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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. PMID:17514495

  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. 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

  4. Biomarkers of myeloperoxidase-derived hypochlorous acid.

    PubMed

    Winterbourn, C C; Kettle, A J

    2000-09-01

    Hypochlorous acid is the major strong oxidant generated by neutrophils. The heme enzyme myeloperoxidase catalyzes the production of hypochlorous acid from hydrogen peroxide and chloride. Although myeloperoxidase has been implicated in the tissue damage that occurs in numerous diseases that involve inflammatory cells, it has proven difficult to categorically demonstrate that it plays a crucial role in any pathology. This situation should soon be rectified with the advent of sensitive biomarkers for hypochlorous acid. In this review, we outline the advantages and limitations of chlorinated tyrosines, chlorohydrins, 5-chlorocytosine, protein carbonyls, antibodies that recognize HOCl-treated proteins, and glutathione sulfonamide as potential biomarkers of hypochlorous acid. Levels of 3-chlorotyrosine and 3,5-dichlorotyrosine are increased in proteins after exposure to low concentrations of hypochlorous acid and we conclude that their analysis by gas chromatography and mass spectrometry is currently the best method available for probing the involvement of oxidation by myeloperoxidase in the pathology of particular diseases. The appropriate use of other biomarkers should provide complementary information.Keywords-Free radicals, Myeloperoxidase, Neutrophil oxidant, Hypochlorous acid, Chlorotyrosine, Chlorohydrin, Oxidant biomarker PMID:11020661

  5. 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

  6. 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. PMID:25919366

  7. Amino Acid Sequence Determination of Protein Biomarkers of Campylobacter upsaliensis and C. helveticus by 'Composite' Sequence Proteomic Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have identified the protein biomarkers observed in the matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF-MS) of cell lysates of five different strains of Campylobacter upsaliensis and one strain of C. helveticus by proteomic techniques. Only one of these strains ...

  8. Nucleic acid-based tissue biomarkers of urologic malignancies.

    PubMed

    Dietrich, Dimo; Meller, Sebastian; Uhl, Barbara; Ralla, Bernhard; Stephan, Carsten; Jung, Klaus; Ellinger, Jörg; Kristiansen, Glen

    2014-08-01

    Molecular biomarkers play an important role in the clinical management of cancer patients. Biomarkers allow estimation of the risk of developing cancer; help to diagnose a tumor, ideally at an early stage when cure is still possible; and aid in monitoring disease progression. Furthermore, they hold the potential to predict the outcome of the disease (prognostic biomarkers) and the response to therapy (predictive biomarkers). Altogether, biomarkers will help to avoid tumor-related deaths and reduce overtreatment, and will contribute to increased survival and quality of life in cancer patients due to personalized treatments. It is well established that the process of carcinogenesis is a complex interplay between genomic predisposition, acquired somatic mutations, epigenetic changes and genomic aberrations. Within this complex interplay, nucleic acids, i.e. RNA and DNA, play a fundamental role and therefore represent ideal candidates for biomarkers. They are particularly promising candidates because sequence-specific hybridization and amplification technologies allow highly accurate and sensitive assessment of these biomarker levels over a broad dynamic range. This article provides an overview of nucleic acid-based biomarkers in tissues for the management of urologic malignancies, i.e. tumors of the prostate, testis, kidney, penis, urinary bladder, renal pelvis, ureter and other urinary organs. Special emphasis is put on genomic, transcriptomic and epigenomic biomarkers (SNPs, mutations [genomic and mitochondrial], microsatellite instabilities, viral and bacterial DNA, DNA methylation and hydroxymethylation, mRNA expression, and non-coding RNAs [lncRNA, miRNA, siRNA, piRNA, snRNA, snoRNA]). Due to the multitude of published biomarker candidates, special focus is given to the general applicability of different molecular classes as biomarkers and some particularly promising nucleic acid biomarkers. Furthermore, specific challenges regarding the development and clinical

  9. Characterization of bacteria that suppress rhizoctonia damping-off in bark compost media by analysis of Fatty Acid biomarkers.

    PubMed

    Tunlid, A; Hoitink, H A; Low, C; White, D C

    1989-06-01

    Examination of cucumber roots (Cucumis sativus L.) grown in bark compost media and of the surrounding edaphic substrate showed profiles of polar lipid fatty acids commonly found in bacteria. The composition of fatty acids in these profiles differed significantly between roots grown in a medium naturally suppressive to Rhizoctonia damping-off and roots from a conducive medium. Cucumber roots from the suppressive medium had higher proportions of cis-vaccenic acid (18:1 omega 7c) and the iso-branched monoenoic fatty acid i17:1 omega 8 but lower proportions of several iso- and anteiso-branched fatty acids compared with roots from the conducive medium. The concentrations of the bacterial fatty acids were significantly lower in the surrounding media. However, the suppressive and conducive growth substrates had differences in the composition of the bacterial fatty acids similar to those found between the cucumber roots proper. These results suggest major differences in bacterial community composition between suppressive and conducive systems. Fatty acid analyses were also utilized to examine the effects on bacterial community composition of root colonization by Flavobacterium balustinum 299, a biocontrol agent. The concentration of the most prominent fatty acid in this bacterium, i17:1 omega 8, was increased on roots produced from inoculated seeds in a medium rendered suppressive by the treatment. This change was concomitant with a significant increase in the concentration of 18:1 omega 7c, not present in the lipids of the antagonist, indicating a shift in the microflora from a conducive to a suppressive bacterial community. PMID:16347930

  10. Alcohol biomarker analysis: simultaneous determination of 5-hydroxytryptophol glucuronide and 5-hydroxyindoleacetic acid by direct injection of urine using ultra-performance liquid chromatography-tandem mass spectrometry.

    PubMed

    Stephanson, Nikolai; Helander, Anders; Beck, Olof

    2007-07-01

    A direct ultra-performance liquid chromatography-tandem mass spectrometry method (UPLC-MS/MS) for simultaneous measurement of urinary 5-hydroxytryptophol glucuronide (GTOL) and 5-hydroxyindoleacetic acid (5-HIAA) was developed. The GTOL/5-HIAA ratio is used as an alcohol biomarker with clinical and forensic applications. The method involved dilution of the urine sample with deuterated analogues (internal standards), reversed-phase chromatography with gradient elution, electrospray ionisation and monitoring of two product ions per analyte in selected reaction monitoring mode. The measuring ranges were 6.7-10 000 nmol/l for GTOL and 0.07-100 micromol/l for 5-HIAA. The intra- and inter-assay imprecision, expressed as the coefficient of variation, was below 7%. Influence from ion suppression was noted for both compounds but was compensated for by the use of co-eluting internal standards. The accuracy in analytical recovery of added substance to urine samples was 96 and 98%, respectively, for GTOL and 5-HIAA. Method comparison with GC-MS for GTOL in 25 authentic patient samples confirmed the accuracy of the method with a median ratio between methods (GC-MS to UPLC-MS/MS) of 1.14 (r(2) = 0.975). The difference is explained by the fact that the GC-MS method also measures unconjugated 5-hydroxytryptophol naturally present in urine. The comparison with data for 5-HIAA obtained by an HPLC method demonstrated a median ratio of 1.05 between the methods. The UPLC-MS/MS method was capable of measuring endogenous GTOL and 5-HIAA levels in urine, which agreed with the literature data. In conclusion, a fully validated and robust direct method for the routine measurement of urinary GTOL and 5-HIAA was developed. PMID:17565712

  11. Preservation of terrestrial plant biomarkers from Nachukui Formation sediments and their viability for stable isotope analysis

    NASA Astrophysics Data System (ADS)

    Kahle, E.; Uno, K. T.; Polissar, P. J.; Lepre, C. J.; deMenocal, P. B.

    2013-12-01

    Plio-Pleistocene sedimentary records from the Turkana Basin in eastern Africa provide a unique opportunity to compare a high-resolution record of climate and terrestrial vegetation with important changes in the record of human evolution. Molecular biomarkers from terrestrial vegetation can yield stable isotope ratios of hydrogen and carbon that reflect ancient climate and vegetation. However, the preservation of long-chain plant wax biomarkers in these paleosol, fluvial, and lacustrine sediments is not known, and this preservation must be studied to establish their utility for molecular stable isotope studies. We investigated leaf wax biomarkers in Nachukui Formation sediments deposited between 2.3 and 1.7 Ma to assess biomarker preservation. We analyzed n alkane and n alkanoic acid concentrations and, where suitable, molecular carbon and hydrogen isotope ratios. Molecular abundance distributions show a great deal of variance in biomarker preservation and plant-type source as indicated by the carbon preference index and average chain length. This variation suggests that some samples are suitable for isotopic analysis, while other samples lack primary terrestrial plant biomarker signatures. The biomarker signal in many samples contains significant additional material from unidentified sources. For example, the n-alkane distributions contain an unresolved complex mixture underlying the short and mid-chain n-alkanes. Samples from lacustrine intervals include long-chain diacids, hydroxy acids and (ω-1) ketoacids that suggest degradation of the original acids. Degradation of poorly preserved samples and the addition of non-terrestrial plant biomarkers may originate from a number of processes including forest fire or microbial alteration. Isotopic analysis of well-preserved terrestrial plant biomarkers will be presented along with examples where the original biomarker distribution has been altered.

  12. Biological reactivity and biomarkers of the neutrophil oxidant, hypochlorous acid.

    PubMed

    Winterbourn, Christine C

    2002-12-27

    Free radicals or reactive oxygen species are thought to contribute to the pathology of many diseases. These include inflammatory conditions, where neutrophils accumulate in large numbers and are stimulated to produce superoxide and other reactive oxidants. Hypochlorous acid (HOCl), produced by myeloperoxidase-catalysed oxidation of chloride by hydrogen peroxide, is the major strong oxidant generated by these cells. Neutrophil-mediated injury may also be important in toxicology when an initial insult is followed by an inflammatory response. It is important to characterize the inflammatory component of such injury and the extent to which it involves reactive oxidants. On the one hand, this requires an understanding of how neutrophil oxidants react with cells and tissue constituents. On the other, specific biomarkers are needed so that oxidative damage can be quantified in clinical material and related to disease severity. This presentation considers biologically relevant reactions of HOCl and the biomarker assays that can be applied to probing the pathological role of myeloperoxidase and its products. PMID:12505315

  13. 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

  14. Integrated Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) Quantitative Proteomic Analysis Identifies Galectin-1 as a Potential Biomarker for Predicting Sorafenib Resistance in Liver Cancer*

    PubMed Central

    Yeh, Chao-Chi; Hsu, Chih-Hung; Shao, Yu-Yun; Ho, Wen-Ching; Tsai, Mong-Hsun; Feng, Wen-Chi; Chow, Lu-Ping

    2015-01-01

    Sorafenib has become the standard therapy for patients with advanced hepatocellular carcinoma (HCC). Unfortunately, most patients eventually develop acquired resistance. Therefore, it is important to identify potential biomarkers that could predict the efficacy of sorafenib. To identify target proteins associated with the development of sorafenib resistance, we applied stable isotope labelling with amino acids in cell culture (SILAC)-based quantitative proteomic approach to analyze differences in protein expression levels between parental HuH-7 and sorafenib-acquired resistance HuH-7 (HuH-7R) cells in vitro, combined with an isobaric tags for relative and absolute quantitation (iTRAQ) quantitative analysis of HuH-7 and HuH-7R tumors in vivo. In total, 2,450 quantified proteins were identified in common in SILAC and iTRAQ experiments, with 81 showing increased expression (>2.0-fold) with sorafenib resistance and 75 showing decreased expression (<0.5-fold). In silico analyses of these differentially expressed proteins predicted that 10 proteins were related to cancer with involvements in cell adhesion, migration, and invasion. Knockdown of one of these candidate proteins, galectin-1, decreased cell proliferation and metastasis in HuH-7R cells and restored sensitivity to sorafenib. We verified galectin-1 as a predictive marker of sorafenib resistance and a downstream target of the AKT/mTOR/HIF-1α signaling pathway. In addition, increased galectin-1 expression in HCC patients' serum was associated with poor tumor control and low response rate. We also found that a high serum galectin-1 level was an independent factor associated with poor progression-free survival and overall survival. In conclusion, these results suggest that galectin-1 is a possible biomarker for predicting the response of HCC patients to treatment with sorafenib. As such, it may assist in the stratification of HCC and help direct personalized therapy. PMID:25850433

  15. 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. PMID:26137879

  16. Applications of microfluidics and microchip electrophoresis for potential clinical biomarker analysis.

    PubMed

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

    2015-09-01

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

  17. 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

  18. 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

  19. Glycodeoxycholic Acid Levels as Prognostic Biomarker in Acetaminophen-Induced Acute Liver Failure Patients

    PubMed Central

    Woolbright, Benjamin L.; McGill, Mitchell R.; Staggs, Vincent S.; Winefield, Robert D.; Gholami, Parviz; Olyaee, Mojtaba; Sharpe, Matthew R.; Curry, Steven C.; Lee, William M.; Jaeschke, Hartmut

    2014-01-01

    Acetaminophen (APAP)-induced acute liver failure (ALF) remains a major clinical problem. Although a majority of patients recovers after severe liver injury, a subpopulation of patients proceeds to ALF. Bile acids are generated in the liver and accumulate in blood during liver injury, and as such, have been proposed as biomarkers for liver injury and dysfunction. The goal of this study was to determine whether individual bile acid levels could determine outcome in patients with APAP-induced ALF (AALF). Serum bile acid levels were measured in AALF patients using mass spectrometry. Bile acid levels were elevated 5–80-fold above control values in injured patients on day 1 after the overdose and decreased over the course of hospital stay. Interestingly, glycodeoxycholic acid (GDCA) was significantly increased in non-surviving AALF patients compared with survivors. GDCA values obtained at peak alanine aminotransferase (ALT) and from day 1 of admission indicated GDCA could predict survival in these patients by receiver-operating characteristic analysis (AUC = 0.70 for day 1, AUC = 0.68 for peak ALT). Of note, AALF patients also had significantly higher levels of serum bile acids than patients with active cholestatic liver injury. These data suggest measurements of GDCA in this patient cohort modestly predicted outcome and may serve as a prognostic biomarker. Furthermore, accumulation of bile acids in serum or plasma may be a result of liver cell dysfunction and not cholestasis, suggesting elevation of circulating bile acid levels may be a consequence and not a cause of liver injury. PMID:25239633

  20. Amino acids as biomarkers in the SOD1(G93A) mouse model of ALS.

    PubMed

    Bame, Monica; Grier, Robert E; Needleman, Richard; Brusilow, William S A

    2014-01-01

    The development of therapies for Amyotrophic Lateral Sclerosis (ALS) has been hindered by the lack of biomarkers for both identifying early disease and for monitoring the effectiveness of drugs. The identification of ALS biomarkers in presymptomatic individuals might also provide clues to the earliest biochemical correlates of the disease. Previous attempts to use plasma metabolites as biomarkers have led to contradictory results, presumably because of heterogeneity in both the underlying genetics and the disease stage in the clinical population. To eliminate these two sources of heterogeneity we have characterized plasma amino acids and other metabolites in the SOD1(G93A) transgenic mouse model for ALS. Presymptomatic SOD1(G93A) mice have significant differences in concentrations of several plasma metabolites compared to wild type animals, most notably in the concentrations of aspartate, cystine/cysteine, and phosphoethanolamine, and in changes indicative of methylation defects. There are significant changes in amino acid compositions between 50 and 70days of age in both the SOD1(G93A) and wild type mice, and several of the age-related and disease-related differences in metabolite concentration were also gender-specific. Many of the SOD1(G93A)-related differences could be altered by treatment of mice with methionine sulfoximine, which extends the lifespan of this mouse, inhibits glutamine synthetase, and modifies brain methylation reactions. These studies show that assaying plasma metabolites can effectively distinguish transgenic mice from wild type, suggesting that one or more plasma metabolites might be useful biomarkers for the disease in humans, especially if genetic and longitudinal analysis is used to reduce population heterogeneity. PMID:24129262

  1. ANALYSIS OF NASAL TISSUE FOR BIOMARKERS OF CHLORINE EXPOSURE

    EPA Science Inventory

    Both 3-chloro-tyrosine (CT) and 3,5-dichloro-tyrosine (dCT) are sensitive and specific biomarkers for evaluating exposure to chlorine gas (Cl2) and hypochlorous acid (HOCl). Previous investigations have focused on the formation of CT and dCT resulting from biochemical responses ...

  2. Occupational Exposure to HDI: Progress and Challenges in Biomarker Analysis

    PubMed Central

    Flack, Sheila L.; Ball, Louise M.; Nylander-French, Leena A.

    2010-01-01

    1,6-hexamethylene diisocyanate (HDI) is extensively used in the automotive repair industry and is a commonly reported cause of occupational asthma in industrialized populations. However, the exact pathological mechanism remains uncertain. Characterization and quantification of biomarkers resulting from HDI exposure can fill important knowledge gaps between exposure, susceptibility, and the rise of immunological reactions and sensitization leading to asthma. Here, we discuss existing challenges in HDI biomarker analysis including the quantification of N-acetyl-1,6-hexamethylene diamine (monoacetyl-HDA) and N,N′-diacetyl-1,6-hexamethylene diamine (diacetyl-HDA) in urine samples based on previously established methods for HDA analysis. In addition, we describe the optimization of reaction conditions for the synthesis of monoacetyl-HDA and diacetyl-HDA, and utilize these standards for the quantification of these metabolites in the urine of three occupationally exposed workers. Diacetyl-HDA was present in untreated urine at 0.015 – 0.060 μg/l. Using base hydrolysis, the concentration range of monoacetyl-HDA in urine was 0.19 – 2.2 μg/l, 60-fold higher than in the untreated samples on average. HDA was detected only in one sample after base hydrolysis (0.026 μg/l). In contrast, acid hydrolysis yielded HDA concentrations ranging from 0.36 to 10.1 μg/l in these three samples. These findings demonstrate HDI metabolism via N-acetylation metabolic pathway and protein adduct formation resulting from occupational exposure to HDI. PMID:20176515

  3. Occupational exposure to HDI: progress and challenges in biomarker analysis.

    PubMed

    Flack, Sheila L; Ball, Louise M; Nylander-French, Leena A

    2010-10-01

    1,6-Hexamethylene diisocyanate (HDI) is extensively used in the automotive repair industry and is a commonly reported cause of occupational asthma in industrialized populations. However, the exact pathological mechanism remains uncertain. Characterization and quantification of biomarkers resulting from HDI exposure can fill important knowledge gaps between exposure, susceptibility, and the rise of immunological reactions and sensitization leading to asthma. Here, we discuss existing challenges in HDI biomarker analysis including the quantification of N-acetyl-1,6-hexamethylene diamine (monoacetyl-HDA) and N,N'-diacetyl-1,6-hexamethylene diamine (diacetyl-HDA) in urine samples based on previously established methods for HDA analysis. In addition, we describe the optimization of reaction conditions for the synthesis of monoacetyl-HDA and diacetyl-HDA, and utilize these standards for the quantification of these metabolites in the urine of three occupationally exposed workers. Diacetyl-HDA was present in untreated urine at 0.015-0.060 μg/l. Using base hydrolysis, the concentration range of monoacetyl-HDA in urine was 0.19-2.2 μg/l, 60-fold higher than in the untreated samples on average. HDA was detected only in one sample after base hydrolysis (0.026 μg/l). In contrast, acid hydrolysis yielded HDA concentrations ranging from 0.36 to 10.1 μg/l in these three samples. These findings demonstrate HDI metabolism via N-acetylation metabolic pathway and protein adduct formation resulting from occupational exposure to HDI. PMID:20176515

  4. 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

  5. Novel biomarkers of the metabolism of caffeic acid derivatives in vivo.

    PubMed

    Rechner, A R; Spencer, J P; Kuhnle, G; Hahn, U; Rice-Evans, C A

    2001-06-01

    The purpose of this study was to investigate biomarkers of the bioavailability and metabolism of hydroxycinnamate derivatives through the determination of the pharmacokinetics of their urinary elimination and identification of the metabolites excreted. Coffee was used as a rich source of caffeic acid derivatives and human supplementation was undertaken. The results show a highly significant increase in the excretion of ferulic, isoferulic, dihydroferulic acid (3-(4-hydroxy-3-methoxyphenyl)-propionic acid), and vanillic acid postsupplementation relative to the levels presupplementation. Thus, ferulic, isoferulic, and dihydroferulic acids are specific biomarkers for the bioavailability and metabolism of dietary caffeic acid esters. Isoferulic acid is a unique biomarker as it is not a dietary component, however, dihydroferulic acid may well derive from other flavonoids with a structurally related B-ring. 3-Hydroxyhippuric acid has also been identified as an indicator for bioavailability and metabolism of phenolic compounds, and shows a highly significant excretion increase postsupplementation. The results reveal isoferulic acid (and possibly dihydroferulic acid) as novel markers of caffeoyl quinic acid metabolism. PMID:11368919

  6. 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

  7. 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. PMID:26540631

  8. 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

  9. 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). PMID:23075272

  10. 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.

  11. 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

  12. 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.

  13. 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...

  14. Characterization of rational biomarkers accompanying fever in yeast-induced pyrexia rats using urine metabolic footprint analysis.

    PubMed

    Guo, Mingxing; Gu, Hao; Song, Yuelin; Peng, Long; Liu, Haiyu; Zhang, Li; Lin, Zhaozhou; Wang, Yun; Gao, Xiaoyan; Qiao, Yanjiang

    2014-07-01

    Fever is a prominent feature of diseases and is an ongoing process that is always accompanied by metabolic changes in the body system. Despite the success of temperature regulation theory, the underlying biological process remains unclear. To truly understand the nature of the febrile response, it is crucial to confirm the biomarkers during the entire biological process. In the current study, a 73-h metabolic footprint analysis of the urine from yeast-induced pyrexia rats was performed using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Potential biomarkers were selected using orthogonal partial least squares-discriminate analysis (OPLS-DA), the rational biomarkers were verified by Pearson correlation analysis, and the predictive power was evaluated using receiver operator characteristic (ROC) curves. A metabolic network constructed using traditional Chinese medicine (TCM) grammar systems was used to validate the rationality of the verified biomarkers. Finally, five biomarkers, including indoleacrylic acid, 3-methyluridine, tryptophan, nicotinuric acid and PI (37:3), were confirmed as rational biomarkers because their correlation coefficients were all greater than 0.87 and because all of the correlation coefficients between any pair of these biomarkers were higher than 0.75. The areas under the ROC curves were all greater than 0.84, and their combined predictive power was considered reliable because the greatest area under the ROC curve was 0.968. A metabolic network also demonstrated the rationality of these five biomarkers. Therefore, these five metabolites can be adopted as rational biomarkers to reflect the process of the febrile response in inflammation-induced pyrexia. PMID:24631712

  15. Identification of potential erythrocyte phospholipid fatty acid biomarkers of advanced lung adenocarcinoma, squamous cell lung carcinoma, and small cell lung cancer.

    PubMed

    Sánchez-Rodríguez, Patricia; Rodríguez, Marina C; Sánchez-Yagüe, Jesús

    2015-07-01

    New biomarkers for lung cancer would be valuable. Our aim was to analyze the fatty acid profiles of the main phospholipid species in erythrocytes from patients with advanced squamous cell lung carcinoma (SCC), lung adenocarcinoma (ADC), and small cell lung cancer (SCLC) and benign lung diseases (chronic obstructive pulmonary disease (COPD) and asthma) to determine the fatty acids that could be use as lung cancer markers. Twenty-eight, 18, 14, 16, and 15 patients with, respectively, SCC, ADC, SCLC, asthma, and COPD and 50 healthy subjects were enrolled in the study. Fatty acid profiles were investigated using gas chromatography/mass spectrometry followed by receiver operating characteristic (ROC) curve analysis. The fatty acid profiles changed significantly in the different pathologies analyzed. Based on the diagnostic yields and operating characteristics, the most significant fatty acids that might be used as biomarkers were as follows: ADC--arachidonic acid (20:4n6) in phosphatidylcholine and oleic acid (18:1n9) in phosphatidylethanolamine (PE); SCC--eicosapentaenoic acid (20:5n3) in PE and palmitic acid (16:0) in phosphatidylserine + phosphatidylinositol (PS+PI); SCLC--eicosadienoic acid (20:2n6) in PS+PI and lignoceric acid (24:0) in sphingomyelin. In conclusion, fatty acids from erythrocyte phospholipid species might serve as biomarkers in the diagnosis, and probably in other aspects related to clinical disease management, of ADC, SCC, and SCLC. PMID:25702090

  16. Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas.

    PubMed

    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; Darb-Esfahani, Silvia; Braicu, Elena Ioana

    2016-02-15

    Ovarian cancer is a heterogeneous disease of low prevalence, but poor survival. Early diagnosis is critical for survival, but it 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 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

  17. 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

  18. Evaluation of serum bile acid profiles as biomarkers of liver injury in rodents.

    PubMed

    Luo, Lina; Schomaker, Shelli; Houle, Christopher; Aubrecht, Jiri; Colangelo, Jennifer L

    2014-01-01

    Bile acids (BAs) have been studied as potential biomarkers of drug-induced liver injury. However, the relationship between levels of individual BAs and specific forms of liver injury remains to be fully understood. Thus, we set out to evaluate cholic acid (CA), glycocholic acid (GCA), and taurocholic acid (TCA) as potential biomarkers of liver injury in rodent toxicity studies. We have developed a sensitive liquid chromatography-tandem mass spectrometry (LC/MS/MS) assay applicable to rat and mouse serum and evaluated levels of the individual BAs in comparison with the classical biomarkers of hepatotoxicity (alanine aminotransferase [ALT], aspartate aminotransferase [AST], glutamate dehydrogenase (GLDH), alkaline phosphatase, total bilirubin, gamma-glutamyl transferase, and total BAs) and histopathology findings in animals treated with model toxicants. The pattern of changes in the individual BAs varied with different forms of liver injury. Animals with histopathologic signs of hepatocellular necrosis showed increases in all 3 BAs tested, as well as increases in ALT, AST, GLDH, and total BAs. Animals with histopathologic signs of bile duct hyperplasia (BDH) displayed increases in only conjugated BAs (GCA and TCA), a pattern not observed with the other toxicants. Because BDH is detectable only via histopathology, our results indicate the potential diagnostic value of examining individual BAs levels in serum as biomarkers capable of differentiating specific forms of liver injury in rodent toxicity studies. PMID:24085190

  19. Oxidative stress markers, secondary bile acids and sulfated bile acids classify the clinical liver injury type: Promising diagnostic biomarkers for cholestasis.

    PubMed

    Masubuchi, Noriko; Sugihara, Masahiro; Sugita, Tomonori; Amano, Katsushi; Nakano, Masanori; Matsuura, Tomokazu

    2016-08-01

    Clinicians sometimes encounter difficulty in choosing a therapeutic strategy due to the uncertainty regarding the type of liver injury. In particular, cholestasis is difficult to diagnose by conventional markers at an early stage of disease. The aim of this study was to identify promising biomarkers for distinguishing the symptom-based types of liver injury (e.g. hepatocellular injury, cholestasis), which was derived from a rigorously statistical perspective. The associations between diagnostic biomarkers (e.g. bile acid components, oxidative stress markers and liver fibrosis markers) and the liver injury types were assessed by a multiple logistic regression analysis using 304 blood samples from patients with liver disease. As a result, reductions in the lithocholic acid (LCA) and deoxycholic acid (DCA) levels, and elevation of the serum sulfated bile acid (SSBA), liver fibrosis marker IV collagen (type IV collagen), hyaluronic acid (HA) and reactive oxygen species (ROS) levels were all significantly associated with cholestasis. On the other hand, elevations in the LCA and type IV collagen levels, and a reduction in the ursodeoxy cholic acid (UDCA) level, were significantly associated with hepatocellular injury. The receiver operating characteristic (ROC) analyses showed that the largest area under the ROC curve (AUC) was found for ROS, followed by DCA, HA, LCA, SSBA and type IV collagen in the cholestatic-type cases. These results indicated that ROS, the secondary bile acid levels such as DCA and LCA, and SSBA are promising biomarkers for cholestasis and for classifying the type of liver injuries. This comprehensive approach will allow for an accurate diagnosis, which will facilitate the selection of an appropriate therapy at the onset of disease. PMID:26325587

  20. 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...

  1. Exhaled breath volatile biomarker analysis for thyroid cancer.

    PubMed

    Guo, Lei; Wang, Changsong; Chi, Chunjie; Wang, Xiaoyang; Liu, Shanshan; Zhao, Wei; Ke, Chaofu; Xu, Guowang; Li, Enyou

    2015-08-01

    Compared with other types of cancer, thyroid cancer incidence rates have increased rapidly worldwide in the past few decades. In recent years, potential thyroid cancer biomarkers have been studied, but these biomarkers have neither specificity nor good positive predictive value. Exhaled breath analysis is a recently developed convenient and noninvasive method for screening and diagnosing the disease. In this study, potential thyroid cancer biomarkers in volatile organic compounds (VOCs) were detected. Exhaled breath was collected from 64 patients with histologically confirmed cases of thyroid disease (including 39 individuals with papillary thyroid carcinoma and 25 individuals with nodular goiters) and 32 healthy volunteers. Solid-phase microextraction-gas chromatography and mass spectrometry was used to assess the exhaled VOCs of the study participants. The statistical methods of principal component analysis and partial least-squares discriminant analysis were performed to process the final data. The VOCs exhibited significant differences between nodular goiter patients and normal controls, papillary thyroid carcinoma patients and normal controls, and papillary thyroid carcinoma patients and nodular goiter patients; 7, 7, and 3 characteristic metabolites played decisive roles in sample classification, respectively. Breath analysis may provide a new, noninvasive, and directly qualitative method for the clinical diagnosis of thyroid disease. PMID:25666355

  2. 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

  3. Immunoproteomic Analysis of Potential Serum Biomarker Candidates in Human Glaucoma

    PubMed Central

    Tezel, Gülgün; Thornton, Ivey L.; Tong, Melissa G.; Luo, Cheng; Yang, Xiangjun; Cai, Jian; Powell, David W.; Soltau, Joern B.; Liebmann, Jeffrey M.; Ritch, Robert

    2012-01-01

    Purpose. Evidence supporting the immune system involvement in glaucoma includes increased titers of serum antibodies to retina and optic nerve proteins, although their pathogenic importance remains unclear. This study using an antibody-based proteomics approach aimed to identify disease-related antigens as candidate biomarkers of glaucoma. Methods. Serum samples were collected from 111 patients with primary open-angle glaucoma and an age-matched control group of 49 healthy subjects without glaucoma. For high-throughput characterization of antigens, serum IgG was eluted from five randomly selected glaucomatous samples and analyzed by linear ion trap mass spectrometry (LC-MS/MS). Serum titers of selected biomarker candidates were then measured by specific ELISAs in the whole sample pool (including an additional control group of diabetic retinopathy). Results. LC-MS/MS analysis of IgG elutes revealed a complex panel of proteins, including those detectable only in glaucomatous samples. Interestingly, many of these antigens corresponded to upregulated retinal proteins previously identified in glaucomatous donors (or that exhibited increased methionine oxidation). Moreover, additional analysis detected a greater immunoreactivity of the patient sera to glaucomatous retinal proteins (or to oxidatively stressed cell culture proteins), thereby suggesting the importance of disease-related protein modifications in autoantibody production/reactivity. As a narrowing-down strategy for selection of initial biomarker candidates, we determined the serum proteins overlapping with the retinal proteins known to be up-regulated in glaucoma. Four of the selected 10 candidates (AIF, cyclic AMP-responsive element binding protein, ephrin type-A receptor, and huntingtin) exhibited higher ELISA titers in the glaucomatous sera. Conclusions. A number of serum proteins identified by this immunoproteomic study of human glaucoma may represent diseased tissue-related antigens and serve as candidate

  4. Amino acid analysis.

    PubMed

    Crabb, J W; West, K A; Dodson, W S; Hulmes, J D

    2001-05-01

    Amino acid analysis (AAA) is one of the best methods to quantify peptides and proteins. Two general approaches to quantitative AAA exist, namely, classical postcolumn derivatization following ion-exchange chromatography and precolumn derivatization followed by reversed-phase HPLC (RP-HPLC). Excellent instrumentation and several specific methodologies are available for both approaches, and both have advantages and disadvantages. This unit focuses on picomole-level AAA of peptides and proteins using the most popular precolumn-derivatization method, namely, phenylthiocarbamyl amino acid analysis (PTC-AAA). It is directed primarily toward those interested in establishing the technology with a modest budget. PTC derivatization and analysis conditions are described, and support and alternate protocols describe additional techniques necessary or useful for most any AAA method--e.g., sample preparation, hydrolysis, instrument calibration, data interpretation, and analysis of difficult or unusual residues such as cysteine, tryptophan, phosphoamino acids, and hydroxyproline. PMID:18429107

  5. Relative acidic compartment volume as a lysosomal storage disorder–associated biomarker

    PubMed Central

    te Vruchte, Danielle; Speak, Anneliese O.; Wallom, Kerri L.; Al Eisa, Nada; Smith, David A.; Hendriksz, Christian J.; Simmons, Louise; Lachmann, Robin H.; Cousins, Alison; Hartung, Ralf; Mengel, Eugen; Runz, Heiko; Beck, Michael; Amraoui, Yasmina; Imrie, Jackie; Jacklin, Elizabeth; Riddick, Kate; Yanjanin, Nicole M.; Wassif, Christopher A.; Rolfs, Arndt; Rimmele, Florian; Wright, Naomi; Taylor, Clare; Ramaswami, Uma; Cox, Timothy M.; Hastings, Caroline; Jiang, Xuntian; Sidhu, Rohini; Ory, Daniel S.; Arias, Begona; Jeyakumar, Mylvaganam; Sillence, Daniel J.; Wraith, James E.; Porter, Forbes D.; Cortina-Borja, Mario; Platt, Frances M.

    2014-01-01

    Lysosomal storage disorders (LSDs) occur at a frequency of 1 in every 5,000 live births and are a common cause of pediatric neurodegenerative disease. The relatively small number of patients with LSDs and lack of validated biomarkers are substantial challenges for clinical trial design. Here, we evaluated the use of a commercially available fluorescent probe, Lysotracker, that can be used to measure the relative acidic compartment volume of circulating B cells as a potentially universal biomarker for LSDs. We validated this metric in a mouse model of the LSD Niemann-Pick type C1 disease (NPC1) and in a prospective 5-year international study of NPC patients. Pediatric NPC subjects had elevated acidic compartment volume that correlated with age-adjusted clinical severity and was reduced in response to therapy with miglustat, a European Medicines Agency–approved drug that has been shown to reduce NPC1-associated neuropathology. Measurement of relative acidic compartment volume was also useful for monitoring therapeutic responses of an NPC2 patient after bone marrow transplantation. Furthermore, this metric identified a potential adverse event in NPC1 patients receiving i.v. cyclodextrin therapy. Our data indicate that relative acidic compartment volume may be a useful biomarker to aid diagnosis, clinical monitoring, and evaluation of therapeutic responses in patients with lysosomal disorders. PMID:24487591

  6. Sterols and fatty acid biomarkers as indicators of changes in soil microbial communities in a uranium mine area.

    PubMed

    Guedes, Maria J; Pereira, Ruth; Duarte, Kátia; Rocha-Santos, Teresa A P; Antunes, Sara C; Gonçalves, Fernando; Duarte, Armando C; Freitas, Ana C

    2011-01-01

    Included in the 2nd tier of a site specific risk assessment that is being carried out in an abandoned uranium mine (Cunha Baixa uranium mine, Central Portugal), fatty acids biomarkers and sterols were analyzed to assess the impact of soil contamination with metals and radionuclides in the structure of the microbial community in seven sampling sites located at different distances from the mine. Surface soil samples were collected in those sampling sites in the four different seasons of the year. Principal component analysis (PCA) was performed on fatty acid biomarkers and sterols. Subsequently PCA scores obtained for both components were used to test the effect of sites and seasons, on soil samples collected in the Cunha Baixa uranium mine, through bi-factorial ANOVAs. Through PCA analysis, two distinct groups were set apart along the first two components. One group included sites at a great distance from the mine which were negatively correlated with higher contents of iC15:0 and iC17:0, both indicators of Gram-positive bacteria, as well as with ergosterol, cholestanol and cholesterol. The second group, in turn, was composed of the sampling sites most impacted by ore exploration, in situ leaching of poor ore, and spread of sludge from the effluent treatment pond. These sites were positively correlated with higher levels of iC16:0 (Gram-positive bacteria indicator), cyC17:0 (generally common in gram negative bacteria) and C18:0 and C17:0 biomarkers of non-specific bacteria. The profile of fatty acids obtained in the sampling sites revealed variable predominance of groups of bacteria which are a clear indication of differences in the soil microbial communities that are directly related to the environmental conditions prevailing in the uranium mine area. PMID:21547821

  7. Chiral amino acid metabolomics for novel biomarker screening in the prognosis of chronic kidney disease.

    PubMed

    Kimura, Tomonori; Hamase, Kenji; Miyoshi, Yurika; Yamamoto, Ryohei; Yasuda, Keiko; Mita, Masashi; Rakugi, Hiromi; Hayashi, Terumasa; Isaka, Yoshitaka

    2016-01-01

    D-Amino acids, the enantiomers of L-amino acids, are increasingly recognized as novel biomarkers. Although the amounts of D-amino acids are usually very trace in human, some of them have sporadically been detected in blood from patients with kidney diseases. This study examined whether multiple chiral amino acids would be associated with kidney functions, comorbidities, and prognosis of chronic kidney disease (CKD) by enantioselective analyses of all chiral amino acids with a micro-two-dimensional high-performance liquid chromatograph (2D-HPLC)-based analytical platform. 16 out of 21 D-amino acids were detected in plasma from 108 CKD patients in a longitudinal cohort. The levels of D-Ser, D-Pro, and D-Asn were strongly associated with kidney function (estimated glomerular filtration ratio), the levels of D-Ala and D-Pro were associated with age, and the level of D-Asp and D-Pro were associated with the presence of diabetes mellitus. D-Ser and D-Asn were significantly associated with the progression of CKD in mutually-adjusted Cox regression analyses; the risk of composite end point (developing to ESKD or death before ESKD) was elevated from 2.7- to 3.8-fold in those with higher levels of plasma D-Ser and D-Asn. These findings identified chiral amino acids as potential biomarkers in kidney diseases. PMID:27188851

  8. Chiral amino acid metabolomics for novel biomarker screening in the prognosis of chronic kidney disease

    PubMed Central

    Kimura, Tomonori; Hamase, Kenji; Miyoshi, Yurika; Yamamoto, Ryohei; Yasuda, Keiko; Mita, Masashi; Rakugi, Hiromi; Hayashi, Terumasa; Isaka, Yoshitaka

    2016-01-01

    D-Amino acids, the enantiomers of L-amino acids, are increasingly recognized as novel biomarkers. Although the amounts of D-amino acids are usually very trace in human, some of them have sporadically been detected in blood from patients with kidney diseases. This study examined whether multiple chiral amino acids would be associated with kidney functions, comorbidities, and prognosis of chronic kidney disease (CKD) by enantioselective analyses of all chiral amino acids with a micro-two-dimensional high-performance liquid chromatograph (2D-HPLC)-based analytical platform. 16 out of 21 D-amino acids were detected in plasma from 108 CKD patients in a longitudinal cohort. The levels of D-Ser, D-Pro, and D-Asn were strongly associated with kidney function (estimated glomerular filtration ratio), the levels of D-Ala and D-Pro were associated with age, and the level of D-Asp and D-Pro were associated with the presence of diabetes mellitus. D-Ser and D-Asn were significantly associated with the progression of CKD in mutually-adjusted Cox regression analyses; the risk of composite end point (developing to ESKD or death before ESKD) was elevated from 2.7- to 3.8-fold in those with higher levels of plasma D-Ser and D-Asn. These findings identified chiral amino acids as potential biomarkers in kidney diseases. PMID:27188851

  9. 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

  10. 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

  11. Anthranilic Acid: A Potential Biomarker and Treatment Target for Schizophrenia

    PubMed Central

    Oxenkrug, Gregory; van der Hart, Marieke; Roeser, Julien; Summergrad, Paul

    2016-01-01

    Dysregulation of Trp-Kyn pathway is the most recent hypothesis of mechanisms of schizophrenia. In particular, over-production of kynurenic acid (KYNA), one of the three immediate downstream metabolites of kynurenine (Kyn) along tryptophan (Trp): Kyn pathway, has been considered as a new target for therapeutic intervention in schizophrenia. Up-regulation of KYNA formation was suggested to occur at the expense of down-regulated production of 3-hydroxyKyn (3-HK), the second immediate downstream metabolite of Kyn. We were interested to assess the third immediate downstream Kyn metabolite, anthranilic acid (AA). Serum AA concentrations were evaluated in schizophrenia patients and control subjects by HPLC-mass spectrometry method. We found 2-fold increase of AA and 3-fold decrease of 3-HK concentrations in serum of schizophrenia patients. Up regulated formation of AA might contribute to mechanisms of schizophrenia considering experimental evidences of AA augmentation of autoimmune processes in rat and mice; clinical findings of AA elevation in rheumatoid arthritis and type 1 diabetes, autoimmune diseases diametrical to schizophrenia; and involvement of autoimmunity in development of schizophrenia. Present data warrant further studies of AA as biological marker in, at least, a subgroup (associated with autoimmune mechanisms) of schizophrenia patients and as a new target for therapeutic intervention. PMID:27042691

  12. Molecular and lipid biomarker analysis of a gypsum-hosted endoevaporitic microbial community.

    PubMed

    Jahnke, L L; Turk-Kubo, K A; N Parenteau, M; Green, S J; Kubo, M D Y; Vogel, M; Summons, R E; Des Marais, D J

    2014-01-01

    Modern evaporitic microbial ecosystems are important analogs for understanding the record of earliest life on Earth. Although mineral-depositing shallow-marine environments were prevalent during the Precambrian, few such environments are now available today for study. We investigated the molecular and lipid biomarker composition of an endoevaporitic gypsarenite microbial mat community in Guerrero Negro, Mexico. The 16S ribosomal RNA gene-based phylogenetic analyses of this mat corroborate prior observations indicating that characteristic layered microbial communities colonize gypsum deposits world-wide despite considerable textural and morphological variability. Membrane fatty acid analysis of the surface tan/orange and lower green mat crust layers indicated cell densities of 1.6 × 10(9) and 4.2 × 10(9)  cells cm(-3) , respectively. Several biomarker fatty acids, ∆7,10-hexadecadienoic, iso-heptadecenoic, 10-methylhexadecanoic, and a ∆12-methyloctadecenoic, correlated well with distributions of Euhalothece, Stenotrophomonas, Desulfohalobium, and Rhodobacterales, respectively, revealed by the phylogenetic analyses. Chlorophyll (Chl) a and cyanobacterial phylotypes were present at all depths in the mat. Bacteriochlorophyl (Bchl) a and Bchl c were first detected in the oxic-anoxic transition zone and increased with depth. A series of monomethylalkanes (MMA), 8-methylhexadecane, 8-methylheptadecane, and 9-methyloctadecane were present in the surface crust but increased in abundance in the lower anoxic layers. The MMA structures are similar to those identified previously in cultures of the marine Chloroflexus-like organism 'Candidatus Chlorothrix halophila' gen. nov., sp. nov., and may represent the Bchl c community. Novel 3-methylhopanoids were identified in cultures of marine purple non-sulfur bacteria and serve as a probable biomarker for this group in the lower anoxic purple and olive-black layers. Together microbial culture and environmental analyses

  13. 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.

  14. Amino acid profiling as a method of discovering biomarkers for early diagnosis of cancer.

    PubMed

    Simińska, Edyta; Koba, Marcin

    2016-06-01

    Cancer is one of the main causes of mortality in the world and its early detection significantly increases chances of patients' survival. High cancer mortality rate is caused mainly by late-stage diagnosis and lack of non-invasive and reliable methods for early diagnosis, such as plasma biomarkers. The incidence of cancers in the world still grows so it is crucial to develop a new, faster, high specificity and more sensitive diagnostic technologies. Several recent researchers indicate amino acids as a potential marker for cancer detection. An ideal cancer biomarker should be characterized by high specificity and sensitivity, reliability, ease of measurement and, what is important, ability to detect disease in its early stage. This study is focused on indicating metabolic amino acid profiling as a method of identifying biomarkers for cancer early detection and screening. Presented results are derived from the most recent studies where patients in early, often asymptomatic stages of disease constituted a large percentage of all the patients and, what is important, where researchers have observed alterations in these patients' amino acid profiles. This review is concentrated on analyzing studies on the most common cancers with high mortality rate. Inventing effective methods of early diagnosis is particularly important in case of such diseases. Research presented in this publication is focused on patients with lung, breast and colon cancer. In all analyzed cases, significant changes in the amino acid profile in cancer patients comparing to healthy controls were observed. This study indicates potential of amino acid profiling as method for early cancer detection. PMID:27033065

  15. 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.

  16. 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.

  17. Extracellular nucleic acids in maternal circulation as potential biomarkers for placental insufficiency.

    PubMed

    Hromadnikova, Ilona

    2012-07-01

    Since the placenta is being continuously remodeled during normal placental development, extracellular nucleic acids of both fetal and placental origin, packed into either trophoblast-derived apoptotic bodies or shedding syncytiotrophoblast microparticles, may be detected in maternal circulation during the course of normal gestation. Placental-insufficiency-related pregnancy complications have been shown to be associated with excessive placental trophoblast apoptosis and shedding of placenta debris. Recent advances in the field are reviewed with a focus on the diagnostic potential of particular molecular biomarkers and their eventual implementation in the currently used predictive and diagnostic algorithms for placental-insufficiency-related pregnancy complications. PMID:22364204

  18. Examination of Oral Cancer Biomarkers by Tissue Microarray Analysis

    PubMed Central

    Choi, Peter; Jordan, C. Diana; Mendez, Eduardo; Houck, John; Yueh, Bevan; Farwell, D. Gregory; Futran, Neal; Chen, Chu

    2008-01-01

    Background Oral squamous cell carcinoma (OSCC) is a major healthcare problem worldwide. Efforts in our laboratory and others focusing on the molecular characterization of OSCC tumors with the use of DNA microarrays have yielded heterogeneous results. To validate the DNA microarray results on a subset of genes from these studies that could potentially serve as biomarkers of OSCC, we elected to examine their expression by an alternate quantitative method and by assessing their protein levels. Design Based on DNA microarray data from our lab and data reported in the literature, we identified six potential biomarkers of OSCC to investigate further. We employed quantitative, real-time polymerase chain reaction (qRT-PCR) to examine expression changes of CDH11, MMP3, SPARC, POSTN, TNC, TGM3 in OSCC and normal control tissues. We further examined validated markers on the protein level by immunohistochemistry (IHC) analysis of OSCC tissue microarray (TMA) sections. Results qRT-PCR analysis revealed up-regulation of CDH11, SPARC, POSTN, and TNC gene expression, and decreased TGM3 expression in OSCC compared to normal controls. MMP3 was not found to be differentially expressed. In TMA IHC analyses, SPARC, periostin, and tenascin C exhibited increased protein expression in cancer compared to normal tissues, and their expression was primarily localized within tumor-associated stroma rather than tumor epithelium. Conversely, transglutaminase-3 protein expression was found only within keratinocytes in normal controls, and was significantly down-regulated in cancer cells. Conclusions Of six potential gene markers of OSCC, initially identified by DNA microarray analyses, differential expression of CDH11, SPARC, POSTN, TNC, and TGM3 were validated by qRT-PCR. Differential expression and localization of proteins encoded by SPARC, POSTN, TNC, and TGM3 were clearly shown by TMA IHC. PMID:18490578

  19. 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. PMID:26170140

  20. Cannabinoid acids analysis.

    PubMed

    Lercker, G; Bocci, F; Frega, N; Bortolomeazzi, R

    1992-03-01

    The cannabinoid pattern of vegetable preparations from Cannabis sativa (hashish, marijuana) allows to recognize the phenotype of the plants, to be used as drug or for fiber. Cannabinoid determination by analytical point of view has represented some problems caused by the complex composition of the hexane extract. Capillary gas chromatography of the hexane extracts of vegetable samples, shows the presence of rather polar constituents that eluted, with noticeable interactions, only on polar phase. The compounds can be methylated by diazomethane and silanized (TMS) by silylating reagents. The methyl and methyl-TMS derivatives are analyzed by high resolution gas chromatography (HRGC) and by gas chromatography-mass spectrometry (GC-MS). The identification of the compounds shows their nature of cannabinoid acids, which the main by quantitative point of view results the cannabidiolic acid (CBDA). It is known that the cannabinoid acids are thermally unstable and are transformed in the corresponding cannabinoids by decarboxilation. This is of interest in forensic analysis with the aim to establish the total amount of THC in the Cannabis preparations, as the active component. PMID:1503600

  1. Cost-effectiveness analysis of acute kidney injury biomarkers in pediatric cardiac surgery

    PubMed Central

    Petrovic, Stanislava; Lakic, Dragana; Peco-Antic, Amira; Vulicevic, Irena; Ivanisevic, Ivana; Kotur-Stevuljevic, Jelena; Jelic-Ivanovic, Zorana

    2015-01-01

    Introduction Acute kidney injury (AKI) is significant problem in children with congenital heart disease (CHD) who undergo cardiac surgery. The economic impact of a biomarker-based diagnostic strategy for AKI in pediatric populations undergoing CHD surgery is unknown. The aim of this study was to perform the cost effectiveness analysis of using serum cystatin C (sCysC), urine neutrophil gelatinase-associated lipocalin (uNGAL) and urine liver fatty acid-binding protein (uL-FABP) for the diagnosis of AKI in children after cardiac surgery compared with current diagnostic method (monitoring of serum creatinine (sCr) level). Materials and methods We developed a decision analytical model to estimate incremental cost-effectiveness of different biomarker-based diagnostic strategies compared to current diagnostic strategy. The Markov model was created to compare the lifetime cost associated with using of sCysC, uNGAL, uL-FABP with monitoring of sCr level for the diagnosis of AKI. The utility measurement included in the analysis was quality-adjusted life years (QALY). The results of the analysis are presented as the incremental cost-effectiveness ratio (ICER). Results Analysed biomarker-based diagnostic strategies for AKI were cost-effective compared to current diagnostic method. However, uNGAL and sCys C strategies yielded higher costs and lower effectiveness compared to uL-FABP strategy. uL-FABP added 1.43 QALY compared to current diagnostic method at an additional cost of $8521.87 per patient. Therefore, ICER for uL-FABP compared to sCr was $5959.35/QALY. Conclusions Our results suggest that the use of uL-FABP would represent cost effective strategy for early diagnosis of AKI in children after cardiac surgery. PMID:26110039

  2. Digital image analysis outperforms manual biomarker assessment in breast cancer.

    PubMed

    Stålhammar, Gustav; Fuentes Martinez, Nelson; Lippert, Michael; Tobin, Nicholas P; Mølholm, Ida; Kis, Lorand; Rosin, Gustaf; Rantalainen, Mattias; Pedersen, Lars; Bergh, Jonas; Grunkin, Michael; Hartman, Johan

    2016-04-01

    In the spectrum of breast cancers, categorization according to the four gene expression-based subtypes 'Luminal A,' 'Luminal B,' 'HER2-enriched,' and 'Basal-like' is the method of choice for prognostic and predictive value. As gene expression assays are not yet universally available, routine immunohistochemical stains act as surrogate markers for these subtypes. Thus, congruence of surrogate markers and gene expression tests is of utmost importance. In this study, 3 cohorts of primary breast cancer specimens (total n=436) with up to 28 years of survival data were scored for Ki67, ER, PR, and HER2 status manually and by digital image analysis (DIA). The results were then compared for sensitivity and specificity for the Luminal B subtype, concordance to PAM50 assays in subtype classification and prognostic power. The DIA system used was the Visiopharm Integrator System. DIA outperformed manual scoring in terms of sensitivity and specificity for the Luminal B subtype, widely considered the most challenging distinction in surrogate subclassification, and produced slightly better concordance and Cohen's κ agreement with PAM50 gene expression assays. Manual biomarker scores and DIA essentially matched each other for Cox regression hazard ratios for all-cause mortality. When the Nottingham combined histologic grade (Elston-Ellis) was used as a prognostic surrogate, stronger Spearman's rank-order correlations were produced by DIA. Prognostic value of Ki67 scores in terms of likelihood ratio χ(2) (LR χ(2)) was higher for DIA that also added significantly more prognostic information to the manual scores (LR-Δχ(2)). In conclusion, the system for DIA evaluated here was in most aspects a superior alternative to manual biomarker scoring. It also has the potential to reduce time consumption for pathologists, as many of the steps in the workflow are either automatic or feasible to manage without pathological expertise. PMID:26916072

  3. 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. PMID:24417263

  4. Hyaluronic acid as a biomarker of fibrosis in chronic liver diseases of different etiologies

    PubMed Central

    ORASAN, OLGA HILDA; CIULEI, GEORGE; COZMA, ANGELA; SAVA, MADALINA; DUMITRASCU, DAN LUCIAN

    2016-01-01

    Chronic liver diseases represent a significant public health problem worldwide. The degree of liver fibrosis secondary to these diseases is important, because it is the main predictor of their evolution and prognosis. Hyaluronic acid is studied as a non-invasive marker of liver fibrosis in chronic liver diseases, in an attempt to avoid the complications of liver puncture biopsy, considered the gold standard in the evaluation of fibrosis. We review the advantages and limitations of hyaluronc acid, a biomarker, used to manage patients with chronic viral hepatitis B or C infection, non-alcoholic fatty liver disease, HIV-HCV coinfection, alcoholic liver disease, primary biliary cirrhosis, biliary atresia, hereditary hemochromatosis and cystic fibrosis. PMID:27004022

  5. 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 (

  6. Quantification of naphthoquinone mercapturic acids in urine as biomarkers of naphthalene exposure.

    PubMed

    Klotz, Katrin; Angerer, Jürgen

    2016-02-15

    Naphthalene shows carcinogenic properties in animal experiments. As the substance is ubiquitary present in the environment and has a possibly high exposure at industrial workplaces, the determination of naphthalene metabolites in humans is of environmental-medical as well as occupational-medical importance. Here, biomarkers of 1,2- and 1,4-naphthoquinone, as possibly carcinogenic metabolites in the naphthalene metabolism, are of outstanding significance. We developed and validated a liquid chromatography-tandem mass-spectrometric (LC-MS/MS) method for the simultaneous determination of the naphthoquinone mercapturic acids of 1,2- and 1,4-naphthoquinone in human urine samples as a sum of naphthoquinone- and dihydroxynaphthalene-mercapturic acid. Except for enzymatic hydrolysis and acidification, no further sample preparation is necessary. For sample clean-up, a column switching procedure is applied. The mercapturic acids are extracted from the urinary matrix on a restricted access material (RAM RP 18) and separated on a reversed phase column (Synergi Polar RP C18). The metabolites were quantified by tandem mass spectrometry using labelled D5-1,4-NQMA as internal standard. The limits of detection are 3μg/l for 1,2-NQMA and 1μg/l for 1,4-NQMA. Intraday- and interday precision for pooled urine (spiked with 10μg/l and 30μg/l of the analytes) ranges from 5.9 to 15.1% for 1,2-NQMA and from 2.0 to 10.8% for 1,4-NQMA. The developed method is suited for the sensitive and specific determination of the mercapturic acids of naphthoquinones in human urine. A good precision and low limits of detection were achieved. Application of those new biomarkers in biomonitoring studies may give deeper insights into the mechanisms of the human naphthalene metabolism. PMID:26812176

  7. 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.

  8. 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. PMID:25802980

  9. Proteomic analysis for early neurodegenerative biomarker detection in an animal model.

    PubMed

    Vincenzetti, Silvia; Nasuti, Cinzia; Fedeli, Donatella; Ricciutelli, Massimo; Pucciarelli, Stefania; Gabbianelli, Rosita

    2016-02-01

    The exposure to xenobiotics in the early stages of life represents the most important component in the etiology of many neurodegenerative disorders. Proteomic analysis of plasma and brain samples from early life treated animal model was performed in order to identify early biomarkers of neurodegeneration. Two-dimensional gel electrophoresis followed by liquid chromatography-tandem mass spectrometry identified four proteins in the plasma of adolescent rats that deviated from the control group. Low expression levels of transthyretin and plasma transferrin, and the absence of long-chain fatty acid transport 1 were measured. On the other hand, the same proteomic approach was done on striatum of an adult rat model of neurodegeneration. Mitochondrial aspartate aminotransferase and voltage-dependent anion channel were under expressed, while mitochondrial malate dehydrogenase, myelin basic protein and ubiquitin-60S ribosomal protein L40 were absent in striatum of animal model compared to control group. Data show that early biomarkers for the diagnosis of neurodegeneration can be obtained by proteomic analysis, starting from adolescent age and the results highlight the time frame for the onset of neurodegeneration due to early exposure to xenobiotics. PMID:26631339

  10. 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

  11. Quantitative analysis of surface electromyography: Biomarkers for convulsive seizures.

    PubMed

    Beniczky, Sándor; Conradsen, Isa; Pressler, Ronit; Wolf, Peter

    2016-08-01

    Muscle activity during seizures is in electroencephalographical (EEG) praxis often considered an irritating artefact. This article discusses ways by surface electromyography (EMG) to turn it into a valuable tool of epileptology. Muscles are in direct synaptic contact with motor neurons. Therefore, EMG signals provide direct information about the electric activity in the motor cortex. Qualitative analysis of EMG has traditionally been a part of the long-term video-EEG recordings. Recent development in quantitative analysis of EMG signals yielded valuable information on the pathomechanisms of convulsive seizures, demonstrating that it was different from maximal voluntary contraction, and different from convulsive psychogenic non-epileptic seizures. Furthermore, the tonic phase of the generalised tonic-clonic seizures (GTCS) proved to have different quantitative features than tonic seizures. The high temporal resolution of EMG allowed detailed characterisation of temporal dynamics of the GTCS, suggesting that the same inhibitory mechanisms that try to prevent the build-up of the seizure activity, contribute to ending the seizure. These findings have clinical implications: the quantitative EMG features provided the pathophysiologic substrate for developing neurophysiologic biomarkers that accurately identify GTCS. This proved to be efficient both for seizure detection and for objective, automated distinction between convulsive and non-convulsive epileptic seizures. PMID:27212115

  12. 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

  13. 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. PMID:20880571

  14. 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

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

    PubMed

    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

  16. 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. PMID:25198158

  17. 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.

  18. Seasonal variation of Fatty acids and stable carbon isotopes in sponges as indicators for nutrition: biomarkers in sponges identified.

    PubMed

    Koopmans, Marieke; van Rijswijk, Pieter; Boschker, Henricus T S; Marco, Houtekamer; Martens, Dirk; Wijffels, Rene H

    2015-02-01

    To get a better understanding of sponge feeding biology and efficiencies, the fatty acid (FA) composition and (13)C natural abundance of sponges and of suspended particulate matter (SPM) from surrounding seawater was studied in different seasons at three locations. Haliclona oculata and Haliclona xena from the Oosterschelde, the Netherlands, Halichondria panicea and H. xena from Lake Veere, the Netherlands, and Aplysina aerophoba and Dysidea avara from the Mediterranean, Spain, were studied. Several FA biomarkers for different algal groups, bacteria and sponge biomass were identified in all sponges. The FA concentration variation in sponges was related to changes in fatty acid concentration in SPM. Stable carbon isotopic ratios (δ(13)C) in sponge specific FAs showed very limited seasonal variation at all sites. Algal FAs in sponges were mainly acquired from the SPM through active filtration in all seasons. At the two sites in the Netherlands only in May (spring), the sponge specific FAs had similar δ(13)C ratios as algal FAs, suggesting that sponges were mainly growing during spring and probably summer. During autumn and winter, they were still actively filtering, but the food collected during this period had little effect on sponge δ(13)C values suggesting limited incorporation of filtered material into the sponge body. The sponge A. aerophoba relied mostly on the symbiotic bacteria. In conclusion, fatty acid composition in combination with stable carbon isotope analysis can be used to analyze the food source of sponges. PMID:25107690

  19. 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

  20. Reverse engineering of Alzheimer's disease based on biomarker pathways analysis.

    PubMed

    Richens, Joanna L; Morgan, Kevin; O'Shea, Paul

    2014-09-01

    Alzheimer's disease (AD) poses an increasingly profound problem to society, yet progress toward a genuine understanding of the disease remains worryingly slow. Perhaps, the most outstanding problem with the biology of AD is the question of its mechanistic origins, that is, it remains unclear wherein the molecular failures occur that underlie the disease. We demonstrate how molecular biomarkers could help define the nature of AD in terms of the early biochemical events that correlate with disease progression. We use a novel panel of biomolecules that appears in cerebrospinal fluid of AD patients. As changes in the relative abundance of these molecular markers are associated with progression to AD from mild cognitive impairment, we make the assumption that by tracking their origins we can identify the biochemical conditions that predispose their presence and consequently cause the onset of AD. We couple these protein markers with an analysis of a series of genetic factors and together this hypothesis essentially allows us to redefine AD in terms of the molecular pathways that underlie the disease. PMID:24684789

  1. Estimation and correlation of cigarette smoke exposure in Canadian smokers as determined by filter analysis and biomarkers of exposure.

    PubMed

    Morin, André; Shepperd, Christopher J; Eldridge, Alison C; Poirier, Nicole; Voisine, Richard

    2011-12-01

    A clinical study conducted in Canada compared two methods of estimating exposure to cigarette smoke in 192 volunteer subjects: 43 smokers of 4-6 mg, 49 of 8-12 mg and 50 of 14-15 mg ISO tar yield cigarettes and 50 non-smokers. Estimates of mouth level exposure (MLE) to nicotine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), pyrene and acrolein were obtained by chemical analysis of spent cigarette filters. Estimates of smoke constituent uptake were achieved by analysis of urinary biomarkers for total nicotine equivalents (nicotine, cotinine, trans-3'-hydroxycotinine plus their glucuronide conjugates), NNK (total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) plus glucuronide), pyrene (1-hydroxy pyrene plus glucuronide) and acrolein (3-hydroxylpropyl-mercapturic acid) plus the nicotine metabolite cotinine in plasma and saliva. The objective of our study was to confirm the correlations between measures of human exposure obtained by filter analysis and biomarkers. Significant correlations (p<0.001) were found between MLE and the relevant biomarker for each smoke constituent. The adjusted values of the Pearson correlation coefficients (r) were 0.80 (nicotine), 0.77 (acrolein) and 0.44 (pyrene). NNK correlations could not be obtained because of the low NNK yield of Canadian cigarettes. Unexpectedly high levels of acrolein biomarker found in non-smokers urine on one of the two days sampled emphasised the need for more than one sampling occasion per period and an awareness of non-tobacco sources of smoke constituents under investigation. No consistent dose response, in line with ISO tar yield smoked, of MLE estimates was found for nicotine, pyrene and acrolein and respective biomarkers. The influence of demographics on our results has also been examined. PMID:20937342

  2. 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.

  3. 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)

  4. Multimarker Analysis for New Biomarkers in Relation to Central Arterial Stiffness and Hemodynamics in a Chinese Community-Dwelling Population.

    PubMed

    Fu, Shihui; Luo, Leiming; Ye, Ping; Xiao, Wenkai

    2015-11-01

    Central arterial stiffness and hemodynamics independently reflect the risk of cardiovascular events. This Chinese community-based analysis was performed to evaluate the relationships of new biomarkers with central arterial stiffness and hemodynamics by a multimarker method. This analysis consisted of 1540 participants who were fully tested for the new biomarkers including N-terminal prohormone of brain natriuretic peptide, lipid accumulation product, triglyceride-high-density lipoprotein cholesterol (TG-HDL-c) ratio, uric acid, high-sensitivity C-reactive protein, and homocysteine. Carotid-femoral pulse wave velocity (cfPWV), central pulse pressure (cPP), and central augmentation index (cAIx) were measured. The median (range) age of entire cohort was 62 years (21-96 years), and 40.5% were males. The median (interquartile range) of cfPWV, cPP, and cAIx was 11.0 m/s (9.6-13.0 m/s), 42 mm Hg (35-52 mm Hg), and 28% (21%-33%), respectively. In multivariate analysis, participants with higher cfPWV had significantly higher age, peripheral pulse pressure, TG, TG-HDL-c ratio, and homocysteine levels compared with others (P < .05 for all). Multimarker analysis in a Chinese community-dwelling population reinforced the potential clinical value of plasma TG-HDL-c ratio and homocysteine levels as the biomarkers of increased arterial stiffness. PMID:25883364

  5. 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.

  6. Biomarker Identification and Pathway Analysis by Serum Metabolomics of Lung Cancer

    PubMed Central

    Chen, Yingrong; Ma, Zhihong; Min, Lishan; Li, Hongwei; Wang, Bin; Zhong, Jing; Dai, Licheng

    2015-01-01

    Lung cancer is one of the most common causes of cancer death, for which no validated tumor biomarker is sufficiently accurate to be useful for diagnosis. Additionally, the metabolic alterations associated with the disease are unclear. In this study, we investigated the construction, interaction, and pathways of potential lung cancer biomarkers using metabolomics pathway analysis based on the Kyoto Encyclopedia of Genes and Genomes database and the Human Metabolome Database to identify the top altered pathways for analysis and visualization. We constructed a diagnostic model using potential serum biomarkers from patients with lung cancer. We assessed their specificity and sensitivity according to the area under the curve of the receiver operator characteristic (ROC) curves, which could be used to distinguish patients with lung cancer from normal subjects. The pathway analysis indicated that sphingolipid metabolism was the top altered pathway in lung cancer. ROC curve analysis indicated that glycerophospho-N-arachidonoyl ethanolamine (GpAEA) and sphingosine were potential sensitive and specific biomarkers for lung cancer diagnosis and prognosis. Compared with the traditional lung cancer diagnostic biomarkers carcinoembryonic antigen and cytokeratin 19 fragment, GpAEA and sphingosine were as good or more appropriate for detecting lung cancer. We report our identification of potential metabolic diagnostic and prognostic biomarkers of lung cancer and clarify the metabolic alterations in lung cancer. PMID:25961003

  7. 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

  8. 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

  9. Utility of bilirubins and bile acids as endogenous biomarkers for the inhibition of hepatic transporters.

    PubMed

    Watanabe, Tomoko; Miyake, Manami; Shimizu, Toshinobu; Kamezawa, Miho; Masutomi, Naoya; Shimura, Takesada; Ohashi, Rikiya

    2015-04-01

    It is useful to identify endogenous substrates for the evaluation of drug-drug interactions via transporters. In this study, we investigated the utility of bilirubins, substrates of OATPs and MRP2, and bile acids and substrates of NTCP and BSEP, as biomarkers for the inhibition of transporters. In rats administered 20 and 80 mg/kg rifampicin, the plasma levels of bilirubin glucuronides were elevated, gradually decreased, and almost returned to the baseline level at 24 hours after administration without an elevation of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). This result indicates the transient inhibition of rOatps and/or rMrp2. Although the correlation between free plasma concentrations and IC50 values of rOatps depended on the substrates used in the in vitro studies, the inhibition of rOatps by rifampicin was confirmed in the in vivo study using valsartan as a substrate of rOatps. In rats administered 10 and 30 mg/kg cyclosporin A, the plasma levels of bile acids were elevated and persisted for up to 24 hours after administration without an elevation of ALT and AST. This result indicates the continuous inhibition of rNtcp and/or rBsep, although there were differences between the free plasma or liver concentrations and IC50 values of rNtcp or rBsep, respectively. This study suggests that the monitoring of bilirubins and bile acids in plasma is useful in evaluating the inhibitory potential of their corresponding transporters. PMID:25581390

  10. 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

  11. Microfluidics in amino acid analysis.

    PubMed

    Pumera, Martin

    2007-07-01

    Microfluidic devices have been widely used to derivatize, separate, and detect amino acids employing many different strategies. Virtually zero-dead volume interconnections and fast mass transfer in small volume microchannels enable dramatic increases in on-chip derivatization reaction speed, while only minute amounts of sample and reagent are needed. Due to short channel path, fast subsecond separations can be carried out. With sophisticated miniaturized detectors, the whole analytical process can be integrated on one platform. This article reviews developments of lab-on-chip technology in amino acid analysis, it shows important design features such as sample preconcentration, precolumn and postcolumn amino acid derivatization, and unlabeled and labeled amino acid detection with focus on advanced designs. The review also describes important biomedical and space exploration applications of amino acid analysis on microfluidic devices. PMID:17542043

  12. Predominance and sources of alkane and fatty acid biomarkers in the surface sediments of Chitrapuzha River (South India).

    PubMed

    Sanil Kumar, K S; Nair, S M

    2015-04-01

    Surface sediment samples were collected from Chitrapuzha (Cochin) estuarine system to identify the natural and anthropogenic origin of organic matter. The distribution and sources of organic matter were assessed with the help of fatty acid and alkane biomarkers. Fatty acids ranging from C12 to C28 were identified and C16:0 was the most abundant fatty acid, which contributed between 23.5 % and 52.4 % to total fatty acids. The low levels of polyunsaturated fatty acids indicate the effective bacterial recycling of algal fatty acids during the whole settling and depositing process. Aliphatic hydrocarbons ranging from C12 to C33 were identified and the total concentration ranged from 7876 to 43,357 ng g(-1). The presence of unresolved complex mixtures and lower pristane to phytane ratios indicates the petroleum contamination in the study area. PMID:25694163

  13. Biomarker-Based Calibration of Retrospective Exposure Predictions of Perfluorooctanoic Acid

    PubMed Central

    2015-01-01

    Estimated historical exposures and serum concentrations of perfluorooctanoic acid (PFOA) have been extensively used in epidemiologic studies that examined associations between PFOA exposures and adverse health outcomes among residents in highly exposed areas in the Mid-Ohio Valley. Using measured serum PFOA levels in 2005–2006, we applied two calibration methods to these retrospective exposure predictions: (1) multiplicative calibration and (2) Bayesian pharmacokinetic calibration with larger adjustments to more recent exposure estimates and smaller adjustments to exposure estimates for years farther in the past. We conducted simulation studies of various hypothetical exposure scenarios and compared hypothetical true historical intake rates with estimates based on mis-specified baseline exposure and pharmacokinetic models to find the method with the least bias. The Bayesian method outperformed the multiplicative method if a change to bottled water consumption was not reported or if the half-life of PFOA was mis-specified. On the other hand, the multiplicative method outperformed the Bayesian method if actual tap water consumption rates were systematically overestimated. If tap water consumption rates gradually decreased over time because of substitution with bottled water or other liquids, neither method clearly outperformed another. Calibration of retrospective exposure estimates using recently collected biomarkers may help reduce uncertainties in environmental epidemiologic studies. PMID:24730513

  14. 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.

  15. Quantitative analysis of gene expression in fixed colorectal carcinoma samples as a method for biomarker validation

    PubMed Central

    OSTASIEWICZ, BEATA; OSTASIEWICZ, PAWEŁ; DUŚ-SZACHNIEWICZ, KAMILA; OSTASIEWICZ, KATARZYNA; ZIÓŁKOWSKI, PIOTR

    2016-01-01

    Biomarkers have been described as the future of oncology. Modern proteomics provide an invaluable tool for the near-whole proteome screening for proteins expressed differently in neoplastic vs. healthy tissues. However, in order to select the most promising biomarkers, an independent method of validation is required. The aim of the current study was to propose a methodology for the validation of biomarkers. Due to material availability the majority of large scale biomarker studies are performed using formalin-fixed paraffin-embedded (FFPE) tissues, therefore these were selected for use in the current study. A total of 10 genes were selected from what have been previously described as the most promising candidate biomarkers, and the expression levels were analyzed with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using calibrator normalized relative quantification with the efficiency correction. For 6/10 analyzed genes, the results were consistent with the proteomic data; for the remaining four genes, the results were inconclusive. The upregulation of karyopherin α 2 (KPNA2) and chromosome segregation 1-like (CSE1L) in colorectal carcinoma, in addition to downregulation of chloride channel accessory 1 (CLCA1), fatty acid binding protein 1 (FABP1), sodium channel, voltage gated, type VII α subunit (SCN7A) and solute carrier family 26 (anion exchanger), member 3 (SLC26A3) was confirmed. With the combined use of proteomic and genetic tools, it was reported, for the first time to the best of our knowledge, that SCN7A was downregulated in colorectal carcinoma at mRNA and protein levels. It had been previously suggested that the remaining five genes served an important role in colorectal carcinogenesis, however the current study provided strong evidence to support their use as biomarkers. Thus, it was concluded that combination of RT-qPCR with proteomics offers a powerful methodology for biomarker identification, which can be used to analyze

  16. Metabonomic analysis of serum of workers occupationally exposed to arsenic, cadmium and lead for biomarker research: a preliminary study.

    PubMed

    Dudka, Ilona; Kossowska, Barbara; Senhadri, Hanna; Latajka, Rafał; Hajek, Julianna; Andrzejak, Ryszard; Antonowicz-Juchniewicz, Jolanta; Gancarz, Roman

    2014-07-01

    Environmental metabonomics is the application of metabonomics to characterize the interactions of organisms with their environment. Metabolic profiling is an exciting addition to the armory of the epidemiologist for the discovery of new disease risk biomarkers and diagnostics. This work is a continuation of research searching for preclinical serum markers in a group of 389 healthy smelter workers exposed to lead, cadmium and arsenic. Changes in the metabolic profiles were studied using Proton Nuclear Magnetic Resonance Spectroscopy on pooled serum samples from both the metal exposed and control groups. These multivariate metabonomic datasets were analyzed with Principal Component Analysis and Partial Least Squares Discriminant Analysis. Analysis of metabolic profiles of people exposed to heavy metals suggests energy metabolism disturbance induced by heavy metals. Changes in lipid fraction (very-low-density lipoprotein - VLDL, low-density lipoprotein - LDL), unsaturated lipids and in the level of amino acids suggest perturbation of the metabolism of lipids and amino acids. This study illustrated the high reliability of NMR-based metabonomic profiling on the study of the biochemical effects induced by the mixture of heavy metals. This approach is capable of identifying intermediate biomarkers of response to toxicants at environmental/occupational concentrations, paving the way to its use in a monitoring of smelter workers exposed to low doses of lead, cadmium and arsenic. PMID:24713610

  17. 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.

  18. Folate Catabolites in Spot Urine as Non-Invasive Biomarkers of Folate Status during Habitual Intake and Folic Acid Supplementation

    PubMed Central

    Niesser, Mareile; Demmelmair, Hans; Weith, Thea; Moretti, Diego; Rauh-Pfeiffer, Astrid; van Lipzig, Marola; Vaes, Wouter; Koletzko, Berthold; Peissner, Wolfgang

    2013-01-01

    Background Folate status, as reflected by red blood cell (RCF) and plasma folates (PF), is related to health and disease risk. Folate degradation products para-aminobenzoylglutamate (pABG) and para-acetamidobenzoylglutamate (apABG) in 24 hour urine have recently been shown to correlate with blood folate. Aim Since blood sampling and collection of 24 hour urine are cumbersome, we investigated whether the determination of urinary folate catabolites in fasted spot urine is a suitable non-invasive biomarker for folate status in subjects before and during folic acid supplementation. Study Design and Methods Immediate effects of oral folic acid bolus intake on urinary folate catabolites were assessed in a short-term pre-study. In the main study we included 53 healthy men. Of these, 29 were selected for a 12 week folic acid supplementation (400 µg). Blood, 24 hour and spot urine were collected at baseline and after 6 and 12 weeks and PF, RCF, urinary apABG and pABG were determined. Results Intake of a 400 µg folic acid bolus resulted in immediate increase of urinary catabolites. In the main study pABG and apABG concentrations in spot urine correlated well with their excretion in 24 hour urine. In healthy men consuming habitual diet, pABG showed closer correlation with PF (rs = 0.676) and RCF (rs = 0.649) than apABG (rs = 0.264, ns and 0.543). Supplementation led to significantly increased folate in plasma and red cells as well as elevated urinary folate catabolites, while only pABG correlated significantly with PF (rs = 0.574) after 12 weeks. Conclusion Quantification of folate catabolites in fasted spot urine seems suitable as a non-invasive alternative to blood or 24 hour urine analysis for evaluation of folate status in populations consuming habitual diet. In non-steady-state conditions (folic acid supplementation) correlations between folate marker (RCF, PF, urinary catabolites) decrease due to differing kinetics. PMID:23457526

  19. Standardization of natural mycolic acid antigen composition and production for use in biomarker antibody detection to diagnose active tuberculosis.

    PubMed

    Ndlandla, F L; Ejoh, V; Stoltz, A C; Naicker, B; Cromarty, A D; van Wyngaardt, S; Khati, M; Rotherham, L S; Lemmer, Y; Niebuhr, J; Baumeister, C R; Al Dulayymi, J R; Swai, H; Baird, M S; Verschoor, J A

    2016-08-01

    Mycobacterium tuberculosis, the causative agent of tuberculosis, is characterized by the abundance of species specific, antigenic cell wall lipids called mycolic acids. These wax-like molecules all share an identical, amphiphilic mycolic motif, but have different functional groups in a long hydrophobic hydrocarbon mero-chain that divide them into three main classes: alpha-, keto- and methoxy-mycolic acids. Whereas alpha-mycolic acids constitutively maintain an abundance of around 50%, the ratio of methoxy- to keto-mycolic acid types may vary depending on, among other things, the growth stage of M. tuberculosis. In human patients, antibodies to mycolic acids have shown potential as diagnostic serum biomarkers for active TB. Variations in mycolic acid composition affect the antigenic properties and can potentially compromise the precision of detection of anti-mycolic acids antibodies in patient sera to natural mixtures. We demonstrate this here with combinations of synthetic mycolic acid antigens, tested against TB patient and control sera. Combinations of methoxy- and α-mycolic acids are more antigenic than combinations of keto- and α-mycolic acids, showing the former to give a more sensitive test for TB biomarker antibodies. Natural mixtures of mycolic acids isolated from mature cultures of M. tuberculosis H37Rv give the same sensitivity as that with synthetic methoxy- and α-mycolic acids in combination, in a surface plasmon resonance inhibition biosensor test. To ensure that the antigenic activity of isolates of natural mycolic acids is reproducible, we cultured M. tuberculosis H37Rv on Middlebrook 7H10 solid agar plates to stationary growth phase in a standardized, optimal way. The proportions of mycolic acid classes in various batches of the isolates prepared from these cultures were compared to a commercially available natural mycolic acid isolate. LC-MS/MS and NMR data for quantitation of mycolic acids class compositions show that the variation in batches

  20. 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. PMID:26744263

  1. 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

  2. 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.

  3. Identification of microRNA as sepsis biomarker based on miRNAs regulatory network analysis.

    PubMed

    Huang, Jie; Sun, Zhandong; Yan, Wenying; Zhu, Yujie; Lin, Yuxin; Chen, Jiajai; Shen, Bairong; Wang, Jian

    2014-01-01

    Sepsis is regarded as arising from an unusual systemic response to infection but the physiopathology of sepsis remains elusive. At present, sepsis is still a fatal condition with delayed diagnosis and a poor outcome. Many biomarkers have been reported in clinical application for patients with sepsis, and claimed to improve the diagnosis and treatment. Because of the difficulty in the interpreting of clinical features of sepsis, some biomarkers do not show high sensitivity and specificity. MicroRNAs (miRNAs) are small noncoding RNAs which pair the sites in mRNAs to regulate gene expression in eukaryotes. They play a key role in inflammatory response, and have been validated to be potential sepsis biomarker recently. In the present work, we apply a miRNA regulatory network based method to identify novel microRNA biomarkers associated with the early diagnosis of sepsis. By analyzing the miRNA expression profiles and the miRNA regulatory network, we obtained novel miRNAs associated with sepsis. Pathways analysis, disease ontology analysis, and protein-protein interaction network (PIN) analysis, as well as ROC curve, were exploited to testify the reliability of the predicted miRNAs. We finally identified 8 novel miRNAs which have the potential to be sepsis biomarkers. PMID:24809055

  4. Temporal dynamics in a shallow coastal benthic food web: Insights from fatty acid biomarkers and their stable isotopes.

    PubMed

    Braeckman, Ulrike; Provoost, Pieter; Sabbe, Koen; Soetaert, Karline; Middelburg, Jack J; Vincx, Magda; Vanaverbeke, Jan

    2015-07-01

    We investigated the temporal variation of pelagic and benthic food sources in the diet of benthic taxa at a depositional site in the Southern Bight of the North Sea by means of fatty acid (FA) biomarkers and compound-specific stable isotope analysis (CSIA). The taxa were the non-selective deposit feeding nematodes (Sabatieria spp. and 'other nematodes'), and three dominant macrobenthic species: two true suspension-deposit feeders (the bivalve Abra alba and the tube dwelling polychaete Owenia fusiformis) and the suspected predatory mud-dwelling anemone Sagartia sp. These species make up on average 16% (Abra alba), 17% (Sagartia sp.) and 20% (Owenia fusiformis) of the biomass in the Abra alba-Kurtiella bidentata community in this area. Phytoplankton dynamics in the suspended particulate matter of the water column as inferred from cell counts, chlorophyll-a and organic carbon content were clearly visible in sediment and animal FA abundance as well, whereas phytodetritus dynamics in the sediment FA composition were less clear, probably due to patchy distribution or stripping of FA by macrofauna. Nematodes appeared to assimilate mainly Polyunsaturated Fatty Acids (PUFAs) from their sedimentary environment and were further non-selectively accumulating more (Sabatieria spp.) or less ('other nematodes') FA from the deposited phytodetritus. In contrast, Abra alba FA composition was consistent with a diatom-dominated diet and consumption of Phaeocystis was observed in Owenia fusiformis, whereas Sagartia sp. showed evidence of a predatory behaviour. While the total FA content in Owenia fusiformis remained constant throughout the year, Sagartia sp. doubled and Abra alba increased its FA level more than 10-fold in response to the organic matter deposition from the phytoplankton bloom. This leads to the conclusion that there is no resource partitioning between non-selective deposit feeding nematodes and the suspension-deposit feeding macrobenthic organisms, suggesting they

  5. Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression

    PubMed Central

    2014-01-01

    Background Prostate cancer is one of the most common complex diseases with high leading cause of death in men. Identifications of prostate cancer associated genes and biomarkers are thus essential as they can gain insights into the mechanisms underlying disease progression and advancing for early diagnosis and developing effective therapies. Methods In this study, we presented an integrative analysis of gene expression profiling and protein interaction network at a systematic level to reveal candidate disease-associated genes and biomarkers for prostate cancer progression. At first, we reconstructed the human prostate cancer protein-protein interaction network (HPC-PPIN) and the network was then integrated with the prostate cancer gene expression data to identify modules related to different phases in prostate cancer. At last, the candidate module biomarkers were validated by its predictive ability of prostate cancer progression. Results Different phases-specific modules were identified for prostate cancer. Among these modules, transcription Androgen Receptor (AR) nuclear signaling and Epidermal Growth Factor Receptor (EGFR) signalling pathway were shown to be the pathway targets for prostate cancer progression. The identified candidate disease-associated genes showed better predictive ability of prostate cancer progression than those of published biomarkers. In context of functional enrichment analysis, interestingly candidate disease-associated genes were enriched in the nucleus and different functions were encoded for potential transcription factors, for examples key players as AR, Myc, ESR1 and hidden player as Sp1 which was considered as a potential novel biomarker for prostate cancer. Conclusions The successful results on prostate cancer samples demonstrated that the integrative analysis is powerful and useful approach to detect candidate disease-associate genes and modules which can be used as the potential biomarkers for prostate cancer progression. The

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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. PMID:21348635

  11. Identification of potential biomarkers for predicting acute dermal irritation by proteomic analysis.

    PubMed

    Zhang, Qihao; Dai, Taoli; Zhang, Lei; Zhang, Minjing; Xiao, Xue; Hu, Hao; Zou, Ping; Liu, Xia; Xiang, Qi; Su, Zhijian; Huang, Yadong; He, Qing-Yu

    2011-11-01

    In vitro alternative tests aiming at replacing the traditional animal test for predicting the irritant potential of chemicals have been developed, but the assessment parameters or endpoints are still not sufficient for analysis. To discover novel endpoints for skin irritation responses, a proteomics approach was used to analyze the protein expression in human keratinocytes exposed to sodium lauryl sulfate in the present study. Among the 20 identified proteins with altered expression, small heat shock protein 27 (HSP27) and superoxide dismutase [Cu-Zn] were down-regulated while cofilin-1 was up-regulated significantly in response to the chemical challenge. Keratinocytes were exposed to acid and basic chemicals for further validation of the proteins. HSP27 displayed the most significant alteration both in mRNA and protein levels, accompanied by nuclear translocation. The irritation also induced an increased production of interleukin-1α in keratinocytes. These findings suggest that these proteins may be combinational biomarkers or additional endpoints for skin hazard assessment. Further investigation into the protein alterations would be helpful for the mechanistic understanding of skin irritation. PMID:21469165

  12. Use of urinary trichloroacetic acid as an exposure biomarker of disinfection by-products in cancer studies.

    PubMed

    Salas, Lucas A; Gracia-Lavedan, Esther; Goñi, Fernando; Moreno, Victor; Villanueva, Cristina M

    2014-11-01

    Urinary trichloroacetic acid (TCAA) has been proposed as a valid exposure biomarker for ingested disinfection by-products (DBP) for reproductive studies. However, it has never been used in epidemiologic studies on cancer. We investigate the performance of urinary TCAA as a biomarker of DBP exposure in the framework of an epidemiologic study on cancer. We conducted home visits to collect tap water, first morning void urine, and a 48h fluid intake diary among 120 controls from a case-control study of colorectal cancer in Barcelona, Spain. We measured urine TCAA and creatinine, and 9 haloacetic acids and 4 trihalomethanes (THM) in tap water. Lifetime THM exposure was estimated based on residential history since age 18 plus routine monitoring data. Robust linear regressions were used to estimate mean change in urinary TCAA adjusted by covariates. Among the studied group, mean age was 74 years (range 63-85) and 41 (34%) were females. Mean total tap water consumption was 2.2l/48h (standard error, 0.1l/48h). Geometric mean urine TCAA excretion rate was 17.3pmol/min [95%CI: 14.0-21.3], which increased 2% for a 10% increase in TCAA ingestion and decreased with total tap water consumption (-17%/l), water intake outside home (-32%), plasmatic volume (-64%/l), in smokers (-79%), and in users of non-steroidal anti-inflammatory drugs (-50%). Urinary TCAA levels were not associated with lifetime THM exposure. In conclusion, our findings support that urine TCAA is not a valid biomarker in case-control studies of adult cancer given that advanced age, comorbidites and medication use are prevalent and are determinants of urine TCAA levels, apart from ingested TCAA levels. In addition, low TCAA concentrations in drinking water limit the validity of urine TCAA as an exposure biomarker. PMID:25462676

  13. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics

    PubMed Central

    Coon, Joshua J.; Zürbig, Petra; Dakna, Mohammed; Dominiczak, Anna F.; Decramer, Stéphane; Fliser, Danilo; Frommberger, Moritz; Golovko, Igor; Good, David M.; Herget-Rosenthal, Stefan; Jankowski, Joachim; Julian, Bruce A.; Kellmann, Markus; Kolch, Walter; Massy, Ziad; Novak, Jan; Rossing, Kasper; Schanstra, Joost P.; Schiffer, Eric; Theodorescu, Dan; Vanholder, Raymond; Weissinger, Eva M.; Mischak, Harald; Schmitt-Kopplin, Philippe

    2010-01-01

    Owing to its availability, ease of collection, and correlation with pathophysiology of diseases, urine is an attractive source for clinical proteomics. However, many proteomic studies have had only limited clinical impact, due to factors such as modest numbers of subjects, absence of disease controls, small numbers of defined biomarkers, and diversity of analytical platforms. Therefore, it is difficult to merge biomarkers from different studies into a broadly applicable human urinary proteome database. Ideally, the methodology for defining the biomarkers should combine a reasonable analysis time with high resolution, thereby enabling the profiling of adequate samples and recognition of sufficient features to yield robust diagnostic panels. Capillary electrophoresis coupled to mass spectrometry (CE-MS), which was used to analyze urine samples from healthy subjects and patients with various diseases, is a suitable approach for this task. The database of these datasets compiled from the urinary peptides enabled the diagnosis, classification, and monitoring of a wide range of diseases. CE-MS exhibits excellent performance for biomarker discovery and allows subsequent biomarker sequencing independent of the separation platform. This approach may elucidate the pathogenesis of many diseases, and better define especially renal and urological disorders at the molecular level. PMID:20130789

  14. 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. PMID:25626423

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

    PubMed

    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

  16. Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis.

    PubMed

    Zhao, Zide; Zhang, Yingying; Gai, Fengchun; Wang, Ying

    2016-09-01

    Despite ongoing research into diabetes and its complications, the underlying molecular associations remain to be elucidated. The systematic identification of molecular interactions in associated diseases may be approached using a network analysis strategy. The biomarker-target interrelated molecules associated with diabetes and its complications were identified via the Comparative Toxicogenomics Database (CTD); the Search Tool for Recurring Instances of Neighboring Genes was utilized for network construction. Functional enrichment analysis was performed with Database for Annotation, Visualization and Integrated Discovery software to investigate connections between diabetes and its complications. A total of 142 (including 122 biomarkers, 10 therapeutic targets and 10 overlapping molecules) biomarker-target interrelated molecules associated with diabetes and its complications were identified via the CTD database, and analysis of the network yielded 1,087 biological processes and fifteen Kyoto Encyclopedia of Genes and Genomes pathways with significant P‑values. Various critical aspects of the networks were examined in the present study: a) Intermolecular horizontal and vertical combinations in biomarkers and therapeutic targets associated with diabetes and its complicationb) network topology properties associated with molecular pathological responsec) contribution of key molecules to integrated regulation; and d) crosstalk between multiple pathways. Based on a multi-dimensional analysis, it was concluded that the integrated molecular pathological development of diabetes and its complications does not proceed randomly, which suggests a requirement for integrated, multi-target intervention. PMID:27430657

  17. 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...

  18. 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.

  19. Tumour-Associated Autoantibodies as Diagnostic Biomarkers for Breast Cancer: A Systematic Review and Meta-Analysis.

    PubMed

    Xia, J; Shi, J; Wang, P; Song, C; Wang, K; Zhang, J; Ye, H

    2016-06-01

    Tumour-associated autoantibodies may be promising biomarkers that could facilitate breast cancer (BC) diagnosis and improve patient outcomes. This review aims to identify the tumour-associated autoantibodies with the greatest diagnostic potential. Systematic searches were conducted using PubMed and Web of Science. The most studied tumour-associated autoantibody was included in a meta-analysis, and its clinical value was determined using Fagan's nomogram. The analysis included 84 studies regarding tumour-associated autoantibodies with the diagnostic value. Anti-p53 antibody was the most frequently studied autoantibody, followed by autoantibodies against MUC1, HER2 and cyclin B1. Although individual tumour-associated autoantibodies showed low diagnostic sensitivity, combinations of autoantibodies offered relatively high sensitivity. Enzyme-linked immunosorbent assay (ELISA) was the most common detection method, and nucleic acid programmable protein microarrays appeared preferable to common protein microarrays. As the most commonly studied autoantibody, anti-p53 antibody was included in a meta-analysis. When it had been detected using ELISA and cut-off values were defined as the mean +2 or 3 standard deviations, the summary area under the receiver operating characteristic curve for the presence of BC was 0.78. Fagan's nomogram showed post-test probabilities of 32% and 6% for positive and negative results, respectively. Mammography might be supplemented by the use of tumour-associated autoantibodies as biomarkers for BC diagnosis in younger women with increased risks of BC. Even though several studies have investigated the diagnostic use of tumour-associated autoantibodies as biomarkers for BC detection, a high-quality prospective study is needed to validate their diagnostic value in practice. PMID:26991924

  20. 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

  1. Promising toxicological biomarkers for the diagnosis of liver injury types: Bile acid metabolic profiles and oxidative stress marker as screening tools in drug development.

    PubMed

    Masubuchi, Noriko; Nishiya, Takayoshi; Imaoka, Masako; Mizumaki, Kiyoko; Okazaki, Osamu

    2016-08-01

    Promising biomarkers were identified in adult male Crl:CD (SD) rats for the screening of new chemical entities for their potential to cause liver injury. We examined the serum biochemistry, liver histopathology, and bile acid profiles by LC-MS/MS, and the mRNA expression of transporters and CYPs by an RT-PCR after the following treatments to male Crl:CD (SD) rats: (a) bile duct ligation (BDL); (b) a single oral dose of 150 mg/kg α-naphthylisothiocyanate (ANIT); and (c) repeated oral doses of a novel pyrrolidinecarboxylic acid derivative (abbreviated as PCA) at 30, 300, and 1000 mg/kg. The serum total bile acid levels and bilirubin concentrations were found to be elevated in all of the groups. However, the bile acid component profiles of the PCA group differed significantly from BDL and ANIT models: deoxycholic acid, lithocholic acid, and sulfated bile acids were upregulated in a dose-dependent manner only in the PCA group. In addition, the PCA group demonstrated high levels of hepatic heme oxygenase-1 expression, whereas the profiles of the mRNA levels of the hepatic transporters and CYPs of all groups were found to be similar. The histopathological findings, for both the BDL and ANIT groups, were of bile duct hyperplasia, hepatocyte degeneration and necrosis. In contrast, only bile duct hyperplasia and hepatocyte degeneration were observed in the PCA group, even at a lethal dose. These results indicated that PCA induced a cholestatic condition and the increase of oxidative stress markers implies that this will also lead hepatocellular injury. In conclusion, the serum bile acid components and sulfated bile acid levels, and the expression of oxidative stress markers could provide information that aids in the diagnosis of liver injury type and helps to elucidate the mechanisms of hepatotoxicity. These findings can be extrapolated into our clinical investigation. The analysis of these crucial biomarkers is likely to be a useful screening tool in the lead

  2. Identification of novel bile acids as biomarkers for the early diagnosis of Niemann-Pick C disease.

    PubMed

    Mazzacuva, Francesca; Mills, Philippa; Mills, Kevin; Camuzeaux, Stephane; Gissen, Paul; Nicoli, Elena-Raluca; Wassif, Christopher; Te Vruchte, Danielle; Porter, Forbes D; Maekawa, Masamitsu; Mano, Nariyasu; Iida, Takashi; Platt, Frances; Clayton, Peter T

    2016-06-01

    This article describes a rapid UPLC-MS/MS method to quantitate novel bile acids in biological fluids and the evaluation of their diagnostic potential in Niemann-Pick C (NPC). Two new compounds, NPCBA1 (3β-hydroxy,7β-N-acetylglucosaminyl-5-cholenoic acid) and NPCBA2 (probably 3β,5α,6β-trihydroxycholanoyl-glycine), were observed to accumulate preferentially in NPC patients: median plasma concentrations of NPCBA1 and NPCBA2 were 40- and 10-fold higher in patients than in controls. However, NPCBA1 concentrations were normal in some patients because they carried a common mutation inactivating the GlcNAc transferase required for the synthesis of this bile acid. NPCBA2, not containing a GlcNAc moiety, is thus a better NPC biomarker. PMID:27139891

  3. Analysis of protein biomarkers in human clinical tumor samples: critical aspects to success from tissue acquisition to analysis.

    PubMed

    Warren, Madhuri V; Chan, W Y Iris; Ridley, John M

    2011-04-01

    There has been increased interest in the analysis of protein biomarkers in clinical tumor tissues in recent years. Tissue-based biomarker assays can add value and aid decision-making at all stages of drug development, as well as being developed for use as predictive biomarkers and for patient stratification and prognostication in the clinic. However, there must be an awareness of the legal and ethical issues related to the sourcing of human tissue samples. This article also discusses the limits of scope and critical aspects on the successful use of the following tissue-based methods: immunohistochemistry, tissue microarrays and automated image analysis. Future advances in standardization of tissue biobanking methods, immunohistochemistry and quantitative image analysis techniques are also discussed. PMID:21473728

  4. Critical analysis of the potential for microRNA biomarkers in breast cancer management

    PubMed Central

    Graveel, Carrie R; Calderone, Heather M; Westerhuis, Jennifer J; Winn, Mary E; Sempere, Lorenzo F

    2015-01-01

    Breast cancer is a complex and heterogeneous disease. Signaling by estrogen receptor (ER), progesterone receptor (PR), and/or human EGF-like receptor 2 (HER2) is a main driver in the development and progression of a large majority of breast tumors. Molecular characterization of primary tumors has identified major subtypes that correlate with ER/PR/HER2 status, and also subgroup divisions that indicate other molecular and cellular features of the tumors. While some of these research findings have been incorporated into clinical practice, several challenges remain to improve breast cancer management and patient survival, for which the integration of novel biomarkers into current practice should be beneficial. microRNAs (miRNAs) are a class of short non-coding regulatory RNAs with an etiological contribution to breast carcinogenesis. miRNA-based diagnostic and therapeutic applications are rapidly emerging as novel potential approaches to manage and treat breast cancer. Rapid technological development enables specific and sensitive detection of individual miRNAs or the entire miRNome in tissues, blood, and other biological specimens from breast cancer patients. This review focuses on recent miRNA research and its potential to address unmet clinical needs and challenges. The four sections presented discuss miRNA findings in the context of the following clinical challenges: biomarkers for early detection; prognostic and predictive biomarkers for treatment decisions using targeted therapies against ER and HER2; diagnostic and prognostic biomarkers for subgrouping of triple-negative breast cancer, for which there are currently no targeted therapies; and biomarkers for monitoring and characterization of metastatic breast cancer. The review concludes with a critical analysis of the current state of miRNA breast cancer research and the need for further studies using large patient cohorts under well-controlled conditions before considering the clinical implementation of mi

  5. 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

  6. CYFRA21-1 levels could be a biomarker for bladder cancer: a meta-analysis.

    PubMed

    Kuang, L I; Song, W J; Qing, H M; Yan, S; Song, F L

    2015-01-01

    The proteolytic region of cytokeratin-19, referred to as CYFRA21-1, is a soluble molecule present in the serum and other body fluids, and is considered a tumor marker in several neoplastic diseases. To examine whether urinary or serum samples containing CYFRA21-1 can be used as biomarkers for bladder cancer, we conducted a comprehensive meta-analysis of 3 case-control studies. In all studies considered, patients with bladder cancer had a higher CYFRA21-1 level than healthy subjects. Subgroup analysis showed that patients with metastatic bladder cancer had a higher CYFRA21-1 level than those with locally invasive disease. However, no significant difference in CYFRA21-1 was observed between patients with stage I and stage II bladder cancer; there was also no difference in patients with stage II local bladder cancer and those with stage III local bladder cancer. Based on our results, CYFRA21-1 level may be a diagnostic biomarker for diagnosing bladder cancer as well as a possible biomarker for differentiation between local and metastatic bladder cancer. However, it cannot be used as a urinary or serum biomarker for differentiating histological stages of local bladder cancer for histological grades I-III. PMID:25966163

  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. Quantitative analysis of gene expression in fixed colorectal carcinoma samples as a method for biomarker validation.

    PubMed

    Ostasiewicz, Beata; Ostasiewicz, Paweł; Duś-Szachniewicz, Kamila; Ostasiewicz, Katarzyna; Ziółkowski, Piotr

    2016-06-01

    Biomarkers have been described as the future of oncology. Modern proteomics provide an invaluable tool for the near‑whole proteome screening for proteins expressed differently in neoplastic vs. healthy tissues. However, in order to select the most promising biomarkers, an independent method of validation is required. The aim of the current study was to propose a methodology for the validation of biomarkers. Due to material availability the majority of large scale biomarker studies are performed using formalin‑fixed paraffin‑embedded (FFPE) tissues, therefore these were selected for use in the current study. A total of 10 genes were selected from what have been previously described as the most promising candidate biomarkers, and the expression levels were analyzed with reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) using calibrator normalized relative quantification with the efficiency correction. For 6/10 analyzed genes, the results were consistent with the proteomic data; for the remaining four genes, the results were inconclusive. The upregulation of karyopherin α 2 (KPNA2) and chromosome segregation 1‑like (CSE1L) in colorectal carcinoma, in addition to downregulation of chloride channel accessory 1 (CLCA1), fatty acid binding protein 1 (FABP1), sodium channel, voltage gated, type VII α subunit (SCN7A) and solute carrier family 26 (anion exchanger), member 3 (SLC26A3) was confirmed. With the combined use of proteomic and genetic tools, it was reported, for the first time to the best of our knowledge, that SCN7A was downregulated in colorectal carcinoma at mRNA and protein levels. It had been previously suggested that the remaining five genes served an important role in colorectal carcinogenesis, however the current study provided strong evidence to support their use as biomarkers. Thus, it was concluded that combination of RT‑qPCR with proteomics offers a powerful methodology for biomarker identification, which

  9. Metabolomics analysis and biomarker identification for brains of rats exposed subchronically to the mixtures of low-dose cadmium and chlorpyrifos.

    PubMed

    Xu, Ming-Yuan; Sun, Ying-Jian; Wang, Pan; Xu, Hai-Yang; Chen, Li-Ping; Zhu, Li; Wu, Yi-Jun

    2015-06-15

    Cadmium (Cd) and chlorpyrifos (CPF) are widespread harmful environmental pollutants with neurotoxicity to mammals. Although the exposure to Cd and CPF at the same time may pose a significant risk to human health, the subchronic combined neurotoxicity of these two chemicals at low levels in the brain is poorly understood. In this study, we treated rats with three doses (low, middle, and high) of Cd, CPF, or their mixture for 90 days. No obvious symptom was observed in the treated animals except those treated with high-dose CPF. Histological results showed that middle and high doses of the chemicals caused neuronal cell damage in brains. GC-MS-based metabonomics analysis revealed that energy and amino acid metabolism were disturbed in the brains of rats exposed to the two chemicals and their combinations even at low doses. We further identified the unique brain metabolite biomarkers for rats treated with Cd, CPF, or both. Two amino acids, tyrosine and l-leucine, were identified as the biomarkers for Cd and CPF treatment, respectively. In addition, a set of five unique biomarkers (1,2-propanediol-1-phosphate, d-gluconic acid, 9H-purine, serine, and 2-ketoisovaleric acid) was identified for the mixtures of Cd and CPF. Therefore, the metabolomics analysis is more sensitive than regular clinical observation and pathological examination for detecting the neurotoxicity of the individual and combined Cd and CPF at low levels. Overall, these results identified the unique biomarkers for Cd and CPF exposure, which provide new insights into the mechanism of their joint toxicity. PMID:25856237

  10. 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

  11. 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. PMID:25455896

  12. 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. PMID:22614361

  13. A Systematic Review and Meta-Analysis of Circulating Biomarkers Associated with Failure of Arteriovenous Fistulae for Haemodialysis

    PubMed Central

    Morris, Dylan R.; Bhandari, Abhishta P.; Moxon, Joseph V.

    2016-01-01

    Background Arteriovenous fistula (AVF) failure is a significant cause of morbidity and expense in patients on maintenance haemodialysis (HD). Circulating biomarkers could be valuable in detecting patients at risk of AVF failure and may identify targets to improve AVF outcome. Currently there is little consensus on the relationship between circulating biomarkers and AVF failure. The aim of this systematic review was to identify circulating biomarkers associated with AVF failure. Methods Studies evaluating the association between circulating biomarkers and the presence or risk of AVF failure were systematically identified from the MEDLINE, EMBASE and Cochrane Library databases. No restrictions on the type of study were imposed. Concentrations of circulating biomarkers of routine HD patients with and without AVF failure were recorded and meta-analyses were performed on biomarkers that were assessed in three or more studies with a composite population of at least 100 participants. Biomarker concentrations were synthesized into inverse-variance random-effects models to calculate standardized mean differences (SMD) and 95% confidence intervals (CI). Results Thirteen studies comprising a combined population of 1512 participants were included after screening 2835 unique abstracts. These studies collectively investigated 48 biomarkers, predominantly circulating molecules which were assessed as part of routine clinical care. Meta-analysis was performed on twelve eligible biomarkers. No significant association between any of the assessed biomarkers and AVF failure was observed. Conclusion This paper is the first systematic review of biomarkers associated with AVF failure. Our results suggest that blood markers currently assessed do not identify an at-risk AVF. Further, rigorously designed studies assessing biological plausible biomarkers are needed to clarify whether assessment of circulating markers can be of any clinical value. PROSPERO registration number CRD42016033845

  14. 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

  15. Diagnostic accuracy of serum biomarkers for head and neck cancer: A systematic review and meta-analysis.

    PubMed

    Guerra, Eliete Neves Silva; Rêgo, Daniela Fortunato; Elias, Silvia Taveira; Coletta, Ricardo D; Mezzomo, Luis André Mendonça; Gozal, David; De Luca Canto, Graziela

    2016-05-01

    Serum biomarkers could be helpful to characterize head and neck squamous cell carcinoma (HNSCC). Thus, the purpose of this systematic review and meta-analysis was to determine the diagnostic capability of serum biomarkers in the assessment of HNSCC patients. Studies were gathered by searching LILACS, PubMed, Science Direct, Scopus and Web of Science up to April 10th, 2015. Studies that focused on serum biomarkers in the diagnosis of HNSCC compared with controls were considered. Sixty-five studies were identified, and the sample size included 9098 subjects. Combined biomarkers demonstrated improved accuracy than those tested individually. Therefore, 12.8% of single and 34.3% of combined indicated that serum biomarkers discriminate patients with HNSCC from controls. The combined biomarkers with better diagnostic capability included Epidermal growth factor receptor (EGFR)+Cyclin D1 and squamous cell cancer-associated antigen (SCCA)+EGFR+Cyclin D1. Beta2-microglobin may also be a promising single biomarker for future studies. Serum biomarkers can be potentially useful in the diagnosis of HNSCC. However, further research is required to validate these biomarkers. PMID:26971993

  16. 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

  17. 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). PMID:21468941

  18. Analysis of Serum Metabolic Profile by Ultra-performance Liquid Chromatography-mass Spectrometry for Biomarkers Discovery: Application in a Pilot Study to Discriminate Patients with Tuberculosis

    PubMed Central

    Feng, Shuang; Du, Yan-Qing; Zhang, Li; Zhang, Lei; Feng, Ran-Ran; Liu, Shu-Ye

    2015-01-01

    Background: Tuberculosis (TB) is a chronic wasting inflammatory disease characterized by multisystem involvement, which can cause metabolic derangements in afflicted patients. Metabolic signatures have been exploited in the study of several diseases. However, the serum that is successfully used in TB diagnosis on the basis of metabolic profiling is not by much. Methods: Orthogonal partial least-squares discriminant analysis was capable of distinguishing TB patients from both healthy subjects and patients with conditions other than TB. Therefore, TB-specific metabolic profiling was established. Clusters of potential biomarkers for differentiating TB active from non-TB diseases were identified using Mann–Whitney U-test. Multiple logistic regression analysis of metabolites was calculated to determine the suitable biomarker group that allows the efficient differentiation of patients with TB active from the control subjects. Results: From among 271 participants, 12 metabolites were found to contribute to the distinction between the TB active group and the control groups. These metabolites were mainly involved in the metabolic pathways of the following three biomolecules: Fatty acids, amino acids, and lipids. The receiver operating characteristic curves of 3D, 7D, and 11D-phytanic acid, behenic acid, and threoninyl-γ-glutamate exhibited excellent efficiency with area under the curve (AUC) values of 0.904 (95% confidence interval [CI]: 0863–0.944), 0.93 (95% CI: 0.893–0.966), and 0.964 (95% CI: 00.941–0.988), respectively. The largest and smallest resulting AUCs were 0.964 and 0.720, indicating that these biomarkers may be involved in the disease mechanisms. The combination of lysophosphatidylcholine (18:0), behenic acid, threoninyl-γ-glutamate, and presqualene diphosphate was used to represent the most suitable biomarker group for the differentiation of patients with TB active from the control subjects, with an AUC value of 0.991. Conclusion: The metabolic

  19. 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

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

    PubMed

    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. Enzyme-based microfluidic chip coupled to graphene electrodes for the detection of D-amino acid enantiomer-biomarkers.

    PubMed

    Batalla, Pilar; Martín, Aída; López, Miguel Ángel; González, María Cristina; Escarpa, Alberto

    2015-01-01

    An electrochemical microfluidic strategy for the separation and enantiomeric detection of D-methionine (D-Met) and D-leucine (D-Leu) is presented. These D-amino acids (D-AAs) act as biomarkers involved in relevant diseases caused by Vibrio cholerae. On a single layout microfluidic chip (MC), highly compatible with extremely low biological sample consumption, the strategy allowed the controlled microfluidic D-AA separation and the specific reaction between D-amino acid oxidase (DAAO) and each D-AA biomarker avoiding the use of additives (i.e., cyclodextrins) for enantiomeric separation as well as any covalent immobilization of the enzyme into the wall channels or on the electrode surface such as in the biosensor-based approaches. Hybrid polymer/graphene-based electrodes were end-channel coupled to the microfluidic system to improve the analytical performance. D-Met and D-Leu were successfully detected becoming this proof-of-the-concept a promising principle for the development of point-of-care (POC) devices for in situ screening of V. cholerae related diseases. PMID:25870911

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

    PubMed

    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

  4. Metabonomic analysis of potential biomarkers and drug targets involved in diabetic nephropathy mice

    PubMed Central

    Wei, Tingting; Zhao, Liangcai; Jia, Jianmin; Xia, Huanhuan; Du, Yao; Lin, Qiuting; Lin, Xiaodong; Ye, Xinjian; Yan, Zhihan; Gao, Hongchang

    2015-01-01

    Diabetic nephropathy (DN) is one of the lethal manifestations of diabetic systemic microvascular disease. Elucidation of characteristic metabolic alterations during diabetic progression is critical to understand its pathogenesis and identify potential biomarkers and drug targets involved in the disease. In this study, 1H nuclear magnetic resonance (1H NMR)-based metabonomics with correlative analysis was performed to study the characteristic metabolites, as well as the related pathways in urine and kidney samples of db/db diabetic mice, compared with age-matched wildtype mice. The time trajectory plot of db/db mice revealed alterations, in an age-dependent manner, in urinary metabolic profiles along with progression of renal damage and dysfunction. Age-dependent and correlated metabolite analysis identified that cis-aconitate and allantoin could serve as biomarkers for the diagnosis of DN. Further correlative analysis revealed that the enzymes dimethylarginine dimethylaminohydrolase (DDAH), guanosine triphosphate cyclohydrolase I (GTPCH I), and 3-hydroxy-3-methylglutaryl-CoA lyase (HMG-CoA lyase) were involved in dimethylamine metabolism, ketogenesis and GTP metabolism pathways, respectively, and could be potential therapeutic targets for DN. Our results highlight that metabonomic analysis can be used as a tool to identify potential biomarkers and novel therapeutic targets to gain a better understanding of the mechanisms underlying the initiation and progression of diseases. PMID:26149603

  5. Metabonomic analysis of potential biomarkers and drug targets involved in diabetic nephropathy mice.

    PubMed

    Wei, Tingting; Zhao, Liangcai; Jia, Jianmin; Xia, Huanhuan; Du, Yao; Lin, Qiuting; Lin, Xiaodong; Ye, Xinjian; Yan, Zhihan; Gao, Hongchang

    2015-01-01

    Diabetic nephropathy (DN) is one of the lethal manifestations of diabetic systemic microvascular disease. Elucidation of characteristic metabolic alterations during diabetic progression is critical to understand its pathogenesis and identify potential biomarkers and drug targets involved in the disease. In this study, (1)H nuclear magnetic resonance ((1)H NMR)-based metabonomics with correlative analysis was performed to study the characteristic metabolites, as well as the related pathways in urine and kidney samples of db/db diabetic mice, compared with age-matched wildtype mice. The time trajectory plot of db/db mice revealed alterations, in an age-dependent manner, in urinary metabolic profiles along with progression of renal damage and dysfunction. Age-dependent and correlated metabolite analysis identified that cis-aconitate and allantoin could serve as biomarkers for the diagnosis of DN. Further correlative analysis revealed that the enzymes dimethylarginine dimethylaminohydrolase (DDAH), guanosine triphosphate cyclohydrolase I (GTPCH I), and 3-hydroxy-3-methylglutaryl-CoA lyase (HMG-CoA lyase) were involved in dimethylamine metabolism, ketogenesis and GTP metabolism pathways, respectively, and could be potential therapeutic targets for DN. Our results highlight that metabonomic analysis can be used as a tool to identify potential biomarkers and novel therapeutic targets to gain a better understanding of the mechanisms underlying the initiation and progression of diseases. PMID:26149603

  6. 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.

  7. 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

  8. Blood metabolomics analysis identifies abnormalities in the citric acid cycle, urea cycle, and amino acid metabolism in bipolar disorder

    PubMed Central

    Yoshimi, Noriko; Futamura, Takashi; Kakumoto, Keiji; Salehi, Alireza M.; Sellgren, Carl M.; Holmén-Larsson, Jessica; Jakobsson, Joel; Pålsson, Erik; Landén, Mikael; Hashimoto, Kenji

    2016-01-01

    Background Bipolar disorder (BD) is a severe and debilitating psychiatric disorder. However, the precise biological basis remains unknown, hampering the search for novel biomarkers. We performed a metabolomics analysis to discover novel peripheral biomarkers for BD. Methods We quantified serum levels of 116 metabolites in mood-stabilized male BD patients (n = 54) and age-matched male healthy controls (n = 39). Results After multivariate logistic regression, serum levels of pyruvate, N-acetylglutamic acid, α-ketoglutarate, and arginine were significantly higher in BD patients than in healthy controls. Conversely, serum levels of β-alanine, and serine were significantly lower in BD patients than in healthy controls. Chronic (4-weeks) administration of lithium or valproic acid to adult male rats did not alter serum levels of pyruvate, N-acetylglutamic acid, β-alanine, serine, or arginine, but lithium administration significantly increased serum levels of α-ketoglutarate. Conclusions The metabolomics analysis demonstrated altered serum levels of pyruvate, N-acetylglutamic acid, β-alanine, serine, and arginine in BD patients. General significance The present findings suggest that abnormalities in the citric acid cycle, urea cycle, and amino acid metabolism play a role in the pathogenesis of BD. PMID:27114925

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

    PubMed

    Horakova, Olga; Hansikova, Jana; 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

  10. 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

  11. Analysis of lipid biomarkers in rocks of Archean crystalline basement

    NASA Astrophysics Data System (ADS)

    Shekhovtsova, Nina V.; Osipov, George A.; Verkhovtseva, Nadejda V.; Pevzner, Lev A.

    2003-01-01

    The Earst-European platform Archean crystalline basement rocks opened by Vorotilov Deep Well (VDW) were studied within depths 2575 - 2805 m. VDW was drilled through Puchezh-Katunki impact structure and opened some rocks characterized by high magnetic saturation. Micro-dispersed structure of magnetite indicated on a possibility of its biogenic origin. Really some pure cultures of magnet-ordered compound producing bacilli were isolated. Thus, the identification of fatty acids and other lipid components of microbial cells inside rocks was made to establish the iron reduction role in common biochemical activity in deep subsurface. 34 microbial lipid markers were detected by gas chromatography -- mass-spectrometry and 22 species were identidied by private database. Bacteria of g. Bacillus reached 6.8% in subsurface communities. However, representatives of gg. Clostridium (37.1 - 33.2%) and Rhodococcus (27.6 - 33.7%) were absolute dominants within studied depth interval. Geochemical conditions in situ as well as physiological features of these micro-organisms allow to constitute a following trophic chain: subsurface fluid hyudrocarbons --> it oxidizing rhodococci --> free aminoacids and biomass proteins (products of rhodococci metabolism) --> it fermenting clostridia. This syntrophic association may be a new basement for subsurface ecosystem and can support the magnet-ordered compounds production.

  12. 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

  13. 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

    2016-02-01

    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

  14. 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

  15. Effects of linseed oil and palm oil on growth performance, tibia fatty acid and biomarkers of bone metabolism in broilers.

    PubMed

    Zhong, X; Gao, S; Wang, J J; Dong, L; Huang, J; Zhang, L L; Wang, T

    2014-01-01

    1. This study was conducted to determine the effects of different dietary fat sources on growth performance, tibia fatty acids and biomarkers of bone metabolism in broilers. 2. One-d-old commercial Arbor Acres broilers were fed with a maize-soya bean basal diet for 42 d, supplemented with oils according to the following 5 treatments: lard (lard group); linseed oil (linseed oil group); palm oil (palm oil group); linseed oil + palm oil (60:40 or 40:60 w/w, LP-1 group and LP-2 group, respectively). 3. No significant differences in weight gain, feed intake and gain/feed ratio were observed between the lard and linseed oil groups. Birds fed on palm oil had significantly greater weight gain and feed intake than those fed on lard or linseed oil. Growth performance in LP-1 and LP-2 was significantly greater than that of single-oil groups. 4. Tibia growth and bone characteristics were not influenced by supplementation with lard, linseed oil, or palm oil alone, but broilers fed on a mixture of fats had significantly greater tibia weight and length compared to broilers fed on linseed oil. Bone mineral density in tibia was significantly increased in LP-1 and LP-2 groups. 5. Supplementation of linseed oil alone or in combination with palm oil enhanced apparent digestibility of calcium, reduced serum calcium and increased tibia calcium concentrations. Moreover, supplementation with linseed oil alone or in combination with palm oil had a positive effect on biomarkers of bone growth. 6. The combination of linseed and palm oils was beneficial for growth performance, tibia growth and biomarkers of bone metabolism. PMID:24641587

  16. 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

  17. Multiplex biomarker analysis biosensor for detection of hepatitis B virus.

    PubMed

    Xu, Hua; Gu, Dayong; He, Jian'an; Shi, Lei; Yao, Jingyu; Liu, Chunxiao; Zhao, Chunzhong; Xu, Yunqing; Jiang, Shengyang; Long, Jun

    2015-01-01

    In this paper, we report the development of a protein microarray-based biosensor for the detection of the hepatitis B virus (HBV) serological markers using surface plasmon resonance (SPR Printing buffer, protein immobilization time and concentration of the capture protein were optimized systematically to determine the best performance of the biosensor. Under optimal conditions, five hepatitis B markers in 20 μL human serum can be simultaneously detected within 30 minutes, whereas other methods such as ELISA and PCR can detect only one marker within four hours. This platform has been validated by analysis of 35 patients known to have hepatitis B, with 85% agreement between the test platform and analysis by commercial enzyme-linked immunosorbent assay (ELISA) kits. The results demonstrate that the protein microarray with SPR displayed a sensitivity of 0.1 ng mL(-1) for HBsAg. In addition to high sensitivity, it also shows excellent specificity, reproducibility and stability. This integrated protein microarray technique combined with SPR is a promising candidate for hepatitis B diagnosis with high-throughput. PMID:26405988

  18. Machine learning and social network analysis applied to Alzheimer's disease biomarkers.

    PubMed

    Di Deco, Javier; González, Ana M; Díaz, Julia; Mato, Virginia; García-Frank, Daniel; Álvarez-Linera, Juan; Frank, Ana; Hernández-Tamames, Juan A

    2013-01-01

    Due to the fact that the number of deaths due Alzheimer is increasing, the scientists have a strong interest in early stage diagnostic of this disease. Alzheimer's patients show different kind of brain alterations, such as morphological, biochemical, functional, etc. Currently, using magnetic resonance imaging techniques is possible to obtain a huge amount of biomarkers; being difficult to appraise which of them can explain more properly how the pathology evolves instead of the normal ageing. Machine Learning methods facilitate an efficient analysis of complex data and can be used to discover which biomarkers are more informative. Moreover, automatic models can learn from historical data to suggest the diagnostic of new patients. Social Network Analysis (SNA) views social relationships in terms of network theory consisting of nodes and connections. The resulting graph-based structures are often very complex; there can be many kinds of connections between the nodes. SNA has emerged as a key technique in modern sociology. It has also gained a significant following in medicine, anthropology, biology, information science, etc., and has become a popular topic of speculation and study. This paper presents a review of machine learning and SNA techniques and then, a new approach to analyze the magnetic resonance imaging biomarkers with these techniques, obtaining relevant relationships that can explain the different phenotypes in dementia, in particular, different stages of Alzheimer's disease. PMID:23548026

  19. Adjacent slice prostate cancer prediction to inform MALDI imaging biomarker analysis

    NASA Astrophysics Data System (ADS)

    Chuang, Shao-Hui; Sun, Xiaoyan; Cazares, Lisa; Nyalwidhe, Julius; Troyer, Dean; Semmes, O. John; Li, Jiang; McKenzie, Frederic D.

    2010-03-01

    Prostate cancer is the second most common type of cancer among men in US [1]. Traditionally, prostate cancer diagnosis is made by the analysis of prostate-specific antigen (PSA) levels and histopathological images of biopsy samples under microscopes. Proteomic biomarkers can improve upon these methods. MALDI molecular spectra imaging is used to visualize protein/peptide concentrations across biopsy samples to search for biomarker candidates. Unfortunately, traditional processing methods require histopathological examination on one slice of a biopsy sample while the adjacent slice is subjected to the tissue destroying desorption and ionization processes of MALDI. The highest confidence tumor regions gained from the histopathological analysis are then mapped to the MALDI spectra data to estimate the regions for biomarker identification from the MALDI imaging. This paper describes a process to provide a significantly better estimate of the cancer tumor to be mapped onto the MALDI imaging spectra coordinates using the high confidence region to predict the true area of the tumor on the adjacent MALDI imaged slice.

  20. 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. PMID:26558960

  1. Hair Cortisol Analysis: A Promising Biomarker of HPA Activation in Older Adults

    PubMed Central

    Wright, Kathy D.; Hickman, Ronald; Laudenslager, Mark L.

    2015-01-01

    Prolonged stress is a potentially harmful and often undetected risk factor for chronic illness in older adults. Cortisol, one indicator of the body’s hormonal responses to stress, is regulated by the hypothalamic-pituitary-adrenal (HPA) axis and is commonly measured in saliva, urine, or blood samples. Cortisol possesses a diurnal pattern and thus collection timing is critical. Hair cortisol is a proxy measure to the total retrospective activity of the HPA axis over the preceding months, much like hemoglobin A1c is a proxy measure of glucose control over the past 3 months. The aim of this review is to examine a novel biomarker, hair cortisol, as a practical measure of long-term retrospective cortisol activity associated with chronic stress in older adults. Hair cortisol analysis advances the science of aging by better characterizing chronic stress as a risk factor for chronic illness progression and as a biomarker of the effectiveness of stress reduction interventions. PMID:26055775

  2. 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.

  3. 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.

  4. 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

  5. Urinary bile acids as biomarkers for liver diseases I. Stability of the baseline profile in healthy subjects.

    PubMed

    Bathena, Sai Praneeth R; Thakare, Rhishikesh; Gautam, Nagsen; Mukherjee, Sandeep; Olivera, Marco; Meza, Jane; Alnouti, Yazen

    2015-02-01

    The role of bile acids (BAs) as biomarkers for liver injury has been proposed for decades. However, the large inter- and intra-individual variability of the BA profile has prevented its clinical application. To this end, we investigated the effect of covariates such as food, gender, age, BMI, and moderate alcohol consumption on the BA profile in healthy human subjects. The BA profile was characterized by the calculation of indices that describe the composition, sulfation, and amidation of total and individual BAs. Both inter- and intra-individual variabilities of BA indices were low in serum and even lower in urine compared with those of absolute concentrations of BAs. Serum BA concentrations increased with consumption of food, whereas urinary BA concentrations were mildly affected by food. Gender differences in the urinary and serum BA profile were minimal. The serum and urinary BA profiles were also not affected by age. BMI showed minimal effect on the urine and serum BA profile. Moderate alcohol consumption did not have a significant effect on the BA profile in both urine and serum. When the effect of the type of alcohol was studied, the results indicate that moderate drinking of beer does not affect BA concentrations and has minimal effect on BA indices, whereas moderate wine consumption slightly increases BA concentrations without affecting the BA indices. In summary, urinary BA indices showed lower variability and higher stability than absolute BA concentrations in serum and showed minimal changes to covariate effects suggesting their utility as biomarkers in clinic. PMID:25344562

  6. Proteomics analysis of urine reveals acute phase response proteins as candidate diagnostic biomarkers for prostate cancer.

    PubMed

    Davalieva, Katarina; Kiprijanovska, Sanja; Komina, Selim; Petrusevska, Gordana; Zografska, Natasha Chokrevska; Polenakovic, Momir

    2015-01-01

    Despite the overall success of prostate specific antigen (PSA) in screening and detection of prostate cancer (PCa), its use has been limited due to the lack of specificity. The principal driving goal currently within PCa research is to identify non-invasive biomarker(s) for early detection of aggressive tumors with greater sensitivity and specificity than PSA. In this study, we focused on identification of non-invasive biomarkers in urine with higher specificity than PSA. We tested urine samples from PCa and benign prostatic hyperplasia (BPH) patients by 2-D DIGE coupled with MS and bioinformatics analysis. Statistically significant (p < 0.05), 1.8 fold variation or more in abundance, showed 41 spots, corresponding to 23 proteins. The Ingenuity Pathway Analysis showed significant association with the Acute Phase Response Signaling pathway. Nine proteins with differential abundances were included in this pathway: AMBP, APOA1, FGA, FGG, HP, ITIH4, SERPINA1, TF and TTR. The expression pattern of 4 acute phase response proteins differed from the defined expression in the canonical pathway. The urine levels of TF, AMPB and HP were measured by immunoturbidimetry in an independent validation set. The concentration of AMPB in urine was significantly higher in PCa while levels of TF and HP were opposite (p < 0.05). The AUC for the individual proteins ranged from 0.723 to 0.754. The combination of HP and AMBP yielded the highest accuracy (AUC = 0.848), greater than PSA. The proposed biomarker set is quickly quantifiable and economical with potential to improve the sensitivity and specificity of PCa detection. PMID:25653573

  7. Cancer biomarkers - current perspectives.

    PubMed

    Bhatt, Anant Narayan; Mathur, Rohit; Farooque, Abdullah; Verma, Amit; Dwarakanath, B S

    2010-08-01

    In the recent years, knowledge about cancer biomarkers has increased tremendously providing great opportunities for improving the management of cancer patients by enhancing the efficiency of detection and efficacy of treatment. Recent technological advancement has enabled the examination of many potential biomarkers and renewed interest in developing new biomarkers. Biomarkers of cancer could include a broad range of biochemical entities, such as nucleic acids, proteins, sugars, lipids, and small metabolites, cytogenetic and cytokinetic parameters as well as whole tumour cells found in the body fluid. A comprehensive understanding of the relevance of each biomarker will be very important not only for diagnosing the disease reliably, but also help in the choice of multiple therapeutic alternatives currently available that is likely to benefit the patients. This review provides a brief account on various biomarkers for diagnosis, prognosis and therapeutic purposes, which include markers already in clinical practice as well as various upcoming biomarkers. PMID:20716813

  8. 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

  9. Biomarkers of Dairy Fatty Acids and Risk of Cardiovascular Disease in the Multi‐Ethnic Study of Atherosclerosis

    PubMed Central

    de Oliveira Otto, Marcia C.; Nettleton, Jennifer A.; Lemaitre, Rozenn N.; M. Steffen, Lyn; Kromhout, Daan; Rich, Stephen S.; Y. Tsai, Michael; Jacobs, David R.; Mozaffarian, Dariush

    2013-01-01

    Background Evidence regarding the role of dairy fat intake in cardiovascular disease (CVD) has been mixed and inconclusive. Most earlier studies have used self‐reported measures of dietary intake and focused on relatively racially homogeneous populations. Circulating biomarkers of dairy fat in a multiethnic cohort provide objective measures of dairy fat intake and facilitate conclusions relevant to populations with different diets and susceptibility to CVD. Methods and Results In a multiethnic cohort of 2837 US adults aged 45 to 84 years at baseline (2000–2002), phospholipid fatty acids including 15:0, 14:0, and trans‐16:1n7 were measured using standardized methods, and the incidence of CVD prospectively adjudicated. Self‐reported whole‐fat dairy and butter intakes had strongest associations with 15:0, rather than 14:0 or trans‐16:1n7. In multivariate models including demographics and lifestyle and dietary habits, each SD‐unit of 15:0 was associated with 19% lower CVD risk (hazard ratio [95% CI] 0.81 [0.68 to 0.98]) and 26% lower coronary heart disease (CHD) risk (0.74 [0.60 to 0.92]). Associations were strengthened after mutual adjustment for 14:0 and trans‐16:1n‐7 and were similar after adjustment for potential mediators. Plasma phospholipid 14:0 and trans‐16:1n‐7 were not significantly associated with incident CVD or CHD. All findings were similar in white, black, Hispanic, and Chinese American participants. Conclusion Plasma phospholipid 15:0, a biomarker of dairy fat, was inversely associated with incident CVD and CHD, while no association was found with phospholipid 14:0 and trans‐16:1n‐7. These findings support the need for further investigation of CVD effects of dairy fat, dairy‐specific fatty acids, and dairy products in general. PMID:23868191

  10. atBioNet– an integrated network analysis tool for genomics and biomarker discovery

    PubMed Central

    2012-01-01

    Background Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. Results atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. Conclusion atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http

  11. 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

  12. Glycoprotein biomarker panel for pancreatic cancer discovered by quantitative proteomics analysis.

    PubMed

    Nie, Song; Lo, Andy; Wu, Jing; Zhu, Jianhui; Tan, Zhijing; Simeone, Diane M; Anderson, Michelle A; Shedden, Kerby A; Ruffin, Mack T; Lubman, David M

    2014-04-01

    Pancreatic cancer is a lethal disease where specific early detection biomarkers would be very valuable to improve outcomes in patients. Many previous studies have compared biosamples from pancreatic cancer patients with healthy controls to find potential biomarkers. However, a range of related disease conditions can influence the performance of these putative biomarkers, including pancreatitis and diabetes. In this study, quantitative proteomics methods were applied to discover potential serum glycoprotein biomarkers that distinguish pancreatic cancer from other pancreas related conditions (diabetes, cyst, chronic pancreatitis, obstructive jaundice) and healthy controls. Aleuria aurantia lectin (AAL) was used to extract fucosylated glycoproteins and then both TMT protein-level labeling and label-free quantitative analysis were performed to analyze glycoprotein differences from 179 serum samples across the six different conditions. A total of 243 and 354 serum proteins were identified and quantified by label-free and TMT protein-level quantitative strategies, respectively. Nineteen and 25 proteins were found to show significant differences in samples between the pancreatic cancer and other conditions using the label-free and TMT strategies, respectively, with 7 proteins considered significant in both methods. Significantly different glycoproteins were further validated by lectin-ELISA and ELISA assays. Four candidates were identified as potential markers with profiles found to be highly complementary with CA 19-9 (p < 0.001). Obstructive jaundice (OJ) was found to have a significant impact on the performance of every marker protein, including CA 19-9. The combination of α-1-antichymotrypsin (AACT), thrombospondin-1 (THBS1), and haptoglobin (HPT) outperformed CA 19-9 in distinguishing pancreatic cancer from normal controls (AUC = 0.95), diabetes (AUC = 0.89), cyst (AUC = 0.82), and chronic pancreatitis (AUC = 0.90). A marker panel of AACT, THBS1, HPT, and CA 19

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

    PubMed Central

    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. PMID:27042856

  14. Negligible contribution from roots to soil-borne phospholipid fatty acid fungal biomarkers 18:2ω6,9 and 18:1ω9

    PubMed Central

    Kaiser, Christina; Frank, Alexander; Wild, Birgit; Koranda, Marianne; Richter, Andreas

    2010-01-01

    The phospholipid fatty acid biomarkers 18:1ω9, 18:2ω6,9 and 18:3ω3,6,9 are commonly used as fungal biomarkers in soils. They have, however, also been found to occur in plant tissues, such as roots. Thus, the use of these PLFAs as fungal biomarkers in sieved soil, which may still contain small remains of roots, has been questioned. We used data from a recent beech tree girdling experiment to calculate the contribution of roots to these biomarkers and were able to demonstrate that not more than 0.61% of 18:1ω9 and 18:2ω6,9 in sieved soil samples originated from roots (but 4% of 18:3ω3,6,9). Additionally, the abundance of the biomarker 18:2ω6,9 in the soil was found to be highly correlated to ectomycorrhizal root colonization, which further corroborates its fungal origin. PLFA biomarkers were substantially reduced in vital roots from girdled trees compared to roots of control trees (by up to 76%), indicating that the major part of PLFAs measured in roots may actually originate from ectomycorrhizal fungi growing inside the roots. We calculated, that even a near to 50% reduction in fine root biomass – as observed in the girdling treatment – accounted for only 0.8% of the measured decrease of 18:2ω6,9. Our results demonstrate that both 18:1ω9 and 18:2ω6,9 are suitable biomarkers for detecting fungal dynamics in soils and that especially 18:2ω6,9 is a reliable biomarker to study mycorrhizal dynamics in beech forests. PMID:21633516

  15. 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.

  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. Metabolomics Analysis Identifies Intestinal Microbiota-Derived Biomarkers of Colonization Resistance in Clindamycin-Treated Mice

    PubMed Central

    Jump, Robin L. P.; Polinkovsky, Alex; Hurless, Kelly; Sitzlar, Brett; Eckart, Kevin; Tomas, Myreen; Deshpande, Abhishek; Nerandzic, Michelle M.; Donskey, Curtis J.

    2014-01-01

    Background The intestinal microbiota protect the host against enteric pathogens through a defense mechanism termed colonization resistance. Antibiotics excreted into the intestinal tract may disrupt colonization resistance and alter normal metabolic functions of the microbiota. We used a mouse model to test the hypothesis that alterations in levels of bacterial metabolites in fecal specimens could provide useful biomarkers indicating disrupted or intact colonization resistance after antibiotic treatment. Methods To assess in vivo colonization resistance, mice were challenged with oral vancomycin-resistant Enterococcus or Clostridium difficile spores at varying time points after treatment with the lincosamide antibiotic clindamycin. For concurrent groups of antibiotic-treated mice, stool samples were analyzed using quantitative real-time polymerase chain reaction to assess changes in the microbiota and using non-targeted metabolic profiling. To assess whether the findings were applicable to another antibiotic class that suppresses intestinal anaerobes, similar experiments were conducted with piperacillin/tazobactam. Results Colonization resistance began to recover within 5 days and was intact by 12 days after clindamycin treatment, coinciding with the recovery bacteria from the families Lachnospiraceae and Ruminococcaceae, both part of the phylum Firmicutes. Clindamycin treatment caused marked changes in metabolites present in fecal specimens. Of 484 compounds analyzed, 146 (30%) exhibited a significant increase or decrease in concentration during clindamycin treatment followed by recovery to baseline that coincided with restoration of in vivo colonization resistance. Identified as potential biomarkers of colonization resistance, these compounds included intermediates in carbohydrate or protein metabolism that increased (pentitols, gamma-glutamyl amino acids and inositol metabolites) or decreased (pentoses, dipeptides) with clindamycin treatment. Piperacillin

  18. Multiplex immunoassay analysis of biomarkers in clinically accessible quantities of human aqueous humor

    PubMed Central

    Rogojina, Anna T.; Chalam, K.V.

    2009-01-01

    Purpose Aqueous humor is intimately related to the cells of the anterior and posterior chambers, which affect its composition. Aqueous analysis provides useful information regarding physiological and pathophysiological processes in the eye. Human aqueous samples are typically less than 100 µl, limiting the usefulness of the analysis with traditional Enzyme-Linked immunoSorbant Assay (ELISA) techniques. The specific aim of this study was to investigate if whether large numbers of analytes can be identified in clinically available samples of aqueous humor and to document the detectability of certain biomarkers in the aqueous. Methods We used a technology developed by Luminex xMAP to analyze hundreds of analytes in a small sample. Aqueous from eight normal and two diabetic patients was analyzed. Results Of the 90 analytes evaluated, 52 (57%) were detectable in the normal aqueous. To place these results in biological context, we analyzed the list of expressed analytes using the MetaCore database. The functional pathways, networks, biological processes, and disease processes that these analytes represented were identified. Several ocular pathology-related processes were represented in the aqueous. The detected analytes represented biomarkers of several relevant disease processes including vascular diseases, arteriosclerosis, ischemia, necrosis, and inflammation. To provide the proof of principle that the aqueous profile could offer useful information about the pathophysiological processes, we analyzed two aqueous samples from diabetic patients. These limited samples showed the differences between normal and diabetic samples, including those relevant to diabetic retinopathy such as vascular endothelial growth factor (VEGF), C reactive protein, glutathione, and cytokines. Several biomarker groups for disease processes relevant to diabetes were perturbed. Conclusions These results demonstrate that multiplex analysis of the aqueous can be a useful tool in screening for any

  19. Paleo-reconstruction: Using multiple biomarker parameters

    NASA Astrophysics Data System (ADS)

    Chen, Zhengzheng

    Advanced technologies have played essential roles in the development of molecular organic geochemistry. In this thesis, we have developed several new techniques and explored their applications, alone and with previous techniques, to paleo-reconstruction. First, we developed a protocol to separate biomarker fractions for accurate measurement of compound-specific isotope analysis. This protocol involves combination of zeolite adduction and HPLC separation. Second, an integrated study of traditional biomarker parameters, diamondoids and compound-specific biomarker isotopes, differentiated oil groups from Saudi Arabia. Specifically, Cretaceous reservoired oils were divided into three groups and the Jurassic reservoired oils were divided into two groups. Third, biomarker acids provide an alternative way to characterize biodegradation. Oils from San Joaquin Valley, U.S.A. and oils from Mediterranean display drastically different acid profiles. These differences in biomarker acids probably reflect different processes of biodegradation. Fourth, by analyzing biomarker distributions in the organic-rich rocks recording the onset of Late Ordovician extinction, we propose that changes in salinity associated with eustatic sea-level fall, contributed at least locally to the extinction of graptolite species.

  20. ASSESSMENT OF NEUROTOXICITY: USE OF GLIAL FIBRILLARY ACIDIC PROTEIN AS A BIOMARKER

    EPA Science Inventory

    Diverse neurotoxic insults results in proliferation and hypertrophy of astrocytes. he hallmark of this response is enhanced expression of the major intermediate filament protein of astrocytes, glial fibrillary acidic protein (GFAP). hese observations suggest that GFAP may be a us...

  1. 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

  2. Microarray Analysis of Transcriptome of Medulla Identifies Potential Biomarkers for Parkinson's Disease

    PubMed Central

    Liao, Xiao-Yang; Yang, Zheng-Hui; Wang, Jun; Lin, Hang; Wang, Qing-Song; Wu, Yu-Xian; Liu, Yu

    2013-01-01

    To complement the molecular pathways contributing to Parkinson's disease (PD) and identify potential biomarkers, gene expression profiles of two regions of the medulla were compared between PD patients and control. GSE19587 containing two groups of gene expression profiles [6 dorsal motor nucleus of the vagus (DMNV) samples from PD patients and 5 from controls, 6 inferior olivary nucleus (ION) samples from PD patients and 5 from controls] was downloaded from Gene Expression Omnibus. As a result, a total of 1569 and 1647 differentially expressed genes (DEGs) were, respectively, screened in DMNV and ION with limma package of R. The functional enrichment analysis by DAVID server (the Database for Annotation, Visualization and Integrated Discovery) indicated that the above DEGs may be involved in the following processes, such as regulation of cell proliferation, positive regulation of macromolecule metabolic process, and regulation of apoptosis. Further analysis showed that there were 365 common DEGs presented in both regions (DMNV and ION), which may be further regulated by eight clusters of microRNAs retrieved with WebGestalt. The genes in the common DEGs-miRNAs regulatory network were enriched in regulation of apoptosis process via DAVID analysis. These findings could not only advance the understandings about the pathogenesis of PD, but also suggest potential biomarkers for this disease. PMID:24350239

  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. Proteomic Analysis of Temporally Stimulated Ovarian Cancer Cells for Biomarker Discovery*

    PubMed Central

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

    2013-01-01

    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 EGF1, 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 monoclonal

  5. 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

  6. 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

  7. Biomarker analysis of liver cells exposed to surfactant-wrapped and oxidized multi-walled carbon nanotubes (MWCNTs).

    PubMed

    Henderson, W Matthew; Bouchard, Dermont; Chang, Xiaojun; Al-Abed, Souhail R; Teng, Quincy

    2016-09-15

    Carbon nanotubes (CNTs) have great potential in industrial, consumer, and mechanical applications, based partly on their unique structural, optical and electronic properties. CNTs are commonly oxidized or treated with surfactants to facilitate aqueous solution processing, and these CNT surface modifications also increase possible human and ecological exposures to nanoparticle-contaminated waters. To determine the exposure outcomes of oxidized and surfactant-wrapped multiwalled carbon nanotubes (MWCNTs) on biochemical processes, metabolomics-based profiling of human liver cells (C3A) was utilized. Cells were exposed to 0, 10, or 100ng/mL of MWCNTs for 24 and 48h; MWCNT particle size distribution, charge, and aggregation were monitored concurrently during exposures. Following MWCNT exposure, cellular metabolites were extracted, lyophilized, and buffered for (1)H NMR analysis. Acquired spectra were subjected to both multivariate and univariate analysis to determine the consequences of nanotube exposure on the metabolite profile of C3A cells. Resulting scores plots illustrated temporal and dose-dependent metabolite responses to all MWCNTs tested. Loadings plots coupled with t-test filtered spectra identified metabolites of interest. XPS analysis revealed the presence of hydroxyl and carboxyl functionalities on both MWCNTs surfaces. Metal content analysis by ICP-AES indicated that the total mass concentration of the potentially toxic impurities in the exposure experiments were extremely low (i.e. [Ni]≤2×10(-10)g/mL). Preliminary data suggested that MWCNT exposure causes perturbations in biochemical processes involved in cellular oxidation as well as fluxes in amino acid metabolism and fatty acid synthesis. Dose-response trajectories were apparent and spectral peaks related to both dose and MWCNT dispersion methodologies were determined. Correlations of the significant changes in metabolites will help to identify potential biomarkers associated with carbonaceous

  8. 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

    2016-03-01

    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. PMID:26820531

  9. Prostate cancer serum biomarker discovery through proteomic analysis of alpha-2 macroglobulin protein complexes

    PubMed Central

    Burgess, Earle F.; Ham, Amy-Joan L.; Tabb, David L.; Billheimer, Dean; Roth, Bruce J.; Chang, Sam S.; Cookson, Michael S.; Hinton, Timothy J.; Cheek, Kristin L.; Hill, Salisha; Pietenpol, Jennifer A.

    2010-01-01

    Alpha-2 macroglobulin (A2M) functions as a universal protease inhibitor in serum and is capable of binding various cytokines and growth factors. In this study, we investigated if immunoaffinity enrichment and proteomic analysis of A2M protein complexes from human serum could improve detection of biologically relevant and novel candidate protein biomarkers in prostate cancer. Serum samples from six patients with androgen-independent, metastatic prostate cancer and six control patients without malignancy were analyzed by immunoaffinity enrichment of A2M protein complexes and MS identification of associated proteins. Known A2M substrates were reproducibly identified from patient serum in both cohorts, as well as proteins previously undetected in human serum. One example is heat shock protein 90 alpha (HSP90α), which was identified only in the serum of cancer patients in this study. Using an ELISA, the presence of HSP90α in human serum was validated on expanded test cohorts and found to exist in higher median serum concentrations in prostate cancer (n = 18) relative to control (n = 13) patients (median concentrations 50.7 versus 27.6 ng/mL, respectively, p = 0.001). Our results demonstrate the technical feasibility of this approach and support the analysis of A2M protein complexes for proteomic-based serum biomarker discovery. PMID:20107526

  10. 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

  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. Proteome analysis of biomarkers in the cerebrospinal fluid of neuromyelitis optica patients

    PubMed Central

    Bai, Shumei; Guo, Xuxiao; Qin, Zhaoyu; Wang, Banqin; Li, Xiaohong; Qin, Yanjiang; Liu, Yi-Hsin

    2009-01-01

    Purpose To better understand the pathophysiological mechanisms underlying neuromyelitis optica (NMO), we developed a proteomics platform for biomarker discovery in the cerebrospinal fluid (CSF) of patients with NMO. Methods Two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) were used to compare the CSF proteome of NMO patients with that of controls. A subsequent ELISA and western blot analysis were performed to verify the results of the proteomic analysis. Pathway Studio 5.0 software was used to determine possible functional interactions among these differentially expressed proteins. Results Using 2-DE and MALDI-TOF MS, we identified 11 differentially expressed proteins and two isoforms of these same proteins. The expression of four proteins was enhanced, whereas the expression of seven proteins was reduced in the NMO group in comparison to the control group. These differences in protein expression were confirmed by performing ELISA and western blot analyses (p<0.01). Protein network analyses revealed biologic interactions and cross-talks among these differentially expressed proteins. Conclusions Because of their unique expression profile in NMO CSFs, these proteins are candidate biomarkers for NMO. Thus, our findings may have important implications for both the diagnosis of NMO and the further understanding of its pathogenesis. PMID:19710940

  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. Alcohol Use Biomarkers Predicting Cognitive Performance: A Secondary Analysis in Veterans With Alcohol Dependence and Posttraumatic Stress Disorder

    PubMed Central

    Kalapatapu, Raj K.; Delucchi, Kevin L.; Lasher, Brooke A.; Vinogradov, Sophia; Batki, Steven L.

    2013-01-01

    Objective We conducted a secondary analysis of baseline data from a recently completed pharmacological pilot clinical trial among 30 veterans with alcohol dependence and posttraumatic stress disorder (PTSD). This trial included baseline measures of alcohol use biomarkers, both indirect (carbohydrate-deficient transferrin, GGT [γ-glutamyltransferase], mean corpuscular volume, AST [aspartate aminotransferase], alanine aminotransferase) and direct (ethyl glucuronide, ethyl sulfate), as well as neurocognitive measures (Trail Making Test parts A and B, Hopkins Verbal Learning Test—Revised, Balloon Analogue Risk Task, Delay Discounting Task). Methods Two regression models were estimated and tested for each neurocognitive measure (dependent measure). The first model included the alcohol use biomarker alone as the predictor. The second model included the alcohol use biomarker along with the following 3 additional predictors: Beck Depression Inventory, Clinician-Administered PTSD Scale, and receiving medications. Results In both models, the indirect biomarkers, such as GGT and AST, significantly predicted performance on the Hopkins Verbal Learning Test—Revised %Retention. GGT alone significantly predicted performance on the Trail Making Test part A. Conclusions Indirect alcohol use biomarkers may have a specific role in identifying those veterans with alcohol dependence and PTSD who have impaired cognitive performance. However, direct alcohol use biomarkers may not share such a role. PMID:24005546

  15. 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. PMID:23639751

  16. A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

    PubMed Central

    Liu, Wanting

    2013-01-01

    Genome-wide microarray technology has facilitated the systematic discovery of diagnostic biomarkers of cancers and other pathologies. However, meta-analyses of published arrays often uncover significant inconsistencies that hinder advances in clinical practice. Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called ‘melanoma driver’ genes involved in MAPK, Ca2+, and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, and WNT4). We have begun to experimentally validate a subset of these genes involved in MAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be over-expressed in metastatic and primary melanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin. While SHC4 has been reported previously to be associated to melanoma, this is the first time CXCL13, COL11A1, and PTPRF have been associated with melanoma on experimental validation. Our computational evaluation indicates that this 12-gene biomarker signature achieves excellent diagnostic power in distinguishing metastatic melanoma from normal skin and benign nevus. Further experimental validation of the role of these 12 genes in a new signaling network may provide new insights into the underlying biological mechanisms driving the progression of melanoma. PMID:23638386

  17. Predicting Cytotoxic T-cell Age from Multivariate Analysis of Static and Dynamic Biomarkers*

    PubMed Central

    Rivet, Catherine A.; Hill, Abby S.; Lu, Hang; Kemp, Melissa L.

    2011-01-01

    Adoptive T-cell transfer therapy relies upon in vitro expansion of autologous cytotoxic T cells that are capable of tumor recognition. The success of this cell-based therapy depends on the specificity and responsiveness of the T cell clones before transfer. During ex vivo expansion, CD8+ T cells present signs of replicative senescence and loss of function. The transfer of nonresponsive senescent T cells is a major bottleneck for the success of adoptive T-cell transfer therapy. Quantitative methods for assessing cellular age and responsiveness will facilitate the development of appropriate cell expansion and selection protocols. Although several biomarkers of lymphocyte senescence have been identified, these proteins in isolation are not sufficient to determine the age-dependent responsiveness of T cells. We have developed a multivariate model capable of extracting combinations of markers that are the most informative to predict cellular age. To acquire signaling information with high temporal resolution, we designed a microfluidic chip enabling parallel lysis and fixation of stimulated cell samples on-chip. The acquisition of 25 static biomarkers and 48 dynamic signaling measurements at different days in culture, integrating single-cell and population based information, allowed the multivariate regression model to accurately predict CD8+ T-cell age. From surface marker expression and early phosphorylation events following T-cell receptor stimulation, the model successfully predicts days in culture and number of population doublings with R2 = 0.91 and 0.98, respectively. Furthermore, we found that impairment of early signaling events following T cell receptor stimulation because of long term culture allows prediction of costimulatory molecules CD28 and CD27 expression levels and the number of population divisions in culture from a limited subset of signaling proteins. The multivariate analysis highlights the information content of both averaged biomarker values and

  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. 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...

  20. Analysis and Characterization of Organic Carbon in Early Holocene Wetland Paleosols using Ramped Pyrolysis 14C and Biomarkers

    NASA Astrophysics Data System (ADS)

    Vetter, L.; Schreiner, K. M.; Fernandez, A.; Rosenheim, B. E.; Tornqvist, T. E.

    2014-12-01

    Radiocarbon analyses are a key tool for quantifying the dynamics of carbon cycling and storage in both modern soils and Quaternary paleosols. Frequently, bulk 14C dates of paleosol organic carbon provide ages older than the time of soil burial, and 14C dates of geochemical fractions such as alkali and acid extracts (operationally defined as humic acids) can provide anomalously old ages when compared to coeval plant macrofossil dates. Ramped pyrolysis radiocarbon analysis of sedimentary organic material has been employed as a tool for investigating 14C age spectra in sediments with multiple organic carbon sources. Here we combine ramped pyrolysis 14C analysis and biomarker analysis (lignin-phenols and other cupric oxide products) to provide information on the source and diagenetic state of the paleosol organic carbon. We apply these techniques to immature early Holocene brackish wetland entisols from three sediment cores in southeastern Louisiana, along with overlying basal peats. Surprisingly, we find narrow 14C age spectra across all thermal aliquots from both paleosols and peats. The weighted bulk 14C ages from paleosols and overlying peats are within analytical error, and are comparable to independently analyzed 14C AMS dates from charcoal fragments and other plant macrofossils from each peat bed. Our results suggest high turnover rates of carbon in soils relative to input of exogenous carbon sources. These data raise broader questions about processes within the active soil and during pedogenesis and burial of paleosols that can effectively homogenize radiocarbon content in soils across the thermochemical spectrum. The concurrence of paleosol and peat 14C ages also suggests that, in the absence of peats with identifiable plant macrofossils, ramped pyrolysis 14C analyses of paleosols may be used to provide ages for sea-level indicators.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26261215

  2. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis

    PubMed Central

    Jakupciak, John P.; Wells, Jeffrey M.; Karalus, Richard J.; Pawlowski, David R.; Lin, Jeffrey S.; Feldman, Andrew B.

    2013-01-01

    Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. PMID:24455204

  3. A Microarray-Based Gene Expression Analysis to Identify Diagnostic Biomarkers for Unknown Primary Cancer

    PubMed Central

    Kurahashi, Issei; Fujita, Yoshihiko; Arao, Tokuzo; Kurata, Takayasu; Koh, Yasuhiro; Sakai, Kazuko; Matsumoto, Koji; Tanioka, Maki; Takeda, Koji; Takiguchi, Yuichi; Yamamoto, Nobuyuki; Tsuya, Asuka; Matsubara, Nobuaki; Mukai, Hirofumi; Minami, Hironobu; Chayahara, Naoko; Yamanaka, Yasuhiro; Miwa, Keisuke; Takahashi, Shin; Takahashi, Shunji; Nakagawa, Kazuhiko; Nishio, Kazuto

    2013-01-01

    Background The biological basis for cancer of unknown primary (CUP) at the molecular level remains largely unknown, with no evidence of whether a common biological entity exists. Here, we assessed the possibility of identifying a common diagnostic biomarker for CUP using a microarray gene expression analysis. Methods Tumor mRNA samples from 60 patients with CUP were analyzed using the Affymetrix U133A Plus 2.0 GeneChip and were normalized by asinh (hyperbolic arc sine) transformation to construct a mean gene-expression profile specific to CUP. A gene-expression profile specific to non-CUP group was constructed using publicly available raw microarray datasets. The t-tests were performed to compare the CUP with non-CUP groups and the top 59 CUP specific genes with the highest fold change were selected (p-value<0.001). Results Among the 44 genes that were up-regulated in the CUP group, 6 genes for ribosomal proteins were identified. Two of these genes (RPS7 and RPL11) are known to be involved in the Mdm2–p53 pathway. We also identified several genes related to metastasis and apoptosis, suggesting a biological attribute of CUP. Conclusions The protein products of the up-regulated and down-regulated genes identified in this study may be clinically useful as unique biomarkers for CUP. PMID:23671674

  4. 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. PMID:26070503

  5. A biomarker found in cadmium exposed residents of Thailand by metabolome analysis.

    PubMed

    Suvagandha, Dhitiwass; Nishijo, Muneko; Swaddiwudhipong, Witaya; Honda, Ruymon; Ohse, Morimasa; Kuhara, Tomiko; Nakagawa, Hideaki; Ruangyuttikarn, Werawan

    2014-04-01

    First, the urinary metabolic profiling by gas chromatography-mass spectrometry (GC-MS), was performed to compare ten cadmium (Cd) toxicosis cases from a Cd-polluted area in Mae Sot (Thailand) with gender-matched healthy controls. Orthogonal partial list square-discrimination analysis was used to identify new biomarker candidates in highly Cd exposed toxicosis cases with remarkable renal tubular dysfunction. The results of the first step of this study showed that urinary citrate was a negative marker and myo-inositol was a positive marker for Cd toxicosis in Thailand. In the second step, we measured urinary citrate in the residents (168 Cd-exposed subjects and 100 controls) and found significantly lower levels of urinary citrate and higher ratios of calcium/citrate and magnesium/citrate, which are risk factors for nephrolithiasis, in highly Cd-exposed residents. Additionally, this inverse association of urinary citrate with urinary Cd was observed after adjustment for age, smoking and renal tubular dysfunction, suggesting a direct effect of Cd on citrate metabolism. These results indicate that urinary citrate is a useful biomarker for the adverse health effects of Cd exposure in a Thai population with a high prevalence of nephrolithiasis. PMID:24699029

  6. Simultaneous analysis of biologically active aminoalkanephosphonic acids.

    PubMed

    Kudzin, Zbigniew H; Gralak, Dorota K; Andrijewski, Grzegorz; Drabowicz, Józef; Luczak, Jerzy

    2003-05-23

    A new approach for simultaneous analysis of biologically active aminoalkanephosphonic acids, namely glyphosate, phosphonoglycine, phosphonosarcosine, phosphonoalanine, phosphono-beta-alanine, phosphonohomoalanine, phosphono-gamma-homoalanine and glufosinate, is presented. This includes a preliminary 31p NMR analysis of these amino acids, their further derivatization to volatile phosphonates (phosphinates) by means of trifluoroacetic acid-trifluoroacetic anhydride-trimethyl orthoacetate reagent and subsequent analysis of derivatization products using MS and/or GC-MS (chemical ionization and/or electron impact ionization). PMID:12862383

  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. PMID:26342574

  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. Development of a gas chromatographic test for the quantitation of the biomarker 2-butoxyacetic acid in urine samples.

    PubMed

    B'Hymer, C

    2007-08-01

    An accurate and precise method is developed and evaluated for the detection and quantitation of 2-butoxyacetic acid (2-BAA), a metabolite and biomarker for human exposure to 2-butoxyethanol. The solvent 2-butoxyethanol (2-BE) is extensively used in various industrial and domestic applications, and it is a health concern owing to its toxicity. Sample preparation consists of liquid-liquid extraction (LLE) of urine, then esterification of 2-BAA to produce the ethyl ester analog. The gas chromatographic conditions utilize a dimethyl polysiloxane phase (HP-1) capillary column and a mass spectrometer (MS) for detection of the analyte. Validation of this method includes a recovery study using fortified urine samples, which demonstrated good accuracy and precision; recovery varied between 100% and 102% of theory, with relative standard deviations of replicate samples at 2.8% and less. The detection limit of this method ranges from 0.005 to 0.015 microg/mL equivalent level of 2-BAA in urine. PMID:17725869

  10. Evaluation of single and joint toxicity of perfluorooctane sulfonate, perfluorooctanoic acid, and copper to Carassius auratus using oxidative stress biomarkers.

    PubMed

    Feng, Mingbao; He, Qun; Meng, Lingjun; Zhang, Xiaoling; Sun, Ping; Wang, Zunyao

    2015-04-01

    Perfluorooctane sulfonate, perfluorooctanoic acid, and copper have been recently regarded as ubiquitous environmental contaminants in aquatic ecosystems worldwide. However, data on their possible combined toxic effects on aquatic organisms are still lacking. In this study, a systematic experimental approach was used to assess the impacts of these chemicals and their mixtures on hepatic antioxidant status of Carassius auratus after 4 days. Oxidative stress was apparently observed for joint exposure by determining biochemical parameters (superoxide dismutase, catalase, glutathione peroxidase, reduced glutathione, and malondialdehyde). The integrated biomarker response index was calculated to rank the toxicity order, from which the synergistic effect was tentatively proposed for joint-toxicity action. In addition, these treatments significantly altered trace element homeostasis in different fish tissues, and the concentration distribution of these test chemicals was also measured. Taken together, these results provided some valuable toxicological data on the joint effects of perfluorinated compounds and heavy metals on aquatic species, which can facilitate further understanding on the potential risks of other coexisting pollutants in the natural aquatic environment. PMID:25697679

  11. 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. PMID:24066126

  12. 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

  13. 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. PMID:25328286

  14. 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...

  15. 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...

  16. 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

  17. 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…

  18. SERS of meso-droplets supported on superhydrophobic wires allows exquisitely sensitive detection of dipicolinic acid, an anthrax biomarker, considerably below the infective dose.

    PubMed

    Cheung, Melody; Lee, Wendy W Y; Cowcher, David P; Goodacre, Royston; Bell, Steven E J

    2016-08-01

    Surface-enhanced Raman measurements of <1 μL analyte/colloid meso-droplets on superhydrophobic wires with hydrophilic tips allowed dipicolinic acid, a spore biomarker for Bacillus anthracis (anthrax), to be detected at 10(-6) mol dm(-3). This is equivalent to 18 spores, significantly below the infective dose of 10(4) spores and 2 orders of magnitude better than previous measurements. PMID:27432481

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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

  1. Estimation of biodiesel cytotoxicity by using acid phosphatase as a biomarker of lysosomal integrity.

    PubMed

    da Cruz, Andrea Cristina Santos; Leite, Maria Bernadete N L; Rodrigues, Luiz Erlon Araújo; Nascimento, Iracema Andrade

    2012-08-01

    Biodiesel is promoted as environmentally less harmful than diesel fuel. Nevertheless its water-soluble-fraction (WSF) may contain methanol, which appears by a reversion of the transesterification reaction, when biodiesel contacts water. This paper evaluated the loss of the lysosomal membrane integrity in liver homogenate of juvenils Tilapia exposed to biodiesels-WSF, through the increase of the acid phosphatase activity, as an evidence of citotoxicity. Differences in the enzyme activity levels (3.4, 2.3 and 0.8 mU mg(-1) total protein over the control value, which was 1.6 mU mg(-1) total protein), found for castor oil, waste cooking-oil and palm oil-biodiesels, respectively, were indicative of their toxicity according to this decreasing trend. WSF-chromatograms suggest the cytotoxicity as related to methanol. PMID:22717620

  2. 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

  3. 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. PMID:25137651

  4. Bias in High-Throughput Analysis of miRNAs and Implications for Biomarker Studies.

    PubMed

    Backes, Christina; Sedaghat-Hamedani, Farbod; Frese, Karen; Hart, Martin; Ludwig, Nicole; Meder, Benjamin; Meese, Eckart; Keller, Andreas

    2016-02-16

    A certain degree of bias in high-throughput molecular technologies including microarrays and next-generation sequencing (NGS) is known. To quantify the actual impact of the biomarker discovery platform on miRNA profiles, we first performed a meta-analysis: raw data of 1 539 microarrays and 705 NGS blood-borne miRNomes were statistically evaluated, suggesting a substantial influence of the technology on biomarker profiles. We observed highly significant dependency of the miRNA nucleotide composition on the expression level. Higher expression in NGS was discovered for uracil-rich miRNAs (p = 7 × 10(-37)), while high expression in microarrays was found predominantly for guanine-rich miRNAs (p = 3 × 10(-33)). To verify the findings, 10 identical replicates of one individual were measured using NGS and microarrays (2 525 miRNAs from miRBase version 21). Overall, we calculated a correlation coefficient of 0.414 for both technologies. Detailed analysis however revealed that the correlation was observed only for miRNAs in the early miRBase versions (<8). The majority of miRNAs (2 013 from miRBase version 8 onward) was not correlated between microarray and NGS. Specifically, we observed 67 miRNAs with a median read count above 10 in NGS, while they were not detected in any of the 10 replicated array experiments. In contrast, 234 miRNAs were discovered in all 10 replicated array measurements but were not found in any of the NGS experiments of the same individual. While the first group had average guanine content of 22%, the latter group consisted of 41% of this nucleotide. Selected concordant and discordant miRNAs were tested in quantitative real-time-polymerase chain reaction (RT-qPCR) experiments again of the same individual, providing further evidence for the substantial bias depending on the base composition. As a consequence, biomarkers that have been discovered by specific high-throughout technologies have to be carefully considered. Especially for validation

  5. Detecting Neuroimaging Biomarkers for Schizophrenia: A Meta-Analysis of Multivariate Pattern Recognition Studies

    PubMed Central

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

    2015-01-01

    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

  6. Analysis of a Ricin Biomarker, Ricinine, in 989 Individual Human Urine Samples

    PubMed Central

    Pittman, Christopher T.; Guido, John; Hamelin, Elizabeth I.; Blake, Thomas A.; Johnson, Rudolph C.

    2015-01-01

    Ricinine (3-cyano-4-methoxy-N-methyl-2-pyridone) is a urinary biomarker which can be measured to confirm human exposure to castor bean products such as ricin. As many consumer products contain castor oil, another castor bean product, ricinine may be detectable in the general population. The following study characterized urinary ricinine concentrations from 989 individuals who were presumed to be unexposed to ricin. An automated diagnostic method was utilized here to simplify the analysis of this large sample set. Sample preparation included a 96-well polystyrene divinylbenzene high throughput extraction and preconcentration step. Purified samples were analyzed by an efficient dual column, reversed phase liquid chromatography separation and 13C-isotope dilution tandem mass spectrometry. In this convenience sample, only 1.2% of the urine samples had detectable amounts of ricinine randomly distributed between 0.186 and 4.15 ng/mL. PMID:23471955

  7. 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. PMID:24819180

  8. Identification of novel biomarkers for preeclampsia on the basis of differential expression network analysis

    PubMed Central

    WU, YUFANG; FU, XIUHUA; WANG, LIN

    2016-01-01

    Preeclampsia (PE) is a severe pregnancy complication, which is a leading cause of maternal and fetal mortality. The present study aimed to screen potential biomarkers for the diagnosis and prediction of PE and to investigate the underlying mechanisms of PE development based on the differential expression network (DEN). The microarray datasets E-GEOD-6573 and E-GEOD-48424 were downloaded from the European Bioinformatics Institute database. Differentially expressed genes (DEGs) between the PE and normal groups were screened by Significant Analysis of Microarrays with the cutoff value of a |log2 fold change| of >2, and a false discovery rate of <0.05. The DEN was constructed based on the differential and non-differential interactions observed. In addition, genes with higher connectivity degrees in the DEN were identified on the basis of centrality analysis, while disease genes were also extracted from the DEN. In order to understand the functional roles of genes in DEN, Gene Ontology (GO) and pathway enrichment analyses were performed. The present results indicated that a total of 225 genes were considered as DEGs in the PE group, while 466 nodes and 314 gene interactions were involved in the DEN. Among these 466 nodes, 4 nodes with higher degrees were identified, including ubiquitin C (UBC), small ubiquitin-like modifier 1 (SUMO1), SUMO2 and RAD21 homolog (S. pombe) (RAD21). Notably, UBC was also found to be a disease gene. UBC, RAD21, SUMO2 and SUMO1 were markedly enriched in the regulation of programmed cell death, as well as in the regulation of apoptosis, cell cycle and chromosomal part. In conclusion, based on these results, we suggest that UBC, RAD21, SUMO2 and SUMO1 may be reliable biomarkers for the prediction of the development and progression of PE. PMID:27347039

  9. Fatty acids in serum and diet--a canonical correlation analysis among toddlers.

    PubMed

    Uusitalo, Liisa; Nevalainen, Jaakko; Salminen, Irma; Ovaskainen, Marja-Leena; Kronberg-Kippilä, Carina; Ahonen, Suvi; Niinistö, Sari; Alfthan, Georg; Simell, Olli; Ilonen, Jorma; Veijola, Riitta; Knip, Mikael; Virtanen, Suvi M

    2013-07-01

    Fatty acid concentrations in blood are potential biomarkers of dietary fat intake, but methodological studies among children are scarce. The large number of fatty acids and their complex interrelationships pose a special challenge in research on fatty acids. Our target was to assess the interrelationships between the total fatty acid profiles in diet and serum of young children. The study subjects were healthy control children from the birth cohort of the Type 1 Diabetes Prediction and Prevention Study. A 3-day food record and a frozen serum sample were available from 135 children at the age of 1 year, from 133 at 2 years, and from 92 at 3 years. The relationship between dietary and serum fatty acid profiles was analysed using canonical correlation analysis. The consumption of fatty milk correlated positively with serum fatty acids, pentadecanoic acid, palmitic acid and conjugated linoleic acid (CLA) at all ages. Correlations between dietary and serum eicosapentaenoic and/or docosahexaenoic acid were observed at 2 and 3 years of age. Serum linoleic acid was positively associated with the consumption of infant formula at the age of 1 year, and with the consumption of vegetable margarine at 2 and 3 years. The results indicate a high quality of the 3-day food records kept by parents and other caretakers of the children, and suitability of non-fasting, un-fractioned serum samples for total fatty acid analyses. The correlation between intake of milk fat and serum proportion of CLA is a novel finding. PMID:22066932

  10. Gamma aminobutyric acid radioreceptor-assay a possible biomarker for human exposure to certain agrochemicals.

    PubMed

    Saleh, M A; Abou Zied, M; el-Baroty, G; Abdel-Reheim, E; Abdel-Rahman, F; Wallace, C; el-Sebae, A H; Blancato, J N

    1993-12-01

    Cyclodiene insecticides, hexachlorocyclohexanes, pyrethroids, bicyclophosphates, the bicycloorthocarboxylate insecticides and some of their metabolites and environmental degradation products are central nervous system toxicants with high specific binding affinity to the chloride channel of the gamma-aminobutyric acid (GABA)A receptor-ionophore sites. [35S] tertiary-butylbicyclophosphorothionate (TBPS) with specific activity higher than 60 Ci/mmole has a high binding affinity to the same sites and is now commercially available and can be used to label the GABAA receptor for the development of a radioreceptor assay technique. The GABA receptor was prepared by ultra centrifugation and dialysis of brain homogenates of either cow, goat, rat or catfish. The receptor was then labeled with [35S] TBPS and the assay was conducted by measuring the displacement of radioactivity following incubation with samples containing the analytes. A radioreceptor assay protocol was developed to measure the amount of the alpha-endosulfan in blood samples. The assay was extremely sensitive, and can detect 0.2 nM of endosulfan at a level equivalent to 0.08 ppb or 8 x 10(-11) gm of endosulfan in each ml of the blood samples. PMID:8270763

  11. 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

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

    PubMed

    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

  13. Integrated biomarker analysis in the earthworm Lumbricus terrestris: application to the monitoring of soil heavy metal pollution.

    PubMed

    Calisi, A; Zaccarelli, N; Lionetto, M G; Schettino, T

    2013-03-01

    As recently recognized exposure and effect assessment of soil contaminants on soil biota is necessary for decision-making related to ecosystem services and habitat protection, establishment of remediation procedures, or pollution monitoring programs. Therefore, biological approaches to soil monitoring, such as the measurement of biomarkers in soil bioindicator organisms, have recently received increasing attention. The aim of the present work was to assess the performance of a suite of cellular and biochemical biomarkers in native earthworms (Lumbricus terrestris) sampled in heavy metal contaminated sites in view of the validation of this biomarker approach in soil monitoring and assessment. Besides well known and standardized biomarkers such as lysosomal membrane stability, metallothionein tissue concentration and acetylcholinesterase activity, novel potential biomarkers such as changes in blood hemoglobin concentration and granulocyte morphometric alterations were analyzed. Both univariate and multivariate (PCA) statistical analysis applied to the data set revealed that the integrated multi-marker approach in native L. terrestris under field conditions produces a sensitive and cost-effective assessment of heavy metal soil pollution, which could be incorporated as a descriptor of environmental status in future soil biomonitoring programmes. PMID:23266410

  14. 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. PMID:26209955

  15. 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

    2015-11-01

    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. PMID:25727266

  16. Urine Injury Biomarkers and Risk of Adverse Outcomes in Recipients of Prevalent Kidney Transplants: The Folic Acid for Vascular Outcome Reduction in Transplantation Trial.

    PubMed

    Bansal, Nisha; Carpenter, Myra A; Weiner, Daniel E; Levey, Andrew S; Pfeffer, Marc; Kusek, John W; Cai, Jianwen; Hunsicker, Lawrence G; Park, Meyeon; Bennett, Michael; Liu, Kathleen D; Hsu, Chi-Yuan

    2016-07-01

    Recipients of kidney transplants (KTR) are at increased risk for cardiovascular events, graft failure, and death. It is unknown whether urine kidney injury biomarkers are associated with poor outcomes among KTRs. We conducted a post hoc analysis of the Folic Acid for Vascular Outcome Reduction in Transplantation (FAVORIT) Trial using a case-cohort study design, selecting participants with adjudicated cardiovascular events, graft failure, or death. Urine neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1), IL-18, and liver-type fatty acid binding protein (L-FABP) were measured in spot urine samples and standardized to urine creatinine concentration. We adjusted for demographics, cardiovascular risk factors, eGFR, and urine albumin-to-creatinine ratio. Patients had 291 cardiovascular events, 257 graft failure events, and 359 deaths. Each log increase in urine NGAL/creatinine independently associated with a 24% greater risk of cardiovascular events (adjusted hazard ratio [aHR], 1.24; 95% confidence interval [95% CI], 1.06 to 1.45), a 40% greater risk of graft failure (aHR, 1.40; 95% CI, 1.16 to 1.68), and a 44% greater risk of death (aHR, 1.44; 95% CI, 1.26 to 1.65). Urine KIM-1/creatinine and IL-18/creatinine independently associated with greater risk of death (aHR, 1.29; 95% CI, 1.03 to 1.61 and aHR, 1.25; 95% CI, 1.04 to 1.49 per log increase, respectively) but not with risk of cardiovascular events or graft failure. Urine L-FABP did not associate with any study outcomes. In conclusion, among prevalent KTRs, higher urine NGAL, KIM-1, and IL-18 levels independently and differentially associated with greater risk of adverse outcomes. PMID:26538631

  17. Nondestructive biomarkers in ecotoxicology.

    PubMed Central

    Fossi, M C

    1994-01-01

    The aim of this article is to attempt a concise review of the state of the art of the nondestructive biomarkers approach in vertebrates, establishing a consensus on the most useful and sensitive nondestructive biomarker techniques, and proposing research priorities for the development and validation of this promising methodology. The following topics are discussed: the advantages of the use of nondestructive strategies in biomonitoring programs and the research fields in which nondestructive biomarkers can be applied; the biological materials suitable for nondestructive biomarkers and residue analysis in vertebrates; which biomarkers lend themselves to noninvasive techniques; and the validation and implementation strategy of the nondestructive biomarker approach. Examples of applications of this methodology in the hazard assessment of endangered species are also presented. Images Figure 1. C PMID:7713034

  18. Heart-Type Fatty Acid Binding Protein: A Better Cardiac Biomarker than CK-MB and Myoglobin in the Early Diagnosis of Acute Myocardial Infarction

    PubMed Central

    Devaranavadagi, Basavaraj B; Sajjannar, Sanjeev L; Nikam, Shashikant V; Shannawaz, Mohd; Sudharani

    2015-01-01

    Background Early diagnosis and therapeutic intervention can improve the outcome of acute myocardial infarction (AMI). However, there are no satisfactory cardiac biomarkers for the diagnosis of AMI within 6 hours of onset of symptoms. Among novel biochemical markers of AMI, heart-type fatty acid binding protein (H-FABP) is of particular interest. Aim To compare the diagnostic value of H-FABP with that of CK-MB and myoglobin in suspected AMI patients within first 6 hours after the onset of symptoms. Settings and Design The study includes 40 AMI cases and 40 non-cardiac chest pain otherwise healthy controls. The cases and controls were further divided into 2 groups depending on the time since chest pain as those subjects within 3 hours and those between 3-6 hours of onset of chest pain. Materials and Methods In all the cases and controls, serum H-FABP, CK-MB and myoglobin concentrations were measured by Immunoturbidimetric method, immuno-inhibition method and Chemiluminescence immunoassay respectively. Statistical Analysis Data is presented as mean ± SD values. Differences between means of two groups were assessed by Student t-test. Sensitivity, Specificity, Positive predictive value, Negative predictive values were calculated and ROC curve analysis was done to assess the diagnostic validity of each study parameter. Results The sensitivity, specificity, PPV, NPV of H-FABP were greater than CK-MB and myoglobin and ROC curve analysis demonstrated highest area under curve for H-FABP followed by myoglobin and CK-MB in patients with suspected AMI both within 3 hours and 3-6 hours after the onset of chest pain. Conclusion The diagnostic efficiency of H-FABP is greater than CK-MB and myoglobin for the early diagnosis of AMI within first 6 hours of chest pain. H-FABP can be used as an additional diagnostic tool for the early diagnosis of AMI. PMID:26557510

  19. Calibration-free concentration analysis of protein biomarkers in human serum using surface plasmon resonance.

    PubMed

    Grover Shah, Veenita; Ray, Sandipan; Karlsson, Robert; Srivastava, Sanjeeva

    2015-11-01

    In complex biological samples such as serum, determination of specific and active concentration of target proteins, independent of a calibration curve, will be valuable in many applications. Calibration-free concentration analysis (CFCA) is a surface plasmon resonance (SPR)-based label-free approach, which calculates active concentration of proteins using their known diffusion coefficient and observed changes in binding rates at different flow rates under diffusion-limited conditions. Here, for the first time we demonstrate the application of CFCA for determining protein biomarker abundance, specifically serum amyloid A (SAA), directly in the serum samples of patients suffering from different infectious and non-infectious diseases. The assay involves preparation of appropriate reaction surfaces by immobilizing antibodies on CM5 chips via amine coupling followed by serum sample preparation and injection over activated and reference surfaces at flow-rates of 5 and 100 μL/min. The system was validated in healthy and diseased (infectious and non-infectious) serum samples by quantifying two different proteins: β2-microglobulin (β2M) and SAA. All concentration assays were performed for nearly 100 serum samples, which showed reliable quantification in unattended runs with high accuracy and sensitivity. The method could detect the serum β2M to as low as 13 ng/mL in 1000-fold serum dilution, indicating the possible utility of this approach to detect low abundance protein biomarkers in body fluids. Applying the CFCA approach, significant difference in serum abundance of SAA was identified in diseased subjects as compared to the healthy controls, which correlated well with our previous proteomic investigations. Estimation of SAA concentration for a subset of healthy and diseased sera was also performed using ELISA, and the trend was observed to be similar in both SPR assay and ELISA. The reproducibility of CFCA in various serum samples made the interpretation of assay

  20. Biomarkers and Molecular Analysis to Improve Bloodstream Infection Diagnostics in an Emergency Care Unit

    PubMed Central

    Loonen, Anne J. M.; de Jager, Cornelis P. C.; Tosserams, Janna; Kusters, Ron; Hilbink, Mirrian; Wever, Peter C.; van den Brule, Adriaan J. C.

    2014-01-01

    Molecular pathogen detection from blood is still expensive and the exact clinical value remains to be determined. The use of biomarkers may assist in preselecting patients for immediate molecular testing besides blood culture. In this study, 140 patients with ≥ 2 SIRS criteria and clinical signs of infection presenting at the emergency department of our hospital were included. C-reactive protein (CRP), neutrophil-lymphocyte count ratio (NLCR), procalcitonin (PCT) and soluble urokinase plasminogen activator receptor (suPAR) levels were determined. One ml EDTA blood was obtained and selective pathogen DNA isolation was performed with MolYsis (Molzym). DNA samples were analysed for the presence of pathogens, using both the MagicPlex Sepsis Test (Seegene) and SepsiTest (Molzym), and results were compared to blood cultures. Fifteen patients had to be excluded from the study, leaving 125 patients for further analysis. Of the 125 patient samples analysed, 27 presented with positive blood cultures of which 7 were considered to be contaminants. suPAR, PCT, and NLCR values were significantly higher in patients with positive blood cultures compared to patients without (p < 0.001). Receiver operating characteristic curves of the 4 biomarkers for differentiating bacteremia from non-bacteremia showed the highest area under the curve (AUC) for PCT (0.806 (95% confidence interval 0.699–0.913)). NLCR, suPAR and CRP resulted in an AUC of 0.770, 0.793, and 0.485, respectively. When compared to blood cultures, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for SepsiTest and MagicPlex Sepsis Test were 11%, 96%, 43%, 80%, and 37%, 77%, 30%, 82%, respectively. In conclusion, both molecular assays perform poorly when one ml whole blood is used from emergency care unit patients. NLCR is a cheap, fast, easy to determine, and rapidly available biomarker, and therefore seems most promising in differentiating BSI from non-BSI patients for

  1. Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

    PubMed Central

    2012-01-01

    Background Accurate outcome prediction in neuroblastoma, which is necessary to enable the optimal choice of risk-related therapy, remains a challenge. To improve neuroblastoma patient stratification, this study aimed to identify prognostic tumor DNA methylation biomarkers. Results To identify genes silenced by promoter methylation, we first applied two independent genome-wide methylation screening methodologies to eight neuroblastoma cell lines. Specifically, we used re-expression profiling upon 5-aza-2'-deoxycytidine (DAC) treatment and massively parallel sequencing after capturing with a methyl-CpG-binding domain (MBD-seq). Putative methylation markers were selected from DAC-upregulated genes through a literature search and an upfront methylation-specific PCR on 20 primary neuroblastoma tumors, as well as through MBD- seq in combination with publicly available neuroblastoma tumor gene expression data. This yielded 43 candidate biomarkers that were subsequently tested by high-throughput methylation-specific PCR on an independent cohort of 89 primary neuroblastoma tumors that had been selected for risk classification and survival. Based on this analysis, methylation of KRT19, FAS, PRPH, CNR1, QPCT, HIST1H3C, ACSS3 and GRB10 was found to be associated with at least one of the classical risk factors, namely age, stage or MYCN status. Importantly, HIST1H3C and GNAS methylation was associated with overall and/or event-free survival. Conclusions This study combines two genome-wide methylation discovery methodologies and is the most extensive validation study in neuroblastoma performed thus far. We identified several novel prognostic DNA methylation markers and provide a basis for the development of a DNA methylation-based prognostic classifier in neuroblastoma. PMID:23034519

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

    DOEpatents

    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.

  3. 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...

  4. 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. PMID:26871867

  5. 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

  6. Development of DNA damage response signaling biomarkers using automated, quantitative image analysis.

    PubMed

    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; Miller, C Ryan

    2014-03-01

    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

  7. 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.

  8. 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

  9. Quantification of the heterogeneity of prognostic cellular biomarkers in ewing sarcoma using automated image and random survival forest analysis.

    PubMed

    Bühnemann, Claudia; Li, Simon; 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

  10. 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. PMID:27154660

  11. [Evaluation on hepatotoxicity caused by Dioscorea bulbifera based on analysis of bile acids].

    PubMed

    Xu, Ying; Chen, Chong-Chong; Yang, Li; Wang, Jun-Ming; Ji, Li-Li; Wang, Zheng-Tao; Hu, Zhi-Bi

    2011-01-01

    Metabolic profile of bile acids was used to evaluate hepatotoxicity of mice caused by ethanol extraction of Dioscorea bulbifera L. (ethanol extraction, ET) and diosbulbin B (DB), separately. Ultra-performance liquid chromatography coupled with quadrupole mass spectrometry (UPLC-MS) was applied to determine the contents of all kinds of endogenous bile acids including free bile acids, taurine conjugates and glycine conjugates. Obvious liver injuries could be observed in mice after administrated with ET and DB. Based on the analysis using principle components analysis (PCA), toxic groups could be distinguished from their control groups, which suggested that the variance of the contents of bile acids could evaluate hepatotoxicity caused by ET and DB. Meanwhile, ET and DB toxic groups were classified in the same trends comparing to control groups in the loading plot, and difference between the two toxic groups could also be observed. DB proved to be one of the toxic components in Dioscorea bulbifera L. Bile acids of tauroursodeoxycholic acid (TUDCA), taurochenodeoxycholic acid (TCDCA), taurocholic acid (TCA), taurodeoxycholic acid (TDCA), cholic acid (CA) and others proved to be important corresponds to ET and DB induced liver injury according to analysis of partial least square-discriminant analysis (PLS-DA) and the statistical analysis showed that there were significant differences between the control groups and toxic groups (P < 0.01). Furthermore, good correlation could be revealed between the foregoing bile acids and ALT, AST. It indicated that taurine conjugated bile acids as TUDCA, TCDCA, TCA and TDCA along with CA could be considered as sensitive biomarkers of ET and DB induced liver injury. This work can provide the base for the further research on the evaluation and mechanism of hepatotoxicity caused by Dioscorea bulbifera L. PMID:21465807

  12. 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. PMID:19968460

  13. BIOMARKERS DATABASE

    EPA Science Inventory

    This database was developed by assembling and evaluating the literature relevant to human biomarkers. It catalogues and evaluates the usefulness of biomarkers of exposure, susceptibility and effect which may be relevant for a longitudinal cohort study. In addition to describing ...

  14. 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.

  15. Foamy Monocytes Are Enriched in cis-7-Hexadecenoic Fatty Acid (16:1n-9), a Possible Biomarker for Early Detection of Cardiovascular Disease.

    PubMed

    Guijas, Carlos; Meana, Clara; Astudillo, Alma M; Balboa, María A; Balsinde, Jesús

    2016-06-23

    Human monocytes respond to arachidonic acid, a secretory product of endothelial cells, by activating the de novo pathway of fatty acid biosynthesis, resulting in the acquisition of a foamy phenotype due to accumulation of cytoplasmic lipid droplets. Recruitment of foamy monocytes to endothelium is a key step in the formation of atherosclerotic plaques. Here we describe that lipid droplets of foamy monocytes are enriched in a rather uncommon fatty acid, cis-7-hexadecenoic acid (16:1n-9), a positional isomer of palmitoleic acid. 16:1n-9 was found to possess an anti-inflammatory activity both in vitro and in vivo that is comparable with that of omega-3 fatty acids and clearly distinguishable from the effects of palmitoleic acid. Selective accumulation in neutral lipids of phagocytic cells of an uncommon fatty acid reveals an early phenotypic change that may provide a biomarker of proatherogenicity, and a potential target for intervention in the early stages of cardiovascular disease. PMID:27265749

  16. 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

  17. 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.

  18. 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

  19. In-depth Proteomic Analysis of Six Types of Exudative Pleural Effusions for Nonsmall Cell Lung Cancer Biomarker Discovery*

    PubMed Central

    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

    2015-01-01

    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

  20. 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.

  1. MicroRNA-18a as a promising biomarker for cancer detection: a meta-analysis

    PubMed Central

    Jin, Shan; Tan, Shi-Sheng; Li, Hang

    2015-01-01

    Patients with cancer discovered at an early stage have relatively high survival rates. Increasing researches have shown the potential of detecting dysregulated microRNA-18a (miR-18a) to diagnose cancer. However, non-uniform results in previous studies were found. Thus, this meta-analysis was conducted to further explore the clinical applicability of miR-18a as an ideal biomarker for cancer detection. Suitable articles were obtained from online databases like PubMed, Embase, Cochrane, CBM and Wanfang. The Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool was used to evaluate the quality of our meta-analysis. The pooled diagnostic parameters like specificity, sensitivity, diagnostic odds ratio (DOR), positive and negative likelihood ratios (PLR and NLR) and area under the summary receiver operator characteristic curve (SROC) were pooled to assess the entire test accuracy. Overall, 10 studies from 9 articles, including 979 patients with cancer and 713 healthy controls were involved in our meta-analysis. The pooled sensitivity was 0.78 (95% CI: 0.70-0.84) and the corresponding specificity was 0.82 (95% CI: 0.73-0.89). The merged PLR was 4.3 (95% CI: 2.8-6.8), NLR was 0.27 (95% CI: 0.20-0.37), and DOR was 16 (95% CI: 8-31). The pooled AUC was 0.86 (95% CI: 0.83-0.89). Our meta-analysis suggested that miR-18a might open up a new field for novel clinical cancer screening with the merits of high accuracy, non-invasiveness, convenience and cheap cost. However, more reliable studies in larger cohort should be conducted before it is used. PMID:26550138

  2. Evaluation of individual and combined applications of serum biomarkers for diagnosis of hepatocellular carcinoma: a meta-analysis.

    PubMed

    Hu, Bin; Tian, Xiaohui; Sun, Jie; Meng, Xiangjun

    2013-01-01

    The clinical value of Serum alpha-fetoprotein (AFP) to detect early hepatocellular carcinoma (HCC) has been questioned due to its low sensitivity and specificity found in recent years. Other than AFP, several new serum biomarkers including the circulating AFP isoform AFP-L3, des-gamma-carboxy prothrombin (DCP) and Golgi protein-73 (GP73) have been identified as useful HCC markers. In this investigation, we review the current knowledge about these HCC-related biomarkers, and sum up the results of our meta-analysis on studies that have addressed the utility of these biomarkers in early detection and prognostic prediction of HCC. A systematic search in PubMed, Web of Science, and the Cochrane Library was performed for articles published in English from 1999 to 2012, focusing on serum biomarkers for HCC detection. Data on sensitivity and specificity of tests were extracted from 40 articles that met the inclusion criteria, and the summary receiver operating characteristic curve (sROC) was obtained. A meta-analysis was carried out in which the area under the curve (AUC) for each biomarker or biomarker combinations (AFP, DCP, GP73, AFP-L3, AFP+DCP, AFP+AFP-L3, and AFP+GP73) was used to compare the diagnostic accuracy of different biomarker tests. The AUC of AFP, DCP, GP73, AFP-L3, AFP+DCP, AFP+AFP-L3, and AFP+GP73 are 0.835, 0.797, 0.914, 0.710, 0.874, 0.748, and 0.932 respectively. A combination of AFP+GP73 is superior to AFP in detecting HCC and differentiating HCC patients from non-HCC patients, and may prove to be a useful marker in the diagnosis and screening of HCC. In addition, the AUC of GP73, AFP+DCP and AFP+GP73 are better than that of AFP. The clinical value of GP73, AFP+DCP, or AFP+GP73 as serological markers for HCC diagnosis needs to be addressed further in future studies. PMID:24317431

  3. Evaluation of Tetrahydrobiopterin Therapy with Large Neutral Amino Acid Supplementation in Phenylketonuria: Effects on Potential Peripheral Biomarkers, Melatonin and Dopamine, for Brain Monoamine Neurotransmitters

    PubMed Central

    Yano, Shoji; Moseley, Kathryn; Fu, Xiaowei; Azen, Colleen

    2016-01-01

    Background Phenylketonuria (PKU) is due to a defective hepatic enzyme, phenylalanine (Phe) hydroxylase. Transport of the precursor amino acids from blood into the brain for serotonin and dopamine synthesis is reported to be inhibited by high blood Phe concentrations. Deficiencies of serotonin and dopamine are involved in neurocognitive dysfunction in PKU. Objective (1) To evaluate the effects of sapropterin (BH4) and concurrent use of large neutral amino acids (LNAA) on the peripheral biomarkers, melatonin and dopamine with the hypothesis they reflect brain serotonin and dopamine metabolism. (2) To evaluate synergistic effects with BH4 and LNAA. (3) To determine the effects of blood Phe concentrations on the peripheral biomarkers concentrations. Methods Nine adults with PKU completed our study consisting of four 4-week phases: (1) LNAA supplementation, (2) Washout, (3) BH4 therapy, and (4) LNAA with BH4 therapy. An overnight protocol measured plasma amino acids, serum melatonin, and 6-sulfatoxymelatonin and dopamine in first void urine after each phase. Results (1) Three out of nine subjects responded to BH4. A significant increase of serum melatonin levels was observed in BH4 responders with decreased blood Phe concentration. No significant change in melatonin, dopamine or Phe levels was observed with BH4 in the subjects as a whole. (2) Synergistic effects with BH4 and LNAA were observed in serum melatonin in BH4 responders. (3) The relationship between serum melatonin and Phe showed a significant negative slope (p = 0.0005) with a trend toward differing slopes among individual subjects (p = 0.066). There was also a negative association overall between blood Phe and urine 6-sulfatoxymelatonin and dopamine (P = 0.040 and 0.047). Conclusion Blood Phe concentrations affected peripheral monoamine neurotransmitter biomarker concentrations differently in each individual with PKU. Melatonin levels increased with BH4 therapy only when blood Phe decreased. Monitoring

  4. The trans/cis ratio of unsaturated fatty acids is not applicable as biomarker for environmental stress in case of long-term contaminated habitats.

    PubMed

    Fischer, Janett; Schauer, Frieder; Heipieper, Hermann J

    2010-06-01

    Cis-trans isomerization of unsaturated fatty acids is a crucial adaptive reaction of Pseudomonas and Vibrio species to toxic organic compounds or other environmental stress factors. In order to test the long-term performance of this adaptive mechanism as well as to assess its application as biomarker for environmental contamination studies were performed in batch cultures and in continuously running sand columns, simulating long-term contamination with bisphenol A (BPA). In short-term grown batch cultures a high correlation between trans/cis ratio and added BPA concentration and toxicity was observed. In contrary, this did not occur in the case of long-term sand columns. An increase in trans/cis ratio of unsaturated fatty acids only appeared in a limited period of time. Afterwards the trans/cis ratio reached the values measured for non-stressed cultures. Cis-trans isomerization is only an urgent response mechanism that is later substituted by other adaptive mechanisms. Therefore, it can be concluded that the trans/cis ratio of unsaturated fatty acids was shown not to be an appropriate biomarker for durable stress in the environment. PMID:20352421

  5. In-depth Proteomic Analysis of Nonsmall Cell Lung Cancer to Discover Molecular Targets and Candidate Biomarkers*

    PubMed Central

    Kikuchi, Takefumi; Hassanein, Mohamed; Amann, Joseph M.; Liu, Qinfeng; Slebos, Robbert J. C.; Rahman, S. M. Jamshedur; Kaufman, Jacob M.; Zhang, Xueqiong; Hoeksema, Megan D.; Harris, Bradford K.; Li, Ming; Shyr, Yu; Gonzalez, Adriana L.; Zimmerman, Lisa J.; Liebler, Daniel C.; Massion, Pierre P.; Carbone, David P.

    2012-01-01

    Advances in proteomic analysis of human samples are driving critical aspects of biomarker discovery and the identification of molecular pathways involved in disease etiology. Toward that end, in this report we are the first to use a standardized shotgun proteomic analysis method for in-depth tissue protein profiling of the two major subtypes of nonsmall cell lung cancer and normal lung tissues. We identified 3621 proteins from the analysis of pooled human samples of squamous cell carcinoma, adenocarcinoma, and control specimens. In addition to proteins previously shown to be implicated in lung cancer, we have identified new pathways and multiple new differentially expressed proteins of potential interest as therapeutic targets or diagnostic biomarkers, including some that were not identified by transcriptome profiling. Up-regulation of these proteins was confirmed by multiple reaction monitoring mass spectrometry. A subset of these proteins was found to be detectable and differentially present in the peripheral blood of cases and matched controls. Label-free shotgun proteomic analysis allows definition of lung tumor proteomes, identification of biomarker candidates, and potential targets for therapy. PMID:22761400

  6. 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.

  7. 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

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

    PubMed

    Lupu, Mihai; Caruntu, Constantin; Ghita, Mihaela Adriana; Voiculescu, Vlad; Voiculescu, Suzana; Rosca, Adrian E; Caruntu, Ana; Moraru, Liliana; Popa, Iris Maria; Calenic, Bogdan; Greabu, Maria; Costea, Daniela Elena

    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

  9. A Proteomic Analysis of Eccrine Sweat: Implications for the Discovery of Schizophrenia Biomarker Proteins

    PubMed Central

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

    2012-01-01

    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 two-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. PMID:22256890

  10. 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

    2012-04-01

    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. PMID:22256890

  11. 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. PMID:26552699

  12. Gene expression profiling via bioinformatics analysis reveals biomarkers in laryngeal squamous cell carcinoma

    PubMed Central

    GUAN, GUO-FANG; ZHENG, YING; WEN, LIAN-JI; ZHANG, DE-JUN; YU, DUO-JIAO; LU, YAN-QING; ZHAO, YAN; ZHANG, HUI

    2015-01-01

    The present study aimed to identify key genes and relevant microRNAs (miRNAs) involved in laryngeal squamous cell carcinoma (LSCC). The gene expression profiles of LSCC tissue samples were analyzed with various bioinformatics tools. A gene expression data set (GSE51985), including ten laryngeal squamous cell carcinoma (LSCC) tissue samples and ten adjacent non-neoplastic tissue samples, was downloaded from the Gene Expression Omnibus. Differential analysis was performed using software package limma of R. Functional enrichment analysis was applied to the differentially expressed genes (DEGs) using the Database for Annotation, Visualization and Integrated Discovery. Protein-protein interaction (PPI) networks were constructed for the protein products using information from the Search Tool for the Retrieval of Interacting Genes/Proteins. Module analysis was performed using ClusterONE (a software plugin from Cytoscape). MicroRNAs (miRNAs) regulating the DEGs were predicted using WebGestalt. A total of 461 DEGs were identified in LSCC, 297 of which were upregulated and 164 of which were downregulated. Cell cycle, proteasome and DNA replication were significantly over-represented in the upregulated genes, while the ribosome was significantly over-represented in the downregulated genes. Two PPI networks were constructed for the up- and downregulated genes. One module from the upregulated gene network was associated with protein kinase. Numerous miRNAs associated with LSCC were predicted, including miRNA (miR)-25, miR-32, miR-92 and miR-29. In conclusion, numerous key genes and pathways involved in LSCC were revealed, which may aid the advancement of current knowledge regarding the pathogenesis of LSCC. In addition, relevant miRNAs were also identified, which may represent potential biomarkers for use in the diagnosis or treatment of the disease. PMID:25936657

  13. 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. PMID:16200529

  14. 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. PMID:26317563

  15. Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers.

    PubMed

    Morris, Heather C; Damon, Michael; Maule, Jake; Monaco, Lisa A; Wainwright, Norm

    2012-09-01

    Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840. PMID:22984871

  16. 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

  17. Acid-labile protein-adducted heterocyclic aromatic amines in human blood are not viable biomarkers of dietary exposure: A systematic study.

    PubMed

    Cooper, Kevin M; Brennan, Sarah F; Woodside, Jayne V; Cantwell, Marie; Guo, Xiaoxiao; Mooney, Mark; Elliott, Christopher T; Cuskelly, Geraldine J

    2016-05-01

    Heterocyclic aromatic amines (HCA) are carcinogenic mutagens formed during cooking of protein-rich foods. HCA residues adducted to blood proteins have been postulated as biomarkers of HCA exposure. However, the viability of quantifying HCAs following hydrolytic release from adducts in vivo and correlation with dietary intake are unproven. To definitively assess the potential of labile HCA-protein adducts as biomarkers, a highly sensitive UPLC-MS/MS method was validated for four major HCAs: 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (4,8-DiMeIQx) and 2-amino-3,7,8-trimethylimidazo[4,5-f]quinoxaline (7,8-DiMeIQx). Limits of detection were 1-5 pg/ml plasma and recoveries 91-115%. Efficacy of hydrolysis was demonstrated by HCA-protein adducts synthesised in vitro. Plasma and 7-day food diaries were collected from 122 fasting adults consuming their habitual diets. Estimated HCA intakes ranged from 0 to 2.5 mg/day. An extensive range of hydrolysis conditions was examined for release of adducted HCAs in plasma. HCA was detected in only one sample (PhIP, 9.7 pg/ml), demonstrating conclusively for the first time that acid-labile HCA adducts do not reflect dietary HCA intake and are present at such low concentrations that they are not feasible biomarkers of exposure. Identification of biomarkers remains important. The search should concentrate on stabilised HCA-peptide markers and use of untargeted proteomic and metabolomic approaches. PMID:26993956

  18. 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

  19. 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

  20. Imaging biomarkers in multiple Sclerosis: From image analysis to population imaging.

    PubMed

    Barillot, Christian; Edan, Gilles; Commowick, Olivier

    2016-10-01

    The production of imaging data in medicine increases more rapidly than the capacity of computing models to extract information from it. The grand challenges of better understanding the brain, offering better care for neurological disorders, and stimulating new drug design will not be achieved without significant advances in computational neuroscience. The road to success is to develop a new, generic, computational methodology and to confront and validate this methodology on relevant diseases with adapted computational infrastructures. This new concept sustains the need to build new research paradigms to better understand the natural history of the pathology at the early phase; to better aggregate data that will provide the most complete representation of the pathology in order to better correlate imaging with other relevant features such as clinical, biological or genetic data. In this context, one of the major challenges of neuroimaging in clinical neurosciences is to detect quantitative signs of pathological evolution as early as possible to prevent disease progression, evaluate therapeutic protocols or even better understand and model the natural history of a given neurological pathology. Many diseases encompass brain alterations often not visible on conventional MRI sequences, especially in normal appearing brain tissues (NABT). MRI has often a low specificity for differentiating between possible pathological changes which could help in discriminating between the different pathological stages or grades. The objective of medical image analysis procedures is to define new quantitative neuroimaging biomarkers to track the evolution of the pathology at different levels. This paper illustrates this issue in one acute neuro-inflammatory pathology: Multiple Sclerosis (MS). It exhibits the current medical image analysis approaches and explains how this field of research will evolve in the next decade to integrate larger scale of information at the temporal, cellular

  1. Adipokines as emerging depression biomarkers: a systematic review and meta-analysis.

    PubMed

    Carvalho, André F; Rocha, Davi Q C; McIntyre, Roger S; Mesquita, Lucas M; Köhler, Cristiano A; Hyphantis, Thomas N; Sales, Paulo M G; Machado-Vieira, Rodrigo; Berk, Michael

    2014-12-01

    Adiponectin, leptin and resistin may play a role in the pathophysiology of major depressive disorder (MDD). However, differences in peripheral levels of these hormones are inconsistent across diagnostic and intervention studies. Therefore, we performed meta-analyses of diagnostic studies (i.e., MDD subjects versus healthy controls) and intervention investigations (i.e., pre-vs. post-antidepressant treatment) in MDD. Adiponectin (N = 1278; Hedge's g = -0.35; P = 0.16) and leptin (N = 893; Hedge's g = -0.018; P = 0.93) did not differ across diagnostic studies. Meta-regression analyses revealed that gender and depression severity explained the heterogeneity observed in adiponectin diagnostic studies, while BMI and the difference in BMI between MDD individuals and controls explained the heterogeneity of leptin diagnostic studies. Subgroup analyses revealed that adiponectin peripheral levels were significantly lower in MDD participants compared to controls when assayed with RIA, but not ELISA. Leptin levels were significantly higher in individuals with mild/moderate depression versus controls. Resistin serum levels were lower in MDD individuals compared to healthy controls (N = 298; Hedge's g = -0.25; P = 0.03). Leptin serum levels did not change after antidepressant treatment. However, heterogeneity was significant and sample size was low (N = 108); consequently meta-regression analysis could not be performed. Intervention meta-analyses could not be performed for adiponectin and resistin (i.e., few studies met inclusion criteria). In conclusion, this systematic review and meta-analysis underscored that relevant moderators/confounders (e.g., BMI, depression severity and type of assay) should be controlled for when considering the role of leptin and adiponectin as putative MDD diagnostic biomarkers. PMID:25183029

  2. Biomarker analysis of Morquio syndrome: identification of disease state and drug responsive markers

    PubMed Central

    2011-01-01

    Background This study was conducted to identify potential biomarkers that could be used to evaluate disease progression and monitor responses to enzyme replacement therapy (ERT) in patients with mucopolysaccharidosis (MPS) IVA. Methods Levels of 88 candidate biomarkers were compared in plasma samples from 50 healthy controls and 78 MPSIVA patients not receiving ERT to test for significant correlations to the presence of MPSIVA. MPSIVA samples were also tested for correlations between candidate biomarkers and age, endurance, or urinary keratin sulfate (KS) levels. Then, levels of the same 88 analytes were followed over 36 weeks in 20 MPSIVA patients receiving ERT to test for significant correlations related to ERT, age, or endurance. Results Nineteen candidate biomarkers were significantly different between MPSIVA and unaffected individuals. Of these, five also changed significantly in response to ERT: alpha-1-antitrypsin, eotaxin, lipoprotein(a), matrix metalloprotein (MMP)-2, and serum amyloid P. Three of these were significantly lower in MPSIVA individuals versus unaffected controls and were increased during ERT: alpha-1-antitrypsin, lipoprotein(a), and serum amyloid P. Conclusions Candidate biomarkers alpha-1-antitrypsin, lipoprotein(a), and serum amyloid P may be suitable markers, in addition to urinary KS, to follow the response to ERT in MPSIVA patients. PMID:22176730

  3. Multiparameter Analysis-Based Electrochemiluminescent Assay for Simultaneous Detection of Multiple Biomarker Proteins on a Single Interface.

    PubMed

    Liang, Wenbin; Fan, Chenchen; Zhuo, Ying; Zheng, Yingning; Xiong, Chengyi; Chai, Yaqin; Yuan, Ruo

    2016-05-01

    Electrochemiluminescent (ECL) assay with high sensitivity has been considered as one of the potential strategies to simultaneously detect multiple biomarker proteins. However, it was essential, but full of challenges, to overcome the limitation caused by cross reactions among different ECL indicators. Herein, the multiparameter analysis of ECL-potential signals demonstrated by multivariate linear algebraic equations was first employed in the simultaneous ECL assay to realize multiple detection of biomarker proteins on a single interface. Additionally, owing to the exponential amplification of self-synthesized nucleotide dendrimer by hybridization chain reaction (HCR) and rolling circle amplification (RCA), the developed simultaneous ECL assay showed improved sensitivity and satisfactory accuracy for the detection of N-terminal of the prohormone brain natriuretic peptide (BNPT) and cardiac troponin I (cTnI). Furthermore, a self-designed magnetic beads-based flow system was also employed to improve the feasibility and analysis speed of the simultaneous ECL assay. Importantly, the proposed strategy enabled simultaneous detection of multiple biomarker proteins simply, which could be readily expanded for the multiplexed estimation of various kinds of proteins and nucleotide sequence also, revealing a new avenue for early disease diagnosis with higher efficiency. PMID:27064937

  4. Quantitative proteomics analysis to identify diffuse axonal injury biomarkers in rats using iTRAQ coupled LC-MS/MS.

    PubMed

    Zhang, Peng; Zhu, Shisheng; Li, Yongguo; Zhao, Minzhu; Liu, Meng; Gao, Jun; Ding, Shijia; Li, Jianbo

    2016-02-01

    Diffuse axonal injury (DAI) is fairly common during a traumatic brain injury (TBI) and is associated with high mortality. Making an early diagnosis, appropriate therapeutic decisions, and an accurate prognostic evaluation of patients with DAI still pose difficulties for clinicians. The detailed mechanisms of axonal injury after head trauma have yet to be clearly defined and no reliable biomarkers are available for early DAI diagnosis. Therefore, this study employed an established DAI animal model in conjunction with an isobaric tag for relative and absolute quantification (iTRAQ)-based protein identification/quantification approach. Alterations in rat cerebral protein expression were quantified using iTRAQ coupled LC-MS/MS, with differentially expressed proteins between the control groups, sham and sham-injured, and the injury groups, animals that died immediately post-injury and those sacrificed at 1h, 6h, 1d, 3d and 7d post-injury, identified. A total of 1858 proteins were identified and quantified and comparative analysis identified ten candidate proteins that warranted further examination. Of the ten candidate DAI biomarkers, four proteins, citrate synthase (CS), synaptosomal-associated protein 25 (Snap25), microtubule-associated protein 1B (MAP1B) and Rho-associated protein kinase 2 (Rock2), were validated by subsequent Western blot and immunohistochemistry analyses. Our studies not only identified several novel biomarkers that may provide insight into the pathophysiological mechanisms of DAI, but also demonstrated the feasibility of iTRAQ-based quantitative proteomic analysis in cerebral tissue research. PMID:26710722

  5. Proteomic analysis of synovial fluid as an analytical tool to detect candidate biomarkers for knee osteoarthritis

    PubMed Central

    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. PMID:26617706

  6. Phase I Study and Biomarker Analysis of Lapatinib and Concurrent Radiation for Locally Advanced Breast Cancer

    PubMed Central

    Horton, Janet K.; Livasy, Chad A.; Shields, Janiel M.; Lawrence, Julia A.; Chiu, WingKeung M.; Ivanova, Anastasia; Ollila, David W.; Carey, Lisa A.; Halle, Jan S.; Sartor, Carolyn I.; Dees, E. Claire

    2012-01-01

    Purpose. This phase I study assessed the toxicity and safety of combining daily lapatinib with radiation therapy. Sequential tumor biopsies were obtained to evaluate changes in biomarkers, such as epidermal growth factor receptor (EGFR) and human EGFR-2 (HER2) signaling pathways. Methods. Eligibility for this dose-escalation study included unresectable and locally recurrent or chemotherapy-refractory and locally advanced breast cancer, and adequate organ function. Patients underwent three serial biopsies: at baseline, after 1 week of lapatinib alone, and after 1 week of lapatinib and radiation. Endpoints included determination of toxicity, maximum tolerated dose, and analysis of the effect of lapatinib with or without radiation on EGFR and HER2 signaling pathways by immunohistochemistry. Results. Doses of lapatinib up to 1,500 mg/day were well tolerated. Toxicity of grade 3 or more was limited to radiation dermatitis and pain. Out of 19 patients treated, in field responses per Response Evaluation Criteria in Solid Tumors criteria were complete in four patients and partial in six patients. Serial biopsies were obtained in 16 patients with no complications. Total Her2 was relatively unchanged while phospho-Her2, phospho-Akt, and phospho-ERK showed variable responses to both lapatinib alone and dual therapy with lapatinib and radiation. Conclusions. The combination of lapatinib and radiation was well tolerated in this patient cohort. Overall local response rates were comparable to those reported in other studies in this patient population. Biopsies were safely performed at all time points. Inhibition of HER2 and downstream signaling pathways was identified, although no strong correlation with response was seen. PMID:23006498

  7. Early Pregnancy Biomarkers in Pre-Eclampsia: A Systematic Review and Meta-Analysis.

    PubMed

    Wu, Pensée; van den Berg, Caroline; Alfirevic, Zarko; O'Brien, Shaughn; Röthlisberger, Maria; Baker, Philip Newton; Kenny, Louise C; Kublickiene, Karolina; Duvekot, Johannes J

    2015-01-01

    Pre-eclampsia (PE) complicates 2%-8% of all pregnancies and is an important cause of perinatal morbidity and mortality worldwide. In order to reduce these complications and to develop possible treatment modalities, it is important to identify women at risk of developing PE. The use of biomarkers in early pregnancy would allow appropriate stratification into high and low risk pregnancies for the purpose of defining surveillance in pregnancy and to administer interventions. We used formal methods for a systematic review and meta-analyses to assess the accuracy of all biomarkers that have been evaluated so far during the first and early second trimester of pregnancy to predict PE. We found low predictive values using individual biomarkers which included a disintegrin and metalloprotease 12 (ADAM-12), inhibin-A, pregnancy associated plasma protein A (PAPP-A), placental growth factor (PlGF) and placental protein 13 (PP-13). The pooled sensitivity of all single biomarkers was 0.40 (95% CI 0.39-0.41) at a false positive rate of 10%. The area under the Summary of Receiver Operating Characteristics Curve (SROC) was 0.786 (SE 0.02). When a combination model was used, the predictive value improved to an area under the SROC of 0.893 (SE 0.03). In conclusion, although there are multiple potential biomarkers for PE their efficacy has been inconsistent and comparisons are difficult because of heterogeneity between different studies. Therefore, there is an urgent need for high quality, large-scale multicentre research in biomarkers for PE so that the best predictive marker(s) can be identified in order to improve the management of women destined to develop PE. PMID:26404264

  8. Early Pregnancy Biomarkers in Pre-Eclampsia: A Systematic Review and Meta-Analysis

    PubMed Central

    Wu, Pensée; van den Berg, Caroline; Alfirevic, Zarko; O’Brien, Shaughn; Röthlisberger, Maria; Baker, Philip Newton; Kenny, Louise C.; Kublickiene, Karolina; Duvekot, Johannes J.

    2015-01-01

    Pre-eclampsia (PE) complicates 2%–8% of all pregnancies and is an important cause of perinatal morbidity and mortality worldwide. In order to reduce these complications and to develop possible treatment modalities, it is important to identify women at risk of developing PE. The use of biomarkers in early pregnancy would allow appropriate stratification into high and low risk pregnancies for the purpose of defining surveillance in pregnancy and to administer interventions. We used formal methods for a systematic review and meta-analyses to assess the accuracy of all biomarkers that have been evaluated so far during the first and early second trimester of pregnancy to predict PE. We found low predictive values using individual biomarkers which included a disintegrin and metalloprotease 12 (ADAM-12), inhibin-A, pregnancy associated plasma protein A (PAPP-A), placental growth factor (PlGF) and placental protein 13 (PP-13). The pooled sensitivity of all single biomarkers was 0.40 (95% CI 0.39–0.41) at a false positive rate of 10%. The area under the Summary of Receiver Operating Characteristics Curve (SROC) was 0.786 (SE 0.02). When a combination model was used, the predictive value improved to an area under the SROC of 0.893 (SE 0.03). In conclusion, although there are multiple potential biomarkers for PE their efficacy has been inconsistent and comparisons are difficult because of heterogeneity between different studies. Therefore, there is an urgent need for high quality, large-scale multicentre research in biomarkers for PE so that the best predictive marker(s) can be identified in order to improve the management of women destined to develop PE. PMID:26404264

  9. Multi-Biomarkers for Early Detection of Type 2 Diabetes, Including 10- and 12-(Z,E)-Hydroxyoctadecadienoic Acids, Insulin, Leptin, and Adiponectin

    PubMed Central

    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

  10. Failure of urinary trans,trans-muconic acid as a biomarker for indoor environmental benzene exposure at PPB levels.

    PubMed

    Sanguinetti, G; Accorsi, A; Barbieri, A; Raffi, G B; Violante, F S

    2001-08-24

    Benzene is a widespread pollutant whose main source in the environment is automotive emission. There is increasing interest in the exposure of the population to this pollutant as benzene is present also in the indoor environment due to cigarette smoke, drinking water, and food. The aim of this study was to evaluate, in an adult nonsmoking population not occupationally exposed to benzene, whether it is possible to detect differences in the urinary concentration of trans,trans-muconic acid (t,t-MA) between low and high environmental exposure to benzene. A study sample of 31 employees working in pharmacies in a large town in Italy with low environmental exposure to benzene (4.8 microg/m3) was compared to a high (8.1 microg/m3) benzene exposure group. Analysis of urinary t,t-MA was carried out by high-performance liquid chromatography (HPLC; photodiode array detector); analysis of environmental benzene samples was by gas chromatography/mass spectroscopy (GC-MS). The statistical analysis revealed no significant differences in urinary levels of t,t-MA of subjects with high (mean concentration: 157.9 microg/g creatinine) versus low exposure (mean concentration: 114.2 microg/g creatinine). Data show that it is difficult to correlate urinary t,t-MA with benzene exposure at parts per billion levels. PMID:11549119

  11. Analysis and validation of tissue biomarkers for renal cell carcinoma using automated high-throughput evaluation of protein expression☆

    PubMed Central

    Abel, E. Jason; Bauman, Tyler M.; Weiker, Madelyn; Shi, Fangfang; Downs, Tracy M.; Jarrard, David F.; Huang, Wei

    2014-01-01

    Summary The objective of this study was to compare the predictive ability of potential tissue biomarkers to known prognostic factors that predict renal cell carcinoma (RCC) recurrence using an automated system of immunohistochemical analysis. After institutional review board approval, a tissue microarray was constructed using tissue from patients who had partial or radical nephrectomy for RCC. Patients with metastatic disease were excluded. Immunohistochemical staining of the tissue microarray for Ki-67, C-reactive protein, carbonic anhydrase 9, and hypoxia-inducible factors 1α and 2α was analyzed using automated image analysis. Univariable and multivariable analyses were performed to evaluate the association of putative biomarkers and known prognostic factors. Of 216 patients who met the entrance criteria, 34 (16%) patients developed metastatic recurrence within a median follow-up interval of 60.9 (interquartile range, 13.9–87.1) months. RCC morphotypes analyzed in this study include clear cell (n = 156), papillary (n = 38), chromophobe (n = 16), and collecting duct/unclassified (n = 6). Univariate analysis identified that only increased Ki-67 was predictive of RCC recurrence among the proteins evaluated, in addition to other known clinicopathological prognostic factors. After multivariate analysis, Ki-67 was identified as an independently predictive risk factor for RCC recurrence (hazard ratio [HR], 3.73 [confidence interval {CI}, 1.60–8.68]). Other independent predictors of RCC recurrence included tumor diameter (HR, 1.20 [CI, 1.02–1.41]) and perinephric fat invasion (HR, 4.49 [CI, 1.11–18.20]). We conclude that Ki-67 positivity is independently predictive of RCC recurrence after surgery in nonmetastatic patients. Automated analysis of tissue protein expression can facilitate a more objective and expedient investigation of tissue biomarkers for RCC. PMID:24746216

  12. Automatic Tumor-Stroma Separation in Fluorescence TMAs Enables the Quantitative High-Throughput Analysis of Multiple Cancer Biomarkers

    PubMed Central

    Lahrmann, Bernd; Halama, Niels; Sinn, Hans-Peter; Schirmacher, Peter; Jaeger, Dirk; Grabe, Niels

    2011-01-01

    The upcoming quantification and automation in biomarker based histological tumor evaluation will require computational methods capable of automatically identifying tumor areas and differentiating them from the stroma. As no single generally applicable tumor biomarker is available, pathology routinely uses morphological criteria as a spatial reference system. We here present and evaluate a method capable of performing the classification in immunofluorescence histological slides solely using a DAPI background stain. Due to the restriction to a single color channel this is inherently challenging. We formed cell graphs based on the topological distribution of the tissue cell nuclei and extracted the corresponding graph features. By using topological, morphological and intensity based features we could systematically quantify and compare the discrimination capability individual features contribute to the overall algorithm. We here show that when classifying fluorescence tissue slides in the DAPI channel, morphological and intensity based features clearly outpace topological ones which have been used exclusively in related previous approaches. We assembled the 15 best features to train a support vector machine based on Keratin stained tumor areas. On a test set of TMAs with 210 cores of triple negative breast cancers our classifier was able to distinguish between tumor and stroma tissue with a total overall accuracy of 88%. Our method yields first results on the discrimination capability of features groups which is essential for an automated tumor diagnostics. Also, it provides an objective spatial reference system for the multiplex analysis of biomarkers in fluorescence immunohistochemistry. PMID:22164226

  13. 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

  14. 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

  15. Network Analysis Identifies SOD2 mRNA as a Potential Biomarker for Parkinson's Disease

    PubMed Central

    Santiago, Jose A.; Scherzer, Clemens R.; Potashkin, Judith A.

    2014-01-01

    Increasing evidence indicates that Parkinson's disease (PD) and type 2 diabetes (T2DM) share dysregulated molecular networks. We identified 84 genes shared between PD and T2DM from curated disease-gene databases. Nitric oxide biosynthesis, lipid and carbohydrate metabolism, insulin secretion and inflammation were identified as common dysregulated pathways. A network prioritization approach was implemented to rank genes according to their distance to seed genes and their involvement in common biological pathways. Quantitative polymerase chain reaction assays revealed that a highly ranked gene, superoxide dismutase 2 (SOD2), is upregulated in PD patients compared to healthy controls in 192 whole blood samples from two independent clinical trials, the Harvard Biomarker Study (HBS) and the Diagnostic and Prognostic Biomarkers in Parkinson's disease (PROBE). The results from this study reinforce the idea that shared molecular networks between PD and T2DM provides an additional source of biologically meaningful biomarkers. Evaluation of this biomarker in de novo PD patients and in a larger prospective longitudinal study is warranted. PMID:25279756

  16. The analysis of disease biomarker data using a mixed hidden Markov model (Open Access publication)

    PubMed Central

    Detilleux, Johann C

    2008-01-01

    A mixed hidden Markov model (HMM) was developed for predicting breeding values of a biomarker (here, somatic cell score) and the individual probabilities of health and disease (here, mastitis) based upon the measurements of the biomarker. At a first level, the unobserved disease process (Markov model) was introduced and at a second level, the measurement process was modeled, making the link between the unobserved disease states and the observed biomarker values. This hierarchical formulation allows joint estimation of the parameters of both processes. The flexibility of this approach is illustrated on the simulated data. Firstly, lactation curves for the biomarker were generated based upon published parameters (mean, variance, and probabilities of infection) for cows with known clinical conditions (health or mastitis due to Escherichia coli or Staphylococcus aureus). Next, estimation of the parameters was performed via Gibbs sampling, assuming the health status was unknown. Results from the simulations and mathematics show that the mixed HMM is appropriate to estimate the quantities of interest although the accuracy of the estimates is moderate when the prevalence of the disease is low. The paper ends with some indications for further developments of the methodology. PMID:18694546

  17. 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. PMID:26833125

  18. Ultratrace level determination and quantitative analysis of kidney injury biomarkers in patient samples attained by zinc oxide nanorods.

    PubMed

    Singh, Manpreet; Alabanza, Anginelle; Gonzalez, Lorelis E; Wang, Weiwei; Reeves, W Brian; Hahm, Jong-in

    2016-02-28

    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

  19. 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

  20. Comparative metabolomics analysis of docosahexaenoic acid fermentation processes by Schizochytrium sp. under different oxygen availability conditions.

    PubMed

    Li, Juan; Ren, Lu-Jing; Sun, Guan-Nan; Qu, Liang; Huang, He

    2013-05-01

    The intracellular metabolic profile characterization of Schizochytrium sp. throughout docosahexaenoic acid fermentation was investigated using gas chromatography-mass spectrometry (GC-MS). Metabolite profiles originating from Schizochytrium sp. under normal and limited oxygen supply conditions were distinctive and distinguished by principal components analysis (PCA). A total of more than 60 intracellular metabolites were detected and quantified with the levels of some metabolites involved in central carbon metabolism varying throughout both processes. Both fermentation processes were differentiated into three main phases by principal components analysis. Potential biomarkers responsible for distinguishing the different fermentation phases were identified as glutamic acid, proline, glycine, alanine, and glucose. In addition, alanine, glutamic acid, glucose, inositol, ornithine, and galactose were found to make great contribution for dry cell weight and fatty acid composition during normal and limited oxygen supply fermentations. Furthermore, significantly higher levels of succinate and several amino acids in cells of limited oxygen supply fermentation revealed that they might play important roles in resisting oxygen deficiency and increasing DHA synthesis during the lipid accumulation. These findings provide novel insights into the metabolomic characteristics during docosahexaenoic acid fermentation processes by Schizochytrium sp. PMID:23586678

  1. 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

  2. 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. PMID:25659366

  3. 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.

  4. Soil water availability and microsite mediate fungal and bacterial phospholipid fatty acid biomarker abundances in Mojave Desert soils exposed to elevated atmospheric CO2

    NASA Astrophysics Data System (ADS)

    Jin, V. L.; Schaeffer, S. M.; Ziegler, S. E.; Evans, R. D.

    2011-06-01

    Changes in the rates of nitrogen (N) cycling, microbial carbon (C) substrate use, and extracellular enzyme activities in a Mojave Desert ecosystem exposed to elevated atmospheric CO2 suggest shifts in the size and/or functional characteristics of microbial assemblages in two dominant soil microsites: plant interspaces and under the dominant shrub Larrea tridentata. We used ester-linked phospholipid fatty acid (PLFA) biomarkers as a proxy for microbial biomass to quantify spatial and temporal differences in soil microbial communities from February 2003 to May 2005. Further, we used the 13C signature of the fossil CO2 source for elevated CO2 plots to trace recent plant C inputs into soil organic matter (SOM) and broad microbial groups using δ13C (‰). Differences between individual δ13CPLFA and δ13CSOM for fungal biomarkers indicated active metabolism of newer C in elevated CO2 soils. Total PLFA-C was greater in shrub microsites compared to plant interspaces, and CO2 treatment differences within microsites increased under higher soil water availability. Total, fungal, and bacterial PLFA-C increased with decreasing soil volumetric water content (VWC) in both microsites, suggesting general adaptations to xeric desert conditions. Increases in fungal-to-bacterial PLFA-C ratio with decreasing VWC reflected functional group-specific responses to changing soil water availability. While temporal and spatial extremes in resource availability in desert ecosystems contribute to the difficulty in identifying common trends or mechanisms driving microbial responses in less extreme environments, we found that soil water availability and soil microsite interacted with elevated CO2 to shift fungal and bacterial biomarker abundances in Mojave Desert soils.

  5. Impact of folic acid fortification on global DNA methylation and one-carbon biomarkers in the Women's Health Initiative Observational Study cohort

    PubMed Central

    Bae, Sajin; Ulrich, Cornelia M; Bailey, Lynn B; Malysheva, Olga; Brown, Elissa C; Maneval, David R; Neuhouser, Marian L; Cheng, Ting-Yuan David; Miller, Joshua W; Zheng, Yingye; Xiao, Liren; Hou, Lifang; Song, Xiaoling; Buck, Katharina; Beresford, Shirley AA; Caudill, Marie A

    2014-01-01

    DNA methylation is an epigenetic mechanism that regulates gene expression and can be modified by one-carbon nutrients. The objective of this study was to investigate the impact of folic acid (FA) fortification of the US food supply on leukocyte global DNA methylation and the relationship between DNA methylation, red blood cell (RBC) folate, and other one-carbon biomarkers among postmenopausal women enrolled in the Women's Health Initiative Observational Study. We selected 408 women from the highest and lowest tertiles of RBC folate distribution matching on age and timing of the baseline blood draw, which spanned the pre- (1994–1995), peri- (1996–1997), or post-fortification (1998) periods. Global DNA methylation was assessed by liquid chromatography-tandem mass spectrometry and expressed as a percentage of total cytosine. We observed an interaction (P = 0.02) between fortification period and RBC folate in relation to DNA methylation. Women with higher (vs. lower) RBC folate had higher mean DNA methylation (5.12 vs. 4.99%; P = 0.05) in the pre-fortification period, but lower (4.95 vs. 5.16%; P = 0.03) DNA methylation in the post-fortification period. We also observed significant correlations between one-carbon biomarkers and DNA methylation in the pre-fortification period, but not in the peri- or post-fortification period. The correlation between plasma homocysteine and DNA methylation was reversed from an inverse relationship during the pre-fortification period to a positive relationship during the post-fortification period. Our data suggest that (1) during FA fortification, higher RBC folate status is associated with a reduction in leukocyte global DNA methylation among postmenopausal women and; (2) the relationship between one-carbon biomarkers and global DNA methylation is dependent on folate availability. PMID:24300587

  6. 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

  7. 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

  8. Nucleic Acid Aptamers for Living Cell Analysis

    NASA Astrophysics Data System (ADS)

    Xiong, Xiangling; Lv, Yifan; Chen, Tao; Zhang, Xiaobing; Wang, Kemin; Tan, Weihong

    2014-06-01

    Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as “chemical antibodies,” have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.

  9. 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. PMID:27402728

  10. Delta-aminolevulinic acid dehydratase activity (ALA-D) in red mullet (Mullus barbatus) from Mediterranean waters as biomarker of lead exposure.

    PubMed

    Fernández, B; Martínez-Gómez, C; Benedicto, J

    2015-05-01

    The enzyme delta-aminolevulinic acid dehydratase (ALA-D) has been investigated as biomarker of lead (Pb) exposure in red mullet (Mullus barbatus) from the Spanish continental shelf. Concentrations of Pb and Zn in muscle and organosomatic indices were also measured to explore causality. Blood ALA-D assay conditions were optimized; the optimum pH for this species has been set to 6.5. Results showed that ALA-D activity ranged from 3.2 to 16.9 nmol PBGmin(-1)mg(-1). No significant differences on ALA-D levels between genders have been detected. ALA-D Baseline level and Background Assessment Criteria (BAC) for this species have been set to 9.1 and 6.6 nmol PBGmin(-1)mg(-1), respectively. There have been detected significant differences on ALA-D activity levels among areas, though the markedly low levels of Pb measured in fish muscle seemed not to be able to produce a relevant suppression on ALA-D. In spite of this, a weak inverse relationship detected between ALA-D and Pb concentrations pointed out the potential of this biomarker in red mullet to reflect Pb bioavailability in marine environment. Nevertheless, subsequent research on ALA-D in marine fish species is recommended to be limited to areas where environmental Pb is effectively accumulated by fish. PMID:25706085

  11. 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. PMID:27240945

  12. Biomarkers of xenobiotic exposures

    SciTech Connect

    Brewster, M.A.

    1988-07-01

    Direct measurement of xenobiotic (foreign) chemicals is not always feasible as an exposure assessment,--owing to rapid metabolism, sequestration into fatty tissues, or lack of suitable assay methods. Furthermore, suspect exposures often involve complex mixtures of organics. In these circumstances, indirect biomarkers of exposure can be most helpful. This paper reviews four urinary parameters that hold promise as biomarkers of exposure in occupational and environmental settings: glucaric acid (end-product of the glucuronidation pathway), thioethers (end-product of glutathione reaction with electrophilic or alkylating agents), porphyrin pattern (altered with disruption in heme biosynthesis), and the Ames mutagenicity test. 112 references.

  13. Analysis and characterisation of bovine oocyte and embryo biomarkers by matrix-assisted desorption ionisation mass spectrometry imaging.

    PubMed

    Gonçalves, Roseli F; Ferreira, Mónica S; de Oliveira, Diogo N; Canevarolo, Rafael; Achilles, Marcos A; D'Ercole, Daniela L; Bols, Peter E; Visintin, Jose A; Killian, Gary J; Catharino, Rodrigo R

    2016-03-01

    In the field of 'single cell analysis', many classical strategies like immunofluorescence and electron microscopy are the primary techniques of choice. However, these methodologies are time consuming and do not permit direct identification of specific molecular classes, such as lipids. In the present study, a novel mass spectrometry-based analytical approach was applied to bovine oocytes and embryos. This new metabolomics-based application uses mass spectrometry imaging (MSI), efficient data processing and multivariate data analysis. Metabolic fingerprinting (MF) was applied to the analysis of unfertilised oocytes, 2-, 4- and 8-cell embryos and blastocysts. A semiquantitative strategy for sphingomyelin [SM (16:0)+Na](+) (m/z 725) and phosphatidylcholine [PC (32:0)+Na](+) (m/z 756) was developed, showing that lipid concentration was useful for selecting the best metabolic biomarkers. This study demonstrates that a combination of MF, MSI features and chemometric analysis can be applied to discriminate cell stages, characterising specific biomarkers and relating them to developmental pathways. This information furthers our understanding of fertilisation and preimplantation events during bovine embryo development. PMID:25228254

  14. A correlation study applied to biomarkers of internal and effective dose for acrylonitrile and 4-aminobiphenyl in smokers

    PubMed Central

    Scherer, Gerhard; Newland, Kirk; Papadopoulou, Ermioni

    2014-01-01

    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. PMID:24754403

  15. Biomarker analysis in 500 kyrs sediment record of Lake Van - potential implications for paleoclimate in eastern Anatolia

    NASA Astrophysics Data System (ADS)

    Randlett, M.-E.; Stockhecke, M.; Kwiecien, O.; Schubert, C.

    2012-04-01

    Biomarkers are organic molecules indicative of specific organisms and/or specific conditions such as salinity, oxygen or temperature. Preserved in the sediment, these molecules represent unique tools for investigating paleoenvironments. The biomarker study presented here is part of the ICDP PALEOVAN project. The main objectives are to distinguish between allochtonous and autochtonous organic fractions and to reconstruct paleotemperatures in eastern Anatolia over glacial-interglacial timescales. Allochtonous and autochtonous organic fractions can be differentiated on the molecular level using lipids typical for land plants and algae. Concentration of fatty acids, sterols and n-alkanes are determined on 60 samples distributed over the entire 219 meters sediment profile. The results are interpreted with the help of the lithostratigraphy and two other proxies measured with a relatively high depth resolution. Total organic carbon (TOC) is indicative of productivity and/or preservation whereas potassium (K) XRF intensity is indicative of detrital input. Temperature reconstructions are widely performed in marine system using a lipid produced by haptophyte algae, so-called alkenones. Alkenones are found in most of the analyzed samples. In order to find an appropriate calibration curve, equations from the literature are tested on sediment trap material. Obtained temperatures are compared with actual measurements from the water column over the years 2008-2011.

  16. 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

  17. 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

  18. Quantitative analysis of single amino acid variant peptides associated with pancreatic cancer in serum by an isobaric labeling quantitative method.

    PubMed

    Nie, Song; Yin, Haidi; Tan, Zhijing; Anderson, Michelle A; Ruffin, Mack T; Simeone, Diane M; Lubman, David M

    2014-12-01

    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

  19. 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

    2016-01-01

    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. PMID:27267954

  20. Biomarker Analysis of Stored Blood Products: Emphasis on Pre-Analytical Issues

    PubMed Central

    Delobel, Julien; Rubin, Olivier; Prudent, Michel; Crettaz, David; Tissot, Jean-Daniel; Lion, Niels

    2010-01-01

    Millions of blood products are transfused every year; many lives are thus directly concerned by transfusion. The three main labile blood products used in transfusion are erythrocyte concentrates, platelet concentrates and fresh frozen plasma. Each of these products has to be stored according to its particular components. However, during storage, modifications or degradation of those components may occur, and are known as storage lesions. Thus, biomarker discovery of in vivo blood aging as well as in vitro labile blood products storage lesions is of high interest for the transfusion medicine community. Pre-analytical issues are of major importance in analyzing the various blood products during storage conditions as well as according to various protocols that are currently used in blood banks for their preparations. This paper will review key elements that have to be taken into account in the context of proteomic-based biomarker discovery applied to blood banking. PMID:21151459

  1. Biomarker analysis of stored blood products: emphasis on pre-analytical issues.

    PubMed

    Delobel, Julien; Rubin, Olivier; Prudent, Michel; Crettaz, David; Tissot, Jean-Daniel; Lion, Niels

    2010-01-01

    Millions of blood products are transfused every year; many lives are thus directly concerned by transfusion. The three main labile blood products used in transfusion are erythrocyte concentrates, platelet concentrates and fresh frozen plasma. Each of these products has to be stored according to its particular components. However, during storage, modifications or degradation of those components may occur, and are known as storage lesions. Thus, biomarker discovery of in vivo blood aging as well as in vitro labile blood products storage lesions is of high interest for the transfusion medicine community. Pre-analytical issues are of major importance in analyzing the various blood products during storage conditions as well as according to various protocols that are currently used in blood banks for their preparations. This paper will review key elements that have to be taken into account in the context of proteomic-based biomarker discovery applied to blood banking. PMID:21151459

  2. Biomarker analysis of combined oxytetracycline and zinc pollution in earthworms (Eisenia fetida).

    PubMed

    Gao, Minling; Qi, Yun; Song, Wenhua; Zhou, Qian

    2015-11-01

    To determine the interactive action of antibiotics and heavy metals, this study assessed pollutant-induced responses of cellular biomarkers in earthworms (Eisenia fetida) exposed to zinc (Zn(2+)) and oxytetracycline (OTC) in soil. Lysosomal membranes were damaged and coelomocyte apoptosis occurred with exposure to the individual and combined pollutants. Compared with Zn(2+) alone, lysosomal membrane stability and coelomocyte apoptosis decreased in the Zn(2+)-OTC combined treatment, possibly as a result of complexation of Zn(2+) and OTC at alkaline pH. Such complexation could reduce the toxicity of the pollutants. Lysosomal membrane stability and coelomocyte apoptosis are sensitive biomarkers and could be economical and rapid tools for the monitoring and assessment of a variety of pollutants. PMID:26134676

  3. 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.

  4. Hypochlorous acid reacts with the N-terminal methionines of proteins to give dehydromethionine, a potential biomarker for neutrophil-induced oxidative stress.

    PubMed

    Beal, Jennifer L; Foster, Steven B; Ashby, Michael T

    2009-11-24

    Electrophilic halogenating agents, including hypohalous acids and haloamines, oxidize free methionine and the N-terminal methionines of peptides and proteins (e.g., Met-1 of anti-inflammatory peptide 1 and ubiquitin) to produce dehydromethionine (a five-membered isothiazolidinium heterocycle). Amide derivatives of methionine are oxidized to the corresponding sulfoxide derivatives under the same reaction conditions (e.g., Met-3 of anti-inflammatory peptide 1). Other biological oxidants, including hydrogen peroxide and peroxynitrite, also produce only the corresponding sulfoxides. Hypothiocyanite does not react with methionine residues. We suggest that dehydromethionine may be a useful biomarker for the myeloperoxidase-induced oxidative stress associated with many inflammatory diseases. PMID:19839600

  5. 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

  6. Synovial tissue analysis for the discovery of diagnostic and prognostic biomarkers in patients with early arthritis.

    PubMed

    de Hair, Maria J H; Harty, Leonard C; Gerlag, Danielle M; Pitzalis, Costantino; Veale, Douglas J; Tak, Paul P

    2011-09-01

    Rheumatoid arthritis (RA) is a chronic disease of unspecified etiology that is manifest by persistent inflammation of the synovium. Considerable efforts have been undertaken globally to study the microenvironment of the inflamed synovium, with many encouraging and enlightening results that bring us closer to unmasking the precise etiologies of RA. Subsequent to these efforts, it has been discovered that CD68-positive macrophages present in abundance in the synovial sublining of the inflamed synovium rescind with treatments that induce clinical improvement in RA. Examination of serial synovial biopsies is now commonly used for screening purposes during early drug development, and the number of centers able to perform synovial tissue biopsy sampling according to standardized methods is increasing. Having implemented the use of serial synovial tissue biopsies to evaluate the effects of new treatments on the group level in early proof of principle studies, it is the ambition of the OMERACT Synovial Tissue Group to identify synovial diagnostic and prognostic biomarkers that could be used in individual patients. Therefore, we started a prospective study termed the Synoviomics Project aimed at the identification of novel diagnostic and prognostic synovial biomarkers. We will use straightforward and powerful technologies to analyze patient material and assess clinical parameters to identify such biomarkers. These markers may be used in the future to identify patients who are at risk of having persistent and destructive disease and to start tailor-made targeted therapies in an early phase to prevent autonomous disease progression and irreversible joint damage. PMID:21885519

  7. Identification of HSPA8 as a candidate biomarker for endometrial carcinoma by using iTRAQ-based proteomic analysis

    PubMed Central

    Shan, Nianchun; Zhou, Wei; Zhang, Shufen; Zhang, Yu

    2016-01-01

    Although there are advances in diagnostic, predictive, and therapeutic strategies, discovering protein biomarker for early detection is required for improving the survival rate of the patients with endometrial carcinoma. In this study, we identify proteins that are differentially expressed between the Stage I endometrial carcinoma and the normal pericarcinous tissues by using isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis. Totally, we screened 1,266 proteins. Among them, 103 proteins were significantly overexpressed, and 30 were significantly downexpressed in endometrial carcinoma. Using the bioinformatics analysis, we identified a list of proteins that might be closely associated with endometrial carcinoma, including CCT7, HSPA8, PCBP2, LONP1, PFN1, and EEF2. We validated the gene overexpression of these molecules in the endometrial carcinoma tissues and found that HSPA8 was most significantly upregulated. We further validated the overexpression of HSPA8 by using immunoblot analysis. Then, HSPA8 siRNA was transferred into the endometrial cancer cells RL-95-2 and HEC-1B. The depletion of HSPA8 siRNAs significantly reduced cell proliferation, promoted cell apoptosis, and suppressed cell growth in both cell lines. Taken together, HSPA8 plays a vital role in the development of endometrial carcinoma. HSPA8 is a candidate biomarker for early diagnosis and therapy of Stage I endometrial carcinoma. PMID:27110132

  8. 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

  9. 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

  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. PMID:25842179

  11. Multivariate analysis of potential biomarkers of oxidative stress in Notopterus notopterus tissues from Mahanadi River as a function of concentration of heavy metals.

    PubMed

    Mohanty, Deepali; Samanta, Luna

    2016-07-01

    In this study, investigation were done on the Mahanadi River water and health of dwelling Indian Knife fish Notopterus notopterus from three sites along the course of the river in an around Cuttack city (Odisha). Oxidative stress biomarker assays such as thiobarbituric acid reactive substances, protein carbonyls, protein and non-protein thionyls, reduced glutathione, metallothionein, superoxide dismutase, catalase, glutathione peroxidase/reductase couple, glutathione-S-transferase, and tissue metal (Fe, Cu, Ni, Cd, Pb and Zn) levels along with water quality assessments were assayed to measure the impacts on fish health. Results indicate that except Fe all other metals studied were within approved limits for fish liver and gill as approved by FAO/WHO. However, the muscle tissue do not have any metal beyond the permissible limit. A site and tissue specific response of the above mentioned oxidative biomarkers as well as metal accumulation in the fish tissues were noticed. Lipid peroxidation and protein carbonylation were increased gradually in the fish tissues collected from experimental sites along the course of the River in comparison to upstream reference site. Glutathione-S-transferase, glutathione peroxidase/reductase couple, reduced glutathione and non-protein thiol content were significantly decreased in fish tissues from experimental sites. An increase in metallothionein content was observed while superoxide dismutase and catalase showed tissue specific responses. Multivariate (Discriminant Function) analysis revealed that lipid peroxidation, protein carbonylation and superoxide dismutase have highest association as predictors of impact in the muscle and liver while that for gill is protein carbonylation, superoxide dismutase and glutathione reductase. PMID:27105150

  12. 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…

  13. 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

    2016-01-01

    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 ((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. PMID:27296761

  14. Data of multiple regressions analysis between selected biomarkers related to glutamate excitotoxicity and oxidative stress in Saudi autistic patients.

    PubMed

    El-Ansary, Afaf

    2016-06-01

    This work demonstrates data of multiple regression analysis between nine biomarkers related to glutamate excitotoxicity and impaired detoxification as two mechanisms recently recorded as autism phenotypes. The presented data was obtained by measuring a panel of markers in 20 autistic patients aged 3-15 years and 20 age and gender matching healthy controls. Levels of GSH, glutathione status (GSH/GSSG), glutathione reductase (GR), glutathione-s-transferase (GST), thioredoxin (Trx), thioredoxin reductase (TrxR) and peroxidoxins (Prxs I and III), glutamate, glutamine, glutamate/glutamine ratio glutamate dehydrogenase (GDH) in plasma and mercury (Hg) in red blood cells were determined in both groups. In Multiple regression analysis, R (2) values which describe the proportion or percentage of variance in the dependent variable attributed to the variance in the independent variables together were calculated. Moreover, β coefficients values which show the direction either positive or negative and the contribution of the independent variable relative to the other independent variables in explaining the variation of the dependent variable were determined. A panel of inter-related markers was recorded. This paper contains data related to and supporting research articles currently published entitled "Mechanism of nitrogen metabolism-related parameters and enzyme activities in the pathophysiology of autism" [1], "Novel metabolic biomarkers related to sulfur-dependent detoxification pathways in autistic patients of Saudi Arabia [2], and "A key role for an impaired detoxification mechanism in the etiology and severity of autism spectrum disorders" [3]. PMID:26933667

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Novel biomarkers and genomic tests in prostate cancer: a critical analysis.

    PubMed

    Falzarano, S M; Ferro, M; Bollito, E; Klein, E A; Carrieri, G; Magi-Galluzzi, C

    2015-09-01

    The aim of this review is to critically analyze the current state of research in selected biomarkers and genomic-based tests for prostate cancer (PCa) diagnosis, staging, prognostication, and monitoring. Although in Western societies, PCa is the most common solid malignancy and the second leading cause of cancer death in men, the vast majority of men with PCa are diagnosed with clinically localized disease. The widespread use of prostate-specific antigen (PSA) testing, on one hand, has resulted in earlier PCa detection at a potentially more curable stage, but on the other hand has led to an increase in the rate of negative biopsies, as well as overdetection and overtreatment of potentially indolent tumors that would not have become life-threatening to a patient. A multitude of molecular tests and algorithms has been developed to enhance diagnostic accuracy, improve pretreatment and post-treatment patient risk stratification, and identify aggressive versus indolent disease to facilitate therapeutic decision-making. PSA and derivatives (PSA kinetics, PSA density, percentage of free PSA) as well as algorithms based on PSA and PSA isoforms measurements (prostate health index, four-kallikrein score), urinary molecular biomarkers-based tests (Prostate Cancer Antigen 3, and the Michigan Health System Prostate Score) and selected genomic/proteomic tests now commercially available for disease prognostication (such as Confirm MDx, Prostate Core Mitomic Test, Oncotype DX, Prolaris, ProMark, and Decipher) are herein discussed to inform the readers about current and future clinical applications and their limitations. Finally, we briefly touch upon potential biomarkers predictive of response to therapy, such as androgen receptor splice variant AR-V7, and detection and quantification of circulating tumor cells in the blood stream. PMID:26054411

  20. 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. PMID:25245419

  1. 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 610ng/μL with correlation coefficient of 0.9998. The precision of the assay was ≤15% RSD and method accuracies between 97 and 108%. PMID:27010352

  2. Metabolomic analysis of amino acid and energy metabolism in rats supplemented with chlorogenic acid

    PubMed Central

    Ruan, Zheng; Yang, Yuhui; Zhou, Yan; Wen, Yanmei; Ding, Sheng; Liu, Gang; Wu, Xin; Deng, Zeyuan; Assaad, Houssein; Wu, Guoyao

    2016-01-01

    This study was conducted to investigate effects of chlorogenic acid (CGA) supplementation on serum and hepatic metabolomes in rats. Rats received daily intragastric administration of either CGA (60 mg/kg body weight) or distilled water (control) for 4 weeks. Growth performance, serum biochemical profiles, and hepatic morphology were measured. Additionally, serum and liver tissue extracts were analyzed for metabolomes by high-resolution 1H nuclear magnetic resonance-based metabolomics and multivariate statistics. CGA did not affect rat growth performance, serum biochemical profiles, or hepatic morphology. However, supplementation with CGA decreased serum concentrations of lactate, pyruvate, succinate, citrate, β-hydroxybutyrate and acetoacetate, while increasing serum concentrations of glycine and hepatic concentrations of glutathione. These results suggest that CGA supplementation results in perturbation of energy and amino acid metabolism in rats. We suggest that glycine and glutathione in serum may be useful biomarkers for biological properties of CGA on nitrogen metabolism in vivo. PMID:24927697

  3. 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

  4. Comparison of Serum Uric Acid, Bilirubin, and C-Reactive Protein as Prognostic Biomarkers of In-Hospital MACE Between Women and Men With ST-Segment Elevation Myocardial Infarction.

    PubMed

    Baumann, Stefan; Huseynov, Aydin; Koepp, Johanna; Jabbour, Claude; Behnes, Michael; Becher, Tobias; Renker, Matthias; Lang, Siegfried; Borggrefe, Martin; Lehmann, Ralf; Akin, Ibrahim

    2016-03-01

    Levels of C-reactive protein (CRP), uric acid (UA), and total bilirubin (TB) are associated with coronary artery disease and major adverse cardiac events (MACEs) in patients with ST-segment elevation myocardial infarction (STEMI). We retrospectively included 1167 patients with STEMI who underwent percutaneous coronary intervention and routine blood sampling. The study cohort consisted of 803 patients (73.1% male, mean age 62.5 ± 13.4 years). In men, the levels of CRP, TB, and UA were significantly higher in the MACE than in the non-MACE group (P < .05). The receiver-operating characteristic (ROC) analysis shows that CRP (area under the curve [AUC]: 0.59; 95% confidence interval [CI]: 0.53-0.66; P = .014) and TB (AUC: 0.58; 95% CI: 0.51-0.65; P = .019) are significantly associated with MACE but not UA (AUC: 0.61; 95% CI: 0.42-0.76; P = .083). Logistic regression revealed CRP (odds ratio [OR] 1.01; 95% CI: 1.00-1.01; P = .006) and TB (OR 2.03; 95% CI: 1.12-3.40; P = .007) as an independent predictor for MACE. In women, none of the biomarkers was associated with MACE by ROC analysis or logistic regression analysis. This study demonstrated that high CRP and TB serum levels have a prognostic association with in-hospital MACE in male patients with STEMI. PMID:26032849

  5. A meta-analysis of gemcitabine biomarkers in patients with pancreatico-biliary cancers

    PubMed Central

    Wei, Christina H.; Gorgan, Tristan R.; Elashoff, David A.; Hines, O. Joe; Farrell, James J.; Donahue, Timothy R.

    2013-01-01

    Objectives To summarize all clinical studies evaluating the prognostic role of gemcitabine metabolic genes in pancreatico-biliary (PB) cancer patients receiving gemcitabine (GEM) therapy in the neoadjuvant, adjuvant or palliative settings. Methods Meta-analyses were performed to calculate the pooled hazard rations (HRs) for each gene by each clinical outcome (overall, disease free, and progression free survivals) using a random-effects approach. Results The search strategy identified 16 eligible studies, comprised of 632 PB patients total, with moderate quality. Compared to low expression, pooled hazards ratios for OS of hENT1, dCK, RRM1, RRM2, and DPD were 0.37 (95%CI, 0.28–0.47), 0.40 (95%CI, 0.20-0.80), 2.21 (95%CI, 1.12-4.36), 2.13 (95%CI, 1.00-4.52), and 1.91 (95%CI, 1.16-3.17), respectively. A similar trend was observed for each of these biomarkers in DFS and PFS prognostication. Subgroup analyses for hENT1 showed a comparable survival correlation in the adjuvant and palliative settings. Conclusions High expression of hENT1 in PB cancer patients receiving GEM-based adjuvant therapy is associated with improved OS and DFS and may be the best examined prognostic marker to date. Evidence for other biomarkers is limited by a small number of publications investigating these markers. PMID:24152955

  6. Long-chain polyunsaturated fatty acid status in obesity: a systematic review and meta-analysis.

    PubMed

    Fekete, K; Györei, E; Lohner, S; Verduci, E; Agostoni, C; Decsi, T

    2015-06-01

    Long-chain polyunsaturated fatty acid (LCPUFA) status has recently been related to the pathogenesis of obesity. Our aims were to systematically review observational studies investigating LCPUFA status from different blood compartments in overweight or obese subjects and to assess the relationship between LCPUFA profile and obesity. The Ovid MEDLINE, Scopus and Cochrane Library CENTRAL databases were searched from inception to January 2014. The meta-analysis showed significant differences in the LCPUFA composition of total plasma lipids, plasma phospholipids and plasma cholesteryl esters between overweight or obese subjects and controls. Dihomo-γ-linolenic acid (DGLA) values were significantly higher in overweight or obese subjects compared with controls in all the investigated biomarkers. In addition, the DGLA/linoleic acid ratio (surrogate parameter for Δ6 desaturase activity) in plasma phospholipids was significantly elevated (mean difference [MD]: 0.05; 95% confidence interval [CI]: 0.02, 0.08; n = 280), while the arachidonic acid/DGLA ratio (surrogate parameter for Δ5 desaturase activity) was significantly decreased (MD: -0.55; 95% CI: -0.71, -0.39; n = 347) in overweight or obese subjects compared with controls. The results of the present meta-analysis confirm that LCPUFA profile is altered in obesity and suggest that the differences observed in desaturase activities may be responsible for the disturbed LCPUFA metabolism in obesity. PMID:25828602

  7. 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.

  8. Coronin-1C is a novel biomarker for hepatocellular carcinoma invasive progression identified by proteomics analysis and clinical validation

    PubMed Central

    2010-01-01

    Background To better search for potential markers for hepatocellular carcinoma (HCC) invasion and metastasis, proteomic approach was applied to identify potential metastasis biomarkers associated with HCC. Methods Membrane proteins were extracted from MHCC97L and HCCLM9 cells, with a similar genetic background and remarkably different metastasis potential, and compared by SDS-PAGE and identified by ESI-MS/MS. The results were further validated by western blot analysis, immunohistochemistry (IHC) of tumor tissues from HCCLM9- and MHCC97L-nude mice, and clinical specimens. Results Membrane proteins were extracted from MHCC97L and HCCLM9 cell and compared by SDS-PAGE analyses. A total of 14 differentially expressed proteins were identified by ESI-MS/MS. Coronin-1C, a promising candidate, was found to be overexpressed in HCCLM9 cells as compared with MHCC97L cells, and validated by western blot and IHC from both nude mice tumor tissues and clinical specimens. Coronin-1C level showed an abrupt upsurge when pulmonary metastasis occurred. Increasing coronin-1C expression was found in liver cancer tissues of HCCLM9-nude mice with spontaneous pulmonary metastasis. IHC study on human HCC specimens revealed that more patients in the higher coronin-1C group had overt larger tumor and more advanced stage. Conclusions Coronin-1C could be a candidate biomarker to predict HCC invasive behavior. PMID:20181269

  9. 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. PMID:25757395

  10. [Validity of urinary 2-thiothiazolidine-4-carboxylic acid (TTCA) as biomarker of exposure to very low concentrations of carbon disulphide: preliminary results].

    PubMed

    Lovreglio, P; Bergonzi, R; Meliddo, G; Pesola, G; Mascia, L; Basso, A; Imbriani, M; Apostoli, P; Soleo, L

    2008-01-01

    The possibility to use urinary 2-thiothiazolidine-4-carboxylic acid (TTCA) as biomarker of occupational exposure to very low doses of carbon disulphide (CS2) was evaluated preliminarily in 10 workers employed in a chemical plant where rubber vulcanization accelerators are produced, and in 10 workers, residents in the same geographical area and not occupationally exposed to CS2 and dithiocarbamates (DTC). Exposure to airborne CS2 was assessed, only for exposed workers, by both personal and area samplers. For the determination of TTCA, a spot urine sample was collected for each worker, exposed and non exposed, at the end of work-shift. A questionnaire probing lifestyle and dietary habits and non occupational exposure to CS2 and DTC was administered to all workers involved in the study. Environmental exposure to CS2 in 2007 ranged between 0.21 mg/m3 and 0.73 mg/m3 for personal sampling, and between 0.23 mg/m3 and 0.41 mg/m3 for area sampling. Urinary TTCA levels resulted very low and did not show any significant difference between exposed (Median: 10.8 microg/g creat; Range: 6.1-26.4 microg/g creat) and non exposed workers (Median: 9.3 microg/g creat; Range: 3.0-33.0 microg/g creat), while higher, but not significant concentrations of TTCA were observed in smokers than in non smokers (p = 0.09). No correlation was found between urinary TTCA levels and environmental exposure to CS2, age, body mass index, smoking and dietary habits. In conclusion, the low sensibility and specificity in the assessment of occupational exposure to low doses of CS2 in workers compared to general population subjects, makes urinary TTCA a biomarker with a low usefulness in biological monitoring. ACGIH, besides, should also introduce "B" (background) notation, at present not considered for the BEI indicated for urinary TTCA. PMID:18700678

  11. 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. PMID:21183322

  12. 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

  13. An analysis of issues concerning acid rain

    SciTech Connect

    Not Available

    1984-01-01

    GAO examines the implications of current scientific knowledge for policy decisions on acid rain and offers a series of observations on the following issues involved in the debate: to what extent has it been scientifically demonstrated that acid rain is resulting in damage to the environment. What are the causes of acid rain and where is it most prevalent. What alternatives exist for controlling acid rain and what are their economic effects.

  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. PMID:19525080

  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. 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.

  17. Strength and limits using 13C phospholipid fatty acid analysis in soil ecology

    NASA Astrophysics Data System (ADS)

    Watzinger, Andrea

    2016-04-01

    This presentation on microbial phospholipid biomarkers, their isotope analysis and their ability to reveal soil functions summarizes experiences gained by the author for more than 10 years. The amount and composition of phospholipid fatty acids (PLFAs) measured in environmental samples strongly depend on the methodology. To achieve comparable results the extraction, separation and methylation method must be kept constant. PLFAs patterns are sensitive to microbial community shifts even though the taxonomic resolution of PLFAs is low. The possibility to easily link lipid biomarkers with stable isotope techniques is identified as a major advantage when addressing soil functions. Measurement of PLFA isotopic ratios is sensitive and enables detecting isotopic fractionation. The difference between the carbon isotopic ratio of single PLFAs and their substrate (δ13C) can vary between -6 and +11‰. This difference derives from the fractionation during biosynthesis and from substrate inhomogeneity. Consequently, natural abundance studies are restricted to quantifying substrate uptake of the total microbial biomass. In contrast, artificial labelling enables quantifying carbon uptake into single PLFAs, but labelling success depends on homogeneous and undisturbed label application. Current developments in microbial ecology (e.g. 13C and 15N proteomics) and isotope techniques (online monitoring of CO2 isotope ratios) will likely improve soil functional interpretations in the future. 13C PLFA analysis will continue to contribute because it is affordable, sensitive and allows frequent sampling combined with the use of small amounts of 13C label.

  18. Liquid chromatography-electrospray ionization-tandem mass spectrometry quantitation of urinary [pyridine-D4]4-hydroxy-4-(3-pyridyl)butanoic acid, a biomarker of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone metabolic activation in smokers.

    PubMed

    Jing, Meng; Wang, Yaohua; Upadhyaya, Pramod; Jain, Vipin; Yuan, Jian-Min; Hatsukami, Dorothy K; Hecht, Stephen S; Stepanov, Irina

    2014-09-15

    4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 1) is a potent tobacco-specific lung carcinogen believed to play a key role in the development of lung cancer in smokers. Metabolic activation of NNK to DNA damaging reactive intermediates proceeds via α-hydroxylation pathways. The end products of these pathways are excreted in the urine of smokers as 4-oxo-4-(3-pyridyl)butanoic acid (keto acid, 3) and 4-hydroxy-4-(3-pyridyl)butanoic acid (hydroxy acid, 4). The sum of these biomarkers (after NaBH4 treatment), referred to as total hydroxy acid, could potentially be used to measure the extent of NNK metabolic activation in smokers. However, the same metabolites are formed from nicotine; therefore, there is a need to distinguish the NNK- and nicotine-derived keto and hydroxy acid in smokers' urine. We previously developed a unique methodology based on the use of [pyridine-D4]NNK ([D4]1), which metabolizes to the correspondingly labeled biomarkers. In this study, we developed a sensitive and reproducible assay for the detection and quantitation of total [pyridine-D4]hydroxy acid ([D4]4) in human urine. A two-step derivatization approach was used to convert [D4]4 to [pyridine-D4]methyl 4-hexanoyl-4-(3-pyridyl)butanoate ([D4]6), and an LC-ESI-MS/MS method was developed for the analysis of this derivative with excellent sensitivity, accuracy, and precision. The robustness and reproducibility of the assay was further confirmed by its application for the analysis of urine samples from 87 smokers who smoked [D4]1-containing cigarettes for 1 week. The measured level averaged 130 fmol/mL urine. The developed assay can be used in future studies that may require evaluation of the relative efficiency of NNK metabolic activation in humans. PMID:25098652

  19. Liquid Chromatography–Electrospray Ionization–Tandem Mass Spectrometry Quantitation of Urinary [Pyridine-D4]4-hydroxy-4-(3-pyridyl)butanoic Acid, a Biomarker of 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone Metabolic Activation in Smokers

    PubMed Central

    2015-01-01

    4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 1) is a potent tobacco-specific lung carcinogen believed to play a key role in the development of lung cancer in smokers. Metabolic activation of NNK to DNA damaging reactive intermediates proceeds via α-hydroxylation pathways. The end products of these pathways are excreted in the urine of smokers as 4-oxo-4-(3-pyridyl)butanoic acid (keto acid, 3) and 4-hydroxy-4-(3-pyridyl)butanoic acid (hydroxy acid, 4). The sum of these biomarkers (after NaBH4 treatment), referred to as total hydroxy acid, could potentially be used to measure the extent of NNK metabolic activation in smokers. However, the same metabolites are formed from nicotine; therefore, there is a need to distinguish the NNK- and nicotine-derived keto and hydroxy acid in smokers’ urine. We previously developed a unique methodology based on the use of [pyridine-D4]NNK ([D4]1), which metabolizes to the correspondingly labeled biomarkers. In this study, we developed a sensitive and reproducible assay for the detection and quantitation of total [pyridine-D4]hydroxy acid ([D4]4) in human urine. A two-step derivatization approach was used to convert [D4]4 to [pyridine-D4]methyl 4-hexanoyl-4-(3-pyridyl)butanoate ([D4]6), and an LC-ESI-MS/MS method was developed for the analysis of this derivative with excellent sensitivity, accuracy, and precision. The robustness and reproducibility of the assay was further confirmed by its application for the analysis of urine samples from 87 smokers who smoked [D4]1-containing cigarettes for 1 week. The measured level averaged 130 fmol/mL urine. The developed assay can be used in future studies that may require evaluation of the relative efficiency of NNK metabolic activation in humans. PMID:25098652

  20. 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

  1. High-throughput transcriptomic analysis nominates proteasomal genes as age-specific biomarkers and therapeutic targets in prostate cancer

    PubMed Central

    Zhao, S G; Jackson, W C; Kothari, V; Schipper, M J; Erho, N; Evans, J R; Speers, C; Hamstra, D A; Niknafs, Y S; Nguyen, P L; Schaeffer, E M; Ross, A E; Den, R B; Klein, E A; Jenkins, R B; Davicioni, E; Feng, F Y

    2015-01-01

    Background: Although prostate cancer (PCa) is hypothesized to differ in nature between younger versus older patients, the underlying molecular distinctions are poorly understood. We hypothesized that high-throughput transcriptomic analysis would elucidate biological differences in PCas arising in younger versus older men, and would nominate potential age-specific biomarkers and therapeutic targets. Methods: The high-density Affymetrix GeneChip platform, encompassing >1 million genomic loci, was utilized to assess gene expression in 1090 radical prostatectomy samples from patients with long-term follow-up. We identified genes associated with metastatic progression by 10 years post-treatment in younger (age<65) versus older (age⩾65) patients, and ranked these genes by their prognostic value. We performed Gene Set Enrichment Analysis (GSEA) to nominate biological concepts that demonstrated age-specific effects, and validated a target by treating with a clinically available drug in three PCa cell lines derived from younger men. Results: Over 80% of the top 1000 prognostic genes in younger and older men were specific to that age group. GSEA nominated the proteasome pathway as the most differentially prognostic in younger versus older patients. High expression of proteasomal genes conferred worse prognosis in younger but not older men on univariate and multivariate analysis. Bortezomib, a Food and Drug Administration approved proteasome inhibitor, decreased proliferation in three PCa cell lines derived from younger patients. Conclusions: Our data show significant global differences in prognostic genes between older versus younger men. We nominate proteasomeal gene expression as an age-specific biomarker and potential therapeutic target specifically in younger men. Limitations of our study include clinical differences between cohorts, and increased comorbidities and lower survival in older patients. These intriguing findings suggest that current models of PCa biology do

  2. 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...

  3. 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

  4. THE TIME-COURSE AND SENSITIVITY OF MUCONIC ACID AS A BIOMARKER FOR HUMAN ENVIRONMENTAL EXPOSURE TO BENZENE

    EPA Science Inventory

    Preliminary results are presented that show the effect of an increased benzene exposure on the urinary elimination of trans,trans-muconic acid (MA) for an adult male. These results were generated from a controlled exposure experiment where by an individual was exposed to benzene ...

  5. MicroRNA-17 family as novel biomarkers for cancer diagnosis: a meta-analysis based on 19 articles.

    PubMed

    Gu, Ronghe; Huang, Shiqing; Huang, Weiguo; Li, Yuming; Liu, Huijiang; Yang, Lijing; Huang, Zhonggui

    2016-05-01

    Cancer remains as the leading cause of death all over the world due to the lack of efficient diagnostic techniques and therapeutic methods. Many studies have reported the potential diagnostic value of microRNA-17 (miRNA-17, miR-17) family members as biomarkers for cancer detection. However, inconsistent results were revealed from a wide range of studies. As a result of this, a meta-analysis based on 19 studies was conducted to assess the diagnostic performance of miR-17 family for cancer detection. A total of 1772 patients with certain types of cancer and 1320 healthy controls were involved in these studies. The overall diagnostic accuracy was measured by the following: sensitivity, 0.67 (95 % confidence interval (CI) 0.60-0.74); specificity, 0.83 (95 % CI 0.74-0.85); positive likelihood ratio (PLR), 3.9 (95 % CI 2.6-5.9); negative likelihood ratio (NLR), 0.40 (95 % CI 0.34-0.48); and diagnostic odds ratio (DOR), 10 (95 % CI 6-16), respectively. Additionally, the pooled area under the summary receiver operator characteristic (SROC) curve (area under the curve (AUC)) was 0.79 (95 % CI 0.75-0.82), indicating a relatively low accuracy of miR-17 family as biomarkers for cancer detection. Subgroup analysis further showed that miR-17 family had more reliable performance in cancer diagnosis for Asian than that for Caucasian. Moreover, multiple miRNAs containing miR-17, -20a/b, and -93 reflected higher diagnostic accuracy than both miR-106a/b (single miRNA) and the overall miR-17 family assay. Therefore, appropriate combinations of miR-17 family may be used as non-invasive screening biomarkers for cancer, and it is necessary to carry out a large-scale population-based study to further assess the potential diagnostic value of miR-17 family. PMID:26631037

  6. Analysis of issues concerning acid rain

    SciTech Connect

    Bowsher, C.A.

    1984-12-11

    Although science has largely determined that man-made emissions cause acid rain, there is uncertainty concerning the extent and timing of its anticipated effects. Thus, at the present time scientific information alone does not lead unequivocally to a conclusion on whether it is appropriate to begin control actions now or to await better understanding. Given this uncertainty, decisionmakers must weigh the risks of further, potentially avoidable environmental damage against the risks of economic impacts from acid rain control actions which may ultimately prove to be unwarranted. GAO examines the implications of current scientific knowledge for policy decisions on acid rain and offers a series of observations on the following issues involved in the debate: To what extent has it been scientifically demonstrated that acid rain is resulting in damage to the environment. What are the causes of acid rain and where is it most prevalent. What alternatives exist for controlling acid rain and what are their economic effects. 5 figures, 20 tables.

  7. 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

  8. An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer

    PubMed Central

    Danforth, David N; Warner, Andrew C; Wangsa, Darawalee; Ried, Thomas; Duelli, Dominik; Filie, Armando C; Prindiville, Sheila A

    2015-01-01

    BACKGROUND There is a strong need to define the molecular changes in normal at-risk breast epithelium to identify biomarkers and new targets for breast cancer prevention and to develop a molecular signature for risk assessment. Improved methods of breast epithelial sampling are needed to promote whole-genome molecular profiling, increase ductal epithelial cell yield, and reduce sample cell heterogeneity. METHODS We developed an improved method of breast ductal sampling with ductal lavage through a 22-gauge catheter and collection of ductal samples with a microaspirator. Women at normal risk or increased risk for breast cancer were studied. Ductal epithelial samples were analyzed for cytopathologic changes, cellular yield, epithelial cell purity, quality and quantity of DNA and RNA, and use in multiple downstream molecular applications. RESULTS We studied 50 subjects, including 40 subjects at normal risk for breast cancer and 37 subjects with non-nipple aspirate fluid-yielding ducts. This method provided multiple 1.0 mL samples of high ductal epithelial cell content (median ≥8 samples per subject of ≥5,000 cells per sample) with 80%–100% epithelial cell purity. Extraction of a single intact ductal sample (fluid and cells) or the separate frozen cellular component provided DNA and RNA for multiple downstream studies, including quantitative reverse transcription- polymerase chain reaction (PCR) for microRNA, quantitative PCR for the human telomerase reverse transcriptase gene, whole-genome DNA amplification, and array comparative genomic hybridization analysis. CONCLUSION An improved breast epithelial sampling method has been developed, which should significantly expand the acquisition and biomarker analysis of breast ductal epithelium in women at risk for breast cancer. PMID:26078587

  9. MicroRNAs as Potential Biomarkers for Diagnosing Cancers of Central Nervous System: a Meta-analysis.

    PubMed

    Wei, Dong; Wan, Qun; Li, Li; Jin, Haifeng; Liu, Yonghong; Wang, Yangang; Zhang, Guangyun

    2015-01-01

    Recent studies have shown abnormal microRNA (miRNA) expression levels in the central nervous system (CNS) of cancer patients, suggesting that miRNAs may serve as promising biomarkers for cancers of CNS. However, other studies have arrived at conflicting results. Therefore, this meta-analysis aims to systematically measure the potential diagnostic value of miRNAs for CNS cancers. Electronic databases as well as other sources were searched until to April 12, 2014 for relevant articles. Data from different studies were pooled using the random-effects model. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative LR (NLR), diagnostic odds ratio (DOR), together with the summary receiver operator characteristic (SROC) curve, and area under the SROC curve (AUC) value were used to estimate overall diagnostic performance. Twenty-three studies from 6 articles were included in the current meta-analysis with a total of 299 CNS cancer patients and 418 controls. The pooled sensitivity, specificity, PLR, NLR, DOR, and AUC were 0.85 (95% CI, 0.80-0.89), 0.83 (95% CI, 0.76-0.88), 5.1 (95% CI, 3.4-7.5), 0.18 (95% CI, 0.12-0.26), 28 (95% CI, 14-58), and 0.91 (95% CI, 0.88-0.93), respectively. Subgroup analyses showed that cerebrospinal fluid (CSF)-based miRNAs assays yielded more accurate results and seemed to be more sensitive in diagnosing of primary central nervous system lymphoma (PCNSL). In conclusion, miRNAs may be suitable for serving as noninvasive biomarkers for CNS cancers detection. However, further validation based on a larger sample of patients and controls is still required. PMID:25081587

  10. 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. PMID:26452500

  11. 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

  12. Biomarkers in orthodontic tooth movement

    PubMed Central

    Kumar, A. Anand; Saravanan, K.; Kohila, K.; Kumar, S. Sathesh

    2015-01-01

    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. PMID:26538871

  13. Serologic Intestinal-Fatty Acid Binding Protein in Necrotizing Enterocolitis Diagnosis: A Meta-Analysis

    PubMed Central

    Cheng, Shupeng; Yu, Jialin; Zhou, Min; Tu, Yan; Lu, Qi

    2015-01-01

    Background. Previous studies showed that intestinal-fatty acid binding protein (I-FABP) may be a valid and promising serologic biomarker for early diagnosis of necrotizing enterocolitis (NEC). Objective. To investigate the early diagnostic value of serologic I-FABP in NEC for the premature neonates. Methods. All major databases were searched from January 1, 1990, to May 1, 2015. We used Meta-Disc 1.4 and Revman5.0 software to calculate the diagnostic accuracy. Results. Seven studies with 444 subjects were identified. The pooled sensitivity of I-FABP was 0.67 for NEC I, 0.74 for NEC II, and 0.83 for NEC III, and the pooled specificity was 0.84, respectively, which showed a moderate diagnostic accuracy. The area under curve (AUC) for each stage was 0.75 (Q⁎ = 0.69), 0.82 (Q⁎ = 0.76), and 0.91 (Q⁎ = 0.84). The diagnostic threshold analysis showed no significant difference in threshold effect. The metaregression showed that the cut-off value has the largest effect on heterogeneity. The funnel plots indicated the existence of publication bias. Conclusion. I-FABP is a valid serologic biomarker for early diagnosis in NEC for the premature neonates with a moderate accuracy. PMID:26798632

  14. Kinetics of acid-induced degradation of tetra- and dihydrobiopterin in relation to their relevance as biomarkers of endothelial function.

    PubMed

    Mortensen, Alan; Lykkesfeldt, Jens

    2013-02-01

    The ratio of the nitric oxide synthase (NOS) cofactor tetrahydrobiopterin (BH(4)) to its oxidized form dihydrobiopterin (BH(2)) has been suggested as an index of endothelial dysfunction. Consequently, much effort has been put into preserving the in vivo equilibrium between these labile analytes. In the present study, we conducted a series of stability experiments in aqueous solutions and blood to identify the most appropriate way of stabilizing BH(4) and BH(2). Based on our results, we are able to recommend that blood samples are immediately stabilized with dithioerythriol and protein precipitation conducted using trichloroacetic acid (TCA). PMID:23066920

  15. 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. PMID:23042767

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

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

    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 on microfabricated capillary electrophoresis (CE) chips (1, 2). To analyze amino acids in situ, 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. The heart of the MOA is the microchip that contains the CE separation channels as well as microfabricated valves and pumps (3) for sample handling. The pneumatic microfabricated valves are created by combining an etched displacement chamber, an actuated PDMS membrane layer, and a discontinuous fluidic channel structure. A microfabricated pump is created by combining three individually-addressable valves in series. These membrane valves and pumps are integrated with the glass separation channel using a novel multilayer design in which sample enters the top fluidic layer for routing and is directed to the bottom glass layers for CE separation and analysis. The microfabricated device is operated by the portable instrument which contains solenoids for controlling fluidic valves, electronics, a 15 mW 400 nm diode laser, confocal detection optics, and a fiber-optic coupled photomultiplier for fluorescence detection. Limits of detection of fluorescamine-labeled amino acids are in the nM to pM range corresponding to part-per-trillion sensitivities in soil samples (4). The portable CE instrument, in combination with the Mars Organic Detector (MOD) (5), was recently successfully field tested on soil samples rich in jarosite from Panoche Valley, CA. Jarosite has recently been detected on Mars

  17. Proteomic Analysis of Cerebrospinal Fluid in Pneumococcal Meningitis Reveals Potential Biomarkers Associated with Survival

    PubMed Central

    Goonetilleke, Upali R.; Scarborough, Matthew; Ward, Stephen A.; Gordon, Stephen B.

    2016-01-01

    Background Patients with pneumococcal meningitis often die or have severe neurological damage despite optimal antibiotic therapy. New or improved therapy is required. The delivery of new interventions will require an improved understanding of the disease pathogenesis. Our objective was to learn more about the pathophysiology of severe meningitis through the interpretation of differences in the proteomic profile of cerebrospinal fluid (CSF) from patients with meningitis. Methods Two-dimensional polyacrylamide gel electrophoresis of CSF from normal subjects (controls, n = 10) and patients with pneumococcal meningitis (n = 20) was analyzed. Spot differences were compared and identified between controls, nonsurvivors (n = 9), and survivors (n = 11). Results Protein concentration in CSF of patients with meningitis was 4-fold higher than in CSF of control subjects (7.0 mg/mL vs 0.23 mg/mL; P < .01). A mean of 2466 discrete protein spots was present in CSF of patients with meningitis. Thirty-four protein spots were differentially expressed in CSF of nonsurvivors, compared with survivors. None of these protein spots were observed in CSF of control subjects. Conclusions Proteomic screening of CSF yields potential biomarkers capable of differentiating control subjects from nonsurvivors and survivors of meningitis. Proteins involved in the inflammatory process and central metabolism were represented in the differentially expressed protein repertoire. PMID:20608875

  18. 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.

  19. 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.

  20. 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.

  1. Increased serum bile acid concentration following low-dose chronic administration of thioacetamide in rats, as evidenced by metabolomic analysis.

    PubMed

    Jeong, Eun Sook; Kim, Gabin; Shin, Ho Jung; Park, Se-Myo; Oh, Jung-Hwa; Kim, Yong-Bum; Moon, Kyoung-Sik; Choi, Hyung-Kyoon; Jeong, Jayoung; Shin, Jae-Gook; Kim, Dong Hyun

    2015-10-15

    A liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS)-based metabolomics approach was employed to identify endogenous metabolites as potential biomarkers for thioacetamide (TAA)-induced liver injury. TAA (10 and 30mg/kg), a well-known hepatotoxic agent, was administered daily to male Sprague-Dawley (SD) rats for 28days. We then conducted untargeted analyses of endogenous serum and liver metabolites. Partial least squares discriminant analysis (PLS-DA) was performed on serum and liver samples to evaluate metabolites associated with TAA-induced perturbation. TAA administration resulted in altered levels of bile acids, acyl carnitines, and phospholipids in serum and in the liver. We subsequently demonstrated and confirmed the occurrence of compromised bile acid homeostasis. TAA treatment significantly increased serum levels of conjugated bile acids in a dose-dependent manner, which correlated well with toxicity. However, hepatic levels of these metabolites were not substantially changed. Gene expression profiling showed that the hepatic mRNA levels of Ntcp, Bsep, and Oatp1b2 were significantly suppressed, whereas those of basolateral Mrp3 and Mrp4 were increased. Decreased levels of Ntcp, Oatp1b2, and Ostα proteins in the liver were confirmed by western blot analysis. These results suggest that serum bile acids might be increased due to the inhibition of bile acid enterohepatic circulation rather than increased endogenous bile acid synthesis. Moreover, serum bile acids are a good indicator of TAA-induced hepatotoxicity. PMID:26222700

  2. Biomarkers to guide clinical therapeutics in rheumatology?

    PubMed Central

    Robinson, William H.; Mao, Rong

    2016-01-01

    Purpose of review The use of biomarkers in rheumatology can help identify disease risk, improve diagnosis and prognosis, target therapy, assess response to treatment, and further our understanding of the underlying pathogenesis of disease. Here, we discuss the recent advances in biomarkers for rheumatic disorders, existing impediments to progress in this field, and the potential of biomarkers to enable precision medicine and thereby transform rheumatology. Recent findings Although significant challenges remain, progress continues to be made in biomarker discovery and development for rheumatic diseases. The use of next-generation technologies, including large-scale sequencing, proteomic technologies, metabolomic technologies, mass cytometry, and other single-cell analysis and multianalyte analysis technologies, has yielded a slew of new candidate biomarkers. Nevertheless, these biomarkers still require rigorous validation and have yet to make their way into clinical practice and therapeutic development. This review focuses on advances in the biomarker field in the last 12 months as well as the challenges that remain. Summary Better biomarkers, ideally mechanistic ones, are needed to guide clinical decision making in rheumatology. Although the use of next-generation techniques for biomarker discovery is making headway, it is imperative that the roadblocks in our search for new biomarkers are overcome to enable identification of biomarkers with greater diagnostic and predictive utility. Identification of biomarkers with robust diagnostic and predictive utility would enable precision medicine in rheumatology. PMID:26720904

  3. Bis-butanediol-mercapturic acid (bis-BDMA) as a urinary biomarker of metabolic activation of butadiene to its ultimate carcinogenic species

    PubMed Central

    Tretyakova, Natalia Y.

    2014-01-01

    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. PMID:24531806

  4. Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke: Systematic review and meta-analysis of 14 015 stroke cases and pooled analysis of primary biomarker data from up to 60 883 individuals

    PubMed Central

    Khan, Tauseef A; Shah, Tina; Prieto, David; Zhang, Weili; Price, Jackie; Fowkes, Gerald R; Cooper, Jackie; Talmud, Philippa J; Humphries, Steve E; Sundstrom, Johan; Hubacek, Jaroslav A; Ebrahim, Shah; Lawlor, Debbie A; Ben-Shlomo, Yoav; Abdollahi, Mohammad R; Slooter, Arjen JC; Szolnoki, Zoltan; Sandhu, Manjinder; Wareham, Nicholas; Frikke-Schmidt, Ruth; Tybjærg-Hansen, Anne; Fillenbaum, Gerda; Heijmans, Bastiaan T; Katsuya, Tomohiro; Gromadzka, Grazyna; Singleton, Andrew; Ferrucci, Luigi; Hardy, John; Worrall, Bradford; Rich, Stephen S; Matarin, Mar; Whittaker, John; Gaunt, Tom R; Whincup, Peter; Morris, Richard; Deanfield, John; Donald, Ann; Davey Smith, George; Kivimaki, Mika; Kumari, Meena; Smeeth, Liam; Khaw, Kay-Tee; Nalls, Michael; Meschia, James; Sun, Kai; Hui, Rutai; Day, Ian; Hingorani, Aroon D; Casas, Juan P

    2013-01-01

    Background At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less clear. We evaluated the association of APOE genotype with risk of ischaemic stroke and assessed whether the observed effect was consistent with the effects of APOE genotype on LDL-C or other lipids and biomarkers of cardiovascular risk. Methods We conducted a systematic review of published and unpublished studies reporting on APOE genotype and ischaemic stroke. We pooled 41 studies (with a total of 9027 cases and 61 730 controls) using a Bayesian meta-analysis to calculate the odds ratios (ORs) for ischaemic stroke with APOE genotype. To better evaluate potential mechanisms for any observed effect, we also conducted a pooled analysis of primary data using 16 studies (up to 60 883 individuals) of European ancestry. We evaluated the association of APOE genotype with lipids, other circulating biomarkers of cardiovascular risk and carotid intima-media thickness (C-IMT). Results The ORs for association of APOE genotypes with ischaemic stroke were: 1.09 (95% credible intervals (CrI): 0.84–1.43) for ε2/ε2; 0.85 (95% CrI: 0.78–0.92) for ε2/ε3; 1.05 (95% CrI: 0.89–1.24) for ε2/ε4; 1.05 (95% CrI: 0.99–1.12) for ε3/ε4; and 1.12 (95% CrI: 0.94–1.33) for ε4/ε4 using the ε3/ε3 genotype as the reference group. A regression analysis that investigated the effect of LDL-C (using APOE as the instrument) on ischaemic stroke showed a positive dose-response association with an OR of 1.33 (95% CrI: 1.17, 1.52) per 1 mmol/l increase in LDL-C. In the separate pooled analysis, APOE genotype was linearly and positively associated with levels of LDL-C (P-trend: 2 × 10−152), apolipoprotein B (P-trend: 8.7 × 10−06) and C-IMT (P-trend: 0.001), and negatively and

  5. 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. PMID:27168482

  6. 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

  7. Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: A systematic review and meta-analysis

    PubMed Central

    Saad, Mohamed N.; Mabrouk, Mai S.; Eldeib, Ayman M.; Shaker, Olfat G.

    2015-01-01

    Genetics of autoimmune diseases represent a growing domain with surpassing biomarker results with rapid progress. The exact cause of Rheumatoid Arthritis (RA) is unknown, but it is thought to have both a genetic and an environmental bases. Genetic biomarkers are capable of changing the supervision of RA by allowing not only the detection of susceptible individuals, but also early diagnosis, evaluation of disease severity, selection of therapy, and monitoring of response to therapy. This review is concerned with not only the genetic biomarkers of RA but also the methods of identifying them. Many of the identified genetic biomarkers of RA were identified in populations of European and Asian ancestries. The study of additional human populations may yield novel results. Most of the researchers in the field of identifying RA biomarkers use single nucleotide polymorphism (SNP) approaches to express the significance of their results. Although, haplotype block methods are expected to play a complementary role in the future of that field. PMID:26843965

  8. 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. PMID:27421103

  9. Network Cluster Analysis of Protein–Protein Interaction Network–Identified Biomarker for Type 2 Diabetes

    PubMed Central

    Li, Zhonghui; Qiao, Zijun

    2015-01-01

    Abstract Type 2 diabetes mellitus (T2DM) is a complex disease that is caused by an impairment in the secretion of β-cell insulin and by a peripheral resistance to insulin. Most patients suffering from T2DM and from obesity exhibit insulin resistance in the muscles, liver, and fat, resulting in a reduced response of these tissues to insulin. In healthy individuals, pancreatic islet β-cells secrete insulin to regulate the increase in blood glucose levels. Once these β-cells fail to function, T2DM develops. Despite the progress achieved in this field in recent years, the genetic causes for insulin resistance and for T2DM have not yet been fully discovered. The present study aims to characterize T2DM by comparing its gene expression with that of normal controls, as well as to identify biomarkers for early T2DM. Gene expression profiles were downloaded from the Gene Expression Omnibus, and differentially expressed genes (DEGs) were identified for type 2 diabetes. Furthermore, functional analyses were conducted for the gene ontology and for the pathway enrichment. In total, 781 DEGs were identified in the T2DM samples relative to healthy controls. These genes were found to be involved in several biological processes, including cell communication, cell proliferation, cell shape, and apoptosis. We constructed a protein–protein interaction (PPI) network, and the clusters in the PPI were analyzed by using ClusterONE. Six functional genes that may play important roles in the initiation of T2DM were identified within the network. PMID:25879401

  10. Diagnostic value of KLK6 as an ovarian cancer biomarker: A meta-analysis

    PubMed Central

    YANG, FAN; HU, ZHI-DE; CHEN, YINGJIAN; HU, CHENG-JIN

    2016-01-01

    Kallikrein-related peptidase 6 (KLK6) is a new potential serum biomarker of ovarian cancer. The aim of the present study was to assess the diagnostic value of KLK6 systematically for ovarian cancer. All the selected studies regarding the changes of KLK6 in ovarian cancer were published prior to April 2015. Five studies involving 485 patients with ovarian cancer, 420 benign cysts and 245 healthy controls met the inclusion criteria. The value of sensitivity, specificity, positive-likelihood ratio (LR+), negative-likelihood ratio (LR-) and area under the receiver operating characteristic curve (ROC) were obtained. All these indices were used to evaluate the diagnostic value of KLK6 for ovarian cancer. The values of sensitivity, specificity, LR+ and LR- (95% confidence interval) of KLK6 were 0.50 (0.47–0.54), 0.91 (0.89–0.93), 7.20 (3.34–15.52) and 0.51 (0.43–0.62), respectively. The area under the summary ROC of KLK6 was 0.86. The index of Q* was 0.79. In conclusion, KLK6 showed high specificity for the diagnosis of ovarian cancer. It can improve the diagnostic accuracy of cancer antigen 125 (CA125). A combined panel of CA125 and KL K6 shows a high diagnostic efficiency for advanced ovarian cancer. Owing to the small number of studies and lack of samples, additional studies meeting the inclusion criteria are required to further analyze the diagnostic value of KLK6 for ovarian cancer. PMID:27284406

  11. 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

  12. 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

  13. The use of the glial fibrillary acidic protein (GFAP) biomarker as an early detection model of chemically induced cancer.

    PubMed

    Capó, M A; Frejo, M T; Sevil, B

    1997-01-01

    Due to the massive industrial development during recent decades, the general population today is exposed to numerous environmental chemicals not only through occupational exposure but also through the daily handling and consumption of products. In our study, we developed a carcinogenesis bioassay for industrial solvents and other pollutants by measuring the gliosis produced by these toxins. We investigated the morphological changes produced by some pollutants in astroglial rat cultures and the increase in GFAP-positive cells. Astroglial primary cultures were obtained from the cerebral hemispheres of neonatal rats. The nutrient medium consisted of Waymouth's medium supplemented with 20% fetal calf serum and antibiotics. The cultures were incubated at 37 degrees C in a humidified particle-filtered room containing an atmosphere of 5% CO2 in air. After being cultured for 22 days, toluene and a mixture of solvents (toluene, carbon tetrachloride, and 1,1,1-trichloroethylene) were applied in concentrations between 10(-4) M and 10(-6) M. Immunofluorescence staining for glial fibrillary acidic protein (GFAP), a specific marker for fibrillary astrocytes, was only occasionally positive in the monolayer of the control cultures; however, it was markedly positive in most cells maintained for 3 or 9 days and exposed to toluene and mixed solvents. This study provides a rapid in vitro assay by which cells exposed to chemicals can be examined. PMID:9256930

  14. Screening biomarkers of bladder cancer using combined miRNA and mRNA microarray analysis.

    PubMed

    Jin, Ning; Jin, Xuefei; Gu, Xinquan; Na, Wanli; Zhang, Muchun; Zhao, Rui

    2015-08-01

    Biomarkers, such as microRNAs (miRNAs) may be useful for the diagnosis of bladder cancer. In order to understand the molecular mechanisms underlying bladder cancer, differentially expressed miRNAs (DE-miRNAs) and their target genes in bladder cancer were analyzed. In the present study, miRNA and mRNA expression profiles (GSE40355) were obtained from the Gene Expression Omnibus. These consisted of healthy bladder samples (n=8) and urothelial carcinoma samples (low-grade, n=8 and high-grade, n=8). DE-miRNAs and differentially expressed genes (DEGs) were identified using the limma package and the Benjamin and Hochberg method from the multtest package in R. Target genes of DE-miRNAs were screened. Associations between DEGs were investigated using STRING, and an interaction network was constructed using Cytoscape. Functional and pathway enrichment analyses were performed for DEGs from the interaction network. 87 DE-miRNAs and 2058 DEGs were screened from low-grade bladder cancer samples, and 40 DE-miRNAs and 2477 DEGs were screened from high-grade bladder cancer samples. DE-target genes were significantly associated with the regulation of cell apoptosis. Bladder cancer, non-small cell lung cancer and pancreatic cancer biological pathways were found to be enriched. The results of the present study demonstrated that E2F transcription factor 1, which is targeted by miR-106b, and cyclin-dependent kinase inhibitor 2A (CDKN2A) and V-Erb-B2 avian erythroblastic leukemia viral oncogene homolog-2, which are targeted by miR-125b, participate in the bladder cancer pathway. In conclusion, DE-miRNAs in bladder cancer tissue samples and DE-targeted genes, such as miR-106b and CDKN2A, which were identified in the present study, may provide the basis for targeted therapy for breast cancer and enhance understanding of its pathogenesis. PMID:25955758

  15. Can Genetic Analysis of Putative Blood Alzheimer's Disease Biomarkers Lead to Identification of Susceptibility Loci?

    PubMed

    Barber, Robert C; Phillips, Nicole R; Tilson, Jeffrey L; Huebinger, Ryan M; Shewale, Shantanu J; Koenig, Jessica L; Mitchel, Jeffrey S; O'Bryant, Sid E; Waring, Stephen C; Diaz-Arrastia, Ramon; Chasse, Scott; Wilhelmsen, Kirk C

    2015-01-01

    Although 24 Alzheimer's disease (AD) risk loci have been reliably identified, a large portion of the predicted heritability for AD remains unexplained. It is expected that additional loci of small effect will be identified with an increased sample size. However, the cost of a significant increase in Case-Control sample size is prohibitive. The current study tests whether exploring the genetic basis of endophenotypes, in this case based on putative blood biomarkers for AD, can accelerate the identification of susceptibility loci using modest sample sizes. Each endophenotype was used as the outcome variable in an independent GWAS. Endophenotypes were based on circulating concentrations of proteins that contributed significantly to a published blood-based predictive algorithm for AD. Endophenotypes included Monocyte Chemoattractant Protein 1 (MCP1), Vascular Cell Adhesion Molecule 1 (VCAM1), Pancreatic Polypeptide (PP), Beta2 Microglobulin (B2M), Factor VII (F7), Adiponectin (ADN) and Tenascin C (TN-C). Across the seven endophenotypes, 47 SNPs were associated with outcome with a p-value ≤1x10(-7). Each signal was further characterized with respect to known genetic loci associated with AD. Signals for several endophenotypes were observed in the vicinity of CR1, MS4A6A/MS4A4E, PICALM, CLU, and PTK2B. The strongest signal was observed in association with Factor VII levels and was located within the F7 gene. Additional signals were observed in MAP3K13, ZNF320, ATP9B and TREM1. Conditional regression analyses suggested that the SNPs contributed to variation in protein concentration independent of AD status. The identification of two putatively novel AD loci (in the Factor VII and ATP9B genes), which have not been located in previous studies despite massive sample sizes, highlights the benefits of an endophenotypic approach for resolving the genetic basis for complex diseases. The coincidence of several of the endophenotypic signals with known AD loci may point to novel

  16. Integrated data analysis reveals uterine leiomyoma subtypes with distinct driver pathways and biomarkers

    PubMed Central

    Mehine, Miika; Kaasinen, Eevi; Heinonen, Hanna-Riikka; Mäkinen, Netta; Kämpjärvi, Kati; Sarvilinna, Nanna; Aavikko, Mervi; Vähärautio, Anna; Pasanen, Annukka; Bützow, Ralf; Heikinheimo, Oskari; Sjöberg, Jari; Pitkänen, Esa; Vahteristo, Pia; Aaltonen, Lauri A.

    2016-01-01

    needed to determine whether the candidate biomarkers presented herein can provide guidance for managing the millions of patients affected by these lesions. PMID:26787895

  17. Can Serum Glypican-3 Be a Biomarker for Effective Diagnosis of Hepatocellular Carcinoma? A Meta-Analysis of the Literature

    PubMed Central

    Yang, Sheng-Li; Fang, Xiefan; Huang, Zao-Zao; Liu, Xiang-Jie; Xiong, Zhi-Fan; Liu, Ping; Yao, Hong-Yi; Li, Chang-Hai

    2014-01-01

    Objective. This review is to evaluate the diagnostic value of serum GPC3 for hepatocellular carcinoma (HCC) due to conflicting results reported. Methods. NCBI PubMed and Embase were comprehensively searched for studies that have used serum GPC3 level as a diagnostic index for HCC. The quality of the included studies was assessed. Subgroup analyses were conducted to evaluate the sensitivity and specificity of GPC3 as a HCC marker. Statistical analysis was performed with the software STATA version 12.0. Results. A total of 22 studies were included. The qualities of included studies were relatively poor. Among them, 18 studies have shown that serum GPC3 is a specific biomarker for HCC, and the pooled sensitivity and specificity of these studies were 69 and 93%, respectively. The other 4 studies have reported conflicting results, which were not caused by races, infection status of HBV and HCV, or assay reagents but due to one common experimental design of enrolling liver cirrhosis patients as control subjects. Conclusions. This meta-analysis indicates that serum GPC3 is elevated in HCC patients compared with healthy individuals, but more studies are needed to evaluate its effectiveness to differentially diagnose HCC and liver cirrhosis. PMID:25378766

  18. Nonesterified fatty acids and spontaneous preterm birth: a factor analysis for identification of risk patterns.

    PubMed

    Catov, Janet M; Bertolet, Marnie; Chen, Yi-Fan; Evans, Rhobert W; Hubel, Carl A

    2014-05-15

    We considered that accumulation of nonesterified (free) fatty acids (NEFAs) in the first trimester of pregnancy would mark women at excess risk of spontaneous preterm birth (sPTB) and examined the interplay between NEFAs, lipids, and other markers to explore pathways to sPTB. In a case-control study nested in the Pregnancy Exposures and Preeclampsia Prevention Study (Pittsburgh, Pennsylvania, 1997-2001), we assayed NEFA levels in nonfasting serum collected at a mean gestational week of 9.4 (range, 4-20 weeks) in 115 women with sPTB (<37 weeks) and 222 women with births occurring at ≥37 weeks. C-reactive protein, total cholesterol, low-density lipoprotein and high-density lipoprotein (HDL) cholesterol, triglycerides, and uric acid were also measured. Polytomous logistic regression models were used to evaluate tertiles of NEFA levels and sPTB at <34 weeks and 34-36 weeks; factor analysis was used to characterize patterns of biomarkers. Women with NEFA levels in the highest tertile versus the lowest were 2.02 (95% confidence interval: 1.13, 3.48) times more likely to have sPTB, after adjustment for covariates. Risk of sPTB before 34 weeks was particularly high among women with high NEFA levels (odds ratio = 3.73, 95% confidence interval: 1.33, 10.44). Six biomarker patterns were identified, and 2 were associated with sPTB: 1) increasing NEFA and HDL cholesterol levels and 2) family history of gestational hypertension. NEFA levels early in pregnancy were independently associated with sPTB, particularly before 34 weeks. We also detected a novel risk pattern suggesting that NEFAs together with HDL cholesterol may be related to sPTB. PMID:24714724

  19. Biomarkers in Barrett's esophagus.

    PubMed

    Reid, Brian J; Blount, Patricia L; Rabinovitch, Peter S

    2003-04-01

    future. Biopsy repositories are now readily available for phase 3 studies that can evaluate and compare biomarkers. There are initiatives for multi-institutional Barrett's Centers of Excellence that could provide rapid progress in biomarker evaluation. In addition to new candidate biomarkers, the human genome project has provided high-throughput methodologies and methods for computer analysis of data, which can provide the volume and quality control required for clinically useful biomarkers. Currently, 17p (p53) LOH has progressed the furthest among molecular biomarkers. The authors do not recommend its routine clinical use at the present time, however. Finally, it is likely that clinicians will want to follow the results of clinical treatment-response studies and epidemiologic studies that evaluate relationship between clinical interventions or environmental risk and protective factors and surrogate endpoints, especially if the endpoints are progessing well along the phases of biomarker validation. These studies are likely to be of clinical interest because they may becoming the basis for randomized clinical trials to prevent cancer in BE. PMID:12916666

  20. Evaluation of Meterorite Amono Acid Analysis Data Using Multivariate Techniques

    NASA Technical Reports Server (NTRS)

    McDonald, G.; Storrie-Lombardi, M.; Nealson, K.

    1999-01-01

    The amino acid distributions in the Murchison carbonaceous chondrite, Mars meteorite ALH84001, and ice from the Allan Hills region of Antarctica are shown, using a multivariate technique known as Principal Component Analysis (PCA), to be statistically distinct from the average amino acid compostion of 101 terrestrial protein superfamilies.

  1. Acid Rain Analysis by Standard Addition Titration.

    ERIC Educational Resources Information Center

    Ophardt, Charles E.

    1985-01-01

    The standard addition titration is a precise and rapid method for the determination of the acidity in rain or snow samples. The method requires use of a standard buret, a pH meter, and Gran's plot to determine the equivalence point. Experimental procedures used and typical results obtained are presented. (JN)

  2. 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.

  3. 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. PMID:22070392

  4. Evaluation of the protective effectiveness of gloves from occupational exposure to 2-methoxyethanol using the biomarkers of 2-methoxyacetic acid levels in the urine and plasma

    PubMed Central

    Chang, H; Lin, C; Shih, T; Chan, H; Chou, J; Huang, Y

    2004-01-01

    Aims: To evaluate the protective effectiveness of gloves from occupational exposure to 2-methoxyethanol (2-ME); and to examine the association of 2-methoxyacetic acid (MAA) in urine and plasma collected simultaneously from low 2-ME exposure and high 2-ME exposure workers in a semiconductor copper laminate circuit board manufacturing plant. Methods: Eight hour time weighted breathing zone monitoring was performed to verify the 2-ME exposure classification between workers in regular and special operations. Urine and plasma samples were simultaneously collected from 74 exposed and 80 non-exposed workers. MAA concentrations in the urine (UMAA) and plasma (PMAA) were measured using previously published methods. Three types of gloves worn by workers (cotton, rubber, and no gloves) were recorded by direct observations in the workplace and validated by person-to-person interview. Protective effectiveness indices (PEI) were used to evaluate the glove effectiveness. Results: There was no detectable 2-ME/MAA in the air, or in urine and plasma samples in non-exposed workers. The average UMAA and PMAA in special operations were 72.63 mg/g Cr. and 29.72 mg/l, significantly higher than values in regular operations (5.44 mg/g Cr. and 2.58 mg/l, respectively). PMAA showed satisfactory correlation to UMAA in all participants from both regular and special operations. The rubber gloves provided significant reduction in 2-ME uptake, whereas cotton gloves provided little protection with fluctuating effectiveness, based on PEI estimates. Conclusions: PMAA, similar to UMAA, could serve as a specific biomarker for 2-ME exposure. Wearing impermeable rubber gloves during high risk tasks can reduce major 2-ME exposure. Other improvements, including engineering control, should be provided to diminish worker exposure to 2-ME in occupational environments. PMID:15258277

  5. 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

  6. 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

  7. 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

    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

  8. Pallidal Index as Biomarker of Manganese Brain Accumulation and Associated with Manganese Levels in Blood: A Meta-Analysis

    PubMed Central

    Huang, Shuang; Huang, Yan-Ni; Li, Xiang-Rong; Chen, Jing-Wen; Li, Yong; Luo, Hai-Lan; Wang, Fang; Ou, Shi-Yan; Jiang, Yue-Ming

    2014-01-01

    Objective The current study was designed to evaluate the sensitivity, feasibility, and effectiveness of the pallidal index (PI) serving as a biomarker of brain manganese (Mn) accumulation, which would be used as an early diagnosis criteria for Mn neurotoxicity. Methods The weighted mean difference (WMD) of the PI between control and Mn-exposed groups was estimated by using a random-effects or fixed-effects meta-analysis with 95% confidence interval (CI) performed by STATA software version 12.1. Moreover, the R package “metacor” was used to estimate correlation coefficients between PI and blood Mn (MnB). Results A total of eight studies with 281 occupationally Mn-exposed workers met the inclusion criteria. Results were pooled and performed with the Meta-analysis. Our data indicated that the PI of the exposed group was significantly higher than that of the control (WMD: 7.76; 95% CI: 4.86, 10.65; I2 = 85.7%, p<0.0001). A random effects model was used to perform meta-analysis. These findings were remarkably robust in the sensitivity analysis, and publication bias was shown in the included studies. Seven out of the eight studies reported the Pearson correlation (r) values. Significantly positive correlation between PI and MnB was observed (r = 0.42; 95% CI, 0.31, 0.52). Conclusions PI can be considered as a sensitive, feasible, effective and semi-quantitative index in evaluating brain Mn accumulation. MnB can also augment the evaluation of brain Mn accumulation levels in the near future. However, the results should be interpreted with caution. PMID:24718592

  9. 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.

  10. 2,2-bis(4-Chlorophenyl)acetic acid (DDA), a water-soluble urine biomarker of DDT metabolism in humans.

    PubMed

    Chen, Zhenshan; Maartens, Francois; Vega, Helen; Kunene, Simon; Gumede, Jonathan; Krieger, Robert I

    2009-01-01

    DDT metabolism in humans yields DDA as the principal urinary metabolite and potential exposure biomarker. A method for DDA analysis in human urine was developed using pentafluorobenzyl bromide and diisopropylethyl amine. Dried hexane extracts were reacted for 1 hour at room temperature. The stable DDA-pentafluorobenzyl-ester derivative was analyzed by gas chromatography-electron capture detector (GC-ECD) and confirmed by gas chromatography-mass spectrometry (GC-MS) in selective ion monitoring mode. The limit of detection for DDA was 0.1 microg/L urine by GC-ECD and 2 microg/L urine by GC-MS, with a relative standard deviation of 12%. Urine specimens from DDT applicators in Swaziland and South Africa were analyzed to evaluate the method. The mean DDA levels during the spray season and post season were 59 and 11 microg/L, respectively. These results must be interpreted cautiously because different groups of workers provided urine specimens in each case. The DDA urinalysis may be a feasible monitoring strategy for low-level occupational and residential DDT exposure assessment in antimalaria campaigns. PMID:19966144

  11. Biomarker Discovery for Heterogeneous Diseases

    PubMed Central

    Wallstrom, Garrick; Anderson, Karen S.; LaBaer, Joshua

    2013-01-01

    Background Modern genomic and proteomic studies reveal that many diseases are heterogeneous, comprising multiple different subtypes. The common notion that one biomarker can be predictive for all patients may need to be replaced by an understanding that each subtype has its own set of unique biomarkers, affecting how discovery studies are designed and analyzed. Methods We used Monte Carlo simulation to measure and compare the performance of eight selection methods with homogeneous and heterogeneous diseases using both single-stage and two-stage designs. We also applied the selection methods in an actual proteomic biomarker screening study of heterogeneous breast cancer cases. Results Different selection methods were optimal and more than 2-fold larger sample sizes were needed for heterogeneous diseases compared with homogeneous diseases. We also found that for larger studies, two-stage designs can achieve nearly the same statistical power as single-stage designs at significantly reduced cost. Conclusions We found that disease heterogeneity profoundly affected biomarker performance. We report sample size requirements and provide guidance on the design and analysis of biomarker discovery studies for both homogeneous and heterogeneous diseases. Impact We have shown that studies to identify biomarkers for the early detection of heterogeneous disease require different statistical selection methods and larger sample sizes than if the disease were homogeneous. These findings provide a methodological platform for biomarker discovery of heterogeneous diseases. PMID:23462916

  12. 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.

  13. Functional Connectivity Analysis of NIRS Data under Rubber Hand Illusion to Find a Biomarker of Sense of Ownership

    PubMed Central

    Arizono, Naoki

    2016-01-01

    The self-identification, which is called sense of ownership, has been researched through methodology of rubber hand illusion (RHI) because of its simple setup. Although studies with neuroimaging technique, such as fMRI, revealed that several brain areas are associated with the sense of ownership, near-infrared spectroscopy (NIRS) has not yet been utilized. Here we introduced an automated setup to induce RHI, measured the brain activity during the RHI with NIRS, and analyzed the functional connectivity so as to understand dynamical brain relationship regarding the sense of ownership. The connectivity was evaluated by multivariate Granger causality. In this experiment, the peaks of oxy-Hb on right frontal and right motor related areas during the illusion were significantly higher compared with those during the nonillusion. Furthermore, by analyzing the NIRS recordings, we found a reliable connectivity from the frontal to the motor related areas during the illusion. This finding suggests that frontal cortex and motor related areas communicate with each other when the sense of ownership is induced. The result suggests that the sense of ownership is related to neural mechanism underlying human motor control, and it would be determining whether motor learning (i.e., neural plasticity) will occur. Thus RHI with the functional connectivity analysis will become an appropriate biomarker for neurorehabilitation. PMID:27413556

  14. Galectin-3: a new biomarker for the diagnosis, analysis and prognosis of acute and chronic heart failure.

    PubMed

    Hrynchyshyn, Nataliya; Jourdain, Patrick; Desnos, Michel; Diebold, Benoit; Funck, François

    2013-10-01

    Heart failure constitutes an important medical, social and economic problem. The prevalence of heart failure is estimated as 2-3% of the adult population and increases with age, despite the scientific progress of the past decade, especially the emergence of natriuretic peptides, which have been widely used as reliable markers for diagnostic and prognostic evaluation. Identification of new reliable markers for diagnosis, analysis, prognosis of mortality and prevention of hospitalization is still necessary. Galectin-3 is a soluble β-galactoside-binding protein secreted by activated macrophages. Its main action is to bind to and activate the fibroblasts that form collagen and scar tissue, leading to progressive cardiac fibrosis. Numerous experimental studies have shown the important role of galectin-3 in cardiac remodelling due to fibrosis, independent of the fibrosis aetiology. Galectin-3 is significantly increased in chronic heart failure (acute or non-acute onset), independent of aetiology. Some clinical studies have confirmed the predictive value of galectin-3 in all-cause mortality in patients with heart failure. In our review, we aim to analyse the role of galectin-3 in the development of heart failure, its value in screening and clinical decision making and its possible predictive application in follow-up as a "routine" test in an addition to established biomarkers, such as B-type natriuretic peptide and N-terminal prohormone of B-type natriuretic peptide. PMID:24090952

  15. Fabry Disease Biomarkers: Analysis of Urinary Lyso-Gb3 and Seven Related Analogs Using Tandem Mass Spectrometry.

    PubMed

    Lavoie, Pamela; Boutin, Michel; Abaoui, Mona; Auray-Blais, Christiane

    2016-01-01

    Fabry disease is an X-linked lysosomal storage disorder caused by the absence or reduction of the enzyme α-galactosidase A activity. Currently, globotriaosylsphingosine (lyso-Gb3 ) and globotriaosylceramide (Gb3 ) are used as biomarkers to diagnose and monitor Fabry patients. However, recent metabolomic studies have shown that several glycosphingolipids are also elevated in biological fluids of affected patients and may be related to disease manifestations. This unit describes a multiplex methodology targeting the analysis of urinary lyso-Gb3 and seven structurally related analogs. A solid-phase extraction process is performed, then lyso-Gb3 and its analogs are analyzed simultaneously with an internal standard by ultra-performance liquid chromatography (UPLC) coupled to a tandem mass spectrometry (MS/MS) system. This methodology can be useful for the diagnosis of Fabry patients, including patients with cardiac variant mutations, but also to monitor the efficacy of therapeutic interventions, considering that lyso-Gb3 analogs are more elevated than lyso-Gb3 itself in urine. © 2016 by John Wiley & Sons, Inc. PMID:27367162

  16. Lower serum soluble-EGFR is a potential biomarker for metastasis of HCC demonstrated by N-glycoproteomic analysis.

    PubMed

    Hu, Heng; Gao, Lingling; Wang, Cun; Li, Yan; Ma, Huiying; Chen, Long; Qin, Jie; Liu, Binbin; Liu, Yinkun; Liang, Chunmin

    2015-05-01

    Hepatocellular carcinoma (HCC) is one of the most deadly cancers in the world due to its high metastatic potential. By using the isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative N-glycoproteomic analysis, 26 differentially expressed serum glycoproteins derived from defined stages in orthotopic xenograft tumor model were identified. Among them, expression level of soluble EGFR (sEGFR) was verified in HCC cell lines. We found that non-metastasis HCC cell lines express significantly more sEGFR than HCC cell lines with metastasis potential both in cell lysates and culture media. Serum samples from 28 non-metastatic HCC patients and 28 metastatic HCC patients were assayed. Compared with the non-metastatic HCC group, serum level of sEGFR in metastatic HCC group was statistically lower (p<0.01). All these results provide evidence that sEGFR is a potential candidate for metastasis-associated biomarkers of HCC. The related molecular mechanism deserves to be further explored. PMID:26105696

  17. Functional Connectivity Analysis of NIRS Data under Rubber Hand Illusion to Find a Biomarker of Sense of Ownership.

    PubMed

    Arizono, Naoki; Ohmura, Yuji; Yano, Shiro; Kondo, Toshiyuki

    2016-01-01

    The self-identification, which is called sense of ownership, has been researched through methodology of rubber hand illusion (RHI) because of its simple setup. Although studies with neuroimaging technique, such as fMRI, revealed that several brain areas are associated with the sense of ownership, near-infrared spectroscopy (NIRS) has not yet been utilized. Here we introduced an automated setup to induce RHI, measured the brain activity during the RHI with NIRS, and analyzed the functional connectivity so as to understand dynamical brain relationship regarding the sense of ownership. The connectivity was evaluated by multivariate Granger causality. In this experiment, the peaks of oxy-Hb on right frontal and right motor related areas during the illusion were significantly higher compared with those during the nonillusion. Furthermore, by analyzing the NIRS recordings, we found a reliable connectivity from the frontal to the motor related areas during the illusion. This finding suggests that frontal cortex and motor related areas communicate with each other when the sense of ownership is induced. The result suggests that the sense of ownership is related to neural mechanism underlying human motor control, and it would be determining whether motor learning (i.e., neural plasticity) will occur. Thus RHI with the functional connectivity analysis will become an appropriate biomarker for neurorehabilitation. PMID:27413556

  18. 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 have not been detectable in biological specimens. Recent analytical advances using tandem liquid chromatography-mass spectrometry suggest prospects for detecting these metabolites. PMID:25835046

  19. Preanalytical Confounding Factors in the Analysis of Cerebrospinal Fluid Biomarkers for Alzheimer’s Disease: The Issue of Diurnal Variation

    PubMed Central

    Cicognola, Claudia; Chiasserini, Davide; Parnetti, Lucilla

    2015-01-01

    Given the growing use of cerebrospinal fluid (CSF) beta-amyloid (Aβ) and tau as biomarkers for early diagnosis of Alzheimer’s disease (AD), it is essential that the diagnostic procedures are standardized and the results comparable across different laboratories. Preanalytical factors are reported to be the cause of at least 50% of the total variability. Among them, diurnal variability is a key issue and may have an impact on the comparability of the values obtained. The available studies on this issue are not conclusive so far. Fluctuations of CSF biomarkers in young healthy volunteers have been previously reported, while subsequent studies have not confirmed those observations in older subjects, the ones most likely to receive this test. The observed differences in circadian rhythms need to be further assessed not only in classical CSF biomarkers but also in novel forthcoming biomarkers. In this review, the existing data on the issue of diurnal variations of CSF classical biomarkers for AD will be analyzed, also evaluating the available data on new possible biomarkers. PMID:26175714

  20. Using artificial neural network tools to analyze microbial biomarker data

    SciTech Connect

    Brandt, C.C.; Schryver, J.C.; Almeida, J.S.; Pfiffner, S.M.; Palumbo, A.V.

    2004-03-17

    A major challenge in the successful implementation of bioremediation is understanding the structure of the indigenous microbial community and how this structure is affected by environmental conditions. Culture-independent approaches that use biomolecular markers have become the key to comparative microbial community analysis. However, the analysis of biomarkers from environmental samples typically generates a large number of measurements. The large number and complex nonlinear relationships among these measurements makes conventional linear statistical analysis of the data difficult. New data analysis tools are needed to help understand these data. We adapted artificial neural network (ANN) tools for relating changes in microbial biomarkers to geochemistry. ANNs are nonlinear pattern recognition methods that can learn from experience to improve their performance. We have successfully applied these techniques to the analysis of membrane lipids and nucleic acid biomarker data from both laboratory and field studies. Although ANNs typically outperform linear data analysis techniques, the user must be aware of several considerations and issues to ensure that analysis results are not misleading: (1) Overfitting, especially in small sample size data sets; (2) Model selection; (3) Interpretation of analysis results; and (4) Availability of tools (code). This poster summarizes approaches for addressing each of these issues. The objectives are: (1) Develop new nonlinear data analysis tools for relating microbial biomolecular markers to geochemical conditions; (2) Apply these nonlinear tools to field and laboratory studies relevant to the NABIR Program; and (3) Provide these tools and guidance in their use to other researchers.

  1. Analysis of fatty acid content and composition in microalgae.

    PubMed

    Breuer, Guido; Evers, Wendy A C; de Vree, Jeroen H; Kleinegris, Dorinde M M; Martens, Dirk E; Wijffels, René H; Lamers, Packo P

    2013-01-01

    A method to determine the content and composition of total fatty acids present in microalgae is described. Fatty acids are a major constituent of microalgal biomass. These fatty acids can be present in different acyl-lipid classes. Especially the fatty acids present in triacylglycerol (TAG) are of commercial interest, because they can be used for production of transportation fuels, bulk chemicals, nutraceuticals (ω-3 fatty acids), and food commodities. To develop commercial applications, reliable analytical methods for quantification of fatty acid content and composition are needed. Microalgae are single cells surrounded by a rigid cell wall. A fatty acid analysis method should provide sufficient cell disruption to liberate all acyl lipids and the extraction procedure used should be able to extract all acyl lipid classes. With the method presented here all fatty acids present in microalgae can be accurately and reproducibly identified and quantified using small amounts of sample (5 mg) independent of their chain length, degree of unsaturation, or the lipid class they are part of. This method does not provide information about the relative abundance of different lipid classes, but can be extended to separate lipid classes from each other. The method is based on a sequence of mechanical cell disruption, solvent based lipid extraction, transesterification of fatty acids to fatty acid methyl esters (FAMEs), and quantification and identification of FAMEs using gas chromatography (GC-FID). A TAG internal standard (tripentadecanoin) is added prior to the analytical procedure to correct for losses during extraction and incomplete transesterification. PMID:24121679

  2. Analysis of Fatty Acid Content and Composition in Microalgae

    PubMed Central

    Breuer, Guido; Evers, Wendy A. C.; de Vree, Jeroen H.; Kleinegris, Dorinde M. M.; Martens, Dirk E.; Wijffels, René H.; Lamers, Packo P.

    2013-01-01

    A method to determine the content and composition of total fatty acids present in microalgae is described. Fatty acids are a major constituent of microalgal biomass. These fatty acids can be present in different acyl-lipid classes. Especially the fatty acids present in triacylglycerol (TAG) are of commercial interest, because they can be used for production of transportation fuels, bulk chemicals, nutraceuticals (ω-3 fatty acids), and food commodities. To develop commercial applications, reliable analytical methods for quantification of fatty acid content and composition are needed. Microalgae are single cells surrounded by a rigid cell wall. A fatty acid analysis method should provide sufficient cell disruption to liberate all acyl lipids and the extraction procedure used should be able to extract all acyl lipid classes. With the method presented here all fatty acids present in microalgae can be accurately and reproducibly identified and quantified using small amounts of sample (5 mg) independent of their chain length, degree of unsaturation, or the lipid class they are part of. This method does not provide information about the relative abundance of different lipid classes, but can be extended to separate lipid classes from each other. The method is based on a sequence of mechanical cell disruption, solvent based lipid extraction, transesterification of fatty acids to fatty acid methyl esters (FAMEs), and quantification and identification of FAMEs using gas chromatography (GC-FID). A TAG internal standard (tripentadecanoin) is added prior to the analytical procedure to correct for losses during extraction and incomplete transesterification. PMID:24121679

  3. Analysis of volatile aldehyde biomarkers in human blood by derivatization and dispersive liquid-liquid microextraction based on solidification of floating organic droplet method by high performance liquid chromatography.

    PubMed

    Lili, Lv; Xu, Hui; Song, Dandan; Cui, Yanfang; Hu, Sheng; Zhang, Ganbing

    2010-04-16

    A new dispersive liquid-liquid microextraction based on solidification of floating organic droplet method (DLLME-SFO) was developed for the determination of volatile aldehyde biomarkers (hexanal and heptanal) in human blood samples. In the derivatization and extraction procedure, 2,4-dinitrophenylhydrazine (DNPH) as derivatization reagent and formic acid as catalyzer were injected into the sample solution for derivatization with aldehydes, then the formed hydrazones was rapidly extracted by dispersive liquid-liquid microextraction with 1-dodecanol as extraction solvent. After centrifugation, the floated droplet was solidified in an ice bath and was easily removed for analysis. The effects of various experimental parameters on derivatization and extraction conditions were studied, such as the kind and volume of extraction solvent and dispersive solvent, the amount of derivatization reagent, derivatization temperature and time, extraction time and salt effect. The limit of detections (LODs) for hexanal and heptanal were 7.90 and 2.34nmolL(-1), respectively. Good reproducibility and recovery of the method were also obtained. The proposed method is an alternative approach to the quantification of volatile aldehyde biomarkers in complex biological samples, being more rapid and simpler and providing higher sensitivity compared with the traditional dispersive liquid-liquid microextraction (DLLME) methods. PMID:20181347

  4. Identification of candidate diagnostic biomarkers for adolescent idiopathic scoliosis using UPLC/QTOF-MS analysis: a first report of lipid metabolism profiles

    PubMed Central

    Sun, Zhi-jian; Jia, Hong-mei; Qiu, Gui-xing; Zhou, Chao; Guo, Shigong; Zhang, Jian-guo; Shen, Jian-xiong; Zhao, Yu; Zou, Zhong-mei

    2016-01-01

    Adolescent idiopathic scoliosis (AIS) is a complex spine deformity, affecting approximately 1–3% adolescents. Earlier diagnosis could increase the likelihood of successful conservative treatment and hence reduce the need for surgical intervention. We conducted a serum metabonomic study to explore the potential biomarkers of AIS for early diagnosis. Serum metabolic profiles were firstly explored between 30 AIS patients and 31 healthy controls by ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Then, the candidate metabolites were validated in an independent cohort including 31 AIS patients and 44 controls. The results showed that metabolic profiles of AIS patients generally deviated from healthy controls in both the discovery set and replication set. Seven differential metabolites were identified as candidate diagnostic biomarkers, including PC(20:4), 2-hexenoylcarnitine, beta-D-glucopyranuronicacid, DG(38:9), MG(20:3), LysoPC(18:2) and LysoPC(16:0). These candidate metabolites indicated disrupted lipid metabolism in AIS, including glycerophospholipid, glycerolipid and fatty acid metabolism. Elevated expressions of adipose triglyceride lipase and hormone sensitive lipase in adipose tissue further corroborated our findings of increased lipid metabolism in AIS. Our findings suggest that differential metabolites discovered in AIS could be used as potential diagnostic biomarkers and that lipid metabolism plays a role in the pathogenesis of AIS. PMID:26928931

  5. Lipid biomarkers provide evolutionary signposts for the oldest known cases of tuberculosis.

    PubMed

    Lee, Oona Y-C; Wu, Houdini H T; Besra, Gurdyal S; Rothschild, Bruce M; Spigelman, Mark; Hershkovitz, Israel; Bar-Gal, Gila Kahila; Donoghue, Helen D; Minnikin, David E

    2015-06-01

    Studies on the evolution of tuberculosis, and the influence of this disease on human and animal development and interaction, require the accumulation of indisputable biomarker evidence. Ideally, the determination of full genomes would provide all the necessary information, but for very old specimens DNA preservation may be compromised and only limited DNA amplification may be a possibility. Mycobacterium tuberculosis is characterised by the presence of unusual cell envelope lipids, with specific biomarker potential. Lipid biomarker recognition has been decisive in pinpointing the oldest known cases of human and animal tuberculosis; the former are a woman and child from a pre-pottery settlement at Atlit-Yam, Israel (∼9,000 ka) and the latter is an extinct Bison antiquus from Natural Trap Cave, Wyoming (∼17,000 ka). Including some new data, it is demonstrated how analysis of a combination of mycolic, mycocerosic and mycolipenic acid and phthiocerol biomarkers provide incontrovertible evidence for tuberculosis in these landmark specimens. PMID:25797611

  6. Surrogate end-point biomarker analysis in a retinol chemoprevention trial in current and former smokers with bronchial dysplasia.

    PubMed

    Lam, Stephen; Xu, Xiaochun; Parker-Klein, Helga; Le Riche, Jean C; Macaulay, Calum; Guillaud, Martial; Coldman, Andy; Gazdar, Adi; Lotan, Reuben

    2003-12-01

    Epidemiological studies suggested that vitamin A may be protective against lung cancer, however, recent chemoprevention trials with beta-carotene, a precursor of vitamin A, demonstrated enhancement of lung carcinogenesis among smokers. Whether vitamin A is beneficial or harmful in chemoprevention of lung cancer in smokers has not been resolved. This study was designed to determine the effect of retinol alone in current and former smokers using bronchial dysplasia, nuclear morphometry and retinoic acid receptor-beta (RAR-beta) mRNA expression as surrogate end-point biomarkers (SEBs). Eighty-one current or former smokers with a smoking history of >/=30 pack-years were randomized to receive either placebo or retinol (50,000 IU per day) for six months. Fluorescence bronchoscopy was performed prior to treatment to localize areas suggestive of dysplasia. At least 4 bronchial biopsies were taken per subject including at least two biopsies from apparently normal areas. The same areas were precisely re-biopsied after 6 months. Any new areas suggestive of dysplasia were also biopsied. Changes in the SEBs were assessed before and after treatment. At baseline, the frequency of biopsies negative for RAR-beta expression was: normal (23%), hyperplasia (28%), metaplasia (41%), mild dysplasia (41%), and moderate/severe dysplasia (44%). There was no significant difference in the regression rate between the retinol and placebo groups using histopathology and nuclear morphometry as SEBs. The likelihood of regression was found to be lower in those who continued to smoke during the study (OR=1.86 for those smoking >10 cigarettes per day, p=0.084 to OR=0.95, p=0.26 for those smoking 20+ per day compared to ex-smokers). Retinol was not effective in the up-regulation of RAR-beta in lesions with bronchial dysplasia. We postulate that the lack of effect of retinol on RAR-beta expression among individuals who continued to smoke while taking retinol may be due to suppressive effect of tobacco

  7. Uptake of algal carbon and the likely 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. M.; Schwartz, M.; Cowie, G.; Whitcraft, C.; Levin, L.; Dick, J. R.; Pond, D. W.

    2014-07-01

    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-labelled 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-labelled and used to simulate a pulse of phytoplankton in two complementary experiments. A lander system was used for in situ incubations at 140 m water depth and for 2.5 days in duration. Shipboard laboratory incubations of cores collected at 140 m incorporated an oxystat system to maintain ambient dissolved oxygen concentrations and were terminated after 5 days. Uptake of diatoms was rapid, with a 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 acid" is often abundant in benthic fauna, yet

  8. Individual and simultaneous determination of uric acid and ascorbic acid by flow injection analysis.

    PubMed

    Almuaibed, A M; Townshend, A

    1992-11-01

    Flow injection methods for the individual and simultaneous determination of ascorbic acid and uric acid are proposed. A spectrophotometer and a miniamperometric detector are connected in sequence. The calibration graphs for uric acid obtained by measuring its absorbance at 293 nm and its current at +0.6 V are linear up to at least 80 and 70 mug/ml, respectively, with an rsd (n = 10) of 1 % for both methods at mid-range concentrations. The calibration graph for ascorbic acid with amperometric detection is linear up to 80 mg/l. with an rsd (n = 10) of 0.8% at 30 mg/l. The simultaneous determination of uric acid and ascorbic acid is based on measurement of the absorbance of uric acid at 393 nm and amperometric determination of both analytes at +0.6 V. The average relative errors of the analysis of binary mixtures of uric acid and ascorbic acid are 2.2 and 4.2%, respectively. PMID:18965554

  9. Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer.

    PubMed

    Győrffy, Balázs; Surowiak, Pawel; Budczies, Jan; Lánczky, András

    2013-01-01

    In the last decade, optimized treatment for non-small cell lung cancer had lead to improved prognosis, but the overall survival is still very short. To further understand the molecular basis of the disease we have to identify biomarkers related to survival. Here we present the development of an online tool suitable for the real-time meta-analysis of published lung cancer microarray datasets to identify biomarkers related to survival. We searched the caBIG, GEO and TCGA repositories to identify samples with published gene expression data and survival information. Univariate and multivariate Cox regression analysis, Kaplan-Meier survival plot with hazard ratio and logrank P value are calculated and plotted in R. The complete analysis tool can be accessed online at: www.kmplot.com/lung. All together 1,715 samples of ten independent datasets were integrated into the system. As a demonstration, we used the tool to validate 21 previously published survival associated biomarkers. Of these, survival was best predicted by CDK1 (p<1E-16), CD24 (p<1E-16) and CADM1 (p = 7E-12) in adenocarcinomas and by CCNE1 (p = 2.3E-09) and VEGF (p = 3.3E-10) in all NSCLC patients. Additional genes significantly correlated to survival include RAD51, CDKN2A, OPN, EZH2, ANXA3, ADAM28 and ERCC1. In summary, we established an integrated database and an online tool capable of uni- and multivariate analysis for in silico validation of new biomarker candidates in non-small cell lung cancer. PMID:24367507

  10. An Optimization-Driven Analysis Pipeline to Uncover Biomarkers and Signaling Paths: Cervix Cancer

    PubMed Central

    Lorenzo, Enery; Camacho-Caceres, Katia; Ropelewski, Alexander J.; Rosas, Juan; Ortiz-Mojer, Michael; Perez-Marty, Lynn; Irizarry, Juan; Gonzalez, Valerie; Rodríguez, Jesús A.; Cabrera-Rios, Mauricio; Isaza, Clara

    2015-01-01

    Establishing how a series of potentially important genes might relate to each other is relevant to understand the origin and evolution of illnesses, such as cancer. High-throughput biological experiments have played a critical role in providing information in this regard. A special challenge, however, is that of trying to conciliate information from separate microarray experiments to build a potential genetic signaling path. This work proposes a two-step analysis pipeline, based on optimization, to approach meta-analysis aiming to build a proxy for a genetic signaling path. PMID:26388997

  11. Urinary Biomarkers of Brain Diseases

    PubMed Central

    An, Manxia; Gao, Youhe

    2016-01-01

    Biomarkers are the measurable changes associated with a physiological or pathophysiological process. Unlike blood, urine is not subject to homeostatic mechanisms. Therefore, greater fluctuations could occur in urine than in blood, better reflecting the changes in human body. The roadmap of urine biomarker era was proposed. Although urine analysis has been attempted for clinical diagnosis, and urine has been monitored during the progression of many diseases, particularly urinary system diseases, whether urine can reflect brain disease status remains uncertain. As some biomarkers of brain diseases can be detected in the body fluids such as cerebrospinal fluid and blood, there is a possibility that urine also contain biomarkers of brain diseases. This review summarizes the clues of brain diseases reflected in the urine proteome and metabolome. PMID:26751805

  12. Integrated miRNA–risk gene–pathway pair network analysis provides prognostic biomarkers for gastric cancer

    PubMed Central

    Cai, Hui; Xu, Jiping; Han, Yifang; Lu, Zhengmao; Han, Ting; Ding, Yibo; Ma, Liye

    2016-01-01

    Purpose This study aimed to identify molecular prognostic biomarkers for gastric cancer. Methods mRNA and miRNA expression profiles of eligible gastric cancer and control samples were downloaded from Gene Expression Omnibus to screen the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs), using MetaDE and limma packages, respectively. Target genes of the DEmiRs were also collected from both predictive and experimentally validated target databases of miRNAs. The overlapping genes between selected targets and DEGs were identified as risk genes, followed by functional enrichment analysis. Human pathways and their corresponding genes were downloaded from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database for the expression analysis of each pathway in gastric cancer samples. Next, co-pathway pairs were selected according to the Pearson correlation coefficients. Finally, the co-pathway pairs, miRNA–target pairs, and risk gene–pathway pairs were merged into a complex interaction network, the most important nodes (miRNAs/target genes/co-pathway pairs) of which were selected by calculating their degrees. Results Totally, 1,260 DEGs and 144 DEmiRs were identified. There were 336 risk genes found in the 9,572 miRNA–target pairs. Judging from the pathway expression files, 45 co-pathway pairs were screened out. There were 1,389 interactive pairs and 480 nodes in the integrated network. Among all nodes in the network, focal adhesion/extracellular matrix–receptor interaction pathways, CALM2, miR-19b, and miR-181b were the hub nodes with higher degrees. Conclusion CALM2, hsa-miR-19b, and hsa-miR-181b might be used as potential prognostic targets for gastric cancer. PMID:27284247

  13. Identification of five candidate lung cancer biomarkers by proteomics analysis of conditioned media of four lung cancer cell lines.

    PubMed

    Planque, Chris; Kulasingam, Vathany; Smith, Chris R; Reckamp, Karen; Goodglick, Lee; Diamandis, Eleftherios P

    2009-12-01

    Detection of lung cancer at an early stage is necessary for successful therapy and improved survival rates. We performed a bottom-up proteomics analysis using a two-dimensional LC-MS/MS strategy on the conditioned media of four lung cancer cell lines of different histological backgrounds (non-small cell lung cancer: H23 (adenocarcinoma), H520 (squamous cell carcinoma), and H460 (large cell carcinoma); small cell lung cancer: H1688) to identify secreted or membrane-bound proteins that could be useful as novel lung cancer biomarkers. Proteomics analysis of the four conditioned media allowed identification of 1,830 different proteins (965, 871, 726, and 847 from H1688, H23, H460, and H520, respectively). All proteins were assigned a subcellular localization, and 38% were classified as extracellular or membrane-bound. We successfully identified the internal control proteins (also detected by ELISA), kallikrein-related peptidases 14 and 11, and IGFBP2. We also identified known or putative lung cancer tumor markers such as squamous cell carcinoma antigen, carcinoembryonic antigen, chromogranin A, creatine kinase BB, progastrin-releasing peptide, neural cell adhesion molecule, and tumor M2-PK. To select the most promising candidates for validation, we performed tissue specificity assays, functional classifications, literature searches for association to cancer, and a comparison of our proteome with the proteome of lung-related diseases and serum. Five novel lung cancer candidates, ADAM-17, osteoprotegerin, pentraxin 3, follistatin, and tumor necrosis factor receptor superfamily member 1A were preliminarily validated in the serum of patients with lung cancer and healthy controls. Our results demonstrate the utility of this cell culture proteomics approach to identify secreted and shed proteins that are potentially useful as serological markers for lung cancer. PMID:19776420

  14. Identification of Five Candidate Lung Cancer Biomarkers by Proteomics Analysis of Conditioned Media of Four Lung Cancer Cell Lines*

    PubMed Central

    Planque, Chris; Kulasingam, Vathany; Smith, Chris R.; Reckamp, Karen; Goodglick, Lee; Diamandis, Eleftherios P.

    2009-01-01

    Detection of lung cancer at an early stage is necessary for successful therapy and improved survival rates. We performed a bottom-up proteomics analysis using a two-dimensional LC-MS/MS strategy on the conditioned media of four lung cancer cell lines of different histological backgrounds (non-small cell lung cancer: H23 (adenocarcinoma), H520 (squamous cell carcinoma), and H460 (large cell carcinoma); small cell lung cancer: H1688) to identify secreted or membrane-bound proteins that could be useful as novel lung cancer biomarkers. Proteomics analysis of the four conditioned media allowed identification of 1,830 different proteins (965, 871, 726, and 847 from H1688, H23, H460, and H520, respectively). All proteins were assigned a subcellular localization, and 38% were classified as extracellular or membrane-bound. We successfully identified the internal control proteins (also detected by ELISA), kallikrein-related peptidases 14 and 11, and IGFBP2. We also identified known or putative lung cancer tumor markers such as squamous cell carcinoma antigen, carcinoembryonic antigen, chromogranin A, creatine kinase BB, progastrin-releasing peptide, neural cell adhesion molecule, and tumor M2-PK. To select the most promising candidates for validation, we performed tissue specificity assays, functional classifications, literature searches for association to cancer, and a comparison of our proteome with the proteome of lung-related diseases and serum. Five novel lung cancer candidates, ADAM-17, osteoprotegerin, pentraxin 3, follistatin, and tumor necrosis factor receptor superfamily member 1A were preliminarily validated in the serum of patients with lung cancer and healthy controls. Our results demonstrate the utility of this cell culture proteomics approach to identify secreted and shed proteins that are potentially useful as serological markers for lung cancer. PMID:19776420

  15. Effects of Exercise Training on Cardiorespiratory Fitness and Biomarkers of Cardiometabolic Health: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

    PubMed Central

    Lin, Xiaochen; Zhang, Xi; Guo, Jianjun; Roberts, Christian K; McKenzie, Steve; Wu, Wen-Chih; Liu, Simin; Song, Yiqing

    2015-01-01

    Background Guidelines recommend exercise for cardiovascular health, although evidence from trials linking exercise to cardiovascular health through intermediate biomarkers remains inconsistent. We performed a meta-analysis of randomized controlled trials to quantify the impact of exercise on cardiorespiratory fitness and a variety of conventional and novel cardiometabolic biomarkers in adults without cardiovascular disease. Methods and Results Two researchers selected 160 randomized controlled trials (7487 participants) based on literature searches of Medline, Embase, and Cochrane Central (January 1965 to March 2014). Data were extracted using a standardized protocol. A random-effects meta-analysis and systematic review was conducted to evaluate the effects of exercise interventions on cardiorespiratory fitness and circulating biomarkers. Exercise significantly raised absolute and relative cardiorespiratory fitness. Lipid profiles were improved in exercise groups, with lower levels of triglycerides and higher levels of high-density lipoprotein cholesterol and apolipoprotein A1. Lower levels of fasting insulin, homeostatic model assessment–insulin resistance, and glycosylated hemoglobin A1c were found in exercise groups. Compared with controls, exercise groups had higher levels of interleukin-18 and lower levels of leptin, fibrinogen, and angiotensin II. In addition, we found that the exercise effects were modified by age, sex, and health status such that people aged <50 years, men, and people with type 2 diabetes, hypertension, dyslipidemia, or metabolic syndrome appeared to benefit more. Conclusions This meta-analysis showed that exercise significantly improved cardiorespiratory fitness and some cardiometabolic biomarkers. The effects of exercise were modified by age, sex, and health status. Findings from this study have significant implications for future design of targeted lifestyle interventions. PMID:26116691