were observed for decreased necrosis (P = 0.0033) and DNA damage biomarkers (P < 0.0001) in the U87MG cell line and increased cytostasis (P < 0.0001) in the U118MG cell line. The effects of FFA also varied between the cell lines, with significant effects observed in decreased cytostasis (P = 0.0022) in the U87MG cell line, whereas increasing cytostasis (P = 0.0144) in the U118MG cell line. Overall, FFA exerted minimal effects on DNA damage biomarkers.

  3. Biomonitoring of concurrent mycotoxin exposure among adults in Sweden through urinary multi-biomarker analysis.

    PubMed

    Wallin, S; Gambacorta, L; Kotova, N; Lemming, E Warensjö; Nälsén, C; Solfrizzo, M; Olsen, M

    2015-09-01

    Mycotoxin producing moulds may contaminate numerous agricultural commodities either before harvest or during storage. A varied diet consisting of different foods may therefore be contaminated with a range of mycotoxins. The aim of the present study was to study concurrent exposure to mycotoxins through urinary multi-biomarker analysis, as well as its possible associations with the diet. Urinary samples from 252 adults, participating in the Swedish national dietary survey Riksmaten 2010-11, were collected together with a 4-day diet record. Concurrent mycotoxin exposure was studied using a multi-biomarker LC-MS/MS method. The results revealed that exposure to mycotoxins is common and concurrent exposure to more than one toxin was found in 69% of the study population. However, when comparing the number of toxins detected with the reported consumption data it was difficult to distinguish food patterns which would indicate an increased risk of exposure to many mycotoxins simultaneously. This is the first study to investigate concurrent mycotoxin exposure and urinary levels of fumonisin B1 (FB1), fumonisin B2 (FB2), nivalenol (NIV), ochratoxin A (OTA), zearalenone (ZEA), α-zearalenol (α-ZOL), β-zearalenol (β-ZOL) and de-epoxydeoxynivalenol (DOM-1) among adults in Sweden.

  4. Biomarker Analysis Revealed Distinct Profiles of Innate and Adaptive Immunity in Infants with Ocular Lesions of Congenital Toxoplasmosis

    PubMed Central

    Machado, Anderson Silva; Carneiro, Ana Carolina Aguiar Vasconcelos; Béla, Samantha Ribeiro; Andrade, Gláucia Manzan Queiroz; Vasconcelos-Santos, Daniel Vitor; Januário, José Nélio; Coelho-dos-Reis, Jordana G.; Ferro, Eloisa Amália Vieira; Teixeira-Carvalho, Andréa; Vitor, Ricardo Wagner Almeida; Martins-Filho, Olindo Assis; —UFMG-CTBG, UFMG Congenital Toxoplasmosis Brazilian Group

    2014-01-01

    Toxoplasma gondii is the main infectious cause of human posterior retinochoroiditis, the most frequent clinical manifestation of congenital toxoplasmosis. This investigation was performed after neonatal screening to identify biomarkers of immunity associated with immunopathological features of the disease by flow cytometry. The study included infected infants without NRL and with retinochoroidal lesions (ARL, ACRL, and CRL) as well as noninfected individuals (NI). Our data demonstrated that leukocytosis, with increased monocytes and lymphocytes, was a relevant hematological biomarker of ARL. Immunophenotypic analysis also revealed expansion of CD14+CD16+HLA-DRhigh monocytes and CD56dim cytotoxic NK-cells in ARL. Moreover, augmented TCRγδ+ and CD8+ T-cell counts were apparently good biomarkers of morbidity. Biomarker network analysis revealed that complex and intricated networks underscored the negative correlation of monocytes with NK- and B-cells in NRL. The remarkable lack of connections involving B-cells and a relevant shift of NK-cell connections from B-cells toward T-cells observed in ARL were outstanding. A tightly connected biomarker network was observed in CRL, with relevant connections of NK- and CD8+ T-cells with a broad range of cell subsets. Our findings add novel elements to the current knowledge on the innate and adaptive immune responses in congenital toxoplasmosis. PMID:25328286

  5. Biomarker analysis revealed distinct profiles of innate and adaptive immunity in infants with ocular lesions of congenital toxoplasmosis.

    PubMed

    Machado, Anderson Silva; Carneiro, Ana Carolina Aguiar Vasconcelos; Béla, Samantha Ribeiro; Andrade, Gláucia Manzan Queiroz; Vasconcelos-Santos, Daniel Vitor; Januário, José Nélio; Coelho-dos-Reis, Jordana G; Ferro, Eloisa Amália Vieira; Teixeira-Carvalho, Andréa; Vitor, Ricardo Wagner Almeida; Martins-Filho, Olindo Assis

    2014-01-01

    Toxoplasma gondii is the main infectious cause of human posterior retinochoroiditis, the most frequent clinical manifestation of congenital toxoplasmosis. This investigation was performed after neonatal screening to identify biomarkers of immunity associated with immunopathological features of the disease by flow cytometry. The study included infected infants without NRL and with retinochoroidal lesions (ARL, ACRL, and CRL) as well as noninfected individuals (NI). Our data demonstrated that leukocytosis, with increased monocytes and lymphocytes, was a relevant hematological biomarker of ARL. Immunophenotypic analysis also revealed expansion of CD14(+)CD16(+)HLA-DR(high) monocytes and CD56(dim) cytotoxic NK-cells in ARL. Moreover, augmented TCRγ δ (+) and CD8(+) T-cell counts were apparently good biomarkers of morbidity. Biomarker network analysis revealed that complex and intricated networks underscored the negative correlation of monocytes with NK- and B-cells in NRL. The remarkable lack of connections involving B-cells and a relevant shift of NK-cell connections from B-cells toward T-cells observed in ARL were outstanding. A tightly connected biomarker network was observed in CRL, with relevant connections of NK- and CD8(+) T-cells with a broad range of cell subsets. Our findings add novel elements to the current knowledge on the innate and adaptive immune responses in congenital toxoplasmosis.

  6. SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis.

    PubMed

    Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G; Treviño, Victor

    2013-01-01

    Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R.

  7. Ultrasensitive electrochemical immunosensor based on horseradish peroxidase (HRP)-loaded silica-poly(acrylic acid) brushes for protein biomarker detection.

    PubMed

    Zhao, Yan; Zheng, Yiqun; Kong, Rongmei; Xia, Lian; Qu, Fengli

    2016-01-15

    We report an ultrasensitive electrochemical immunosensor designed for the detection of protein biomarkers using horseradish peroxidase (HRP)-loaded silica-poly(acrylic acid) brushes (SiO2-SPAABs) as labels. HRP could be efficiently and stably accommodated in the three-dimensional architecture of the SiO2-SPAABs and the SiO2-SPAABs-HRP exhibited high catalytic performance towards o-phenylenediamine (OPD) oxidation in the presence of H2O2, which resulted in significant differential pulse voltammetric (DPV) response change and color change. Using human IgG (HIgG) as a model analyte, a sandwich-type immunosensor was constructed. In particular, graphene oxide (GO) and SiO2-SPAABs-HRP were used to immobilize capture antibody (Ab1) and bind a layer of detection antibody (Ab2), respectively. The current biosensor exhibited a good linear response of HIgG from 100pg/mL to 100μg/mL with a detection limit of 50pg/mL (S/N=5). The sensitivity was 6.70-fold higher than the conventional enzyme-linked immunosorbent assays. The immunosensor results were validated through the detection of HIgG in serum samples.

  8. Fatty Acid-Binding Protein 4 (FABP4): Pathophysiological Insights and Potent Clinical Biomarker of Metabolic and Cardiovascular Diseases

    PubMed Central

    Furuhashi, Masato; Saitoh, Shigeyuki; Shimamoto, Kazuaki; Miura, Tetsuji

    2014-01-01

    Over the past decade, evidences of an integration of metabolic and inflammatory pathways, referred to as metaflammation in several aspects of metabolic syndrome, have been accumulating. Fatty acid-binding protein 4 (FABP4), also known as adipocyte FABP (A-FABP) or aP2, is mainly expressed in adipocytes and macrophages and plays an important role in the development of insulin resistance and atherosclerosis in relation to metaflammation. Despite lack of a typical secretory signal peptide, FABP4 has been shown to be released from adipocytes in a non-classical pathway associated with lipolysis, possibly acting as an adipokine. Elevation of circulating FABP4 levels is associated with obesity, insulin resistance, diabetes mellitus, hypertension, cardiac dysfunction, atherosclerosis, and cardiovascular events. Furthermore, ectopic expression and function of FABP4 in several types of cells and tissues have been recently demonstrated. Here, we discuss both the significant role of FABP4 in pathophysiological insights and its usefulness as a biomarker of metabolic and cardiovascular diseases. PMID:25674026

  9. Comparison of blood lead and blood and plasma δ-aminolevulinic acid concentrations as biomarkers for lead poisoning in cattle.

    PubMed

    Kang, Hwan Goo; Bischoff, Karyn; Ebel, Joseph G; Cha, Sang Ho; McCardle, James; Choi, Cheong Up

    2010-11-01

    Lead (Pb) concentrations in whole blood and δ-aminolevulinic acid (ALA) concentrations in plasma and whole blood from 37 cattle with suspected Pb exposure were determined in order to investigate the usefulness of ALA as a biological indicator for Pb poisoning in cattle. Cows were divided into 4 groups based on blood Pb, as follows: <30 ppb (group 1), 30-100 ppb (group 2), 100-300 ppb (group 3), and >300 ppb (group 4). The derivatization reaction for ALA was improved by a greater than 2-fold measure in whole blood and by a 10-fold measure in plasma by adding 75 and 50 µl of 0.1 N HCl, respectively. Blood Pb concentrations ranged from <25 ppb to 1,006 ppb (185.5 ± 254.9 ppb), with 17 samples containing >50 ppb Pb. Delta-aminolevulinic acid concentrations in whole blood and plasma ranged from <62.7 ppb to 96.9 ppb (77.4 ± 8.4 ppb) and from <5.0 ppb to 24.0 ppb (4.6 ± 3.8 ppb), respectively. Whole blood ALA did not correlate with blood lead concentrations in any group. Increase in plasma ALA concentration was dependent on blood Pb concentration. There was no correlation between blood Pb concentration and plasma ALA concentration in group 2 (n  =  4), but correlation coefficients were 0.736 in group 3 and 0.807 in group 4, respectively. The correlation coefficient was increased to 0.851 when groups 3 and 4 were combined. Based on these observations, in cattle, plasma ALA is a more reliable biological biomarker for Pb exposure than is blood ALA.

  10. Fish scale deformation analysis using scanning electron microscope: New potential biomarker in aquatic environmental monitoring of aluminum and iron contamination

    SciTech Connect

    Hidayati, Dewi; Sulaiman, Norela; Othman, Shuhaimi; Ismail, B. S.

    2013-11-27

    Fish scale has the potential to be a rapid biomarker due to its structure and high possibility to come into contact with any pollutant in the aquatic environment. The scale structure consists of osteoblastic cells and other bone materials such as collagen where it is possible to form a molecular complex with heavy metals such as aluminum and iron. Hence, aluminum and iron in water could possibly destroy the scale material and marked as a scale deformation that quantitatively could be analyzed by comparing it to the normal scale structure. Water sampling and fish cage experiment were performed between June and July 2011 in Porong river which represented the water body that has high aluminum and iron contamination. The filtered water samples were preserved and extracted using the acid-mixture procedure prior to measurement of the aluminum and iron concentrations using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), while samples for total suspended solid (TSS) analysis were kept at 4 °C in cool-boxes. The scales were cleaned with sterile water, then dehydrated in 30, 50, 70, and 90% ethanol and dried on filter papers. They were then mounted on an aluminum stub and coated with gold in a sputter coater prior to Scanning Electron Microscope (SEM) observation. According to the SEM analysis, it was found that there were several deformations on the scale samples taken from sites that have high concentrations of aluminum and iron i.e. the increasing number of pits, deformation and decreasing number of spherules and ridges while the control scale exhibited the normal features. However, the site with higher TSS and pH indicated lower aluminum effect. A moderate correlation was found between the number of pits with aluminum (r=0.43) and iron (r=0.41) concentrations. Fish scale deformation using SEM analysis can potentially be a rapid biomarker in aquatic monitoring of aluminum and iron contamination. However, the measurement must be accompanied by pH and

  11. Feeding strategies of four dominant copepod species in Prydz Bay, Antarctica: Insights from a combined fatty acid biomarker and stable isotopic approach

    NASA Astrophysics Data System (ADS)

    Yang, Guang; Li, Chaolun; Guilini, Katja; Peng, Quancai; Wang, Yanqing; Zhang, Ye; Zhang, Yongshan

    2016-08-01

    Using fatty acid biomarkers and stable isotopic signatures, we investigated the feeding strategies and dietary preferences of four dominant copepod species (Calanoides acutus, Calanus propinquus, Metridia gerlachei and Rhincalanus gigas) sampled during the late austral summer in Prydz Bay, Antarctica. Our results show that diatoms, dinoflagellates and ciliates dominated copepod food sources (hypothesized to be phytoplankton and particulate organic matter) in the inner bay regions more than in the oceanic regions of Prydz Bay. Regional differences in the composition and abundance of food sources were also reflected in the fatty acid biomarkers and stable isotopic values. In the inner bay region, the total fatty acid contents of these food sources were nearly twofold higher, including greater contributions from fatty acids of dinoflagellate origin; these samples also had higher δ13C and δ15N values. Fatty acid biomarkers and stable isotopic values in copepod species roughly mirrored the spatial patterns in food sources. As found in the primary producers, the concentrations of dinoflagellate fatty acids and δ13C and δ15N values were higher in copepods from the inner bay regions. Additionally, there were inter-species differences in the fatty acids and stable isotopic values of copepods. C. acutus and C. propinquus did not exhibit significant regional differences in their total fatty acid contents. In contrast, M. gerlachei from the inner bay region had higher fatty acid values. C. acutus and C. propinquus had higher compositions of the long chain fatty acids 20:1n-9, 22:1n-9 and 22:1n-1, while docosahexaenoic acid (DHA) was higher in M. gerlachei. The δ15N values indicate that C. acutus occupies a higher trophic level than the other copepod species. Similarly, higher fatty acid ratios in M. gerlachei, including DHA/EPA(eicosapntemacnioc acid) and 18:1n-9/18:1n-7, indicate that this species feeds more opportunistically and prefers a carnivorous diet. Insights from

  12. Validation of an HPLC-MS/MS method for the simultaneous determination of phenylmercapturic acid, benzylmercapturic acid and o-methylbenzyl mercapturic acid in urine as biomarkers of exposure to benzene, toluene and xylenes.

    PubMed

    Sabatini, Laura; Barbieri, Anna; Indiveri, Paolo; Mattioli, Stefano; Violante, Francesco Saverio

    2008-02-15

    A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and fully validated, according to U.S. Food and Drug Administration guidance, for the simultaneous determination of phenylmercapturic acid, benzylmercapturic acid and o-methylbenzyl mercapturic acid in human urine as biomarkers of exposure to benzene, toluene and xylenes (BTX). After solid phase extraction and LC separation, samples were analyzed by a triple-quadrupole mass spectrometer operated in negative ion mode, using isotope-labeled analogs as internal standards (ISs). The method meets all the validation criteria required. The limits of detection of the three analytes, ranging from 0.30 to 0.40microgl(-1), and the high throughput make the method suitable for the routine biological monitoring of co-exposure to BTX both in the occupational and environmental settings. The validated method was applied to assess exposure to BTX in a group of 354 urban traffic wardens.

  13. The Influence of α-Lipoic Acid and Garlic Administration on Biomarkers of Oxidative Stress and Inflammation in Rabbits Exposed to Oxidized Nutrition Oils

    PubMed Central

    Zalejska-Fiolka, Jolanta; Wielkoszyński, Tomasz; Rokicki, Wojciech; Dąbrowska, Natalia; Strzelczyk, Joanna Katarzyna; Kasperczyk, Aleksandra; Owczarek, Aleksander; Błaszczyk, Urszula; Kasperczyk, Sławomir; Stawiarska-Pięta, Barbara; Birkner, Ewa; Gamian, Andrzej

    2015-01-01

    We hypothesized that addition of substances with antioxidant activity could decrease the concentrations of biomarkers of oxidative stress and inflammatory process, thus inhibiting nonalcoholic steatohepatitis development. We investigated the influence of α-lipoic acid (ALA) and garlic administration on the development of adverse changes in rabbit liver and serum under oxidative stress conditions induced with HFD from oxidized oils. We determined 8-hydroxy-2′-deoxyguanosine (8OHdG) and malondialdehyde (MDA) in liver homogenates, total oxidant status (TOS), lipid peroxides (LOO) and tumor necrosis factor alpha (TNFα) in blood serum, and TNFα and IL-1α genes expression in liver. The results indicate that the intake of dietary ALA and garlic was significantly associated with decreases of 8OHdG and MDA levels in rabbits' liver tissue as well as TOS and LOO levels in rabbits' serum. Similarly, TNFα and IL-1α gene expressions were suppressed due to ALA and garlic supplementation. The histopathological analysis confirmed that HFD results in liver disorder leading to steatosis. This adverse effect of HFD was ameliorated by the supplementation of ALA and garlic. The obtained results indicate a beneficial effect of ALA and garlic administration by reducing the oxidative stress intensity and the levels of some proinflammatory cytokines in rabbits fed HFD. PMID:26634212

  14. Quantification of fatty acid ethyl esters (FAEE) and ethyl glucuronide (EtG) in meconium for detection of alcohol abuse during pregnancy: Correlation study between both biomarkers.

    PubMed

    Cabarcos, Pamela; Tabernero, María Jesús; Otero, José Luís; Míguez, Martha; Bermejo, Ana María; Martello, Simona; De Giovanni, Nadia; Chiarotti, Marcello

    2014-11-01

    This article presents results from 47 meconium samples, which were analyzed for fatty acid ethyl esters (FAEE) and ethyl glucuronide (EtG) for detection of gestational alcohol consumption. A validated microwave assisted extraction (MAE) method in combination with GC-MS developed in the Institute of Forensic Science (Santiago de Compostela) was used for FAEE and the cumulative concentration of ethyl myristate, ethyl palmitate and ethyl stearate with a cut-off of 600ng/g was applied for interpretation. A simple method for identification and quantification of EtG has been evaluated by ultrasonication followed solid phase extraction (SPE). Successful validation parameters were obtained for both biochemical markers of alcohol intake. FAEE and EtG concentrations in meconium ranged between values lower than LOD and 32,892ng/g or 218ng/g respectively. We have analyzed FAEE and EtG in the same meconium aliquot, enabling comparison of the efficiency of gestational ethanol exposure detection. Certain agreement between the two biomarkers was found as they are both a very specific alcohol markers, making it a useful analysis for confirmation.

  15. High-performance liquid chromatography-tandem mass spectrometry assay of fatty acid amide hydrolase (FAAH) in blood: FAAH inhibition as clinical biomarker.

    PubMed

    Yapa, Udeni; Prusakiewicz, Jeffery J; Wrightstone, Ann D; Christine, Lori J; Palandra, Joe; Groeber, Elizabeth; Wittwer, Arthur J

    2012-02-15

    Fatty acid amide hydrolase (FAAH) is one of the main enzymes responsible for the degradation of the endocannabinoid anandamide (N-arachidonoylethanolamine, AEA). FAAH inhibitors may be useful in treating many disorders involving inflammation and pain. Although brain FAAH may be the relevant target for inhibition, rat studies show a correlation between blood and brain FAAH inhibition, allowing blood FAAH activity to be used as a target biomarker. Building on experience with a rat leukocyte FAAH activity assay using [³H]AEA, we have developed a human leukocyte assay using stably labeled [²H₄]AEA as substrate. The deuterium-labeled ethanolamine reaction product ([²H₄]EA) was analyzed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) in the positive electrospray ionization (ESI) mode. The response for [²H₄]EA was linear from 10 nM to 10 μM, and the analysis time was less than 6 min/sample. Results using the [²H₄]AEA and HPLC-MS/MS method agreed well with those obtained using the [³H]AEA radiometric assay. In addition to using a nonradioactive substrate, the HPLC-MS/MS method had increased sensitivity with lower background. Importantly, the assay preserved partial FAAH inhibition resulting from ex vivo treatment with a time-dependent irreversible inhibitor, suggesting its utility with clinical samples. The assay has been used to profile the successful inhibition of FAAH in recent clinical trials.

  16. A chromo- and fluorogenic sensor for probing the cancer biomarker lysophosphatidic acid.

    PubMed

    Zhao, Wenwen; Liu, Weimin; Zhang, Wenjun; Zeng, Lintao; Fan, Zhiyuan; Wu, Jiasheng; Wang, Pengfei

    2012-04-21

    A novel chromo- and fluorogenic sensor, 4-(4-dimethylaminostyryl)-1-hexadecylpyridinium (DSHP) for lysophosphatidic acid (LPA) was successfully developed by incorporating a long alkyl chain into the cyanine molecule. DSHP shows excellent selectivity and high sensitivity towards LPA with a detection limit of about 7.09 × 10(-7) M based on electrostatic and hydrophobic interactions between the sensor and LPA. Upon addition of LPA ranging from 0 to 7.5 × 10(-4) M, DSHP displays an 'on-off-on' fluorescence response and obvious colour change. Good linear relationships between the fluorescence intensity and LPA concentrations were achieved in the fluorescence quenching ranges of 0-28 μM and 34-52 μM, which could be attributed to the combined effects of the photoinduced electron transfer and LPA-induced aggregation of the sensor molecules.

  17. Aptamer-initiated on-particle template-independent enzymatic polymerization (aptamer-OTEP) for electrochemical analysis of tumor biomarkers.

    PubMed

    Wang, Pengjuan; Wan, Ying; Deng, Shengyuan; Yang, Shulin; Su, Yan; Fan, Chunhai; Aldalbahi, Ali; Zuo, Xiaolei

    2016-12-15

    Herein, an aptamer-initiated on-particle template-independent enzymatic polymerization (aptamer-OTEP) strategy for electrochemical aptasensor (E-aptasensor) is developed for analysis of cancer biomarker carcino-embryonic antigen (CEA). A pair of DNA aptamers is employed which can be specifically bond with CEA simultaneously. One of the aptamer is thiolated at 3'-terminal and immobilized onto the gold electrode as a capture probe, while the other one has a thiol group at its 5'-terminal and is modified onto the gold nanoparticles surface to form a nanoprobe. In the present of target, the two aptamers can "sandwich" the target, thus the nanoprobe is attached to the electrode. Then terminal deoxynucleotidyl transferase (TdT) is employed to catalyze the incorporation of biotin labeled dNTPs into the 3'-OH terminals of the DNA aptamer on the nanoprobe. The as-generated long DNA oligo tentacles allow specific binding of numerous avidin modified horseradish peroxidase (Av-HRP), resulting in tens of thousands of HRP catalyzed reduction of hydrogen peroxide and sharply increasing electrochemical signals. Taking advantage of the enzyme based nucleic acid amplification and nanoprobe, this strategy is demonstrated to possess the outstanding amplification efficiency.

  18. Nanotechnologic biosensor ellipsometry and biomarker pattern analysis in the evaluation of atherosclerotic risk profile.

    PubMed

    Siegel, G; Rodríguez, M; Sauer, F; Abletshauser, C; de Mey, C; Schötz, K; Ringstad, L; Malmsten, M; Schäfer, P

    2009-01-01

    A proteoheparan sulfate coated, hydrophobic silica surface serves as lipoprotein receptor at which the Ca(2+)-driven arteriosclerotic nanoplaque formation can be pursued by laser-based ellipsometry. Any lipoprotein from human blood can be very sensitively tested for its atherogenic properties. From the same blood sample, it is possible to determine the concentration and activity of a series of interacting biomarker molecules which, through a pattern analysis, allow to assess the state of health with respect to cardiovascular diseases. These two interlinked and complementary biosensors make a prospective cardio-cerebro-vascular risk stratification feasible, especially the sequelae of an underlying arteriosclerotic disease. Based on these diagnostic tools, an optimized therapy decision for the patient can be taken and the necessary preventive measures for the still healthy person.

  19. Monitoring concussion in a knocked-out boxer by CSF biomarker analysis.

    PubMed

    Neselius, Sanna; Brisby, Helena; Granholm, Fredrik; Zetterberg, Henrik; Blennow, Kaj

    2015-09-01

    Concussion is common in many sports, and the incidence is increasing. The medical consequences after a sport-related concussion have received increased attention in recent years since it is known that concussions cause axonal and glial damage, which disturbs the cerebral physiology and makes the brain more vulnerable for additional concussions. This study reports on a knocked-out amateur boxer in whom cerebrospinal fluid (CSF) neurofilament light (NFL) protein, reflecting axonal damage, was used to identify and monitor brain damage. CSF NFL was markedly increased during 36 weeks, suggesting that neuronal injury persists longer than expected after a concussion. CSF biomarker analysis may be valuable in the medical counselling of concussed athletes and in return-to-play considerations.

  20. Retracted: Identification of Novel Biomarkers for Pancreatic Cancer Using Integrated Transcriptomics With Functional Pathways Analysis.

    PubMed

    Zhang, Xuan; Tong, Pan; Chen, Jinyun; Pei, Zenglin; Zhang, Xiaoyan; Chen, Weiping; Xu, Jianqing; Wang, Jin

    2016-02-22

    Retraction: 'Identification of Novel Biomarkers for Pancreatic Cancer Using Integrated Transcriptomics With Functional Pathways Analysis' by Zhang, X., Tong, P., Chen, J., Pei, Z., Zhang, X., Chen, W., Xu, J. and Wang, J. The above article from the Journal of Cellular Physiology, published online on 10 March 2016 in Wiley Online Library as Early View (http://onlinelibrary.wiley.com/enhanced/doi/10.1002/jcp.25353/), has been retracted by agreement between Gary Stein, the journal's Editor-in-Chief, and Wiley Periodicals, Inc. The retraction has been agreed following an investigation at the University of Texas, MD Anderson Cancer Center, which confirmed that the article was submitted and approved for publication by Dr. Jin Wang without acknowledgement of NIH funding received or the consent and authorship of Dr. Ann Killary and Dr. Subrata Sen, with whom the manuscript was originally drafted.

  1. Amino acid isotopic analysis in agricultural systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A relatively new approach to stable isotopic analysis—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino acids (glutamic acid and phenylalanine). CSIA has recently been used to generate trophic position estimates among anima...

  2. Principal component analysis of phenolic acid spectra

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenolic acids are common plant metabolites that exhibit bioactive properties and have applications in functional food and animal feed formulations. The ultraviolet (UV) and infrared (IR) spectra of four closely related phenolic acid structures were evaluated by principal component analysis (PCA) to...

  3. New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces

    PubMed Central

    Sistiaga, Ainara; Wrangham, Richard; Rothman, Jessica M.; Summons, Roger E.

    2015-01-01

    Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets. PMID:26061730

  4. Boric Acid in Kjeldahl Analysis

    ERIC Educational Resources Information Center

    Cruz, Gregorio

    2013-01-01

    The use of boric acid in the Kjeldahl determination of nitrogen is a variant of the original method widely applied in many laboratories all over the world. Its use is recommended by control organizations such as ISO, IDF, and EPA because it yields reliable and accurate results. However, the chemical principles the method is based on are not…

  5. Biomarker- versus drug-driven tumor growth inhibition models: an equivalence analysis.

    PubMed

    Sardu, Maria Luisa; Poggesi, Italo; De Nicolao, Giuseppe

    2015-12-01

    The mathematical modeling of tumor xenograft experiments following the dosing of antitumor drugs has received much attention in the last decade. Biomarker data can further provide useful insights on the pathological processes and be used for translational purposes in the early clinical development. Therefore, it is of particular interest the development of integrated pharmacokinetic-pharmacodynamic (PK-PD) models encompassing drug, biomarker and tumor-size data. This paper investigates the reciprocal consistency of three types of models: drug-to-tumor, such as established drug-driven tumor growth inhibition (TGI) models, drug-to-biomarker, e.g. indirect response models, and biomarker-to-tumor, e.g. the more recent biomarker-driven TGI models. In particular, this paper derives a mathematical relationship that guarantees the steady-state equivalence of the cascade of drug-to-biomarker and biomarker-to-tumor models with a drug-to-tumor TGI model. Using the Simeoni TGI model as a reference, conditions for steady-state equivalence are worked out and used to derive a new biomarker-driven model. Simulated and real data are used to show that in realistic cases the steady-state equivalence extends also to transient responses. The possibility of predicting the drug-to-tumor potency of a new candidate drug based only on biomarker response is discussed.

  6. Biomarkers for the Detection of Prenatal Alcohol Exposure: A Review.

    PubMed

    Bager, Heidi; Christensen, Lars Porskjaer; Husby, Steffen; Bjerregaard, Lene

    2017-02-01

    Alcohol exposure during pregnancy can cause adverse effects to the fetus, because it interferes with fetal development, leading to later physical and mental impairment. The most common clinical tool to determine fetal alcohol exposure is maternal self-reporting. However, a more objective and useful method is based on the use of biomarkers in biological specimens alone or in combination with maternal self-reporting. This review reports on clinically relevant biomarkers for detection of prenatal alcohol exposure (PAE). A systematic search was performed to ensure a proper overview in existing literature. Studies were selected to give an overview on clinically relevant neonatal and maternal biomarkers. The direct biomarkers fatty acid ethyl esters (FAEEs), ethyl glucuronide (EtG), ethyl sulfate, and phosphatidylethanol (PEth) were found to be the most appropriate biomarkers in relation to detection of PAE. To review each biomarker in a clinical context, we have compared the advantages and disadvantages of each biomarker, in relation to its window of detectability, ease of collection, and the ease and cost of analysis of each biomarker. The biomarkers PEth, FAEEs, and EtG were found to be applicable for detection of even low levels of alcohol exposure. Meconium is an accessible matrix for determination of FAEEs and EtG, and blood an accessible matrix for determination of PEth.

  7. High throughput HPLC-ESI(-)-MS/MS methodology for mercapturic acid metabolites of 1,3-butadiene: Biomarkers of exposure and bioactivation.

    PubMed

    Kotapati, Srikanth; Esades, Amanda; Matter, Brock; Le, Chap; Tretyakova, Natalia

    2015-11-05

    1,3-Butadiene (BD) is an important industrial and environmental carcinogen present in cigarette smoke, automobile exhaust, and urban air. The major urinary metabolites of BD in humans are 2-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene/1-(N-acetyl-L-cystein-S-yl)-2-hydroxybut-3-ene (MHBMA), 4-(N-acetyl-L-cystein-S-yl)-1,2-dihydroxybutane (DHBMA), and 4-(N-acetyl-L-cystein-S-yl)-1,2,3-trihydroxybutyl mercapturic acid (THBMA), which are formed from the electrophilic metabolites of BD, 3,4-epoxy-1-butene (EB), hydroxymethyl vinyl ketone (HMVK), and 3,4-epoxy-1,2-diol (EBD), respectively. In the present work, a sensitive high-throughput HPLC-ESI(-)-MS/MS method was developed for simultaneous quantification of MHBMA and DHBMA in small volumes of human urine (200 μl). The method employs a 96 well Oasis HLB SPE enrichment step, followed by isotope dilution HPLC-ESI(-)-MS/MS analysis on a triple quadrupole mass spectrometer. The validated method was used to quantify MHBMA and DHBMA in urine of workers from a BD monomer and styrene-butadiene rubber production facility (40 controls and 32 occupationally exposed to BD). Urinary THBMA concentrations were also determined in the same samples. The concentrations of all three BD-mercapturic acids and the metabolic ratio (MHBMA/(MHBMA+DHBMA+THBMA)) were significantly higher in the occupationally exposed group as compared to controls and correlated with BD exposure, with each other, and with BD-hemoglobin biomarkers. This improved high throughput methodology for MHBMA and DHBMA will be useful for future epidemiological studies in smokers and occupationally exposed workers.

  8. An integrated transcriptomic and computational analysis for biomarker identification in human glioma.

    PubMed

    Xing, Wenli; Zeng, Chun

    2016-06-01

    Malignant glioma is one of the most common primary brain tumors and is among the deadliest of human cancers. The molecular mechanism for human glioma is poorly understood. Early prognosis of this disease and early treatment are vital. Thus, it is crucial to target the key genes controlling pathogenesis in the early stage of glioma. In this study, differentially expressed genes in human glioma and paired peritumoral tissues were detected by transcriptome microarray analysis. Following gene microarray analysis, the gene expression profile in the differential grade glioma was further validated by bioinformatic analyses, co-expression network construction. Microarray analysis revealed that 1725 genes were differentially expressed and classified into different glioma stage. The analysis revealed 14 genes that were significantly associated with survival with a false discovery rate. Among these genes, macrophage capping protein (CAPG), a member of the actin-regulatory protein, was the key gene in a 20-gene network that modulates cell motility by interacting with the cytoskeleton. Furthermore, the prognostic impact of CAPG was validated by use of quantitative real-time polymerase chain reaction (qPCR) and immunohistochemistry on human glioma tissue. CAPG protein was significantly upregulated in clinical high-grade glioblastoma as compared with normal brain tissues. Overexpression of CAPG levels also predict shorter overall survival of glioma patients. These data demonstrated CAPG protein expression in human glioma was associated with tumorigenesis and may be a biomarker for identification of the pathological grade of glioma.

  9. Homovanillic acid and 5-hydroxyindole acetic acid as biomarkers for dementia with Lewy bodies and coincident Alzheimer’s disease: An autopsy-confirmed study

    PubMed Central

    Takao, Masaki; Hatsuta, Hiroyuki; Nishina, Yasushi; Komiya, Tadashi; Sengoku, Renpei; Nakano, Yuta; Uchino, Akiko; Sumikura, Hiroyuki; Saito, Yuko; Kanemaru, Kazutomi; Murayama, Shigeo

    2017-01-01

    Dementia with Lewy bodies (DLB) and Alzheimer’s disease (AD) are the two most common causes of dementia. Both pathologies often coexist, and AD patients with concomitant neocortical LB pathology (referred to as the Lewy body variant of AD) generally show faster cognitive decline and accelerated mortality relative to patients with pure AD. Thus, discriminating among patients with DLB, AD, and coincident DLB and AD is important in clinical practice. We examined levels of homovanillic acid (HVA), 5-hydroxyindole acetic acid (5-HIAA), tau, phosphorylated tau (p-tau), and beta-amyloid (Aβ) 1–42 in cerebrospinal fluid (CSF) to evaluate their viability as biomarkers to discriminate among different forms of dementia. We obtained a total of 3498 CSF samples from patients admitted to our hospital during the period from 1996 to 2015. Of these patients, we were able to carry out a brain autopsy in 94 cases. Finally, 78 neuropathologically diagnosed cases (10 AD, six DLB, five DLB with AD, five controls without neurological diseases, and 52 cases with other neurological diseases) were studied. CSF levels of HVA and 5-HIAA were consistently decreased in pathologically advanced Lewy body disorder (LBD; Braak LB stages >3) compared with pathologically incipient LBD (Braak LB stages <2). These results suggest that if an individual has LB pathology in the central nervous system, CSF levels of HVA and 5-HIAA may decrease after the onset of clinical symptoms. In addition, CSF levels of HVA and 5-HIAA decreased with LB pathology, and were especially low in cases of DLB and DLB with AD. Furthermore, the combination of HVA, 5-HIAA, and brain specific proteins t-tau, p-tau, and Aβ 1–42 in CSF were useful for discriminating among DLB, DLB with AD, and AD with high diagnostic accuracy. PMID:28166276

  10. Use of fish farms to assess river contamination: combining biomarker responses, active biomonitoring, and chemical analysis.

    PubMed

    Quesada-García, Alba; Valdehita, Ana; Torrent, Fernando; Villarroel, Morris; Hernando, M Dolores; Navas, José M

    2013-09-15

    Here we addressed the possible effects of trace levels of contaminants on fish by means of a combination of biomarker responses, active biomonitoring (ABM), and chemical analysis. In environmental studies, cytochromes P4501A (Cyp1A) and Cyp3A and related enzyme activities (7-ethoxyresorufin-O-deethylase, EROD, and benzyloxy-4-[trifluoromethyl]-coumarin-O-debenzyloxylase, BFCOD, respectively) are commonly used as biomarkers for evidencing exposure to a variety of contaminants. In a rainbow trout (Oncorhynchus mykiss) fish farm that is routinely sampled to obtain references regarding normal levels of such enzyme activities in freshwater fish, we observed a strong and punctual increase in these activities at the end of 2011. In order to shed light on the causes of this induction, we transferred some fish to a fish farm with controlled conditions and examined them using an active biomonitoring (ABM) approach. EROD activity showed a decrease of 80% from the original values after 7 days in the control farm, while BFCOD activity was also reduced after 15 days. Although not significant, a decrease in cyp1A and cyp3A mRNA levels was also observed. To determine the presence of pollutants, water and sediment samples from the river feeding the fish farm were analyzed by two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-TOF-MS). The screening study reflected a weak inflow of pollutants in the monitored area, which is located far from any industrial activity or densely populated cities. Trace levels of polyaromatic hydrocarbons (PAHs) and personal care products (the polycyclic musk fragrance HHCB, and triclosan) were detected in sediments, at concentrations ranging from 0.01 to 38 ng/g dry weight, and in water from 4 to 441 ng/L. The approach followed in this study proved useful as a biomonitoring technique for the early detection of trace contaminants.

  11. Multi-analyte analysis of saliva biomarkers as predictors of periodontal and pre-implant disease

    SciTech Connect

    Braun, Thomas; Giannobile, William V; Herr, Amy E; Singh, Anup K; Shelburne, Charlie

    2015-04-07

    The present invention relates to methods of measuring biomarkers to determine the probability of a periodontal and/or peri-implant disease. More specifically, the invention provides a panel of biomarkers that, when used in combination, can allow determination of the probability of a periodontal and/or peri-implant disease state with extremely high accuracy.

  12. ANALYSIS OF UNCERTAINTIES IN DOSE RECONSTRUCTION FROM BIOMARKERS: IMPACT ON STUDY DESIGN

    EPA Science Inventory

    The absorbed dose is defined as the quantity which has passed through the barriers (skin, GI tract, The absorbed dose of a pesticide can be estimated from its established urinary biomarker. ungs). For an exposure study, there are several options for biomarker collection, each w...

  13. Pathway Analysis of Proteomics Profiles in Rabies Infection: Towards Future Biomarkers?

    PubMed

    Mehta, Shraddha; Sreenivasamurthy, Sreelakshmi; Banerjee, Shefali; Mukherjee, Sandeepan; Prasad, Keshava; Chowdhary, Abhay

    2016-02-01

    Rabies is a zoonotic viral disease that invariably leads to fatal encephalitis, which can be prevented provided post-exposure prophylaxis is initiated timely. Ante-mortem diagnostic tests are inconclusive, and rabies is nontreatable once the clinical signs appear. A large number of host factors are responsible for the altered neuronal functions observed in rabies; however their precise role remains uninvestigated. We therefore used two-dimensional electrophoresis and mass spectrometry analysis to identify differentially expressed host proteins in an experimental murine model of rabies. We identified 143 proteins corresponding to 45 differentially expressed spots (p < 0.05) in neuronal tissues of Swiss albino mice in response to infection with neurovirulent rabies strains. Time series analyses revealed that a majority of the alterations occur at 4 to 6 days post infection, in particular affecting the host's cytoskeletal architecture. Extensive pathway analysis and protein interaction studies using the bioinformatic tools such as Ingenuity Pathway Analysis and STRING revealed novel pathways and molecules (e.g., protein ubiquitination) unexplored hitherto. Further activation/inhibition studies of these pathway molecular leads would be relevant to identify novel biomarkers and mechanism-based therapeutics for rabies, a disease that continues to severely impact global health.

  14. Identification of new biomarkers for human papillary thyroid carcinoma employing NanoString analysis.

    PubMed

    Chitikova, Zhanna; Pusztaszeri, Marc; Makhlouf, Anne-Marie; Berczy, Margaret; Delucinge-Vivier, Celine; Triponez, Frederic; Meyer, Patrick; Philippe, Jacques; Dibner, Charna

    2015-05-10

    We previously reported an upregulation of the clock transcript BMAL1, correlating with TIMP1 expression in fresh-frozen samples from papillary thyroid carcinoma (PTC). Since frozen postoperative biopsy samples are difficult to obtain, we aimed to validate the application of high-precision NanoString analysis for formalin-fixed paraffin-embedded (FFPE) thyroid nodule samples and to screen for potential biomarkers associated with PTC. No significant differences were detected between fresh-frozen and FFPE samples. NanoString analysis of 51 transcripts in 17 PTC and 17 benign nodule samples obtained from different donors and in 24 pairs of benign and PTC nodules, obtained from the same donor (multinodular goiters), confirmed significant alterations in the levels of BMAL1, c-MET, c-KIT, TIMP1, and other transcripts. Moreover, we identified for the first time alterations in CHEK1 and BCL2 levels in PTC. A predictive score was established for each sample, based on the combined expression levels of BMAL1, CHEK1, c-MET, c-KIT and TIMP1. In combination with BRAF mutation analysis, this predictive score closely correlated with the clinicopathological characteristics of the analyzed thyroid nodules. Our study identified new thyroid transcripts with altered levels in PTC using the NanoString approach. A predictive score correlation coefficient might contribute to improve the preoperative diagnosis of thyroid nodules.

  15. Development of DNA Damage Response Signaling Biomarkers using Automated, Quantitative Image Analysis

    PubMed Central

    Nikolaishvilli-Feinberg, Nana; Cohen, Stephanie M.; Midkiff, Bentley; Zhou, Yingchun; Olorvida, Mark; Ibrahim, Joseph G.; Omolo, Bernard; Shields, Janiel M.; Thomas, Nancy E.; Groben, Pamela A.; Kaufmann, William K.

    2014-01-01

    The DNA damage response (DDR) coordinates DNA repair with cell cycle checkpoints to ameliorate or mitigate the pathological effects of DNA damage. Automated quantitative analysis (AQUA) and Tissue Studio are commercial technologies that use digitized immunofluorescence microscopy images to quantify antigen expression in defined tissue compartments. Because DDR is commonly activated in cancer and may reflect genetic instability within the lesion, a method to quantify DDR in cancer offers potential diagnostic and/or prognostic value. In this study, both AQUA and Tissue Studio algorithms were used to quantify the DDR in radiation-damaged skin fibroblasts, melanoma cell lines, moles, and primary and metastatic melanomas. Digital image analysis results for three markers of DDR (γH2AX, P-ATM, P-Chk2) correlated with immunoblot data for irradiated fibroblasts, whereas only γH2AX and P-Chk2 correlated with immunoblot data in melanoma cell lines. Melanoma cell lines displayed substantial variation in γH2AX and P-Chk2 expression, and P-Chk2 expression was significantly correlated with radioresistance. Moles, primary melanomas, and melanoma metastases in brain, lung and liver displayed substantial variation in γH2AX expression, similar to that observed in melanoma cell lines. Automated digital analysis of immunofluorescent images stained for DDR biomarkers may be useful for predicting tumor response to radiation and chemotherapy. PMID:24309508

  16. Nutritional aspects of metabolic inflammation in relation to health--insights from transcriptomic biomarkers in PBMC of fatty acids and polyphenols.

    PubMed

    Afman, Lydia; Milenkovic, Dragan; Roche, Helen M

    2014-08-01

    Recent research has highlighted potential important interaction between metabolism and inflammation, within the context of metabolic health and nutrition, with a view to preventing diet-related disease. In addition to this, there is a paucity of evidence in relation to accurate biomarkers that are capable of reflecting this important biological interplay or relationship between metabolism and inflammation, particularly in relation to diet and health. Therefore the objective of this review is to highlight the potential role of transcriptomic approaches as a tool to capture the mechanistic basis of metabolic inflammation. Within this context, this review has focused on the potential of peripheral blood mononuclear cells transcriptomic biomarkers, because they are an accessible tissue that may reflect metabolism and subacute chronic inflammation. Also these pathways are often dysregulated in the common diet-related diseases obesity, type 2 diabetes, and cardiovascular disease, thus may be used as markers of systemic health. The review focuses on fatty acids and polyphenols, two classes of nutrients/nonnutrient food components that modulate metabolism/inflammation, which we have used as an example of a proof-of-concept with a view to understanding the extent to which transcriptomic biomarkers are related to nutritional status and/or sensitive to dietary interventions. We show that both nutritional components modulate inflammatory markers at the transcriptomic level with the capability of profiling pro- and anti-inflammatory mechanisms in a bidirectional fashion; to this end transcriptomic biomarkers may have potential within the context of metabolic inflammation. This transcriptomic biomarker approach may be a sensitive indicator of nutritional status and metabolic health.

  17. Quantification of the Heterogeneity of Prognostic Cellular Biomarkers in Ewing Sarcoma Using Automated Image and Random Survival Forest Analysis

    PubMed Central

    Yu, Haiyue; Branford White, Harriet; Schäfer, Karl L.; Llombart-Bosch, Antonio; Machado, Isidro; Picci, Piero; Hogendoorn, Pancras C. W.; Athanasou, Nicholas A.; Noble, J. Alison; Hassan, A. Bassim

    2014-01-01

    Driven by genomic somatic variation, tumour tissues are typically heterogeneous, yet unbiased quantitative methods are rarely used to analyse heterogeneity at the protein level. Motivated by this problem, we developed automated image segmentation of images of multiple biomarkers in Ewing sarcoma to generate distributions of biomarkers between and within tumour cells. We further integrate high dimensional data with patient clinical outcomes utilising random survival forest (RSF) machine learning. Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithms. Each cell nucleus and cytoplasm were identified in relation to DAPI and CD99, respectively, and protein biomarkers (e.g. Ki67, pS6, Foxo3a, EGR1, MAPK) localised relative to nuclear and cytoplasmic regions of each cell in order to generate image feature distributions. The image distribution features were analysed with RSF in relation to known overall patient survival from three separate cohorts (185 informative cases). Variation in pre-analytical processing resulted in elimination of a high number of non-informative images that had poor DAPI localisation or biomarker preservation (67 cases, 36%). The distribution of image features for biomarkers in the remaining high quality material (118 cases, 104 features per case) were analysed by RSF with feature selection, and performance assessed using internal cross-validation, rather than a separate validation cohort. A prognostic classifier for Ewing sarcoma with low cross-validation error rates (0.36) was comprised of multiple features, including the Ki67 proliferative marker and a sub-population of cells with low cytoplasmic/nuclear ratio of CD99. Through elimination of bias, the evaluation of high-dimensionality biomarker distribution within cell populations of a tumour using random forest analysis in quality controlled tumour

  18. Chiral Biomarkers and Microfossils in Carbonaceous Meteorites

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.

    2010-01-01

    Homochirality of the biomolecules (D-sugars of DNA and RNA and L-amino acids of proteins) is a fundamental property of all life on Earth. Abiotic mechanisms yield racemic mixtures (D/L=1) of chiral molecules and after the death of an organism, the enantiopure chiral biomolecules slowly racemize. Several independent investigators have now established that the amino acids present in CI1 and CM2 carbonaceous meteorites have a moderate to strong excess of the L-enantiomer. Stable isotope data have established that these amino acids are both indigenous and extraterrestrial. Carbonaceous meteorites also contain many other strong chemical biomarkers including purines and pyrimidines (nitrogen heterocycles of nucleic acids); pristine and phytane (components of the chlorophyll pigment) and morphological biomarkers (microfossils of filamentous cyanobacteria). Energy dispersive X-ray Spectroscopy (EDS) analysis reveals that nitrogen is below the detectability level in most of the meteorite filaments as well as in Cambrian Trilobites and filaments of 2.7 Gya Archaean cyanobacteria from Karelia. The deficiency of nitrogen in the filaments and the total absence of sugars, of twelve of the life-critical protein amino acids, and two of the nucleobases of DNA and RNA provide clear and convincing evidence that these filaments are not modern biological contaminants. This paper reviews the chiral, chemical biomarkers morphological biomarkers and microfossils in carbonaceous meteorites. This paper reviews chiral and morphological biomarkers and discusses the missing nitrogen, sugars, protein amino acids, and nucleobases as ?bio-discriminators? that exclude modern biological contaminants as a possible explanation for the permineralized cyanobacterial filaments found in the meteorites.

  19. An approach to remove alpha amylase for proteomic analysis of low abundance biomarkers in human saliva.

    PubMed

    Deutsch, Omer; Fleissig, Yoram; Zaks, Batia; Krief, Guy; Aframian, Doron J; Palmon, Aaron

    2008-11-01

    Proteomic characterization of human whole saliva for the identification of disease-specific biomarkers is guaranteed to be an easy-to-use and powerful diagnostic tool for defining the onset, progression and prognosis of human systemic diseases and, in particular, oral diseases. The high abundance of proteins, mainly alpha amylase, hampers the detection of low abundant proteins appearing in the disease state and therefore should be removed. In the present study a 2-DE was used to analyze human whole saliva following the removal of alpha amylase by affinity adsorption to potato starch. After alpha amylase removal whole saliva was analyzed by SDS-PAGE showing at least sixfold removal efficiency and by an alpha amylase activity assay showing 97% reduced activity. MS identification of the captured alpha amylase after elution demonstrated specific removal; 2-DE analysis showed the selective removal of alpha amylase and consequently increased gel resolution. MS identification of protein spots in the 60 kDa area revealed 15 proteins, which were masked before alpha amylase removal. In conclusion, treatment of human whole saliva with an alpha amylase removal device increases gel resolution and enables a higher protein sample for analysis.

  20. Biomarkers present in asphaltenes

    SciTech Connect

    Philp, R.P.

    1985-01-01

    The significance and distribution of biomarkers in sediments, source rocks and crude oils are well documented in the literature. Little attention has been directed towards the biomarkers that are present in the asphaltene fractions of crude oils and source rock extracts. Asphaltene fractions by definition are insoluble in certain solvents and consist of high molecular components which makes them difficult to analyze by techniques commonly used to characterize the soluble extracts. Asphaltenes are ideally suited for analysis by microscale pyrolysis techniques (py) combined with gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). Utilization of the multiple ion detection technique in conjunction with the py-GC-MS analyses permits the distribution of the steranes, triterpanes and other biomarker produced by pyrolysis of the asphaltenes to be easily determined. It is proposed in this paper to discuss the pyrolysis of asphaltene from a variety of source rocks and analysis of the biomarkers, released by the pyrolysis. These biomarkers distributions can be used to obtain information on source and maturity of the organic matter in a similar manner to using the soluble biomarkers. It is proposed to discuss the asphaltene biomarker distributions and also to speculate as to why certain biomarkers are present only in the extracts and asphaltenes and not produced by pyrolysis of the kerogens.

  1. A fluorescence-based analysis of aristolochic acid-derived DNA adducts.

    PubMed

    Romanov, Victor; Sidorenko, Victoria; Rosenquist, Thomas A; Whyard, Terry; Grollman, Arthur P

    2012-08-01

    Aristolochic acids (AAs), major components of plant extracts from Aristolochia species, form (after metabolic activation) pro-mutagenic DNA adducts in renal tissue. The DNA adducts can be used as biomarkers for studies of AA toxicity. Identification of these adducts is a complicated and time-consuming procedure. We present here a fast, nonisotopic, fluorescence-based assay for the detection of AA-DNA adducts in multiple samples. This approach allows analysis of AA adducts in synthetic DNA with known nucleotide composition and analysis of DNA adducts formed from chemically diverse AAs in vitro. The method can be applied to compare AA-DNA adduct formation in cells and tissues.

  2. Analysis of Chiral Carboxylic Acids in Meteorites

    NASA Technical Reports Server (NTRS)

    Burton, A. S.; Elsila, J. E.; Hein, J. E.; Aponte, J. C.; Parker, E. T.; Glavin, D. P.; Dworkin, J. P.

    2015-01-01

    our efforts to develop highly sensitive LC-MS methods for the analysis of chiral carboxylic acids including hydroxy acids.

  3. Amino acid analysis for pharmacopoeial purposes.

    PubMed

    Wahl, Oliver; Holzgrabe, Ulrike

    2016-07-01

    The impurity profile of amino acids depends strongly on the production process. Since there are many different production methods (e.g. fermentation, protein hydrolysis or chemical synthesis) universal, state of the art methods are required to determine the impurity profile of amino acids produced by all relevant competitors. At the moment TLC tests provided by the Ph. Eur. are being replaced by a very specific amino acid analysis procedure possibly missing out on currently unknown process related impurities. Production methods and possible impurities as well as separation and detection methods suitable for said impurities are subject to this review.

  4. An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum.

    PubMed

    Ahmed, Nuzhat; Barker, Gillian; Oliva, Karen; Garfin, David; Talmadge, Kenneth; Georgiou, Harry; Quinn, Michael; Rice, Greg

    2003-10-01

    Proteomic technologies are being used to discover and identify disease-associated biomarkers. The application of these technologies in the search for potential diagnostic/prognostic biomarkers in the serum of patients has been limited by the presence of highly abundant albumin and immunoglobulins that constitute approximately 60-97% of the total serum proteins. The purpose of the study was to evaluate whether treatment of human serum with Affi-Gel Blue alone or in combination with Protein A (Aurum serum protein mini kit, Bio-Rad) before two-dimensional gel electrophoresis (2-DE) analysis removed high abundance proteins to allow the visualization of low abundant proteins. Serum samples were treated with either Affi-Gel Blue or Aurum kit and then subjected to 2-DE using 11 cm, pH 4-7 isoelectric focussing strips for the first dimension and 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis for second dimension. Protein spots were visualized using a fluorescent protein dye (SYPRO Ruby, Bio-Rad). Comparison between treatment methods showed significant removal of albumin by both Affi-Gel Blue and Aurum kit and considerable differences in the protein profile of the gels after each treatment. Direct comparison between treatments revealed twenty-eight protein spots unique to Affi-Gel Blue while only two spots were unique after Aurum kit treatment. Unique spots in Affi-Gel Blue and Aurum kit treated serum were not visualized in untreated serum. Sixteen hours of Affi-Gel Blue treatment resulted in enhanced visualization of fifty-three protein spots by two-fold, thirty-one by five-fold, twelve by ten-fold and six by twenty-fold. In parallel after Aurum kit treatment two-, five-, ten- and twenty-fold enhancements of thirty, thirteen, eight and five protein spots, respectively, were observed. The pattern of increased visualization of protein spots with both treatment methods was similar. In conclusion, treatment of serum samples with Affi-Gel Blue or Aurum kit before

  5. Capillary Electrophoresis Analysis of Organic Amines and Amino Acids in Saline and Acidic Samples Using the Mars Organic Analyzer

    NASA Astrophysics Data System (ADS)

    Stockton, Amanda M.; Chiesl, Thomas N.; Lowenstein, Tim K.; Amashukeli, Xenia; Grunthaner, Frank; Mathies, Richard A.

    2009-11-01

    The Mars Organic Analyzer (MOA) has enabled the sensitive detection of amino acid and amine biomarkers in laboratory standards and in a variety of field sample tests. However, the MOA is challenged when samples are extremely acidic and saline or contain polyvalent cations. Here, we have optimized the MOA analysis, sample labeling, and sample dilution buffers to handle such challenging samples more robustly. Higher ionic strength buffer systems with pKa values near pH 9 were developed to provide better buffering capacity and salt tolerance. The addition of ethylaminediaminetetraacetic acid (EDTA) ameliorates the negative effects of multivalent cations. The optimized protocol utilizes a 75 mM borate buffer (pH 9.5) for Pacific Blue labeling of amines and amino acids. After labeling, 50 mM (final concentration) EDTA is added to samples containing divalent cations to ameliorate their effects. This optimized protocol was used to successfully analyze amino acids in a saturated brine sample from Saline Valley, California, and a subcritical water extract of a highly acidic sample from the Río Tinto, Spain. This work expands the analytical capabilities of the MOA and increases its sensitivity and robustness for samples from extraterrestrial environments that may exhibit pH and salt extremes as well as metal ions.

  6. Capillary electrophoresis analysis of organic amines and amino acids in saline and acidic samples using the Mars organic analyzer.

    PubMed

    Stockton, Amanda M; Chiesl, Thomas N; Lowenstein, Tim K; Amashukeli, Xenia; Grunthaner, Frank; Mathies, Richard A

    2009-11-01

    The Mars Organic Analyzer (MOA) has enabled the sensitive detection of amino acid and amine biomarkers in laboratory standards and in a variety of field sample tests. However, the MOA is challenged when samples are extremely acidic and saline or contain polyvalent cations. Here, we have optimized the MOA analysis, sample labeling, and sample dilution buffers to handle such challenging samples more robustly. Higher ionic strength buffer systems with pK(a) values near pH 9 were developed to provide better buffering capacity and salt tolerance. The addition of ethylaminediaminetetraacetic acid (EDTA) ameliorates the negative effects of multivalent cations. The optimized protocol utilizes a 75 mM borate buffer (pH 9.5) for Pacific Blue labeling of amines and amino acids. After labeling, 50 mM (final concentration) EDTA is added to samples containing divalent cations to ameliorate their effects. This optimized protocol was used to successfully analyze amino acids in a saturated brine sample from Saline Valley, California, and a subcritical water extract of a highly acidic sample from the Río Tinto, Spain. This work expands the analytical capabilities of the MOA and increases its sensitivity and robustness for samples from extraterrestrial environments that may exhibit pH and salt extremes as well as metal ions.

  7. Exosome analysis: a promising biomarker system with special attention to saliva.

    PubMed

    Zheng, Xiaowen; Chen, Feng; Zhang, Jieni; Zhang, Qian; Lin, Jiuxiang

    2014-11-01

    Today, exosome-related studies have become a focus in science and technology. Recently, three scientists won the Nobel Prize for determining the mechanisms of exosomal transport, making exosomes a promising biomarker system for disease diagnosis and treatment. This review provides a general introduction of exosomes and explores the recent progress on the function, application, isolation, and identification of exosomes as biomarkers in blood and other body fluids, especially in saliva. Detailed information of exosomal proteins and RNAs is discussed in the paper because of their ability to determine the function of exosomes. Due to their noninvasive assessment for quick and convenient diagnosis of diseases, salivary exosomes may well be promising biomarkers.

  8. Integrated analysis of genome-wide DNA methylation and gene expression profiles identifies potential novel biomarkers of rectal cancer

    PubMed Central

    Zhang, Jinning; Zhou, Yuhui; Dang, Shuwei; Chen, Hongsheng; Wu, Qiong; Liu, Ming

    2016-01-01

    DNA methylation was regarded as the promising biomarker for rectal cancer diagnosis. However, the optimal methylation biomarkers with ideal diagnostic performance for rectal cancer are still limited. To identify new molecular markers for rectal cancer, we mapped DNA methylation and transcriptomic profiles in the six rectal cancer and paired normal samples. Further analysis revealed the hypermethylated probes in cancer prone to be located in gene promoter. Meanwhile, transcriptome analysis presented 773 low-expressed and 1,161 over-expressed genes in rectal cancer. Correction analysis identified a panel of 36 genes with an inverse correlation between methylation and gene expression levels, including 10 known colorectal cancer related genes. From the other 26 novel marker genes, GFRA1 and GSTM2 were selected for further analysis on the basis of their biological functions. Further experiment analysis confirmed their methylation and expression status in a larger number (44) of rectal cancer samples, and ROC curves showed higher AUC than SEPT9, which has been used as a biomarker in rectal cancer. Our data suggests that aberrant DNA methylation of contiguous CpG sites in methylation array may be potential diagnostic markers of rectal cancer. PMID:27566576

  9. In-depth proteomic analysis of six types of exudative pleural effusions for nonsmall cell lung cancer biomarker discovery.

    PubMed

    Liu, Pei-Jun; Chen, Chi-De; Wang, Chih-Liang; Wu, Yi-Cheng; Hsu, Chia-Wei; Lee, Chien-Wei; Huang, Lien-Hung; Yu, Jau-Song; Chang, Yu-Sun; Wu, Chih-Ching; Yu, Chia-Jung

    2015-04-01

    Pleural effusion (PE), a tumor-proximal body fluid, may be a promising source for biomarker discovery in human cancers. Because a variety of pathological conditions can lead to PE, characterization of the relative PE proteomic profiles from different types of PEs would accelerate discovery of potential PE biomarkers specifically used to diagnose pulmonary disorders. Using quantitative proteomic approaches, we identified 772 nonredundant proteins from six types of exudative PEs, including three malignant PEs (MPE, from lung, breast, and gastric cancers), one lung cancer paramalignant PE, and two benign diseases (tuberculosis and pneumonia). Spectral counting was utilized to semiquantify PE protein levels. Principal component analysis, hierarchical clustering, and Gene Ontology of cellular process analyses revealed differential levels and functional profiling of proteins in each type of PE. We identified 30 candidate proteins with twofold higher levels (q<0.05) in lung cancer MPEs than in the two benign PEs. Three potential markers, MET, DPP4, and PTPRF, were further verified by ELISA using 345 PE samples. The protein levels of these potential biomarkers were significantly higher in lung cancer MPE than in benign diseases or lung cancer paramalignant PE. The area under the receiver-operator characteristic curve for three combined biomarkers in discriminating lung cancer MPE from benign diseases was 0.903. We also observed that the PE protein levels were more clearly discriminated in effusions in which the cytological examination was positive and that they would be useful in rescuing the false negative of cytological examination in diagnosis of nonsmall cell lung cancer-MPE. Western blotting analysis further demonstrated that MET overexpression in lung cancer cells would contribute to the elevation of soluble MET in MPE. Our results collectively demonstrate the utility of label-free quantitative proteomic approaches in establishing differential PE proteomes and

  10. Transcriptomic analysis and biomarkers (Rag1 and Igμ) for probing the immune system development in Pacific cod, Gadus macrocephalus.

    PubMed

    Mao, Ming-Guang; Li, Xing; Perálvarez-Marín, Alejandro; Jiang, Jie-Lan; Jiang, Zhi-Qiang; Wen, Shi-Hui; Lü, Hui-Qian

    2015-06-01

    Mortality (>90%) is a big concern in larval rearing facilities of Pacific cod, Gadus macrocephalus, limiting its culture presently still in the experimental stages. Understanding the immune system development of G. macrocephalus is crucial to optimize the aquaculture of this species, to improve the use of economic resources and to avoid abuse of antibiotics. For the transcriptome analysis, using an Illumina sequencing platform, 61,775,698 raw reads were acquired. After a de novo assembly, 77,561 unigenes were obtained. We have classified functionally these transcripts by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). 27 genes mainly related to hematopoietic or lymphoid organ development and somatic diversification of immune receptors have been reported for the first time in Pacific cod, and 14 Ig heavy chain (μ chain) locuses were assembled using Trinity. Based on our previous achievement, we have chosen Rag1 and Igμ as immune system development biomarkers. Full length cDNA of Rag1 and Igμ as biomarkers were obtained respectively using RACE PCR. Concerning Rag1, the deduced amino acid of Rag1 and protein immunodetection revealed a Rag1 isoform of 69 kDa, significantly different from other fish orthologs, such as Oncorhynchus mykiss (121 kDa). Phylogenetic analysis reveals a unique immune system for the Gadus genre, not exclusive for Atlantic cod, among vertebrates. Meanwhile, full length cDNA of Igμ included an ORF of 1710 bp and the deduced amino acid was composed of a leader peptide, a variable domain, CH1, CH2, Hinge, CH3, CH4 and C-terminus, which was in accordance with most teleost. Absolute quantification PCR revealed that significant expression of Rag1 appeared earlier than Igμ, 61 and 95 dph compared to 95 dph, respectively. Here we report the first transcriptomic analysis of G. macrocephalus as the starting point for genetic research on immune system development towards improving the Pacific cod aquaculture.

  11. Relation between stable isotope ratios in human red blood cells and hair: implications for using the nitrogen isotope ratio of hair as a biomarker of eicosapentaenoic acid and docosahexaenoic acid1234

    PubMed Central

    Nash, Sarah H; Kristal, Alan R; Boyer, Bert B; King, Irena B; Metzgar, Jordan S

    2009-01-01

    Background: The nitrogen isotope ratio (expressed as δ15N) of red blood cells (RBCs) is highly correlated with the RBC long-chain ω−3 (n−3) fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in Yup'ik Eskimos. Because δ15N can also be measured in hair samples, it could provide a noninvasive, retrospective biomarker for EPA and DHA intakes. Objectives: We investigated the agreement between δ15N in hair and RBCs and then evaluated the relations between hair δ15N and RBC EPA and DHA. We also assessed the agreement in carbon isotope ratios (δ13C) between hair and RBCs, because δ13C has been proposed as a dietary biomarker in other populations. Design: We assessed relations between hair and RBC δ15N and δ13C in a community-based sample of 144 Yup'ik Eskimos and examined the correlations between δ15N and RBC EPA and DHA in a subset of these participants (n = 44). Results: We showed a 1:1 relation with good agreement between hair and RBC δ15N (r = 0.91) and δ13C (r = 0.87). Hair isotope ratios were greater than RBC ratios by 1.5‰ for δ15N and by 2.3‰ for δ13C. There were strong correlations between hair δ15N and RBC EPA and DHA (r = 0.83 and 0.84, respectively). Conclusions: These results support the use of hair δ15N values as a biomarker of EPA and DHA intakes. Because hair collection is noninvasive and the samples require no special processing, studies of EPA and DHA intakes in large populations could use biomarkers rather than self-reports to assess these fatty acids. PMID:19864410

  12. The Integrated Oncology Program of the Italian Ministry of Health. Analytical and clinical validation of new biomarkers for early diagnosis: network, resources, methodology, quality control, and data analysis.

    PubMed

    Paradiso, Angelo; Mangia, Anita; Orlando, Claudio; Verderio, Paolo; Belfiglio, Maurizio; Marchetti, Antonio; Bertario, Lucio; Chiappetta, Gennaro; Gion, Massimo; Tonini, Gian Paolo; Podo, Franca; Vocaturo, Amina; Silvestrini, Rosella; Romani, Massimo; Belloni, Elena; Cavallo, Delia; Ulivi, Paola; Tommasi, Stefania; Steffan, Agostino; Russo, Antonio; Alessio, Massimo; Calistri, Daniele; Zancan, Matelda; Parrela, Paola; Broggini, Massimo; Giuseppe, Antonio; Buttitta, Fiamma; Finocchiaro, Gaetano; Mazzocco, Katia; Veronesi, Giulia; Landuzzi, Lorena; Benevolo, Maria; Mariani, Luciano; De Marco, Federico; Venuti, Aldo; Giannelli, Gianluigi; Quaranta, Michele; Trojano, Vito

    2009-01-01

    In 2007, an Italian cancer research group proposed a specific concerted action aimed at the "analytical and clinica validation of new biomarkers for early diagnosis: Network, resources, methodology, quality control, and data analysis." The proposal united 37 national operative units involved in different biomarker studies and it created a strong coordinative body with the necessary expertise in methodologies, statistical analysis, quality control, and biological resources to perform ad hoc validation studies for new biomarkers of early cancer diagnosis. The action, financed by the Italian Ministry of Health within the Integrated Oncology Program (PIO) coordinated by NCI-Istituto Tumori Bari, started in 2007 and activated 7 projects, each of which focused on disease-specific biomarker studies. Overall, the 37 participating units proposed studies on 50 biomarkers, including analytical and clinical validation procedures. Clusters of units were specifically involved in research of early-detection biomarkers for cancers of the lung, digestive tract, prostate/bladder, and nervous system, as well as female cancers. Furthermore, a cluster involved in biomarkers for bioimaging and infection-related cancers was created. The first investigators' meeting, "Analytical and clinical validation of new biomarkers for early diagnosis," was held on 9 September 2008 in Bari. During this meeting, methodological aspects, scientific programs and preliminary results were presented and discussed.

  13. Meta-Analysis of Long-Chain Omega-3 Polyunsaturated Fatty Acids (LCω-3PUFA) and Prostate Cancer

    PubMed Central

    Alexander, Dominik D.; Bassett, Julie K.; Weed, Douglas L.; Barrett, Erin Cernkovich; Watson, Heather; Harris, William

    2015-01-01

    We conducted a systematic review and meta-analysis to estimate the potential association between LCω-3PUFAs and prostate cancer (PC). A comprehensive literature search was performed through 2013 to identify prospective studies that examined dietary intakes of long-chain omega-3 polyunsaturated fatty acids (LCω-3PUFA) or blood biomarkers of LCω-3PUFA status and risk of PC. Random-effects meta-analyses were conducted to generate summary relative risk estimates (SRREs) for LCω-3PUFAs and total PC, and by stage and grade. Subgroup analyses were also conducted for specific fatty acids and other study characteristics. Twelve self-reported dietary intake and 9 biomarker studies from independent study populations were included in the analysis, with 446,243 and 14,897 total participants, respectively. No association between LCω-3PUFAs and total PC was observed (SRRE = 1.00, 95% CI: 0.93–1.09) for the dietary intake studies (high vs. low LCω-3PUFAs category comparison) or for the biomarker studies (SRRE of 1.07, 95% CI: 0.94–1.20). In general, most summary associations for the dietary intake studies were in the inverse direction, whereas the majority of summary associations for the biomarker studies were in the positive direction, but all were weak in magnitude. The results from this meta-analysis do not support an association between LCω-3PUFAs and PC. PMID:25826711

  14. Proteomic analysis of eccrine sweat: implications for the discovery of schizophrenia biomarker proteins.

    PubMed

    Raiszadeh, Michelle M; Ross, Mark M; Russo, Paul S; Schaepper, Mary Ann; Zhou, Weidong; Deng, Jianghong; Ng, Daniel; Dickson, April; Dickson, Cindy; Strom, Monica; Osorio, Carolina; Soeprono, Thomas; Wulfkuhle, Julia D; Petricoin, Emanuel F; Liotta, Lance A; Kirsch, Wolff M

    2012-04-06

    Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and multiple reaction monitoring mass spectrometry (MRM-MS) proteomics analyses were performed on eccrine sweat of healthy controls, and the results were compared with those from individuals diagnosed with schizophrenia (SZ). This is the first large scale study of the sweat proteome. First, we performed LC-MS/MS on pooled SZ samples and pooled control samples for global proteomics analysis. Results revealed a high abundance of diverse proteins and peptides in eccrine sweat. Most of the proteins identified from sweat samples were found to be different than the most abundant proteins from serum, which indicates that eccrine sweat is not simply a plasma transudate and may thereby be a source of unique disease-associated biomolecules. A second independent set of patient and control sweat samples were analyzed by LC-MS/MS and spectral counting to determine qualitative protein differential abundances between the control and disease groups. Differential abundances of selected proteins, initially determined by spectral counting, were verified by MRM-MS analyses. Seventeen proteins showed a differential abundance of approximately 2-fold or greater between the SZ pooled sample and the control pooled sample. This study demonstrates the utility of LC-MS/MS and MRM-MS as a viable strategy for the discovery and verification of potential sweat protein disease biomarkers.

  15. Gene Expression and Proteome Analysis as Sources of Biomarkers in Basal Cell Carcinoma

    PubMed Central

    Ghita, Mihaela Adriana; Voiculescu, Suzana; Rosca, Adrian E.; Moraru, Liliana; Greabu, Maria

    2016-01-01

    Basal cell carcinoma (BCC) is the world's leading skin cancer in terms of frequency at the moment and its incidence continues to rise each year, leading to profound negative psychosocial and economic consequences. UV exposure is the most important environmental factor in the development of BCC in genetically predisposed individuals, this being reflected by the anatomical distribution of lesions mainly on sun-exposed skin areas. Early diagnosis and prompt management are of crucial importance in order to prevent local tissue destruction and subsequent disfigurement. Although various noninvasive or minimal invasive techniques have demonstrated their utility in increasing diagnostic accuracy of BCC and progress has been made in its treatment options, recurrent, aggressive, and metastatic variants of BCC still pose significant challenge for the healthcare system. Analysis of gene expression and proteomic profiling of tumor cells and of tumoral microenvironment in various tissues strongly suggests that certain molecules involved in skin cancer pathogenic pathways might represent novel predictive and prognostic biomarkers in BCC. PMID:27578920

  16. Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods

    PubMed Central

    Valavanis, Ioannis; Pilalis, Eleftherios; Georgiadis, Panagiotis; Kyrtopoulos, Soterios; Chatziioannou, Aristotelis

    2015-01-01

    DNA methylation profiling exploits microarray technologies, thus yielding a wealth of high-volume data. Here, an intelligent framework is applied, encompassing epidemiological genome-scale DNA methylation data produced from the Illumina’s Infinium Human Methylation 450K Bead Chip platform, in an effort to correlate interesting methylation patterns with cancer predisposition and, in particular, breast cancer and B-cell lymphoma. Feature selection and classification are employed in order to select, from an initial set of ~480,000 methylation measurements at CpG sites, predictive cancer epigenetic biomarkers and assess their classification power for discriminating healthy versus cancer related classes. Feature selection exploits evolutionary algorithms or a graph-theoretic methodology which makes use of the semantics information included in the Gene Ontology (GO) tree. The selected features, corresponding to methylation of CpG sites, attained moderate-to-high classification accuracies when imported to a series of classifiers evaluated by resampling or blindfold validation. The semantics-driven selection revealed sets of CpG sites performing similarly with evolutionary selection in the classification tasks. However, gene enrichment and pathway analysis showed that it additionally provides more descriptive sets of GO terms and KEGG pathways regarding the cancer phenotypes studied here. Results support the expediency of this methodology regarding its application in epidemiological studies. PMID:27600245

  17. A conditional likelihood approach for regression analysis using biomarkers measured with batch-specific error.

    PubMed

    Wang, Ming; Flanders, W Dana; Bostick, Roberd M; Long, Qi

    2012-12-20

    Measurement error is common in epidemiological and biomedical studies. When biomarkers are measured in batches or groups, measurement error is potentially correlated within each batch or group. In regression analysis, most existing methods are not applicable in the presence of batch-specific measurement error in predictors. We propose a robust conditional likelihood approach to account for batch-specific error in predictors when batch effect is additive and the predominant source of error, which requires no assumptions on the distribution of measurement error. Although a regression model with batch as a categorical covariable yields the same parameter estimates as the proposed conditional likelihood approach for linear regression, this result does not hold in general for all generalized linear models, in particular, logistic regression. Our simulation studies show that the conditional likelihood approach achieves better finite sample performance than the regression calibration approach or a naive approach without adjustment for measurement error. In the case of logistic regression, our proposed approach is shown to also outperform the regression approach with batch as a categorical covariate. In addition, we also examine a 'hybrid' approach combining the conditional likelihood method and the regression calibration method, which is shown in simulations to achieve good performance in the presence of both batch-specific and measurement-specific errors. We illustrate our method by using data from a colorectal adenoma study.

  18. Serum proteomic analysis reveals potential serum biomarkers for occupational medicamentosa-like dermatitis caused by trichloroethylene.

    PubMed

    Huang, Peiwu; Ren, Xiaohu; Huang, Zhijun; Yang, Xifei; Hong, Wenxu; Zhang, Yanfang; Zhang, Hang; Liu, Wei; Huang, Haiyan; Huang, Xinfeng; Wu, Desheng; Yang, Linqing; Tang, Haiyan; Zhou, Li; Li, Xuan; Liu, Jianjun

    2014-08-17

    Trichloroethylene (TCE) is an industrial solvent with widespread occupational exposure and also a major environmental contaminant. Occupational medicamentosa-like dermatitis induced by trichloroethylene (OMLDT) is an autoimmune disease and it has become one major hazard in China. In this study, sera from 3 healthy controls and 3 OMLDT patients at different disease stages were used for a screening study by 2D-DIGE and MALDI-TOF-MS/MS. Eight proteins including transthyretin (TTR), retinol binding protein 4 (RBP4), haptoglobin, clusterin, serum amyloid A protein (SAA), apolipoprotein A-I, apolipoprotein C-III and apolipoprotein C-II were found to be significantly altered among the healthy, acute-stage, healing-stage and healed-stage groups. Specifically, the altered expression of TTR, RBP4 and haptoglobin were further validated by Western blot analysis and ELISA. Our data not only suggested that TTR, RBP4 and haptoglobin could serve as potential serum biomarkers of OMLDT, but also indicated that measurement of TTR, RBP4 and haptoglobin or their combination could help aid in the diagnosis, monitoring the progression and therapy of the disease.

  19. Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

    PubMed

    Kaczkowski, Bogumil; Tanaka, Yuji; Kawaji, Hideya; Sandelin, Albin; Andersson, Robin; Itoh, Masayoshi; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R

    2016-01-15

    Genes that are commonly deregulated in cancer are clinically attractive as candidate pan-diagnostic markers and therapeutic targets. To globally identify such targets, we compared Cap Analysis of Gene Expression profiles from 225 different cancer cell lines and 339 corresponding primary cell samples to identify transcripts that are deregulated recurrently in a broad range of cancer types. Comparing RNA-seq data from 4,055 tumors and 563 normal tissues profiled in the The Cancer Genome Atlas and FANTOM5 datasets, we identified a core transcript set with theranostic potential. Our analyses also revealed enhancer RNAs, which are upregulated in cancer, defining promoters that overlap with repetitive elements (especially SINE/Alu and LTR/ERV1 elements) that are often upregulated in cancer. Lastly, we documented for the first time upregulation of multiple copies of the REP522 interspersed repeat in cancer. Overall, our genome-wide expression profiling approach identified a comprehensive set of candidate biomarkers with pan-cancer potential, and extended the perspective and pathogenic significance of repetitive elements that are frequently activated during cancer progression.

  20. Biomarker Analysis of Samples Visually Identified as Microbial in the Eocene Green River Formation: An Analogue for Mars.

    PubMed

    Olcott Marshall, Alison; Cestari, Nicholas A

    2015-09-01

    One of the major exploration targets for current and future Mars missions are lithofacies suggestive of biotic activity. Although such lithofacies are not confirmation of biotic activity, they provide a way to identify samples for further analyses. To test the efficacy of this approach, we identified carbonate samples from the Eocene Green River Formation as "microbial" or "non-microbial" based on the macroscale morphology of their laminations. These samples were then crushed and analyzed by gas chromatography/mass spectroscopy (GC/MS) to determine their lipid biomarker composition. GC/MS analysis revealed that carbonates visually identified as "microbial" contained a higher concentration of more diverse biomarkers than those identified as "non-microbial," suggesting that this could be a viable detection strategy for selecting samples for further analysis or caching on Mars.

  1. On-line sample preconcentration with chemical derivatization of bacterial biomarkers by capillary electrophoresis: a dual strategy for integrating sample pretreatment with chemical analysis.

    PubMed

    Ptolemy, Adam S; Le Bihan, Marianne; Britz-McKibbin, Philip

    2005-11-01

    Simple, selective yet sensitive methods to quantify low-abundance bacterial biomarkers derived from complex samples are required in clinical, biological, and environmental applications. In this report, a new strategy to integrate sample pretreatment with chemical analysis is investigated using on-line preconcentration with chemical derivatization by CE and UV detection. Single-step enantioselective analysis of muramic acid (MA) and diaminopimelic acid (DAP) was achieved by CE via sample enrichment by dynamic pH junction with ortho-phthalaldehyde/N-acetyl-L-cysteine labeling directly in-capillary. The optimized method resulted in up to a 100-fold enhancement in concentration sensitivity compared to conventional off-line derivatization procedures. The method was also applied toward the detection of micromolar levels of MA and DAP excreted in the extracellular medium of Escherichia coli bacterial cell cultures. On-line preconcentration with chemical derivatization by CE represents a unique approach for conducting rapid, sensitive, and high-throughput analyses of other classes of amino acid and amino sugar metabolites with reduced sample handling, where the capillary functions simultaneously as a concentrator, microreactor, and chiral selector.

  2. Identification of Cardiac Myosin-binding Protein C as a Candidate Biomarker of Myocardial Infarction by Proteomics Analysis*

    PubMed Central

    Jacquet, Sebastien; Yin, Xiaoke; Sicard, Pierre; Clark, James; Kanaganayagam, Gajen S.; Mayr, Manuel; Marber, Michael S.

    2009-01-01

    Acute myocardial infarction (AMI) is a common cause of death for which effective treatments are available provided that diagnosis is rapid. The current diagnostic gold standards are circulating cardiac troponins I and T. However, their slow release delays diagnosis, and their persistence limits their utility in the identification of reinfarction. The aim was to identify candidate biomarkers of AMI. Isolated mouse hearts were perfused with oxygenated protein-free buffer, and coronary effluent was collected after ischemia or during matched normoxic perfusion. Effluents were analyzed using proteomics approaches based on one- or two-dimensional initial separation. Of the 459 proteins identified after ischemia with one-dimensional separation, 320 were not detected in the control coronary effluent. Among these were all classic existing biomarkers of AMI. We also identified the cardiac isoform of myosin-binding protein C in its full-length form and as a 40-kDa degradation product. This protein was not detected in the other murine organs examined, increased markedly with even trivial myocardial infarction, and could be detected in the plasma after myocardial infarction in vivo, a profile compatible with a biomarker of AMI. Two-dimensional fluorescence DIGE of ischemic and control coronary effluents identified more than 200 asymmetric spots verified by swapping dyes. Once again existing biomarkers of injury were confirmed as well as posttranslational modifications of antioxidant proteins such as peroxiredoxins. Perfusing hearts with protein-free buffers provides a platform of graded ischemic injury that allows detailed analysis of protein release and identification of candidate cardiac biomarkers like myosin-binding protein C. PMID:19721077

  3. Analysis of amino acids by miniaturised isotachophoresis.

    PubMed

    Prest, Jeff E; Baldock, Sara J; Fielden, Peter R; Goddard, Nicholas J; Brown, Bernard J Treves

    2004-10-08

    A method allowing the miniaturised isotachophoretic analysis of amino acids has been developed. To overcome the problems of carbonate contamination which occur when performing separations at alkaline pH levels glycolate was used as the leading ion. Addition of magnesium to the leading electrolyte as a counter species was found to improve the separations. The method has been used on a poly(methyl methacrylate) microdevice with integrated on-column conductivity detectors. The behaviour of a range of common amino acids was investigated and successful separations of up to seven amino acids were made. Good linearity was observed with calibration curves for aspartic acid and phenylalanine over the range 0.063-1.0 mM. Limits of detection for these two species were calculated to be 0.060 and 0.018 mM, respectively.

  4. Vibrational analysis of α-cyanohydroxycinnamic acid

    NASA Astrophysics Data System (ADS)

    Mojica, Elmer-Rico E.; Vedad, Jayson; Desamero, Ruel Z. B.

    2015-08-01

    In the present study, a comparative Raman vibrational analysis of alpha-cyano-4-hydroxycinnamic acid (4CHCA) and its derivative, alpha-cyano-3-hydroxycinnamic acid (3CHCA), was performed. The Raman spectra of the 4CHCA and 3CHCA in solid form were obtained and analyzed to determine differences between the two structurally similar derivatives. For comparison, the CHCA derivatives cyanocinnamic acid (CCA) and coumaric acid (CA) were also studied. The plausible vibrational assignments were made and matched with those obtained theoretically using density functional theory (DFT) based method employing a 6-31 g basis set. The computational wavenumbers obtained were in good agreement with the observed experimental results. This was the first reported Raman study of CCA, 3CHCA and 4CHCA.

  5. A method for the simultaneous determination of mercapturic acids as biomarkers of exposure to 2-chloroprene and epichlorohydrin in human urine.

    PubMed

    Eckert, Elisabeth; Leng, Gabriele; Gries, Wolfgang; Göen, Thomas

    2012-03-15

    We developed and validated an analytical method for the simultaneous determination of several chlorine and non-chlorine containing mercapturic acids in urine as specific metabolites of the hazardous chemicals 2-chloroprene and epichlorohydrin. The method involves an online column switching arrangement for online solid phase extraction of the analytes with subsequent analytical separation and detection using LC-MS/MS. The developed method enables for the first time the determination of Cl-MA-I (4-chloro-3-oxobutyl mercapturic acid), Cl-MA-II (4-chloro-3-hydroxybutyl mercapturic acid), Cl-MA-III (3-chloro-2-hydroxy-3-butenyl mercapturic acid) and HOBMA (4-hydroxy-3-oxobutyl mercapturic acid) as potential biomarkers of 2-chloroprene in urine. Additionally, CHPMA (3-chloro-2-hydroxypropyl mercapturic acid) as a specific metabolite of epichlorohydrin in urine and DHBMA (3,4-dihydroxybutyl mercapturic acid) can be determined. The analytical method proved to be both sensitive and reliable with detection limits ranging from 1.4 μg/L (for Cl-MA-III) to 4.2 μg/L (for HOBMA). Intra- and interday imprecision was determined to range from 4.7 to 11.8%. Due to the good accuracy and precision and the low limits of detection the developed method is well suited for application in biomonitoring studies in order to determine occupational exposure to 2-chloroprene and epichlorohydrin.

  6. Bioinformatics Multivariate Analysis Determined a Set of Phase-Specific Biomarker Candidates in a Novel Mouse Model for Viral Myocarditis

    PubMed Central

    Omura, Seiichi; Kawai, Eiichiro; Sato, Fumitaka; Martinez, Nicholas E.; Chaitanya, Ganta V.; Rollyson, Phoebe A.; Cvek, Urska; Trutschl, Marjan; Alexander, J. Steven; Tsunoda, Ikuo

    2015-01-01

    Background Myocarditis is an inflammatory disease of the cardiac muscle and is mainly caused by viral infections. Viral myocarditis has been proposed to be divided into 3 phases: the acute viral phase, the subacute immune phase, and the chronic cardiac remodeling phase. Although individualized therapy should be applied depending on the phase, no clinical or experimental studies have found biomarkers that distinguish between the 3 phases. Theiler’s murine encephalomyelitis virus belongs to the genus Cardiovirus and can cause myocarditis in susceptible mouse strains. Methods and Results Using this novel model for viral myocarditis induced with Theiler’s murine encephalomyelitis virus, we conducted multivariate analysis including echocardiography, serum troponin and viral RNA titration, and microarray to identify the biomarker candidates that can discriminate the 3 phases. Using C3H mice infected with Theiler’s murine encephalomyelitis virus on 4, 7, and 60 days post infection, we conducted bioinformatics analyses, including principal component analysis and k-means clustering of microarray data, because our traditional cardiac and serum assays, including 2-way comparison of microarray data, did not lead to the identification of a single biomarker. Principal component analysis separated heart samples clearly between the groups of 4, 7, and 60 days post infection. Representative genes contributing to the separation were as follows: 4 and 7 days post infection, innate immunity–related genes, such as Irf7 and Cxcl9; 7 and 60 days post infection, acquired immunity–related genes, such as Cd3g and H2-Aa; and cardiac remodeling–related genes, such as Mmp12 and Gpnmb. Conclusions Sets of molecules, not single molecules, identified by unsupervised principal component analysis, were found to be useful as phase-specific biomarkers. PMID:25031303

  7. iTRAQ-Based Quantitative Proteomic Analysis Identified HSC71 as a Novel Serum Biomarker for Renal Cell Carcinoma

    PubMed Central

    Zhang, Yushi; Cai, Yi; Yu, Hongyan; Li, Hanzhong

    2015-01-01

    Renal cell carcinoma (RCC) is one of the most lethal urologic cancers and about 80% of RCC are of the clear-cell type (ccRCC). However, there are no serum biomarkers for the accurate diagnosis of RCC. In this study, we performed a quantitative proteomic analysis on serum samples from ccRCC patients and control group by using isobaric tag for relative and absolute quantitation (iTRAQ) labeling and LC-MS/MS analysis to access differentially expressed proteins. Overall, 16 proteins were significantly upregulated (ratio > 1.5) and 14 proteins were significantly downregulated (ratio < 0.67) in early-stage ccRCC compared to control group. HSC71 was selected and subsequently validated by Western blot in six independent sets of patients. ELISA subsequently confirmed HSC71 as a potential serum biomarker for distinguishing RCC from benign urologic disease with an operating characteristic curve (ROC) area under the curve (AUC) of 0.86 (95% confidence interval (CI), 0.76~0.96), achieving sensitivity of 87% (95% CI 69%~96%) at a specificity of 80% (95% CI 61~92%) with a threshold of 15 ng/mL. iTRAQ-based quantitative proteomic analysis led to identification of serum HSC71 as a novel serum biomarker of RCC, particularly useful in early diagnosis of ccRCC. PMID:26425554

  8. Novel biochip platform for nucleic acid analysis.

    PubMed

    Pernagallo, Salvatore; Ventimiglia, Giorgio; Cavalluzzo, Claudia; Alessi, Enrico; Ilyine, Hugh; Bradley, Mark; Diaz-Mochon, Juan J

    2012-01-01

    This manuscript describes the use of a novel biochip platform for the rapid analysis/identification of nucleic acids, including DNA and microRNAs, with very high specificity. This approach combines a unique dynamic chemistry approach for nucleic acid testing and analysis developed by DestiNA Genomics with the STMicroelectronics In-Check platform, which comprises two microfluidic optimized and independent PCR reaction chambers, and a sequential microarray area for nucleic acid capture and identification by fluorescence. With its compact bench-top "footprint" requiring only a single technician to operate, the biochip system promises to transform and expand routine clinical diagnostic testing and screening for genetic diseases, cancers, drug toxicology and heart disease, as well as employment in the emerging companion diagnostics market.

  9. PD-L1 expression as predictive biomarker in patients with NSCLC: a pooled analysis

    PubMed Central

    Natoli, Clara; Rizzo, Sergio; Galvano, Antonio; Listì, Angela; Cicero, Giuseppe; Rolfo, Christian; Santini, Daniele; Russo, Antonio

    2016-01-01

    Background Clinical trials of immune checkpoints modulators, including both programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) inhibitors, have recently shown promising activity and tolerable toxicity in pre-treated NSCLC patients. However the predictive role of PD-L1 expression is still controversial. This pooled analysis aims to clarify the association of clinical objective responses to anti PD-1/PD-L1 monoclonal antibodies (MoAbs) and tumor PD-L1 expression in pre-treated NSCLC patients. Methods Data from published studies, that evaluated efficacy and safety of PD-1/PD-L1 inhibitors in pre-treated NSCLC patients, stratified by tumor PD-L1 expression status (immunohistochemistry, cut-off point 1%), were collected by searching in PubMed, Cochrane Library, American Society of Clinical Oncology, European Society of Medical Oncology and World Conference of Lung Cancer, meeting proceedings. Pooled Odds ratio (OR) and 95% confidence intervals (95% CIs) were calculated for the Overall Response Rate (ORR) (as evaluated by Response Evaluation Criteria in Solid Tumors, version 1.1), according to PD-L1 expression status. Results A total of seven studies, with 914 patients, were eligible. Pooled analysis showed that patients with PD-L1 positive tumors (PD-L1 tumor cell staining ≥1%), had a significantly higher ORR, compared to patients with PD-L1 negative tumors (OR: 2.44; 95% CIs: 1.61-3.68). Conclusions PD-L1 tumor over-expression seems to be associated with higher clinical activity of anti PD-1/PD-L1 MoAbs, in pre-treated NSCLC patients, suggesting a potential role of PD-L1 expression, IHC cut-off point 1%, as predictive biomarker for the selection of patients to treat with immune-checkpoint inhibitors. PMID:26918451

  10. The Relationship between Fatty Acids and Different Depression-Related Brain Regions, and Their Potential Role as Biomarkers of Response to Antidepressants

    PubMed Central

    Fernandes, Maria Fernanda; Mutch, David M.; Leri, Francesco

    2017-01-01

    Depression is a complex disorder influenced by a variety of biological and environmental factors. Due to significant heterogeneity, there are remarkable differences in how patients respond to treatment. A primary objective of psychiatric research is to identify biological markers that could be used to better predict and enhance responses to antidepressant treatments. Diet impacts various aspects of health, including depression. The fatty acid composition of the Western diet, which has a high ratio of n-6:n-3 polyunsaturated fatty acids, is associated with increased incidence of depression. The brain is rich in lipids, and dietary fatty acids act within specific brain regions to regulate processes that impact emotional behavior. This manuscript reviews existing evidence demonstrating brain region-specific fatty acid profiles, and posits that specific fatty acids may serve as predictive biomarkers of response to antidepressants. Furthermore, increasing blood levels of certain fats, such as n-3s, via dietary intervention may serve as an adjunct to improve the efficacy of antidepressants. Notably, most of the existing research regarding fats and depression-related brain regions has focused on n-3s, as compared to n-6s, monounsaturated, and saturated fats. This review article will help guide future work investigating the relationships between fatty acids, brain regions, and antidepressant efficacy. PMID:28304335

  11. Identification of EBP50 as a Specific Biomarker for Carcinogens Via the Analysis of Mouse Lymphoma Cellular Proteome

    PubMed Central

    Lee, Yoen Jung; Choi, In-Kwon; Sheen, Yhun Yhong; Park, Sue Nie; Kwon, Ho Jeong

    2012-01-01

    To identify specific biomarkers generated upon exposure of L5178Y mouse lymphoma cells to carcinogens, 2-DE and MALDI-TOF MS analysis were conducted using the cellular proteome of L5178Y cells that had been treated with the known carcinogens, 1,2-dibromoethane and O-nitrotoluene and the noncarcinogens, emodin and D-mannitol. Eight protein spots that showed a greater than 1.5-fold increase or decrease in intensity following carcinogen treatment compared with treatment with noncarcinogens were selected. Of the identified proteins, we focused on the candidate biomarker ERM-binding phosphoprotein 50 (EBP50), the expression of which was specifically increased in response to treatment with the carcinogens. The expression level of EBP50 was determined by western analysis using polyclonal rabbit anti-EBP50 antibody. Further, the expression level of EBP50 was increased in cells treated with seven additional carcinogens, verifying that EBP50 could serve as a specific biomarker for carcinogens. PMID:22434383

  12. LncRNAs act as prognostic and diagnostic biomarkers in renal cell carcinoma: a systematic review and meta-analysis

    PubMed Central

    Gu, Liangyou; Li, Xintao; Gao, Yu; Lyu, Xiangjun; Chen, Luyao; Luo, Guoxiong; Wang, Lei; Xie, Yongpeng; Duan, Junyao; Peng, Cheng; Ma, Xin

    2016-01-01

    We conducted a systematic review and meta-analysis to investigate the clinical values, including clinicopathology, prognosis, and diagnosis of different long non-coding RNAs (lncRNAs) in renal cell carcinoma (RCC). A total of 14 eligible studies, including 10 on clinicopathological features, 11 on prognosis, and 3 on diagnosis were identified. Results revealed that metastasis-associated lung adenocarcinoma transcript 1(MALAT1) expression was associated with tumor stage (odds ratio [OR], 3.46; 95% confidence interval [CI], 1.63-7.36; p=0.001). The high expression of MALAT1 could be considered a biomarker of the early detection of lymph node metastasis and predictor of poor survival in RCC patients, who likely manifested short overall survival (OS; hazard ratio [HR], 2.97; 95% CI, 1.68-5.28; p<0.001). For diagnostic value, the pooled result showed that lncRNA maintained a sensitivity of 0.89 and specificity of 0.91 in RCC diagnosis, The area under the curve of 0.94 (95% CI, 0.92-0.96) for lncRNA in RCC diagnosis also indicated a significant advantage over other biomarkers. Our systematic review and meta-analysis demonstrated that lncRNAs could be considered biomarkers to detect lymph node metastasis and distant metastasis in early stages. LncRNAs could function as potential prognostic markers in RCC. LncRNAs could also display high accuracy for RCC diagnosis. PMID:27527868

  13. Biomarker panel of cardiac and skeletal muscle troponins, fatty acid binding protein 3 and myosin light chain 3 for the accurate diagnosis of cardiotoxicity and musculoskeletal toxicity in rats.

    PubMed

    Tonomura, Yutaka; Matsushima, Shuuichi; Kashiwagi, Emi; Fujisawa, Kae; Takagi, Shingo; Nishimura, Yoko; Fukushima, Ryou; Torii, Mikinori; Matsubara, Mitsunobu

    2012-12-16

    Cardiotoxicity and musculoskeletal toxicity can be life-threatening, and thus have strong impact on both the development and marketing of drugs. Because the conventional biomarkers such as aspartate aminotransferase (AST), lactate dehydrogenase (LDH), and creatine kinase (CK) have low detection power, there has been increasing interest in developing biomarkers with higher detection power. The current study examined the usefulness of several promising biomarkers, cardiac and skeletal muscle troponins (cTnI, cTnT and sTnI), fatty acid binding protein 3 (FABP3) and myosin light chain 3 (MYL3), and compared the obtained data to AST, LDH and CK in rat models treated with various myotoxic and non-myotoxic compounds (isoproterenol, metaproterenol, doxorubicin, mitoxantrone, allylamine, cyclosporine A, cyclophosphamide, aminoglutethimide, acetaminophen, methapyrilene, allylalcohol and α-naphthylisothiocyanate). These promising biomarkers were found to be superior to the conventional biomarkers, as they had a specific and abundant distribution within the heart and/or skeletal muscles; exhibited a positive correlation between the amplitude of increases and the degree of pathological alterations; had higher diagnostic accuracy for detecting pathological alterations; and had the additive effect of improving the diagnostic accuracy of conventional biomarkers. However, these promising biomarkers have several drawbacks including a rapid clearance, the fact that they are affected by renal dysfunction, and different reactivity to the mode of action of individual myotoxicants. In conclusion, the promising biomarkers cTnI, cTnT, FABP3, MYL3, and sTnI demonstrated sensitivity and specificity for cardiac and skeletal myotoxicity that was superior to those of conventional biomarkers, while we should pay attention to the drawbacks of these biomarkers when used in toxicity studies.

  14. Proteomic analysis of synovial fluid as an analytical tool to detect candidate biomarkers for knee osteoarthritis.

    PubMed

    Liao, Weixiong; Li, Zhongli; Zhang, Hao; Li, Ji; Wang, Ketao; Yang, Yimeng

    2015-01-01

    We conducted research to detect the proteomic profiles in synovial fluid (SF) from knee osteoarthritis (OA) patients to better understand the pathogenesis and aetiology of OA. Our long-term goal is to identify reliable candidate biomarkers for OA in SF. The SF proteins obtained from 10 knee OA patients and 10 non-OA patients (9 of whom were patients with a meniscus injury in the knee; 1 had a discoid meniscus in the knee, and all exhibited intact articular cartilage) were separated by two-dimensional electrophoresis (2-DE). The repeatability of the obtained protein spots regarding their intensity was tested via triplicate 2-DE of selected samples. The observed protein expression patterns were subjected to statistical analysis, and differentially expressed protein spots were identified via matrix-assisted laser desorption/ionisation-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS). Our analyses showed low intrasample variability and clear intersample variation. Among the protein spots observed on the gels, there were 29 significant differences, of which 22 corresponded to upregulation and 7 to downregulation in the OA group. One of the upregulated protein spots was confirmed to be haptoglobin by mass spectrometry, and the levels of haptoglobin in SF are positively correlated with the severity of OA (r = 0.89, P < 0.001). This study showed that 2-DE could be used under standard conditions to screen SF samples and identify a small subset of proteins in SF that are potential markers associated with OA. Spots of interest identified by mass spectrometry, such as haptoglobin, may be associated with OA severity.

  15. Crowdsourcing for translational research: analysis of biomarker expression using cancer microarrays

    PubMed Central

    Lawson, Jonathan; Robinson-Vyas, Rupesh J; McQuillan, Janette P; Paterson, Andy; Christie, Sarah; Kidza-Griffiths, Matthew; McDuffus, Leigh-Anne; Moutasim, Karwan A; Shaw, Emily C; Kiltie, Anne E; Howat, William J; Hanby, Andrew M; Thomas, Gareth J; Smittenaar, Peter

    2017-01-01

    Background: Academic pathology suffers from an acute and growing lack of workforce resource. This especially impacts on translational elements of clinical trials, which can require detailed analysis of thousands of tissue samples. We tested whether crowdsourcing – enlisting help from the public – is a sufficiently accurate method to score such samples. Methods: We developed a novel online interface to train and test lay participants on cancer detection and immunohistochemistry scoring in tissue microarrays. Lay participants initially performed cancer detection on lung cancer images stained for CD8, and we measured how extending a basic tutorial by annotated example images and feedback-based training affected cancer detection accuracy. We then applied this tutorial to additional cancer types and immunohistochemistry markers – bladder/ki67, lung/EGFR, and oesophageal/CD8 – to establish accuracy compared with experts. Using this optimised tutorial, we then tested lay participants' accuracy on immunohistochemistry scoring of lung/EGFR and bladder/p53 samples. Results: We observed that for cancer detection, annotated example images and feedback-based training both improved accuracy compared with a basic tutorial only. Using this optimised tutorial, we demonstrate highly accurate (>0.90 area under curve) detection of cancer in samples stained with nuclear, cytoplasmic and membrane cell markers. We also observed high Spearman correlations between lay participants and experts for immunohistochemistry scoring (0.91 (0.78, 0.96) and 0.97 (0.91, 0.99) for lung/EGFR and bladder/p53 samples, respectively). Conclusions: These results establish crowdsourcing as a promising method to screen large data sets for biomarkers in cancer pathology research across a range of cancers and immunohistochemical stains. PMID:27959886

  16. Biomarkers for neuromyelitis optica.

    PubMed

    Chang, Kuo-Hsuan; Ro, Long-Sun; Lyu, Rong-Kuo; Chen, Chiung-Mei

    2015-02-02

    Neuromyelitis optica (NMO) is an acquired, heterogeneous inflammatory disorder, which is characterized by recurrent optic neuritis and longitudinally extensive spinal cord lesions. The discovery of the serum autoantibody marker, anti-aquaporin 4 (anti-AQP4) antibody, revolutionizes our understanding of pathogenesis of NMO. In addition to anti-AQP4 antibody, other biomarkers for NMO are also reported. These candidate biomarkers are particularly involved in T helper (Th)17 and astrocytic damages, which play a critical role in the development of NMO lesions. Among them, IL-6 in the peripheral blood is associated with anti-AQP4 antibody production. Glial fibrillary acidic protein (GFAP) in CSF demonstrates good correlations with clinical severity of NMO relapses. Detecting these useful biomarkers may be useful in the diagnosis and evaluation of disease activity of NMO. Development of compounds targeting these biomarkers may provide novel therapeutic strategies for NMO. This article will review the related biomarker studies in NMO and discuss the potential therapeutics targeting these biomarkers.

  17. Multi-Biomarkers for Early Detection of Type 2 Diabetes, Including 10- and 12-(Z,E)-Hydroxyoctadecadienoic Acids, Insulin, Leptin, and Adiponectin.

    PubMed

    Umeno, Aya; Yoshino, Kohzoh; Hashimoto, Yoshiko; Shichiri, Mototada; Kataoka, Masatoshi; Yoshida, Yasukazu

    2015-01-01

    We have previously found that fasting plasma levels of totally assessed 10- and 12-(Z,E)-hydroxyoctadecadienoic acid (HODE) correlated well with levels of glycated hemoglobin (HbA1c) and glucose during oral glucose tolerance tests (OGTT); these levels were determined via liquid chromatography-mass spectrometry after reduction and saponification. However, 10- and 12-(Z,E)-HODE alone cannot perfectly detect early impaired glucose tolerance (IGT) and/or insulin resistance, which ultimately lead to diabetes. In this study, we randomly recruited healthy volunteers (n = 57) who had no known history of any diseases, and who were evaluated using the OGTT, the HODE biomarkers, and several additional proposed biomarkers, including retinol binding protein 4 (RBP4), adiponectin, leptin, insulin, glycoalbumin, and high sensitivity-C-reactive protein. The OGTT revealed that our volunteers included normal individuals (n = 44; Group N), "high-normal" individuals (fasting plasma glucose 100-109 mg/dL) with IGT (n = 11; Group HN+IGT), and diabetic individuals (n = 2; Group D). We then used these groups to evaluate the potential biomarkers for the early detection of type 2 diabetes. Plasma levels of RBP4 and glycoalbumin were higher in Group HN+IGT, compared to those in Group N, and fasting levels of 10- and 12-(Z,E)-HODE/linoleic acids were significantly correlated with levels of RBP4 (p = 0.003, r = 0.380) and glycoalbumin (p = 0.006, r = 0.316). Furthermore, we developed a stepwise multiple linear regression models to predict the individuals' insulin resistance index (the Matsuda Index 3). Fasting plasma levels of 10- and 12-(Z,E)-HODE/linoleic acids, glucose, insulin, and leptin/adiponectin were selected as the explanatory variables for the models. The risks of type 2 diabetes, early IGT, and insulin resistance were perfectly predicted by comparing fasting glucose levels to the estimated Matsuda Index 3 (fasting levels of 10- and 12-(Z,E)-HODE/linoleic acids, insulin, and leptin/adiponectin).

  18. A new and fast methodology to assess oxidative damage in cardiovascular diseases risk development through eVol-MEPS-UHPLC analysis of four urinary biomarkers.

    PubMed

    Mendes, Berta; Silva, Pedro; Mendonça, Isabel; Pereira, Jorge; Câmara, José S

    2013-11-15

    In this work, a new, fast and reliable methodology using a digitally controlled microextraction by packed sorbent (eVol(®)-MEPS) followed by ultra-high pressure liquid chromatography (UHPLC) analysis with photodiodes (PDA) detection, was developed to establish the urinary profile levels of four putative oxidative stress biomarkers (OSBs) in healthy subjects and patients evidencing cardiovascular diseases (CVDs). This data was used to verify the suitability of the selected OSBs (uric acid-UAc, malondialdehyde-MDA, 5-(hydroxymethyl)uracil-5-HMUra and 8-hydroxy-2'-deoxyguanosine-8-oxodG) as potential biomarkers of CVDs progression. Important parameters affecting the efficiency of the extraction process were optimized, particularly stationary phase selection, pH influence, sample volume, number of extraction cycles and washing and elution volumes. The experimental conditions that allowed the best extraction efficiency, expressed in terms of total area of the target analytes and data reproducibility, includes a 10 times dilution and pH adjustment of the urine samples to 6.0, followed by a gradient elution through the C8 adsorbent with 5 times 50 µL of 0.01% formic acid and 3×50 µL of 20% methanol in 0.01% formic acid. The chromatographic separation of the target analytes was performed with a HSS T3 column (100 mm × 2.1 mm, 1.7 µm in particle size) using 0.01% formic acid 20% methanol at 250 µL min(-1). The methodology was validated in terms of selectivity, linearity, instrumental limit of detection (LOD), method limit of quantification (LOQ), matrix effect, accuracy and precision (intra-and inter-day). Good results were obtained in terms of selectivity and linearity (r(2)>0.9906), as well as the LOD and LOQ, whose values were low, ranging from 0.00005 to 0.72 µg mL(-1) and 0.00023 to 2.31 µg mL(-1), respectively. The recovery results (91.1-123.0%), intra-day (1.0-8.3%), inter-day precision (4.6-6.3%) and the matrix effect (60.1-110.3%) of e

  19. An Integrated Analysis of Heterogeneous Drug Responses in Acute Myeloid Leukemia That Enables the Discovery of Predictive Biomarkers.

    PubMed

    Chen, Weihsu C; Yuan, Julie S; Xing, Yan; Mitchell, Amanda; Mbong, Nathan; Popescu, Andreea C; McLeod, Jessica; Gerhard, Gitte; Kennedy, James A; Bogdanoski, Goce; Lauriault, Stevan; Perdu, Sofie; Merkulova, Yulia; Minden, Mark D; Hogge, Donna E; Guidos, Cynthia; Dick, John E; Wang, Jean C Y

    2016-03-01

    Many promising new cancer drugs proceed through preclinical testing and early-phase trials only to fail in late-stage clinical testing. Thus, improved models that better predict survival outcomes and enable the development of biomarkers are needed to identify patients most likely to respond to and benefit from therapy. Here, we describe a comprehensive approach in which we incorporated biobanking, xenografting, and multiplexed phospho-flow (PF) cytometric profiling to study drug response and identify predictive biomarkers in acute myeloid leukemia (AML) patients. To test the efficacy of our approach, we evaluated the investigational JAK2 inhibitor fedratinib (FED) in 64 patient samples. FED robustly reduced leukemia in mouse xenograft models in 59% of cases and was also effective in limiting the protumorigenic activity of leukemia stem cells as shown by serial transplantation assays. In parallel, PF profiling identified FED-mediated reduction in phospho-STAT5 (pSTAT5) levels as a predictive biomarker of in vivo drug response with high specificity (92%) and strong positive predictive value (93%). Unexpectedly, another JAK inhibitor, ruxolitinib (RUX), was ineffective in 8 of 10 FED-responsive samples. Notably, this outcome could be predicted by the status of pSTAT5 signaling, which was unaffected by RUX treatment. Consistent with this observed discrepancy, PF analysis revealed that FED exerted its effects through multiple JAK2-independent mechanisms. Collectively, this work establishes an integrated approach for testing novel anticancer agents that captures the inherent variability of response caused by disease heterogeneity and in parallel, facilitates the identification of predictive biomarkers that can help stratify patients into appropriate clinical trials.

  20. Wastewater analysis to monitor use of caffeine and nicotine and evaluation of their metabolites as biomarkers for population size assessment.

    PubMed

    Senta, Ivan; Gracia-Lor, Emma; Borsotti, Andrea; Zuccato, Ettore; Castiglioni, Sara

    2015-05-01

    The use of caffeine, nicotine and some major metabolites was investigated by wastewater analysis in 13 sewage treatment plants (STPs) across Italy, and their suitability was tested as qualitative and quantitative biomarkers for assessing population size and dynamics. A specific analytical method based on mass spectrometry was developed and validated in raw urban wastewater, and included two caffeine metabolites, 1-methylxanthine and 7-methylxanthine, never reported in wastewater before. All these compounds were found widely at the μg/L level. Mass loads, calculated by multiplying concentrations by the wastewater daily flow rate and normalized to the population served by each plant, were used to compare the profiles from different cities. Some regional differences were observed in the mass loads, especially for nicotine metabolites, which were significantly higher in the south than in the center and north of Italy, reflecting smoking prevalences from population surveys. There were no significant weekly trends, although the mean mass loads of caffeine and its metabolites were slightly lower during the weekend. Most caffeine and nicotine metabolites fulfilled the requirements for an ideal biomarker for the assessment of population size, i.e. being easily detectable in wastewater, stable in sewage and during sampling, and reflecting human metabolism. Nicotine metabolites were tested as quantitative biomarkers to estimate population size and the results agreed well with census data. Caffeine and its metabolites were confirmed as good qualitative biomarkers, but additional information is needed on the caffeine metabolism in relation to the multiple sources of its main metabolites. This exploratory study opens the way to the routine use of nicotine metabolites for estimating population size and dynamics.

  1. Urinary Nerve Growth Factor Could Be a Biomarker for Interstitial Cystitis/Painful Bladder Syndrome: A Meta-Analysis

    PubMed Central

    Qu, Hong-Chen; Zhang, Wei; Yan, Shi; Liu, Yi-Li; Wang, Ping

    2014-01-01

    To examine whether urinary nerve growth factor (NGF) could serve as a biomarker for interstitial cystitis/painful bladder syndrome (IC/PBS), we conducted a comprehensive meta-analysis of 9 studies. Among the studies considered, patients with IC/PBS had higher urinary NGF and NGF/Cr levels compared to those of healthy people (SMD = 1.94, 95%CI = 0.79–3.08, P = 0.0009 and SMD = 1.79, 95%CI = 0.65–2.93, P = 0.002, respectively). In addition, there was a significant difference between patients with IC/PBS and patients with overactive bladder (OAB) symptoms with respect to the urinary NGF and NGF/Cr levels (SMD = −0.62, 95%CI = −1.00–−0.24, P = 0.001 and SMD = −0.70, 95%CI = −1.01–−0.39, P<0.0001, respectively). Furthermore, patients had a significantly lower urinary NGF level after successful treatment (SMD = 1.74, 95%CI = 0.32–3.17, P = 0.02). In conclusion, urinary NGF could be a useful biomarker for the diagnosis of OAB, a urinary biomarker for the differential diagnosis of IC/PBS and OAB (when a critical urinary NGF or NGF/Cr level is needed), and a predictive biomarker to help guide treatment. PMID:25181532

  2. Role of Urinary Biomarkers in the Diagnosis of Adenoma and Colorectal Cancer: A Systematic Review and Meta-Analysis

    PubMed Central

    Altobelli, Emma; Angeletti, Paolo Matteo; Latella, Giovanni

    2016-01-01

    The growing interest in enhancing and spreading colorectal cancer (CRC) screening has been stimulating the exploration of novel biomarkers with greater sensitivity and specificity than immunochemical faecal occult blood test (iFOBT). The present study provides i) a systematic review of the urinary biomarkers that have been tested to achieve early CRC diagnosis and assess the risk of colorectal adenoma and adenocarcinoma, and ii) a meta-analysis of the data regarding the urinary prostaglandin (PG) metabolite PGE-M. As regard to gene markers, we found significantly different percent methylation of the vimentin gene in CRC patients and healthy controls (HC) (p<0.0001). Respect to metabolism of nitrogenous bases, cytidine, 1-methyladenosine, and adenosine, have higher concentrations in CRC patients than in HC (respectively, p<0.01, p=0.01, and p<0.01). As regard to spermine we found that N1,N12 diacetyl spermine (DiAcSpm) and N1, N8 diacetylspermidine (DiAcSpd) were significantly higher in CRC than in HC (respectively p=0.01 and p<0.01). Respect to PGE-M, levels were higher in CRC than in those with multiple polyposis (p<0.006) and HC subjects (p<0.0004). PGE-M seems to be the most interesting and promising urinary marker for CRC and adenoma risk assessment and for CRC screening. In conclusion, evidence suggests that urinary biomarker could have a potential role as urinary biomarkers in the diagnosis of colorectal cancer. Particularly, PGE-M seems to be the most promising urinary marker for CRC early detection. PMID:27877214

  3. Ultratrace Level Determination and Quantitative Analysis of Kidney Injury Biomarkers in Patient Samples Attained by Zinc Oxide Nanorods

    PubMed Central

    Singh, Manpreet; Alabanza, Anginelle; Gonzalez, Lorelis E.; Wang, Weiwei; Reeves, W. Brian; Hahm, Jong-in

    2016-01-01

    Determining ultratrace amounts of protein biomarkers in patient samples in a straightforward and quantitative manner is extremely important for early disease diagnosis and treatment. Here, we successfully demonstrate the novel use of zinc oxide nanorods (ZnO NRs) in the ultrasensitive and quantitative detection of two acute kidney injury (AKI)-related protein biomarkers, tumor necrosis factor (TNF)-α and interleukin (IL)-8, directly from patient samples. We first validate the ZnO NRs-based IL-8 results via comparison with those obtained from using a conventional enzyme-linked immunosorbent method in samples from 38 individuals. We further assess the full detection capability of the ZnO NRs-based technique by quantifying TNF-α, whose levels in human urine are often below the detection limits of conventional methods. Using the ZnO NR platforms, we determine the TNF-α concentrations of all 46 patient samples tested, down to the fg/mL level. Subsequently, we screen for TNF-α levels in approximately 50 additional samples collected from different patient groups in order to demonstrate a potential use of the ZnO NRs-based assay in assessing cytokine levels useful for further clinical monitoring. Our research efforts demonstrate that ZnO NRs can be straightforwardly employed in the rapid, ultrasensitive, quantitative, and simultaneous detection of multiple AKI-related biomarkers directly in patient urine samples, providing an unparalleled detection capability beyond those of conventional analysis methods. Additional key advantages of the ZnO NRs-based approach include a fast detection speed, low-volume assay condition, multiplexing ability, and easy automation/integration capability to existing fluorescence instrumentation. Therefore, we anticipate that our ZnO NRs-based detection method will be highly beneficial for overcoming the frequent challenges in early biomarker development and treatment assessment, pertaining to the facile and ultrasensitive quantification of

  4. Renal cell carcinoma: a critical analysis of metabolomic biomarkers emerging from current model systems.

    PubMed

    Rodrigues, Daniela; Monteiro, Márcia; Jerónimo, Carmen; Henrique, Rui; Belo, Luís; Bastos, Maria de Lourdes; Guedes de Pinho, Paula; Carvalho, Márcia

    2017-02-01

    Metabolomics, an emerging field of "omics" sciences, has caught wide scientific attention in the area of biomarker research for cancers in which early diagnostic biomarkers have the potential to greatly improve patient outcome, such as renal cell carcinoma (RCC). Metabolomic approaches have been successfully applied to various human RCC model systems, mostly ex vivo neoplastic renal tissues and biofluids (urine and serum) from patients with RCC. Importantly, in contrast to other cancers, only a few studies have addressed the RCC metabolome using cancer cell culture-based in vitro models. Herein, we first carried out a comprehensive review of current metabolomic data in RCC, with emphasis on metabolite disturbances and dysregulated metabolic pathways identified in each of these experimental models. We then critically analyzed the consistency of evidence in this field and whether metabolites found altered in tumor cell and tissue microenvironment are reflected in biofluids, which constitute the rationale underlying the translation of discovered metabolic biomarkers into noninvasive diagnostic tools. Finally, dominant metabolic pathways and promising metabolites as biomarkers for diagnosis and prognosis of RCC are outlined.

  5. Lipid biomarker and compound-specific isotope analysis of cave sediments: a new approach to investigating past vegetation change

    NASA Astrophysics Data System (ADS)

    Blyth, A.; Griffiths, T.; Robson, S.

    2009-12-01

    Caves are vital archives for records of terrestrial palaeoenvironmental change, as they form sheltered sediment traps capable of preserving long environmental sequences. Due to their unique role in the landscape, they are also intimately connected to the archaeology and palaeoecology of the parent region. Chemical proxy records preserved in speleothems (chemically precipitated cave deposits) have long been used as a tool in palaeoclimatic research, but clastic sediments deposited by air, water, and breakdown of the surrounding rock also have much to contribute. However, although well researched in a sedimentary context, the geochemical records contained in these deposits, especially organic parameters, have been less well-studied. Here we present the first in-depth study of the organic geochemistry of cave sediment sequences, using samples from two south-east Asian caves, and focusing on plant-derived lipid biomarkers and their associated compound-specific carbon isotope records. The work aimed to establish: whether routine extraction and analysis of compounds was feasible in this context at acceptable sample sizes; whether there was a significant vegetation-derived contribution to the record; whether the depositional mode of the sediment (colluvium, midden, channel fill etc) affects the organic composition; and whether the records show coherent and interpretable variation through time. Two sites were studied: Niah Cave in Borneo, where the sediments recovered are a mixture of colluvium and channel fill and date back to >40 ka; and Hang Boi in Vietnam, where the principal deposit is a Holocene occupation midden dominated by land-snail shells. To recover the lipid fraction 7 g aliquots of freeze-dried sediment were extracted by sonication in 95:5 dichloromethane:methanol. Excess solvent was then removed via rotary evaporation and the extracts derivatised with BF3-Methanol and BSTFA prior to analysis by GC-MS. The lipid extracts contain a range of compounds including

  6. Breast Cancer With Brain Metastases: Clinicopathologic Features, Survival, and Paired Biomarker Analysis

    PubMed Central

    Shen, Qi; Hess, Kenneth R.; Suki, Dima; Aldape, Kenneth D.; Sawaya, Raymond; Ibrahim, Nuhad K.

    2015-01-01

    Background. The aim of this study was to describe clinicopathologic features of patients with breast cancer brain metastasis (BCBM); to evaluate survival after diagnosis of BCBM; and to compare estrogen receptor (ER), progesterone receptor (PR), and HER2 expression in the paired primary and brain tumors. Materials and Methods. We identified 140 consecutive patients who underwent craniotomy for BCBM (either for diagnostic purpose or with therapeutic intent) at the University of Texas MD Anderson Cancer Center between 2002 and 2009. Results. Most patients had invasive ductal histology (91%), grade 3 tumors (67%), and positive axillary lymph node (64%). Of the tumors, 56% were ER-negative, 62% were PR-negative, 44% were HER2-positive, and 28% were triple negative (TN). Brain metastasis (BM) was solitary in 51% of patients. Median interval from breast cancer diagnosis to BM was 46 months; median survival after BM was 14.1 months. In the univariate analysis, younger age, solitary brain metastasis, and ER or PR positivity in the breast tumors were associated with longer survival. There was a statistical trend toward increased survival in HER2-positive patients compared with HER2-negative patients (18 vs. 11 months). In the multivariate analysis, predictors for longer survival included younger age, solitary brain lesion, and HER2 positivity in the breast cancer. Biomarkers were evaluated in paired primary and brain tumors in 35 patients for ER status, 34 for PR status, and 36 for HER2 status. Discordant rates were 28% for ER, 20% for PR, and 3% for HER2. Conclusion. Compared with unselected breast cancer patients at the same institution, patients with breast cancer who had brain metastases had a higher proportion of hormone receptor-negative, HER2-positive, and TN tumors. Younger age, solitary brain lesion, and HER2 expression were independent predictors of better survival in patients with BCBM. HER2 status was highly concordant between the paired primary and brain tumors

  7. Biomarker profiling and reproducibility study of MALDI-MS measurements of Escherichia coli by analysis of variance-principal component analysis.

    PubMed

    Chen, Ping; Lu, Yao; Harrington, Peter B

    2008-03-01

    Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has proved useful for the characterization of bacteria and the detection of biomarkers. Key challenges for MALDI-MS measurements of bacteria are overcoming the relatively large variability in peak intensities. A soft tool, combining analysis of variance and principal component analysis (ANOVA-PCA) (Harrington, P. D.; Vieira, N. E.; Chen, P.; Espinoza, J.; Nien, J. K.; Romero, R.; Yergey, A. L. Chemom. Intell. Lab. Syst. 2006, 82, 283-293. Harrington, P. D.; Vieira, N. E.; Espinoza, J.; Nien, J. K.; Romero, R.; Yergey, A. L. Anal. Chim. Acta. 2005, 544, 118-127) was applied to investigate the effects of the experimental factors associated with MALDI-MS studies of microorganisms. The variance of the measurements was partitioned with ANOVA and the variance of target factors combined with the residual error was subjected to PCA to provide an easy to understand statistical test. The statistical significance of these factors can be visualized with 95% Hotelling T2 confidence intervals. ANOVA-PCA is useful to facilitate the detection of biomarkers in that it can remove the variance corresponding to other experimental factors from the measurements that might be mistaken for a biomarker. Four strains of Escherichia coli at four different growth ages were used for the study of reproducibility of MALDI-MS measurements. ANOVA-PCA was used to disclose potential biomarker proteins associated with different growth stages.

  8. Analysis of cutin and suberin biomarker patterns in alluvial sedi-ments

    NASA Astrophysics Data System (ADS)

    Herschbach, Jennifer; Sesterheim, Anna; König, Frauke; Fuchs, Elmar

    2015-04-01

    Cutin and suberin are the primary source of hydrolysable aliphatic lipid polyesters in soil organic matter (SOM). They are known as geochemical biomarkers to estimate the contribution of different plant species and tissues to SOM. Despite their potential as biomarkers, cutin and suberin have received less attention as flood plain sediment biomarkers. The objectives of this study were to investigate the efficiency of cutin and suberin as biomarkers in floodplains. Therefore similarities between the lipid pattern in alluvial sediments and in the actual vegetation were considered. Lipids of plant tissues (roots, twigs, leaves) from different species (reed (e.g. Phalaris arun-diacea), Salix alba, Ulmus laevis and grassland (e.g. Carex spec.)) and of the un-derlying soils and sediments were obtained and investigated at four sites in the nature reserve Knoblauchsaue (Hessen, Germany). The four sampling sites differ not only with respect to their vegetation, but also within their distance to the river Rhine. Cutin and suberin monomers of plants and soils were analysed by alkaline hydrolysis, methylation and acetylation and subsequent gas chromatography-mass spectrometry. Resulting lipid patterns were specific for the appropriate plant species and tissues. However, the traceability of single selected lipids was decreasing alongside the soil profile, with the exception of monomers in softwood floodplain soils. Selected tissue specific lipid ratios showed a higher traceability due to strong attributions of lipid ratios in soils and roots of U. laevis and Carex spec. and in leaves of U. laevis and S. alba. In contrast, there was no accordance between the suberin specific lipid ratios in soils and roots of S. alba and P. arundiacea. The most robust interpretations were afforded when a set of multiple biomarkers (i.e. a combination of free lipid ratios and ratios of hydrolysable lipids) was used to collectively reconstruct the source vegetation of different sediment layers.

  9. Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications.

    PubMed

    Ruijter, Jan M; Pfaffl, Michael W; Zhao, Sheng; Spiess, Andrej N; Boggy, Gregory; Blom, Jochen; Rutledge, Robert G; Sisti, Davide; Lievens, Antoon; De Preter, Katleen; Derveaux, Stefaan; Hellemans, Jan; Vandesompele, Jo

    2013-01-01

    RNA transcripts such as mRNA or microRNA are frequently used as biomarkers to determine disease state or response to therapy. Reverse transcription (RT) in combination with quantitative PCR (qPCR) has become the method of choice to quantify small amounts of such RNA molecules. In parallel with the democratization of RT-qPCR and its increasing use in biomedical research or biomarker discovery, we witnessed a growth in the number of gene expression data analysis methods. Most of these methods are based on the principle that the position of the amplification curve with respect to the cycle-axis is a measure for the initial target quantity: the later the curve, the lower the target quantity. However, most methods differ in the mathematical algorithms used to determine this position, as well as in the way the efficiency of the PCR reaction (the fold increase of product per cycle) is determined and applied in the calculations. Moreover, there is dispute about whether the PCR efficiency is constant or continuously decreasing. Together this has lead to the development of different methods to analyze amplification curves. In published comparisons of these methods, available algorithms were typically applied in a restricted or outdated way, which does not do them justice. Therefore, we aimed at development of a framework for robust and unbiased assessment of curve analysis performance whereby various publicly available curve analysis methods were thoroughly compared using a previously published large clinical data set (Vermeulen et al., 2009) [11]. The original developers of these methods applied their algorithms and are co-author on this study. We assessed the curve analysis methods' impact on transcriptional biomarker identification in terms of expression level, statistical significance, and patient-classification accuracy. The concentration series per gene, together with data sets from unpublished technical performance experiments, were analyzed in order to assess the

  10. Identification and quantification of 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid glucuronide (THC-COOH-glu) in hair by ultra-performance liquid chromatography tandem mass spectrometry as a potential hair biomarker of cannabis use.

    PubMed

    Pichini, Simona; Marchei, Emilia; Martello, Simona; Gottardi, Massimo; Pellegrini, Manuela; Svaizer, Fiorenza; Lotti, Andrea; Chiarotti, Marcello; Pacifici, Roberta

    2015-04-01

    We developed and validated an ultra-high-pressure liquid chromatography-tandem mass spectrometry method to identify and quantify 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid glucuronide in hair of cannabis consumers. After hair washing with methyl alcohol and diethyl ether and subsequent addition of amiodarone as internal standard hair samples were treated with 500 μl VMA-T M3 buffer reagent for 1 h at 100 °C. After cooling, 10 μl VMA-T M3 extract were injected into chromatographic system. Chromatographic separation was carried out on a reversed phase column using a linear gradient elution with two solvents: 5 mM ammonium formate pH 3.0 (solvent A) and 0.1% formic acid in acetonitrile (solvent B). The flow rate was kept constant at 0.4 ml/min during the analysis. The separated analytes were detected with a triple quadrupole mass spectrometer operated in multiple reaction monitoring mode via positive electrospray ionization. Linear calibration curves were obtained for 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid glucuronide with correlation coefficients (r(2)) of 0.99 and a limit of quantification of 0.25 pg/mg hair. Analytical recovery was between 79.6% and 100.7% and intra- and inter-assay imprecision and inaccuracy were always lower than 15%. Ultra-high-pressure liquid chromatography-tandem mass spectrometry analysis of 20 different hair samples of cannabis consumers disclosed the presence of 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid glucuronide in the range of 0.5-8.6 pg/mg hair. These data provided a good start to consider 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid glucuronide as alternative hair biomarker of cannabis consumption.

  11. Association between n-3 polyunsaturated fatty acid content of red blood cells and inflammatory biomarkers in patients with peripheral artery disease

    PubMed Central

    Grenon, S. Marlene; Conte, Michael S.; Nosova, Emily; Alley, Hugh; Chong, Karen; Harris, William S.; Vittinghoff, Eric; Owens, Christopher D.

    2014-01-01

    Objective The n-3 polyunsaturated fatty acids (PUFA) are dietary components derived from fish oil with beneficial cardiovascular effects that may relate in part to anti-inflammatory properties. Peripheral artery disease (PAD) is characterized by a marked pro-inflammatory state. We hypothesized that the n-3 PUFA content of red blood cells (omega-3 index) would be correlated with biomarkers of inflammation and vascular function in a PAD cohort. Methods This was a cross-sectional study of subjects who presented to an outpatient vascular surgery clinic for evaluation of PAD. We used linear regression to evaluate the independent association between the omega-3 index, inflammatory biomarkers [C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), interleukin-6 (IL-6), and tumor-necrosis-factor-α (TNF-α)] and endothelial function (brachial artery flow mediated dilation [FMD]). Results 64 subjects (61 claudicants and 3 with critical limb ischemia) were recruited for the study. The mean CRP level was 5.0 ± 5.0 mg/L and the mean omega-3 index was 5.0% ± 1.8%. In an unadjusted model, the omega-3 index was negatively associated with CRP (38% increase in CRP for one standard deviation decrease in the omega-3 index; P=.007) which remained significant after adjustment for age, body-mass index, smoking, the ABI and HDL (33%; P=.04). There was also evidence for independent associations between the omega-3 index and IL-6 (P=.001). There were no significant associations between the omega-3 index and vascular function tests. Conclusions In a cohort of patients with PAD, the omega-3 index was inversely associated with biomarkers of inflammation even after adjustment for covariates including the ABI. Because patients with PAD have a high inflammatory burden, further studies should be conducted to determine if manipulation of omega-3 index via dietary changes or fish oil supplementation could improve inflammation and symptoms in these patients. PMID:23830313

  12. Singlet oxygen induced products of linoleates, 10- and 12-(Z,E)-hydroxyoctadecadienoic acids (HODE), can be potential biomarkers for early detection of type 2 diabetes.

    PubMed

    Umeno, Aya; Shichiri, Mototada; Ishida, Noriko; Hashimoto, Yoshiko; Abe, Kaori; Kataoka, Masatoshi; Yoshino, Kohzoh; Hagihara, Yoshihisa; Aki, Nanako; Funaki, Makoto; Asada, Yasuhiko; Yoshida, Yasukazu

    2013-01-01

    Current diagnostic tests such as glycemic indicators have limitations for early detection of impaired glucose tolerance (IGT), which leads to diabetes. Oxidative stress induced by various oxidants in a random and destructive manner is considered to play an important role in the pathophysiology of a number of human disorders and diseases such as impaired glucose tolerance. We have developed an improved method for the measurement of in vivo lipid peroxidation, where the presence of 8-iso-prostaglandin F2α (8-iso-PGF2α), hydroxyoctadecadienoic acids (HODEs), hydroxyeicosatetraenoic acids (HETEs), and 7-hydroxycholesterol (7-OHCh), as well as their parent molecules, linoleic acid (LA) and cholesterol (Ch), was determined by performing LC-MS/MS (for 8-iso-PGF2α, HODE, and HETE) and GC-MS (for 7-OHCh, LA, and Ch) after reduction with triphenyl phosphine and saponification by potassium hydroxide. We then applied this method to volunteers (n = 57), including normal type (n = 43), "high-normal" (fasting plasma glucose, 100-109 mg/dL, n = 7), pre-diabetic type (IGT, n = 5), and diabetic type (n = 2) subjects who are diagnosed by performing oral glucose tolerance tests (OGTTs). Several biomarkers in plasma, such as insulin, leptin, adiponectin, interleukin-6, tumor necrosis factor-α, high sensitivity-C-reactive protein, HbA1c, and glucose levels were measured during OGTT. We found that the fasting levels of (10- and 12-(Z,E)- HODE)/LA increased significantly with increasing levels of HbA1c and glucose during OGTT and with insulin secretion and resistance index. In conclusion, 10- and 12-(Z,E)-HODE may be prominent biomarkers for the early detection of IGT and "high-normal" type without OGTT.

  13. Prediction of transition from ultra-high risk to first-episode psychosis using a probabilistic model combining history, clinical assessment and fatty-acid biomarkers.

    PubMed

    Clark, S R; Baune, B T; Schubert, K O; Lavoie, S; Smesny, S; Rice, S M; Schäfer, M R; Benninger, F; Feucht, M; Klier, C M; McGorry, P D; Amminger, G P

    2016-09-20

    Current criteria identifying patients with ultra-high risk of psychosis (UHR) have low specificity, and less than one-third of UHR cases experience transition to psychosis within 3 years of initial assessment. We explored whether a Bayesian probabilistic multimodal model, combining baseline historical and clinical risk factors with biomarkers (oxidative stress, cell membrane fatty acids, resting quantitative electroencephalography (qEEG)), could improve this specificity. We analyzed data of a UHR cohort (n=40) with a 1-year transition rate of 28%. Positive and negative likelihood ratios were calculated for predictor variables with statistically significant receiver operating characteristic curves (ROCs), which excluded oxidative stress markers and qEEG parameters as significant predictors of transition. We clustered significant variables into historical (history of drug use), clinical (Positive and Negative Symptoms Scale positive, negative and general scores and Global Assessment of Function) and biomarker (total omega-3, nervonic acid) groups, and calculated the post-test probability of transition for each group and for group combinations using the odds ratio form of Bayes' rule. Combination of the three variable groups vastly improved the specificity of prediction (area under ROC=0.919, sensitivity=72.73%, specificity=96.43%). In this sample, our model identified over 70% of UHR patients who transitioned within 1 year, compared with 28% identified by standard UHR criteria. The model classified 77% of cases as very high or low risk (P>0.9, <0.1) based on history and clinical assessment, suggesting that a staged approach could be most efficient, reserving fatty-acid markers for 23% of cases remaining at intermediate probability following bedside interview.

  14. Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity.

    PubMed

    Malik, Zulezwan Ab; Cobley, James N; Morton, James P; Close, Graeme L; Edwards, Ben J; Koch, Lauren G; Britton, Steven L; Burniston, Jatin G

    2013-12-01

    Two-dimensional gel electrophoresis provides robust comparative analysis of skeletal muscle, but this technique is laborious and limited by its inability to resolve all proteins. In contrast, orthogonal separation by SDS-PAGE and reverse-phase liquid chromatography (RPLC) coupled to mass spectrometry (MS) affords deep mining of the muscle proteome, but differential analysis between samples is challenging due to the greater level of fractionation and the complexities of quantifying proteins based on the abundances of their tryptic peptides. Here we report simple, semi-automated and time efficient (i.e., 3 h per sample) proteome profiling of skeletal muscle by 1-dimensional RPLC electrospray ionisation tandem MS. Solei were analysed from rats (n = 5, in each group) bred as either high- or low-capacity runners (HCR and LCR, respectively) that exhibited a 6.4-fold difference (1,625 ± 112 m vs. 252 ± 43 m, p < 0.0001) in running capacity during a standardized treadmill test. Soluble muscle proteins were extracted, digested with trypsin and individual biological replicates (50 ng of tryptic peptides) subjected to LC-MS profiling. Proteins were identified by triplicate LC-MS/MS analysis of a pooled sample of each biological replicate. Differential expression profiling was performed on relative abundances (RA) of parent ions, which spanned three orders of magnitude. In total, 207 proteins were analysed, which encompassed almost all enzymes of the major metabolic pathways in skeletal muscle. The most abundant protein detected was type I myosin heavy chain (RA = 5,843 ± 897) and the least abundant protein detected was heat shock 70 kDa protein (RA = 2 ± 0.5). Sixteen proteins were significantly (p < 0.05) more abundant in HCR muscle and hierarchal clustering of the profiling data highlighted two protein subgroups, which encompassed proteins associated with either the respiratory chain or fatty acid oxidation. Heart-type fatty acid binding protein (FABPH) was 1.54-fold (p

  15. Analysis of plasma free amino acid profiles in canine brain tumors

    PubMed Central

    Utsugi, Shinichi; Azuma, Kazuo; Osaki, Tomohiro; Murahata, Yusuke; Tsuka, Takeshi; Ito, Norihiko; Imagawa, Tomohiro; Okamoto, Yoshiharu

    2017-01-01

    Canine brain tumors are best diagnosed using magnetic resonance imaging (MRI). However, opportunities of MRI examination are restricted due to its limited availability in veterinary facilities; thus, numerous canine brain tumors are diagnosed at an advanced stage. Therefore, development of a noninvasive diagnostic biomarker is required for the early detection of brain tumors. In the present study, plasma free amino acid (PFAA) profiles between dogs with and without brain tumors were compared. A total of 12 dogs with brain tumors, diagnosed based on clinical signs, and on the results of intracranial MRI and/or pathological examination were evaluated. In addition, eight dogs diagnosed with idiopathic epilepsy and 16 healthy dogs were also included. A liquid chromatography system with automated pre-column derivatization functionality was used to measure the levels of 20 amino acids. As a result, the levels of three amino acids (alanine, proline and isoleucine) were increased significantly (1.6-, 1.5- and 1.6-fold, respectively) in the plasma of dogs with brain tumors as compared with the levels in control dogs (all P<0.05). Thus, the PFAA levels of dogs with brain tumors differed from those of healthy dogs. The present study demonstrated that analysis of PFAA levels of dogs with brain tumors may serve as a useful biomarker for the early detection of canine brain tumors. PMID:28357072

  16. Association between erythrocyte n-3 polyunsaturated fatty acids and biomarkers of inflammation and oxidative stress in patients with and without depression.

    PubMed

    Baek, Dawon; Park, Yongsoon

    2013-10-01

    Associations between n-3 polyunsaturated fatty acids (PUFAs), inflammation, oxidative stress and the risk of depression have been suggested. We hypothesize that erythrocyte n-3 PUFAs are inversely associated with biomarkers for inflammation and oxidative stress in Koreans with and without depression. Study participants comprised 80 cases diagnosed with depression based on the Center for Epidemiological Studies Depression Scale Korea version (CES-D-K) scores ≥25 and psychiatrist confirmation and 80 age- and sex-matched healthy controls without histories of depression. Depressed patients had lower levels of n-3 PUFAs and higher circulating levels of inducible nitric oxide synthase (iNOS), superoxide dismutase, interferon-γ, and nitrotyrosine compared to the controls. CES-D-K scores and levels of iNOS and tumor necrosis factor (TNF)-α were negatively associated with Omega-3 Index (erythrocyte levels of eicosapentaenoic acid and docosahexaenoic acid) after adjusting for confounding factors. Concentrations of iNOS, TNF-α, thiobarbituric acid reactive substances, and nitrotyrosine were negatively correlated with erythrocyte levels of n-3 PUFAs, but positively with erythrocyte levels of n-6 PUFAs. Erythrocyte levels of n-3 PUFAs were inversely associated with circulating markers of inflammation and oxidative stress in Koreans with and without depression in this case control study. Future randomized controlled trials are needed to determine whether dietary or supplemental n-3 PUFAs can reduce inflammation and oxidative stress, and reduce depressive symptoms in humans.

  17. Quantitative proteomic analysis by iTRAQ for identification of candidate biomarkers in plasma from acute respiratory distress syndrome patients.

    PubMed

    Chen, Xia; Shan, Qiang; Jiang, Li; Zhu, Bo; Xi, Xiuming

    2013-11-08

    Acute respiratory distress syndrome (ARDS) is a major cause of morbidity and mortality in critical patients. Proteomic analysis of plasma from individuals with ARDS could elucidate new biomarkers for diagnosis and pathophysiology and identify potential ARDS treatment targets. In this study, we recruited 26 patients (15 controls, 11 ARDS). The ARDS group was subdivided into two groups depending on the type of injury: (1) direct lung injury (AD) and (2) indirect lung injury (AI). Using iTRAQ (isobaric tags for relative and absolute quantitation) analysis, we identified 2429 peptides representing 132 plasma proteins. Among these, 16 were differentially expressed in ARDS patients, including 11 overlapping proteins between the AI and AD group and 5 AI-specific proteins. Protein annotation revealed that lipid transport and complement activation were significantly enriched in the biological process category, and lipid transporter, transporter, and serine-type peptidase activities were significantly enriched in the molecular function category. IPA (Ingenuity Pathway Analysis) signaling pathways revealed that the overlapping proteins were involved in a variety of signaling pathways, including those underlying acute phase response; liver X receptor/retinoid X receptor (LXR/RXR) and farnesoid X (FXR)/RXR activation; clathrin-mediated endocytosis; atherosclerosis; interleukin (IL)-12; complement system; and cytokine, nitric oxide, and reactive oxygen species production in macrophages. We present the first proteomic analysis of ARDS plasma using the iTRAQ approach. Our data provide new biomarker candidates and shed light on potential pathological mechanisms underlying ARDS.

  18. Accounting for measurement error in biomarker data and misclassification of subtypes in the analysis of tumor data.

    PubMed

    Nevo, Daniel; Zucker, David M; Tamimi, Rulla M; Wang, Molin

    2016-12-30

    A common paradigm in dealing with heterogeneity across tumors in cancer analysis is to cluster the tumors into subtypes using marker data on the tumor, and then to analyze each of the clusters separately. A more specific target is to investigate the association between risk factors and specific subtypes and to use the results for personalized preventive treatment. This task is usually carried out in two steps-clustering and risk factor assessment. However, two sources of measurement error arise in these problems. The first is the measurement error in the biomarker values. The second is the misclassification error when assigning observations to clusters. We consider the case with a specified set of relevant markers and propose a unified single-likelihood approach for normally distributed biomarkers. As an alternative, we consider a two-step procedure with the tumor type misclassification error taken into account in the second-step risk factor analysis. We describe our method for binary data and also for survival analysis data using a modified version of the Cox model. We present asymptotic theory for the proposed estimators. Simulation results indicate that our methods significantly lower the bias with a small price being paid in terms of variance. We present an analysis of breast cancer data from the Nurses' Health Study to demonstrate the utility of our method. Copyright © 2016 John Wiley & Sons, Ltd.

  19. Nontargeted metabolomic analysis and "commercial-homophyletic" comparison-induced biomarkers verification for the systematic chemical differentiation of five different parts of Panax ginseng.

    PubMed

    Qiu, Shi; Yang, Wen-Zhi; Yao, Chang-Liang; Qiu, Zhi-Dong; Shi, Xiao-Jian; Zhang, Jing-Xian; Hou, Jin-Jun; Wang, Qiu-Rong; Wu, Wan-Ying; Guo, De-An

    2016-07-01

    A key segment in authentication of herbal medicines is the establishment of robust biomarkers that embody the intrinsic metabolites difference independent of the growing environment or processing technics. We present a strategy by nontargeted metabolomics and "Commercial-homophyletic" comparison-induced biomarkers verification with new bioinformatic vehicles, to improve the efficiency and reliability in authentication of herbal medicines. The chemical differentiation of five different parts (root, leaf, flower bud, berry, and seed) of Panax ginseng was illustrated as a case study. First, an optimized ultra-performance liquid chromatography/quadrupole time-of-flight-MS(E) (UPLC/QTOF-MS(E)) approach was established for global metabolites profiling. Second, UNIFI™ combined with search of an in-house library was employed to automatically characterize the metabolites. Third, pattern recognition multivariate statistical analysis of the MS(E) data of different parts of commercial and homophyletic samples were separately performed to explore potential biomarkers. Fourth, potential biomarkers deduced from commercial and homophyletic root and leaf samples were cross-compared to infer robust biomarkers. Fifth, discriminating models by artificial neutral network (ANN) were established to identify different parts of P. ginseng. Consequently, 164 compounds were characterized, and 11 robust biomarkers enabling the differentiation among root, leaf, flower bud, and berry, were discovered by removing those structurally unstable and possibly processing-related ones. The ANN models using the robust biomarkers managed to exactly discriminate four different parts and root adulterant with leaf as well. Conclusively, biomarkers verification using homophyletic samples conduces to the discovery of robust biomarkers. The integrated strategy facilitates authentication of herbal medicines in a more efficient and more intelligent manner.

  20. CYP3A Specifically Catalyzes 1β-Hydroxylation of Deoxycholic Acid: Characterization and Enzymatic Synthesis of a Potential Novel Urinary Biomarker for CYP3A Activity.

    PubMed

    Hayes, Martin A; Li, Xue-Qing; Grönberg, Gunnar; Diczfalusy, Ulf; Andersson, Tommy B

    2016-09-01

    The endogenous bile acid metabolite 1β-hydroxy-deoxycholic acid (1β-OH-DCA) excreted in human urine may be used as a sensitive CYP3A biomarker in drug development reflecting in vivo CYP3A activity. An efficient and stereospecific enzymatic synthesis of 1β-OH-DCA was developed using a Bacillus megaterium (BM3) cytochrome P450 (P450) mutant, and its structure was confirmed by nuclear magnetic resonance (NMR) spectroscopy. A [(2)H4]-labeled analog of 1β-OH-DCA was also prepared. The major hydroxylated metabolite of deoxycholic acid (DCA) in human liver microsomal incubations was identified as 1β-OH-DCA by comparison with the synthesized reference analyzed by UPLC-HRMS. Its formation was strongly inhibited by CYP3A inhibitor ketoconazole. Screening of 21 recombinant human cytochrome P450 (P450) enzymes showed that, with the exception of extrahepatic CYP46A1, the most abundant liver P450 subfamily CYP3A, including CYP3A4, 3A5, and 3A7, specifically catalyzed 1β-OH-DCA formation. This indicated that 1β-hydroxylation of DCA may be a useful marker reaction for CYP3A activity in vitro. The metabolic pathways of DCA and 1β-OH-DCA in human hepatocytes were predominantly via glycine and, to a lesser extent, via taurine and sulfate conjugation. The potential utility of 1β-hydroxylation of DCA as a urinary CYP3A biomarker was illustrated by comparing the ratio of 1β-OH-DCA:DCA in a pooled spot urine sample from six healthy control subjects to a sample from one patient treated with carbamazepine, a potent CYP3A inducer; 1β-OH-DCA:DCA was considerably higher in the patient versus controls (ratio 2.8 vs. 0.4). Our results highlight the potential of 1β-OH-DCA as a urinary biomarker in clinical CYP3A DDI studies.

  1. MicroRNAs are novel non-invasive diagnostic biomarkers for pulmonary embolism: a meta-analysis

    PubMed Central

    Deng, Han-Yu; Li, Gang; Luo, Jun; Wang, Zhi-Qiang; Yang, Xiao-Yan; Liu, Lun-Xu

    2016-01-01

    Backgrounds The diagnosis of pulmonary embolism (PE) still remains difficult in clinical practice. MicroRNAs (miRNAs) have been widely investigated as biomarkers for various diseases. However, the diagnostic biomarker value of miRNAs in the diagnosis of PE is unclear. Therefore, we conducted this meta-analysis to establish the diagnostic power of miRNAs for PE diagnosis. Methods A systematic literature search in PubMed and Embase was conducted to identify relevant studies dated up to July 22, 2016. Data on sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR) were pooled from those included studies. Summary receiver operating characteristic (SROC) curves were used to summarize overall diagnostic power of miRNAs for PE diagnosis. Results A total of three studies with five types of miRNAs covering 254 participants were included in our meta-analysis. The overall pooled results for sensitivity, specificity, PLR, NLR, and DOR of miRNAs for PE diagnosis were 0.83 [95% confidence intervals (CI): 0.67–0.92], 0.85 (95% CI: 0.72–0.92), 5.4 (95% CI: 2.7–10.9), 0.20 (95% CI: 0.10–0.44), and 26.00 (95% CI: 7.00–101.00), respectively. The area under the SROC curve was 0.90 (95% CI: 0.87–0.92). Even though heterogeneity was observed in the analysis of sensitivity, there was no evidence of publication bias. Conclusions MiRNAs could serve as novel non-invasive diagnostic biomarkers of PE with a relatively high diagnostic power. More researches, however, are needed to explore the diagnostic as well as therapeutic values of miRNAs for PE. PMID:28149552

  2. A correlation study applied to biomarkers of internal and effective dose for acrylonitrile and 4-aminobiphenyl in smokers.

    PubMed

    Scherer, Gerhard; Newland, Kirk; Papadopoulou, Ermioni; Minet, Emmanuel

    2014-06-01

    The urinary metabolites 2-cyanoethylmercapturic acid and 4-aminobiphenyl have been correlated with tobacco smoke exposure. Similarly, 2-cyanoethylvaline and 4-aminobiphenyl haemoglobin adducts have been used as biomarkers of effective dose for the exposure to acrylonitrile and 4-aminobiphenyl, respectively. Each pair of biomarkers is derived from the same parent chemical; however, the correlation between the urinary and the haemoglobin biomarkers has not been investigated. Using clinical study samples, we report a weak correlation between urinary and haemoglobin biomarkers due to different accumulation and elimination rates. Time course analysis showed that a reduction in exposure was paralleled by a delayed reduction in haemoglobin adducts.

  3. An online automatic sample cleanup system for the quantitative detection of the benzene exposure biomarker S-phenylmercapturic acid in human urine by electrospray ionization tandem mass spectrometry.

    PubMed

    Liao, Pao-Chi; Li, Chien-Ming; Lin, Lung-Cheng; Hung, Chien-Wen; Shih, Tung-Sheng

    2002-01-01

    An online automatic sample cleanup system was developed for use with electrospray ionization tandem mass spectrometry (ESI-MS-MS) for the quantitative detection of the benzene exposure biomarker S-phenylmercapturic acid (S-PMA) in human urine. The sample clean-up system was constructed with an autosampling device, a reversed-phase C18 trap cartridge, a two-position switching valve, and controlling computer software and hardware. The sample cleanup system was interfaced directly with the ESI source of a triple-stage-quadrupole MS using multiple reaction monitoring of negative product ions derived from S-PMA and the internal standard as the detection mode. The calibration curve was linear using human urine spiked at concentrations from 0.23 to 100 mg/L S-PMA (R2 = 0.997). The detection limit of the analytical system for neat S-PMA standard solution was 0.04 microg/L, whereas the detection limit was estimated to be lower than 0.35 microg/L for a urine matrix containing trace amounts of S-PMA. Without tedious manual sample cleanup procedures, the analytical system is fully automatic and therefore useful for high-throughput urinary S-PMA determination. With the selectivity and the sensitivity provided by MS-MS detection, the analytical system can be used for high-throughput and accurate determination of S-PMA levels in human urinary samples as a biomarker for benzene exposure.

  4. Assimilation of toluene carbon along a bacteria-protist food chain determined by 13C-enrichment of biomarker fatty acids.

    PubMed

    Mauclaire, Laurie; Pelz, Oliver; Thullner, Martin; Abraham, Wolf-Rainer; Zeyer, Josef

    2003-12-01

    A food chain consisting of toluene, toluene-degrading Pseudomonas sp. PS+ and a bacterivorous flagellated amoebae Vahlkampfia sp. was established in a batch culture. This culture was amended with [U-13C]toluene and served as a model system to elucidate the flux of carbon in the food chain by quantifying bacterial biovolumes and 13C enrichment of phospholipid fatty acid (PLFA) biomarkers of the bacteria and the heterotrophic protists. Major PLFA detected in the batch co-culture included those derived from Pseudomonas sp. PS+ (16:1omega7c and 18:1omega7c) and Vahlkampfia sp. (20:4omega6c and 20:3omega6c). A numerical model including consumption of toluene by the bacteria and predation of the bacteria by the heterotrophic protists was adjusted to the measured toluene carbon, bacterial carbon and delta13C values of bacterial and protist biomass. Using this model, we estimated that 28+/-7% of the consumed toluene carbon was transformed into bacterial biomass, and 12+/-4% of the predated bacterial carbon was incorporated into heterotrophic protist biomass. Our study showed that the 13C enrichment of PLFA biomarkers coupled to biomass determination via biovolume calculations is a suitable method to trace carbon fluxes in protist-inclusive microbial food chains because it does not require the separation of protist cells from bacterial cells and soil particles.

  5. Monitoring urinary mercapturic acids as biomarkers of human dietary exposure to acrylamide in combination with acrylamide uptake assessment based on duplicate diets.

    PubMed

    Ruenz, Meike; Bakuradze, Tamara; Eisenbrand, Gerhard; Richling, Elke

    2016-04-01

    The present human intervention study investigated the relation between the intake of acrylamide (AA) in diets with minimized, low, and high AA contents and the levels of urinary exposure biomarkers. As biomarkers, the mercapturic acids, N-acetyl-S-(carbamoylethyl)-L-cysteine (AAMA), and N-acetyl-S-(1-carbamoyl-2-hydroxyethyl)-L-cysteine (GAMA) were monitored. The study was performed with 14 healthy male volunteers over a period of 9 days, under controlled conditions excluding any inadvertent AA exposure. Dietary exposure to AA was measured by determining AA contents in duplicates of all meals consumed by the volunteers. The study design included an initial washout period of 3 days on AA-minimized diet, resulting in dietary AA exposure not exceeding 41 ng/kg bw/d. Identical washout periods of 2 days each followed the AA exposure days (day 4, low exposure, and day 7, high exposure). At the respective AA intake days, volunteers ingested 0.6-0.8 (low exposure) or 1.3-1.8 (high exposure) μg AA/kg bw/d with their food. Both low and high AA intakes resulted in an AAMA output within 72 h corresponding to 58 % of the respective AA intake. At the end of the initial 3-day washout period, an AAMA baseline level of 93 ± 31 nmol/d was recorded, suggestive for an assumed net AA baseline exposure level of 0.2-0.3 μg AA/kg bw/d.

  6. Combined heavy mineral and biomarker analysis in silt: a novel approach for provenance studies (Indus Fan, IODP Expedition 355)

    NASA Astrophysics Data System (ADS)

    Andò, Sergio; Bratenkov, Sophia; Hahn, Annette; George, Simon; Clift, Peter D.; Garzanti, Eduardo

    2016-04-01

    A high-resolution mineralogical study of Indus Fan turbiditic sediments cored during IODP Expedition 355 (Arabian Sea Monsoon) in the Laxmi Basin was carried out to investigate and quantify the different compositional signatures encoded in the sand, silt, and clay fractions. The turbidite deposits recovered at IODP Sites U1456 and U1457 in sedimentological Unit II were chosen as the best candidate for such a study. The integrated dataset presented here was obtained by coupling traditional and innovative bulk-sediment to single-grain analytical techniques, including bulk petrography, heavy-mineral and biomarker analyses on the same samples. Reliable quantitative results even in the medium to fine silt classes, which represent the dominant sediment sizes encountered in the recovered cores, were obtained by point-counting under the microscope, assisted by Micro-Raman spectroscopy (Andò et al., 2011; 2014). Preliminary data from the studied turbidites document rich and diverse heavy mineral assemblages in both the sand and silty-sand fractions. Heavy-mineral concentrations, as well as the number of mineral species, reach a maximum in sand and tend to decrease with grain size, becoming minimal in the clay fraction. Conversely, the biomarker analysis is generally focused on the finer sediment fractions and clay, where better preservation of biomarker compounds are obtained. The two approaches are thus complementary. Because biomarkers tend to be depleted in sand and heavy minerals in clay, the medium silt fraction represents the most suitable size window for the joint application of these two techniques. Comparing heavy-mineral assemblages with biomarkers allows us to evaluate both continental and marine inputs in turbidites and the hemipelagic deposits of the Indus Fan. This new methodological approach plays a key role in the identification of the effects of climate change on marine depositional environments and helps us to differentiate among the diverse Himalayan

  7. Analysis of sea ice and phytoplankton biomarkers in marine sediments from the Nordic Seas - a calibration study

    NASA Astrophysics Data System (ADS)

    Navarro Rodriguez, A.; Cabedo Sanz, P.; Belt, S.; Brown, T.; Knies, J.; Husum, K.; Giraudeau, J.

    2012-04-01

    The work presented here is part of the Changing Arctic and SubArctic Environment program (EU CASE) which is an Initial Training Network (ITN) on climate change and marine environment and is an interdisciplinary project focussing on biological proxies. One of these proxies is the sea ice diatom biomarker IP25 which is a highly branched isoprenoid (HBI) alkene synthesised by some Arctic sea-ice diatoms and has been shown to be a specific, stable and sensitive proxy measure of Arctic sea ice when detected in underlying sediments (Belt et al., 2007). The current study focuses on two key elements: (1) An analytical calibration of IP25 isolated from marine sediments and purified using a range of chromatographic methods was conducted in order to improve the quantification of this biomarker in sediment extracts. (2) Analysis of >30 near-surface sediments from the Nordic Seas was carried out to quantify biomarkers previously suggested as indicators of open-water phytoplankton (brassicasterol) (Müller et al., 2011) and sea-ice (IP25) conditions (Belt et al., 2010). The outcomes of the biomarker analyses were used to make comparisons between proxy data and known sea ice conditions in the study area derived from satellite record over the last 20 years. The results of this study should inform longer timescale reconstructions of sea ice conditions in the Nordic sea in the future. Belt, S.T., Massé, G., Rowland. S.J., Poulin. M., Michel. C., LeBlanc. B., (2007). A novel chemical fossil of palaeo sea ice : IP25 . Organic Geochemistry 38 (16-27). Belt, S. T., Vare, L. L., Massé, G., Manners, H. R., Price, J. C., MacLachlan, S. E., Andrews, J. T. & Schmidt, S. (2010) 'Striking similarities in temporal changes to spring sea ice occurrence across the central Canadian Arctic Archipelago over the last 7000 years', Quaternary Science Reviews, 29 (25-26), pp. 3489-3504. Müller, J., Wagner, A., Fahl, K., Stein, R., Prange, M., & Lohmann, G. (2011). Towards quantitative sea ice

  8. BDNF DNA methylation changes as a biomarker of psychiatric disorders: literature review and open access database analysis.

    PubMed

    Zheleznyakova, Galina Y; Cao, Hao; Schiöth, Helgi B

    2016-06-06

    Brain-derived neurotrophic factor (BDNF) plays an important role in nervous system development and function and it is well established that BDNF is involved in the pathogenesis of a wide range of psychiatric disorders. Recently, numerous studies have associated the DNA methylation level of BDNF promoters with certain psychiatric phenotypes. In this review, we summarize data from current literature as well as from our own analysis with respect to the correlation of BDNF methylation changes with psychiatric disorders and address questions about whether DNA methylation related to the BDNF can be useful as biomarker for specific neuropsychiatric disorders.

  9. Applications of cellular fatty acid analysis.

    PubMed Central

    Welch, D F

    1991-01-01

    More than ever, new technology is having an impact on the tools of clinical microbiologists. The analysis of cellular fatty acids by gas-liquid chromatography (GLC) has become markedly more practical with the advent of the fused-silica capillary column, computer-controlled chromatography and data analysis, simplified sample preparation, and a commercially available GLC system dedicated to microbiological applications. Experience with applications in diagnostic microbiology ranges from substantial success in work with mycobacteria, legionellae, and nonfermentative gram-negative bacilli to minimal involvement with fungi and other nonbacterial agents. GLC is a good alternative to other means for the identification of mycobacteria or legionellae because it is rapid, specific, and independent of other specialized testing, e.g., DNA hybridization. Nonfermenters show features in their cellular fatty acid content that are useful in identifying species and, in some cases, subspecies. Less frequently encountered nonfermenters, including those belonging to unclassified groups, can ideally be characterized by GLC. Information is just beginning to materialize on the usefulness of cellular fatty acids for the identification of gram-positive bacteria and anaerobes, despite the traditional role of GLC in detecting metabolic products as an aid to identification of anaerobes. When species identification of coagulase-negative staphylococci is called for, GLC may offer an alternative to biochemical testing. Methods for direct analysis of clinical material have been developed, but in practical and economic terms they are not yet ready for use in the clinical laboratory. Direct analysis holds promise for detecting markers of infection due to an uncultivable agent or in clinical specimens that presently require cultures and prolonged incubation to yield an etiologic agent. PMID:1747860

  10. Hydrocyclone/Filter for Concentrating Biomarkers from Soil

    NASA Technical Reports Server (NTRS)

    Ponce, Adrian; Obenhuber, Donald

    2008-01-01

    The hydrocyclone-filtration extractor (HFE), now undergoing development, is a simple, robust apparatus for processing large amounts of soil to extract trace amounts of microorganisms, soluble organic compounds, and other biomarkers from soil and to concentrate the extracts in amounts sufficient to enable such traditional assays as cell culturing, deoxyribonucleic acid (DNA) analysis, and isotope analysis. Originally intended for incorporation into a suite of instruments for detecting signs of life on Mars, the HFE could also be used on Earth for similar purposes, including detecting trace amounts of biomarkers or chemical wastes in soils.

  11. A Microfluidic Immunostaining System Enables Quality Assured and Standardized Immunohistochemical Biomarker Analysis

    PubMed Central

    Kwon, Seyong; Cho, Chang Hyun; Kwon, Youngmee; Lee, Eun Sook; Park, Je-Kyun

    2017-01-01

    Immunohistochemistry (IHC) plays an important role in biomarker-driven cancer therapy. Although there has been a high demand for standardized and quality assured IHC, it has rarely been achieved due to the complexity of IHC testing and the subjective validation-based process flow of IHC quality control. We present here a microfluidic immunostaining system for the standardization of IHC by creating a microfluidic linearly graded antibody (Ab)-staining device and a reference cell microarray. Unlike conventional efforts, our system deals primarily with the screening of biomarker staining conditions for quantitative quality assurance testing in IHC. We characterized the microfluidic matching of Ab staining intensity using three HER2 Abs produced by different manufacturers. The quality of HER2 Ab was also validated using tissues of breast cancer patients, demonstrating that our system is an efficient and powerful tool for the standardization and quality assurance of IHC. PMID:28378835

  12. The 3-hydroxy fatty acids as biomarkers for quantification and characterization of endotoxins and Gram-negative bacteria in atmospheric aerosols in Hong Kong

    NASA Astrophysics Data System (ADS)

    Lee, Alex K. Y.; Chan, Chak K.; Fang, Ming; Lau, Arthur P. S.

    Endotoxins from Gram-negative bacteria have received much attention because they could elicit strong pro-inflammatory responses in the human respiratory tract. In this study, 3-hydroxy fatty acids (3-OH FAs) with carbon chain lengths from 10 to 18 (C10-C18) were employed as biomarkers to quantify and characterize the endotoxins and Gram-negative bacterial community in atmospheric aerosols. Gas chromatography-mass spectrometry (GC-MS) was utilized for quantification of this biomarker in fine (PM 2.5) and coarse (PM 2.5-10) particulates collected by high volume samplers simultaneously at a rural and an urban site in Hong Kong. The geometric mean concentrations of the endotoxins were 5.5 and 1.35 ng m -3 in fine and coarse particulates at the rural site, respectively. At the urban site, the corresponding concentrations were 9.4 and 2.80 ng m -3 in fine and coarse particulates, respectively. It is found that 70-80% of the total endotoxins are associated with the fine particulates. Significant higher endotoxin levels at the urban site were observed throughout the 8-month study period. This could possibly relate to the heavier human activities in the urban areas. The distribution patterns of the 3-OH FAs with respect to carbon number are similar between the rural and urban sites regardless of particle sizes. The C10 and C16 were predominant and accounted for about 40-50% of the total 3-OH FAs. Furthermore, the odd carbon chain length 3-OH FAs constituted a non-negligible fraction (15-25%) of the total 3-OH FAs. The biologically active endotoxins estimated as the sum of C12 and C14 portions in this study ranged from 0.6-3.7 and 1.9-4.8 ng m -3 at the rural and urban sites, respectively. Applying the biomarker-to-microbial mass conversion factors, the dry mass loading of the Gram-negative bacteria are in the order of 10-10 2 ng m -3 in atmospheric aerosol. This study also demonstrates that the biomarker (3-OH FAs) approach yields much more quantitative information such as

  13. [Analysis of citric acid and citrates. Citric acid and urolithiasis].

    PubMed

    Leskovar, P

    1979-08-01

    In the first part the physico-chemical, analytic chemical and physiologic biochemical properties of the citric acid are discussed. In the second part the author enters the role of the citric acid in the formation of uric calculi. In the third part is reported on the individual methods of the determination of citric acid and the method practised in the author's laboratory is described.

  14. Biomarker identification and pathway analysis of preeclampsia based on serum metabolomics.

    PubMed

    Chen, Tingting; He, Ping; Tan, Yong; Xu, Dongying

    2017-02-07

    Preeclampsia presents serious risk of both maternal and fetal morbidity and mortality. Biomarkers for the detection of preeclampsia are critical for risk assessment and targeted intervention. The goal of this study is to screen potential biomarkers for the diagnosis of preeclampsia and to illuminate the pathogenesis of preeclampsia development based on the differential expression network. Two groups of subjects, including healthy pregnant women, subjects with preeclampsia, were recruited for this study. The metabolic profiles of all of the subjects' serum were obtained by liquid chromatography quadruple time-of-flight mass spectrometry. Correlation between metabolites was analyzed by bioinformatics technique. Results showed that the PC(14:0/00), proline betaine and proline were potential sensitive and specific biomarkers for preeclampsia diagnosis and prognosis. Perturbation of corresponding biological pathways, such as iNOS signaling, nitric oxide signaling in the cardiovascular system, mitochondrial dysfunction were responsible for the pathogenesis of preeclampsia. This study indicated that the metabolic profiling had a good clinical significance in the diagnosis of preeclampsia as well as in the study of its pathogenesis.

  15. Microdevices integrating affinity columns and capillary electrophoresis for multi-biomarker analysis in human serum

    PubMed Central

    Yang, Weichun; Yu, Ming; Sun, Xiuhua; Woolley, Adam T.

    2010-01-01

    Summary Biomarkers in human body fluids have great potential for use in screening for diseases such as cancer and diabetes, diagnosis, determining the effectiveness of treatments, and detecting recurrence. Present 96-well immunoassay technology effectively analyzes large numbers of samples; however, this approach is more expensive and less time effective on single or a few samples. In contrast, microfluidic systems are well suited for assaying small numbers of specimens in a point-of-care setting, provided suitable procedures are developed to work within peak capacity constraints when analyzing complex mixtures like human blood serum. Here, we developed integrated microdevices with an affinity column and capillary electrophoresis channels to isolate and quantitate a panel of proteins in complex matrices. To form an affinity column, a thin film of a reactive polymer was photopolymerized in a microchannel, and four antibodies were covalently immobilized to it. The retained protein amounts were consistent from chip to chip, demonstrating reproducibility. Furthermore, the signals from four fluorescently labeled proteins captured on-column were in the same range after rinsing, indicating the column has little bias toward any of the four antibodies or their antigens. These affinity columns have been integrated with capillary electrophoresis separation, enabling us to simultaneously quantify four protein biomarkers in human blood serum in the low ng/mL range using either a calibration curve or standard addition. Our systems provide a fast, integrated and automated platform for multiple biomarker quantitation in complex media such as human blood serum. PMID:20664867

  16. Global transcriptome analysis of formalin-fixed prostate cancer specimens identifies biomarkers of disease recurrence

    PubMed Central

    Long, Qi; Xu, Jianpeng; Osunkoya, Adeboye O.; Sannigrahi, Soma; Johnson, Brent A.; Zhou, Wei; Gillespie, Theresa; Park, Jong Y.; Nam, Robert K.; Sugar, Linda; Stanimirovic, Aleksandra; Seth, Arun K.; Petros, John A.; Moreno, Carlos S.

    2014-01-01

    Prostate cancer remains the second leading cause of cancer death in American men and there is an unmet need for biomarkers to identify patients with aggressive disease. In an effort to identify biomarkers of recurrence, we performed global RNA sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, defining a 24-gene signature panel. The 24 genes in this panel function in cell cycle progression, angiogenesis, hypoxia, apoptosis, PI3K signaling, steroid metabolism, translation, chromatin modification and transcription. Sixteen genes have been associated with cancer with five specifically associated with prostate cancer (BTG2, IGFBP3, SIRT1, MXI1 and FDPS). Validation was performed on an independent publicly available dataset of 140 patients, where the new signature panel outperformed markers published previously in terms of predicting biochemical recurrence (BCR). Our work also identified differences in gene expression between Gleason Pattern 4+3 and 3+4 tumors, including several genes involved in the epithelial to mesenchymal transition and developmental pathways. Overall, this study defines a novel biomarker panel that has the potential to improve the clinical management of prostate cancer. PMID:24713434

  17. Critical analysis of soil invertebrate biomarkers: a field case study in Avonmouth, UK.

    PubMed

    Weeks, Jason M; Spurgeon, David J; Svendsen, Claus; Hankard, Peter K; Kammenga, Jan E; Dallinger, Reinhard; Köhler, Heinz-R; Simonsen, Vibeke; Scott-Fordsmand, Janeck

    2004-11-01

    During the period 1996-1999 a joint field research programme (BIOPRINT-II) funded by the European Union was undertaken. The main objective of this project was the deployment of biochemical fingerprint techniques of soil invertebrate biomarkers for assessing the exposure and effect of toxicants on soil invertebrates in the field. The aim was to apply these techniques in the field focusing on a a chronically polluted field near a lead and zinc smelter in Avonmouth (UK). Therefore six sites were selected from which organisms were either sampled or transplanted to or from the laboratory. The project has provided a unique opportunity to apply a series of biological test methodologies in order to determine the hazard posed to soil sustainability and by inference soil biodiversity and function. This work has attempted to understand the linkage between effects measured at the molecular or cellular level and relate these to changes at higher levels of biological organisation. Here we evaluated the links between biomarkers and soil function parameters. The paper aims to summarize and explore the necessary caveats that must be understood before soil biomarker test systems may be used to strengthen the risk assessment process.

  18. Ultra-high-resolution paleoenvironmental records via direct laser-based analysis of lipid biomarkers in sediment core samples

    PubMed Central

    Wörmer, Lars; Elvert, Marcus; Fuchser, Jens; Lipp, Julius Sebastian; Buttigieg, Pier Luigi; Zabel, Matthias; Hinrichs, Kai-Uwe

    2014-01-01

    Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and used in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single submillimeter-sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional liquid chromatography/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-µm resolution (∼4-y temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the ∼200-y de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and environmental factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments. PMID:25331871

  19. Custom microarray construction and analysis for determining potential biomarkers of subchronic androgen exposure in the Eastern Mosquitofish (Gambusia holbrooki)

    PubMed Central

    2013-01-01

    Background The eastern mosquitofish (Gambusia holbrooki) has the potential to become a bioindicator organism of endocrine disrupting chemicals (EDCs) due to its androgen-driven secondary sexual characteristics. However, the lack of molecular information on G. holbrooki hinders its use as a bioindicator coupled with biomarker data. While traditional gene-by-gene approaches provide insight for biomarker development, a holistic analysis would provide more rapid and expansive determination of potential biomarkers. The objective of this study was to develop and utilize a mosquitofish microarray to determine potential biomarkers of subchronic androgen exposure. To achieve this objective, two specific aims were developed: 1) Sequence a G. holbrooki cDNA library, and 2) Use microarray analysis to determine genes that are differentially regulated by subchronic androgen exposure in hepatic tissues of 17β-trenbolone (TB) exposed adult female G. holbrooki. Results A normalized library of multiple organs of male and female G. holbrooki was prepared and sequenced by the Illumina GA IIx and Roche 454 XLR70. Over 30,000 genes with e-value ≤ 10-4 were annotated and 14,758 of these genes were selected for inclusion on the microarray. Hepatic microarray analysis of adult female G. holbrooki exposed to the vehicle control or 1 μg/L of TB (a potent anabolic androgen) revealed 229 genes upregulated and 279 downregulated by TB (one-way ANOVA, p < 0.05, FDR α = 0.05, fold change > 1.5 and < −1.5). Fifteen gene ontology biological processes were enriched by TB exposure (Fisher’s Exact Test, p < 0.05). The expression levels of 17β-hydroxysteroid dehydrogenase 3 and zona pellucida glycoprotein 2 were validated by quantitative polymerase chain reaction (qPCR) (Student’s t-test, p < 0.05). Conclusions Coupling microarray data with phenotypic changes driven by androgen exposure in mosquitofish is key for developing this organism into a bioindicator for

  20. Quantitative Analysis of Single Amino Acid Variant Peptides Associated with Pancreatic Cancer in Serum by an Isobaric Labeling Quantitative Method

    PubMed Central

    2015-01-01

    Single amino acid variations are highly associated with many human diseases. The direct detection of peptides containing single amino acid variants (SAAVs) derived from nonsynonymous single nucleotide polymorphisms (SNPs) in serum can provide unique opportunities for SAAV associated biomarker discovery. In the present study, an isobaric labeling quantitative strategy was applied to identify and quantify variant peptides in serum samples of pancreatic cancer patients and other benign controls. The largest number of SAAV peptides to date in serum including 96 unique variant peptides were quantified in this quantitative analysis, of which five variant peptides showed a statistically significant difference between pancreatic cancer and other controls (p-value < 0.05). Significant differences in the variant peptide SDNCEDTPEAGYFAVAVVK from serotransferrin were detected between pancreatic cancer and controls, which was further validated by selected reaction monitoring (SRM) analysis. The novel biomarker panel obtained by combining α-1-antichymotrypsin (AACT), Thrombospondin-1 (THBS1) and this variant peptide showed an excellent diagnostic performance in discriminating pancreatic cancer from healthy controls (AUC = 0.98) and chronic pancreatitis (AUC = 0.90). These results suggest that large-scale analysis of SAAV peptides in serum may provide a new direction for biomarker discovery research. PMID:25393578

  1. Genome-Wide Association Analysis of Blood Biomarkers in Chronic Obstructive Pulmonary Disease

    PubMed Central

    Kim, Deog Kyeom; Cho, Michael H.; Hersh, Craig P.; Lomas, David A.; Miller, Bruce E.; Kong, Xiangyang; Bakke, Per; Gulsvik, Amund; Agustí, Alvar; Wouters, Emiel; Celli, Bartolome; Coxson, Harvey; Vestbo, Jørgen; MacNee, William; Yates, Julie C.; Rennard, Stephen; Litonjua, Augusto; Qiu, Weiliang; Beaty, Terri H.; Crapo, James D.; Riley, John H.; Tal-Singer, Ruth

    2012-01-01

    Rationale: A genome-wide association study (GWAS) for circulating chronic obstructive pulmonary disease (COPD) biomarkers could identify genetic determinants of biomarker levels and COPD susceptibility. Objectives: To identify genetic variants of circulating protein biomarkers and novel genetic determinants of COPD. Methods: GWAS was performed for two pneumoproteins, Clara cell secretory protein (CC16) and surfactant protein D (SP-D), and five systemic inflammatory markers (C-reactive protein, fibrinogen, IL-6, IL-8, and tumor necrosis factor-α) in 1,951 subjects with COPD. For genome-wide significant single nucleotide polymorphisms (SNPs) (P < 1 × 10−8), association with COPD susceptibility was tested in 2,939 cases with COPD and 1,380 smoking control subjects. The association of candidate SNPs with mRNA expression in induced sputum was also elucidated. Measurements and Main Results: Genome-wide significant susceptibility loci affecting biomarker levels were found only for the two pneumoproteins. Two discrete loci affecting CC16, one region near the CC16 coding gene (SCGB1A1) on chromosome 11 and another locus approximately 25 Mb away from SCGB1A1, were identified, whereas multiple SNPs on chromosomes 6 and 16, in addition to SNPs near SFTPD, had genome-wide significant associations with SP-D levels. Several SNPs affecting circulating CC16 levels were significantly associated with sputum mRNA expression of SCGB1A1 (P = 0.009–0.03). Several SNPs highly associated with CC16 or SP-D levels were nominally associated with COPD in a collaborative GWAS (P = 0.001–0.049), although these COPD associations were not replicated in two additional cohorts. Conclusions: Distant genetic loci and biomarker-coding genes affect circulating levels of COPD-related pneumoproteins. A subset of these protein quantitative trait loci may influence their gene expression in the lung and/or COPD susceptibility. Clinical trial registered with www.clinicaltrials.gov (NCT 00292552). PMID

  2. Simultaneous Quantification of Serum Nonesterified and Esterified Fatty Acids as Potential Biomarkers to Differentiate Benign Lung Diseases from Lung Cancer

    PubMed Central

    Ren, Junling; Zhang, Dan; Liu, Yujie; Zhang, Ruiqing; Fang, Huiling; Guo, Shuai; Zhou, Dan; Zhang, Mo; Xu, Yupin; Qiu, Ling; Li, Zhili

    2016-01-01

    In this study, we have employed graphene oxide as a matrix to simultaneously and directly quantify serum nonesterified and esterified fatty acids (FAs) using matrix-assisted laser/desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS). Twelve serum nonesterified FAs combined with their individual esterified FAs (i.e., C16:0, C16:1, C18:0, C18:1, C18:2, C18:3, C20:2, C20:3, C20:4, C20:5, C22:5, and C22:6) were quantified based on their calibration curves with the correlation coefficients of >0.99, along with the analytical time of <1 min each sample. As a result, serum levels of twelve total FAs (TFAs) in 1440 serum samples from 487 healthy controls (HCs), 479 patients with benign lung diseases (BLDs) and 474 patients with lung cancer (LC) were determined. Statistical analysis indicated that significantly increased levels of C16:0, C16:1, C18:0, C18:1, C18:3, C20:3, and C22:6 and decreased levels of C20:5 were observed in LC patients compared with BLDs. Receiver operating characteristic (ROC) analysis revealed that panel a (C18:2, C20:3, C20:4, C20:5, C22:5, and C22:6), panel b (C18:0, C20:4, C20:5, and C22:6), and panel c (C16:1, C18:0, C18:1, C20:3, and C22:6) have exhibited good diagnostic ability to differentiate BLDs from LC relative to clinical uses of tumor markers (CEA and Cyfra 21-1). PMID:27687250

  3. Tissue-Specific Molecular Biomarker Signatures of Type 2 Diabetes: An Integrative Analysis of Transcriptomics and Protein-Protein Interaction Data.

    PubMed

    Calimlioglu, Beste; Karagoz, Kubra; Sevimoglu, Tuba; Kilic, Elif; Gov, Esra; Arga, Kazim Yalcin

    2015-09-01

    Type 2 diabetes mellitus is a major global public health burden. A complex metabolic disease, type 2 diabetes affects multiple different tissues, demanding a "systems medicine" approach to biomarker and novel diagnostic discovery, not to mention data integration across omics-es. In the present study, transcriptomics data from different tissues including beta-cells, pancreatic islets, arterial tissue, peripheral blood mononuclear cells, liver, and skeletal muscle of 228 samples were integrated with protein-protein interaction data and genome scale metabolic models to unravel the molecular and tissue-specific biomarker signatures of type 2 diabetes mellitus. Classifying differentially expressed genes, reconstruction and topological analysis of active protein-protein interaction subnetworks indicated that genomic reprogramming depends on the type of tissue, whereas there are common signatures at different levels. Among all tissue and cell types, Mannosidase Alpha Class 1A Member 2 was the common signature at genome level, and activation-ppara reaction, which stimulates a nuclear receptor protein, was found out as the mutual reporter at metabolic level. Moreover, miR-335 and miR-16-5p came into prominence in regulation of transcription at different tissues. On the other hand, distinct signatures were observed for different tissues at the metabolome level. Various coenzyme-A derivatives were significantly enriched metabolites in pancreatic islets, whereas skeletal muscle was enriched for cholesterol, malate, L-carnitine, and several amino acids. Results have showed utmost importance concerning relations between T2D and cancer, blood coagulation, neurodegenerative diseases, and specific metabolic and signaling pathways.

  4. Insulin resistance, atherogenicity, and iron metabolism in multiple sclerosis with and without depression: Associations with inflammatory and oxidative stress biomarkers and uric acid.

    PubMed

    Oliveira, Sayonara Rangel; Kallaur, Ana Paula; Lopes, Josiane; Colado Simão, Andrea Name; Vissoci Reiche, Edna Maria; de Almeida, Elaine Regina Delicato; Morimoto, Helena Kaminami; de Carvalho Jennings de Pereira, Wildea Lice; Alfieri, Daniela Frizon; Flauzino, Tamires; de Meleck Proença, Caio; Gomes, Anna Maria; Kaimen-Maciel, Damacio Ramón; Maes, Michael

    2017-04-01

    Depression is accompanied by metabolic disorders in iron metabolism, lipoproteins, and insulin resistance. We measured plasma levels of ferritin, iron, lipids, insulin, and glucose and computed the homeostasis model assessment (HOMA2IR) and atherogenic index of plasma (AIP) in MS patients with and without depression and healthy controls. Explanatory variables were serum uric acid, interleukin (IL)-6, lipid hydroperoxides (CL-LOOH), albumin, and C-reactive protein (CRP). Depression was assessed using the Hospital Anxiety and Depression Scale (HADS), neurological disability using the Expanded Disability Status Scale (EDSS), and disease progression using ∆EDSS over five years earlier. HOMA2IR and insulin were predicted by diagnosis (increased in MS), age and body mass index (BMI); AIP by diagnosis, sex, BMI, CRP, and uric acid; triglycerides by diagnosis (higher in MS without depression), age, BMI and uric acid; ferritin by diagnosis (higher in MS), sex, CRP, and albumin; and iron by albumin. The HADS score was significantly predicted by ∆EDSS, gastro-intestinal symptoms, iron (inverse), and age. MS is characterized by significantly increased insulin resistance, which is determined by increased insulin levels; and increased ferritin, a biomarker of inflammation. Depression in MS is not associated with increased insulin resistance and atherogenicity but with lowered iron.

  5. Cholesterol, 24-Hydroxycholesterol, and 27-Hydroxycholesterol as Surrogate Biomarkers in Cerebrospinal Fluid in Mild Cognitive Impairment and Alzheimer's Disease: A Meta-Analysis.

    PubMed

    Wang, Hua-Long; Wang, Yan-Yong; Liu, Xin-Gang; Kuo, Sheng-Han; Liu, Na; Song, Qiao-Yun; Wang, Ming-Wei

    2016-01-01

    Abnormal cholesterol metabolism is an established feature of Alzheimer's disease (AD). Cerebrospinal fluid (CSF) is the fluid surrounding the central nervous system, and the protein and lipid content alterations in the CSF could be biomarkers for degenerative changes in the brain. The laboratory diagnosis of AD is limited to the analysis of three biomarkers in CSF: Aβ42, total tau, and phospho-tau. The purpose of this analysis is to systematically analyze the available data describing the biomarkers of cholesterol and its metabolites in the CSF of subjects with AD. MEDLINE, EMBASE, and the Cochrane Central database were systematically queried to collect studies that have evaluated the markers of cholesterol and its metabolites in the CSF of subjects with mild cognitive impairment (MCI) or AD and age-matched controls. Analysis of the published data shows that the levels of cholesterol are increased in MCI subjects; 24-hydroxycholesterol and 27-hydroxycholesterol are elevated in AD and MCI subjects compared to controls. There is a significant dysfunction of cholesterol metabolism in the CSF of AD subjects. This analysis indicates that in addition to the available biomarkers in the CSF, such as Aβ42, total tau, and phospho-tau, 24-hydroxycholesterol, 27-hydroxycholesterol, and cholesterol appear to be sensitive biomarkers for the evaluation of MCI and AD.

  6. Differential integrative omic analysis for mechanism insights and biomarker discovery of abnormal Savda syndrome and its unique Munziq prescription.

    PubMed

    Guo, Xia; Bakri, Iskandar; Abudula, Abulizi; Arken, Kalbinur; Mijit, Mahmut; Mamtimin, Batur; Upur, Halmurat

    2016-06-14

    Research has shown that many cancers have acommon pathophysiological origin and often present with similar symptoms. In terms of Traditional Uighur Medicine (TUM) Hilit (body fluid) theory, abnormal Savda syndrome (ASS) formed by abnormal Hilit is the common phenotype of complex diseases and in particular tumours. Abnormal Savda Munziq (ASMq), one representative of TUM, has been effective in the treatment of cancer since ancient times. Despite the physiopathology of ASS, the relationship between causative factors and the molecular mechanism of ASMq are not fully understood. The current study expanded upon earlier work by integrating traditional diagnostic approaches with others utilizing systems biology technology for the analysis of proteomic (iTRAQ) and metabolomic ((1)H-NMR) profiles of Uighur Medicine target organ lesion (liver) tumours. The candidate proteins were analyzed by enrichment analysis of the biological process and biomarker filters. Subsequently, 3Omics web-based tools were used to determine the relationships between proteins and appropriate metabolites. ELISA assay and IHC methods were used to verify the proteomic result; the protein von Willebrand factor (vWF) may be the "therapeutic window" of ASMq and biomarkers of ASS. This study is likely to be of great significance for the standardization and modernization of TUM.

  7. Differential integrative omic analysis for mechanism insights and biomarker discovery of abnormal Savda syndrome and its unique Munziq prescription

    PubMed Central

    Guo, Xia; Bakri, Iskandar; Abudula, Abulizi; Arken, Kalbinur; Mijit, Mahmut; Mamtimin, Batur; Upur, Halmurat

    2016-01-01

    Research has shown that many cancers have acommon pathophysiological origin and often present with similar symptoms. In terms of Traditional Uighur Medicine (TUM) Hilit (body fluid) theory, abnormal Savda syndrome (ASS) formed by abnormal Hilit is the common phenotype of complex diseases and in particular tumours. Abnormal Savda Munziq (ASMq), one representative of TUM, has been effective in the treatment of cancer since ancient times. Despite the physiopathology of ASS, the relationship between causative factors and the molecular mechanism of ASMq are not fully understood. The current study expanded upon earlier work by integrating traditional diagnostic approaches with others utilizing systems biology technology for the analysis of proteomic (iTRAQ) and metabolomic (1H-NMR) profiles of Uighur Medicine target organ lesion (liver) tumours. The candidate proteins were analyzed by enrichment analysis of the biological process and biomarker filters. Subsequently, 3Omics web-based tools were used to determine the relationships between proteins and appropriate metabolites. ELISA assay and IHC methods were used to verify the proteomic result; the protein von Willebrand factor (vWF) may be the “therapeutic window” of ASMq and biomarkers of ASS. This study is likely to be of great significance for the standardization and modernization of TUM. PMID:27296761

  8. Cancer biomarker discovery and validation

    PubMed Central

    Goossens, Nicolas; Nakagawa, Shigeki; Sun, Xiaochen; Hoshida, Yujin

    2015-01-01

    With the emergence of genomic profiling technologies and selective molecular targeted therapies, biomarkers play an increasingly important role in the clinical management of cancer patients. Single gene/protein or multi-gene “signature”-based assays have been introduced to measure specific molecular pathway deregulations that guide therapeutic decision-making as predictive biomarkers. Genome-based prognostic biomarkers are also available for several cancer types for potential incorporation into clinical prognostic staging systems or practice guidelines. However, there is still a large gap between initial biomarker discovery studies and their clinical translation due to the challenges in the process of cancer biomarker development. In this review we summarize the steps of biomarker development, highlight key issues in successful validation and implementation, and overview representative examples in the oncology field. We also discuss regulatory issues and future perspectives in the era of big data analysis and precision medicine. PMID:26213686

  9. A preliminary analysis of microRNA as potential clinical biomarker for schizophrenia.

    PubMed

    Sun, Xin-yang; Zhang, Jin; Niu, Wei; Guo, Wei; Song, Hong-tao; Li, Heng-yu; Fan, Hui-min; Zhao, Lin; Zhong, Ai-fang; Dai, Yun-hua; Guo, Zhong-min; Zhang, Li-yi; Lu, Jim; Zhang, Qiao-li

    2015-04-01

    MicroRNAs (miRNA, miR) have been implicated as promising blood-based biomarkers for schizophrenia patients. This study aimed to clinically validate miRNA as potential schizophrenia biomarkers. Plasma levels of 10 miRNAs were analyzed using qPCR in a cohort of 61 schizophrenia patients and 62 normal controls, as well as 25 patients particularly selected for a six-week antipsychotic treatment course. Positive And Negative Syndrome Scale (PANSS), Global Assessment Scale (GAS) and Clinical Global Impression (CGI) were administered to assess the clinical symptoms. The results demonstrated that a panel of miRNAs consisting of miR-30e, miR-181b, miR-34a, miR-346 and miR-7 had significantly increased expression levels with significant combined diagnostic value (AUC:0.713; sensitivity:35.5%; specificity:90.2%). In response to pharmacological treatment, expression levels of miR-132, miR-181b, miR-432 and miR-30e were significantly decreased. In addition, the improvement of clinical symptomatology was significantly correlated with the changes of miR-132, miR-181b, miR-212 and miR-30e expression levels. Furthermore, the decreases of plasma levels of miR-132 and miR-432 were significantly greater in high-effect subgroup than those in low-effect subgroup after six-week treatment course. We conclude that miR-30e, miR-181b, miR-34a, miR-346 and miR-7 combined as a panel are potentially useful non-invasive biomarkers for schizophrenia diagnosis. Markers miR-132, miR-181b, miR-30e and miR-432 are potential indicators for symptomatology improvements, treatment responses and prognosis for schizophrenia patients.

  10. Secretome analysis using a hollow fiber culture system for cancer biomarker discovery.

    PubMed

    Chiu, Kuo-Hsun; Chang, Ying-Hua; Liao, Pao-Chi

    2013-11-01

    Secreted proteins, collectively referred to as the secretome, were suggested as valuable biomarkers in disease diagnosis and prognosis. However, some secreted proteins from cell cultures are difficult to detect because of their intrinsically low abundance; they are frequently masked by the released proteins from lysed cells and the substantial amounts of serum proteins used in culture medium. The hollow fiber culture (HFC) system is a commercially available system composed of small fibers sealed in a cartridge shell; cells grow on the outside of the fiber. Recently, because this system can help cells grow at a high density, it has been developed and applied in a novel analytical platform for cell secretome collection in cancer biomarker discovery. This article focuses on the advantages of the HFC system, including the effectiveness of the system for collection of secretomes, and reviews the process of cell secretome collection by the HFC system and proteomic approaches to discover cancer biomarkers. The HFC system not only provides a high-density three-dimensional (3D) cell culture system to mimic tumor growth conditions in vivo but can also accommodate numerous cells in a small volume, allowing secreted proteins to be accumulated and concentrated. In addition, cell lysis rates can be greatly reduced, decreasing the amount of contamination by abundant cytosolic proteins from lysed cells. Therefore, the HFC system is useful for preparing a wide range of proteins from cell secretomes and provides an effective method for collecting higher amounts of secreted proteins from cancer cells. This article is part of a Special Issue entitled: An Updated Secretome.

  11. Novel Biomarkers of Periodontitis and/or Obesity in Saliva – An Exploratory Analysis

    PubMed Central

    Recker, Erica N.; Brogden, Kim A.; Avila-Ortiz, Gustavo; Fischer, Carol L.; Pagan-Rivera, Keyla; Dawson, Deborah V.; Smith, Katherine M.; Elangovan, Satheesh

    2015-01-01

    Objective Recent studies point to the clinical and research utility of saliva as a valuable diagnostic aid for monitoring periodontal health. The objectives of this study were to detect novel biomarkers attributed to chronic inflammation in saliva and to determine if the levels of these markers correlate with severity of periodontitis and with standard obesity measures in participants in a periodontal maintenance program. Design In this cross-sectional assessment of 63 participants, unstimulated whole saliva was collected after recording anthropometric and clinical parameters of obesity and periodontitis, respectively. The levels of interleukin-1 receptor antagonist (IL-1ra), sCD40L, granzyme B and alpha-fetoprotein (AFP) in saliva were determined using multiplex proteomic immunoassays. The correlation between the four tested biomarker concentrations and obesity/periodontal measures was determined. Results Positive correlation between fat% and granzyme B levels (r=0.292; p=0.020) and negative correlation between BMI and sCD40L (r=0.256;p=0.043) was observed. In addition, positive correlation between severity of periodontal disease and levels of IL1-ra (r=0.253; p=0.046) and negative correlation between periodontitis severity and sCD40L salivary levels (r=0.272; p=0.031) was noted. None of the above correlations remained statistically significant after multiple comparisons adjustment. After adjustment for clinical covariates, the relationship between sCD40L and periodontal severity remained suggestive (p=0.081). Conclusions Levels of four novel biomarkers of periodontitis were detectable in saliva of subjects enrolled in a periodontal maintenance program. Prospective studies with larger sample sizes and other populations are warranted to explore the diagnostic applicability of these markers. PMID:26263539

  12. Statistical considerations when analyzing biomarker data.

    PubMed

    Beam, Craig A

    2015-11-01

    Biomarkers have become, and will continue to become, increasingly important to clinical immunology research. Yet, biomarkers often present new problems and raise new statistical and study design issues to scientists working in clinical immunology. In this paper I discuss statistical considerations related to the important biomarker problems of: 1) The design and analysis of clinical studies which seek to determine whether changes from baseline in a biomarker are associated with changes in a metabolic outcome; 2) The conditions that are required for a biomarker to be considered a "surrogate"; 3) Considerations that arise when analyzing whether or not a predictive biomarker could act as a surrogate endpoint; 4) Biomarker timing relative to the clinical endpoint; 5) The problem of analyzing studies that measure many biomarkers from few subjects; and, 6) The use of statistical models when analyzing biomarker data arising from count data.

  13. Comprehensive profiling of mercapturic acid metabolites from dietary acrylamide as short-term exposure biomarkers for evaluation of toxicokinetics in rats and daily internal exposure in humans using isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry.

    PubMed

    Zhang, Yu; Wang, Qiao; Cheng, Jun; Zhang, Jingshun; Xu, Jiaojiao; Ren, Yiping

    2015-09-24

    Mercapturic acid metabolites from dietary acrylamide are important short-term exposure biomarkers for evaluating the in vivo toxicity of acrylamide. Most of studies have focused on the measurement of two metabolites, N-acetyl-S-(2-carbamoylethyl)-L-cysteine (AAMA) and N-acetyl-S-(2-carbamoyl-2-hydroxyethyl)-L-cysteine (GAMA). Thus, the comprehensive profile of acrylamide urinary metabolites cannot be fully understood. We developed an isotope dilution ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for the simultaneous determination of all four mercapturic acid adducts of acrylamide and its primary metabolite glycidamide under the electroscopy ionization negative (ESI-) mode in the present study. The limit of detection (LOD) and limit of quantification (LOQ) of the analytes ranged 0.1-0.3 ng/mL and 0.4-1.0 ng/mL, respectively. The recovery rates with low, intermediate and high spiking levels were calculated as 95.5%-105.4%, 98.2%-114.0% and 92.2%-108.9%, respectively. Acceptable within-laboratory reproducibility (RSD<7.0%) substantially supported the use of current method for robust analysis. Rapid pretreatment procedures and short run time (8 min per sample) ensured good efficiency of metabolism profiling, indicating a wide application for investigating short-term internal exposure of dietary acrylamide. Our proposed UHPLC-MS/MS method was successfully applied to the toxicokinetic study of acrylamide in rats. Meanwhile, results of human urine analysis indicated that the levels of N-acetyl-S-(2-carbamoylethyl)-L-cysteine-sulfoxide (AAMA-sul), which did not appear in the mercapturic acid metabolites in rodents, were more than the sum of GAMA and N-acetyl-S-(1-carbamoyl-2-hydroxyethyl)-L-cysteine (iso-GAMA). Thus, AAMA-sul may alternatively become a specific biomarker for investigating the acrylamide exposure in humans. Current proposed method provides a substantial methodology support for comprehensive profiling of

  14. Using Willie's Acid-Base Box for Blood Gas Analysis

    ERIC Educational Resources Information Center

    Dietz, John R.

    2011-01-01

    In this article, the author describes a method developed by Dr. William T. Lipscomb for teaching blood gas analysis of acid-base status and provides three examples using Willie's acid-base box. Willie's acid-base box is constructed using three of the parameters of standard arterial blood gas analysis: (1) pH; (2) bicarbonate; and (3) CO[subscript…

  15. Dynamics of sinking particles in northern Japan trench in the western North Pacific: biogenic chemical components and fatty acids biomarkers

    NASA Astrophysics Data System (ADS)

    Shin, K. H.; Noriki, S.; Itou, M.; Tsunogai, S.

    Biogenic opal was predominant component, and had strongly positive correlation with organic carbon in both traps. The average atomic ratios of biogenic opal and calcium carbonate (CaCO 3) were also large (7.1 and 11 in the shallow and deep trap, respectively) and the highest ratio was found in May 1995, when the biogenic opal proportion (%) to the total particle flux and C org/C inorg ratio increased concomitantly. However, transient switching of the biogenic opal and CaCO 3 ratios (0.6 and 0.8) was observed in winter 1995, which seems to be related to a warm-core ring developed in the northwestern Pacific. Downward fluxes of fatty acids as molecular markers were determined and compared with major biogenic chemical components in sinking particles. As a diatom index of fatty acids, the 16:1(n-7)/16:0 ratio is positively related to biogenic opal contribution (%) to the sinking particles in the shallow and deep traps. 20:5(n-3) proportion (%) was also correlated with opal content (%) in sinking particles in the 1-km trap. In addition, a major source of sinking fatty acids in the western North Pacific might be characterized by algal fatty acids as a diatom marker (16:1(n-7)), comparing to a zooplankton fatty acid (18:1(n-9)) in the central North Pacific and fecal pellets and coccolithophores in the eastern North Pacific, respectively. Also, PUFA index (a measure of polyunsaturated fatty acids contribution to the total fatty acids) correlated well with Chl a inventory in surface 0-50 m water. These results suggest that undegraded diatomaceous fatty acids are present in sinking particles, and the composition of fatty acids is useful to understand the origin of sinking organic particles.

  16. Integrated plasma and urine metabolomics coupled with HPLC/QTOF-MS and chemometric analysis on potential biomarkers in liver injury and hepatoprotective effects of Er-Zhi-Wan.

    PubMed

    Yao, Weifeng; Gu, Haiwei; Zhu, Jiangjiang; Barding, Gregory; Cheng, Haibo; Bao, Beihua; Zhang, Li; Ding, Anwei; Li, Wei

    2014-11-01

    Metabolomics techniques are the comprehensive assessment of endogenous metabolites in a biological system and may provide additional insight into the molecular mechanisms. Er-Zhi-Wan (EZW) is a traditional Chinese medicine formula, which contains Fructus Ligustri Lucidi (FLL) and Herba Ecliptae (HE). EZW is widely used to prevent and treat various liver injuries through the nourishment of the liver. However, the precise molecular mechanism of hepatoprotective effects has not been comprehensively explored. Here, an integrated metabolomics strategy was designed to assess the effects and possible mechanisms of EZW against carbon tetrachloride-induced liver injury, a commonly used model of both acute and chronic liver intoxication. High-performance chromatography/quadrupole time-of-flight mass spectrometry (HPLC/QTOF-MS) combined with chemometric approaches including principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were used to discover differentiating metabolites in metabolomics data of rat plasma and urine. Results indicate six differentiating metabolites, tryptophan, sphinganine, tetrahydrocorticosterone, pipecolic acid, L-2-amino-3-oxobutanoic acid and phosphoribosyl pyrophosphate, in the positive mode. Functional pathway analysis revealed that the alterations in these metabolites were associated with tryptophan metabolism, sphingolipid metabolism, steroid hormone biosynthesis, lysine degradation, glycine, serine and threonine metabolism, and pentose phosphate pathway. Of note, EZW has a potential pharmacological effect, which might be through regulating multiple perturbed pathways to the normal state. Our findings also showed that the robust integrated metabolomics techniques are promising for identifying more biomarkers and pathways and helping to clarify the function mechanisms of traditional Chinese medicine.

  17. Integrative transcriptomic meta-analysis of Parkinson’s disease and depression identifies NAMPT as a potential blood biomarker for de novo Parkinson’s disease

    PubMed Central

    Santiago, Jose A.; Littlefield, Alyssa M.; Potashkin, Judith A.

    2016-01-01

    Emerging research indicates that depression could be one of the earliest prodromal symptoms or risk factors associated with the pathogenesis of Parkinson’s disease (PD), the second most common neurodegenerative disorder worldwide, but the mechanisms underlying the association between both diseases remains unknown. Understanding the molecular networks linking these diseases could facilitate the discovery of novel diagnostic and therapeutics. Transcriptomic meta-analysis and network analysis of blood microarrays from untreated patients with PD and depression identified genes enriched in pathways related to the immune system, metabolism of lipids, glucose, fatty acids, nicotinamide, lysosome, insulin signaling and type 1 diabetes. Nicotinamide phosphoribosyltransferase (NAMPT), an adipokine that plays a role in lipid and glucose metabolism, was identified as the most significant dysregulated gene. Relative abundance of NAMPT was upregulated in blood of 99 early stage and drug-naïve PD patients compared to 101 healthy controls (HC) nested in the cross-sectional Parkinson’s Progression Markers Initiative (PPMI). Thus, here we demonstrate that shared molecular networks between PD and depression provide an additional source of biologically relevant biomarkers. Evaluation of NAMPT in a larger prospective longitudinal study including samples from other neurodegenerative diseases, and patients at risk of PD is warranted. PMID:27680512

  18. p-Coumaric acid, a novel and effective biomarker for quantifying hypoxic stress by HILIC-ESI-MS.

    PubMed

    Silina, Yuliya E; Fink-Straube, Claudia; Hanselmann, Rainer G; Peuschel, Henrike; Volmer, Dietrich A

    2016-05-01

    In this study, we report p-coumaric acid as novel and effective response marker for indirectly measuring the levels of hypoxia in normal primary bronchial epithelial cells. We developed a simple and rapid technique based on hydrophilic interaction chromatography-electrospray ionization-mass spectrometry (HILIC-ESI-MS). During 168h of hypoxia without induction of reactive oxygen species (ROS), an almost linear increase of p-coumaric acid levels was observed. We interpret the increasing p-coumaric acid concentrations during hypoxia as a result of cell damage, triggered by reduced co-enzyme Q10 levels, because the oxidative cascade was not able to supply sufficient energy. The HILIC-ESI-MS assay within p-coumaric acid exhibited a linear dynamic range from 60 to 610 ng/μL with correlation coefficient of 0.9998. The precision of the assay was ≤15% RSD and method accuracies between 97 and 108%.

  19. Ultratrace level determination and quantitative analysis of kidney injury biomarkers in patient samples attained by zinc oxide nanorods

    NASA Astrophysics Data System (ADS)

    Singh, Manpreet; Alabanza, Anginelle; Gonzalez, Lorelis E.; Wang, Weiwei; Reeves, W. Brian; Hahm, Jong-In

    2016-02-01

    Determining ultratrace amounts of protein biomarkers in patient samples in a straightforward and quantitative manner is extremely important for early disease diagnosis and treatment. Here, we successfully demonstrate the novel use of zinc oxide nanorods (ZnO NRs) in the ultrasensitive and quantitative detection of two acute kidney injury (AKI)-related protein biomarkers, tumor necrosis factor (TNF)-α and interleukin (IL)-8, directly from patient samples. We first validate the ZnO NRs-based IL-8 results via comparison with those obtained from using a conventional enzyme-linked immunosorbent method in samples from 38 individuals. We further assess the full detection capability of the ZnO NRs-based technique by quantifying TNF-α, whose levels in human urine are often below the detection limits of conventional methods. Using the ZnO NR platforms, we determine the TNF-α concentrations of all 46 patient samples tested, down to the fg per mL level. Subsequently, we screen for TNF-α levels in approximately 50 additional samples collected from different patient groups in order to demonstrate a potential use of the ZnO NRs-based assay in assessing cytokine levels useful for further clinical monitoring. Our research efforts demonstrate that ZnO NRs can be straightforwardly employed in the rapid, ultrasensitive, quantitative, and simultaneous detection of multiple AKI-related biomarkers directly in patient urine samples, providing an unparalleled detection capability beyond those of conventional analysis methods. Additional key advantages of the ZnO NRs-based approach include a fast detection speed, low-volume assay condition, multiplexing ability, and easy automation/integration capability to existing fluorescence instrumentation. Therefore, we anticipate that our ZnO NRs-based detection method will be highly beneficial for overcoming the frequent challenges in early biomarker development and treatment assessment, pertaining to the facile and ultrasensitive quantification

  20. Tolfenamic acid downregulates BACE1 and protects against lead-induced upregulation of Alzheimer's disease related biomarkers.

    PubMed

    Adwan, Lina; Subaiea, Gehad M; Zawia, Nasser H

    2014-04-01

    Environmental exposure to lead (Pb) early in life results in a latent upregulation of genes and products associated with Alzheimer's disease (AD), particularly the plaque forming protein amyloid beta (Aβ). Furthermore, animals exposed to Pb as infants develop cognitive decline and memory impairments in old age. Studies from our lab demonstrated that tolfenamic acid lowers the levels of the amyloid β precursor protein (APP) and its aggregative cleavage product Aβ by inducing the degradation of the transcription factor specificity protein 1 (Sp1). These changes were accompanied by cognitive improvement in transgenic APP knock-in mice. In this study, we examined the effects of tolfenamic acid on beta site APP cleaving enzyme 1 (BACE1) which is responsible for Aβ production and tested its ability to reverse Pb-induced upregulation in the amyloidogenic pathway. Mice were administered tolfenamic acid for one month and BACE1 gene expression as well as its enzymatic activity were analyzed in the cerebral cortex. Tolfenamic acid was also tested for its ability to reverse changes in Sp1, APP and Aβ that were upregulated by Pb in vitro. Differentiated SH-SY5Y neuroblastoma cells were either left unexposed, or sequentially exposed to Pb followed by tolfenamic acid. Our results show that tolfenamic acid reduced BACE1 gene expression and enzyme activity in mice. In neuroblastoma cells, Pb upregulated Sp1, APP and Aβ, while tolfenamic acid lowered their expression. These results along with previous data from our lab provide evidence that tolfenamic acid, a drug that has been used for decades for migraine, represents a candidate which can reduce the pathology of AD and may mitigate the damage of environmental risk factors associated with this disease.

  1. Probability of success for phase III after exploratory biomarker analysis in phase II.

    PubMed

    Götte, Heiko; Kirchner, Marietta; Sailer, Martin Oliver

    2017-02-23

    The probability of success or average power describes the potential of a future trial by weighting the power with a probability distribution of the treatment effect. The treatment effect estimate from a previous trial can be used to define such a distribution. During the development of targeted therapies, it is common practice to look for predictive biomarkers. The consequence is that the trial population for phase III is often selected on the basis of the most extreme result from phase II biomarker subgroup analyses. In such a case, there is a tendency to overestimate the treatment effect. We investigate whether the overestimation of the treatment effect estimate from phase II is transformed into a positive bias for the probability of success for phase III. We simulate a phase II/III development program for targeted therapies. This simulation allows to investigate selection probabilities and allows to compare the estimated with the true probability of success. We consider the estimated probability of success with and without subgroup selection. Depending on the true treatment effects, there is a negative bias without selection because of the weighting by the phase II distribution. In comparison, selection increases the estimated probability of success. Thus, selection does not lead to a bias in probability of success if underestimation due to the phase II distribution and overestimation due to selection cancel each other out. We recommend to perform similar simulations in practice to get the necessary information about the risk and chances associated with such subgroup selection designs.

  2. Assessing the toxicity of TBBPA and HBCD by zebrafish embryo toxicity assay and biomarker analysis.

    PubMed

    Hu, Jun; Liang, Yong; Chen, Minjie; Wang, Xiaorong

    2009-08-01

    Tetrabromobisphenol A (TBBPA) and hexabromocyclododecane (HBCD) are two of the most widely used brominated flame retardants (BFRs). The biological toxicity effect of TBBPA and HBCD was studied by means of zebrafish embryo toxicity assays in combination with three biomarkers, including superoxide dismutase (SOD), lipid peroxidation, (LPO), and heat shock protein (Hsp70). The standard zebrafish embryo assay showed that high concentrations of TBBPA (> or =0.75 mg/L) can cause lethality or malformation. For HBCD within the concentration range (0.002-10 mg/L), no endpoint was observed. Furthermore, SOD activities of zebrafish embryos exposed to TBBPA were increased with the increasing concentrations. SOD activities in the group treated by HBCD showed an increase followed by a decline. Regardless of TBBPA or HBCD, LPO were increased along with the increase of the concentration. The change pattern of Hsp70 levels was the same with LPO. All these results showed that TBBPA and HBCD could cause oxidative stress and Hsp70 overexpression, inducing acute toxicity to zebrafish embryo in a short-term exposure. The study also indicates that the zebrafish embryo assay in combination with the biomarkers is effective in aquatic environmental toxicology and risk assessment.

  3. Oncosecretomics coupled to bioenergetics identifies α-amino adipic acid, isoleucine and GABA as potential biomarkers of cancer: Differential expression of c-Myc, Oct1 and KLF4 coordinates metabolic changes.

    PubMed

    Bellance, Nadège; Pabst, Lisa; Allen, Genevara; Rossignol, Rodrigue; Nagrath, Deepak

    2012-11-01

    Bioenergetic profiling of tumors is a new challenge of cancer research and medicine as therapies are currently being developed. Meanwhile, methodological means must be proposed to gather information on tumor metabolism in order to adapt these potential therapies to the bioenergetic specificities of tumors. Studies performed on tumors and cancer cell lines have shown that cancer cells bioenergetics is highly variable. This profile changes with microenvironmental conditions (eg. substrate availability), the oncogenes activated (and the tumor suppressors inactivated) and the interaction with the stroma (i.e. reverse Warburg effect). Here, we assessed the power of metabolic footprinting (MFP) to unravel the bioenergetics and associated anabolic changes induced by three oncogenes, c-Myc, KLF4 and Oct1. The MFP approach provides a quantitative analysis of the metabolites secreted and consumed by cancer cells. We used ultra performance liquid chromatography for quantifying the amino acid uptake and secretion. To investigate the potential oncogene-mediated alterations in mitochondrial metabolism, we measured oxygen consumption rate and ATP production as well as the glucose uptake and lactate release. Our findings show that c-Myc deficiency initiates the Warburg effect along with a reduction of mitochondrial respiration. KLF4 deficiency also stimulated glycolysis, albeit without cellular respiration impairment. In contrast, Oct1 deficiency reduced glycolysis and enhanced oxidative phosphorylation efficiency. MFP revealed that c-Myc, KLF4 and Oct1 altered amino acid metabolism with specific patterns. We identified isoleucine, α-aminoadipic acid and GABA (γ-aminoisobutyric acid) as biomarkers related. Our findings establish the impact of Oct1, KLF4 and c-Myc on cancer bioenergetics and evidence a link between oncosecretomics and cellular bioenergetics profile.

  4. Cell Surface Profiling Using High-Throughput Flow Cytometry: A Platform for Biomarker Discovery and Analysis of Cellular Heterogeneity

    PubMed Central

    Gedye, Craig A.; Hussain, Ali; Paterson, Joshua; Smrke, Alannah; Saini, Harleen; Sirskyj, Danylo; Pereira, Keira; Lobo, Nazleen; Stewart, Jocelyn; Go, Christopher; Ho, Jenny; Medrano, Mauricio; Hyatt, Elzbieta; Yuan, Julie; Lauriault, Stevan; Kondratyev, Maria; van den Beucken, Twan; Jewett, Michael; Dirks, Peter; Guidos, Cynthia J.; Danska, Jayne; Wang, Jean; Wouters, Bradly; Neel, Benjamin; Rottapel, Robert; Ailles, Laurie E.

    2014-01-01

    Cell surface proteins have a wide range of biological functions, and are often used as lineage-specific markers. Antibodies that recognize cell surface antigens are widely used as research tools, diagnostic markers, and even therapeutic agents. The ability to obtain broad cell surface protein profiles would thus be of great value in a wide range of fields. There are however currently few available methods for high-throughput analysis of large numbers of cell surface proteins. We describe here a high-throughput flow cytometry (HT-FC) platform for rapid analysis of 363 cell surface antigens. Here we demonstrate that HT-FC provides reproducible results, and use the platform to identify cell surface antigens that are influenced by common cell preparation methods. We show that multiple populations within complex samples such as primary tumors can be simultaneously analyzed by co-staining of cells with lineage-specific antibodies, allowing unprecedented depth of analysis of heterogeneous cell populations. Furthermore, standard informatics methods can be used to visualize, cluster and downsample HT-FC data to reveal novel signatures and biomarkers. We show that the cell surface profile provides sufficient molecular information to classify samples from different cancers and tissue types into biologically relevant clusters using unsupervised hierarchical clustering. Finally, we describe the identification of a candidate lineage marker and its subsequent validation. In summary, HT-FC combines the advantages of a high-throughput screen with a detection method that is sensitive, quantitative, highly reproducible, and allows in-depth analysis of heterogeneous samples. The use of commercially available antibodies means that high quality reagents are immediately available for follow-up studies. HT-FC has a wide range of applications, including biomarker discovery, molecular classification of cancers, or identification of novel lineage specific or stem cell markers. PMID:25170899

  5. Nano optical sensor binuclear Pt-2-pyrazinecarboxylic acid -bipyridine for enhancement of the efficiency of 3-nitrotyrosine biomarker for early diagnosis of liver cirrhosis with minimal hepatic encephalopathy.

    PubMed

    Attia, M S; Al-Radadi, Najlaa S

    2016-12-15

    A new, precise, and very selective method for increasing the impact and assessment of 3-nitrotyrosine (3-Nty) as a biomarker for early diagnosis of liver cirrhosis with minimal hepatic encephalopathy (MHE) disease was developed. The method depends on the formation of the ion pair associate between 3-nitrotyrosine and the optical sensor binuclear Pt-2-pyrazinecarboxylic acid (pca)-Bipyridine (bpy) complex doped in sol-gel matrix in buffer solution of pH 7.3. The binuclear Pt (pca)(bpy) has +II net charge which is very selective and sensitive for [3-Nty](-2) at pH 7.3 in serum sample of liver cirrhosis with MHE diseases. 3-nitrotyrosine (3-Nty) quenches the luminescence intensity of the nano optical sensor binuclear Pt(pca) (bpy) at 528nm after excitation at 370nm, pH 7.3. The remarkable quenching of the luminescence intensity at 528nm of nano binuclear Pt(pca) (bpy) doped in sol-gel matrix by various concentrations of the 3-Nty was successfully used as an optical sensor for the assessment of 3-Nty in different serum samples of (MHE) in patients with liver cirrhosis. The calibration plot was achieved over the concentration range 1.85×10(-5) - 7.95×10(-10)molL(-1) 3-Nty with a correlation coefficient of (0.999) and a detection limit of (4.7×10(-10)molL(-1)). The method increases the sensitivity (93.75%) and specificity (96.45%) of 3-Nty as a biomarker for early diagnosis of liver cirrhosis with MHE in patients.

  6. Evaluating the potential of long chain n-alkanes and n-carboxylic acids as biomarkers for past vegetation

    NASA Astrophysics Data System (ADS)

    Lanny, Verena; Zech, Roland; Eglinton, Timothy

    2014-05-01

    Leaf waxes, such as long chain n-alkanes and n-carboxylic acids, may have a great potential for the reconstruction of past environmental and climate conditions (e.g. (Zech R. et al., 2013). While n-C27 and n-C29 alkanes often predominantly occur in trees and shrubs, n-C31 and n-C33 are more abundant in grasses and herbs. However, little is known about chain-length distributions of n-carboxylic acids, and very few studies have systematically investigated leaf waxes in top soils. We analyzed n-alkanes and n-carboxylic acids in ~100 litter and topsoil samples from Southern Germany to Sweden. Our results show that sites under deciduous trees often contain a lot of C27 n-alkanes and C28 n-carboxylic acids. Coniferous sites are characterized by dominance in n-alkanes C29 and C31 and have relatively high concentrations of n-carboxylic acids C22 and C24. Grass sites show a Cmax at C31 for n-alkanes and at C24 or C26 for n-carboxylic acids. Differences in homologue patterns are most pronounced in the litter samples, but are well preserved also in the topsoils (0-3 cm depth, a little less in the lower topsoils from 3-10 cm). Our results illustrate the potential of combining n-alkane and n-carboxylic acid analyses for paleo-vegetation reconstructions, yet indicate that the degree of degradation may have to be taken into consideration (Zech M. et al., 2013). References: Zech, M. et al. (2013) Quat. Int. 296, 108-116. Zech, R. et al. (2013) Palaeo3, 387, 165-175.

  7. Modulatory effects of vitamin E, acetyl-L-carnitine and α-lipoic acid on new potential biomarkers for Alzheimer's disease in rat model.

    PubMed

    Ahmed, Hanaa H

    2012-09-01

    Alzheimer's disease (AD) is the most common chronic neurodegenerative disorder associated with aging. This study aimed to explore new markers for AD as total homocysteine (tHcy), insulin, insulin like growth factor-1 (IGF-1), interlukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α); to determine the modulatory effects of vitamin E (VE), acetyl-L-carnitine (ALC) and α-lipoic acid (LA) on the investigated parameters and to evaluate the possible therapeutic role of these nutraceutical in AD-induced in rats. Our results revealed that brain acetylcholine esterase (AChE) activity and tHcy levels were significantly increased in AD model. Folic acid, vitamin B(12) levels and Na(+)/K(+) ATPase activity were markedly reduced. Plasma insulin and IGF-1 levels were noticeably decreased but plasma TNF-α and IL-1β concentrations were significantly increased, confirming that abnormal inflammatory response is associated with AD. Treatment by VE, ALC and LA restored the above mentioned parameters to about normal levels comparable to those of donepezil, indicating that tHcy, insulin, IGF-1, IL-1β and TNF-α may be considered as new biomarkers for AD. The study points to the potential restoring effects of VE, ALC and LA in AD model. Our study provides evidence for the importance of dietary supplementation in delaying the progression of age-related neurodegenerative diseases.

  8. Intact Capture and In-situ Analysis System for Possible Biomarkers of Enceladus Plume Particles

    NASA Astrophysics Data System (ADS)

    Yano, Hajime; Fujishima, Kosuke; Rothschild, Lynn; Carbonnier, Benjamin; Guerrouache, Mohamed; Dziomba, Szymon; Tabata, Makoto

    2016-07-01

    A combination of intact capture and in-situ detection of organic molecules from extraterrestrial environments is a key step towards understanding the variety and distribution of the building blocks of life other than the terrestrial one. The best candidate in terms of technical feasibility of our time is to sample currently ejecting icy plumes of the Satrun's satellite Enceladus. While gas chromatography/mass spectrometry (GC/MS) has been dominantly used as successful and robust organic detection system in space, it is not suited for the separation and detection of non-volatile, heat-degradable organic molecules. Using polypeptides as a candidate molecule target, we we able to separate 16 out of the 17 tripeptides consisting of abiotically available amino acids by using capillary electrophoresis (CE). This can be regarded an example of possible bio-signatures that can be found in habitable extraterrestrial environments such as deep habitats of internal oceans of satellites of gas giants like Enceladus. We further used these peptides for the simulated Enceladus sample return using hypervelocity impact experiment facility at the same encountering velocity (i.e., 4-6 km/s) as flying through sampling mission to its plumes like the LIFE mission concept. As a result by using the space-proven 0.01g/cc aerogels, two peptide peaks corresponding to negatively charged peptides were detected, thus representing a full simulation of the capture, extraction and analysis of peptides from plume particles. Since the aerogel module is crushable and can be soaked with the electrophoresis agents/solutions and injected to capillary, this media can be used for in-situ wet analysis, in addition to previously known usage for sample return missions.

  9. Standardizing methylation method during phospholipid fatty acid analysis to profile soil microbial communities.

    PubMed

    Chowdhury, Taniya Roy; Dick, Richard P

    2012-02-01

    Phospholipid fatty acid (PLFA) as biomarkers, is widely used to profile microbial communities in environmental samples. However, PLFA extraction and derivatization protocols are not standardized and have widely varied among published studies. Specifically investigators have used either HCl/MeOH or KOH/MeOH or both for the methylation step of PLFA analysis, without justification or research to support either one. It seems likely that each method could have very different outcomes and conclusions for PLFA based studies. Therefore, the objective of this study was to determine the effect of catalyst type for methylation on detecting PLFAs and implications for interpreting microbial profiling in soil. Fatty acid samples extracted from soils obtained from a wetland, an intermittently flooded site, and an adjacent upland site were subjected to HCl/MeOH or KOH/MeOH catalyzed methylation procedures during PLFA analyses. The methylation method using HCl/MeOH resulted in significantly higher concentrations of most PLFAs than the KOH/MeOH method. Another important outcome was that fatty acids with a methyl group (18:1ω,7c 11Me, TBSA 10Me 18:0, 10Me 18:0, 17:0 10Me and 16:0 10Me being an actinomycetes biomarker) could not be detected by HCl/MeOH catalyzed methylation but were found in appreciable concentrations with KOH/MeOH method. From our results, because the HCl/MeOH method did not detect the fatty acids containing methyl groups that could strongly influence the microbial community profile, we recommend that the KOH/MeOH catalyzed transesterification method should become the standard procedure for PLFA profiling of soil microbial communities.

  10. Proteomic Analysis of Urine to Identify Breast Cancer Biomarker Candidates Using a Label-Free LC-MS/MS Approach

    PubMed Central

    Beretov, Julia; Wasinger, Valerie C.; Millar, Ewan K. A.; Schwartz, Peter; Graham, Peter H.; Li, Yong

    2015-01-01

    Introduction Breast cancer is a complex heterogeneous disease and is a leading cause of death in women. Early diagnosis and monitoring progression of breast cancer are important for improving prognosis. The aim of this study was to identify protein biomarkers in urine for early screening detection and monitoring invasive breast cancer progression. Method We performed a comparative proteomic analysis using ion count relative quantification label free LC-MS/MS analysis of urine from breast cancer patients (n = 20) and healthy control women (n = 20). Results Unbiased label free LC-MS/MS-based proteomics was used to provide a profile of abundant proteins in the biological system of breast cancer patients. Data analysis revealed 59 urinary proteins that were significantly different in breast cancer patients compared to the normal control subjects (p<0.05, fold change >3). Thirty-six urinary proteins were exclusively found in specific breast cancer stages, with 24 increasing and 12 decreasing in their abundance. Amongst the 59 significant urinary proteins identified, a list of 13 novel up-regulated proteins were revealed that may be used to detect breast cancer. These include stage specific markers associated with pre-invasive breast cancer in the ductal carcinoma in-situ (DCIS) samples (Leucine LRC36, MAST4 and Uncharacterized protein CI131), early invasive breast cancer (DYH8, HBA, PEPA, uncharacterized protein C4orf14 (CD014), filaggrin and MMRN2) and metastatic breast cancer (AGRIN, NEGR1, FIBA and Keratin KIC10). Preliminary validation of 3 potential markers (ECM1, MAST4 and filaggrin) identified was performed in breast cancer cell lines by Western blotting. One potential marker MAST4 was further validated in human breast cancer tissues as well as individual human breast cancer urine samples with immunohistochemistry and Western blotting, respectively. Conclusions Our results indicate that urine is a useful non-invasive source of biomarkers and the profile patterns

  11. Biomarkers in pediatrics: children as biomarker orphans.

    PubMed

    Savage, William J; Everett, Allen D

    2010-12-01

    Biomarkers have enormous potential to improve patient care by establishing tests of diagnosis, prognosis, and treatment effects. Successfully translating a biomarker from discovery to clinical application demands high-quality discovery research and high-quality clinical studies for biomarker validation; however, there are additional challenges that face biomarker research in pediatrics. There are also additional characteristics of pediatric medicine that make biomarker research especially needed. This review focuses on the fundamentals of biomarkers, the additional considerations needed for applying biomarker research to children, and recommendations for advancing pediatric biomarker research.

  12. Group-based trajectory analysis applications for prognostic biomarker model development in severe TBI: a practical example.

    PubMed

    Niyonkuru, Christian; Wagner, Amy K; Ozawa, Haishin; Amin, Krutika; Goyal, Akash; Fabio, Anthony

    2013-06-01

    Over the last decade, biomarker research has identified potential biomarkers for the diagnosis, prognosis, and management of traumatic brain injury (TBI). Several cerebrospinal fluid (CSF) and serum biomarkers have shown promise in predicting long-term outcome after severe TBI. Despite this increased focus on identifying biomarkers for outcome prognostication after a severe TBI, several challenges still exist in effectively modeling the significant heterogeneity observed in TBI-related pathology, as well as the biomarker-outcome relationships. Biomarker data collected over time are usually summarized into single-point estimates (e.g., average or peak biomarker levels), which are, in turn, used to examine the relationships between biomarker levels and outcomes. Further, many biomarker studies to date have focused on the prediction power of biomarkers without controlling for potential clinical and demographic confounders that have been previously shown to affect long-term outcome. In this article, we demonstrate the application of a practical approach to delineate and describe distinct subpopulations having similar longitudinal biomarker profiles and to model the relationships between these biomarker profiles and outcomes while taking into account potential confounding factors. As an example, we demonstrate a group-based modeling technique to identify temporal S100 calcium-binding protein B (S100b) profiles, measured from CSF over the first week post-injury, in a sample of adult subjects with TBI, and we use multivariate logistic regression to show that the prediction power of S100b biomarker profiles can be superior to the prediction power of single-point estimates.

  13. Proteomics analysis of dendritic cell activation by contact allergens reveals possible biomarkers regulated by Nrf2.

    PubMed

    Mussotter, Franz; Tomm, Janina Melanie; El Ali, Zeina; Pallardy, Marc; Kerdine-Römer, Saadia; Götz, Mario; von Bergen, Martin; Haase, Andrea; Luch, Andreas

    2016-12-15

    Allergic contact dermatitis is a widespread disease with high clinical relevance affecting approximately 20% of the general population. Typically, contact allergens are low molecular weight electrophilic compounds which can activate the Keap1/Nrf2 pathway. We performed a proteomics study to reveal possible biomarkers for dendritic cell (DC) activation by contact allergens and to further elucidate the role of Keap1/Nrf2 signaling in this process. We used bone marrow derived dendritic cells (BMDCs) of wild-type (nrf2(+/+)) and Nrf2 knockout (nrf2(-/-)) mice and studied their response against the model contact sensitizers 2,4-dinitrochlorobenzene (DNCB), cinnamaldehyde (CA) and nickel(II) sulfate by 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE) in combination with electrospray ionization tandem mass spectrometry (ESI-MS/MS). Sodium dodecyl sulfate (SDS, 100μM) served as irritant control. While treatment with nickel(II) sulfate and SDS had only little effects, CA and DNCB led to significant changes in protein expression. We found 18 and 30 protein spots up-regulated in wild-type cells treated with 50 and 100μM CA, respectively. For 5 and 10μM DNCB, 32 and 37 spots were up-regulated, respectively. Almost all of these proteins were not differentially expressed in nrf2(-/-) BMDCs, indicating an Nrf2-dependent regulation. Among them proteins were detected which are involved in oxidative stress and heat shock responses, as well as in signal transduction or basic cellular pathways. The applied approach allowed us to differentiate between Nrf2-dependent and Nrf2-independent cellular biomarkers differentially regulated upon allergen-induced DC activation. The data presented might contribute to the further development of suitable in vitro testing methods for chemical-mediated sensitization.

  14. Recent trends in the advanced analysis of bioactive fatty acids.

    PubMed

    Ruiz-Rodriguez, Alejandro; Reglero, Guillermo; Ibañez, Elena

    2010-01-20

    The consumption of dietary fats have been long associated to chronic diseases such as obesity, diabetes, cancer, arthritis, asthma, and cardiovascular disease; although some controversy still exists in the role of dietary fats in human health, certain fats have demonstrated their positive effect in the modulation of abnormal fatty acid and eicosanoid metabolism, both of them associated to chronic diseases. Among the different fats, some fatty acids can be used as functional ingredients such as alpha-linolenic acid (ALA), arachidonic acid (AA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), gamma-linolenic acid (GLA), stearidonic acid (STA) and conjugated linoleic acid (CLA), among others. The present review is focused on recent developments in FAs analysis, covering sample preparation methods such as extraction, fractionation and derivatization as well as new advances in chromatographic methods such as GC and HPLC. Special attention is paid to trans fatty acids due its increasing interest for the food industry.

  15. GENETIC ANALYSIS OF ABSCISIC ACID BIOSYNTHESIS

    SciTech Connect

    MCCARTY D R

    2012-01-10

    The carotenoid cleavage dioxygenases (CCD) catalyze synthesis of a variety of apo-carotenoid secondary metabolites in plants, animals and bacteria. In plants, the reaction catalyzed by the 11, 12, 9-cis-epoxy carotenoid dioxygenase (NCED) is the first committed and key regulated step in synthesis of the plant hormone, abscisic acid (ABA). ABA is a key regulator of plant stress responses and has critical functions in normal root and seed development. The molecular mechanisms responsible for developmental control of ABA synthesis in plant tissues are poorly understood. Five of the nine CCD genes present in the Arabidopsis genome encode NCED's involved in control of ABA synthesis in the plant. This project is focused on functional analysis of these five AtNCED genes as a key to understanding developmental regulation of ABA synthesis and dissecting the role of ABA in plant development. For this purpose, the project developed a comprehensive set of gene knockouts in the AtNCED genes that facilitate genetic dissection of ABA synthesis. These mutants were used in combination with key molecular tools to address the following specific objectives: (1) the role of ABA synthesis in root development; (2) developmental control of ABA synthesis in seeds; (3) analysis of ATNCED over-expressers; (4) preliminary crystallography of the maize VP14 protein.

  16. Modulation of Breast Cancer Risk Biomarkers by High Dose Omega-3 Fatty Acids: Phase II Pilot Study in Pre-menopausal Women

    PubMed Central

    Fabian, Carol J; Kimler, Bruce F.; Phillips, Teresa A.; Box, Jessica A.; Kreutzjans, Amy L.; Carlson, Susan E.; Hidaka, Brandon H.; Metheny, Trina; Zalles, Carola M.; Mills, Gordon B.; Powers, Kandy R.; Sullivan, Debra K.; Petroff, Brian K.; Hensing, Whitney L.; Fridley, Brooke L.; Hursting, Stephen D

    2015-01-01

    Higher intakes of the omega-3 eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) relative to the omega-6 arachidonic acid (AA) have been variably associated with reduced risk of premenopausal breast cancer. The purpose of this pilot trial was to assess feasibility and explore effects of high dose EPA and DHA on blood and benign breast tissue risk biomarkers prior to design of a placebo controlled Phase IIB trial. Premenopausal women with evidence of hyperplasia +/- atypia by baseline random periareolar fine needle aspiration (RPFNA) were given 1860 mg of EPA + 1500 mg of DHA ethyl esters daily for 6 months. Blood and benign breast tissue were sampled during the same menstrual cycle phase pre-study and a median of 3 weeks after last dose. Additional blood was obtained within 24 hours of last dose. Feasibility which was pre-defined as 50% uptake, 85% retention and 70% compliance, was demonstrated with 46% uptake, 94% completion, and 85% compliance. Cytologic atypia decreased from 77 to 38% (p=0.002), and Ki-67 from a median of 2.1 to 1.0 % (p=0.021) with an increase in the ratio of EPA + DHA to AA in erythrocyte phospholipids but no change in blood hormones, adipokines, or cytokines. Exploratory breast proteomics assessment showed decreases in several proteins involved in hormone and cytokine signaling with mixed effects on those in the AKT/mTOR pathways. Further investigation of EPA plus DHA for breast cancer prevention in a placebo controlled trial in premenopausal women is warranted. PMID:26276744

  17. Imaging Biomarkers or Biomarker Imaging?

    PubMed Central

    Mitterhauser, Markus; Wadsak, Wolfgang

    2014-01-01

    Since biomarker imaging is traditionally understood as imaging of molecular probes, we highly recommend to avoid any confusion with the previously defined term “imaging biomarkers” and, therefore, only use “molecular probe imaging (MPI)” in that context. Molecular probes (MPs) comprise all kinds of molecules administered to an organism which inherently carry a signalling moiety. This review highlights the basic concepts and differences of molecular probe imaging using specific biomarkers. In particular, PET radiopharmaceuticals are discussed in more detail. Specific radiochemical and radiopharmacological aspects as well as some legal issues are presented. PMID:24967536

  18. Blood-based biomarkers for Parkinson's disease.

    PubMed

    Chahine, Lama M; Stern, Matthew B; Chen-Plotkin, Alice

    2014-01-01

    There is a pressing need for biomarkers to diagnose Parkinson's disease (PD), assess disease severity, and prognosticate course. Various types of biologic specimens are potential candidates for identifying biomarkers--defined here as surrogate indicators of physiological or pathophysiological states--but blood has the advantage of being minimally invasive to obtain. There are, however, several challenges to identifying biomarkers in blood. Several candidate biomarkers identified in other diseases or in other types of biological fluids are being pursued as blood-based biomarkers in PD. In addition, unbiased discovery is underway using techniques including metabolomics, proteomics, and gene expression profiling. In this review, we summarize these techniques and discuss the challenges and successes of blood-based biomarker discovery in PD. Blood-based biomarkers that are discussed include α-synuclein, DJ-1, uric acid, epidermal growth factor, apolipoprotein-A1, and peripheral inflammatory markers.

  19. Trophic spectra under the lens of amino acid isotopic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in compound specific isotopic ratio analysis (CSIRA) have allowed researchers to measure trophic fractionation of 15N in specific amino acids, namely glutamic acid and phenylalanine. These amino acids have proven useful in food web studies because of the wide and consistent disparity...

  20. Biomarkers in orthodontic tooth movement.

    PubMed

    Kumar, A Anand; Saravanan, K; Kohila, K; Kumar, S Sathesh

    2015-08-01

    Tooth movement by orthodontic treatment is characterized by remodeling changes in the periodontal ligament, alveolar bone, and gingiva. A reflection of these phenomenons can be found in the gingival crevicular fluid (GCF) of moving teeth, with significant elevations in the concentrations of its components like, cytokines, neurotransmitters, growth Factors, and a arachidonic acid metabolites. GCF arises at the gingival margin and can be described as a transudate or an exudate. Several studies have focused on the composition of GCF and the changes that occur during orthodontic tooth movement (OTM). GCF component analysis is a non-invasive method for studying the cellular response of the underlying periodontium. Clinically, GCF can be easily collected using platinum loops, filter paper strips, gingival washings, and micropipettes. A number of GCF biomarkers involve in bone remodeling during OTM. The data suggest that knowledge of all the biomarkers present in the GCF that can be used to mark the changes in tooth that is undergoing orthodontic treatment may be of clinical usefulness leading to proper choice of mechanical stress to improve and to shorten treatment time and avoid side effects.

  1. Protective effect of rosmarinic acid against oxidative stress biomarkers in liver and kidney of strepotozotocin-induced diabetic rats.

    PubMed

    Mushtaq, Nadia; Schmatz, Roberta; Ahmed, Mushtaq; Pereira, Luciane Belmonte; da Costa, Pauline; Reichert, Karine Paula; Dalenogare, Diéssica; Pelinson, Luana Paula; Vieira, Juliano Marchi; Stefanello, Naiara; de Oliveira, Lizielle Souza; Mulinacci, Nadia; Bellumori, Maria; Morsch, Vera Maria; Schetinger, Maria Rosa

    2015-12-01

    In the present study, we investigated the efficiency of rosmarinic acid (RA) in preventing the alteration of oxidative parameters in the liver and kidney of diabetic rats induced by streptozotocin (STZ). The animals were divided into six groups (n = 8): control, ethanol, RA 10 mg/kg, diabetic, diabetic/ethanol, and diabetic/RA 10 mg/kg. After 3 weeks of treatment, we found that TBARS levels in liver and kidney were significantly increased in the diabetic/saline group and the administration of RA prevented this increase in the liver and kidney (P < 0.05). Diabetes caused a significant decrease in the activity of superoxide dismutase (SOD) and catalase (CAT) in the diabetes/saline group (P < 0.05). However, the treatment with 10 mg/kg RA (antioxidant) prevented this alteration in SOD and CAT activity in the diabetic RA group (P < 0.05). In addition, RA reverses the decrease in ascorbic acid and non-protein-thiol (NPSH) levels in diabetic rats. The treatment with RA also prevented the decrease in the Delta-aminolevulinic acid dehydratase (ALA-D) activity in the liver and kidney of diabetic rats. Furthermore, RA did not have any effect on glycemic levels. These results indicate that RA effectively reduced the oxidative stress induced by STZ, suggesting that RA is a potential candidate for the prevention and treatment of pathological conditions in diabetic models.

  2. Functional analysis of rat acidic calponin.

    PubMed

    Fujii, Toshihiro; Yabe, Sachiko; Nakamura, Kouta; Koizumi, Youichi

    2002-05-01

    Recombinant acidic calponin, a member of the calponin family, interacted with F-actin, but not with microtubules, desmin filaments, tropomyosin, calmodulin, S100 and phosphatidylserine (PS) vesicles with significant affinity. The bindings of acidic calponin to F-actin occurred in a concentration-dependent manner and were saturated at a molar ratio of about 1 acidic calponin to 1-2 actin molecules. The apparent Kd value of acidic calponin to F-actin was calculated to be 1.6 x 10(5) M(-1). Chemical cross-linking experiments indicated that a 1:1 molar covalent complex of acidic calponin and actin monomer was produced as in the case of basic calponinactin binding. No significant morphologic change of F-actin was observed by the addition of acidic calponin. Acidic calponin had little effect on actomyosin Mg2+-ATPase activity unlike basic calponin. Basic calponin partially competed with acidic calponin for binding to F-actin. Domain mapping with V8 protease revealed that acidic calponin binding site resided within the C-terminal 16 kDa fragment of actin, where the binding of basic calponin also occurs. However, both calponins showed reversal effects on fluorescence intensity of pyrene-labeled F-actin. Fragments of acidic calponin with 30 and 22 kDa, lacking the C-terminal acidic tail, were bound to F-actin. Interestingly, both the fragments became bound to PS vesicles, but not to other components. Circular dichroism studies showed that limited digestion of acidic calponin resulted in about 30% decrease of alpha-helix and beta contents. The present results suggest that acidic calponin is functionally distinct from basic calponin and expresses a novel characteristic after removal of the acidic tail region.

  3. Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Cholestasis and Intervention Effect of Paeonia lactiflora Pall.

    PubMed Central

    Ma, Xiao; Chi, Yong-Hui; Niu, Ming; Zhu, Yun; Zhao, Yan-Ling; Chen, Zhe; Wang, Jia-Bo; Zhang, Cong-En; Li, Jian-Yu; Wang, Li-Fu; Gong, Man; Wei, Shi-Zhang; Chen, Chang; Zhang, Lu; Wu, Ming-Quan; Xiao, Xiao-He

    2016-01-01

    Background: The dried root of Paeonia lactiflora Pall. (PLP) is a classical Chinese herbal medicine that has been used to treat hepatic disease for 1000s of years. Our previous work suggested that PLP can be used to treat hepatitis with severe cholestasis. This study explored the mechanism by which PLP affects ANIT-induced cholestasis in rats using a metabolomics approach. Methods: The effects of PLP on serum indices (TBIL, DBIL, AST, ALT, ALP, and TBA) and the histopathology of the liver were analyzed. Moreover, UHPLC-Q-TOF was performed to identify the possible effect of PLP on metabolites. The pathway analysis was conducted to illustrate the pathways and network by which PLP treats cholestasis. Result: High-dose PLP remarkably down-regulated the serum indices and alleviated histological damage to the liver. Metabolomics analyses showed that the therapeutic effect of high-dose PLP is mainly associated with the regulation of several metabolites, such as glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, L(D)-arginine, and L-tryptophan. A pathway analysis showed that the metabolites were related to bile acid secretion and amino acid metabolism. In addition, the significant changes in bile acid transporters also indicated that bile acid metabolism might be involved in the therapeutic effect of PLP on cholestasis. Moreover, a principal component analysis indicated that the metabolites in the high-dose PLP group were closer to those of the control, whereas those of the moderate dose or low-dose PLP group were closer to those of the ANIT group. This finding indicated that metabolites may be responsible for the differences between the effects of low-dose and moderate-dose PLP. Conclusion: The therapeutic effect of high-dose PLP on cholestasis is possibly related to regulation of bile acid secretion and amino acid metabolism. Moreover, these findings may help better understand the mechanisms of disease and provide a potential therapy for cholestasis. PMID

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

    SciTech Connect

    MCClay, Joseph L.; Adkins, Daniel E.; Isern, Nancy G.; O'Connell, Thomas M.; Wooten, Jan B.; Zedler, Barbara K.; Dasika, Madhukar S.; Webb, B. T.; Webb-Robertson, Bobbie-Jo M.; Pounds, Joel G.; Murrelle, Edward L.; Leppert, Mark F.; van den Oord, Edwin J.

    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 correcting 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.

  5. Dental panoramic image analysis for enhancement biomarker of mandibular condyle for osteoporosis early detection

    NASA Astrophysics Data System (ADS)

    Suprijanto; Azhari; Juliastuti, E.; Septyvergy, A.; Setyagar, N. P. P.

    2016-03-01

    Osteoporosis is a degenerative disease characterized by low Bone Mineral Density (BMD). Currently, a BMD level is determined by Dual Energy X-ray Absorptiometry (DXA) at the lumbar vertebrae and femur. Previous studies reported that dental panoramic radiography image has potential information for early osteoporosis detection. This work reported alternative scheme, that consists of the determination of the Region of Interest (ROI) the condyle mandibular in the image as biomarker and feature extraction from ROI and classification of bone conditions. The minimum value of intensity in the cavity area is used to compensate an offset on the ROI. For feature extraction, the fraction of intensity values in the ROI that represent high bone density and the ROI total area is perfomed. The classification will be evaluated from the ability of each feature and its combinations for the BMD detection in 2 classes (normal and abnormal), with the artificial neural network method. The evaluation system used 105 panoramic image data from menopause women which consist of 36 training data and 69 test data that were divided into 2 classes. The 2 classes of classification obtained 88.0% accuracy rate and 88.0% sensitivity rate.

  6. Proteomic Analysis of Saliva Identifies Potential Biomarkers for Orthodontic Tooth Movement

    PubMed Central

    Ellias, Mohd Faiz; Zainal Ariffin, Shahrul Hisham; Karsani, Saiful Anuar; Abdul Rahman, Mariati; Senafi, Shahidan; Megat Abdul Wahab, Rohaya

    2012-01-01

    Orthodontic treatment has been shown to induce inflammation, followed by bone remodelling in the periodontium. These processes trigger the secretion of various proteins and enzymes into the saliva. This study aims to identify salivary proteins that change in expression during orthodontic tooth movement. These differentially expressed proteins can potentially serve as protein biomarkers for the monitoring of orthodontic treatment and tooth movement. Whole saliva from three healthy female subjects were collected before force application using fixed appliance and at 14 days after 0.014′′ Niti wire was applied. Salivary proteins were resolved using two-dimensional gel electrophoresis (2DE) over a pH range of 3–10, and the resulting proteome profiles were compared. Differentially expressed protein spots were then identified by MALDI-TOF/TOF tandem mass spectrometry. Nine proteins were found to be differentially expressed; however, only eight were identified by MALDI-TOF/TOF. Four of these proteins—Protein S100-A9, immunoglobulin J chain, Ig alpha-1 chain C region, and CRISP-3—have known roles in inflammation and bone resorption. PMID:22919344

  7. Application of Mass Spectrometry for the Analysis of Vitellogenin, a Unique Biomarker for Xenobiotic Compounds

    NASA Astrophysics Data System (ADS)

    Cohen, Alejandro M.; Banoub, Joseph H.

    Vitellogenin is a complex phosphoglycolipoprotein that is secreted into the bloodstream of sexually mature, female, oviparous animals in response to circulating estrogens. It is then incorporated into the ovaries by receptor mediated endocytosis, where it is further cleaved to form the major constituents of the egg yolk proteins. It is generally accepted that these protein and peptide products serve as the main nutritional reserve for the developing embryo. Quantification of vitellogenin in blood is useful for different purposes. The reproductive status and degree of sexual maturation of oviparous animals can be assessed according to the levels of vitellogenin in plasma. The expression of this protein can also be induced in males under the effect of estrogenic compounds. Relying on this observation, vitellogenin has been used as a unique biomarker of environmental endocrine disruption in many species. In this respect, vitellogenin levels could potentially be used to assess the use of chemical warefare compounds with estrogenic activity. In this paper we review a technique developed for measuring vitellogenin plasma levels of different fish species using high performance liquid chromatography coupled to tandem mass spectrometry.

  8. Detection of Impaired Sympathetic Cerebrovascular Control Using Functional Biomarkers Based on Principal Dynamic Mode Analysis

    PubMed Central

    Saleem, Saqib; Tzeng, Yu-Chieh; Kleijn, W. Bastiaan; Teal, Paul D.

    2017-01-01

    This study sought to determine whether models of cerebrovascular function based on Laguerre-Volterra kernels that account for nonlinear cerebral blood flow (CBF) dynamics can detect the effects of functional cerebral sympathetic blockade. We retrospectively analyzed continuous beat-to-beat blood pressure, middle cerebral blood velocity, and partial-pressure of end-tidal CO2 (PETCO2) recordings from eighteen healthy individuals who were treated with either an oral dose of the α1-adrenergic receptor blocker Prazosin or a placebo treatment. The global principal dynamic modes (PDMs) were analyzed using Laguerre-Volterra kernels to examine the nonlinear system dynamics. Our principal findings were: (1) very low frequency (<0.03 Hz) linear components of first-order kernels for BP and PETCO2 are mutually coupled to CBF dynamics with the ability to separate individuals between control and blockade conditions, and (2) the gains of the nonlinear functions associated with low-pass and ≈0.03 Hz global PDMs for the BP are sensitive to sympathetic blockade. Collectively these results suggest that very low frequency global PDMs for BP may have potential utility as functional biomarkers of sympathetic neurovascular dysfunction which can occur in conditions like autonomic failure, stroke and traumatic brain injury. PMID:28119628

  9. Conductive hydrogel composed of 1,3,5-benzenetricarboxylic acid and Fe(3+) used as enhanced electrochemical immunosensing substrate for tumor biomarker.

    PubMed

    Wang, Huiqiang; Han, Hongliang; Ma, Zhanfang

    2017-04-01

    In this work, a new conductive hydrogel was prepared by a simple cross-linking coordination method using 1,3,5-benzenetricarboxylic acid as the ligand and Fe(3+) as the metal ion. The hydrogel film was formed on a glassy carbon electrode (GCE) by a drop coating method, which can dramatically facilitate the transport of electrons. A sensitive label-free electrochemical immunosensor was fabricated following electrodeposition of gold nanoparticles (AuNPs) on a hydrogel film and immobilization of an antibody. Neuron-specific enolase (NSE), a lung cancer biomarker, was used as the model analyte to be detected. The proposed immunosensor exhibited a wide linear detection range of 1pgmL(-1) to 200ngmL(-1) and a limit of detection of 0.26pgmL(-1) (the ratio of signal to noise (S/N)=3). Moreover, the detection of NSE in human serum samples showed satisfactory accuracy compared with the data determined by enzyme-linked immunosorbent assay (ELISA), indicating good analytical performance of the immunoassay.

  10. Microfluidic immunosensor based on mesoporous silica platform and CMK-3/poly-acrylamide-co-methacrylate of dihydrolipoic acid modified gold electrode for cancer biomarker detection.

    PubMed

    Regiart, Matías; Fernández-Baldo, Martin A; Villarroel-Rocha, Jhonny; Messina, Germán A; Bertolino, Franco A; Sapag, Karim; Timperman, Aaron T; Raba, Julio

    2017-04-22

    We report a hybrid glass-poly (dimethylsiloxane) microfluidic immunosensor for epidermal growth factor receptor (EGFR) determination, based on the covalent immobilization of anti-EGFR antibody (anti-EGFR) on amino-functionalized mesoporous silica (AMS) retained in the central channel of a microfluidic device. The synthetized AMS was characterized by N2 adsorption-desorption isotherm, scanning electron microscopy (SEM), energy dispersive spectrometry (EDS) and infrared spectroscopy. The cancer biomarker was quantified in human serum samples by a direct sandwich immunoassay measuring through a horseradish peroxidase-conjugated anti-EGFR. The enzymatic product was detected at -100 mV by amperometry on a sputtering gold electrode, modified with an ordered mesoporous carbon (CMK-3) in a matrix of poly-acrylamide-co-methacrylate of dihydrolipoic acid (poly(AC-co-MDHLA)) through in situ copolymerization. CMK-3/poly(AC-co-MDHLA)/gold was characterized by cyclic voltammetry, EDS and SEM. The measured current was directly proportional to the level of EGFR in human serum samples. The linear range was from 0.01 ng mL(-1) to 50 ng mL(-1). The detection limit was 3.03 pg mL(-1), and the within- and between-assay coefficients of variation were below 5.20%. The microfluidic immunosensor is a very promising device for the diagnosis of several kinds of epithelial origin carcinomas.

  11. Biomarker genes highlight intraspecific and interspecific variations in the responses of Pinus taeda L. and Pinus radiata D. Don to Sirex noctilio F. acid gland secretions.

    PubMed

    Bordeaux, John Michael; Lorenz, W Walter; Dean, Jeffrey F D

    2012-10-01

    Sirex noctilio F., a Eurasian horntail woodwasp recently introduced into North America, oviposits in pines and other conifers and in the process spreads a phytopathogenic fungus that serves as a food source for its larvae. During oviposition the woodwasp also deposits mucus produced in its acid (venom) gland that alters pine defense responses and facilitates infection by the fungus. A 26,496-feature loblolly pine cDNA microarray was used to survey gene expression of pine tissue responding to S. noctilio venom. Six genes were selected for further assessment by quantitative real-time polymerase chain reaction (qRT-PCR), including one that encoded an apparent PR-4 protein and another that encoded a thaumatin-like protein. Expression of both was strongly induced in response to venom, while expression of an apparent actin gene (ACT1) was stable in response to the venom. The pattern of gene response was similar in Pinus taeda L. and Pinus radiata D. Don, but the magnitude of response in P. radiata was significantly stronger for each of the induced genes. The magnitude of the biomarker gene response to venom also varied according to genotype within these two species. The qRT-PCR assay was used to demonstrate that the primary bioactive component in S. noctilio venom is a polypeptide.

  12. Discovery of biomarkers for oxidative stress based on cellular metabolomics.

    PubMed

    Wang, Ningli; Wei, Jianteng; Liu, Yewei; Pei, Dong; Hu, Qingping; Wang, Yu; Di, Duolong

    2016-07-01

    Oxidative stress has a close relationship with various pathologic physiology phenomena and the potential biomarkers of oxidative stress may provide evidence for clinical diagnosis or disease prevention. Metabolomics was employed to identify the potential biomarkers of oxidative stress. High-performance liquid chromatography-diode array detector, mass spectrometry and partial least squares discriminate analysis were used in this study. The 10, 15 and 13 metabolites were considered to discriminate the model group, vitamin E-treated group and l-glutathione-treated group, respectively. Some of them have been identified, namely, malic acid, vitamin C, reduced glutathione and tryptophan. Identification of other potential biomarkers should be conducted and their physiological significance also needs to be elaborated.

  13. Analysis of Valproic Acid, Salicylic Acid and Ibuprofen in Whole Blood by GC-MS.

    PubMed

    Stephenson, Jon B; Flater, Melanie L; Bain, Lisa T

    2016-10-01

    The Georgia Bureau of Investigation utilized a silylation method of analysis for low molecular weight carboxylic acids in the past. Due to the negative impact such derivatizations can have on gas chromatography-mass spectrometry (GC-MS) systems an alternative means of analysis was investigated. The described method is a whole blood solid phase extraction of valproic acid, salicylic acid and ibuprofen utilizing butylation for sensitivity and improved chromatography by GC-MS. The method produced a limit of detection and limit of quantitation at 1 mg/L for valproic acid, 2 mg/L for salicylic acid and 0.25 mg/L for ibuprofen. The variability based upon the middle of the calibration curve estimated to be 7% for valproic acid, 8% for salicylic acid and 11% for ibuprofen established upon a 95% confidence interval, with the highest percent coefficient of variation being 5.3% for ibuprofen.

  14. Plasma concentrations of arginine and related amino acids following traumatic brain injury: Proline as a promising biomarker of brain damage severity.

    PubMed

    Louin, G; Neveux, N; Cynober, L; Plotkine, M; Marchand-Leroux, C; Jafarian-Tehrani, M

    2007-09-01

    The aim of this study was to find a plasma biomarker, in relation with nitric oxide (NO), as a sign of brain damage severity following traumatic brain injury (TBI). We first investigated the post-traumatic evolution of the plasma concentrations of NO via the level of NO end-products metabolites (nitrite plus nitrate, NO(x)), that of l-arginine (Arg) and amino acids involved in its metabolism as well as the time course of neurological score in a rat model of lateral fluid percussion brain injury. First, the level of NO(x) was increased in plasma at 24 and 48 h post-TBI with a marked increase at 72 h. In contrast, this elevation was neither accompanied by a modification of plasma concentrations of Arg, nor of amino acids involved in NO and Arg metabolism, l-ornithine (Orn), l-glutamate (Glu), and l-glutamine (Gln). Second, TBI induced a fall of plasma l-proline (Pro) concentrations. The time course of post-TBI neurological deficit showed also a decrease of neurological score at 24, 48, and 72 h. Furthermore, there is a weak negative correlation between the neurological score and the plasma level of NO(x) (r=-0.305; P<0.05), while a marked positive correlation has been found between the neurological score and the plasma level of Pro (r=0.563; P<0.001). In conclusion, the plasma concentrations of Pro could be a promising marker of post-traumatic neurological deficit.

  15. Bis-butanediol-mercapturic acid (bis-BDMA) as a urinary biomarker of metabolic activation of butadiene to its ultimate carcinogenic species.

    PubMed

    Kotapati, Srikanth; Sangaraju, Dewakar; Esades, Amanda; Hallberg, Lance; Walker, Vernon E; Swenberg, James A; Tretyakova, Natalia Y

    2014-06-01

    Human carcinogen 1,3-butadiene (BD) undergoes metabolic activation to 3,4-epoxy-1-butene (EB), hydroxymethylvinyl ketone (HMVK), 3,4-epoxy-1,2-butanediol (EBD) and 1,2,3,4-diepoxybutane (DEB). Among these, DEB is by far the most genotoxic metabolite and is considered the ultimate carcinogenic species of BD. We have shown previously that BD-exposed laboratory mice form 8- to 10-fold more DEB-DNA adducts than rats exposed at the same conditions, which may be responsible for the enhanced sensitivity of mice to BD-mediated cancer. In the present study, we have identified 1,4-bis-(N-acetyl-L-cystein-S-yl)butane-2,3-diol (bis-BDMA) as a novel DEB-specific urinary biomarker. Isotope dilution high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry was employed to quantify bis-BDMA and three other BD-mercapturic acids, 2-(N-acetyl-L-cystein-S-yl)-1-hydroxybut-3-ene/1-(N-acetyl-L-cystein-S-yl)-2-hydroxy-but-3-ene (MHBMA, from EB), 4-(N-acetyl-L-cystein-S-yl)-1,2-dihydroxybutane (DHBMA, from HMVK) and 4-(N-acetyl-L-cystein-S-yl)-1,2,3-trihydroxybutane (THBMA, from EBD), in urine of confirmed smokers, occupationally exposed workers and BD-exposed laboratory rats. Bis-BDMA was formed in a dose-dependent manner in urine of rats exposed to 0-200 p.p.m. BD by inhalation, although it was a minor metabolite (1%) as compared with DHBMA (47%) and THBMA (37%). In humans, DHBMA was the most abundant BD-mercapturic acid excreted (93%), followed by THBMA (5%) and MHBMA (2%), whereas no bis-BDMA was detected. These results reveal significant differences in metabolism of BD between rats and humans.

  16. Hop rho iso-alpha acids, berberine, vitamin D3 and vitamin K1 favorably impact biomarkers of bone turnover in postmenopausal women in a 14-week trial.

    PubMed

    Holick, Michael F; Lamb, Joseph J; Lerman, Robert H; Konda, Veera R; Darland, Gary; Minich, Deanna M; Desai, Anuradha; Chen, Tai C; Austin, Melissa; Kornberg, Jacob; Chang, Jyh-Lurn; Hsi, Alex; Bland, Jeffrey S; Tripp, Matthew L

    2010-05-01

    Osteoporosis is a major health issue facing postmenopausal women. Increased production of pro-inflammatory cytokines resulting from declining estrogen leads to increased bone resorption. Nutrition can have a positive impact on osteoporosis prevention and amelioration. The objective of this study was to investigate the impact of targeted phytochemicals and nutrients essential for bone health on bone turnover markers in healthy postmenopausal women. In this 14-week, single-blinded, 2-arm placebo-controlled pilot study, all women were instructed to consume a modified Mediterranean-style low-glycemic-load diet and to engage in limited aerobic exercise; 17 randomized to the placebo and 16 to the treatment arm (receiving 200 mg hop rho iso-alpha acids, 100 mg berberine sulfate trihydrate, 500 IU vitamin D(3) and 500 microg vitamin K(1), twice daily). Thirty-two women completed the study. Baseline nutrient intake did not differ between arms. At 14 weeks, the treatment arm exhibited an estimated 31% mean reduction (P = 0.02) in serum osteocalcin (a marker of bone turnover), whereas the placebo arm exhibited a 19% increase (P = 0.03) compared to baseline. Serum 25-hydroxyvitamin D (25(OH)D) increased by 13% (P = 0.24) in the treatment arm and decreased by 25% (P < 0.01) in the placebo arm. The between-arm differences for OC and 25(OH)D were statistically significant. Serum IGF-I was increased in both arms, but the increase was more significant in the treatment arm at 14 weeks (P < 0.01). Treatment with hop rho iso-alpha acids, berberine sulfate trihydrate, vitamin D(3) and vitamin K(1) produced a more favorable bone biomarker profile that supports a healthy bone metabolism.

  17. Quantification of Arachidonic Acid and Its Metabolites in Rat Tissues by UHPLC-MS/MS: Application for the Identification of Potential Biomarkers of Benign Prostatic Hyperplasia

    PubMed Central

    Bian, Qiaoxia; Wang, Weihui; Wang, Nannan; Peng, Yan; Ma, Wen; Dai, Ronghua

    2016-01-01

    To evaluate the potential relationship between benign prostatic hyperplasia (BPH) and the arachidonic acid (AA) metabolome, a UHPLC—MS/MS method has been developed and validated for simultaneous determination of AA and its cyclooxygenase(COX) and lipoxygenase(LOX) pathway metabolites (15-HETE, 12-HETE, TXA2, 5-HETE, AA, PGI2, PGF2α, 8-HETE, PGD2, PGE2 and LTB4) in rat tissues. The analytes were extracted from tissue samples with a protein precipitation procedure and then separated on a Shim-pack XR-ODSC18 column with 0.05% formic acid in water (pH adjusted with dilute ammonia) and methanol:acetonitrile (20:80, v/v). Detection was performed on a UHPLC—MS/MS system with electrospray negative ionization (ESI) and a multiple reaction-monitoring mode. The lower limits of quantification (LLOQ) were 0.25–50 ng/mL for all of the analytes in the prostate, seminal, bladder, liver and kidney tissues. The absolute recoveries of the analytes from all of the tissues were more than 50%. By means of the method developed, the AA metabolites in tissue samples from Sham and BPH group rats were determined. The eleven biomarkers in the BPH group prostate, seminal, bladder, liver and kidney tissues were significantly higher than those of the sham group, indicating that BPH fortified the inducible expression of COX and LOX, as well as increased the production of AA and eicosanoids. The method described here offers a useful tool for the evaluation of complex regulatory eicosanoids responses in vivo. PMID:27893755

  18. Application of quantitative proteomic analysis using tandem mass tags for discovery and identification of novel biomarkers in periodontal disease.

    PubMed

    Tsuchida, Sachio; Satoh, Mamoru; Kawashima, Yusuke; Sogawa, Kazuyuki; Kado, Sayaka; Sawai, Setsu; Nishimura, Motoi; Ogita, Mayumi; Takeuchi, Yasuo; Kobyashi, Hiroaki; Aoki, Akira; Kodera, Yoshio; Matsushita, Kazuyuki; Izumi, Yuichi; Nomura, Fumio

    2013-08-01

    Periodontal disease is a bacterial infection that destroys the gingiva and surrounding tissues of the oral cavity. Gingival crevicular fluid (GCF) is extracted from the gingival sulcus and pocket. Analysis of biochemical markers in GCF, which predict the progression of periodontal disease, may facilitate disease diagnosis. However, no useful GCF biochemical markers with high sensitivity for detecting periodontal disease have been identified. Thus, the search for biochemical markers of periodontal disease is of continued interest in experimental and clinical periodontal disease research. Using tandem mass tag (TMT) labeling, we analyzed GCF samples from healthy subjects and patients with periodontal disease, and identified a total of 619 GCF proteins based on proteomic analysis. Of these, we focused on two proteins, matrix metalloproteinase (MMP)-9 and neutrophil gelatinase-associated lipocalin (LCN2), which are involved in the progression of periodontal disease. Western blot analysis revealed that the levels of MMP-9 and LCN2 were significantly higher in patients with periodontal disease than in healthy subjects. In addition, ELISA also detected significantly higher levels of LCN2 in patients with periodontal disease than in healthy subjects. Thus, LC-MS/MS analyses of GCF using TMT labeling led to the identification of LCN2, which may be a promising GCF biomarker for the detection of periodontal disease.

  19. Integrated biomarker response in catfish Hypostomus ancistroides by multivariate analysis in the Pirapó River, southern Brazil.

    PubMed

    Ghisi, Nédia C; Oliveira, Elton C; Mendonça Mota, Thais F; Vanzetto, Guilherme V; Roque, Aliciane A; Godinho, Jayson P; Bettim, Franciele Lima; Silva de Assis, Helena Cristina da; Prioli, Alberto J

    2016-10-01

    Aquatic pollutants produce multiple consequences in organisms, populations, communities and ecosystems, affecting the function of organs, reproductive state, population size, species survival and even biodiversity. In order to monitor the health of aquatic organisms, biomarkers have been used as effective tools in environmental risk assessment. The aim of this study is to evaluate, through a multivariate and integrative analysis, the response of the native species Hypostomus ancistroides over a pollution gradient in the main water supply body of northwestern Paraná state (Brazil). The condition factor, micronucleus test and erythrocyte nuclear abnormalities (ENA), comet assay, measurement of the cerebral and muscular enzyme acetylcholinesterase (AChE), and histopathological analysis of liver and gill were evaluated in fishes from three sites of the Pirapó River during the dry and rainy seasons. The multivariate general result showed that the interaction between the seasons and the sites was significant: there are variations in the rates of alterations in the biological parameters, depending on the time of year researched at each site. In general, the best results were observed for the site nearest the spring, and alterations in the parameters at the intermediate and downstream sites. In sum, the results of this study showed the necessity of a multivariate analysis, evaluating several biological parameters, to obtain an integrated response to the effects of the environmental pollutants on the organisms.

  20. Diagnostic and Prognostic Biomarkers in Melanoma

    PubMed Central

    Leininger, Jennifer; Hamby, Carl; Safai, Bijan

    2014-01-01

    Melanoma is a lethal melanocytic neoplasm. Unfortunately, the histological diagnosis can be difficult at times. Distinguishing ambiguous melanocytic neoplasms that are benign nevi from those that represent true melanoma is important both for treatment and prognosis. Diagnostic biomarkers currently used to assist in the diagnosis of melanoma are usually specific only for melanocytic neoplasms and not necessarily for their ability to metastasize. Traditional prognostic biomarkers include depth of invasion and mitotic count. Newer diagnostic and prognostic biomarkers utilize immunohistochemical staining as well as ribonucleic acid, micro-ribonucleic acid, and deoxyribonucleic acid assays and fluorescence in situ hybridization. Improved diagnostic and prognostic biomarkers are of increasing importance in the treatment of melanoma with the development of newer and more targeted therapies. Herein, the authors review many of the common as well as newer diagnostic and prognostic biomarkers used in melanoma. PMID:25013535

  1. Effects of Valproic Acid and Dexamethasone Administration on Early Bio-Markers and Gene Expression Profile in Acute Kidney Ischemia-Reperfusion Injury in the Rat

    PubMed Central

    Speir, Ryan W.; Stallings, Jonathan D.; Andrews, Jared M.; Gelnett, Mary S.; Brand, Timothy C.; Salgar, Shashikumar K.

    2015-01-01

    Renal ischemia-reperfusion (IR) causes acute kidney injury (AKI) with high mortality and morbidity. The objective of this investigation was to ameliorate kidney IR injury and identify novel biomarkers for kidney injury and repair. Under general anesthesia, left renal ischemia was induced in Wister rats by occluding renal artery for 45 minutes, followed by reperfusion and right nephrectomy. Thirty minutes prior to ischemia, rats (n = 8/group) received Valproic Acid (150 mg/kg; VPA), Dexamethasone (3 mg/kg; Dex) or Vehicle (saline) intraperitoneally. Animals were sacrificed at 3, 24 or 120 h post-IR. Plasma creatinine (mg/dL) at 24 h was reduced (P<0.05) in VPA (2.7±1.8) and Dex (2.3±1.2) compared to Vehicle (3.8±0.5) group. At 3 h, urine albumin (mg/mL) was higher in Vehicle (1.47±0.10), VPA (0.84±0.62) and Dex (1.04±0.73) compared to naïve (uninjured/untreated control) (0.14±0.26) group. At 24 h post-IR urine lipocalin-2 (μg/mL) was higher (P<0.05) in VPA, Dex and Vehicle groups (9.61–11.36) compared to naïve group (0.67±0.29); also, kidney injury molecule-1 (KIM-1; ng/mL) was higher (P<0.05) in VPA, Dex and Vehicle groups (13.7–18.7) compared to naïve group (1.7±1.9). Histopathology demonstrated reduced (P<0.05) ischemic injury in the renal cortex in VPA (Grade 1.6±1.5) compared to Vehicle (Grade 2.9±1.1). Inflammatory cytokines IL1β and IL6 were downregulated and anti-apoptotic molecule BCL2 was upregulated in VPA group. Furthermore, kidney DNA microarray demonstrated reduced injury, stress, and apoptosis related gene expression in the VPA administered rats. VPA appears to ameliorate kidney IR injury via reduced inflammatory cytokine, apoptosis/stress related gene expression, and improved regeneration. KIM-1, lipocalin-2 and albumin appear to be promising early urine biomarkers for the diagnosis of AKI. PMID:25970334

  2. Identification of Potential Novel Biomarkers and Signaling Pathways Related to Otitis Media Induced by Diesel Exhaust Particles Using Transcriptomic Analysis in an In Vivo System

    PubMed Central

    Kwon, Jee Young; Kim, Yeo Jin; Hun Kang, Seung; Jang, Won-Hee; Lee, Jun Ho; Seo, Myung-Whan; Song, Jae-Jun; Seo, Young Rok; Park, Moo Kyun

    2016-01-01

    Introduction Air pollutants are associated with inflammatory diseases such as otitis media (OM). Significantly higher incidence rates of OM are reported in regions with air pollution. Diesel exhaust particles (DEPs) comprise a major class of contaminants among numerous air pollutants, and they are characterized by a carbonic mixture of polycyclic aromatic hydrocarbons (PAHs), nitro-PAHs, and small amounts of sulfate, nitrate, metals and other trace elements. DEP exposure is a risk factor for inflammatory diseases. Our previous study identified potential biomarkers using gene expression microarray and pathway analyses in an in vitro system. Although in vitro investigations have been conducted to elucidate plausible biomarkers and molecular mechanisms related to DEP exposure, in vivo studies are necessary to identify the exact biological relevance regarding the incidence of OM caused by DEP exposure. In this study, we identified potential molecular biomarkers and pathways triggered by DEP exposure in a rodent model. Methods Transcriptomic analysis was employed to identify novel potential biomarkers in the middle ear of DEP-exposed mice. Results A total of 697 genes were differentially expressed in the DEP-exposed mice; 424 genes were upregulated and 273 downregulated. In addition, signaling pathways among the differentially expressed genes mediated by DEP exposure were predicted. Several key molecular biomarkers were identified including cholinergic receptor muscarinic 1 (CHRM1), erythropoietin (EPO), son of sevenless homolog 1 (SOS1), estrogen receptor 1 (ESR1), cluster of differentiation 4 (CD4) and interferon alpha-1 (IFNA1). Conclusions Our results shed light on the related cell processes and gene signaling pathways affected by DEP exposure. The identified biomarkers might be potential candidates for determining early diagnoses and effective treatment strategies for DEP-mediated disorders. PMID:27832168

  3. Biomarker analysis of Upper Permian lacustrine oil shales, Junggar basin, NW China

    SciTech Connect

    Carroll, A. )

    1990-05-01

    Upper Permian lacustrine oil shales containing up to 34% TOC (total organic carbon) underlie approximately 50,000 km{sup 2} of the Junggar basin in western China, and appear to be the principal source of oils in the giant Karamay field in the northwestern Junggar and in several recent discoveries in other areas of the basin. The siliceous oil shales were deposited in a sediment-starved foreland basin during a period of predominantly humid climate. Previous biomarker studies of crude oils from Karamay field have documented an abundance of {beta}-carotane (which in some cases dominates the aliphatic hydrocarbon distribution) and gammacerane, suggesting a source bed deposited under hypersaline conditions. However, relatively complete outcrop exposures of finely laminated oil shales in the southern Junggar conspicuously lack evaporites, extensive dessication horizons, or other sedimentological evidence of playa lake environments. Indeed, the aliphatic hydrocarbon distribution in bitumen extracts from southern Junggar oil shales appear characteristic of freshwater to brakish water deposition of organic matter in an anoxic lake. Normal alkanes show a slight odd-over-even preference with relatively low levels of the C{sub 22}, n-alkane, pristane/phytane ratios close to unity, low {beta}-carotane and gammacerane levels, and the absence of C{sub 34}-C{sub 35} hopanes. This apparent difference in source bed depositional environments may be due to tectonic partitioning between separate depocenters of the Late Permian Junggar basin. Alternatively, hypersaline oil shale facies may be limited to deeper basinal areas, whereas upslope southern Junggar sediments record highstands in lake level or influx of fresh water from the adjacent drainage areas.

  4. Ion-exchange chromatographic analysis of peroxynitric acid.

    PubMed

    Nakashima, Yoichi; Ikawa, Satoshi; Tani, Atsushi; Kitano, Katsuhisa

    2016-01-29

    Ion-exchange chromatographic analysis of peroxynitric acid (O2NOOH) was performed by combining an acidic eluate with an UV-vis detector and immersing the separation column in an ice-water bath. The decomposition behavior of peroxynitric acid in the solution was also studied using this system. The fraction for the peroxynitric acid peak was collected. Ion-exchange chromatographic analysis of this fraction, after standing at room temperature for 24h, showed that the decomposition products were mainly nitrate ions with a very small amount of nitrous acid. The peroxynitric acid peak area correlated perfectly with the total amount of decomposition products. The ion-exchange chromatographic isolation allowed us to evaluate the molar extinction coefficient of peroxynitric acid precisely in a wider wavelength range than previous reports. The value decreases monotonically from 1729±26M(-1)cm(-1) at 200nm to 12.0±0.5M(-1)cm(-1) at 290nm.

  5. Chiral Biomarkers in Meteorites

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.

    2010-01-01

    The chirality of organic molecules with the asymmetric location of group radicals was discovered in 1848 by Louis Pasteur during his investigations of the rotation of the plane of polarization of light by crystals of sodium ammonium paratartrate. It is well established that the amino acids in proteins are exclusively Levorotary (L-aminos) and the sugars in DNA and RNA are Dextrorotary (D-sugars). This phenomenon of homochirality of biological polymers is a fundamental property of all life known on Earth. Furthermore, abiotic production mechanisms typically yield recemic mixtures (i.e. equal amounts of the two enantiomers). When amino acids were first detected in carbonaceous meteorites, it was concluded that they were racemates. This conclusion was taken as evidence that they were extraterrestrial and produced by abiologically. Subsequent studies by numerous researchers have revealed that many of the amino acids in carbonaceous meteorites exhibit a significant L-excess. The observed chirality is much greater than that produced by any currently known abiotic processes (e.g. Linearly polarized light from neutron stars; Circularly polarized ultraviolet light from faint stars; optically active quartz powders; inclusion polymerization in clay minerals; Vester-Ulbricht hypothesis of parity violations, etc.). This paper compares the measured chirality detected in the amino acids of carbonaceous meteorites with the effect of these diverse abiotic processes. IT is concluded that the levels observed are inconsistent with post-arrival biological contamination or with any of the currently known abiotic production mechanisms. However, they are consistent with ancient biological processes on the meteorite parent body. This paper will consider these chiral biomarkers in view of the detection of possible microfossils found in the Orgueil and Murchison carbonaceous meteorites. Energy dispersive x-ray spectroscopy (EDS) data obtained on these morphological biomarkers will be

  6. Predictive urinary biomarkers for steroid-resistant and steroid-sensitive focal segmental glomerulosclerosis using high resolution mass spectrometry and multivariate statistical analysis

    PubMed Central

    2014-01-01

    Background Focal segmental glomerulosclerosis (FSGS) is a glomerular scarring disease diagnosed mostly by kidney biopsy. Since there is currently no diagnostic test that can accurately predict steroid responsiveness in FSGS, prediction of the responsiveness of patients to steroid therapy with noninvasive means has become a critical issue. In the present study urinary proteomics was used as a noninvasive tool to discover potential predictive biomarkers. Methods Urinary proteome of 10 patients (n = 6 steroid-sensitive, n = 4 steroid-resistant) with biopsy proven FSGS was analyzed using nano-LC-MS/MS and supervised multivariate statistical analysis was performed. Results Twenty one proteins were identified as discriminating species among which apolipoprotein A-1 and Matrix-remodeling protein 8 had the most drastic fold changes being over- and underrepresented, respectively, in steroid sensitive compared to steroid resistant urine samples. Gene ontology enrichment analysis revealed acute inflammatory response as the dominant biological process. Conclusion The obtained results suggest a panel of predictive biomarkers for FSGS. Proteins involved in the inflammatory response are shown to be implicated in the responsiveness. As a tool for biomarker discovery, urinary proteomics is especially fruitful in the area of prediction of responsiveness to drugs. Further validation of these biomarkers is however needed. PMID:25182141

  7. Cellphone-based detection platform for rbST biomarker analysis in milk extracts using a microsphere fluorescence immunoassay.

    PubMed

    Ludwig, Susann K J; Zhu, Hongying; Phillips, Stephen; Shiledar, Ashutosh; Feng, Steve; Tseng, Derek; van Ginkel, Leendert A; Nielen, Michel W F; Ozcan, Aydogan

    2014-11-01

    Current contaminant and residue monitoring throughout the food chain is based on sampling, transport, administration, and analysis in specialized control laboratories. This is a highly inefficient and costly process since typically more than 99% of the samples are found to be compliant. On-site simplified prescreening may provide a scenario in which only samples that are suspect are transported and further processed. Such a prescreening can be performed using a small attachment on a cellphone. To this end, a cellphone-based imaging platform for a microsphere fluorescence immunoassay that detects the presence of anti-recombinant bovine somatotropin (rbST) antibodies in milk extracts was developed. RbST administration to cows increases their milk production, but is illegal in the EU and a public health concern in the USA. The cellphone monitors the presence of anti-rbST antibodies (rbST biomarker), which are endogenously produced upon administration of rbST and excreted in milk. The rbST biomarker present in milk extracts was captured by rbST covalently coupled to paramagnetic microspheres and labeled by quantum dot (QD)-coupled detection antibodies. The emitted fluorescence light from these captured QDs was then imaged using the cellphone camera. Additionally, a dark-field image was taken in which all microspheres present were visible. The fluorescence and dark-field microimages were analyzed using a custom-developed Android application running on the same cellphone. With this setup, the microsphere fluorescence immunoassay and cellphone-based detection were successfully applied to milk sample extracts from rbST-treated and untreated cows. An 80% true-positive rate and 95% true-negative rate were achieved using this setup. Next, the cellphone-based detection platform was benchmarked against a newly developed planar imaging array alternative and found to be equally performing versus the much more sophisticated alternative. Using cellphone-based on-site analysis in

  8. Extraterrestrial material analysis: loss of amino acids during liquid-phase acid hydrolysis

    NASA Astrophysics Data System (ADS)

    Buch, Arnaud; Brault, Amaury; Szopa, Cyril; Freissinet, Caroline

    2015-04-01

    Searching for building blocks of life in extraterrestrial material is a way to learn more about how life could have appeared on Earth. With this aim, liquid-phase acid hydrolysis has been used, since at least 1970 , in order to extract amino acids and other organic molecules from extraterrestrial materials (e.g. meteorites, lunar fines) or Earth analogues (e.g. Atacama desert soil). This procedure involves drastic conditions such as heating samples in 6N HCl for 24 h, either under inert atmosphere/vacuum, or air. Analysis of the hydrolyzed part of the sample should give its total (free plus bound) amino acid content. The present work deals with the influence of the 6N HCl hydrolysis on amino acid degradation. Our experiments have been performed on a standard solution of 17 amino acids. After liquid-phase acid hydrolysis (6N HCl) under argon atmosphere (24 h at 100°C), the liquid phase was evaporated and the dry residue was derivatized with N-Methyl-N-(t-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) and dimethylformamide (DMF), followed by gas chromatography-mass spectrometry analysis. After comparison with derivatized amino acids from the standard solution, a significant reduction of the chromatographic peak areas was observed for most of the amino acids after liquid-phase acid hydrolysis. Furthermore, the same loss pattern was observed when the amino acids were exposed to cold 6N HCl for a short amount of time. The least affected amino acid, i.e. glycine, was found to be 73,93% percent less abundant compared to the non-hydrolyzed standard, while the most affected, i.e. histidine, was not found in the chromatograms after hydrolysis. Our experiments thereby indicate that liquid-phase acid hydrolysis, even under inert atmosphere, leads to a partial or total loss of all of the 17 amino acids present in the standard solution, and that a quick cold contact with 6N HCl is sufficient to lead to a loss of amino acids. Therefore, in the literature, the reported increase

  9. Microarray analysis identifies keratin loci as sensitive biomarkers for thyroid hormone disruption in the salamander Ambystoma mexicanum.

    PubMed

    Page, Robert B; Monaghan, James R; Samuels, Amy K; Smith, Jeramiah J; Beachy, Christopher K; Voss, S Randal

    2007-02-01

    Ambystomatid salamanders offer several advantages for endocrine disruption research, including genomic and bioinformatics resources, an accessible laboratory model (Ambystoma mexicanum), and natural lineages that are broadly distributed among North American habitats. We used microarray analysis to measure the relative abundance of transcripts isolated from A. mexicanum epidermis (skin) after exogenous application of thyroid hormone (TH). Only one gene had a >2-fold change in transcript abundance after 2 days of TH treatment. However, hundreds of genes showed significantly different transcript levels at days 12 and 28 in comparison to day 0. A list of 123 TH-responsive genes was identified using statistical, BLAST, and fold level criteria. Cluster analysis identified two groups of genes with similar transcription patterns: up-regulated versus down-regulated. Most notably, several keratins exhibited dramatic (1000 fold) increases or decreases in transcript abundance. Keratin gene expression changes coincided with morphological remodeling of epithelial tissues. This suggests that keratin loci can be developed as sensitive biomarkers to assay temporal disruptions of larval-to-adult gene expression programs. Our study has identified the first collection of loci that are regulated during TH-induced metamorphosis in a salamander, thus setting the stage for future investigations of TH disruption in the Mexican axolotl and other salamanders of the genus Ambystoma.

  10. Is hair analysis for dialkyl phosphate metabolites a suitable biomarker for assessing past acute exposure to organophosphate pesticides?

    PubMed

    Tsatsakis, A M; Tutudaki, M; Tzatzarakis, M N; Dawson, A; Mohamed, F; Christaki, M; Alegakis, A K

    2012-03-01

    In the present paper, the possibility to use dialkyl phosphate metabolites (DAPs) hair segmental analysis as a biomarker of past acute exposure to organophosphates is examined. Hair samples of four acute poisoning survivors were collected and segmental hair analysis was performed. The total hair samples were divided to 1 cm segments and analysed by gas chromatography-mass spectrometry (GC-MS) for the presence of four DAP metabolites, dimethyl phosphate (DMP), diethyl phosphate (DEP), diethyl thiophosphate (DETP) and diethyl dithiophosphate (DEDTP). Results were examined under the light of pesticide type and time of hair sample collection. Although DAPs were detected all along the hair shaft, higher concentrations (peaks) were detected in the segments proximate to the suicide period. It was also observed that the elevated concentrations of the present metabolites corresponded to the ones produced by the ingested parent compound. Conclusively, measurements of DAPs in the appropriate hair segments of OP-poisoned patients can be used for assessing past acute exposure to organophosphates in certain cases.

  11. Comparative biochemical and RAPD analysis in two varieties of rice (Oryza sativa) under arsenic stress by using various biomarkers.

    PubMed

    Ahmad, Mohd Anwar; Gaur, Rashmi; Gupta, Meetu

    2012-05-30

    Multiple biomarker systems have been frequently used to measure the genotoxic effects of environmental pollutants (including heavy metals) on living organisms. In this study, we used leaves of hydroponically grown 14 days old seedlings of rice (Oryza sativa) varieties (PB1 and IR64) treated with 50, 150 and 300 μM arsenite (As(III)) for 24 and 96 h duration. Reduction in seed germination, root-shoot length, chlorophyll and protein were observed with increasing As(III) concentration and duration in both varieties, being more in IR64. Increase/decrease of antioxidant enzymes and stress related parameters showed much changes at higher concentration for 24 and 96 h duration in both varieties. Eleven primers were found in RAPD analysis to produce polymorphic band pattern and produced a total of 51 (control), 79 (treated) and 42 (control) and 29 (treated) bands in PB1 and IR64 varieties, respectively. These results indicated that genomic template stability (GTS, changes in RAPD profile) was significantly affected at all tested As(III) concentration, when compared with other parameters. Differential response was observed in both varieties with PB1 being more tolerant. We concluded that DNA polymorphism detected by RAPD analysis in conjunction with other biochemical parameters could be a powerful eco-toxicological tool in bio-monitoring arsenic pollution.

  12. Nanopore Back Titration Analysis of Dipicolinic Acid

    PubMed Central

    Han, Yujing; Zhou, Shuo; Wang, Liang; Guan, Xiyun

    2015-01-01

    Here we report a novel label-free nanopore back titration method for the detection of dipicolinic acid, a marker molecule for bacterial spores. By competitive binding of the target analyte and a large ligand probe to metal ions, dipicolinic acid could be sensitively and selectively detected. This nanopore back titration approach should find useful applications in the detection of other species of medical, biological, or environmental importance if their direct detection is difficult to achieve. PMID:25074707

  13. Biomarkers for Heart Failure in Asia.

    PubMed

    Richards, Arthur Mark

    2015-10-01

    Contributions from the Asian biomedical community to knowledge of biomarkers in heart failure have grown rapidly since 2000. Japan has made world-leading contributions in the discovery and application of cardiac natriuretic peptides as biomarkers in heart failure, but there has been rapid growth in reports from China. Contributions also come from Taiwan, South Korea, Singapore, and Hong Kong. Centers in Asia have established clinical cohorts providing powerful platforms for the discovery and validation of biomarkers in heart failure. This century, Asian enquiry into biomarkers in heart failure will include peptides, cytokines, metabolites, nucleic acids, and other analytes.

  14. Biomarkers for diagnosis of neonatal infections: A systematic analysis of their potential as a point-of-care diagnostics

    PubMed Central

    Meem, Mahbuba; Modak, Joyanta K.; Mortuza, Roman; Morshed, Mahboob; Islam, Mohammad Shahidul; Saha, Samir K.

    2011-01-01

    Background Neonatal infections annually claim lives of 1.4 million neonates worldwide. Until now, there is no ideal diagnostic test for detecting sepsis and thus management of possible sepsis cases often depends on clinical algorithm leading to empirical treatment. This often results in unnecessary antibiotic use, which may lead to emergence of antibiotic resistance. Biomarkers have shown great promise in diagnosis of sepsis and guiding appropriate treatment of neonates. In this study, we conducted a literature review of existing biomarkers to analyze their status for use as a point-of-care diagnostic in developing countries. Methods PubMed and EMBASE database were searched with keywords, ‘infections’, ‘neonates’, and ‘biomarkers’ to retrieve potentially relevant papers from the period 1980 to 2010. Leading hospitals and manufacturers were communicated to inquire about the cost, laboratory requirements and current standing of biomarkers in clinical use. Results The search returned 6407 papers on biomarkers; 65 were selected after applying inclusion and exclusion criteria. Among the studies, C-reactive protein (CRP), procalcitonin (PCT) and interleukin 6 (IL-6) were the most widely studied biomarkers and were considered to be most promising for diagnosing neonatal infections. About 90% of the studies were from developed countries; more than 50% were from Europe. Conclusions Extensive work is being performed to find the diagnostic and prognostic value of biomarkers. However, the methodologies and study design are highly variable. Despite numerous research papers on biomarkers, their use in clinical setting is limited to CRP. The methods for detection of biomarkers are far too advanced to be used at the community level where most of the babies are dying. It is important that a harmonized multi-site study is initiated to find a battery of biomarkers for diagnosis of neonatal infections. PMID:23198119

  15. A New Antibody for Category 1 Biomarker Detection

    NASA Technical Reports Server (NTRS)

    Maule, J.; Steele, A.; Toporski, J.; McKay, D. S.

    2003-01-01

    At least two questions arise in developing a life-detection strategy: What do we look for and what will positive detection tell us? Unfortunately, many 'biomarkers' are not conclusive markers of biology. For example, sugars, amino acids, polycyclic aromatic hydrocarbons (PAH) and certain bacteria-like morphologies can all be produced non-biologically. Inferences of life following the detection of several inconclusive biomarkers in one sample will always be questioned. Although DNA, RNA and proteins are excellent markers of biology, and preserved on Earth for several millions of years, their survival over longer periods of time is low. Ideally, we should target biomarkers which are both stable over time and formed exclusively from biological processes, i.e. a 'category 1' biomarker under the new classification system of Mckay. We have used antibodies to detect category 1 and other biomarkers in rock samples. Extraction takes a few minutes and analysis a few hours. We have presented use of new antibodies to detect hopanes and have shown proof of operation during martian gravity.

  16. Metabolic profiling of Parkinson's disease: evidence of biomarker from gene expression analysis and rapid neural network detection

    PubMed Central

    Ahmed, Shiek SSJ; Santosh, Winkins; Kumar, Suresh; Christlet, Hema T Thanka

    2009-01-01

    Background Parkinson's disease (PD) is a neurodegenerative disorder. The diagnosis of Parkinsonism is challenging because currently none of the clinical tests have been proven to help in diagnosis. PD may produce characteristic perturbations in the metabolome and such variations can be used as the marker for detection of disease. To test this hypothesis, we used proton NMR and multivariate analysis followed by neural network pattern detection. Methods & Results 1H nuclear magnetic resonance spectroscopy analysis was carried out on plasma samples of 37 healthy controls and 43 drug-naive patients with PD. Focus on 22 targeted metabolites, 17 were decreased and 5 were elevated in PD patients (p < 0.05). Partial least squares discriminant analysis (PLS-DA) showed that pyruvate is the key metabolite, which contributes to the separation of PD from control samples. Furthermore, gene expression analysis shows significant (p < 0.05) change in expression of PDHB and NPFF genes leading to increased pyruvate concentration in blood plasma. Moreover, the implementation of 1H- NMR spectral pattern in neural network algorithm shows 97.14% accuracy in the detection of disease progression. Conclusion The results increase the prospect of a robust molecular definition in detection of PD through the early symptomatic phase of the disease. This is an ultimate opening for therapeutic intervention. If validated in a genuinely prospective fashion in larger samples, the biomarker trajectories described here will go a long way to facilitate the development of useful therapies. Moreover, implementation of neural network will be a breakthrough in clinical screening and rapid detection of PD. PMID:19594911

  17. Hydroxyproline, a Serum Biomarker Candidate for Gastric Ulcer in Rats: A Comparison Study of Metabolic Analysis of Gastric Ulcer Models Induced by Ethanol, Stress, and Aspirin

    PubMed Central

    Takeuchi, Kenichiro; Ohishi, Maki; Endo, Keiko; Suzumura, Kenichi; Naraoka, Hitoshi; Ohata, Takeji; Seki, Jiro; Miyamae, Yoichi; Honma, Masashi; Soga, Tomoyoshi

    2014-01-01

    Gastrointestinal symptoms are a common manifestation of adverse drug effects. Non-steroid anti-inflammatory drugs (NSAIDs) are widely prescribed drugs that induce the serious side effect of gastric mucosal ulceration. Biomarkers for these side effects have not been identified and ulcers are now only detectable by endoscopy. We previously identified five metabolites as biomarker candidates for NSAID-induced gastric ulcer using capillary electrophoresis–mass spectrometry (CE–MS)-based metabolomic analysis of serum and stomach from rats. Here, to clarify mechanism of changes and limitations of indications of biomarker candidates, we performed CE–MS-based metabolomic profiling in stomach and serum from rats with gastric ulcers induced by ethanol, stress, and aspirin. The results suggest that a decrease in hydroxyproline reflects the induction of gastric injury and may be useful in identifying gastric ulcer induced by multiple causes. While extrapolation to humans requires further study, hydroxyproline can be a new serum biomarker of gastric injury regardless of cause. PMID:25125970

  18. Oral rosmarinic acid-enhanced Mentha spicata modulates synovial fluid biomarkers of inflammation in horses challenged with intra-articular LPS.

    PubMed

    Pearson, W; Fletcher, R S; Kott, L S

    2012-10-01

    A biological extract of high-rosmarinic acid mint (HRAM) has previously demonstrated inhibitory effects on lipopolysaccharide (LPS)-induced prostaglandin E(2) (PGE(2)), nitric oxide (NO) and glycosaminoglycan (GAG) release in vitro. This study was undertaken to determine whether HRAM added to feed produces similar effects in horses challenged with intra-articular LPS. Eight horses received HRAM (0 or 28.1 ± 1.3 g/day; n = 4 per group) in their feed for 24 days in a blinded manner. On day 21, all horses received an intra-articular injection of LPS (0.3 ng) into their left or right intercarpal joint. Synovial fluid (SF) samples were taken on postinjection day (PID)-21 (i.e. prior to commencement of supplementation), PID0, PID0.25, PID0.5, PID1 and PID3 and analysed for PGE(2), GAG, NO, protein and total nucleated cells counts. Blood biochemistry and haematology screens were conducted at PID-21, PID0, PID1 and PID3. There was a significant reduction in LPS-induced PGE(2) and GAG in SF in horses supplemented with HRAM compared with controls and a tendency to increase complement recognition protein accumulation in synovial fluid of HRAM horses. Plasma from HRAM horses had reduced total white blood cells, segmented neutrophils (compared with baseline concentrations) and lymphocytes (compared with controls), and increased SF nucleated cell count (compared with baseline concentrations and controls). It is concluded that HRAM offered as part of the feed alter biomarkers of inflammation in SF of LPS-challenged horses. Larger studies that seek to clarify effects of HRAM on synovial fluid cell counts and possible role of HRAM-induced interference with complement signalling are warranted.

  19. Glial Fibrillary Acidic Protein and Ubiquitin C-Terminal Hydrolase-L1 Are Not Specific Biomarkers for Mild CT-Negative Traumatic Brain Injury.

    PubMed

    Posti, Jussi P; Hossain, Iftakher; Takala, Riikka S K; Liedes, Hilkka; Newcombe, Virginia; Outtrim, Joanne; Katila, Ari J; Frantzén, Janek; Ala-Seppälä, Henna; Coles, Jonathan P; Kyllönen, Anna; Maanpää, Henna-Riikka; Tallus, Jussi; Hutchinson, Peter J; van Gils, Mark; Menon, David K; Tenovuo, Olli

    2017-01-27

    Glial fibrillary acidic protein (GFAP) and ubiquitin C-terminal hydrolase-L1 (UCH-L1) have been studied as potential biomarkers of mild traumatic brain injury (mTBI). We report the levels of GFAP and UCH-L1 in patients with acute orthopedic injuries without central nervous system involvement, and relate them to the type of extracranial injury, head magnetic resonance imaging (MRI) findings, and levels of GFAP and UCH-L1 in patients with CT-negative mTBI. Serum UCH-L1 and GFAP were longitudinally measured from 73 patients with acute orthopedic injury on arrival and on days 1, 2, 3, 7 after admission, and on the follow-up visit 3-10 months after the injury. The injury types were recorded, and 71% patients underwent also head MRI. The results were compared with those found in patients with CT-negative mTBI (n = 93). The levels of GFAP were higher in patients with acute orthopedic trauma than in patients with CT-negative mTBI (p = 0.026) on arrival; however, no differences were found on the following days. The levels of UCH-L1 were not significantly different between these two groups at any measured point of time. Levels of GFAP and UCH-L1 were not able to distinguish patients with CT-negative mTBI from patients with orthopedic trauma. Patients with orthopedic trauma and high levels of UCH-L1 or GFAP values may be falsely diagnosed as having a concomitant mTBI, predisposing them to unwarranted diagnostics and unnecessary brain imaging. This casts a significant doubt on the diagnostic value of GFAP and UCH-L1 in cases with mTBI.

  20. Meeting Report--NASA Radiation Biomarker Workshop

    SciTech Connect

    Straume, Tore; Amundson, Sally A,; Blakely, William F.; Burns, Frederic J.; Chen, Allen; Dainiak, Nicholas; Franklin, Stephen; Leary, Julie A.; Loftus, David J.; Morgan, William F.; Pellmar, Terry C.; Stolc, Viktor; Turteltaub, Kenneth W.; Vaughan, Andrew T.; Vijayakumar, Srinivasan; Wyrobek, Andrew J.

    2008-05-01

    A summary is provided of presentations and discussions from the NASA Radiation Biomarker Workshop held September 27-28, 2007, at NASA Ames Research Center in Mountain View, California. Invited speakers were distinguished scientists representing key sectors of the radiation research community. Speakers addressed recent developments in the biomarker and biotechnology fields that may provide new opportunities for health-related assessment of radiation-exposed individuals, including for long-duration space travel. Topics discussed include the space radiation environment, biomarkers of radiation sensitivity and individual susceptibility, molecular signatures of low-dose responses, multivariate analysis of gene expression, biomarkers in biodefense, biomarkers in radiation oncology, biomarkers and triage following large-scale radiological incidents, integrated and multiple biomarker approaches, advances in whole-genome tiling arrays, advances in mass-spectrometry proteomics, radiation biodosimetry for estimation of cancer risk in a rat skin model, and confounding factors. Summary conclusions are provided at the end of the report.

  1. Biomarkers for Gastroesophageal Reflux in Respiratory Diseases

    PubMed Central

    Gíslason, Þórarinn; Olin, Anna-Carin; Janson, Christer; Ólafsson, Ísleifur

    2013-01-01

    Gastroesophageal reflux (GER) is commonly associated with respiratory symptoms, either through a vagal bronchoconstrictive reflex or through microaspiration of gastric contents. No diagnostic test is available, however, to diagnose when respiratory illnesses are caused by GER and when not, but research in this field has been moving forward. Various biomarkers in different types of biosamples have been studied in this context. The aim of this review is to summarize the present knowledge in this field. GER patients with respiratory diseases seem to have a different biochemical profile from similar patients without GER. Inflammatory biomarkers differ in asthmatics based on GER status, tachykinins are elevated in patients with GER-related cough, and bile acids are elevated in lung transplant patients with GER. However, studies on these biomarkers are often limited by their small size, methods of analysis, and case selections. The two pathogenesis mechanisms are associated with different respiratory illnesses and biochemical profiles. A reliable test to identify GER-induced respiratory disorders needs to be developed. Bronchoalveolar lavage is too invasive to be of use in most patients. Exhaled breath condensate samples need further evaluation and standardization. The newly developed particles in exhaled air measurements remain to be studied further. PMID:23653634

  2. Uptake of algal carbon and the synthesis of an "essential" fatty acid by Uvigerina ex. gr. semiornata (Foraminifera) within the Pakistan margin oxygen minimum zone: evidence from fatty acid biomarker and 13C tracer experiments

    NASA Astrophysics Data System (ADS)

    Larkin, K. E.; Gooday, A. J.; Woulds, C.; Jeffreys, R.; Schwartz, M.; Cowie, G.; Whitcraft, C.; Levin, L.; Dick, J. R.; Pond, D. W.

    2014-01-01

    Foraminifera are an important component of benthic communities in oxygen depleted settings, where they potentially play a~significant role in the processing of organic matter. We tracked the uptake of a 13C-labeled algal food source into individual fatty acids in the benthic foraminiferal species, Uvigerina ex. gr. semiornata, from the Arabian Sea oxygen minimum zone (OMZ). The tracer experiments were conducted on the Pakistan Margin during the late/post monsoon period (August-October 2003). A monoculture of the diatom Thalassiosira weisflogii was 13C-labeled and used to simulate a pulse of phytoplankton in two complementary experiments. A lander system was used for in situ incubations at 140 m and for 2.5 days duration, whilst a laboratory incubation used an oxystat system to maintain ambient dissolved oxygen concentrations. These shipboard experiments were terminated after 5 days. Uptake of diatoms was rapid, with high incorporation of diatom fatty acids into foraminifera after ~2 days in both experiments. Ingestion of the diatom food source was indicated by the increase over time in the quantity of diatom biomarker fatty acids in the foraminifera and by the high percentage of 13C in many of the fatty acids present at the endpoint of both in~situ and laboratory-based experiments. These results indicate that U. ex. gr. semiornata rapidly ingested the diatom food source and that this foraminifera will play an important role in the short-term cycling of organic matter within this OMZ environment. The experiments also suggested that U. ex. gr. semiornata consumed non-labeled bacterial food items, particularly bacteria, and synthesised the polyunsaturated fatty acid 20:4(n-6) de novo. 20:4(n-6) is often abundant in benthic fauna yet its origins and function have remained unclear. This study demonstrates that U. ex. gr. semiornata is capable of de novo synthesis of this "essential fatty acid" and is potentially a major source of this dietary nutrient in benthic food

  3. How To Expoit Chirality As A Biomarker; GC-MS Analysis Of The Martian Soil In The Moma Experiment

    NASA Astrophysics Data System (ADS)

    Freissinet, Caroline; Buch, A.; Sternberg, R.; Szopa, C.; Coll, P.; Rodier, C.; Stambouli, M.; Raulin, F.; Goesmann, F.; MOMA GC-team

    2009-09-01

    One of the goal of the next European Martian mission Exomars 2016 will be to find traces of life. In this aim the MOMA experiment will be dedicated to the search of organic compounds such as amino acids and possible presence of chiral compounds. Then, this work deals with the development of a space compatible analysis technique of chiral organic molecules using dimethyl-formamide dimethylacetal (DMF-DMA). This study involves three steps, extraction, derivatization and GC-MS analysis, which are firstly considered one by one, and then studied as a whole. This work shows that as well as its intrinsic qualities such as light weight derivatives and great resistance to drastic operating conditions, DMF-DMA allows simple and fast derivatization suitable with in situ analysis within the constraints of a space mission. It allows the identification of 19 out of the 20 proteogenic amino acids, and the enantiomeric separation of 10. Moreover, other amino and carboxylic acids, found on meteorites, and nucleic bases are also detected with the same parameters. Racemization of the molecules has been studied within the different conditions of derivatization. Measurement of the limit of detection show that the proposed method is suitable for a quantitative determination of enantiomers of several amino acids as the limit of detection is lower than the ppb level of organic molecules already detected in Martian meteorites. The extraction-derivatization-analysis combined in one pot raises more issues, as it added the constraints of each step to the whole. A single pot is used as the extraction reactor of the organic molecules from complex soils, the derivatization reactor with DMF-DMA and the injection tool to the gas chromatograph. Preliminary results let us very optimistic since from different soils, in a one-step one-pot reaction, one can detect and identify amino and carboxylic acids, as well as nucleic bases.

  4. Milk fat biomarkers and cardiometabolic disease

    PubMed Central

    Risérus, Ulf; Marklund, Matti

    2017-01-01

    Purpose of review Dairy is a major food group with potential impact on cardiometabolic health. Self-reported dairy intake has limitations that can partly be avoided by using biomarkers. This review aims to summarize the evidence of odd-chain saturated fatty acids (OCFAs), that is, pentadecanoic acid (C15 : 0) and heptadecanoic acid (17 : 0), as biomarkers of dairy fat intake. In addition, the associations of OCFA biomarkers with cardiometabolic disease will be overviewed. Recent findings Adipose tissue 15 : 0 is the preferred biomarker but also circulating 15 : 0, and to a weaker extent 17 : 0, reflects both habitual and changes in dairy intake. Whereas results from studies assessing cardiovascular outcomes are inconsistent, OCFA biomarkers are overall associated with lower diabetes risk. Residual confounding should however be considered until interventional data and mechanisms are available. Although OCFA biomarkers mainly reflect dairy fat intake, recently proposed endogenous synthesis and metabolism do motivate further research. Summary Taking into account the study population diet and limitations of OCFA biomarkers, both adipose and circulating levels of 15 : 0, in particular, are useful for estimating total dairy fat intake. OCFA biomarkers are overall not linked to cardiovascular disease risk, but a possible beneficial role of dairy foods in diabetes prevention warrant further study. PMID:27906713

  5. Rapid isolation of biomarkers for compound specific radiocarbon dating using high-performance liquid chromatography and flow injection analysis-atmospheric pressure chemical ionisation mass spectrometry.

    PubMed

    Smittenberg, Rienk H; Hopmans, Ellen C; Schouten, Stefan; Sinninghe Damsté, Jaap S

    2002-11-29

    Repeated semi-preparative normal-phase HPLC was performed to isolate selected biomarkers from sediment extracts for radiocarbon analysis. Flow injection analysis-mass spectrometry was used for rapid analysis of collected fractions to evaluate the separation procedure, taking only 1 min per fraction. In this way 100-1000 microg of glycerol dialkyl glycerol tetraethers, sterol fractions and chlorophyll-derived phytol were isolated from typically 100 g of marine sediment, i.e., in sufficient quantities for radiocarbon analysis, without significant carbon isotopic fractionation or contamination.

  6. Evaluation of the oxidative deoxyribonucleic acid damage biomarker 8-hydroxy-2'-deoxyguanosine in the urine of leukemic children by micellar electrokinetic capillary chromatography.

    PubMed

    Zhang, Pingping; Lian, Kaoqi; Wu, Xiaoli; Yao, Min; Lu, Xin; Kang, Weijun; Jiang, Lingling

    2014-04-04

    Determining the level of urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG), an oxidative DNA damage biomarker, is vital to the study of clinical pathogenesis and drug toxicity. The principal limitation of capillary electrophoresis (CE) with UV detection is its low sensitivity. To overcome this shortcoming, we developed a micellar electrokinetic capillary chromatography (MEKC) with solid-phase extraction (SPE) for urinary 8-OHdG analysis. The sensitivity of MEKC-UV was improved using a reasonable UV system, injection mode, and SPE. The parameters affecting MEKC and SPE were also optimized. The calibration curve was linear within the range from 1 to 500 μg L(-1). The limits of detection and quantification were 0.27 μg L(-1) and 0.82 μg L(-1), respectively. Interday and intraday precision were both <5.6%. The recovery of 8-OHdG in urine ranged from 94.5% to 103.2%. This method was used to measure urinary 8-OHdG from eight normal children, eight newly diagnosed leukemic children, and eight leukemic children undergoing chemotherapy. The results show that the proposed method can be used to assess oxidative stress in patients and the side effects of chemotherapeutic drugs by measuring urinary 8-OHdG.

  7. Biomarkers of Selenium Status

    PubMed Central

    Combs, Gerald F.

    2015-01-01

    The essential trace element, selenium (Se), has multiple biological activities, which depend on the level of Se intake. Relatively low Se intakes determine the expression of selenoenzymes in which it serves as an essential constituent. Higher intakes have been shown to have anti-tumorigenic potential; and very high Se intakes can produce adverse effects. This hierarchy of biological activities calls for biomarkers informative at different levels of Se exposure. Some Se-biomarkers, such as the selenoproteins and particularly GPX3 and SEPP1, provide information about function directly and are of value in identifying nutritional Se deficiency and tracking responses of deficient individuals to Se-treatment. They are useful under conditions of Se intake within the range of regulated selenoprotein expression, e.g., for humans <55 μg/day and for animals <20 μg/kg diet. Other Se-biomarkers provide information indirectly through inferences based on Se levels of foods, tissues, urine or feces. They can indicate the likelihood of deficiency or adverse effects, but they do not provide direct evidence of either condition. Their value is in providing information about Se status over a wide range of Se intake, particularly from food forms. There is need for additional Se biomarkers particularly for assessing Se status in non-deficient individuals for whom the prospects of cancer risk reduction and adverse effects risk are the primary health considerations. This would include determining whether supranutritional intakes of Se may be required for maximal selenoprotein expression in immune surveillance cells. It would also include developing methods to determine low molecular weight Se-metabolites, i.e., selenoamino acids and methylated Se-metabolites, which to date h