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Sample records for chromatography mutation analysis

  1. Denaturing high-performance liquid chromatography mutation analysis in patients with reduced Protein S levels

    DEFF Research Database (Denmark)

    Bathum, Lise; Münster, Anna-Marie; Nybo, Mads;

    2008-01-01

    diagnosis and risk estimation. The aim was to design a high-throughput genetic analysis based on denaturing high-performance liquid chromatography to identify sequence variations in the gene coding for Protein S. PATIENTS: In total, 55 patients referred to the Section of Thrombosis and Haemostasis, Odense...... were missense mutations (c.932T>G; c.1367A>G; c.1378T>C). Furthermore, four patients carried the same mutation (c.1045G>A), while two carried the Heerlen mutation (c.1378T>C). CONCLUSIONS: The reported method will be useful for rapidly detecting sequence variations in the gene coding for Protein S...

  2. Comparison of fluorescent single-strand conformation polymorphism analysis and denaturing high-performance liquid chromatography for detection of EXT1 and EXT2 mutations in hereditary multiple exostoses.

    Science.gov (United States)

    Dobson-Stone, C; Cox, R D; Lonie, L; Southam, L; Fraser, M; Wise, C; Bernier, F; Hodgson, S; Porter, D E; Simpson, A H; Monaco, A P

    2000-01-01

    EXT1 and EXT2 are two genes responsible for the majority of cases of hereditary multiple exostoses (HME), a dominantly inherited bone disorder. In order to develop an efficient screening strategy for mutations in these genes, we performed two independent blind screens of EXT1 and EXT2 in 34 unrelated patients with HME, using denaturing high-performance liquid chromatography (DHPLC) and fluorescent single-strand conformation polymorphism analysis (F-SSCP). The mutation likely to cause HME was found in 29 (85%) of the 34 probands: in 22 of these (76%), the mutation was in EXT1; seven patients (24%) had EXT2 mutations. Nineteen of these disease mutations have not been previously reported. Of the 42 different amplicon variants identified in total in the cohort, 40 were detected by DHPLC and 39 by F-SSCP. This corresponds to mutation detection efficiencies of 95% and 93% respectively. We have also found that we can confidently distinguish between different sequence variants in the same fragment using F-SSCP but not DHPLC. In light of this, and the similarly high sensitivities of the two techniques, we propose to continue screening with F-SSCP. PMID:10713884

  3. Rapid Mutation Scanning of Genes Associated with Familial Cancer Syndromes Using Denaturing High-Performance Liquid Chromatography

    Directory of Open Access Journals (Sweden)

    Deborah J. Marsh

    2001-01-01

    Full Text Available Germline mutations in tumor suppressor genes, or less frequently oncogenes, have been identified in up to 19 familial cancer syndromes including Li-Fraumeni syndrome, familial paraganglioma, familial adenomatous polyposis coli and breast and ovarian cancers. Multiple genes have been associated with some syndromes as approximately 26 genes have been linked to the development of these familial cancers. With this increased knowledge of the molecular determinants of familial cancer comes an equal expectation for efficient genetic screening programs. We have trialled denaturing highperformance liquid chromatography (dHPLC as a tool for rapid germline mutation scanning of genes implicated in three familial cancer syndromes - Cowden syndrome (PTEN mutation, multiple endocrine neoplasia type 2 (RET mutation and von Hippel-Lindau disease (VHL mutation. Thirty-two mutations, including 21 in PTEN, 9 in RET plus a polymorphism, and 2 in VHL, were analyzed using the WAVE DNA fragment analysis system with 100% detection efficiency. In the case of the tumor suppressor gene PTEN, mutations were scattered along most of the gene. However, mutations in the RET proto-oncogene associated with multiple endocrine neoplasia type 2 were limited to specific clusters or “hot spots”. The use of GC-clamped primers to scan for mutations scattered along PTEN exons was shown to greatly enhance the sensitivity of detection of mutant hetero- and homoduplex peaks at a single denaturation temperature compared to fragments generated using non-GC-clamped primers. Thus, when scanning tumor suppressor genes for germline mutation using dHPLC, the incorporation of appropriate GCclamped primers will likely increase the efficiency of mutation detection.

  4. Discordant diagnoses obtained by different approaches in antithrombin mutation analysis

    DEFF Research Database (Denmark)

    Feddersen, Søren; Nybo, Mads

    OBJECTIVES: In hereditary antithrombin (AT) deficiency it is important to determine the underlying mutation since the future risk of thromboembolism varies considerably between mutations. DNA investigations are in general thought of as flawless and irrevocable, but the diagnostic approach can be...... critical. We therefore investigated mutation results in the AT gene, SERPINC1, with two different approaches. DESIGN AND METHODS: Sixteen patients referred to the Centre for Thrombosis and Haemostasis, Odense University Hospital, with biochemical indications of AT deficiency, but with a negative denaturing...... high-performance liquid chromatography (DHPLC) mutation screening (routine approach until recently) were included. As an alternative mutation analysis, direct sequencing of all exons and exon-intron boundaries without pre-selection by DHPLC was performed. RESULTS: Out of sixteen patients with a...

  5. Christhin: Quantitative Analysis of Thin Layer Chromatography

    CERN Document Server

    Barchiesi, Maximiliano; Renaudo, Carlos; Rossi, Pablo; Pramparo, María de Carmen; Nepote, Valeria; Grosso, Nelson Ruben; Gayol, María Fernanda

    2012-01-01

    Manual for Christhin 0.1.36 Christhin (Chromatography Riser Thin) is software developed for the quantitative analysis of data obtained from thin-layer chromatographic techniques (TLC). Once installed on your computer, the program is very easy to use, and provides data quickly and accurately. This manual describes the program, and reading should be enough to use it properly.

  6. A Comparison Between Denaturing Gradient Gel Electrophoresis and Denaturing High Performance Liquid Chromatography in Detecting Mutations in Genes Associated with Hereditary Non-Polyposis Colorectal Cancer (HNPCC and the Identification of 9 New Mutations Previously Unidentified by DGGE

    Directory of Open Access Journals (Sweden)

    Meldrum Cliff J

    2003-12-01

    Full Text Available Abstract Denaturing high performance liquid chromatography is a relatively new method by which heteroduplex structures formed during the PCR amplification of heterozygote samples can be rapidly identified. The use of this technology for mutation detection in hereditary non-polyposis colorectal cancer (HNPCC has the potential to appreciably shorten the time it takes to analyze genes associated with this disorder. Prior to acceptance of this method for screening genes associated with HNPCC, assessment of the reliability of this method should be performed. In this report we have compared mutation and polymorphism detection by denaturing gradient gel electrophoresis (DGGE with denaturing high performance liquid chromatography (DHPLC in a set of 130 families. All mutations/polymorphisms representing base substitutions, deletions, insertions and a 23 base pair inversion were detected by DHPLC whereas DGGE failed to identify four single base substitutions and a single base pair deletion. In addition, we show that DHPLC has been used for the identification of 5 different mutations in exon 7 of hMSH2 that could not be detected by DGGE. From this study we conclude that DHPLC is a more effective and rapid alternative to the detection of mutations in hMSH2 and hMLH1 with the same or better accuracy than DGGE. Furthermore, this technique offers opportunities for automation, which have not been realised for the majority of other methods of gene analysis.

  7. Germline mutation analysis of MLH1 and MSH2 in Malaysian Lynch syndrome patients

    Institute of Scientific and Technical Information of China (English)

    Mohd Nizam Zahary; Gurjeet Kaur; Muhammad Radzi Abu Hassan; Harjinder Singh; Venkatesh R Naik; Ravindran Ankathil

    2012-01-01

    AIM:To investigate the protein expression profile of mismatch repair (MMR) genes in suspected cases of Lynch syndrome and to characterize the associated germline mutations.METHODS:Immunohistochemical analysis of tumor samples was performed to determine the protein expression profile of MMR protein.Germline mutation screening was carried out on peripheral blood samples.The entire exon regions of MLH1 and MSH2 genes were amplified by polymerase chain reaction,screened by denaturing high performance liquid chromatography (dHPLC) and analyzed by DNA sequencing to characterize the germline mutations.RESULTS:Three out of 34 tissue samples (8.8%) and four out of 34 tissue samples (11.8%) showed loss of nuclear staining by immunohistochemistry,indicating the absence of MLH1 and MSH2 protein expression in carcinoma cells,respectively.dHPLC analysis followed by DNA sequencing showed these samples to have germline mutations of MSH2 gene.However,no deleterious mutations were identified in any of the 19 exons or coding regions of MLH1 gene,but we were able to identify MLH1 promoter polymorphism,-93G >A (rs1800734),in 21 out of 34 patients (61.8%).We identified one novel mutation,transversion mutation c.2005G > C,which resulted in a missense mutation (Gly669Arg),a transversion mutation in exon 1,c.142G > T,which resulted in a nonsense mutation (Glu48Stop)and splice-site mutation,c.2006-6T > C,which was adjacent to exon 13 of MSH2 gene.CONCLUSION:Germline mutations were identified in four Malaysian Lynch syndrome patients.Immunohistochemical analysis of tumor tissue proved to be a good pre-screening test before proceeding to germline mutation analysis of DNA MMR genes.

  8. Targeted analysis of glycomics liquid chromatography/mass spectrometry data

    OpenAIRE

    Dreyfuss, Jonathan M.; Jacobs, Christopher; Gindin, Yevgeniy; Benson, Gary; Staples, Gregory O.; Zaia, Joseph

    2010-01-01

    Hydrophilic interaction chromatography (HILIC) liquid chromatography/mass spectrometry (LC/MS) is appropriate for all native and reductively aminated glycan classes. HILIC carries the advantage that retention times (RTs) vary predictably according to oligosaccharide composition. Chromatographic conditions are compatible with sensitive and reproducible glycomics analysis of large numbers of samples. The data are extremely useful for quantitative profiling of glycans expressed in biological tis...

  9. Liquid chromatography - mass spectrometry analysis of pharmaceuticals

    International Nuclear Information System (INIS)

    The drugs represent mostly non-volatile and thermally labile solutes, often available only in small amounts like it is in case of radiopharmaceuticals. Therefor, the favourable separation techniques for such compounds are HPLC, capillary electrophoresis and also TLC 1. Liquid chromatography with mass spectrometric detector (LC/MS) is especially powerful for their microanalysis. Mass spectrometry separating the ions in high vacuum was presumably used as detector for gas chromatography effluent but the on-line coupling with liquid eluant flow 0.1-1 mL/min is far more challenging. New types of ion sources were constructed for simultaneous removal of solvent and ionisation of solutes at atmospheric pressure (API). At present, a relatively wide choice of successfully designed commercial equipment is available either for small organic molecules and larger biomolecules (Perkin-Elmer, Agilent, Jeol, Bruker Daltonics, ThermoQuest, Shimadzu). The features of the LC/MS systems are presented. LC/MS as a new quality control tool for [F-18]fluorodeoxyglucose (FDG) radiopharmaceutical, which has became the most spread radiopharmaceutical for positron emission tomography (PET), was proposed. Other applications of the LC/MS are reviewed. (author)

  10. Using Single Drop Microextraction for Headspace Analysis with Gas Chromatography

    Science.gov (United States)

    Riccio, Daniel; Wood, Derrick C.; Miller, James M.

    2008-01-01

    Headspace (HS) gas chromatography (GC) is commonly used to analyze samples that contain non-volatiles. In 1996, a new sampling technique called single drop microextraction, SDME, was introduced, and in 2001 it was applied to HS analysis. It is a simple technique that uses equipment normally found in the undergraduate laboratory, making it ideal…

  11. Automotive gasoline quality analysis by gas chromatography: study of adulteration

    Energy Technology Data Exchange (ETDEWEB)

    Moreira, L.S.; Azevedo, D.A. [Dept. de Quimica Organica, Univ. Federal do Rio de Janeiro, Ilha do Fundao, Rio de Janeiro, RJ (Brazil); d' Avila, L.A. [Dept. de Processos Organicos, Univ. Federal do Rio de Janeiro, Ilha do Fundao, Rio de Janeiro, RJ (Brazil)

    2003-10-01

    The addition of organic solvents (light aliphatic, heavy aliphatic and aromatic hydrocarbons) in Brazilian gasoline is unfortunately very frequent, and this illicit practice impares gasoline quality. Gas chromatography (GC) and gas chromatography coupled to mass spectrometry (GC-MS) analyses can be used as a procedure to improve the detection of adulterated gasoline. The results showed that adulterated samples and also the type of organic solvent used in adulteration can be detected by comparison of chromatographic profiles (standard samples versus adulterated samples). However, a single GC analysis can detect an adulterated gasoline, and so decrease the number of adulterated samples approved as presenting good quality. (orig.)

  12. Application of fast liquid chromatography for antioxidants analysis

    Directory of Open Access Journals (Sweden)

    Agnieszka Drożdżyńska

    2012-03-01

    Full Text Available Background. An intensive development of the Fast Liquid Chromatography (FLC has been recently observed. It makes possible to reduce time analysis and improve resolution as well as sensitivity. The aim of this study was to separate the chosen antioxidants optimization using the FLC method. Material  and methods. The three various procedures for antioxidants analysis were compared. Mobile phases containing aqueous solution of formic acid, acetic acid, acetonitrile, and methanol were tested. Limit of detection (LOD, limit of quantification (LOQ, linearity and repeatability of each procedures were determined. Results. Developed procedure enabled to separate all analytes and allowed to get low LOD levels and good repeatability. This procedure was used for antioxidants analysis in buckwheat and buckwheat products. Conclusion. Fast Liquid Chromatography allows to  reduce time analysis and  obtain good  validation parameters.

  13. Application of fast liquid chromatography for antioxidants analysis

    OpenAIRE

    Agnieszka Drożdżyńska; Krzysztof Dziedzic; Alicja Kośmider; Katarzyna Leja; Katarzyna Czaczyk; Danuta Górecka

    2012-01-01

    Background. An intensive development of the Fast Liquid Chromatography (FLC) has been recently observed. It makes possible to reduce time analysis and improve resolution as well as sensitivity. The aim of this study was to separate the chosen antioxidants optimization using the FLC method. Material  and methods. The three various procedures for antioxidants analysis were compared. Mobile phases containing aqueous solution of formic acid, acetic acid, acetonitrile, and methanol were t...

  14. KIT mutation analysis in mast cell neoplasms

    DEFF Research Database (Denmark)

    Arock, M; Sotlar, K; Akin, C;

    2015-01-01

    Although acquired mutations in KIT are commonly detected in various categories of mastocytosis, the methodologies applied to detect and quantify the mutant type and allele burden in various cells and tissues are poorly defined. We here propose a consensus on methodologies used to detect KIT mutat...

  15. Multiple-injection high-throughput gas chromatography analysis.

    Science.gov (United States)

    Schafer, Wes; Wang, Heather; Welch, Christopher J

    2016-08-01

    Multiple-injection techniques have been shown to be a simple way to perform high-throughput analysis where the entire experiment resides in a single chromatogram, simplifying the data analysis and interpretation. In this study, multiple-injection techniques are applied to gas chromatography with flame ionization detection and mass detection to significantly increase sample throughput. The unique issues of implementing a traditional "Fast" injection mode of multiple-injection techniques with gas chromatography and mass spectrometry are discussed. Stacked injections are also discussed as means to increase the throughput of longer methods where mass detection is unable to distinguish between analytes of the same mass and longer retentions are required to resolve components of interest. Multiple-injection techniques are shown to increase instrument throughput by up to 70% and to simplify data analysis, allowing hits in multiple parallel experiments to be identified easily. PMID:27292909

  16. Mutation analysis and prenatal diagnosis of EXT1 gene mutations in Chinese patients with multiple osteochondromas

    Institute of Scientific and Technical Information of China (English)

    ZHU Hai-yan; HU Ya-li; YANG Ying; WU Xing; ZHU Rui-fang; ZHU Xiang-yu; DUAN Hong-lei; ZHANG Ying; ZHOU Jin-yong

    2011-01-01

    Background Multiple osteochondromas (MO), an inherited autosomal dominant disorder, is characterized by the presence of multiple exostoses on the long bones. MO is caused by mutations in the EXT1 or EXT2 genes which encode glycosyltransferases implicated in heparin sulfate biosynthesis.Methods In this study, efforts were made to identify the underlying disease-causing mutations in patients from two MO families in China.Results Two novel EXT1 gene mutations were identified and no mutation was found in EXT2 gene. The mutation c.497T>A in exon 1 of the EXT1 gene was cosegregated with the disease phenotype in family 1 and formed a stop codon at amino acid site 166. The fetus of the proband was diagnosed negative. In family 2, the mutation c. 1430-1431delCC in exon 6 of the EXT1 gene would cause frameshift and introduce a premature stop codon after the reading frame being open for 42 amino acids. The fetus of this family inherited this mutation from the father.Conclusions Mutation analysis of two MO families in this study demonstrates its further application in MO genetic counseling and prenatal diagnosis.

  17. Phytonutrient analysis of gamma rays mutated tomato

    International Nuclear Information System (INIS)

    Full text: With increasing of world population and reducing land resources, good quality food production has become even more important. Mutant breeding is an inevitable way for producing of vegetable crops which are sustainable under varied agro-climatic conditions and have high nutrient capacity. The use of nuclear techniques in plant breeding has been mostly directed for inducing mutations. Since the use of ionizing radiation, such as X-rays, gamma rays, e-beam and neutrons for inducing variation, has become an established technology. Induced mutations have been used in the economic value improvement of major crops such as cereals and solanaceae, which are seed propagated. The economic value of a new variety can be assessed from several parameters. From these not only area planted to the variety and percentage of the area under the crop in the region, increased yield and savings in water but also increased nutritive value, and enhanced quality are also very important parameters which should have taken into consideration. Often, induced mutations lead to more advantages than a simple desired phenotypic change.In this study, tomato seeds were irradiated at the dose of 150 Gy by using 60Co gamma rays irradiator at a fixed dose rate of 0.654 kGy/h. These seeds were planted and M4 stage mutant lines were analysed for phytonutrient capacity by using HPLC system with different types of detectors depending on the analytes to be determined (vitamin C, carotenoids and vitamin E). Accelerated Solvent Extraction technique was used for the extraction of vitamin C from the samples under high pressure of nitrogen gas. For carotenoids and tocopherols extractions, liquid-liquid partition technique was used. Photodiode Array, UV and Fluorescence detectors were used for the determination of vitamin C (L-ascorbic acid), some carotenoids (lutein, β-carotene, lycopene) and vitamin E ( α-, γ-, δ tocopherols), respectively. Results obtained from these analysis were found as follows

  18. Principles of Micellar Electrokinetic Capillary Chromatography Applied in Pharmaceutical Analysis

    Directory of Open Access Journals (Sweden)

    Árpád Gyéresi

    2013-02-01

    Full Text Available Since its introduction capillary electrophoresis has shown great potential in areas where electrophoretic techniques have rarely been used before, including here the analysis of pharmaceutical substances. The large majority of pharmaceutical substances are neutral from electrophoretic point of view, consequently separations by the classic capillary zone electrophoresis; where separation is based on the differences between the own electrophoretic mobilities of the analytes; are hard to achieve. Micellar electrokinetic capillary chromatography, a hybrid method that combines chromatographic and electrophoretic separation principles, extends the applicability of capillary electrophoretic methods to neutral analytes. In micellar electrokinetic capillary chromatography, surfactants are added to the buffer solution in concentration above their critical micellar concentrations, consequently micelles are formed; micelles that undergo electrophoretic migration like any other charged particle. The separation is based on the differential partitioning of an analyte between the two-phase system: the mobile aqueous phase and micellar pseudostationary phase. The present paper aims to summarize the basic aspects regarding separation principles and practical applications of micellar electrokinetic capillary chromatography, with particular attention to those relevant in pharmaceutical analysis.

  19. Mutation detection in the human HSP70B′ gene by denaturing high-performance liquid chromatography

    OpenAIRE

    Hecker, Karl H.; Asea, Alexzander; Kobayashi, Kaoru; Green, Stacy; Tang, Dan; Calderwood, Stuart K

    2000-01-01

    Variances, particularly single nucleotide polymorphisms (SNP), in the genomic sequence of individuals are the primary key to understanding gene function as it relates to differences in the susceptibility to disease, environmental influences, and therapy. In this report, the HSP70B′ gene is the target sequence for mutation detection in biopsy samples from human prostate cancer patients undergoing combined hyperthermia and radiation therapy at the Dana-Farber Cancer Institute, using temperature...

  20. Identification and functional analysis of novel THAP1 mutations.

    Science.gov (United States)

    Lohmann, Katja; Uflacker, Nils; Erogullari, Alev; Lohnau, Thora; Winkler, Susen; Dendorfer, Andreas; Schneider, Susanne A; Osmanovic, Alma; Svetel, Marina; Ferbert, Andreas; Zittel, Simone; Kühn, Andrea A; Schmidt, Alexander; Altenmüller, Eckart; Münchau, Alexander; Kamm, Christoph; Wittstock, Matthias; Kupsch, Andreas; Moro, Elena; Volkmann, Jens; Kostic, Vladimir; Kaiser, Frank J; Klein, Christine; Brüggemann, Norbert

    2012-02-01

    Mutations in THAP1 have been associated with dystonia 6 (DYT6). THAP1 encodes a transcription factor that represses the expression of DYT1. To further evaluate the mutational spectrum of THAP1 and its associated phenotype, we sequenced THAP1 in 567 patients with focal (n = 461), segmental (n = 68), or generalized dystonia (n = 38). We identified 10 novel variants, including six missense substitutions within the DNA-binding Thanatos-associated protein domain (Arg13His, Lys16Glu, His23Pro, Lys24Glu, Pro26Leu, Ile80Val), a 1bp-deletion downstream of the nuclear localization signal (Asp191Thrfs*9), and three alterations in the untranslated regions. The effect of the missense variants was assessed using prediction tools and luciferase reporter gene assays. This indicated the Ile80Val substitution as a benign variant. The subcellular localization of Asp191Thrfs*9 suggests a disturbed nuclear import for this mutation. Thus, we consider six of the 10 novel variants as pathogenic mutations accounting for a mutation frequency of 1.1%. Mutation carriers presented mainly with early onset dystonia (<12 years in five of six patients). Symptoms started in an arm or neck and spread to become generalized in three patients or segmental in two patients. Speech was affected in four mutation carriers. In conclusion, THAP1 mutations are rare in unselected dystonia patients and functional analysis is necessary to distinguish between benign variants and pathogenic mutations. PMID:21847143

  1. Micro analysis of disolved gases by the gas chromatography technique

    International Nuclear Information System (INIS)

    A technique which allows the quantitative analysis of small concentration of disolved gases such as CO2 and H2 in the order of 10-6 - 10-3M is discussed. For the extraction, separation and quantification a Toepler pump was used. This is in tandem to a gas chromatography. This method also can be applied for the analysis of other gases like CO, CH4, CH3-CH3 etc. This technique may be applied in fields such as radiation chemistry, oceanography and environmental studies. (author)

  2. Molecular analysis of mucopolysaccharidosis IVA: Common mutations and racial difference

    Energy Technology Data Exchange (ETDEWEB)

    Tomatsu, S.; Hori, T.; Nakashima, Y. [Gifu Univ. (Japan)] [and others

    1994-09-01

    Mucopolysaccharidosis IVA (MPS IVA) is an autosomal recessive disorder caused by a deficiency in N-acetylgalactosamine -6-sulfate sulfatase (GALNS). Studies on the molecular basis of MPS IVA have been facilitated following cloning of the full-length cDNA and genomic DNA. In this study we detected mutations from 20 Caucasian and 19 Japanese MPS IVA patients using SSCP system and compared mutations of Caucasian origin with those of Japanese origin. The results showed the presence of 16 various mutations (3 small, deletions, 2 nonsense and 11 missense mutations) for Caucasian patients and 15 (1 deletion, 1 large alteration and 13 missense mutations) for Japanese. Moreover, two common mutations existed; one is double gene deletion characteristic for Japanese (6 alleles; 15%) and the other is a point mutation (1113F A{yields}T transition) characteristic for Caucasian (9 alleles; 22.5%). And the clear genotype/phenotype relationship among 1342delCA, IVS1(-2), P151S, Q148X, R386C, I113F, Q473X, W220G, P151L, A291T, R90W, and P77R, for a severe type, G96B N204K and V138A for a milder type, was observed. Only R386 mutation was seen in both of the populations. Further, the precise DNA analysis for double gene deletion of a common double gene deletion has been performed by defining the breakpoints and the results showed that one deletion was caused by homologous recombination due to Alu repetitive sequences and the other was due to nonhomologous recombination of short direct repeat. Haplotype analysis for six alleles with double deletion were different, indicating the different origin of this mutation or the frequent recombination events before a mutational event. Thus the mutations in GALNS gene are very heterogeneous and the racial difference is characteristic.

  3. Mutational Analysis of Merkel Cell Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Erstad, Derek J. [Department of Surgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114 (United States); Cusack, James C. Jr., E-mail: jcusack@mgh.harvard.edu [Division of Surgical Oncology, Harvard Medical School, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114 (United States)

    2014-10-17

    Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine malignancy that is associated with a poor prognosis. The pathogenesis of MCC is not well understood, and despite a recent plethora of mutational analyses, we have yet to find a set of signature mutations implicated in the majority of cases. Mutations, including TP53, Retinoblastoma and PIK3CA, have been documented in subsets of patients. Other mechanisms are also likely at play, including infection with the Merkel cell polyomavirus in a subset of patients, dysregulated immune surveillance, epigenetic alterations, aberrant protein expression, posttranslational modifications and microRNAs. In this review, we summarize what is known about MCC genetic mutations and chromosomal abnormalities, and their clinical significance. We also examine aberrant protein function and microRNA expression, and discuss the therapeutic and prognostic implications of these findings. Multiple clinical trials designed to selectively target overexpressed oncogenes in MCC are currently underway, though most are still in early phases. As we accumulate more molecular data on MCC, we will be better able to understand its pathogenic mechanisms, develop libraries of targeted therapies, and define molecular prognostic signatures to enhance our clinicopathologic knowledge.

  4. OGG1 Mutations and Risk of Female Breast Cancer: Meta-Analysis and Experimental Data

    OpenAIRE

    Kashif Ali; Ishrat Mahjabeen; Maimoona Sabir; Humera Mehmood; Mahmood Akhtar Kayani

    2015-01-01

    In first part of this study association between OGG1 polymorphisms and breast cancer susceptibility was explored by meta-analysis. Second part of the study involved 925 subjects, used for mutational analysis of OGG1 gene using PCR-SSCP and sequencing. Fifteen mutations were observed, which included five intronic mutations, four splice site mutations, two 3′UTR mutations, three missense mutations, and a nonsense mutation. Significantly (p < 0.001) increased (~29 fold) breast cancer risk was as...

  5. Imatinib resistance mutation analysis: experience from a tertiary oncology center

    Directory of Open Access Journals (Sweden)

    Mallekavu Suresh Babu

    2015-01-01

    Full Text Available Purpose: BCR-ABL kinase domain (KD mutations account for 50-90% of the imatinib resistance observed in patients of CML-chronic phase. In CML-CP patients receiving imatinib first-line, mutation analysis is recommended in case of failure or suboptimal response using European LeukemiaNet (ELN criteria. The present study was carried out at a tertiary oncology centre in south India to assess which mutations accounted for resistance to imatinib among patients of chronic phase CML being treated with imatinib.Methods: This was a retrospective observational study. We analyzed patients who were tested for imatinib resistance mutation in view of suboptimal responses while on imatinib or imatinib failure. Direct sequencing of the BCR-ABL transcript by the Sanger method was used for IRMA testing.Results: Out of 120 tested for IRMA, 36 (30% had detectable mutations. We observed a higher frequency of mutations at amino acids T315, F359 and M351T.Conclusions: Among the patients who were tested for imatinib resistance mutation in view of suboptimal responses while on imatinib or imatinib failure, 30% had IRMA +ve mutations. The high incidence of imatinib resistance in present study may be attributed to the fact that our patients were given higher dose of imatinib (600 mg, if they failed to achieve CCyR at 12 months or CHR at 3 months as they could not afford second generation TKIs.

  6. RADIA: RNA and DNA integrated analysis for somatic mutation detection.

    Directory of Open Access Journals (Sweden)

    Amie J Radenbaugh

    Full Text Available The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA to also sequence the tumor RNA. Here we present RADIA (RNA and DNA Integrated Analysis, a novel computational method combining the patient-matched normal and tumor DNA with the tumor RNA to detect somatic mutations. The inclusion of the RNA increases the power to detect somatic mutations, especially at low DNA allelic frequencies. By integrating an individual's DNA and RNA, we are able to detect mutations that would otherwise be missed by traditional algorithms that examine only the DNA. We demonstrate high sensitivity (84% and very high precision (98% and 99% for RADIA in patient data from endometrial carcinoma and lung adenocarcinoma from TCGA. Mutations with both high DNA and RNA read support have the highest validation rate of over 99%. We also introduce a simulation package that spikes in artificial mutations to patient data, rather than simulating sequencing data from a reference genome. We evaluate sensitivity on the simulation data and demonstrate our ability to rescue back mutations at low DNA allelic frequencies by including the RNA. Finally, we highlight mutations in important cancer genes that were rescued due to the incorporation of the RNA.

  7. RADIA: RNA and DNA integrated analysis for somatic mutation detection.

    Science.gov (United States)

    Radenbaugh, Amie J; Ma, Singer; Ewing, Adam; Stuart, Joshua M; Collisson, Eric A; Zhu, Jingchun; Haussler, David

    2014-01-01

    The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA) to also sequence the tumor RNA. Here we present RADIA (RNA and DNA Integrated Analysis), a novel computational method combining the patient-matched normal and tumor DNA with the tumor RNA to detect somatic mutations. The inclusion of the RNA increases the power to detect somatic mutations, especially at low DNA allelic frequencies. By integrating an individual's DNA and RNA, we are able to detect mutations that would otherwise be missed by traditional algorithms that examine only the DNA. We demonstrate high sensitivity (84%) and very high precision (98% and 99%) for RADIA in patient data from endometrial carcinoma and lung adenocarcinoma from TCGA. Mutations with both high DNA and RNA read support have the highest validation rate of over 99%. We also introduce a simulation package that spikes in artificial mutations to patient data, rather than simulating sequencing data from a reference genome. We evaluate sensitivity on the simulation data and demonstrate our ability to rescue back mutations at low DNA allelic frequencies by including the RNA. Finally, we highlight mutations in important cancer genes that were rescued due to the incorporation of the RNA. PMID:25405470

  8. Liquid chromatography mass spectrometry for analysis of microbial metabolites

    DEFF Research Database (Denmark)

    Klitgaard, Andreas

    as signaling, defense, or pigmentation. Compounds from microorganisms have a dual impact on human society: they have been used as drugs, or as inspiration for the development of drugs for centuries. However, fungal infection of crops and the subsequent contamination by mycotoxins, continue to pose a threat...... are still to be discovered. The main analytical technique used to investigate production of products from these diverse organisms is liquid-chromatography coupled to mass spectrometry (LC-MS). With the development of new and improved analytical instrumentation for chemical analysis, the time needed...

  9. Permanent gas analysis using gas chromatography with vacuum ultraviolet detection.

    Science.gov (United States)

    Bai, Ling; Smuts, Jonathan; Walsh, Phillip; Fan, Hui; Hildenbrand, Zacariah; Wong, Derek; Wetz, David; Schug, Kevin A

    2015-04-01

    The analysis of complex mixtures of permanent gases consisting of low molecular weight hydrocarbons, inert gases, and toxic species plays an increasingly important role in today's economy. A new gas chromatography detector based on vacuum ultraviolet (VUV) spectroscopy (GC-VUV), which simultaneously collects full scan (115-240 nm) VUV and UV absorption of eluting analytes, was applied to analyze mixtures of permanent gases. Sample mixtures ranged from off-gassing of decomposing Li-ion and Li-metal batteries to natural gas samples and water samples taken from private wells in close proximity to unconventional natural gas extraction. Gas chromatography separations were performed with a porous layer open tubular column. Components such as C1-C5 linear and branched hydrocarbons, water, oxygen, and nitrogen were separated and detected in natural gas and the headspace of natural gas-contaminated water samples. Of interest for the transport of lithium batteries were the detection of flammable and toxic gases, such as methane, ethylene, chloromethane, dimethyl ether, 1,3-butadiene, CS2, and methylproprionate, among others. Featured is the capability for deconvolution of co-eluting signals from different analytes. PMID:25724098

  10. Heat exchanger scale deposits analysis: application of ion chromatography

    International Nuclear Information System (INIS)

    Concentration level of leachable sulphate ions in the scale samples can be used as reliable indicators in analysis of failed heat exchanger tubes at Desalination Division, BARC. Determination of sulphate in non standard/rare samples like scale deposits need method development and method validation. Screening of scale deposit using X-ray fluorescence (EDXRF) was carried out to know the matrix and the suitable pretreatment procedure to be adopted before ion chromatography analysis. EDXRF studies showed that the sample contains calcium, iron, nickel, copper, silicon, as major elements and titanium, potassium as minor elements. The present study was carried out to develop a simple, rapid and accurate analytical methodology for the determination of sulphate in the above matrix. Scale sample was sonicated and supernatant was treated with H-guard cartridge to remove interfering metal ions. The quantitative determination of different anions was accomplished by anion exchange chromatography with conductometric detection in suppressed mode. A Dionex AS11-HC anion analytical column (4 mm X 250 mm) connected in series with a Dionex AG11-HC guard column (4 mm X 20 mm) was used for separation of anions. The mobile phase was a solution of 35 mM NaOH with a flow rate of 1.0 mL min-1. The column temperature was 30℃ and suppressor current was 112 mA. The optimum resolution and elution time for different anions were found under these conditions. The limit of detection for different anions was in the range 0.3-3 μg g-1 and the relative standard deviation was < 6% for the overall method

  11. Mutational analysis of the human MAOA gene

    Energy Technology Data Exchange (ETDEWEB)

    Tivol, E.A.; Shalish, C.; Schuback, D.E.; Breakefield, X.O. [Harvard Medical School, Boston, MA (United States); Hsu, Yun-Pung [VA Medical Center, West Roxbury, MA (United States)

    1996-02-16

    The monoamine oxidases (MAO-A and MAO-B) are the enzymes primarily responsible for the degradation of amine neurotransmitters, such as dopamine, norepinephrine, and serotonin. Wide variations in activity of these isozymes have been reported in control humans. The MAOA and MAOB genes are located next to each other in the p11.3-11.4 region of the human X chromosome. Our recent documentation of an MAO-A-deficiency state, apparently associated with impulsive aggressive behavior in males, has focused attention on genetic variations in the MAOA gene. In the present study, variations in the coding sequence of the MAOA gene were evaluated by RT-PCR, SSCP, and sequencing of mRNA or genomic DNA in 40 control males with >100-fold variations in MAOA activity, as measured in cultured skin fibroblasts. Remarkable conservation of the coding sequence was found, with only 5 polymorphisms observed. All but one of these were in the third codon position and thus did not alter the deduced amino acid sequence. The one amino acid alteration observed, lys{r_arrow}arg, was neutral and should not affect the structure of the protein. This study demonstrates high conservation of coding sequence in the human MAOA gene in control males, and provides primer sets which can be used to search genomic DNA for mutations in this gene in males with neuropsychiatric conditions. 47 refs., 1 fig., 2 tabs.

  12. Functional analysis of mutations in TGIF associated with holoprosencephaly

    Science.gov (United States)

    El-Jaick, Kenia B.; Powers, Shannon E.; Bartholin, Laurent; Myers, Kenneth R.; Hahn, Jin; Orioli, Ieda M.; Ouspenskaia, Maia; Lacbawan, Felicitas; Roessler, Erich; Wotton, David; Muenke, Maximilian

    2007-01-01

    Holoprosencephaly (HPE) is the most common structural malformation of the forebrain and face in humans. Our current understanding of the pathogenesis of HPE attempts to integrate genetic susceptibility, evidenced by mutations in the known HPE genes, with the epigenetic influence of environmental factors. Mutations or deletions of the human TGIF gene have been associated with HPE in multiple population cohorts. Here we examine the functional effects of all previously reported mutations, and describe four additional variants. Of the eleven sequence variations in TGIF, all but four can be demonstrated to be functionally abnormal. In contrast, no potentially pathogenic sequence alterations were detected in the related gene TGIF2. These results provide further evidence of a role for TGIF in HPE and demonstrate the importance of functional analysis of putative disease-associated alleles. PMID:16962354

  13. The Use of Gas Chromatography for Biogas Analysis

    Science.gov (United States)

    Andersen, Amanda; Seeley, John; Aurandt, Jennifer

    2010-04-01

    Energy from natural gas accounts for 24 percent of energy consumed in the US. Natural gas is a robust form of energy which is rich in methane content and is low in impurities. This quality suggests that it is a very clean and safe gas; it can be used in providing heat, a source for cooking, and in powering vehicles. The downside is that it is a non-renewable resource. On the contrary, methane rich gas that is produced by the breakdown of organic material in an anaerobic environment, called biogas, is a renewable energy source. This research focuses on the gas analysis portion of the creation of the anaerobic digestion and verification laboratory where content and forensic analysis of biogas is performed. Gas Chromatography is implemented as the optimal analytical tool for quantifying the components of the biogas including methane, carbon dioxide, hydrogen sulfide and siloxanes. In addition, the problems associated with the undesirable components are discussed. Anaerobic digestion of primary sludge has consistently produced about 55 percent methane; future goals of this research include studying different substrates to increase the methane yield and decrease levels of impurities in the gas.

  14. Microemulsion electrokinetic chromatography for analysis of phthalates in soft drinks.

    Science.gov (United States)

    Hsieh, Sung-Yu; Wang, Chun-Chi; Wu, Shou-Mei

    2013-12-15

    Microemulsion electrokinetic chromatography (MEEKC) is proposed for analysis of di-n-butyl phthalate (DBP) and di-(2-ethylhexyl) phthalate (DEHP) in soft drinks. However, the instability of microemulsion is a critical issue. In this research, a novel material, Pluronic® F-127, which has the properties of polymer and surfactant, was added for stabilizing the microemulsion in the MEEKC system. Our data demonstrate that the presence of Pluronic® F-127 (0.05-0.30%) also helps enhance resolution of highly hydrophobic compounds, DBP and DEHP. The electrokinetic injection of sodium dodecyl sulphate (SDS) including sample (-10 kV, 20 s) was introduced in this MEEKC system and this yielded about 25-fold sensitivity enhancement compared with hydrodynamic injection (1 psi, 10 s). During method validation, calibration curves were linear (r≥0.99), within a range of 75-500 ng/mL for DBP and 150-1000 ng/mL for DEHP. As the precision and accuracy assays, absolute values of relative standard deviation (RSD) and relative error (RE) in intraday (n=3) and interday (n=5) observations were less than 4.93%. This method was further applied for analyzing six commercial soft drinks and one was found containing 453.67 ng/mL of DEHP. This method is considered feasible for serving as a tool for analysis of highly hydrophobic molecules. PMID:23993511

  15. Biomedical Mutation Analysis (BMA): A software tool for analyzing mutations associated with antiviral resistance

    Science.gov (United States)

    Salvatierra, Karina; Florez, Hector

    2016-01-01

    Introduction: Hepatitis C virus (HCV) is considered a major public health problem, with 200 million people infected worldwide. The treatment for HCV chronic infection with pegylated interferon alpha plus ribavirin inhibitors is unspecific; consequently, the treatment is effective in only 50% of patients infected. This has prompted the development of direct-acting antivirals (DAA) that target virus proteins. These DAA have demonstrated a potent effect in vitro and in vivo; however, virus mutations associated with the development of resistance have been described. Objective: To design and develop an online information system for detecting mutations in amino acids known to be implicated in resistance to DAA. Materials and methods:    We have used computer applications, technological tools, standard languages, infrastructure systems and algorithms, to analyze positions associated with resistance to DAA for the NS3, NS5A, and NS5B genes of HCV. Results: We have designed and developed an online information system named Biomedical Mutation Analysis (BMA), which allows users to calculate changes in nucleotide and amino acid sequences for each selected sequence from conventional Sanger and cloning sequencing using a graphical interface. Conclusion: BMA quickly, easily and effectively analyzes mutations, including complete documentation and examples. Furthermore, the development of different visualization techniques allows proper interpretation and understanding of the results. The data obtained using BMA will be useful for the assessment and surveillance of HCV resistance to new antivirals, and for the treatment regimens by selecting those DAA to which the virus is not resistant, avoiding unnecessary treatment failures. The software is available at: http://bma.itiud.org.

  16. Mutation Analysis Approach to Develop Reliable Object-Oriented Software

    Directory of Open Access Journals (Sweden)

    Monalisa Sarma

    2014-01-01

    Full Text Available In general, modern programs are large and complex and it is essential that they should be highly reliable in applications. In order to develop highly reliable software, Java programming language developer provides a rich set of exceptions and exception handling mechanisms. Exception handling mechanisms are intended to help developers build robust programs. Given a program with exception handling constructs, for an effective testing, we are to detect whether all possible exceptions are raised and caught or not. However, complex exception handling constructs make it tedious to trace which exceptions are handled and where and which exceptions are passed on. In this paper, we address this problem and propose a mutation analysis approach to develop reliable object-oriented programs. We have applied a number of mutation operators to create a large set of mutant programs with different type of faults. We then generate test cases and test data to uncover exception related faults. The test suite so obtained is applied to the mutant programs measuring the mutation score and hence verifying whether mutant programs are effective or not. We have tested our approach with a number of case studies to substantiate the efficacy of the proposed mutation analysis technique.

  17. Quantitative analysis of soil chromatography. I. Water and radionuclide transport

    Energy Technology Data Exchange (ETDEWEB)

    Reeves, M.; Francis, C.W.; Duguid, J.O.

    1977-12-01

    Soil chromatography has been used successfully to evaluate relative mobilities of pesticides and nuclides in soils. Its major advantage over the commonly used suspension technique is that it more accurately simulates field conditions. Under such conditions the number of potential exchange sites is limited both by the structure of the soil matrix and by the manner in which the carrier fluid moves through this structure. The major limitation of the chromatographic method, however, has been its qualitative nature. This document represents an effort to counter this objection. A theoretical basis is specified for the transport both of the carrier eluting fluid and of the dissolved constituent. A computer program based on this theory is developed which optimizes the fit of theoretical data to experimental data by automatically adjusting the transport parameters, one of which is the distribution coefficient k/sub d/. This analysis procedure thus constitutes an integral part of the soil chromatographic method, by means of which mobilities of nuclides and other dissolved constituents in soils may be quantified.

  18. The use of microemulsion electrokinetic chromatography in pharmaceutical analysis.

    Science.gov (United States)

    Miola, M F; Snowden, M J; Altria, K D

    1998-12-01

    The use of a single set of microemulsion electrokinetic chromatography (MEEKC) separation conditions has been assessed for its applicability in the analysis of a range of pharmaceutical compounds. Particular emphasis was placed on neutral or very hydrophobic compounds, which can be difficult to analyse by conventional capillary electrophoresis. The microemulsion employed for the majority of separations consisted of 0.81% w/w octane, 6.61% w/w 1-butanol, 3.31% w/w sodium dodecyl sulphate and 89.27% w/w 10 mM sodium tetraborate buffer. Good separations of methyl, ethyl, butyl and propyl hydroxybenzoates, and a range of ionic and neutral water soluble and insoluble compounds was achieved using a single set of separation conditions. A number of novel applications of MEEKC were developed included the simultaneous determination of the active components and preservatives in liquid formulation and determination of drug related impurities. Improved performance was obtained through use of internal standards and preparation of the samples dissolved in the microemulsion solution. Validation aspects such as linearity, repeatability, accuracy, injection precision and sensitivity were successfully assessed. PMID:9919981

  19. Protein Mobility Shifts Contribute to Gel Electrophoresis Liquid Chromatography Analysis

    OpenAIRE

    Carruthers, Nicholas J.; Parker, Graham C.; Gratsch, Theresa; Caruso, Joseph A.; Stemmer, Paul M.

    2015-01-01

    Profiling of cellular and subcellular proteomes by liquid chromatography with tandem mass spectrometry (MS) after fractionation by SDS-PAGE is referred to as GeLC (gel electrophoresis liquid chromatography)-MS. The GeLC approach decreases complexity within individual MS analyses by size fractionation with SDS-PAGE. SDS-PAGE is considered an excellent fractionation technique for intact proteins because of good resolution for proteins of all sizes, isoelectric points, and hydrophobicities. Addi...

  20. Analysis of Some Biogenic Amines by Micellar Liquid Chromatography

    OpenAIRE

    Irena Malinowska; Katarzyna E. Stępnik

    2012-01-01

    Micellar liquid chromatography (MLC) with the use of high performance liquid chromatography (HPLC) was used to determine some physicochemical parameters of six biogenic amines: adrenaline, dopamine, octopamine, histamine, 2-phenylethylamine, and tyramine. In this paper, an influence of surfactant’s concentration and pH of the micellar mobile phase on the retention of the tested substances was examined. To determine the influence of surfactant’s concentration on the retention of the tested ami...

  1. RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

    OpenAIRE

    Radenbaugh, Amie J.; Ma, Singer; Ewing, Adam; Stuart, Joshua M.; Collisson, Eric A.; Zhu, Jingchun; Haussler, David

    2014-01-01

    The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on comparing the normal and tumor genomes from the same individual. In recent years, it has become routine for projects like The Cancer Genome Atlas (TCGA) to also sequence the tumor RNA. Here we present RADIA (RNA and DNA Integrated Analysis), a method that combines the patient-matched normal and tumor DNA with the tumor RN...

  2. Detection of Epidermal Growth Factor Receptor Mutations in Non-small Cell Lung Cancer Tumor Specimens from Various Ways by Denaturing High-performance Liquid Chromatography

    Directory of Open Access Journals (Sweden)

    Siyuan CHEN

    2010-09-01

    Full Text Available Background and objective Epidermal growth factor receptor (EGFR is the most important therapeutic target in non-small cell lung cancer (NSCLC. EGFR mutations may predict responsiveness to tyrosine kinase inhibitors (TKIs. These mutations are commonly identified using direct sequencing, which is considered the gold standard. But direct sequencing is time-consuming and hyposensitive. In addition, this method requires a lot of tumor specimens. Denaturing highperformance liquid chromatography (DHPLC is a rapid automated sensitive and specific method in mutant gene detection. The aim of this study is to evaluate DHPLC as a rapid detection method for EGFR mutations in NSCLC tumor specimens. Methods DHPLC was used to evaluate the accuracy and sensitivity of detection the serial dilutions of mutant and wild type EGFR plasma DNA. Frozen tumor specimens of 83 NSCLC patients from various ways had been included, after DNA extraction and polymerase chain reaction (PCR on EGFR exon 19 and 21, the results from the direct sequencing and DHPLC were compared. Results Mutant plasma DNA can be detected in the serial dilution of 1:100 by DHPLC and 1:10 by direct sequencing respectively. The results from DHPLC showed 22 EGFR mutations were detected in 83 NSCLC patients, and only 19 mutation samples had been conformed by direct sequencing. Moreover, the other 61 samples were deemed as wild type by DHPLC and direct sequencing. The sensitivity and specificity of DHPLC was 100% and 95.13% respectively. The detection of the tumor specimens from CT-guided transthoracic needle lung biopsy, lymph node biopsy and surgical resection all showed high sensitivity and specificity. EGFR mutation has strong correlation with gender and pathologic type, but irrelevant to age and smoking status. Conclusion DHPLC was a precise rapid preliminary screening method for detection of NSCLC EGFR genotype.

  3. Analysis of chemical signals in red fire ants by gas chromatography and pattern recognition techniques

    Science.gov (United States)

    The combination of gas chromatography and pattern recognition (GC/PR) analysis is a powerful tool for investigating complicated biological problems. Clustering, mapping, discriminant development, etc. are necessary to analyze realistically large chromatographic data sets and to seek meaningful relat...

  4. Nucleic acid analysis using liquid chromatography and electrospray ionization mass spectrometry

    International Nuclear Information System (INIS)

    tandem repeat loci used in forensic science. Mass spectrometry emerged as one of the most important tools for the characterization of biological macromolecules after the introduction of soft ionization techniques like electrospray ionization. It yields information useful to determine or confirm the structure and sequence of biomolecules; it enables the detection of mutations and modifications in nucleic acids. We compared the characteristics of three different mass spectrometers, namely a quadrupole ion trap, a triple stage quadrupole and a sector-field instrument, in mass spectrometric analysis of nucleic acids. To prepare the online coupling of liquid chromatography and mass spectrometry, we optimized the conditions of the electrospray process in terms of utilized solvent, sheath liquid and concentration of ion-pair reagent. (author)

  5. HD gas analysis with Gas Chromatography and Quadrupole Mass Spectrometer

    CERN Document Server

    Ohta, T; Didelez, J -P; Fujiwara, M; Fukuda, K; Kohri, H; Kunimatsu, T; Morisaki, C; Ono, S; Rouille, G; Tanaka, M; Ueda, K; Uraki, M; Utsuro, M; Wang, S Y; Yosoi, M

    2011-01-01

    A gas analyzer system has been developed to analyze Hydrogen-Deuteride (HD) gas for producing frozen-spin polarized HD targets, which are used for hadron photoproduction experiments at SPring-8. Small amounts of ortho-H$_{2}$ and para-D$_{2}$ gas mixtures ($\\sim$0.01%) in the purified HD gas are a key to realize a frozen-spin polarized target. In order to obtain reliable concentrations of these gas mixtures in the HD gas, we produced a new gas analyzer system combining two independent measurements with the gas chromatography and the QMS. The para-H$_{2}$, ortho-H$_{2}$, HD, and D$_{2}$ are separated using the retention time of the gas chromatography and the mass/charge. It is found that the new gas analyzer system can measure small concentrations of $\\sim$0.01% for the otho-H$_2$ and D$_2$ with good S/N ratios.

  6. Molecular weight analysis by size exclusion chromatography with multiple detection

    Czech Academy of Sciences Publication Activity Database

    Netopilík, Miloš

    Bangalore : Central Power Research Institute, 2007, s. 1-6. [International Conference on Polymeric Materials in Power Engineering. Bangalore (IN), 04.10.2007-06.10.2007] R&D Projects: GA AV ČR IAA400500703; GA ČR GA203/07/0659 Institutional research plan: CEZ:AV0Z40500505 Keywords : size exclusion chromatography * viscometric detection * number- average molecular weight Subject RIV: CF - Physical ; Theoretical Chemistry

  7. [Analysis of 5'-deoxyribonucleotides by high-effective liquid chromatography].

    Science.gov (United States)

    Galkina, O V; Pupkova, V I

    1980-01-01

    The paper describes a method of analyzing 5'-deoxyribonucleotides by high-effective liquid chromatography on the strong-basic anion exchange resin Aminex A-27 in a nongradient phosphate borate buffer with ethanol addition. This method is useful for simultaneous separation of up to 6 UV-absorbing impurities--mononucleotides and nucleosides--with a sensitivity of 0.01 to 0.025 microgram. PMID:7384015

  8. THE ANALYSIS OF NF2 GENE MUTATION IN SPORADIC SCHWANNOMAS

    Institute of Scientific and Technical Information of China (English)

    卞留贯; 孙青芳; 沈建康; 赵卫国; 罗其中

    2002-01-01

    Objective To analyze the mutation of NF2 gene (exon 2,4,6 and 13) in schwannomas. Methods The NF2 gene mutation in 36 schwannomas were observed by PCR-SSCP and DNA sequence. The proliferative index of schwannoma was detected by immunohistochemistry. Results We found 13 mutations in 36 schwannomas, including 6 deletion or insertion resulting in a frameshift, 2 nonsense mutations, 2 missense mutations, and 3 alterations affecting acceptor or donor of splicing sites in E4,E6,E13. The proliferative index of schwannomas with mutation were significantly higher than those without mutation (P< 0.05). Conclusion NF2 gene mutation is the frequent event in the tumorigenesis of schwannomas, and there is some correlation between the mutation and clinical behavior(tumor proliferation).

  9. Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma

    OpenAIRE

    Palavalli, Lavanya H.; Prickett, Todd D.; Wunderlich, John R.; Wei, Xiaomu; Burrell, Allison S.; Porter-Gill, Patricia; Davis, Sean; Wang, Chenwei; Cronin, Julia C.; Agrawal, Neena S.; Lin, Jimmy C.; Westbroek, Wendy; Hoogstraten-Miller, Shelley; Molinolo, Alfredo A; Fetsch, Patricia

    2009-01-01

    A mutational analysis of the matrix metalloproteinase (MMP) gene family in human melanoma identified somatic mutations in 23% of melanomas. Five mutations in one of the most commonly mutated genes, MMP8, reduced MMP enzyme activity. Expression of wild-type but not mutant MMP8 in human melanoma cells inhibited growth on soft agar in vitro and tumor formation in vivo, suggesting that wild-type MMP-8 has the ability to inhibit melanoma progression.

  10. COLD-PCR enhanced melting curve analysis improves diagnostic accuracy for KRAS mutations in colorectal carcinoma

    OpenAIRE

    Joseph Loren; Reddy Poluru L; Akagi Laura; Pritchard Colin C; Tait Jonathan F

    2010-01-01

    Abstract Background KRAS mutational analysis is the standard of care prior to initiation of treatments targeting the epidermal growth factor receptor (EGFR) in patients with metastatic colorectal cancer. Sensitive methods are required to reliably detect KRAS mutations in tumor samples due to admixture with non-mutated cells. Many laboratories have implemented sensitive tests for KRAS mutations, but the methods often require expensive instrumentation and reagents, parallel reactions, multiple ...

  11. Thin-layer chromatography in analysis of inorganic substances

    International Nuclear Information System (INIS)

    The use of thin-layer chromatography (TLC) for separation and determination of inorganic compounds is briefly considered. Universal character of the method, its simplicity, rapidness, high efficiency, clear separation and visual demonstration of results are pointed out, which permits to use TLC extensively for solving scientific and practical problems related to the determination of trace amounts of inorganic substances. TLC method permits to work with nano- and microgram amounts of substances and ensures the absolute limit of determination in the optimal conditions, which is 10-2-10-7 g. Techniques of chromatographic determination of Te, rare earths, Y, Pu in various objects and their metrological characteristics are presented

  12. Analysis of Some Biogenic Amines by Micellar Liquid Chromatography

    Directory of Open Access Journals (Sweden)

    Irena Malinowska

    2012-01-01

    Full Text Available Micellar liquid chromatography (MLC with the use of high performance liquid chromatography (HPLC was used to determine some physicochemical parameters of six biogenic amines: adrenaline, dopamine, octopamine, histamine, 2-phenylethylamine, and tyramine. In this paper, an influence of surfactant’s concentration and pH of the micellar mobile phase on the retention of the tested substances was examined. To determine the influence of surfactant’s concentration on the retention of the tested amines, buffered solutions (at pH 7.4 of ionic surfactant—sodium dodecyl sulfate SDS (at different concentrations with acetonitrile as an organic modifier (0.8/0.2 v/v were used as the micellar mobile phases. To determine the influence of pH of the micellar mobile phase on the retention, mobile phases contained buffered solutions (at different pH values of sodium dodecyl sulfate SDS (at 0.1 M with acetonitrile (0.8/0.2 v/v. The inverse of value of retention factor (1/ versus concentration of micelles ( relationships were examined. Other physicochemical parameters of solutes such as an association constant analyte—micelle (ma—and partition coefficient of analyte between stationary phase and water (hydrophobicity descriptor (swΦ were determined by the use of Foley’s equation.

  13. Chromatography analysis of Jatropha Curcas L oil raw and refined

    International Nuclear Information System (INIS)

    The chromatography of gases is one of the most versatile methods utilized in the chemical laboratory, which permits the determinations of the percentages and types of fatty acids present in vegetable oils. The objective of this work was to carry out a comparative study of the composition of the fatty acids, of the mechanically extracted oil from the seed of the Jatropha curcas L plant in the raw and refined state, using the data obtained by gas chromatography. The fatty acids of the oil were determined as methylic esteres. The analyst was carried out in a gas chromatographer, with a detector of ionization by way of flame (FID), Agilent 7890A (Agilent, USA) coupled to HP Pentium 4 computer, with a data processing program. The temperatures of the injector and of the detector were 250℃ and 260℃ respectively. The data obtained chromatographically of the oil of Jatropha curcas L, raw and refined indicates that the refinery process did not vary the composition of the fatty acid, because there are no significant differences between them. Also, the results obtained by other investigators, showed that the predominant fatty acids obtained from the oil of the Jatropha curcas L were palmitic and stearic in the saturated fatty acids, and oleic and linoleic in the unsaturated fatty acids

  14. Chromatography Analysis of Jatropha Curcas L Oil Raw and Refined

    International Nuclear Information System (INIS)

    The chromatography of gases is one of the most versatile methods utilized in the chemical laboratory, which permits the determinations of the percentages and types of fatty acids present in vegetable oils. The objective of this work was to carry out a comparative study of the composition of the fatty acids, of the mechanically extracted oil from the seed of the Jatropha curcas L plant in the raw and refined state, using the data obtained by gas chromatography. The fatty acids of the oil were determined as methylic esteres. The analyst was carried out in a gas chromatographer, with a detector of ionization by way of flame (FID), Agilent 7890A (Agilent, USA) coupled to HP Pentium 4 computer, with a data processing program. The temperatures of the injector and of the detector were 250 °C and 260 °C respectively. The data obtained chromatographically of the oil of Jatropha curcas L, raw and refined indicates that the refinery process did not vary the composition of the fatty acid, because there are no significant differences between them. Also, the results obtained by other investigators, showed that the predominant fatty acids obtained from the oil of the Jatropha curcas L were palmitic and stearic in the saturated fatty acids, and oleic and linoleic in the unsaturated fatty acids

  15. Comparison of gas chromatography/isotope ratio mass spectrometry and liquid chromatography/isotope ratio mass spectrometry for carbon stable-isotope analysis of carbohydrates

    OpenAIRE

    Moerdijk-Poortvliet, T.C.W.; Schierbeek, H.; Houtekamer, M; Engeland, T.; D. Derrien; Stal, L.J.; Boschker, H.T.S.

    2015-01-01

    We compared gas chromatography/isotope ratio mass spectrometry (GC/IRMS) and liquid chromatography/isotope ratio mass spectrometry (LC/IRMS) for the measurement of d13C values in carbohydrates. Contrary to GC/IRMS, no derivatisation is needed for LC/IRMS analysis of carbohydrates. Hence, although LC/IRMS is expected to be more accurate and precise, no direct comparison has been reported

  16. Functional diversity and mutational analysis of Agrobacterium 6B oncoproteins.

    Science.gov (United States)

    Helfer, A; Pien, S; Otten, L

    2002-07-01

    Many Agrobacterium T-DNA genes belong to a diverse family of T-DNA genes, the rolB family. These genes cause various growth abnormalities but their modes of action remain largely unknown. So far, none of the RolB-like proteins has been subjected to mutational analysis. The RolB-like oncoprotein 6B, which induces tumours on species such as Nicotiana glauca and Kalanchoe tubiflora, was chosen to investigate the role of the most conserved amino acid residues within the RolB family. We first determined which of the natural 6B variants had the strongest oncogenic activity; to this end, six 6b coding sequences (A- 6b, AB- 6b, C- 6b, CG- 6b, S- 6b and T- 6b) were placed under the control of the strong constitutive 2x35S promoter and compared for tumour induction on N. glauca, N. tabacum and K. daigremontiana. Oncogenicity increased in the order C- 6b/CG- 6b, A- 6b/AB- 6b, and S- 6b/T- 6b. The most conserved amino acid residues in the strongly oncogenic T-6B protein were mutated and shown to be required for oncogenicity and accumulation of the T-6B protein in planta but not in bacteria. Hybrids between T-6B and the weakly oncogenic A-6B protein revealed an additional oncogenic determinant required for the formation of large tumours. PMID:12172796

  17. Sensitive KIT D816V mutation analysis of blood as a diagnostic test in mastocytosis

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Vestergaard, Hanne; Bindslev-Jensen, Carsten; Møller, Michael Boe; Broesby-Olsen, Sigurd

    2014-01-01

    The recent progress in sensitive KIT D816V mutation analysis suggests that mutation analysis of peripheral blood (PB) represents a promising diagnostic test in mastocytosis. However, there is a need for systematic assessment of the analytical sensitivity and specificity of the approach in order to...... establish its value in clinical use. We therefore evaluated sensitive KIT D816V mutation analysis of PB as a diagnostic test in an entire case-series of adults with mastocytosis. We demonstrate for the first time that by using a sufficiently sensitive KIT D816V mutation analysis, it is possible to detect...... the mutation in PB in nearly all adult mastocytosis patients. The mutation was detected in PB in 78 of 83 systemic mastocytosis (94%) and 3 of 4 cutaneous mastocytosis patients (75%). The test was 100% specific as determined by analysis of clinically relevant control patients who all tested negative...

  18. BRCA1 and BRCA2 germline mutation analysis among Indian women from south India: identification of four novel mutations and high-frequency occurrence of 185delAG mutation

    Indian Academy of Sciences (India)

    Kannan Vaidyanathan; Smita Lakhotia; H M Ravishankar; Umaira Tabassum; Geetashree Mukherjee; Kumaravel Somasundaram

    2009-09-01

    Mutations in the BRCA1 and BRCA2 genes profoundly increase the risk of developing breast and/or ovarian cancer among women. To explore the contribution of BRCA1 and BRCA2 mutations in the development of hereditary breast cancer among Indian women, we carried out mutation analysis of the BRCA1 and BRCA2 genes in 61 breast or ovarian cancer patients from south India with a positive family history of breast and/or ovarian cancer. Mutation analysis was carried out using conformation-sensitive gel electrophoresis (CSGE) followed by sequencing. Mutations were identified in 17 patients (28.0%); 15 (24.6%) had BRCA1 mutations and two (3.28%) had BRCA2 mutations. While no specific association between BRCA1 or BRCA2 mutations with cancer type was seen, mutations were more often seen in families with ovarian cancer. While 40% (4/10) and 30.8% (4/12) of families with ovarian or breast and ovarian cancer had mutations, only 23.1% (9/39) of families with breast cancer carried mutations in the BRCA1 and BRCA2 genes. In addition, while BRCA1 mutations were found in all age groups, BRCA2 mutations were found only in the age group of ≤ 40 years. Of the BRCA1 mutations, there were three novel mutations (295delCA; 4213T → A; 5267T → G) and three mutations that have been reported earlier. Interestingly, 185delAG, a BRCA1 mutation which occurs at a very high frequency in Ashkenazi Jews, was found at a frequency of 16.4% (10/61). There was one novel mutation (4866insT) and one reported mutation in BRCA2. Thus, our study emphasizes the importance of mutation screening in familial breast and/or ovarian cancers, and the potential implications of these findings in genetic counselling and preventive therapy.

  19. On-line coupled high performance liquid chromatography-gas chromatography for the analysis of contamination by mineral oil. Part 1: method of analysis.

    Science.gov (United States)

    Biedermann, Maurus; Grob, Koni

    2012-09-14

    For the analysis of mineral oil saturated hydrocarbons (MOSH) and mineral oil aromatic hydrocarbons (MOAH), on-line coupled high performance liquid chromatography-gas chromatography-flame ionization detection (HPLC-GC-FID) offers important advantages: it separates MOSH and MOAH in robust manner, enables direct injection of large aliquots of raw extracts (resulting in a low detection limit), avoids contamination of the sample during preparation and is fully automated. This review starts with an overview of the technology, particularly the fundamentals of introducing large volumes of solvent into GC, and their implementation into various transfer techniques. The main part deals with the concepts of MOSH and MOAH analysis, with a thorough discussion of the choices made. It is followed by a description of the method. Finally auxiliary tools are summarized to remove interfering components, enrich the sample in case of a high fat content and obtain additional information about the MOSH and MOAH composition. PMID:22770383

  20. Quantitative analysis of complex casein hydrolysates based on chromatography and membrane

    Institute of Scientific and Technical Information of China (English)

    Qi Wei; Yu Yanjun; He Zhimin

    2006-01-01

    The enzymatic hydrolysates of casein are so complex that there is no effective method to do quantitative analysis.The common techniques,such as high performance chromatography and SDS-PAGE,can only carry out qualitative analysis.On the basis of membrane separation and high performance size exclusion chromatography (HPSEC),standard peptides with different molecular mass range were prepared,and the linear relationships between mass concentration of the standard peptides and the ultraviolet absorption of corresponding peak areas were established.Consequently,mass concentration of the different hydrolysates at different reaction times could be accurately calculated.The combination of chromatography and membrane separation is of great importance to the quantitative analysis of the complex hydrolysates,which can also be applied to the other macromolecular systems,such as carbohydrates.

  1. SERPINA1 Full-Gene Sequencing Identifies Rare Mutations Not Detected in Targeted Mutation Analysis.

    Science.gov (United States)

    Graham, Rondell P; Dina, Michelle A; Howe, Sarah C; Butz, Malinda L; Willkomm, Kurt S; Murray, David L; Snyder, Melissa R; Rumilla, Kandelaria M; Halling, Kevin C; Highsmith, W Edward

    2015-11-01

    Genetic α-1 antitrypsin (AAT) deficiency is characterized by low serum AAT levels and the identification of causal mutations or an abnormal protein. It needs to be distinguished from deficiency because of nongenetic causes, and diagnostic delay may contribute to worse patient outcome. Current routine clinical testing assesses for only the most common mutations. We wanted to determine the proportion of unexplained cases of AAT deficiency that harbor causal mutations not identified through current standard allele-specific genotyping and isoelectric focusing (IEF). All prospective cases from December 1, 2013, to October 1, 2014, with a low serum AAT level not explained by allele-specific genotyping and IEF were assessed through full-gene sequencing with a direct sequencing method for pathogenic mutations. We reviewed the results using American Council of Medical Genetics criteria. Of 3523 cases, 42 (1.2%) met study inclusion criteria. Pathogenic or likely pathogenic mutations not identified through clinical testing were detected through full-gene sequencing in 16 (38%) of the 42 cases. Rare mutations not detected with current allele-specific testing and IEF underlie a substantial proportion of genetic AAT deficiency. Full-gene sequencing, therefore, has the ability to improve accuracy in the diagnosis of AAT deficiency. PMID:26321041

  2. Determination of site selectivity of different carcinogens for preferential mutational hot spots in oligonucleotide fragments by ion-pair reversed-phase nano liquid chromatography tandem mass spectrometry.

    Science.gov (United States)

    Sharma, Vaneet K; Xiong, Wennan; Glick, James; Vouros, Paul

    2014-01-01

    Ion-pair reversed-phase nano liquid chromatography coupled with nanospray ion trap mass spectrometry was used to investigate site selectivity of the known carcinogens N-acetoxy-2-acetylaminofluorene, N-hydroxy-4-aminobiphenyl and (+/-)-anti-benzo[a]pyrene diol epoxide with the synthetic double-strand 14-mer long oligonucleotide fragment of the p53 gene containing two mutational hot-spot codons (5'-P-ACC155 CGC156 GTC157 CGC158 GC/5'-GCG CGG ACG CGG GT). The investigation was performed using a monolithic polystyrene divinylbenzene capillary column and triethylammonium bicarbonate as an ion-pair reagent. The exact location of the carcinogen on the modified oligonucleotide backbone was determined using characteristic collision-induced dissociation fragmentation patterns obtained under negative-ion mode ionization. In all these cases, the adducted, isomeric oligonucleotides formed were chromatographically resolved and structural identification was performed without any prior deoxyribonucleic acid cleavage or hydrolysis. The knowledge of the site specificity of a carcinogen, especially at purported mutational hot spots, is of paramount importance (1) in establishing the identity of biomarkers for an early risk assessment of the formed DNA adducts, (2) developing repair mechanisms for the formed carcinogen adducted DNA, and (3) understanding the nature of the covalent bond formed and mapping the frequency of the adduction process. PMID:24881456

  3. Analysis of moniliformin in maize plants using hydrophilic interaction chromatography

    DEFF Research Database (Denmark)

    Sørensen, Jens Laurids; Nielsen, Kristian Fog; Thrane, Ulf

    2007-01-01

    A novel HPLC method was developed for detection of the Fusarium mycotoxin, moniliformin in whole maize plants. The method is based on hydrophilic interaction chromatography (HILIC) on a ZIC zwitterion column combined with diode array detection and negative electrospray mass spectrometry (ESI......−-MS). Samples were extracted using acetonitrile–water (85:15), and the extracts were cleaned up on strong anion exchange columns. By this procedure we obtained a recovery rate of 57–74% moniliformin with a limit of detection at 48 ng/g and a limit of quantification at 96 ng/g using UV detection at 229 nm, which...... is comparable to current methods used. Limit of detection and quantification using ESI−-MS detection was 1 and 12 ng/g, respectively. Screening of maize samples infected with the moniliformin producing fungi F. avenaceum, F. tricinctum, or F. subglutinans detected moniliformin levels of 1–12 ng/g in...

  4. Single base pair mutation analysis by PNA directed PCR clamping

    DEFF Research Database (Denmark)

    Ørum, H.; Nielsen, P.E.; Egholm, M.; Berg, R.H.; Buchardt, O.; Stanley, C.

    1993-01-01

    A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and bind to their complementary nucleic acid sequences with higher thermal stability and specificity...... than the corresponding deoxyribooligonucleotides and that they cannot function as primers for DNA polymerases. We show that a PNA/DNA complex can effectively block the formation of a PCR product when the PNA is targeted against one of the PCR primer sites. Furthermore, we demonstrate that this blockage...... allows selective amplification/suppression of target sequences that differ by only one base pair. Finally we show that PNAs can be designed in such a way that blockage can be accomplished when the PNA target sequence is located between the PCR primers....

  5. PKU in Minas Gerais State, Brazil: mutation analysis.

    Science.gov (United States)

    Santos, L L; Castro-Magalhães, M; Fonseca, C G; Starling, A L P; Januário, J N; Aguiar, M J B; Carvalho, M R S

    2008-11-01

    This work was undertaken in order to ascertain the PKU mutational spectrum in Minas Gerais, Brazil, the relative frequency of the mutations in the State and the origin of these mutations by haplotype determination. Minas Gerais is a trihybrid population formed by miscegenation from Europeans, Africans and Amerindians. All 13 exons of the PAH gene from 78 PKU patients were analyzed, including splicing sites and the promoter region. We identified 30 different mutations and 98% of the PAH alleles were established. A new mutation (Q267X) was identified as well. The most common mutations found were V388M (21.2), R261Q (16.0%), IVS10-11G>A (15.3%), I65T (5.8%), IVS2+5G>C (5.8%), R252W (5.1%), IVS2+5G>A (4.5%), P281L (3.8%) and L348V (3.2%). These nine mutations correspond to 80% of the PKU alleles in the state. Haplotypes were determined to characterize the origin of the PAH alleles. The majority of the mutations found, with respective haplotypes, are frequent in the Iberian Peninsula. However, there were some mutations that are rare in Europe and four previously unreported mutation-haplotype associations. I65T and Q267X were found in association with haplotype 38 and may be African in origin or the result of miscegenation in the Brazilian population. PMID:18798839

  6. Quantitative analysis of abused drugs in physiological fluids by gas chromatography/chemical ionization mass spectrometry

    International Nuclear Information System (INIS)

    Methods have been developed for quantitative analysis of commonly abused drugs in physiological fluids using gas chromatography/chemical ionization mass spectrometry. The methods are being evaluated in volunteer analytical and toxicological laboratories, and analytical manuals describing the methods are being prepared. The specific drug and metabolites included in this program are: Δ9-tetrahydrocannabinol, methadone, phencyclidine, methaqualone, morphine, amphetamine, methamphetamine, mescaline, 2,5-dimethoxy-4-methyl amphetamine, cocaine, benzoylecgonine, diazepam, and N-desmethyldiazepam. The current analytical methods utilize relatively conventional instrumentation and procedures, and are capable of measuring drug concentrations as low as 1 ng/ml. Various newer techniques such as sample clean-up by high performance liquid chromatography, separation by glass capillary chromatography, and ionization by negative ion chemical ionization are being investigated with respect to their potential for achieving higher sensitivity and specificity, as well as their ability to facilitate simultaneous analysis of more than one drug and metabolite. (Auth.)

  7. Mutation analysis in South American patients with Mucopolysaccharidosis type I

    OpenAIRE

    Matte, Ursula; Leistner, Sandra; Schwartz, Ida; Lima, Luciane; Chamoles, Néstor; Yogalingam, Gouri; Brooks, Doug; Hopwood, John; Giugliani, Roberto

    2001-01-01

    Mucopolysaccharidosis type I (MPS I) is a lysosomal storage disorder due to the deficiency of-L-iduronidase (IDUA). Severely affected patients show coarse faces, hepatosplenomegaly and mental retardation. Mild cases have facial features, joint stiffness, short stature but no CNS involvement. The gene encoding IDUA was cloned in 1990 and more than 55 disease-causing mutations have been described so far. Mutation frequency varies worldwide but W402X is the most frequent mutation found in Europe...

  8. Functional analysis of mutations in TGIF associated with holoprosencephaly

    OpenAIRE

    El-Jaick, Kenia B.; Powers, Shannon E.; Bartholin, Laurent; Myers, Kenneth R; Hahn, Jin; Ieda M. Orioli; Ouspenskaia, Maia; Lacbawan, Felicitas; Roessler, Erich; Wotton, David; Muenke, Maximilian

    2006-01-01

    Holoprosencephaly (HPE) is the most common structural malformation of the forebrain and face in humans. Our current understanding of the pathogenesis of HPE attempts to integrate genetic susceptibility, evidenced by mutations in the known HPE genes, with the epigenetic influence of environmental factors. Mutations or deletions of the human TGIF gene have been associated with HPE in multiple population cohorts. Here we examine the functional effects of all previously reported mutations, and de...

  9. Mutational analysis of the encephalomyocarditis virus primary cleavage.

    OpenAIRE

    Hahn, H.; Palmenberg, A C

    1996-01-01

    Sixteen substitution mutations of the conserved DvExNPGP sequence, implicated in cardiovirus and aphthovirus primary polyprotein cleavage, were created in encephalomyocarditis virus cDNA, expressed, and characterized for processing activity. Nearly all the mutations severely decreased the efficiency of the primary cleavage reaction during cell-free synthesis of viral precursors, indicating a stringent requirement for the natural sequence in this processing event. When representative mutations...

  10. Hierarchical Bayesian analysis of somatic mutation data in cancer

    OpenAIRE

    Ding, Jie; Trippa, Lorenzo; Zhong, Xiaogang; Parmigiani, Giovanni

    2013-01-01

    Identifying genes underlying cancer development is critical to cancer biology and has important implications across prevention, diagnosis and treatment. Cancer sequencing studies aim at discovering genes with high frequencies of somatic mutations in specific types of cancer, as these genes are potential driving factors (drivers) for cancer development. We introduce a hierarchical Bayesian methodology to estimate gene-specific mutation rates and driver probabilities from somatic mutation data ...

  11. Analysis of RAS oncogene mutations in human lymphoid malignancies.

    OpenAIRE

    Neri, A.; Knowles, D M; Greco, A.; McCormick, F; Dalla-Favera, R

    1988-01-01

    We investigated the frequency of mutations activating RAS oncogenes in human lymphoid malignancies, including B- and T-cell-derived acute lymphoblastic leukemia, chronic lymphocytic leukemia, and non-Hodgkin lymphoma. By the polymerase chain reaction/oligonucleotide hybridization method, DNA from 178 cases was analyzed for activating mutations involving codons 12 and 61 of the HRAS, KRAS and NRAS genes and codon 13 of the NRAS gene. Mutations involving codons 12 or 13 of the NRAS gene were de...

  12. OGG1 Mutations and Risk of Female Breast Cancer: Meta-Analysis and Experimental Data

    Directory of Open Access Journals (Sweden)

    Kashif Ali

    2015-01-01

    Full Text Available In first part of this study association between OGG1 polymorphisms and breast cancer susceptibility was explored by meta-analysis. Second part of the study involved 925 subjects, used for mutational analysis of OGG1 gene using PCR-SSCP and sequencing. Fifteen mutations were observed, which included five intronic mutations, four splice site mutations, two 3′UTR mutations, three missense mutations, and a nonsense mutation. Significantly (pG and 3′UTR variant g.9798848G>A. Among intronic mutations, highest (~15 fold increase in breast cancer risk was associated with g.9793680G>A (p<0.009. Similarly ~14-fold increased risk was associated with Val159Gly (p<0.01, ~17-fold with Gly221Arg (p<0.005, and ~18-fold with Ser326Cys (p<0.004 in breast cancer patients compared with controls, whereas analysis of nonsense mutation showed that ~13-fold (p<0.01 increased breast cancer risk was associated with Trp375STOP in patients compared to controls. In conclusion, a significant association was observed between OGG1 germ line mutations and breast cancer risk. These findings provide evidence that OGG1 may prove to be a good candidate of better diagnosis, treatment, and prevention of breast cancer.

  13. Comparison of microemulsion electrokinetic chromatography with high-performance liquid chromatography for fingerprint analysis of resina draconis.

    Science.gov (United States)

    Cao, Yuhua; Gong, Wenjun; Li, Nan; Yin, Changna; Wang, Yun

    2008-11-01

    Microemulsion electrokinetic chromatography (MEEKC) has been developed for fingerprint analysis of resina draconis, a substitute for sanguis draconis in the Chinese market. The microemulsion as the running buffer was made up of 3.3% (w/v) sodium dodecyl sulfate (SDS), 6.6% (w/v) n-butanol, 0.8% (w/v) n-octane, and 10 mmol/L sodium tetraborate buffer (pH 9.2), which was also used as the solvent for ultrasonic extraction of both water- and fat-soluble compounds in the traditional Chinese medicine samples. Four batches of resina draconis obtained from different pharmaceutical factories located in different geographic regions were used to establish the electrophoretic fingerprint. MEEKC was performed using a Beckman PACE/MDQ system equipped with a diode-array detector and with monitoring at 280 nm. The fingerprint of resina draconis comprised 27 common peaks within 100 min. The relative standard deviations of the relative migration time of these common peaks were less than 2.1%. Through repetitive injection of the sample solution six times in 24 h, all relative standard deviations of the migration time and peak area of loureirin A and loureirin B were less than 2.5 and 3.8%, which demonstrated that the method had good stability and reproducibility. The relative peak areas of these common peaks in the electropherograms of four batches of resina draconis were processed with two mathematical methods, the correlation coefficient and the interangle cosine, to valuate the similarity. The values of the similarity degree of all samples were more than 0.91, which showed resina draconis samples from different origins were consistent. On the other hand, high-performance liquid chromatography (HPLC) coupled with photodiode-array detection was also applied to establish the fingerprint of resina draconis. The samples were separated with a LiChrospher C(18) column using acetonitrile (solvent A) and water containing 0.1% H(3)PO(4) (solvent B) as the mobile phase in linear gradient

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

    Science.gov (United States)

    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...

  15. Quantitative analysis of target components by comprehensive two-dimensional gas chromatography

    NARCIS (Netherlands)

    Mispelaar, V.G. van; Tas, A.C.; Smilde, A.K.; Schoenmakers, P.J.; Asten, A.C. van

    2003-01-01

    Quantitative analysis using comprehensive two-dimensional (2D) gas chromatography (GC) is still rarely reported. This is largely due to a lack of suitable software. The objective of the present study is to generate quantitative results from a large GC x GC data set, consisting of 32 chromatograms. I

  16. A multivariate statistical analysis approach to analyze gas chromatography-olfactometry data of tangerine hybrids

    Science.gov (United States)

    Gas chromatography (GC) hyphenated with olfactometry (O) when a human subject smells the effluent of the GC is a useful technique to identify aroma activity of volatile compounds in a food. Many techniques have been developed, based on olfactory thresholds (CHARM analysis, AEDA), or based on psychop...

  17. High-performance liquid chromatography for analysis of 32P-Postlabeled DNA adducts

    OpenAIRE

    Zeisig, Magnus

    1996-01-01

    High-Performance Liquid Chromatography for Analysis of 32P-Postlabeled DNA Adducts Magnus Zeisig Center for Nutrition and Toxicology, Department of Bioscience at Novum, Karolinska Institutet, Novum, S-141 57 Huddinge, SwedenThe formation of DNA adducts, i.e. the covalent binding of chemicals and chemical groups to DNA,isbelieved to be an important step in chemical carciwg...

  18. Analysis and Identification of Acid-Base Indicator Dyes by Thin-Layer Chromatography

    Science.gov (United States)

    Clark, Daniel D.

    2007-01-01

    Thin-layer chromatography (TLC) is a very simple and effective technique that is used by chemists by different purposes, including the monitoring of the progress of a reaction. TLC can also be easily used for the analysis and identification of various acid-base indicator dyes.

  19. New trends in fast liquid chromatography for food and environmental analysis.

    Science.gov (United States)

    Núñez, Oscar; Gallart-Ayala, Héctor; Martins, Claudia P B; Lucci, Paolo

    2012-03-01

    There is an increasing need for applications in food and environmental areas able to cope with a large number of analytes in very complex matrices. The new analytical procedures demand sensitivity, robustness and high resolution within an acceptable analysis time. The purpose of this review is to describe new trends based on fast liquid chromatography applied to the food and environmental analysis. It includes different column technologies, such as monolithic, sub-2 μm, porous shell, as well as different stationary phases such as reversed phase (C8 and C18), hydrophilic interaction liquid chromatography (HILIC) and fluorinated columns. Additionally, recent sample extraction and clean-up methodologies applied to reduce sample manipulation and total analysis time in food and environmental analysis--QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe), on line solid phase extraction coupled to ultrahigh pressure liquid chromatography (on line SPE-UHPLC), turbulent flow chromatography (TFC) and molecularly imprinted polymers (MIPs), were also addressed. The advantages and drawbacks of these methodologies applied to the fast and sensitive analyses of food and environmental samples are going to be discussed. PMID:22153282

  20. Regiospecific Analysis of Marine Oil Triacylglycerols Using Boric Acid High-Performance Thin-Layer Chromatography

    OpenAIRE

    ANDO, Yasuhiro; Haba, Yusuke; Takase, Kiwamu; Sakai, Shinya

    2007-01-01

    This paper presents a smaller-sized procedure for regiospecific analysis of triacylglycerols (TAG) using boric acid high-performance thin-layer chromatography (HPTLC). Cod liver/mackerel, bonito head, and seal oils TAG (2mg) were partially hydrolyzed by ethyl magnesium bromide, and resulting 1(3)-and 2-monoacylglycerols (MAG) were isolated by the HPTLC. Fatty acids of the 1(3)-and 2-MAG were analyzed by gas-liquid chromatography (GLC). Positional distributions of fatty acids in TAG observed f...

  1. Mutation analysis in mitochondrial fatty acid oxidation defects

    DEFF Research Database (Denmark)

    Gregersen, N; Andresen, B S; Corydon, M J;

    2001-01-01

    systems may help to assess the balance between genetic and environmental factors in the clinical expression of a given mutation. The realization that the effect of the monogene, such as disease-causing mutations in the VLCAD, MCAD, and SCAD genes, may be modified by variations in other genes presages the...

  2. High resolution gas chromatography analysis of rice bran oil

    Science.gov (United States)

    Yu, Fengxiang; Lin, Qinlu; Chen, Xu; Wei, Xiaojun

    To assess the nutritional value and safety quality of rice bran oil (RBO) ,fatty acids of RBO from 15 species rice come from Hunan Province were analyzed by high resolution gas chromatography (HRGC). Crude RBOs were extracted by hexane 3-times using a solvent-to-rice bran ratio of 3:1 (w/w) at 40°C and composition of RBOs was analyzed by HRGC. The result showed that main fatty acids of 15 kinds of RBO include myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1), linoleic acid (C18:2), linolenic acid (C18:3), arachidic acid (C20:0), arachidonic acid (C20:1). It is strange that arachidonic acid (C20:1) is not listed in Chinese standard of RBO (GB11192-2003), and it exists in our samples of RBO. The average value of linolenic acid in RBOs is 1.6304% (range from 1.2425% to 2.131%), and it showed higher level comparing with Chinese standard that linolenic acid is less than 1.0%. The average value of USFA and SFA are 76.81% (range 75.96% to 82.06% ) and 20.15% (range 13.72% to 23.06%) respectively, and USFA content is close to olive oil (83.75%), peanut oil (81.75%) and soybean oil (85.86%). USFA in Jingyou 13 RBO is the highest content. The ratio of USFA to SFA content is 4:1 (range from 3.32 to 5.98:1). The ratio of SFA: MUFA: PUFA of 15 RBOs is 1: 2.2: 1.8, and ω6/ω3 ratio is 21.69 (range from16.54 to 27.28) and it is close to the 26:1 which is reported to be helpful to increase SOD activity. The oleic acid /linoleic acid ratio of 15 RBOs is 1.23:1 (rang from 1.04:1 to 1.42:1). Our data analyzed composition of RBOs from 15 species rice of China and will provide new evidence to revise RBO standard. It also helps us to assess nutritional value of RBOs and identify different RBOs from various species rice and places of origin.

  3. Hotspot-Mutation Analysis of the EGFR/KRAS/BRAF Pathway Using Mutation Surveyor® Software

    Science.gov (United States)

    Hulce, D.; LeVan, K.; Shouyong, N.; Liu, J.

    2011-01-01

    Hotspot-mutation analysis of the EGFR/KRAS/BRAF pathway (or other clinically relevant pathway) can quickly genotype patients as candidates who may respond favorably to specific drug treatments and therapies or into other groups where treatment options are limited and less favorable. Sanger sequencing analysis using Mutation Surveyor software provides high-throughput, high-sensitivity variation detection. Increased efficiency can be achieved using flexible and customizable reporting-sequencing results can be organized by patient identifiers, variation type (reported or unreported, pathogenic or benign or drug sensitive), by gene/exon/amplicon, or quality metrics, and other options. GenBank sequence files from NCBI for EGFR exons 18, 19, 20, and 21; KRAS exons 2 and 3; and BRAF exon 15 were edited to contain reported variations. These reported variations included polymorphisms from dbSNP (downloaded with the GenBank file), pathogenic and drug-sensitivity variations for EGFR (obtained from http://www.egfr.org/), activating mutations for KRAS, and constitutive mutations for BRAF. Bidirectional sequencing data for twelve, simulated (mutations obtained from sequencing reports in the scientific literature), patients were developed and compared to the customized GenBank sequences. Sequencing analysis results were grouped by patient-specific identifiers. Any unmatched or low quality data files are identified in the report, indicating which samples require resequencing. Mutations that match reported variations added to the GenBank sequences are highlighted-SNP identifiers or color coding of SNP type quickly indicate which variations are pathogenic or drug-sensitive or reported in dbSNP. Unreported variations are not highlighted and may be benign or variations of unknown significance. The gene column displays the gene and accession number for that gene used for the analysis. The exon column displays the exon number of the gene, and accession numbers of the mRNA and protein

  4. Analysis of radioactive mixed hazardous waste using derivatization gas chromatography/mass spectrometry, liquid chromatography, and liquid chromatography/mass spectrometry

    International Nuclear Information System (INIS)

    Six samples of core segments from Tank 101-SY were analyzed for chelators, chelator fragments, and several carboxylic acids by derivatization gas chromatography/mass spectrometry. The major components detected were ethylenediaminetetraacetic acid, nitroso-iminodiacetic acid, nitrilotriacetic acid, citric acid, succinic acid, and ethylenediaminetriacetic acid. The chelator of highest concentration was ethylenediaminetetraacetic acid in all six samples analyzed. Liquid chromatography was used to quantitate low molecular weight acids including oxalic, formic, glycolic, and acetic acids, which are present in the waste as acid salts. From 23 to 61% of the total organic carbon in the samples analyzed was accounted for by these acids

  5. Molecular Analysis Expands the Spectrum of Phenotypes Associated with GLI3 Mutations

    NARCIS (Netherlands)

    J.J. Johnston; J.C. Sapp; J.T. Turner; D. Amor; S. Aftimos; K.A. Aleck; M. Bocian; J.N. Bodurtha; G.F. Cox; C.J. Curry; R. Day; D. Donnai; M. Field; I. Fujiwara; M. Gabbett; M. Gal; J.M. Graham Jr; P. Hedera; R.C.M. Hennekam; J.H. Hersh; R.J. Hopkin; H. Kayserili; A.M.J. Kidd; V. Kimonis; A.E. Lin; S.A. Lynch; M. Maisenbacher; S. Mansour; J. McGaughran; L. Mehta; H. Murphy; M. Raygada; N.H. Robin; A.F. Rope; K.N. Rosenbaum; G.B. Schaefer; A. Shealy; W. Smith; M. Soller; A Sommer; H.J. Stalker; B. Steiner; M.J. Stephan; D. Tilstra; S. Tomkins; P. Trapane; A.C.H. Tsai; M.I. van Allen; P.C. Vasudevan; B. Zabel; J. Zunich; G.C.M. Black; L.G. Biesecker

    2010-01-01

    A range of phenotypes including Greig cephalopolysyndactyly and Pallister-Hall syndromes (GCPS, PHS) are caused by pathogenic mutation of the GLI3 gene. To characterize the clinical variability of GLI3 mutations, we present a subset of a cohort of 174 probands referred for GLI3 analysis. Eighty-one

  6. Limited diagnostic value of enzyme analysis in patients with mitochondrial tRNA mutations

    DEFF Research Database (Denmark)

    Wibrand, Flemming; Jeppesen, Tina Dysgaard; Frederiksen, Anja L;

    2010-01-01

    We evaluated the diagnostic value of respiratory chain (RC) enzyme analysis of muscle in adult patients with mitochondrial myopathy (MM). RC enzyme activity was measured in muscle biopsies from 39 patients who carry either the 3243A>G mutation, other tRNA point mutations, or single, large...

  7. Indication for CDKN2A-mutation analysis in familial pancreatic cancer families without melanomas

    NARCIS (Netherlands)

    Harinck, Femme; Kluijt, Irma; van der Stoep, Nienke; Oldenburg, Rogier A.; Wagner, Anja; Aalfs, Cora M.; Sijmons, Rolf H.; Poley, Jan-Werner; Kuipers, Ernst J.; Fockens, Paul; van Os, Theo A. M.; Bruno, Marco J.

    2012-01-01

    Background CDKN2A-mutation carriers run a high risk of developing melanomas and have an increased risk of developing pancreatic cancer (PC). Familial PC (FPC) patients with a personal history or family history of melanomas are therefore offered CDKN2A-mutation analysis. In contrast, CDKN2A testing i

  8. Mutation analysis and evaluation of the cardiac localization of TMEM43 in arrhythmogenic right ventricular cardiomyopathy

    DEFF Research Database (Denmark)

    Christensen, A H; Andersen, C B; Tybjærg-Hansen, A;

    2011-01-01

    Christensen AH, Andersen CB, Tybjærg-Hansen A, Haunso S, Svendsen JH. Mutation analysis and evaluation of the cardiac localization of TMEM43 in arrhythmogenic right ventricular cardiomyopathy. A single report has associated mutations in TMEM43 (LUMA) with a distinctive form of arrhythmogenic righ...

  9. [An analysis of maicaodi by high performance liquid chromatography].

    Science.gov (United States)

    Yang, H; Chen, R; Jiang, M

    1997-05-01

    Maicaodi has recently been developed and produced by the pesticide plant of Nanjing Agricultural University. The quantitative analysis of the effective components--tribenuron methyl and R (-)napropamide in wettable powder of Maicaode, by a high performance liquid chromatographic method was carried out with a Lichrosorb Si-60 20cm x 0.46cm i.d. column, mobile phase of petroleum ether/isopropanol/methanol/acetonitrile/chloroform mixture solvent (80:5:5:5:5) and internal standard of diisooctyl phthalate. The sample was detected by ultraviolet absorption at 254 nm. The retention times of tribenuron methyl and R (-)napropamide were 10-11min and 6-7min respectively. The coefficient of variation of this analysis was 0.34% with a recovery of 99.51%-100.32%. The coefficient of linear correlation was 0.9999. PMID:15739379

  10. Mutational Analysis of Influenza A Virus Nucleoprotein: Identification of Mutations That Affect RNA Replication

    OpenAIRE

    Mena, Ignacio; Jambrina, Enrique; Albo, Carmen; Perales, Beatriz; Ortín, Juan; Arrese, Marta; Vallejo, Dolores; Portela, Agustín

    1999-01-01

    The influenza A virus nucleoprotein (NP) is a multifunctional polypeptide which plays a pivotal role in virus replication. To get information on the domains and specific residues involved in the different NP activities, we describe here the preparation and characterization of 20 influenza A virus mutant NPs. The mutations, mostly single-amino-acid substitutions, were introduced in a cDNA copy of the A/Victoria/3/75 NP gene and, in most cases, affected residues located in regions that were hig...

  11. Preventive doping control analysis: Liquid and gas chromatography time-to-flight mass spectrometry for detection of designer steriods

    NARCIS (Netherlands)

    Georgakopoulos, C.G.; Vonaparti, A.; Stamou, M.; Kiousi, P.; Lyris, E.; Angelis, Y.S.; Tsoupras, G.; Wuest, B.; Nielen, M.W.F.; Panderi, I.; Koupparis, M.

    2007-01-01

    A new combined doping control screening method for the analysis of anabolic steroids in human urine using liquid chromatography/electrospray ionization orthogonal acceleration time-of-flight mass spectrometry (LCoaTOFMS) and gas chromatography/electron ionization orthogonal acceleration time-of-flig

  12. Onsite analysis of petroleum hydrocarbons using thin-layer chromatography

    International Nuclear Information System (INIS)

    This paper reports that the analysis of environmental samples for petroleum hydrocarbons is complicated by the large number and wide variety in the types of compounds that can be present. Many of these compounds originate in the crude oil from which most of our petroleum products are made. The highly volatile compounds present in soil and water following a release often come from refined petroleum products such as gasoline or solvents. Weathering of petroleum products will add or remove compounds that were present in the initial release. Each weathering process will change the petroleum product in different and often predictable ways

  13. Molecular analysis of the APC gene in 71 Israeli families: 17 novel mutations.

    Science.gov (United States)

    Gavert, Nancy; Yaron, Yuval; Naiman, Tova; Bercovich, Dani; Rozen, Paul; Shomrat, Ruth; Legum, Cyril; Orr-Urtreger, Avi

    2002-06-01

    Familial adenomatous polyposis (FAP) is caused by germline mutations in the APC gene. This study included 71 Israeli families referred for molecular analysis of the APC gene. Analysis was performed by the protein truncation test (PTT) of exon 15, and if negative, by direct sequencing of exon 1 to 14. Mutations were found in 36 (50.7%) probands. Mutation detection rates depended on the pattern of referral, such that among the 40 probands referred from the Service for Hereditary Cancer the mutation detection rate was 70%, whereas among the 31 probands referred by other gastroenterologists detection rate was significantly lower (25.8%). Of the 36 mutations detected, 21 were within exon 15, 13 within exons 1 to 14 and 2 were newly-described splicing mutations in introns 9 and 14. A relatively high proportion of the mutations was detected in exon 9 (6/36), five of them newly described. Altogether, we describe here 17 new mutations. Within the two major ethnic groups in Israel, patients of Ashkenazi and non-Ashkenazi origin, there was no significant differences in the mutation detection rate or the distribution of mutations within the APC gene. No founder mutation was detected in any of these populations. Our data confirm that higher detection rates may be expected in patients referred by clinical services specializing in hereditary colon cancer. These results further underscore the importance of complete analysis of all exons and exon/intron boundaries, in order to achieve maximal detection rate in patients suspected of FAP. PMID:12007223

  14. Analysis of SLX4/FANCP in non-BRCA1/2-mutated breast cancer families

    International Nuclear Information System (INIS)

    Genes that, when mutated, cause Fanconi anemia or greatly increase breast cancer risk encode for proteins that converge on a homology-directed DNA damage repair process. Mutations in the SLX4 gene, which encodes for a scaffold protein involved in the repair of interstrand cross-links, have recently been identified in unclassified Fanconi anemia patients. A mutation analysis of SLX4 in German or Byelorussian familial cases of breast cancer without detected mutations in BRCA1 or BRCA2 has been completed, with globally negative results. The genomic region of SLX4, comprising all exons and exon-intron boundaries, was sequenced in 94 Spanish familial breast cancer cases that match a criterion indicating the potential presence of a highly-penetrant germline mutation, following exclusion of BRCA1 or BRCA2 mutations. This mutational analysis revealed extensive genetic variation of SLX4, with 21 novel single nucleotide variants; however, none could be linked to a clear alteration of the protein function. Nonetheless, genotyping 10 variants (nine novel, all missense amino acid changes) in a set of controls (138 women and 146 men) did not detect seven of them. Overall, while the results of this study do not identify clearly pathogenic mutations of SLX4 contributing to breast cancer risk, further genetic analysis, combined with functional assays of the identified rare variants, may be warranted to conclusively assess the potential link with the disease

  15. Molecular analysis of heavy ion induced mutations in the budding yeast

    International Nuclear Information System (INIS)

    The aim of this study is to elucidate the relation between linear energy transfer (LET) and mutagenesis. Carbon ion beams with varied LET generated by Heavy Ion Medical Accelerator in Chiba (HIMAC) synchrotron were irradiated to several types of yeast cells, and we examined the survival rate and mutation frequencies. The results showed that the survival rates were reduced along with the LET, while the mutation frequencies were enhanced along with the LET, and the mutation frequencies increased consistently with LET. The sequencing analysis of mutations showed that the low LET carbon ion beams induced more deletion and insertion mutations than high LET carbon ion beams did. Furthermore, we also examined the gene expression analysis of RAD50, RAD52 and OGG1 after ion beam radiation to cells. The result indicated that the high-LET carbon-ion beams induced the expression of RAD50 gene. (author)

  16. Venus lower atmospheric composition - Analysis by gas chromatography

    Science.gov (United States)

    Oyama, V. I.; Carle, G. C.; Woeller, F.; Pollack, J. B.

    1979-01-01

    The first gas chromatographic analysis of the lower atmosphere of Venus is reported. Three atmospheric samples were analyzed. The third of these samples showed carbon dioxide (96.4 percent), molecular nitrogen (3.41 percent), water vapor (0.135 percent), molecular oxygen (69.3 ppm), argon (18.6 ppm), neon (4.31 ppm), and sulfur dioxide (186 ppm). The amounts of water vapor and sulfur dioxide detected are roughly compatible with the requirements of greenhouse models of the high surface temperature of Venus. The large positive gradient of sulfur dioxide, molecular oxygen, and water vapor from the cloud tops to their bottoms, as implied by Earth-based observations and these results, gives added support for the presence of major quantities of aqueous sulfuric acid in the clouds. A comparison of the inventory of inert gases found in the atmospheres of Venus, Earth, and Mars suggests that these components are due to outgassing from the planetary interiors.

  17. Simplifying the detection of MUTYH mutations by high resolution melting analysis

    International Nuclear Information System (INIS)

    MUTYH-associated polyposis (MAP) is a disorder caused by bi-allelic germline MUTYH mutation, characterized by multiple colorectal adenomas. In order to identify mutations in MUTYH gene we applied High Resolution Melting (HRM) genotyping. HRM analysis is extensively employed as a scanning method for the detection of heterozygous mutations. Therefore, we applied HRM to show effectiveness in detecting homozygous mutations for these clinically important and frequent patients. In this study, we analyzed phenotype and genotype data from 82 patients, with multiple (>= 10) synchronous (19/82) or metachronous (63/82) adenomas and negative APC study (except one case). Analysis was performed by HRM-PCR and direct sequencing, in order to identify mutations in MUTYH exons 7, 12 and 13, where the most prevalent mutations are located. In monoallelic mutation carriers, we evaluated entire MUTYH gene in search of another possible alteration. HRM-PCR was performed with strict conditions in several rounds: the first one to discriminate the heteroduplex patterns and homoduplex patterns and the next ones, in order to refine and confirm parameters. The genotypes obtained were correlated to phenotypic features (number of adenomas (synchronous or metachronous), colorectal cancer (CRC) and family history). MUTYH germline mutations were found in 15.8% (13/82) of patients. The hot spots, Y179C (exon 7) and G396D (exon 13), were readily identified and other mutations were also detected. Each mutation had a reproducible melting profile by HRM, both heterozygous mutations and homozygous mutations. In our study of 82 patients, biallelic mutation is associated with being a carrier of ≥10 synchronous polyps (p = 0.05) and there is no association between biallelic mutation and CRC (p = 0.39) nor family history (p = 0.63). G338H non-pathogenic polymorphism (exon 12) was found in 23.1% (19/82) of patients. In all cases there was concordance between HRM (first and subsequent rounds) and sequencing

  18. Chromatography and its hyphenation to mass spectrometry for extracellular vesicle analysis.

    Science.gov (United States)

    Pocsfalvi, Gabriella; Stanly, Christopher; Fiume, Immacolata; Vékey, Károly

    2016-03-25

    Extracellular vesicles (EVs), such as exosomes, microvesicles and apoptotic bodies are released by cells, both under physiological and pathological conditions. EVs can participate in a novel type of intercellular communication and deliver cargo of nucleic acids, proteins and lipids near or to distant host cells. EV research is proceeding at a fast pace; now they start to appear as promising therapeutic targets, diagnostic tools and drug delivery systems. Isolation and analysis of EVs are prerequisites for understanding their biological roles and for their clinical exploitation. In this process chromatography and mass spectrometry (MS)-based strategies are rapidly gaining importance; and are reviewed in the present communication. Isolation and purification of EVs is mostly performed by ultracentrifugation at present. Chromatography-based strategies are gaining ground, among which affinity and size exclusion chromatography (SEC) are particularly strong contenders. Their major advantages are the relative simplicity, robustness and throughput. Affinity chromatography has the added advantage of separating EV subtypes based on molecular recognition of EV surface motifs. SEC has the advantage that isolated EVs may retain their biological activity. EVs are typically isolated in small amounts, therefore high sensitivity is required for their analysis. Study of the molecular content of EVs (all compounds beside nucleic acids) is predominantly based on liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. The chromatographic separation is mostly performed by reverse phase, nanoscale, ultra high performance LC technique. The MS analysis relying typically on nano-electrospray ionization MS/MS provides high sensitivity, selectivity and resolution, so that thousand(s) of proteins can be detected/identified/quantified in a EV sample. Beside protein identification, quantitation and characterization of protein post-translational modifications (PTMs), like glycosylation

  19. Detection of somatic mutations by high-resolution DNA melting (HRM analysis in multiple cancers.

    Directory of Open Access Journals (Sweden)

    Jesus Gonzalez-Bosquet

    Full Text Available Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each. HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

  20. Laminin-5 mutational analysis in an Italian cohort of patients with junctional epidermolysis bullosa.

    Science.gov (United States)

    Posteraro, Patrizia; De Luca, Naomi; Meneguzzi, Guerrino; El Hachem, May; Angelo, Corrado; Gobello, Tommaso; Tadini, Gianluca; Zambruno, Giovanna; Castiglia, Daniele

    2004-10-01

    Junctional epidermolysis bullosa (JEB) is a rare genodermatosis characterized by dermal-epidermal separation that is caused by mutations in the genes encoding hemidesmosomal components and laminin-5, the major epithelial adhesion ligand. Here, we report on the mutational analysis of LAMA3, LAMB3, and LAMC2 genes encoding laminin-5 chains in 19 Italian patients, 11 affected with the severe Herlitz (H JEB) and eight with the mild non-Herlitz variant of JEB (non-H JEB). Eighteen mutations, seven of which were novel, were identified and their consequences analyzed at the mRNA and protein level. Premature termination codon mutations in both alleles of LAMB3 or LAMC2 genes were found in nine of the 11 H JEB patients, with a prevalence of mutations in LAMC2. In one case, a homozygous frameshift mutation in LAMB3 was associated to illegitimate splicing leading to non-H JEB. One H JEB patient showed a large intragenic duplication within LAMC2, a genetic defect so far uncovered in laminin-5 genes. Splicing or missense mutations, were prevalent in non-H JEB patients. Collectively, five mutations appeared to be frequent in laminin-5 JEB patients: R635X, 29insC, E210K, W143X in LAMB3 and R95X in LAMC2. These recurrent mutations account for approximately 44% of laminin-5 JEB alleles in Italian patients. PMID:15373767

  1. Mutation Analysis of CFTR Gene in 70 Iranian Cystic Fibrosis Patients

    Directory of Open Access Journals (Sweden)

    Reza Alibakhshi Mahdi Zamani

    2006-03-01

    Full Text Available Cystic fibrosis (CF is the most common inherited disorder in Caucasian populations, with over 1400 cystic fibrosis transmembrane conductance regulator (CFTR mutations. The type of mutations and their distributions varies widely between different countries and/or ethnic groups. Seventy Iranian cystic fibrosis patients were screened for the CFTR gene mutation using ARMS/PCR (amplification refractory mutation system for the following mutations: ∆F508, N1303K, G542X, 1717-1G>A, R553X, W1282X, G551D, 621+1G>T, ∆I507 and R560T. Single strand conformation polymorphism (SSCP analysis of exons 3, 7, 10, 11 and 17b, including both the exon/intron junctions, of the CFTR gene was performed in patients in whom no mutation could be identified on one or both CFTR genes. As a result of this screening, only three mutations were found: ∆F508 mutation was found in 25 (17.8% alleles, N1303K in six (4.3% alleles and G542X in five (3.6% alleles. Thus, a total of 3 mutations cover 25.7% of CF alleles. These finding will be used for planning future screening and appropriate genetic counseling programs in Iranian CF patients.

  2. nfxB as a novel target for analysis of mutation spectra in Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Mariela R Monti

    Full Text Available nfxB encodes a negative regulator of the mexCD-oprJ genes for drug efflux in the opportunistic pathogen Pseudomonas aeruginosa. Inactivating mutations in this transcriptional regulator constitute one of the main mechanisms of resistance to ciprofloxacin (Cip(r. In this work, we evaluated the use of nfxB/Cip(r as a new test system to study mutation spectra in P. aeruginosa. The analysis of 240 mutations in nfxB occurring spontaneously in the wild-type and mutator backgrounds or induced by mutagens showed that nfxB/Cip(r offers several advantages compared with other mutation detection systems. Identification of nfxB mutations was easy since the entire open reading frame and its promoter region were sequenced from the chromosome using a single primer. Mutations detected in nfxB included all transitions and transversions, 1-bp deletions and insertions, >1-bp deletions and duplications. The broad mutation spectrum observed in nfxB relies on the selection of loss-of-function changes, as we confirmed by generating a structural model of the NfxB repressor and evaluating the significance of each detected mutation. The mutation spectra characterized in the mutS, mutT, mutY and mutM mutator backgrounds or induced by the mutagenic agents 2-aminopurine, cisplatin and hydrogen peroxide were in agreement with their predicted mutational specificities. Additionally, this system allowed the analysis of sequence context effects since point mutations occurred at 85 different sites distributed over the entire nfxB. Significant hotspots and preferred sequence contexts were observed for spontaneous and mutagen-induced mutation spectra. Finally, we demonstrated the utility of a luminescence-based reporter for identification of nfxB mutants previous to sequencing analysis. Thus, the nfxB/Cip(r system in combination with the luminescent reporter may be a valuable tool for studying mutational processes in Pseudomonas spp. wherein the genes encoding the NfxB repressor and

  3. Extended RAS and BRAF Mutation Analysis Using Next-Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Kazuko Sakai

    Full Text Available Somatic mutations in KRAS, NRAS, and BRAF genes are related to resistance to anti-EGFR antibodies in colorectal cancer. We have established an extended RAS and BRAF mutation assay using a next-generation sequencer to analyze these mutations. Multiplexed deep sequencing was performed to detect somatic mutations within KRAS, NRAS, and BRAF, including minor mutated components. We first validated the technical performance of the multiplexed deep sequencing using 10 normal DNA and 20 formalin-fixed, paraffin-embedded (FFPE tumor samples. To demonstrate the potential clinical utility of our assay, we profiled 100 FFPE tumor samples and 15 plasma samples obtained from colorectal cancer patients. We used a variant calling approach based on a Poisson distribution. The distribution of the mutation-positive population was hypothesized to follow a Poisson distribution, and a mutation-positive status was defined as a value greater than the significance level of the error rate (α = 2 x 10(-5. The cut-off value was determined to be the average error rate plus 7 standard deviations. Mutation analysis of 100 clinical FFPE tumor specimens was performed without any invalid cases. Mutations were detected at a frequency of 59% (59/100. KRAS mutation concordance between this assay and Scorpion-ARMS was 92% (92/100. DNA obtained from 15 plasma samples was also analyzed. KRAS and BRAF mutations were identified in both the plasma and tissue samples of 6 patients. The genetic screening assay using next-generation sequencer was validated for the detection of clinically relevant RAS and BRAF mutations using FFPE and liquid samples.

  4. Venus lower atmospheric composition: analysis by gas chromatography.

    Science.gov (United States)

    Oyama, V I; Carle, G C; Woeller, F; Pollack, J B

    1979-02-23

    The first gas chromatographic analysis of the lower atmosphere of Venus is reported. Three atmospheric samples were analyzed. The third of these samples showed carbon dioxide (96.4 percent), molecular nitrogen (3.41 percent), water vapor (0.135 percent), molecular oxygen [69.3 parts per million (ppm)], argon (18.6 ppm), neon (4.31 ppm), and sulfuir dioxide (186 ppm). The amounts of water vapor and sulfur dioxide detected are roughly compatible with the requirements of greenhouse models of the high surface temperature of Venus. The large positive gradient of sulfur dioxide, molecular oxygen, and water vapor from the clould tops to their bottoms, as implied by Earth-based observations and these resuilts, gives added support for the presence of major quantities of aqueous sulfuric acid in the clouds. A comparison of the inventory of inert gases found in the atmospheres of Venus, Earth, and Mars suggests that these components are due to outgassing from the planetary interiors. PMID:17833004

  5. Analysis of 23 polycyclic aromatic hydrocarbons in smokeless tobacco by gas chromatography-mass spectrometry

    OpenAIRE

    Stepanov, Irina; Villalta, Peter W.; Knezevich, Aleksandar; Jensen, Joni; Hatsukami, Dorothy; Hecht, Stephen S

    2010-01-01

    Smokeless tobacco contains 28 known carcinogens and causes precancerous oral lesions and oral and pancreatic cancer. A recent study conducted by our research team identified 8 different polycyclic aromatic hydrocarbons (PAH) in U.S. moist snuff, encouraging further investigations of this group of toxicants and carcinogens in smokeless tobacco products. In this study, we developed a gas chromatography-mass spectrometry method that allows simultaneous analysis of 23 various PAH in smokeless tob...

  6. Mutation analysis and molecular genetics of epidermolysis bullosa.

    Science.gov (United States)

    Pulkkinen, L; Uitto, J

    1999-02-01

    Cutaneous basement membrane zone (BMZ) consists of a number of attachment structures that are critical for stable association of the epidermis to the underlying dermis. These include hemidesmosomes, anchoring filaments and anchoring fibrils which form an interconnecting network extending from the intracellular milieu of basal keratinocytes across the dermal-epidermal basement membrane to the underlying dermis. Aberrations in this network structure, e.g. due to genetic lesions in the corresponding genes, can result in fragility of the skin at the level of the cutaneous BMZ. The prototype of such diseases is epidermolysis bullosa (EB), a heterogeneous group of genodermatoses characterized by fragility and blistering of the skin, often associated with extracutaneous manifestations, and inherited either in an autosomal dominant or autosomal recessive manner. Based on constellations of the phenotypic manifestations, severity of the disease, and the level of tissue separation within the cutaneous BMZ, EB has been divided into clinically distinct subcategories, including the simplex, hemidesmosomal, junctional and dystrophic variants. Elucidation of BMZ gene/protein systems and development of mutation detection strategies have allowed identification of mutations in 10 different BMZ genes which can explain the clinical heterogeneity of EB. These include mutations in the type VII collagen gene (COL7A1) in the dystrophic (severely scarring) forms of EB; mutations in the laminin 5 genes (LAMA3, LAMB3 and LAMC2) in a lethal (Herlitz) variant of junctional EB; aberrations in the type XVII collagen gene (COL17A1) in non-lethal forms of junctional EB; mutations in the alpha6 and beta4 integrin genes in a distinct hemidesmosomal variant of EB with congenital pyloric atresia; and mutations in the plectin gene (PLEC1) in a form of EB associated with late-onset muscular dystrophy. Identification of mutations in these gene/protein systems attests to their critical importance in the

  7. Pesticide analysis in rose wines by micellar electrokinetic chromatography.

    Science.gov (United States)

    Ravelo-Pérez, Lidia M; Hernández-Borges, Javier; Borges-Miquel, Teresa M; Rodríguez-Delgado, Miguel Angel

    2007-12-01

    In this work, the determination of 11 pesticides (pirimicarb, metalaxyl, pyrimethanil, procymidone, nuarimol, azoxystrobin, tebufenozide, fenarimol, benalaxyl, penconazole, and tetradifon) in rose wines by micellar EKC (MEKC) using reversed electrode polarity stacking mode (REPSM) as online preconcentration strategy is described. The MEKC buffer consisted of 100 mM sodium tetraborate and 30 mM SDS at pH 8.5 with 6% v/v 1-propanol. A solid-phase microextraction (SPME) procedure using PDMS/divinylbenzene (PDMS/DVB) fibers was applied to extract the selected pesticides from the rose wine samples. The comparison between the calibration curves obtained from hydroalcoholic solutions (12% v/v ethanol) and from rose wines (matrix matched calibration) showed the existence of a strong matrix effect. Furthermore, a comparison with calibration curves obtained with white wine samples also showed significant differences for most of the analyzed pesticides. As a result, a matrix matched calibration was developed. Quantitative extraction from spiked wine samples was carried out in triplicate at two levels of concentration (range 0.18-6.00 mg/L). LODs between 0.040 and 0.929 mg/L were achieved, which are below the maximum residue limits (MRLs) established for wine grapes (except for pirimicarb) by the EU and Spain legislation as well as by the Codex Alimentarius. The established method - which is solvent free, cost effective, and fast - was also applied to the analysis of several homemade rose wine samples and a commercial one. Two of the selected pesticides were found in some of the analyzed samples. PMID:18027361

  8. Fast gas chromatography for pesticide residues analysis using analyte protectants.

    Science.gov (United States)

    Kirchner, Michal; Húsková, Renáta; Matisová, Eva; Mocák, Ján

    2008-04-01

    Fast GC-MS with narrow-bore columns combined with effective sample preparation technique (QuEChERS method) was used for evaluation of various calibration approaches in pesticide residues analysis. In order to compare the performance of analyte protectants (APs) with matrix-matched standards calibration curves of selected pesticides were searched in terms of linearity of responses, repeatability of measurements and reached limit of quantifications utilizing the following calibration standards in the concentration range 1-500 ng mL(-1)(the equivalent sample concentration 1-500 microg kg(-1)): in neat solvent (acetonitrile) with/without addition of APs, matrix-matched standards with/without addition of APs. For APs results are in a good agreement with matrix-matched standards. To evaluate errors of determination of concentration synthetic samples at concentration level of pesticides 50 ng mL(-1) (50 microg kg(-1)) were analyzed and quantified using the above given standards. For less troublesome pesticides very good estimation of concentration was obtained utilizing APs, while for more troublesome pesticides such as methidathion, malathion, phosalone and deltamethrin significant overestimation reaching up to 80% occurred. According to presented results APs can be advantegously used for "easy" pesticides determination. For "difficult" pesticides an alternative calibration approach is required for samples potentially violating MRLs. An example of real sample measurement is shown. In this paper also the use of internal standards (triphenylphosphate (TPP) and heptachlor (HEPT)) for peak areas normalization is discussed in terms of repeatability of measurements and quantitative data obtained. TPP normalization provided slightly better results than the use of absolute peak areas measurements on the contrary to HEPT. PMID:17920613

  9. Thin layer chromatography coupled to paper spray ionization mass spectrometry for cocaine and its adulterants analysis.

    Science.gov (United States)

    De Carvalho, Thays C; Tosato, Flavia; Souza, Lindamara M; Santos, Heloa; Merlo, Bianca B; Ortiz, Rafael S; Rodrigues, Rayza R T; Filgueiras, Paulo R; França, Hildegardo S; Augusti, Rodinei; Romão, Wanderson; Vaz, Boniek G

    2016-05-01

    Thin layer chromatography (TLC) is a simple and inexpensive type of chromatography that is extensively used in forensic laboratories for drugs of abuse analysis. In this work, TLC is optimized to analyze cocaine and its adulterants (caffeine, benzocaine, lidocaine and phenacetin) in which the sensitivity (visual determination of LOD from 0.5 to 14mgmL(-1)) and the selectivity (from the study of three different eluents: CHCl3:CH3OH:HCOOHglacial (75:20:5v%), (C2H5)2O:CHCl3 (50:50v%) and CH3OH:NH4OH (100:1.5v%)) were evaluated. Aiming to improve these figures of merit, the TLC spots were identified and quantified (linearity with R(2)>0.98) by the paper spray ionization mass spectrometry (PS-MS), reaching now lower LOD values (>1.0μgmL(-1)). The method developed in this work open up perspective of enhancing the reliability of traditional and routine TLC analysis employed in the criminal expertise units. Higher sensitivity, selectivity and rapidity can be provided in forensic reports, besides the possibility of quantitative analysis. Due to the great simplicity, the PS(+)-MS technique can also be coupled directly to other separation techniques such as the paper chromatography and can still be used in analyses of LSD blotter, documents and synthetic drugs. PMID:26970868

  10. TP53 Mutations and Survival in Osteosarcoma Patients: A Meta-Analysis of Published Data

    Directory of Open Access Journals (Sweden)

    Zhe Chen

    2016-01-01

    Full Text Available Several research groups have examined the association between TP53 mutations and prognosis in human osteosarcoma. However, the results were controversial. The purpose of this study was to evaluate the prognostic value of TP53 mutations in osteosarcoma patients. A meta-analysis was conducted with all eligible studies which quantitatively evaluated the relationship between TP53 mutations and clinical outcome of osteosarcoma patients. Eight studies with a total of 210 patients with osteosarcoma were included in this meta-analysis. The risk ratio (RR with a 95% confidence interval (95% CI was calculated to assess the effect of TP53 mutations on 2-year overall survival. The quantitative synthesis of 8 published studies showed that TP53 mutations were associated with 2-year overall survival in osteosarcoma patients. These data suggested that TP53 mutations had an unfavorable impact on 2-year overall survival when compared to the counterparts with wild type (WT TP53 (RR: 1.79; 95% CI: 1.12 to 2.84; P=0.01; I2=0%. There was no between-study heterogeneity. TP53 mutations are an effective prognostic marker for survival of patients with osteosarcoma. However, further large-scale prospective trials should be performed to clarify the prognostic value of TP53 mutations on 3- or 5-year survival in osteosarcoma patients.

  11. Mutation analysis of cathepsin C gene in a Chinese patient with pre-pubertal periodontitis

    Institute of Scientific and Technical Information of China (English)

    YANG Yuan; BAI Xiao-wen; SONG Shu-juan; GE Li-hong; CAO Cai-fang

    2005-01-01

    @@ Pre-pubertal periodontitis (PPP) is a rare and rapidly progressive form of early onset periodontitis resulting in premature tooth loss of primary and permanent dentitions. Mutations in cathepsin C (CTSC) gene have been found in patients with pre-pubertal periodontitis and Papillon-Lefevre syndrome which also characterized with severe periodontitis and palmoplantar hyperkera-tosis.1-3 To date, more than 40 mutations of CTSC gene have been identified in ethnically diverse people worldwide.4 However, there is no such genetic analysis in China. In the present study, we report the mutation analysis of a Chinese patient with PPP.

  12. Mutational analysis of Btk, the defective gene in X-linked agammaglobulinemia

    Energy Technology Data Exchange (ETDEWEB)

    Conley, M.E.; Fitch-Hilgenberg, M.E.; Rohrer, J. [St. Jude Children`s Research Hospital, Memphis, TN (United States)

    1994-09-01

    Recent studies have shown that X-linked agammaglobulinemia (XLA), a disorder of B cell development, is due to mutations in an scr-like cytoplasmic tyrosine kinase, Btk. Thus far, mutations in this gene have been identified by sequencing of cDNA. To permit the detection of mutations in genomic DNA, we determined the structure of Btk and identified 19 exons in 37 kb of DNA. PCR primers were designed to amplify each exon with its splice sites. Two overlapping PCR products were employed for exons longer than 230 base pairs. Single strand conformation polymorphism (SSCP) analysis was used to screen genomic DNA from 30 unrelated families presumed to carry a mutation in Btk. It was possible to amplify DNA in every reaction from every patient. None of the DNA samples demonstrated more than one aberrant SSCP pattern. Twenty three mutations were detected in 25 families. Seven point mutations resulting in amino acid substitutions were seen. An additional 7 base pair substitutions gave rise to premature stop codons. Two splice defects were noted. Small insertions or deletions, all resulting in frameshifts and premature stop codons were seen in eight patients. One patient had an A to G transition in the ATG start codon. Two mutations, both at CpG dinucleotides, were seen in more than one family. Haplotype analysis, using CA repeats closely linked to Btk, demonstrated that the mutations in these families arose independently. We conclude from these studies that the mutations in Btk in patients with XLA are highly variable. Large deletions are uncommon, although small 1 to 4 bp insertions or deletions constitute as many as one third of the mutations. Further analysis of patients with amino acid substitutions will permit structure/function correlations.

  13. Detection of Somatic Mutations by High-Resolution DNA Melting (HRM) Analysis in Multiple Cancers

    OpenAIRE

    Jesus Gonzalez-Bosquet; Jacob Calcei; Wei, Jun S.; Montserrat Garcia-Closas; Sherman, Mark E.; Stephen Hewitt; Joseph Vockley; Jolanta Lissowska; Yang, Hannah P.; Javed Khan; Stephen Chanock

    2011-01-01

    Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounde...

  14. Ion Chromatography.

    Science.gov (United States)

    Mulik, James D.; Sawicki, Eugene

    1979-01-01

    Accurate for the analysis of ions in solution, this form of analysis enables the analyst to directly assay many compounds that previously were difficult or impossible to analyze. The method is a combination of the methodologies of ion exchange, liquid chromatography, and conductimetric determination with eluant suppression. (Author/RE)

  15. Detailed analysis of petroleum cuts by multidimensional gas chromatography; Analyse detaillee de coupes petrolieres par chromatographie en phase gazeuse multidimensionnelle

    Energy Technology Data Exchange (ETDEWEB)

    Vendeuvre, C.

    2006-01-15

    The limitations of petroleum resources implying a better valorisation of crude oil through the optimisation of production, refinery and petrochemistry processes, as well as the environmental regulations have strengthened the necessity of more detailed characterisation of petroleum products. In order to take up this challenge, efficient analytical tools have to be developed. This work demonstrates that comprehensive two-dimensional gas chromatography (GCxGC) constitutes a major advance compared to GC owing to its improved resolution power and to the structured chromatograms indicating the polarity and the volatility of hydrocarbons. The principle of GCxGC is based on the analysis of a whole sample in two independent dimensions of separation achieved using two GC columns of different selectivities; between the two columns a modulator device samples, focuses and re-injects small portions of the effluent from the first column into the second one. Since its introduction in 1991, GCxGC has known a rapid growth and has received a wide acceptance by the analytical science community. The competitive situation has considerably evolved during this thesis with the introduction of commercial systems and the two first sessions of an international symposium dedicated to this technique (Volendam, 2003 and Atlanta, 2004). The key points of the thesis concern the development of a GCxGC prototype system using dual jets CO{sub 2} technology and a data processing program; the evaluation of a retention model allowing a rational choice of operating conditions; and the application of this technique to various and complex issues. Thus, effluents from petrochemistry, refinery or pollution areas have been analysed according to the chemical classes of hydrocarbons and to their number of carbon atoms; a new method for obtaining distillation curves for each chemical group was also presented. Furthermore, the hyphenation of GCxGC with a specific sulphur detector revealed a great interest for

  16. DETECTION OF K-RAS AND P53 MUTATIONS IN SPUTUM SAMPLES OF LUNG CANCER PATIENTS USING LASER CAPTURE MICRODISSECTION MICROSCOPE AND MUTATION ANALYSIS

    Science.gov (United States)

    Detection of K-ras and p53 Mutations in Sputum Samples of Lung Cancer Patients Using Laser Capture Microdissection Microscope and Mutation AnalysisPhouthone Keohavong a,*, Wei-Min Gao a, Kui-Cheng Zheng a, Hussam Mady b, Qing Lan c, Mona Melhem b, and Judy Mumford d.<...

  17. Denaturing high-performance liquid chromatography of the myotubularin-related 2 gene (MTMR2) in unrelated patients with Charcot-Marie-Tooth disease suggests a low frequency of mutation in inherited neuropathy.

    Science.gov (United States)

    Bolino, A; Lonie, L J; Zimmer, M; Boerkoel, C F; Takashima, H; Monaco, A P; Lupski, J R

    2001-03-01

    Charcot-Marie-Tooth type 4B (CMT4B), an autosomal recessive demyelinating neuropathy characterized by focally folded myelin sheaths in the peripheral nerve, has been associated with mutations in the gene encoding myotubularin-related protein 2, MTMR2, on chromosome 11q22. To investigate whether mutations in MTMR2 may also cause different forms of CMT, we screened 183 unrelated patients with a broad spectrum of CMT and related neuropathies using denaturing high-performance liquid chromatography. We identified four frequent and three rare exonic variants; two of the rare variants were identified in two unrelated patients with congenital hypomyelinating neuropathy and not in the normal controls. Our results suggest that loss-of-function mutations in MTMR2 are preferentially associated with the CMT4B phenotype. PMID:11354824

  18. Multiresidue analysis of pesticides in traditional Chinese medicines using gas chromatography - negative chemical ionization tandem mass spectrometry

    Science.gov (United States)

    In this study, a residue analysis method for the simultaneous determination of 107 pesticides in the traditional Chinese medicines (TCMs), Angelica sinensis, Angelica dahurica, Leonurus heterophyllus Sweet, Pogostemon cablin, and Lonicera japonica Thunb, was developed using gas chromatography couple...

  19. Spectrum of mutations and genotype-phenotype analysis in Currarino syndrome.

    Science.gov (United States)

    Köchling, J; Karbasiyan, M; Reis, A

    2001-08-01

    The triad of a presacral tumour, sacral agenesis and anorectal malformation constitutes the Currarino syndrome which is caused by dorsal-ventral patterning defects during embryonic development. The syndrome occurs in the majority of patients as an autosomal dominant trait associated with mutations in the homeobox gene HLXB9 which encodes the nuclear protein HB9. However, genotype-phenotype analyses have been performed only in a few families and there are no reports about the specific impact of HLXB9 mutations on HB9 function. We performed a mutational analysis in 72 individuals from nine families with Currarino syndrome. We identified a total of five HLXB9 mutations, four novel and one known mutation, in four out of four families and one out of five sporadic cases. Highly variable phenotypes and a low penetrance with half of all carriers being clinically asymptomatic were found in three families, whereas affected members of one family showed almost identical phenotypes. However, an obvious genotype-phenotype correlation was not found. While HLXB9 mutations were diagnosed in 23 patients, no mutation or microdeletion was detected in four sporadic patients with Currarino syndrome. The distribution pattern of here and previously reported HLXB9 mutations indicates mutational predilection sites within exon 1 and the homeobox. Furthermore, sequence homology to Drosophila homeobox genes suggest that some of these mutations located within the homeobox may alter the DNA-binding specificity of HB9 while those in sequences homologous to a recently identified NLS motif of the human homeobox gene PDX-1 may impair nuclear translocation of the mutated protein. PMID:11528505

  20. Functional analysis of 'a' determinant mutations associated with occult HBV in HIV-positive South Africans.

    Science.gov (United States)

    Powell, Eleanor A; Boyce, Ceejay L; Gededzha, Maemu P; Selabe, Selokela G; Mphahlele, M Jeffrey; Blackard, Jason T

    2016-07-01

    Occult hepatitis B is defined by the presence of hepatitis B virus (HBV) DNA in the absence of hepatitis B surface antigen (HBsAg). Occult HBV is associated with the development of hepatocellular carcinoma, reactivation during immune suppression, and virus transmission. Viral mutations contribute significantly to the occult HBV phenotype. Mutations in the 'a' determinant of HBsAg are of particular interest, as these mutations are associated with immune escape, vaccine escape and diagnostic failure. We examined the effects of selected occult HBV-associated mutations identified in a population of HIV-positive South Africans on HBsAg production in vitro. Mutations were inserted into two different chronic HBV backbones and transfected into a hepatocyte-derived cell line. HBsAg levels were quantified by enzyme-linked immunosorbent assay (ELISA), while the detectability of mutant HBsAg was determined using an HA-tagged HBsAg expression system. Of the seven mutations analysed, four (S132P, C138Y, N146D and C147Y) resulted in decreased HBsAg expression in one viral background but not in the second viral background. One mutation (N146D) led to a decrease in HBsAg detected as compared to HA-tag, indicating that this mutation compromises the ability of the ELISA to detect HBsAg. The contribution of occult-associated mutations to the HBsAg-negative phenotype of occult HBV cannot be determined adequately by testing the effect of the mutation in a single viral background, and rigorous analysis of these mutations is required. PMID:27031988

  1. Supercritical fluid chromatography with photodiode array detection for pesticide analysis in papaya and avocado samples.

    Science.gov (United States)

    Pano-Farias, Norma S; Ceballos-Magaña, Silvia G; Gonzalez, Jorge; Jurado, José M; Muñiz-Valencia, Roberto

    2015-04-01

    To improve the analysis of pesticides in complex food matrices with economic importance, alternative chromatographic techniques, such as supercritical fluid chromatography, can be used. Supercritical fluid chromatography has barely been applied for pesticide analysis in food matrices. In this paper, an analytical method using supercritical fluid chromatography coupled to a photodiode array detection has been established for the first time for the quantification of pesticides in papaya and avocado. The extraction of methyl parathion, atrazine, ametryn, carbofuran, and carbaryl was performed through the quick, easy, cheap, effective, rugged, and safe methodology. The method was validated using papaya and avocado samples. For papaya, the correlation coefficient values were higher than 0.99; limits of detection and quantification ranged from 130-380 and 220-640 μg/kg, respectively; recovery values ranged from 72.8-94.6%; precision was lower than 3%. For avocado, limit of detection values were ˂450 μg/kg; precision was lower than 11%; recoveries ranged from 50.0-94.2%. Method feasibility was tested for lime, banana, mango, and melon samples. Our results demonstrate that the proposed method is applicable to methyl parathion, atrazine, ametryn, and carbaryl, toxics pesticides used worldwide. The methodology presented in this work could be applicable to other fruits. PMID:25641906

  2. On the possibility of shear-driven chromatography: a theoretical performance analysis.

    Science.gov (United States)

    Desmet, G; Baron, G V

    1999-09-01

    The use of shear forces for the generation of the mobile phase flow in chromatographic separations is proposed. This novel chromatographic operating principle, referred to as shear-driven chromatography (SDC), completely circumvents the pressure-drop limitation of conventional pressure-driven GC and LC without affecting the operational flexibility (choice of mobile and stationary phases, possibility of solvent and/or temperature programming, etc.). In the present paper, the expression for the height equivalent to a theoretical plate in SDC in a channel with a flat rectangular cross-section is established and is used to demonstrate the large gain in analysis speed under LC, GC and supercritical fluid chromatography conditions. PMID:10514973

  3. Analysis of quality of aviation lubricating oils by means of liquid and gas-liquid chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Kholostova, G.G.; Bakunin, V.N.; Shimonaev, G.S.

    1987-01-01

    The authors examine the basic methodological aspects of chromatographic analysis of the quality of oils for aircraft gas turbine engines, and certain relationships in oil aging that have been established on this basis. A commercial ester (designated PEE) was selected for investigation of pentaerythritol and C/sub 5/-C/sub 9/ synthetic fatty acids (SFA) which serves as the synthetic base stock for a number of aviation oils. The changes in PEE composition upon oxidation, with or without additives, were evaluated by means of gas-liquid chromatography in a Tsvet-100 chromatograph with a flame ionization detector. The results from examination of the original and oxidized PEE samples by means of gas and liquid chromatography are presented.

  4. Application of high-temperature gas chromatography to the analysis of used frying fats

    International Nuclear Information System (INIS)

    The determination of polar compounds is the most commonly applied technique in the analysis of used frying fats and oils. High-temperature gas chromatography allows for a quantitative determination of oxidized monomeric FAME and dimeric FAME thus giving extra information on oil degradation starting from the fraction of polar compounds. Polar compounds are trans esterified and methyl esters are separated in a VF-5ht Ultimetal column (150 degree centigrade -held for 5 min- rising at 5 degree centigrade min-1 to 370 degree centigrade and held for 5 min) using methyl tricosanoate as internal standard. Results are compared with those obtained by more complex alternative methodology using high-performance size-exclusion chromatography. (Author)

  5. Application of high-temperature gas chromatography to the analysis of used frying fats

    Energy Technology Data Exchange (ETDEWEB)

    Aguirre, M.; Marmesat, S.; Ruiz Mendez, M. V.; Dobarganes, M. C.

    2010-07-01

    The determination of polar compounds is the most commonly applied technique in the analysis of used frying fats and oils. High-temperature gas chromatography allows for a quantitative determination of oxidized monomeric FAME and dimeric FAME thus giving extra information on oil degradation starting from the fraction of polar compounds. Polar compounds are trans esterified and methyl esters are separated in a VF-5ht Ultimetal column (150 degree centigrade -held for 5 min- rising at 5 degree centigrade min-1 to 370 degree centigrade and held for 5 min) using methyl tricosanoate as internal standard. Results are compared with those obtained by more complex alternative methodology using high-performance size-exclusion chromatography. (Author)

  6. Analysis of antimycin A by reversed-phase liquid chromatography/nuclear magnetic-resonance spectrometry

    Science.gov (United States)

    Ha, Steven T.K.; Wilkins, Charles L.; Abidi, Sharon L.

    1989-01-01

    A mixture of closely related streptomyces fermentation products, antimycin A, Is separated, and the components are identified by using reversed-phase high-performance liquid chromatography with directly linked 400-MHz proton nuclear magnetic resonance detection. Analyses of mixtures of three amino acids, alanine, glycine, and valine, are used to determine optimal measurement conditions. Sensitivity increases of as much as a factor of 3 are achieved, at the expense of some loss in chromatographic resolution, by use of an 80-μL NMR cell, Instead of a smaller 14-μL cell. Analysis of the antimycin A mixture, using the optimal analytical high performance liquid chromatography/nuclear magnetic resonance conditions, reveals it to consist of at least 10 closely related components.

  7. Whole exome analysis identifies frequent CNGA1 mutations in Japanese population with autosomal recessive retinitis pigmentosa.

    Directory of Open Access Journals (Sweden)

    Satoshi Katagiri

    Full Text Available OBJECTIVE: The purpose of this study was to investigate frequent disease-causing gene mutations in autosomal recessive retinitis pigmentosa (arRP in the Japanese population. METHODS: In total, 99 Japanese patients with non-syndromic and unrelated arRP or sporadic RP (spRP were recruited in this study and ophthalmic examinations were conducted for the diagnosis of RP. Among these patients, whole exome sequencing analysis of 30 RP patients and direct sequencing screening of all CNGA1 exons of the other 69 RP patients were performed. RESULTS: Whole exome sequencing of 30 arRP/spRP patients identified disease-causing gene mutations of CNGA1 (four patients, EYS (three patients and SAG (one patient in eight patients and potential disease-causing gene variants of USH2A (two patients, EYS (one patient, TULP1 (one patient and C2orf71 (one patient in five patients. Screening of an additional 69 arRP/spRP patients for the CNGA1 gene mutation revealed one patient with a homozygous mutation. CONCLUSIONS: This is the first identification of CNGA1 mutations in arRP Japanese patients. The frequency of CNGA1 gene mutation was 5.1% (5/99 patients. CNGA1 mutations are one of the most frequent arRP-causing mutations in Japanese patients.

  8. Quantitative Analysis of Rutin in Buckwheat (Fagopyrum sp.) by High Performance Liquid Chromatography

    OpenAIRE

    Minami, M; Kitabayashi, H; Ujihara, A

    1998-01-01

    For the quantitative analysis of rutin in common buckwheat (Fagopyrum esculentum) and tartary buckwheat (F. tataricum), the operating condition of high performance liquid chromatography (HPLC) and methods of sample preparation and extraction were investigated. Reliable analysis method with less than 5 g of sample was established as follows; ① drying samples for 24 hours at 70℃ by using forced air flow oven,② grinding 5 g of seed and 2 g of leaf samples into powder for 30 seconds,③ extracting ...

  9. Inferring loop invariants by mutation, dynamic analysis, and static checking

    OpenAIRE

    Galeotti, J.P.; Furia, C.A.; May, E.; Fraser, G.; Zeller, A.

    2015-01-01

    Verifiers that can prove programs correct against their full functional specification require, for programs with loops, additional annotations in the form of loop invariants - properties that hold for every iteration of a loop. We show that significant loop invariant candidates can be generated by systematically mutating postconditions; then, dynamic checking (based on automatically generated tests) weeds out invalid candidates, and static checking selects provably valid ones. We present a fr...

  10. Mutational analysis of PI3K/AKT and RAS/RAF pathway activation in malignant salivary gland tumours with a new mutation of PIK3CA.

    Science.gov (United States)

    Shalmon, B; Drendel, M; Wolf, M; Hirshberg, A; Cohen, Y

    2016-06-01

    The phosphoinositide 3-kinase (PIK3)/v-akt murine thymoma (AKT) oncogene pathway and the RAS/RAF pathway are involved in regulating the signalling of multiple biological processes, including apoptosis, metabolism, cell proliferation, and cell growth. Mutations in the genes within these pathways are frequently found in several tumours. The aim of this study was to investigate the frequency of mutations in the PIK3CA, BRAF, and KRAS genes in cases of malignant salivary gland tumours. Mutational analysis of the PIK3CA, KRAS, and BRAF genes was performed by direct sequencing of material from 21 patients with malignant salivary gland tumours who underwent surgery between 1992 and 2001. No mutations were found in the KRAS exon 2, BRAF exon 15, or PIK3CA exon 9 genes. However, an unpublished mutation of the PIK3CA gene in exon 20 (W1051 stop mutation) was found in one case of adenocarcinoma NOS. The impact of this mutation on the biological behaviour of the tumour has yet to be explored, however the patient with adenocarcinoma NOS harbouring this mutation has survived for over 20 years following surgery despite a high stage at presentation. Further studies with more homogeneous patient cohorts are needed to address whether this mutation reflects a different clinical presentation and may benefit from targeted treatment strategies. PMID:26811072

  11. Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute

    Science.gov (United States)

    Churkin, Alexander; Barash, Danny

    2006-12-01

    We introduce here for the first time the RNAMute package, a pattern-recognition-based utility to perform mutational analysis and detect vulnerable spots within an RNA sequence that affect structure. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called "riboswitches" and other known RNA switches, without an organized utility that analyzes all single-point mutations and can be further expanded. The RNAMute package allows a comprehensive categorization, given an RNA sequence that has functional relevance, by exploring the patterns of all single-point mutants. For illustration, we apply the RNAMute package on an RNA transcript for which individual point mutations were shown experimentally to inactivate spectinomycin resistance in Escherichia coli. Functional analysis of mutations on this case study was performed experimentally by creating a library of point mutations using PCR and screening to locate those mutations. With the availability of RNAMute, preanalysis can be performed computationally before conducting an experiment.

  12. Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute

    Directory of Open Access Journals (Sweden)

    Churkin Alexander

    2006-01-01

    Full Text Available We introduce here for the first time the RNAMute package, a pattern-recognition-based utility to perform mutational analysis and detect vulnerable spots within an RNA sequence that affect structure. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called "riboswitches" and other known RNA switches, without an organized utility that analyzes all single-point mutations and can be further expanded. The RNAMute package allows a comprehensive categorization, given an RNA sequence that has functional relevance, by exploring the patterns of all single-point mutants. For illustration, we apply the RNAMute package on an RNA transcript for which individual point mutations were shown experimentally to inactivate spectinomycin resistance in Escherichia coli. Functional analysis of mutations on this case study was performed experimentally by creating a library of point mutations using PCR and screening to locate those mutations. With the availability of RNAMute, preanalysis can be performed computationally before conducting an experiment.

  13. The TREAT-NMD DMD Global Database: analysis of more than 7,000 Duchenne muscular dystrophy mutations.

    Science.gov (United States)

    Bladen, Catherine L; Salgado, David; Monges, Soledad; Foncuberta, Maria E; Kekou, Kyriaki; Kosma, Konstantina; Dawkins, Hugh; Lamont, Leanne; Roy, Anna J; Chamova, Teodora; Guergueltcheva, Velina; Chan, Sophelia; Korngut, Lawrence; Campbell, Craig; Dai, Yi; Wang, Jen; Barišić, Nina; Brabec, Petr; Lahdetie, Jaana; Walter, Maggie C; Schreiber-Katz, Olivia; Karcagi, Veronika; Garami, Marta; Viswanathan, Venkatarman; Bayat, Farhad; Buccella, Filippo; Kimura, En; Koeks, Zaïda; van den Bergen, Janneke C; Rodrigues, Miriam; Roxburgh, Richard; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Zimowski, Janusz; Santos, Rosário; Neagu, Elena; Artemieva, Svetlana; Rasic, Vedrana Milic; Vojinovic, Dina; Posada, Manuel; Bloetzer, Clemens; Jeannet, Pierre-Yves; Joncourt, Franziska; Díaz-Manera, Jordi; Gallardo, Eduard; Karaduman, A Ayşe; Topaloğlu, Haluk; El Sherif, Rasha; Stringer, Angela; Shatillo, Andriy V; Martin, Ann S; Peay, Holly L; Bellgard, Matthew I; Kirschner, Jan; Flanigan, Kevin M; Straub, Volker; Bushby, Kate; Verschuuren, Jan; Aartsma-Rus, Annemieke; Béroud, Christophe; Lochmüller, Hanns

    2015-04-01

    Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations). PMID:25604253

  14. The TREAT-NMD DMD Global Database: Analysis of More than 7,000 Duchenne Muscular Dystrophy Mutations

    Science.gov (United States)

    Bladen, Catherine L; Salgado, David; Monges, Soledad; Foncuberta, Maria E; Kekou, Kyriaki; Kosma, Konstantina; Dawkins, Hugh; Lamont, Leanne; Roy, Anna J; Chamova, Teodora; Guergueltcheva, Velina; Chan, Sophelia; Korngut, Lawrence; Campbell, Craig; Dai, Yi; Wang, Jen; Barišić, Nina; Brabec, Petr; Lahdetie, Jaana; Walter, Maggie C; Schreiber-Katz, Olivia; Karcagi, Veronika; Garami, Marta; Viswanathan, Venkatarman; Bayat, Farhad; Buccella, Filippo; Kimura, En; Koeks, Zaïda; van den Bergen, Janneke C; Rodrigues, Miriam; Roxburgh, Richard; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Zimowski, Janusz; Santos, Rosário; Neagu, Elena; Artemieva, Svetlana; Rasic, Vedrana Milic; Vojinovic, Dina; Posada, Manuel; Bloetzer, Clemens; Jeannet, Pierre-Yves; Joncourt, Franziska; Díaz-Manera, Jordi; Gallardo, Eduard; Karaduman, A Ayşe; Topaloğlu, Haluk; El Sherif, Rasha; Stringer, Angela; Shatillo, Andriy V; Martin, Ann S; Peay, Holly L; Bellgard, Matthew I; Kirschner, Jan; Flanigan, Kevin M; Straub, Volker; Bushby, Kate; Verschuuren, Jan; Aartsma-Rus, Annemieke; Béroud, Christophe; Lochmüller, Hanns

    2015-01-01

    Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations). PMID:25604253

  15. Flavor characterization of ripened cod roe by gas chromatography, sensory analysis, and electronic nose.

    Science.gov (United States)

    Jonsdottir, Rosa; Olafsdottir, Gudrun; Martinsdottir, Emilia; Stefansson, Gudmundur

    2004-10-01

    Characterization of the flavors of ripened roe products is of importance to establish a basis for a standardized product. Flavor profiles of commercially processed ripened roe from Iceland and Norway were studied by sensory analysis, gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS), and an electronic nose to characterize the headspace of ripened roe. Sensory analysis showed that ripened roe odor and flavor in combination with caviar flavor and whey/caramel-like odor give the overall positive effect of the complex characteristic roe flavor. Analysis of volatiles by GC-MS and electronic nose confirmed the presence of aroma compounds contributing to the typical ripening and spoilage flavors detected by the sensory analysis. Methional, 1-octen-3-ol, and 2,6-nonadienal were the most important compounds contributing to ripened roe odor. Spoilage flavors were partly contributed by 3-methyl-1-butanol and 3-methylbutanal, which can be measured by the electronic nose and are suggested as quality indicators for objectively assessing the ripening of roe. Principal component analysis of the overall data showed that GC-O correlated well with sensory evaluation and the electronic nose measurements. PMID:15453695

  16. Mutational analysis of ATP7B in Chinese Wilson disease patients.

    Science.gov (United States)

    Hua, Rui; Hua, Fang; Jiao, Yonggeng; Pan, Yu; Yang, Xu; Peng, Shanshan; Niu, Junqi

    2016-01-01

    Wilson Disease (WD) is an inborn error of copper metabolism inherited in an autosomal recessive manner caused by the mutations in the P-type ATPase gene (ATP7B). In this study, we screen and detect the mutations of the ATP7B gene in unrelated Chinese WD patients. A total of 68 individuals from ten provinces of China with WD were recruited. Of them, 43 were males and 25 were females, and their onset ages were from 1 to 48 years with a median onset age of 22.2 years. All the exons and exon/intron boundaries of ATP7B gene of the patients were sequenced and aligned to the referred ATP7B gene sequence. The results suggested that 66 of the 68 patents carried with at least one mutation and 48 different mutations were identified including 34 missense, one synonymous, two nonsense, two splicing, and nine frameshift mutations (five insertion and four deletion). Among these mutations, c.2333G>T, c.2310C>G, c.2975C>T, and c.3443T>C were the most prevalent mutants and c.2310C>G always linked with c.2333G>T. The eighth, 11(th), and 18(th) exons carried more mutations (6/48, 5/48, and 5/48, respectively) than others. After comparing with the mutations reported previously, 22 out of the 48 mutations were identified as novel mutations. A popular algorithm, Polyphen-2, was used to predict the effects of the amino-acid substitution due to the mutations on the structure and function of ATP7B function and the predicted results indicated that all the missense mutations were unfavorable except c.121A>G and c.748G>A. Phenotype/genotype correlation analysis suggested that the patients with c.2975C>T or c.3809A>G often presented WD features before 12 years old while the patients with c.3443T>C almost presented WD after 12 years old. This is the first time to identify the common mutations contributing to early onset age in Chinese WD patients. Our study will broaden our knowledge about ATP7B mutations in WD patients. PMID:27398169

  17. Bioinformatic analysis of pathogenic missense mutations of activin receptor like kinase 1 ectodomain.

    Directory of Open Access Journals (Sweden)

    Claudia Scotti

    Full Text Available Activin A receptor, type II-like kinase 1 (also called ALK1, is a serine-threonine kinase predominantly expressed on endothelial cells surface. Mutations in its ACVRL1 encoding gene (12q11-14 cause type 2 Hereditary Haemorrhagic Telangiectasia (HHT2, an autosomal dominant multisystem vascular dysplasia. The study of the structural effects of mutations is crucial to understand their pathogenic mechanism. However, while an X-ray structure of ALK1 intracellular domain has recently become available (PDB ID: 3MY0, structure determination of ALK1 ectodomain (ALK1(EC has been elusive so far. We here describe the building of a homology model for ALK1(EC, followed by an extensive bioinformatic analysis, based on a set of 38 methods, of the effect of missense mutations at the sequence and structural level. ALK1(EC potential interaction mode with its ligand BMP9 was then predicted combining modelling and docking data. The calculated model of the ALK1(EC allowed mapping and a preliminary characterization of HHT2 associated mutations. Major structural changes and loss of stability of the protein were predicted for several mutations, while others were found to interfere mainly with binding to BMP9 or other interactors, like Endoglin (CD105, whose encoding ENG gene (9q34 mutations are known to cause type 1 HHT. This study gives a preliminary insight into the potential structure of ALK1(EC and into the structural effects of HHT2 associated mutations, which can be useful to predict the potential effect of each single mutation, to devise new biological experiments and to interpret the biological significance of new mutations, private mutations, or non-synonymous polymorphisms.

  18. Evaluation of vermicompost maturity using scanning electron microscopy and paper chromatography analysis.

    Science.gov (United States)

    Senthil Kumar, D; Satheesh Kumar, P; Rajendran, N M; Uthaya Kumar, V; Anbuganapathi, G

    2014-04-01

    Vermicompost was produced from flower waste inoculated with biofertilizers using the earthworm Eisenia fetida. Principal component analysis (PCA) and cluster analysis (CA) were carried out on the basis of physicochemical parameters of vermicomposted samples. From the results of the PCA and CA, it was possible to classify two different groups of vermicompost samples in the following categories: E2 and E5; and E1, E3, E4, and control. Scanning electron microscopy and biodynamic circular paper chromatography analysis were used to investigate the changes in surface morphology and functional groups in the control and vermicompost products. SEM analysis of E1-E5 shows more fragment and pores than the control. Chromatographic analysis of vermicompost indicated the mature condition of the compost materials. PMID:24634991

  19. Coupling Charge Reduction Mass Spectrometry to Liquid Chromatography for Complex Mixture Analysis.

    Science.gov (United States)

    Stutzman, John R; Crowe, Matthew C; Alexander, James N; Bell, Bruce M; Dunkle, Melissa N

    2016-04-01

    Electrospray ionization (ESI) of solution mixtures often generates complex mass spectra, even following liquid chromatography (LC), due to analyte multiple charging. Multiple charge state distributions can lead to isobaric interferences, mass spectral congestion, and ambiguous ion identification. As a consequence, data interpretation increases in complexity. Several charge reduction mass spectrometry (MS) approaches have been previously developed to reduce the average charge state of gaseous ions; however, all of these techniques have been restricted to direct infusion MS. In this study, synthetic polyols and surfactants separated by liquid chromatography and ionized by positive mode ESI have been subjected to polonium-210 α-particle radiation to reduce the average charge state to singly charged cations prior to mass analysis. LC/MS analysis of 5000 molecular weight poly(ethylene glycol) (PEG5000) generated an average charge state of 5.88+; whereupon, liquid chromatography/electrospray ionization/charge reduction/mass spectrometry (LC/CR/MS) analysis of PEG 5000 generated an average charge state of 1.00+. The PEG5000 results demonstrated a decrease in spectral complexity and enabled facile interpretation. Other complex solution mixtures representing specific MS challenges (i.e., competitive ionization and isobaric ion overlap) were explored and analyzed with LC/CR/MS to demonstrate the benefits of coupling LC to CR/MS. For example, polyol information related to initiator, identity/relative amount of monomer, and estimated molecular weight was characterized in random and triblock ethylene oxide/propylene oxide polyols using LC/CR/MS. LC/CR/MS is a new analytical technique for the analysis of complex mixtures. PMID:26971559

  20. Reducing Dilution and Analysis Time in Online Comprehensive Two-Dimensional Liquid Chromatography by Active Modulation.

    Science.gov (United States)

    Gargano, Andrea F G; Duffin, Mike; Navarro, Pablo; Schoenmakers, Peter J

    2016-02-01

    Online comprehensive two-dimensional liquid chromatography (LC × LC) offers ways to achieve high-performance separations in terms of peak capacity (exceeding 1000) and additional selectivity to realize applications that cannot be addressed with one-dimensional chromatography (1D-LC). However, the greater resolving power of LC × LC comes at the price of higher dilutions (thus, reduced sensitivity) and, often, long analysis times (>100 min). The need to preserve the separation attained in the first dimension ((1)D) causes greater dilution for LC × LC, in comparison with 1D-LC, and long analysis times to sample the (1)D with an adequate number of second dimension separations. A way to significantly reduce these downsides is to introduce a concentration step between the two chromatographic dimensions. In this work we present a possible active-modulation approach to concentrate the fractions of (1)D effluent. A typical LC × LC system is used with the addition of a dilution flow to decrease the strength of the (1)D effluent and a modulation unit that uses trap columns. The potential of this approach is demonstrated for the separation of tristyrylphenol ethoxylate phosphate surfactants, using a combination of hydrophilic interaction and reversed-phase liquid chromatography. The modified LC × LC system enabled us to halve the analysis time necessary to obtain a similar degree of separation efficiency with respect to UHPLC based LC × LC and of 5 times with respect to HPLC instrumentation (40 compared with 80 and 200 min, respectively), while at the same time reducing dilution (DF of 142, 299, and 1529, respectively) and solvent consumption per analysis (78, 120, and 800 mL, respectively). PMID:26709410

  1. Applications of capillary electrophoresis in DNA mutation analysis of genetic disorders.

    OpenAIRE

    Le, H; Fung, D.; Trent, R.J.

    1997-01-01

    AIM: To facilitate DNA mutation analysis by use of capillary electrophoresis. METHODS: The usefulness and applications of capillary electrophoresis in DNA fragment sizing and sequencing were evaluated. RESULTS: DNA mutation testing in disorders such as cystic fibrosis, Huntington disease, alpha thalassaemia, and hereditary fructose intolerance were undertaken effectively. However, sizing the (CAG)n repeat in the case of Huntington disease was a potential problem when using capillary electroph...

  2. Phylogenetic analysis of mitochondrial DNA:detection of mutations in patients with occipital stroke

    OpenAIRE

    Finnilä, S. (Saara)

    2000-01-01

    Abstract A mitochondrial disorder may be one of the rare aetiologies of occipital stroke. Clinical and molecular analysis has suggested that 10% of young patients with occipital stroke have a mitochondrial disorder and 6% harbour the mutation 3243A>G in mitochondrial DNA (mtDNA), causing the MELAS syndrome. To identify other possible mtDNA mutations involved, we studied mtDNA genotypes in patients who had suffered an occipital stroke and in whom the common pathogenic m...

  3. Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations.

    Directory of Open Access Journals (Sweden)

    Alex S Holehouse

    Full Text Available Protein post-translational modifications (PTMs are an important aspect of protein regulation. The number of PTMs discovered within the human proteome, and other proteomes, has been rapidly expanding in recent years. As a consequence of the rate in which new PTMs are identified, analysis done in one year may result in different conclusions when repeated in subsequent years. Among the various functional questions pertaining to PTMs, one important relationship to address is the interplay between modifications and mutations. Specifically, because the linear sequence surrounding a modification site often determines molecular recognition, it is hypothesized that mutations near sites of PTMs may be more likely to result in a detrimental effect on protein function, resulting in the development of disease.We wrote an application programming interface (API to make analysis of ProteomeScout, a comprehensive database of PTMs and protein information, easy and reproducible. We used this API to analyze the relationship between PTMs and human mutations associated with disease (based on the 'Clinical Significance' annotation from dbSNP. Proteins containing pathogenic mutations demonstrated a significant study bias which was controlled for by analyzing only well-studied proteins, based on their having at least one pathogenic mutation. We found that pathogenic mutations are significantly more likely to lie within eight amino acids of a phosphoserine, phosphotyrosine or ubiquitination site when compared to mutations in general, based on a Fisher's Exact test. Despite the skew of pathogenic mutations occurring on positively charged arginines, we could not account for this relationship based only on residue type. Finally, we hypothesize a potential mechanism for a pathogenic mutation on RAF1, based on its proximity to a phosphorylation site, which represents a subtle regulation difference that may explain why its biochemical effect has failed to be uncovered

  4. Graphitized carbon in gas-liquid-solid chromatography and gas chromatography/mass spectrometric analysis of high boiling hydrocarbon mixtures

    International Nuclear Information System (INIS)

    Gas--liquid--solid chromatography (GLSC) employing a poly(phenyl ether) (PPE 20) liquid phase on graphitized carbon black (GCB) is applicable to the analyses of crude oils and distillates of sedimentary rocks. The elution of C4 to C40 hydrocarbons which consist of n-alkanes, isoprenoid-type alkanes, steranes, olefins, and aromatic hydrocarbons can be handled in a single GC run. A GLSC column in tandem with a mass spectrometer provides an excellent means for the identification of geochemically significant organic compounds in complex natural mixtures. 8 figures, 4 tables

  5. Rapid chemical profiling of saponins in the flower buds of Panax notoginseng by integrating MCI gel column chromatography and liquid chromatography/mass spectrometry analysis.

    Science.gov (United States)

    Yang, Wen-Zhi; Bo, Tao; Ji, Shuai; Qiao, Xue; Guo, De-An; Ye, Min

    2013-08-15

    The flower buds of Panax notoginseng (Notoginseng flower, FBP) are used as the traditional Chinese medicine San-Qi-Hua. In this study, we conducted column chromatography fractionation and liquid chromatography/mass spectrometry (LC/MS) analysis to comprehensively profile bioactive notoginseng saponins (ginsenosides) in FBP. MCI gel column chromatography allowed separation and enrichment of minor saponins. Electrospray ionization tandem mass spectrometry of [M-H](-) and [M+Na](+) precursor ions of the saponins provided reliable structural information for the sapogenin, and sequence of sugar chains. Confirmed by high-accuracy Q-TOF analysis, 170 notoginseng saponins were characterized from FBP, and 91 of them were reported from Panax species for the first time. The new ginsenosides contain acyl groups on α-chain, malonyl group at 20-OH, or di-malonyl groups. This study also indicated that the flower buds of P. notoginseng contained more protopanaxadiol-type but less protopanaxatriol-type ginsenosides than the roots. PMID:23561171

  6. Isotopic analysis of H2, HD, D2 mixtures and analysis of ortho-para-hydrogen mixtures by gas chromatography

    International Nuclear Information System (INIS)

    This communication describes the present situation concerning the possibilities of vapor phase chromatography for the separation and analysis of mixtures of H2, HD and D2 and of ortho- and para-hydrogen mixtures. Separation factors for physical adsorption of the various varieties of hydrogen have been deduced from chromatograms and have also been measured directly with a static method - the agreements is good. (author)

  7. Molecular genetic analysis of regions of the murine genome associated with radiation-induced mutations

    International Nuclear Information System (INIS)

    The authors are exploiting the large array of radiation-induced mutations to develop both detailed molecular and functional maps of selected small model regions (as opposed to specific genes) within the mouse genome. Through the integrated use of recombinant DNA technology and classical genetic and cytogenetic analysis, they hope to relate the structure and function of these regions to the study of both normal and abnormal mammalian development. Over the years, the germ-line mutagenesis program has generated a valuable array of induced mutations at several specific loci scattered throughout the murine genome. Many of these mutations are multilocus deletions of chromosomal DNA. Genetic analysis of these types of lesions has detected passenger mutations of wide-ranging effect and severity, and has generated gross functional maps of entire chromosomal regions. They have initiated a program to expand the molecular analysis of these types of deletion mutations. This program exploits the deletion mutations and other chromosomal rearrangements to obtain molecular clones of wild-type DNA that map to regions absent in mutants carrying the deletions. These clones will then be used to correlate the resultant molecular/physical map of the chromosomal region with the genetic/functional map in both mutant and wild-type individuals. Such correlations are essential to a strategy for identifying as many of the genes as possible in a particular region of the genome and for ascertaining their role(s) in the normal development of the mouse

  8. Mutation analysis of the PKU population in England and Scotland - how and why

    Energy Technology Data Exchange (ETDEWEB)

    Tyfield, L.A.; Stephenson, A. [Southmead Hospital, Bristol (United Kingdom); Bidwell, J. [Univ. of Bristol (United Kingdom)] [and others

    1994-09-01

    To date, over 150 disease-causing mutations have been defined at the phenylalanine hydroxylase (PAH) locus. Because of their varied effects on enzyme activity as determined in in vitro expression systems, it is to be anticipated that different combinations would result in a continuum of phenotypes ranging from severe classical PKU to non-PKU hyperphenylalaninaemia requiring no dietary phenylalanine restriction. To examine this, it is essential to characterize the mutations on both alleles in as many affected individuals as possible. Using heteroduplex analysis with synthetic DNA constructs, we are able to characterize 14 different mutations in 3 exons (12, 3 and 7) of the PAH gene. In the PKU populations of England and Scotland, we have screened over 370 independent mutant chromosomes from 200 affected individuals or their parents. Analysis of these exons in conjunction with screening for two specific mutations in exon 2 and intron 10 enables us to identify the mutations on 60 to 65% of mutant chromosomes. These are found in 21 different combinations in 81 affected individuals in whom both mutations could be identified. Analysis of various parameters measuring the degree of dietary restrictions and management in these patients should give some indication whether genotype can be used as an independent predictor of the severity of the disorder.

  9. In situ search for organics by gas chromatography analysis: new derivatization / thermochemolysis approach

    Science.gov (United States)

    Geffroy, Claude; Buch, Arnaud; David, Marc; Aissat, Lyes; El Mufleh, Amel; Papot, S.; Sternberg, Robert

    Many organic molecules are present in interstellar clouds and might be carried to the early Earth by comets and meteorites during the heavy bombardment phase in the first few hundred million years of the solar system. It has been suggested that extraterrestrial organic material may well represent an important part of the organic material available for the origin of life. Until samples, brought by future space missions, are available on Earth, in situ measurements are one of the way to get unaltered and non-contaminated samples for analysis. The analytical technique has to be robust, sensitive and non-specific due to the large scope of targets molecules. The only currently flight qualified technique of analysis of organic molecules in space is gas chromatography (Viking, Cassini-Huygens, SAM-MSL, COSAC-Rosetta). The main objective of this work is to present a new approach with multi step analysis using derivatisation and thermochemolysis reagents for a one pot in situ analysis of volatile and refractory organics in surface or sub-surface samples (Mars, comets).Indeed, no single technology enables to identify all organic compounds because naturally occurring molecules have different polarities, molecular weights, being extractible or recalcitrant, bonded trapped or adsorbed on minerals. Thus, we propose to wider the scope of chemical reagent already validated for in situ wet chemistry such as MTBSTFA (Rodier et al. 2001, 2002), DMF-DMA (Rodier et al. 2002), or TMAH (Rodier et al, 2005, Geffroy-Rodier et al; 2009) to analyze enantiomers of amino acids, carbohydrates and lipids in a one pot several steps sub system using a multi reagent and multi step approach. Thus using a new derivatizing agent, we successfully identified twenty one amino acids including twelve of the twenty proteinic amino acids without inhibiting following multi step thermochemolysis. *Geffroy-Rodier C, Grasset L, Sternberg R. Buch A. Amblès A. (2009) Thermochemolysis in search for organics in

  10. Analysis of Gas Chromatography x Gas Chromatography Time-of-Flight Mass Spectrometry of essential oils from Globba patens var. patens

    International Nuclear Information System (INIS)

    Leaf, stem, and rhizome essential oils of Globba patens var. patens (Zingiberaceae) were obtained by hydro distillation at 0.0021 %, in small quantity, and also small quantity. Their chemical components and each percentage were determined from analysis by using gas chromatography x gas chromatography-time-of-flight mass spectrometry (GC x GC-TOFMS). Terpenes were the oils major contributor with the rhizome gave the lowest amount of 30.56 %. Major compounds in the leaf oil were β-thujene (11.45%, 1), β-selinene (7.82 %, 2), and α-pinene (5.27 %, 3); the stem, β-pinene (2.77 %, 4), myrtenol (2.30 %, 5), and β-elemene/ ledene oxide (2.23 %, 6/ 7); the rhizome, caryophyllene oxide (2.74 %, 8), D-limonene (2.71 %, 9), and 7-(1-methylethylidene)-bicyclo[4.1.0] heptane (1.93 %, 10). (author)

  11. Qualitative and quantitative analysis of vetiver essential oils by comprehensive two-dimensional gas chromatography and comprehensive two-dimensional gas chromatography/mass spectrometry.

    Science.gov (United States)

    Filippi, Jean-Jacques; Belhassen, Emilie; Baldovini, Nicolas; Brevard, Hugues; Meierhenrich, Uwe J

    2013-05-01

    Vetiver essential oils (VEO) are important raw ingredients used in perfume industry, entering the formula of numerous modern fragrances. Vetiver oils are considered to be among the most complex essential oils, resulting most of the time in highly coeluted chromatograms whatever the analytical technique. In this context, conventional gas chromatography has failed to provide a routine tool for the accurate qualitative and quantitative analysis of their constituents. Applying comprehensive two-dimensional gas chromatography techniques (GC×GC-FID/MS) afforded the mean to separate efficiently vetiver oil constituents in order to identify them in a more reliable way. Moreover, this is the first time that a complete true quantitation of each constituent is carried out on such complex oils by means of internal calibration. Finally, we have studied the influence of the injection mode on the determined chemical composition, and showed that several alcohols underwent dehydration under defined chromatographic conditions (splitless mode) usually recommended for quantitation purposes. PMID:23522261

  12. Mutational Analysis of Oculocutaneous Albinism: A Compact Review

    OpenAIRE

    2014-01-01

    Oculocutaneous albinism (OCA) is an autosomal recessive disorder caused by either complete lack of or a reduction of melanin biosynthesis in the melanocytes. The OCA1A is the most severe type with a complete lack of melanin production throughout life, while the milder forms OCA1B, OCA2, OCA3, and OCA4 show some pigment accumulation over time. Mutations in TYR, OCA2, TYRP1, and SLC45A2 are mainly responsible for causing oculocutaneous albinism. Recently, two new genes SLC24A5 and C10orf11 are ...

  13. Genetic Analysis of Mating Locus Linked Mutations in CHLAMYDOMONAS REINHARDII

    OpenAIRE

    Galloway, R. E.; Goodenough, U. W.

    1985-01-01

    The mating-type (mt) locus of Chlamydomonas reinhardii has been analyzed using four mutant strains (imp-1, imp-10, imp-11 and imp-12). All have been shown, or are shown here, to carry mutations linked to either the plus (mt+) or the minus (mt-) locus, and their behavior in complementation tests has allowed us to define several distinct functions for each locus. Specifically, we propose that the mt+ locus contains the following genes or regulatory elements: a locus designated sfu, which is n...

  14. A parylene-based dual channel micro-electrophoresis system for rapid mutation detection via heteroduplex analysis

    NARCIS (Netherlands)

    Sukas, Sertan; Erson, Ayse Elif; Sert, Cuneyt; Kulah, Haluk

    2008-01-01

    A new dual channel micro-electrophoresis system for rapid mutation detection based on heteroduplex analysis was designed and implemented. Mutation detection was successfully achieved in a total separation length of 250 μm in less than 3 min for a 590 bp DNA sample harboring a 3 bp mutation causing a

  15. Discrimination of honeys using colorimetric sensor arrays, sensory analysis and gas chromatography techniques.

    Science.gov (United States)

    Tahir, Haroon Elrasheid; Xiaobo, Zou; Xiaowei, Huang; Jiyong, Shi; Mariod, Abdalbasit Adam

    2016-09-01

    Aroma profiles of six honey varieties of different botanical origins were investigated using colorimetric sensor array, gas chromatography-mass spectrometry (GC-MS) and descriptive sensory analysis. Fifty-eight aroma compounds were identified, including 2 norisoprenoids, 5 hydrocarbons, 4 terpenes, 6 phenols, 7 ketones, 9 acids, 12 aldehydes and 13 alcohols. Twenty abundant or active compounds were chosen as key compounds to characterize honey aroma. Discrimination of the honeys was subsequently implemented using multivariate analysis, including hierarchical clustering analysis (HCA) and principal component analysis (PCA). Honeys of the same botanical origin were grouped together in the PCA score plot and HCA dendrogram. SPME-GC/MS and colorimetric sensor array were able to discriminate the honeys effectively with the advantages of being rapid, simple and low-cost. Moreover, partial least squares regression (PLSR) was applied to indicate the relationship between sensory descriptors and aroma compounds. PMID:27041295

  16. Discrimination of three mutational events that result in a disruption of the R122 primary autolysis site of the human cationic trypsinogen (PRSS1 by denaturing high performance liquid chromatography

    Directory of Open Access Journals (Sweden)

    Férec Claude

    2001-11-01

    Full Text Available Abstract Background R122, the primary autolysis site of the human cationic trypsinogen (PRSS1, constitutes an important "self-destruct" or "fail-safe" defensive mechanism against premature trypsin activation within the pancreas. Disruption of this site by a missense mutation, R122H, was found to cause hereditary pancreatitis. In addition to a c.365G>A (CGC>CAC single nucleotide substitution, a c.365~366GC>AT (CGC>CAT gene conversion event in exon 3 of PRSS1 was also found to result in a R122H mutation. This imposes a serious concern on the genotyping of pancreatitis by a widely used polymerase chain reaction-restriction fragment length polymorphism assay, which could only detect the commonest c.365G>A variant. Materials and methods DNA samples containing either the known c.365G>A or c.365~366GC>AT variant in exon 3 of PRSS1 were used as positive controls to establish a denaturing high performance liquid chromatography (DHPLC assay. Results DHPLC could readily discriminate the two known different mutational events resulting in the R122H mutation. More importantly, under the same experimental conditions, it identified a further mutational event that also occurs in the R122 primary autolysis site but results in a different amino acid substitution: c.364C>T (CGC>TGC; R122C. Conclusions A rapid, simple, and low-cost assay for detecting both the known and new mutations occuring in the R122 primary autolysis site of PRSS1 was established. In addition, the newly found R122C variant represents a likely pancreatitis-predisposing mutation.

  17. A rapid analysis of plasma/serum ethylene and propylene glycol by headspace gas chromatography

    OpenAIRE

    Ehlers, Alexandra; Morris, Cory; Krasowski, Matthew D

    2013-01-01

    A rapid headspace-gas chromatography (HS-GC) method was developed for the analysis of ethylene glycol and propylene glycol in plasma and serum specimens using 1,3-propanediol as the internal standard. The method employed a single-step derivitization using phenylboronic acid, was linear to 200 mg/dL and had a lower limit of quantitation of 1 mg/dL suitable for clinical analyses. The analytical method described allows for laboratories with HS-GC instrumentation to analyze ethanol, methanol, iso...

  18. Development of conjugate methods with gas chromatography for inorganic compounds analysis

    International Nuclear Information System (INIS)

    The application of gas chromatography combined with mass spectrometry or with nuclear methods for the analysis of inorganic compounds is studied. The advantages of the use of a gas chromatograph coupled with a quadrupole mass spectrometer or with a high resolution radiation detector, are discussed. We also studied the formation and solvent extraction of metal chelates; an aliquot of the organic phase was directly injected into the gas chromatograph and the eluted compounds were detected by mass spectrometry or, when radioactive, by nuclear methods. (author)

  19. Simple, specific analysis of organophosphorus and carbamate pesticides in sediments using column extraction and gas chromatography

    Science.gov (United States)

    Belisle, A.A.; Swineford, D.M.

    1988-01-01

    A simple, specific procedure was developed for the analysis of organophosphorus and carbamate pesticides in sediment. The wet soil was mixed with anhydrous sodium sulfate to bind water and the residues were column extracted in acetone:methylene chloride (1:l,v/v). Coextracted water was removed by additional sodium sulfate packed below the sample mixture. The eluate was concentrated and analyzed directly by capillary gas chromatography using phosphorus and nitrogen specific detectors. Recoveries averaged 93 % for sediments extracted shortly after spiking, but decreased significantly as the samples aged.

  20. Approach to hydrophilic interaction chromatography column selection: application to neurotransmitters analysis.

    Science.gov (United States)

    Chirita, Raluca-Ioana; West, Caroline; Finaru, Adriana-Luminita; Elfakir, Claire

    2010-04-30

    This paper presents the comparison between 12 hydrophilic interaction liquid chromatography columns that are commercially available. The main factors influencing the retention and selectivity toward 12 neurotransmitters for these different HILIC systems have been studied. For additional information, the retention data have been analyzed statistically by factor analysis. Principal component analyses (PCA) were calculated to evidence different separation behaviour between the stationary phases, based on the retention data measured for three compound classes: anionic acidic compounds, cationic basic compounds and zwitterionic amino acids. Finally, a generic procedure is suggested for optimization of HILIC analyses, depending on the ionization state of the analytes. PMID:20338567

  1. Issues pertaining to the analysis of buprenorphine and its metabolites by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Wang, Yu-Shan; Lin, Dong-Liang; Yang, Shu-Ching; Wu, Meng-Yan; Liu, Ray H; Su, Lien-Wen; Cheng, Pai-Sheng; Liu, Chiareiy; Fuh, Ming-Ren

    2010-03-01

    "Substitution therapy" and the use of buprenorphine (B) as an agent for treating heroin addiction continue to gain acceptance and have recently been implemented in Taiwan. Mature and widely utilized gas chromatography-mass spectrometry (GC-MS) technology can complement the low cost and highly sensitive immunoassay (IA) approach to facilitate the implementation of analytical tasks supporting compliance monitoring and pharmacokinetic/pharmacogenetic studies. Issues critical to GC-MS analysis of B and norbuprenorphine (NB) (free and as glucuronides), including extraction, hydrolysis, derivatization, and quantitation approaches were studied, followed by comparing the resulting data against those derived from IA and two types of liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods. Commercial solid-phase extraction devices, highly effective for recovering all metabolites, may not be suitable for the analysis of free B and NB; acetyl-derivatization products exhibit the most favorable chromatographic, ion intensity, and cross-contribution characteristics for GC-MS analysis. Evaluation of IA, GC-MS, and LC-MS/MS data obtained in three laboratories has proven the 2-aliquot GC-MS protocol effective for the determination of free B and NB and their glucuronides. PMID:20122691

  2. Identification of five novel FBN1 mutations by non-radioactive single-strand conformation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Liu, W.; Qian, C.; Comeau, K.; Francke, U. [Stanford Univ. Medical Center, Stanford, CA (United States)

    1994-09-01

    Marfan syndrome (MFS), one of the most common genetic disorders of connective tissue, is characterized by variable manifestations in skeletal, cardiovascular and ocular systems. Mutations in the fibrillin gene on chromosome 15 (FBN1) have been shown to cause MFS. To examine the relationship between FBN1 gene mutations, fibrillin protein function and MFS phenotypes, we screened for alternations in the fibrillin coding sequence in fibroblast derived cDNA from MFS patients. To date, abnormally migrating bands in more than 20 unrelated MFS patients have been identified by using non-radioactive single-strand conformation analysis and silver staining. Five altered bands have been directly sequenced. Two missense mutations and three splice site mutations have been identified. Both missense mutations substitute another amino acid for a cysteine residue (C1402W and C1672R) in EGF-like motifs of the fibrillin polypeptide chain. The two splice site mutations are at nucleotide positions 6994+1 (G{yields}A), and 7205-2 (A{yields}G) and result in in-frame skipping of exon 56 and 58, respectively. Skipping of exon 56 occurs in 50% of mutant transcripts. Use of a cryptic splice site 51 bp upstream of the normal donor site results in half of the mutant transcripts containing part of exon 56. Both products contain in-frame deletions. Another splice site mutation, identified by exon screening from patient genomic DNA using intron primers, is at nucleotide position 2293+2 (T{yields}A), but the predicted exon skipping has not been detected at the RT-PCR level. This may be due to instability of the mutant transcript. Including the mutations reported here, a total of 8 out of 36 published FBN1 gene mutations involve exon skipping. It may be inferred that FBN1 exon skipping plays an important pathogenic role in MFS.

  3. The use of selection in recovery of transgenic targets for mutation analysis.

    Science.gov (United States)

    Lundberg, K S; Kretz, P L; Provost, G S; Short, J M

    1993-02-01

    Transgenic animal mutagenesis assays using lambda shuttle vectors have recently been described for isolation and characterization of spontaneous and chemical induced DNA mutations. Extensive information on lambda and E. coli genetics provides a wealth of techniques to allow selection of mutant target genes. Here we describe the modification of an E. coli host which permits two methods for the direct selection of mutant genes. These methods reduce the number of plates needed to be screened for a comparable amount of frequency data by 20-100-fold and thus provide a significant savings of the materials and time required for the screening of mutations. In addition, mutants selected by these approaches described here may alter or broaden the spectrum of mutations that are recoverable. Ultimately, a combination of selective and nonselective techniques may prove valuable for the analysis of mutations produced in vivo in transgenic animals. PMID:7678177

  4. Analysis of human transforming growth factor β-induced gene mutation in corneal dystrophy

    Institute of Scientific and Technical Information of China (English)

    李杨; 孙旭光; 任慧媛; 董冰; 王智群; 孙秀英

    2004-01-01

    Background Corneal dystrophy is a group of inherited blinding diseases of the cornea. This study was to identify the mutations of the keratoepithelin (KE) gene for proper diagnosis of corneal dystrophy. Methods Three families with corneal dystrophy were analysed. Thirteen individuals at risk for corneal dystrophy in family A, the proband and her son in family B, and the proband in family C were examined after their blood samples were obtained. Mutation screening of human transforming growth factor β-induced gene (BIGH3 gene) was performed. Results Five individuals in family A were found by clinical evaluation to be affected with granular corneal dystrophy and carried the BIGH3 mutation W555R. However, both probands in families B and C, also diagnosed with granular corneal dystrophy, harboured the BIGH3 mutation R124H. Conclusion Molecular genetic analysis can improve accurate diagnosis of corneal dystrophy.

  5. Analysis of P53 mutations and their expression in 56 colorectal cancer cell lines

    DEFF Research Database (Denmark)

    Liu, Ying; Bodmer, Walter F

    2006-01-01

    A comprehensive analysis of the TP53 gene and its protein status was carried out on a panel of 56 colorectal cancer cell lines. This analysis was based on a combination of denaturing HPLC mutation screening of all exons of the p53 gene, sequencing the cDNA, and assessing the function of the p53 p...

  6. Multiresidue analysis of 30 organochlorine pesticides in milk and milk powder by gel permeation chromatography-solid phase extraction-gas chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Zheng, Guocan; Han, Chao; Liu, Yi; Wang, Jing; Zhu, Meiwen; Wang, Chengjun; Shen, Yan

    2014-10-01

    A method for simultaneous determination of the 30 organochlorine pesticides (OCP) in milk and milk powder samples has been developed. Prior to the gas chromatography-tandem mass spectrometric analysis, the residual OCP in samples were extracted with n-hexane and acetone mixture (1/1, vol/vol) and cleaned up by gel permeation chromatography and solid phase extraction. Selected reaction monitoring mode was used for gas chromatography-tandem mass spectrometric data acquisition to identify and quantify the OCP. To avoid the matrix effects, matrix-matched calibration solutions ranging from 2 to 50 ng/mL were used to record the calibration curve. Limits of quantification of all OCP were 0.8 μg/kg. With the exception of endrin, limits of quantification are significantly lower than maximum residue limits set by the European Union and China. The average recoveries were in the range of 70.1 to 114.7% at 3 spiked concentration levels (0.8, 2.0, and 10.0 μg/kg) with residual standard deviation lower than 12.9%. The developed method was successfully applied to analyze the OCP in commercial milk products. PMID:25087035

  7. Analysis of PIK3CA Mutations and Activation Pathways in Triple Negative Breast Cancer.

    Directory of Open Access Journals (Sweden)

    Paolo Cossu-Rocca

    Full Text Available Triple Negative Breast Cancer (TNBC accounts for 12-24% of all breast carcinomas, and shows worse prognosis compared to other breast cancer subtypes. Molecular studies demonstrated that TNBCs are a heterogeneous group of tumors with different clinical and pathologic features, prognosis, genetic-molecular alterations and treatment responsivity. The PI3K/AKT is a major pathway involved in the regulation of cell survival and proliferation, and is the most frequently altered pathway in breast cancer, apparently with different biologic impact on specific cancer subtypes. The most common genetic abnormality is represented by PIK3CA gene activating mutations, with an overall frequency of 20-40%. The aims of our study were to investigate PIK3CA gene mutations on a large series of TNBC, to perform a wider analysis on genetic alterations involving PI3K/AKT and BRAF/RAS/MAPK pathways and to correlate the results with clinical-pathologic data.PIK3CA mutation analysis was performed by using cobas® PIK3CA Mutation Test. EGFR, AKT1, BRAF, and KRAS genes were analyzed by sequencing. Immunohistochemistry was carried out to identify PTEN loss and to investigate for PI3K/AKT pathways components.PIK3CA mutations were detected in 23.7% of TNBC, whereas no mutations were identified in EGFR, AKT1, BRAF, and KRAS genes. Moreover, we observed PTEN loss in 11.3% of tumors. Deregulation of PI3K/AKT pathways was revealed by consistent activation of pAKT and p-p44/42 MAPK in all PIK3CA mutated TNBC.Our data shows that PIK3CA mutations and PI3K/AKT pathway activation are common events in TNBC. A deeper investigation on specific TNBC genomic abnormalities might be helpful in order to select patients who would benefit from current targeted therapy strategies.

  8. Variation analysis of space mutation in winter wheat varieties

    International Nuclear Information System (INIS)

    Seeds of eight winter wheat varieties were carried into space by satellite Shijian No.8 and returned to the earth. After years' consecutive planting and choices, the mutagenic effects of space condition on the the yield in the SP3 generation, high whiteness and strong gluten materials appeared in the mutation progenies of Zhoumai 18 with a whiteness value of 82.9 and stability time of 80 min in the SP2 and SP3 generations were studied. The results showed that the variation of phenotype in progenies could be induced, while different varieties and traits responded differently to the space conditions. The mutant frequency of Xinmai 18 and Zhengmai 336 was 13.2% and 12.5% respectively. The variation was significant in plant height, ear length yield and quality trail. Segregation and inheritance occurred in the successive progenies, most of which were tended to be stable after the selection of single ear or plant. (authors)

  9. Analysis of odour compounds from scented consumer products using gas chromatography-mass spectrometry and gas chromatography-olfactometry.

    Science.gov (United States)

    Bartsch, Jennifer; Uhde, Erik; Salthammer, Tunga

    2016-01-21

    Scented consumer products are being bought in increasing amounts and gaining more popularity. There is, however, relatively little information available about their ingredients, emissions and allergenic potential. Frequently, a mixture of different fragrance substances and not solely an individual substance contributes to the overall desired smell. The aim of this study was to investigate the odorous volatile organic compounds (OVOCs) in consumer products containing fragrances. Over 44 products were selected: various scented candles, printing products with different scent types and other products types particularly meant to be used indoors. Measurements were carried out in a desiccator. Air samples were collected on thermal desorption tubes to determine the released fragrance substances by means of gas chromatography-mass spectrometry (GC-MS). Moreover, gas chromatography-olfactometry (GC-O) was used to obtain sensory data and to ensure no important odorant was overlooked. Using both methods it was possible to distinguish between odour active and inactive compounds and subsequently to identify almost 300 different odorants across all scented products. Besides the advantage of differentiation, as the human nose is a very sensitive detector, GC-O was found to be a useful tool for detecting traces and chosen target compounds. One focus in this study lay on the 26 EU-regulated fragrance allergens to prove their relevance in scented consumer goods. In total, 18 of them were identified, with at least one substance being present in almost every product. Benzyl alcohol, cinnamaldehyde, citronellol, eugenol, linalool and limonene were the prevalently detected allergens. Particularly linalool and limonene were observed in over 50% of the products. In addition, eugenol appeared to be one of the most frequently detected compounds in trace-level concentrations in the candle emissions. PMID:26724768

  10. COLD-PCR enhanced melting curve analysis improves diagnostic accuracy for KRAS mutations in colorectal carcinoma

    Directory of Open Access Journals (Sweden)

    Joseph Loren

    2010-11-01

    Full Text Available Abstract Background KRAS mutational analysis is the standard of care prior to initiation of treatments targeting the epidermal growth factor receptor (EGFR in patients with metastatic colorectal cancer. Sensitive methods are required to reliably detect KRAS mutations in tumor samples due to admixture with non-mutated cells. Many laboratories have implemented sensitive tests for KRAS mutations, but the methods often require expensive instrumentation and reagents, parallel reactions, multiple steps, or opening PCR tubes. Methods We developed a highly sensitive, single-reaction, closed-tube strategy to detect all clinically significant mutations in KRAS codons 12 and 13 using the Roche LightCycler® instrument. The assay detects mutations via PCR-melting curve analysis with a Cy5.5-labeled sensor probe that straddles codons 12 and 13. Incorporating a fast COLD-PCR cycling program with a critical denaturation temperature (Tc of 81°C increased the sensitivity of the assay >10-fold for the majority of KRAS mutations. Results We compared the COLD-PCR enhanced melting curve method to melting curve analysis without COLD-PCR and to traditional Sanger sequencing. In a cohort of 61 formalin-fixed paraffin-embedded colorectal cancer specimens, 29/61 were classified as mutant and 28/61 as wild type across all methods. Importantly, 4/61 (6% were re-classified from wild type to mutant by the more sensitive COLD-PCR melting curve method. These 4 samples were confirmed to harbor clinically-significant KRAS mutations by COLD-PCR DNA sequencing. Five independent mixing studies using mutation-discordant pairs of cell lines and patient specimens demonstrated that the COLD-PCR enhanced melting curve assay could consistently detect down to 1% mutant DNA in a wild type background. Conclusions We have developed and validated an inexpensive, rapid, and highly sensitive clinical assay for KRAS mutations that is the first report of COLD-PCR combined with probe

  11. Analysis of the photo catalytic degradation of the 4-chloro phenol and endosulfan by gas chromatography

    International Nuclear Information System (INIS)

    The water and soil pollution by organic compounds of considerable toxicity, is every time more alarming. The phenols and organo chlorinated compounds are some of the pollutants of more environmental concern. The present work shows the degradation by heterogeneous photo catalysis of the 4-chloro phenol and endosulfan in watery solutions using a photo reactor at laboratory scale, under ultraviolet irradiation as energy source and titanium dioxide TiO2 Degussa P25 as catalyst. Solutions of both compounds at concentrations of 10, 20, 30 and 40 mg/L were used, analyzing the more important operation parameters with those that the maxima degradation levels were reached. The analyzed variables were catalyst concentration and irradiation time, the analytical techniques of ultraviolet-visible spectroscopy and gas chromatography were used as process control. By means of ultraviolet-visible spectroscopy it was settled down that starting from the quantitative analysis, the 4-chloro phenol presented bigger degradation at smaller concentrations. Under the operation conditions mentioned in this work, it was observed that the photo catalytic processes obey a first order behavior in the chemical kinetics being adjusted to the Langmuir-Hinshelwood model (L-H). With the purpose of checking the degradation of the same ones it was used the gas chromatography, which is an advanced technique for the process pursuit, auxiliary in the quantification and analysis of the photo catalytic degradation of the 4-chloro phenol and endosulfan. It was based on the development and validation of the analytical method, by means of which was proven that the method is good and reliable in the research environment. The results of the quantitative analysis by gas chromatography and ultraviolet-visible, derived of the photo catalytic degradation of the 4-chloro phenol, in the maximum time of study (180 minutes), using the concentrations of 10, 20, 30 and 40 mg/L was found, by gas chromatography, a maximum

  12. Multivariate analysis of progressive thermal desorption coupled gas chromatography-mass spectrometry.

    Energy Technology Data Exchange (ETDEWEB)

    Van Benthem, Mark Hilary; Mowry, Curtis Dale; Kotula, Paul Gabriel; Borek, Theodore Thaddeus, III

    2010-09-01

    Thermal decomposition of poly dimethyl siloxane compounds, Sylgard{reg_sign} 184 and 186, were examined using thermal desorption coupled gas chromatography-mass spectrometry (TD/GC-MS) and multivariate analysis. This work describes a method of producing multiway data using a stepped thermal desorption. The technique involves sequentially heating a sample of the material of interest with subsequent analysis in a commercial GC/MS system. The decomposition chromatograms were analyzed using multivariate analysis tools including principal component analysis (PCA), factor rotation employing the varimax criterion, and multivariate curve resolution. The results of the analysis show seven components related to offgassing of various fractions of siloxanes that vary as a function of temperature. Thermal desorption coupled with gas chromatography-mass spectrometry (TD/GC-MS) is a powerful analytical technique for analyzing chemical mixtures. It has great potential in numerous analytic areas including materials analysis, sports medicine, in the detection of designer drugs; and biological research for metabolomics. Data analysis is complicated, far from automated and can result in high false positive or false negative rates. We have demonstrated a step-wise TD/GC-MS technique that removes more volatile compounds from a sample before extracting the less volatile compounds. This creates an additional dimension of separation before the GC column, while simultaneously generating three-way data. Sandia's proven multivariate analysis methods, when applied to these data, have several advantages over current commercial options. It also has demonstrated potential for success in finding and enabling identification of trace compounds. Several challenges remain, however, including understanding the sources of noise in the data, outlier detection, improving the data pretreatment and analysis methods, developing a software tool for ease of use by the chemist, and demonstrating our belief

  13. Reaction flow chromatography for rapid post column derivatisations: the analysis of antioxidants in natural products.

    Science.gov (United States)

    Camenzuli, M; Ritchie, H J; Dennis, G R; Shalliker, R A

    2013-08-16

    The analysis of antioxidants from complex samples is conveniently achieved using liquid chromatography, which provides sample fraction, coupled with an on-line antioxidant assay, which provides detection. One particularly useful on-line antioxidant assay that has routinely been coupled with HPLC involves the diphenylpicrylhydrazyl radical (DPPH), which provides a positive test for phenolic antioxidants through a decolorisation of the DPPH reagent. A limitation of this assay, however, is the need to employ a reaction coil, which is often large with respect to the peak volume, consequently adding substantial band broadening to the separation. In this study we introduce a new concept that can be employed for systems requiring post column derivatisations, such as the DPPH assay. We have termed this 'reaction flow' chromatography, whereby, the derivatisation reagent can be added directly into one of the outlet ports of a parallel segmented flow column. Subsequently, the mixing between the derivatising reagent and the solute is very efficient removing the need to employ reaction coils. The concept is tested here using the DPPH assay for the analysis of antioxidants in samples derived from natural origin. PMID:23849586

  14. Gas chromatography-vacuum ultraviolet spectroscopy for analysis of fatty acid methyl esters.

    Science.gov (United States)

    Fan, Hui; Smuts, Jonathan; Bai, Ling; Walsh, Phillip; Armstrong, Daniel W; Schug, Kevin A

    2016-03-01

    A new vacuum ultraviolet (VUV) detector for gas chromatography was recently developed and applied to fatty acid methyl ester (FAME) analysis. VUV detection features full spectral acquisition in a wavelength range of 115-240nm, where virtually all chemical species absorb. VUV absorption spectra of 37 FAMEs, including saturated, monounsaturated, and polyunsaturated types were recorded. Unsaturated FAMEs show significantly different gas phase absorption profiles than saturated ones, and these classes can be easily distinguished with the VUV detector. Another advantage includes differentiating cis/trans-isomeric FAMEs (e.g. oleic acid methyl ester and linoleic acid methyl ester isomers) and the ability to use VUV data analysis software for deconvolution of co-eluting signals. As a universal detector, VUV also provides high specificity, sensitivity, and a fast data acquisition rate, making it a powerful tool for fatty acid screening when combined with gas chromatography. The fatty acid profile of several food oil samples (olive, canola, vegetable, corn, sunflower and peanut oils) were analyzed in this study to demonstrate applicability to real world samples. PMID:26471553

  15. A single center analysis of nucleophosmin in acute myeloid leukemia: value of combining immunohistochemistry with molecular mutation analysis.

    Science.gov (United States)

    Woolthuis, Carolien M; Mulder, André B; Verkaik-Schakel, Rikst Nynke; Rosati, Stefano; Diepstra, Arjan; van den Berg, Eva; Schuringa, Jan Jacob; Vellenga, Edo; Kluin, Philip M; Huls, Gerwin

    2013-10-01

    Mutations of nucleophosmin 1 are frequently found in acute myeloid leukemia and lead to aberrant cytoplasmic accumulation of nucleophosmin protein. Immunohistochemical staining is therefore recommended as the technique of choice in front-line screening. In this study, we assessed the sensitivity and specificity of immunohistochemistry on formalin-fixed bone marrow biopsies compared with gold standard molecular analysis to predict nucleophosmin 1 mutation status in 119 patients with acute myeloid leukemia. Discrepant cases were further characterized by gene expression analyses and fluorescence in situ hybridization. A large overlap between both methods was observed. Nevertheless, nine patients demonstrated discordant results at initial screening. Five cases demonstrated nuclear staining of nucleophosmin 1 by immunohistochemistry, but a nucleophosmin 1 mutation by molecular analysis. In two cases this could be attributed to technical issues and in three cases minor subpopulations of myeloblasts had not been discovered initially. All tested cases exhibited the characteristic nucleophosmin-mutated gene expression pattern. Four cases had cytoplasmic nucleophosmin 1 staining and a nucleophosmin-mutated gene expression pattern without a detectable nucleophosmin 1 mutation. In two of these cases we found the chromosomal translocation t(3;5)(q25;q35) encoding the NPM-MLF1 fusion protein. In the other discrepant cases the aberrant cytoplasmic nucleophosmin staining and gene expression could not be explained. In total six patients (5%) had true discordant results between immunohistochemistry and mutation analysis. We conclude that cytoplasmic nucleophosmin localization is not always caused by a conventional nucleophosmin 1 mutation and that in the screening for nucleophosmin 1 abnormalities, most information will be obtained by combining immunohistochemistry with molecular analysis. PMID:23716555

  16. A cautionary lesson on the use of targeted methods for EGFR mutation analysis: a case report.

    Science.gov (United States)

    Walsh, K; Wallace, W A; Butler, R; Mackean, M J; Harrison, D J; Stirling, D; Oniscu, A

    2014-08-01

    Epidermal growth factor receptor (EGFR) mutation analysis is recommended for lung cancer patients prior to the prescription of first-line EGFR tyrosine kinase inhibitors in order to predict response to treatment. There are many methods available to identify mutations in the EGFR gene; a large number of clinical laboratories use the therascreen EGFR RGQ PCR kit (Qiagen). We report a case where this kit detected an exon 19 deletion, predicting sensitivity to tyrosine kinase inhibitors (TKIs), which on further analysis was found to be a 2 bp indel (c.2239_2240delinsCC, p.(Leu747Pro)). Two of four published cases with this mutation were found to be associated with resistance to EGFR TKI. The sample was also tested using two other commercial kits, one of which indicated a deletion. This is a rare mutation making the erroneous detection of a deletion unlikely; however, it is important that clinical laboratories are aware of the potential failings of two commercial kits for EGFR mutation analysis. PMID:24811487

  17. Ion chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Tarter, J.G.

    1987-01-01

    Similar in many ways to other liquid chromatographic techniques, ion chromatography (IC) is an invaluable method that is used all too rarely in chemical analysis. Its application is particularly promising in the analysis of inorganic anions, an area where more information is needed. Ion Chromatogrphy identifies the merits of this technique. Serving as a review and reference for experienced ion chromatographers and as a teaching aid for individuals new to the field, it provides the information necessary for determining the potential usefulness of IC for a given situation. Among the areas treated, this volume focuses on eluant-suppressed IC, especially for anion and cation analysis, single-column IC, plus ancillary techniques and applications, electrochemical, spectroscopic, and other detecting methods, ion chromatography exclusion (ICE), including its limits and applications.

  18. High performance thin layer chromatography (HPTLC) and high performance liquid chromatography (HPLC) for the qualitative and quantitative analysis of Calendula officinalis-advantages and limitations.

    Science.gov (United States)

    Loescher, Christine M; Morton, David W; Razic, Slavica; Agatonovic-Kustrin, Snezana

    2014-09-01

    Chromatography techniques such as HPTLC and HPLC are commonly used to produce a chemical fingerprint of a plant to allow identification and quantify the main constituents within the plant. The aims of this study were to compare HPTLC and HPLC, for qualitative and quantitative analysis of the major constituents of Calendula officinalis and to investigate the effect of different extraction techniques on the C. officinalis extract composition from different parts of the plant. The results found HPTLC to be effective for qualitative analysis, however, HPLC was found to be more accurate for quantitative analysis. A combination of the two methods may be useful in a quality control setting as it would allow rapid qualitative analysis of herbal material while maintaining accurate quantification of extract composition. PMID:24880991

  19. Analysis of mutations in the entire coding sequence of the factor VIII gene

    Energy Technology Data Exchange (ETDEWEB)

    Bidichadani, S.I.; Lanyon, W.G.; Connor, J.M. [Glascow Univ. (United Kingdom)] [and others

    1994-09-01

    Hemophilia A is a common X-linked recessive disorder of bleeding caused by deleterious mutations in the gene for clotting factor VIII. The large size of the factor VIII gene, the high frequency of de novo mutations and its tissue-specific expression complicate the detection of mutations. We have used a combination of RT-PCR of ectopic factor VIII transcripts and genomic DNA-PCRs to amplify the entire essential sequence of the factor VIII gene. This is followed by chemical mismatch cleavage analysis and direct sequencing in order to facilitate a comprehensive search for mutations. We describe the characterization of nine potentially pathogenic mutations, six of which are novel. In each case, a correlation of the genotype with the observed phenotype is presented. In order to evaluate the pathogenicity of the five missense mutations detected, we have analyzed them for evolutionary sequence conservation and for their involvement of sequence motifs catalogued in the PROSITE database of protein sites and patterns.

  20. Somatic mutation analysis of MYH11 in breast and prostate cancer

    International Nuclear Information System (INIS)

    MYH11 (also known as SMMHC) encodes the smooth-muscle myosin heavy chain, which has a key role in smooth muscle contraction. Inversion at the MYH11 locus is one of the most frequent chromosomal aberrations found in acute myeloid leukemia. We have previously shown that MYH11 mutations occur in human colorectal cancer, and may also be associated with Peutz-Jeghers syndrome. The mutations found in human intestinal neoplasia result in unregulated proteins with constitutive motor activity, similar to the mutant myh11 underlying the zebrafish meltdown phenotype characterized by disrupted intestinal architecture. Recently, MYH1 and MYH9 have been identified as candidate breast cancer genes in a systematic analysis of the breast cancer genome. The aim of this study was to investigate the role of somatic MYH11 mutations in two common tumor types; breast and prostate cancers. A total of 155 breast cancer and 71 prostate cancer samples were analyzed for those regions in MYH11 (altogether 8 exons out of 42 coding exons) that harboured mutations in colorectal cancer in our previous study. In breast cancer samples only germline alterations were observed. One prostate cancer sample harbored a frameshift mutation c.5798delC, which we have previously shown to result in a protein with unregulated motor activity. Little evidence for a role of somatic MYH11 mutations in the formation of breast or prostate cancers was obtained in this study

  1. Mutational analysis of whole mitochondrial DNA in patients with MELAS and MERRF diseases.

    Science.gov (United States)

    Choi, Byung-Ok; Hwang, Jung Hee; Cho, Eun Min; Jeong, Eun Hye; Hyun, Young Se; Jeon, Hyeon Jeong; Seong, Ki Min; Cho, Nam Soo; Chung, Ki Wha

    2010-06-30

    Mitochondrial diseases are clinically and genetically heterogeneous disorders, which make the exact diagnosis and classification difficult. The purpose of this study was to identify pathogenic mtDNA mutations in 61 Korean unrelated families (or isolated patients) with MELAS or MERRF. In particular, the mtDNA sequences were completely determined for 49 patients. From the mutational analysis of mtDNA obtained from blood, 5 confirmed pathogenic mutations were identified in 17 families, and 4 unreported pathogenically suspected mutations were identified in 4 families. The m.3243A>G in the tRNA(Leu(UUR))was predominantly observed in 10 MELAS families, and followed by m.8344A>G in the tRNA(Lys) of 4 MERRF families. Most pathogenic mutations showed heteroplasmy, and the rates were considerably different within the familial members. Patients with a higher rate of mutations showed a tendency of having more severe clinical phenotypes, but not in all cases. This study will be helpful for the molecular diagnosis of mitochondrial diseases, as well as establishment of mtDNA database in Koreans. PMID:20440095

  2. Mutation analysis of GJB2 gene and prenatal diagnosis in a non-syndromic deafness family

    Directory of Open Access Journals (Sweden)

    Xiao-hua CHEN

    2014-08-01

    Full Text Available Objective To identify the pathogenic gene in a non-syndromic deafness family, provide an accurate genetic consultation and early intervention for deaf family to reduce the incidence of congenital deafness. Methods Mutation analysis was carried out by polymerase chain reaction followed by DNA sequencing of coding region of GJB2 gene. The fetal DNA was extracted from the amniotic fluid cells by amniocentesis at 20 weeks during pregnancy. The genotype of the fetus was characterized for predicting the status of hearing. Results Complex heterozygous mutations 235delC and 176-191del16bp were detected in the proband of the family, heterozygous mutation 176-191del16bp was detected in the father, and 235delC was detected in the mother. Fetus carried 235delC heterozygous mutation inherited from his mother. Conclusions The proband's hearing loss is resulted from the complex heterozygous mutations 235delC and 176-191del16bp in GJB2 gene. Fetus is a heterozygous mutation 235delC carrier. Prenatal diagnosis for deafness assisted by genetic test can provide efficient guidance about offspring's hearing condition, and prevent another deaf-mute member from birth. DOI: 10.11855/j.issn.0577-7402.2014.07.09

  3. Mutation analysis of the PALB2 gene in unselected pancreatic cancer patients in the Czech Republic.

    Science.gov (United States)

    Borecka, M; Zemankova, P; Vocka, M; Soucek, P; Soukupova, J; Kleiblova, P; Sevcik, J; Kleibl, Z; Janatova, M

    2016-05-01

    Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis among common solid cancer diagnoses. It has been shown that up to 10% of PDAC cases have a familial component. Characterization of PDAC-susceptibility genes could reveal high-risk individuals and patients that may benefit from tailored therapy. Hereditary mutations in PALB2 (Partner and Localizer of BRCA2) gene has been shown to predispose, namely to PDAC and breast cancers; however, frequencies of mutations vary among distinct geographical populations. Using the combination of sequencing, high-resolution melting and multiplex ligation-dependent probe amplification analyses, we screened the entire PALB2 gene in 152 unselected Czech PDAC patients. Truncating mutations were identified in three (2.0%) patients. Genotyping of found PALB2 variants in 1226 control samples revealed one carrier of PALB2 truncating variant (0.08%; P = 0.005). The mean age at PDAC diagnosis was significantly lower among PALB2 mutation carriers (51 years) than in non-carriers (63 years; P = 0.016). Only one patient carrying germline PALB2 mutation had a positive family breast cancer history. Our results indicate that hereditary PALB2 mutation represents clinically considerable genetic factor increasing PDAC susceptibility in our population and that analysis of PALB2 should be considered not only in PDAC patients with familial history of breast or pancreatic cancers but also in younger PDAC patients without family cancer history. PMID:27106063

  4. Identification of novel KIF11 mutations in patients with familial exudative vitreoretinopathy and a phenotypic analysis.

    Science.gov (United States)

    Li, Jia-Kai; Fei, Ping; Li, Yian; Huang, Qiu-Jing; Zhang, Qi; Zhang, Xiang; Rao, Yu-Qing; Li, Jing; Zhao, Peiquan

    2016-01-01

    KIF11 gene mutations cause a rare autosomal dominant inheritable disease called microcephaly with or without chorioretinopathy, lymphedema, or mental retardation (MCLMR). Recently, such mutations were also found to be associated with familial exudative vitreoretinopathy (FEVR). Here, we report 7 novel KIF11 mutations identified by targeted gene capture in a cohort of 142 probands with FEVR who were diagnosed in our clinic between March 2015 and November 2015. These mutations were: p.L171V, c.790-2A>C, p.Q525*, p.Q842*, p.S936*, p.L983fs and p.R1025G. Phenotypic analysis revealed that all of the affected probands had advanced FEVR (stage 4 or above). Three had microcephaly, and one had chorioretinopathy, which indicated a phenotypic overlap with MCLMR. Two mutations were also found in the families of the affected probands. One parent with a p.R1025G mutation had an avascular peripheral retina and abnormal looping vessels. However, one parent with p.L983fs had normal retina, which indicated incomplete penetration of the genotype. Our results further confirmed that KIF11 is causative of FEVR in an autosomal dominant manner. We also suggest the examination of MCLMR-like features, such as microcephaly, chorioretinopathy, for patients with FEVR and wide-field fundus photography for patients with MCLMR in future practice. PMID:27212378

  5. Structural analysis of thermostabilizing mutations of cocaine esterase

    Energy Technology Data Exchange (ETDEWEB)

    Narasimhan, Diwahar; Nance, Mark R.; Gao, Daquan; Ko, Mei-Chuan; Macdonald, Joanne; Tamburi, Patricia; Yoon, Dan; Landry, Donald M.; Woods, James H.; Zhan, Chang-Guo; Tesmer, John J.G.; Sunahara, Roger K. (Michigan); (Columbia); (Kentucky)

    2010-09-03

    Cocaine is considered to be the most addictive of all substances of abuse and mediates its effects by inhibiting monoamine transporters, primarily the dopamine transporters. There are currently no small molecules that can be used to combat its toxic and addictive properties, in part because of the difficulty of developing compounds that inhibit cocaine binding without having intrinsic effects on dopamine transport. Most of the effective cocaine inhibitors also display addictive properties. We have recently reported the use of cocaine esterase (CocE) to accelerate the removal of systemic cocaine and to prevent cocaine-induced lethality. However, wild-type CocE is relatively unstable at physiological temperatures ({tau}{sub 1/2} {approx} 13 min at 37 C), presenting challenges for its development as a viable therapeutic agent. We applied computational approaches to predict mutations to stabilize CocE and showed that several of these have increased stability both in vitro and in vivo, with the most efficacious mutant (T172R/G173Q) extending half-life up to 370 min. Here we present novel X-ray crystallographic data on these mutants that provide a plausible model for the observed enhanced stability. We also more extensively characterize the previously reported variants and report on a new stabilizing mutant, L169K. The improved stability of these engineered CocE enzymes will have a profound influence on the use of this protein to combat cocaine-induced toxicity and addiction in humans.

  6. Analysis of Soft Drinks: UV Spectrophotometry, Liquid Chromatography, and Capillary Electrophoresis

    Science.gov (United States)

    McDevitt, Valerie L.; Rodriguez, Alejandra; Williams, Kathryn R.

    1998-05-01

    Instrumental analysis students analyze commercial soft drinks in three successive laboratory experiments. First, UV multicomponent analysis is used to determine caffeine and benzoic acid in Mello YelloTM using the spectrophotometer's software and manually by the simultaneous equations method. The following week, caffeine, benzoic acid and aspartame are determined in a variety of soft drinks by reversed-phase liquid chromatography using 45% methanol/55% aqueous phosphate, pH 3.0, as the mobile phase. In the third experiment, the same samples are analyzed by capillary electrophoresis using a pH 9.4 borate buffer. Students also determine the minimum detection limits for all three compounds by both LC and CE. The experiments demonstrate the analytical use and limitations of the three instruments. The reports and prelab quizzes also stress the importance of the chemistry of the three compounds, especially the relationships of acid/base behavior and polarity to the LC and CE separations.

  7. Saffron authentication based on liquid chromatography high resolution tandem mass spectrometry and multivariate data analysis.

    Science.gov (United States)

    Rubert, Josep; Lacina, Ondrej; Zachariasova, Milena; Hajslova, Jana

    2016-08-01

    Saffron is one of the oldest and most expensive spices, which is often target of fraudulent activities. In this research, a new strategy of saffron authentication based on metabolic fingerprinting was developed. In the first phase, a solid liquid extraction procedure was optimized, the main aim was to isolate as maximal representation of small molecules contained in saffron as possible. In the second step, a detection method based on liquid chromatography coupled with high-resolution mass spectrometry was developed. Initially, principal component analysis (PCA) revealed clear differences between saffron cultivated and packaged in Spain, protected designation of origin (PDO), and saffron packaged in Spain of unknown origin, labeled Spanish saffron. Afterwards, orthogonal partial least square discriminant analysis (OPLS-DA) was favorably used to discriminate between Spanish saffron. The tentative identification of markers showed glycerophospholipids and their oxidized lipids were significant markers according to their origin. PMID:26988494

  8. [Analysis of amines in water samples by high performance liquid chromatography-laser induced fluorescence detection].

    Science.gov (United States)

    Liu, Fan; Gao, Fangyuan; Tang, Tao; Sun, Yuanshe; Li, Tong; Zhang, Weibing

    2013-11-01

    A sensitive high performance liquid chromatography (HPLC)-laser induced fluorescence detection (LIFD) method was developed for the determination of amines. The derivatization and separation conditions were investigated. Under the optimized conditions, spermidine, putrescine and histamine were analyzed. The limits of detection (LODs) of the three biogenic amines (S/N = 3) were as low as 10(-10) mol/L. This method showed excellent stability. The RSDs of retention times and peak areas of the three biogenic amines were lower than 0.3% and 3%, respectively. This method was applied in biogenic amine analysis in water samples, and the average recoveries were in the range of 94.99%-104.7%. Furthermore, the amines in seven tea samples were analyzed by this method, and satisfactory results were achieved. The developed assay is of excellent sensitivity and good reproducibility, which can be used in the analysis of the amines in water samples. PMID:24558849

  9. Core-Shell Columns in High-Performance Liquid Chromatography: Food Analysis Applications

    Science.gov (United States)

    Preti, Raffaella

    2016-01-01

    The increased separation efficiency provided by the new technology of column packed with core-shell particles in high-performance liquid chromatography (HPLC) has resulted in their widespread diffusion in several analytical fields: from pharmaceutical, biological, environmental, and toxicological. The present paper presents their most recent applications in food analysis. Their use has proved to be particularly advantageous for the determination of compounds at trace levels or when a large amount of samples must be analyzed fast using reliable and solvent-saving apparatus. The literature hereby described shows how the outstanding performances provided by core-shell particles column on a traditional HPLC instruments are comparable to those obtained with a costly UHPLC instrumentation, making this novel column a promising key tool in food analysis. PMID:27143972

  10. Analysis of 5-hydroxymethylfurfural in foods by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Teixidó, E; Santos, F J; Puignou, L; Galceran, M T

    2006-11-24

    A new, simple and selective method for the analysis of 5-hydroxymethylfurfural (HMF) in foods by gas chromatography coupled to mass spectrometry (GC-MS) is proposed. Several derivatising procedures based on the formation of an HMF silylated derivative using different reagents were studied. Among the derivatising reagents examined, N,O-bis-trimethylsilyltrifluoroacetamide (BSTFA) provided the best derivatisation yield. Sample clean-up was also optimised, using either liquid-liquid extraction with dichloromethane or solid-phase extraction (SPE) with several commercially available cartridges, and the best results were obtained using ENV+ cartridges. Quality parameters such as day-to-day and run-to-run precision (RSD<10%), linearity (between 25 and 700 ng g(-1)) and detection limit (6 ng g(-1)) were established. This method was successfully applied to the analysis of HMF content in several Spanish food samples from a local market, such as jam, honey, orange juice and bakery products. PMID:17010355

  11. Structural analysis of mitochondrial mutations reveals a role for bigenomic protein interactions in human disease.

    Directory of Open Access Journals (Sweden)

    Rhiannon E Lloyd

    Full Text Available Mitochondria are the energy producing organelles of the cell, and mutations within their genome can cause numerous and often severe human diseases. At the heart of every mitochondrion is a set of five large multi-protein machines collectively known as the mitochondrial respiratory chain (MRC. This cellular machinery is central to several processes important for maintaining homeostasis within cells, including the production of ATP. The MRC is unique due to the bigenomic origin of its interacting proteins, which are encoded in the nucleus and mitochondria. It is this, in combination with the sheer number of protein-protein interactions that occur both within and between the MRC complexes, which makes the prediction of function and pathological outcome from primary sequence mutation data extremely challenging. Here we demonstrate how 3D structural analysis can be employed to predict the functional importance of mutations in mtDNA protein-coding genes. We mined the MITOMAP database and, utilizing the latest structural data, classified mutation sites based on their location within the MRC complexes III and IV. Using this approach, four structural classes of mutation were identified, including one underexplored class that interferes with nuclear-mitochondrial protein interactions. We demonstrate that this class currently eludes existing predictive approaches that do not take into account the quaternary structural organization inherent within and between the MRC complexes. The systematic and detailed structural analysis of disease-associated mutations in the mitochondrial Complex III and IV genes significantly enhances the predictive power of existing approaches and our understanding of how such mutations contribute to various pathologies. Given the general lack of any successful therapeutic approaches for disorders of the MRC, these findings may inform the development of new diagnostic and prognostic biomarkers, as well as new drugs and targets for

  12. Analysis of starch in food systems by high-performance size exclusion chromatography.

    Science.gov (United States)

    Ovando-Martínez, Maribel; Whitney, Kristin; Simsek, Senay

    2013-02-01

    Starch has unique physicochemical characteristics among food carbohydrates. Starch contributes to the physicochemical attributes of food products made from roots, legumes, cereals, and fruits. It occurs naturally as distinct particles, called granules. Most starch granules are a mixture of 2 sugar polymers: a highly branched polysaccharide named amylopectin and a basically linear polysaccharide named amylose. The starch contained in food products undergoes changes during processing, which causes changes in the starch molecular weight and amylose to amylopectin ratio. The objective of this study was to develop a new, simple, 1-step, and accurate method for simultaneous determination of amylose and amylopectin ratio as well as weight-averaged molecular weights of starch in food products. Starch from bread flour, canned peas, corn flake cereal, snack crackers, canned kidney beans, pasta, potato chips, and white bread was extracted by dissolving in KOH, urea, and precipitation with ethanol. Starch samples were solubilized and analyzed on a high-performance size exclusion chromatography (HPSEC) system. To verify the identity of the peaks, fractions were collected and soluble starch and beta-glucan assays were performed additional to gas chromatography analysis. We found that all the fractions contain only glucose and soluble starch assay is correlated to the HPSEC fractionation. This new method can be used to determine amylose amylopectin ratio and weight-averaged molecular weight of starch from various food products using as low as 25 mg dry samples. PMID:23330715

  13. Hydrocarbon group-type analysis by thin layer chromatography and scanning densitometry

    Energy Technology Data Exchange (ETDEWEB)

    Membrado, L.; Cebolla, V.L.; Matt, M.; Galvez, E.M.; Domingo, M.P.; Vela, J.; Beregovtsova, N. [CSIC, Zaragoza (Spain)

    2002-07-01

    Hydrocarbon group-type analysis (HGTA) is a common technique for characterization of complex mixtures derived from raw materials such as coal, petroleum, or biomass. In these and other, related, samples, trying to achieve extensive separation of all the components would be very difficult at least, and most of the relevant properties of the samples can be related to the amounts of the different types of hydrocarbon. Groups of interest depend mainly on the nature of the sample, and some kind of liquid chromatography is usually involved in the most common HGTA methods. Thin-layer chromatography (TLC) can nowadays usually be used instead of HPLC, resulting in several advantages in terms of speed, cost, and general convenience. Detection and quantification of the different peaks might involve the use of special equipment, e.g. in TLC-flame ionization detection (FID) methods, although it can also be accomplished by means of UV and fluorescence scanning densitometry. This paper describes a series of TLC-based HGTA methods developed for coal-, biomass-, and petroleum-derived products that give a reasonably general overview of the possibilities of TLC applied to HGTA.

  14. Analysis of aristolochic acids, aristololactams and their analogues using liquid chromatography tandem mass spectrometry.

    Science.gov (United States)

    Yu, Jie; Ma, Chao-Mei; Wang, Xuan; Shang, Ming-Ying; Hattori, Masao; Xu, Feng; Jing, Yu; Dong, Shi-Wen; Xu, Yu-Qiong; Zhang, Cui-Ying; Cai, Shao-Qing

    2016-08-01

    More than 80 aristolochic acids (AAs) and aristololactams (ALs) have been found in plants of the Aristolochiaceae family, but relatively few have been fully studied. The present study aimed at developing and validating a liquid chromatography tandem mass spectrometry (LC/MS(n)) for the analysis of these compounds. We characterized the fragmentation behaviors of 31 AAs, ALs, and their analogues via high performance liquid chromatography coupled with electrospray ionization mass spectrometry. We summarized their fragmentation rules and used these rules to identify the constituents contained in Aristolochia contorta, Ar. debilis, Ar. manshurensis, Ar. fangchi, Ar. cinnabarina, and Ar. mollissima. The AAs and ALs showed very different MS behaviors. In MS(1) of AAs, the characteristic pseudomolecular ions were [M + NH4](+), [M + H](+), and [M + H - H2O](+). However, only [M + H](+) was found in the MS(1) of ALs, which was simpler than that of AAs. Distinct MS(n)fragmentation patterns were found for AAs and ALs, showing the same skeleton among the different substituent groups. The distribution of the 31 constituents in the 6 species of Aristolochia genus was reported for the first time. 25 Analogues of AAs and ALs were detected in this genus. A hierarchical schemes and a calculating formula of the molecular formula of these nitrophenanthrene carboxylic acids and their lactams were proposed. In conclusion, this method could be applied to identification of similar unknown constituents in other plants. PMID:27608953

  15. Timing of the uv mutagenesis in yeast: a pedigree analysis of induced recessive mutation

    International Nuclear Information System (INIS)

    The mechanism of uv-induced mutation in eukaryotes was studied in individual yeast cells by a procedure that combined pedigree analysis and tetrad analysis. The technique involved the induction of recessive lethals and semilethals in G1 diploid cells. Induced frequencies were 25 and 61% at survival levels of 90 and 77%, respectively. No evidence of gross chromosome aberrations was detected. Recessive mutations that affect only one strand or that affect both strands of the DNA molecule are induced much at random among a population of cells, and both types can occur within the same cell. However, the data confirm that two-strand mutations are in the majority after a low level of irradiation. The simplest explanation involves a mechanism whereby most mutations are fixed in both strands prior to the first round of post-irradiation DNA replication. The recessive mutational consequences of irradiation are exhausted at the conclusion of the first post-irradiation cell division, although dominant-lethal sectoring continues at a high level through the second post-irradiation division. It is concluded that pyrimidine dimers that persist to the second round of DNA replication are rare or ineffective

  16. RFLP Analysis of rice semi dwarf mutation induced by high energy argon ion radiation

    International Nuclear Information System (INIS)

    Two Indica rice varieties, Bianpizhan and Xiangzhan, and their semi dwarf mutants induced by high energy argon ion radiation, Ar 10, and Xiang Ar 1, were examined with restriction fragment length polymorphism(RFLP)analysis by using 97 rice single copy genomic clones mapped on 12 chromosomes of molecular genetic map, combined with 5 restriction enzymes.Among the markers screened, 9 detected polymorphism were between Bianpizhan and Ar 10, and 11 detected polymorphism were between Xiangzhan and Xiang Ar 1.Moreover, two or more restriction enzymes could generate RFLP patterns when screened with a given marker for several polymorphic markers. Based on the polymorphic allelic loci, the mutation frequencies were estimated as 5 15% and 6 39% for Ar 10 and Xiang Ar 1 respectively.These results suggested that the nature of mutation on the DNA level was probably large genetic changes rather than point mutation.Genetic analysis and gene tagging of semi dwarf mutation in one of the mutant line, Ar 10, indicated that this mutation was controlled by a major recessive gene, which was preliminary located on chromosome 4. (author)

  17. [Detection of NPM1, FLT3 and C-KIT mutations in acute myeloid leukemia and their prognostic analysis].

    Science.gov (United States)

    Li, Ling; Lyu, Xiao-Dong; Mi, Rui-Hua; Ding, Jing; Chen, Lin; Wang, Qian; Yin, Qing-Song; Hu, Jie-Ying; Fan, Rui-Hua; Wei, Xu-Dong

    2013-06-01

    This study was aimed to evaluate the frequencies and prognostic significance of the nucleophosmin 1 (NPM1) mutation, the fms-like tyrosine kinase 3 (FLT3) mutation and c-KIT mutation in acute myeloid leukemia (AML) and to explore their relevance to clinical characteristics, cytogenetics and survival. Genomic DNA from 78 newly diagnosed AML from August 2010 to October 2012 was screened by PCR and sequencing or capillary electrophoresis (CE) for NPM1, FLT3 and c-KIT mutations. The results showed that the incidence of NPM1 mutation was 14.1% in AML patients and 26.7% in normal karyotype AML patients. NPM1 mutant cases were significantly associated with old age (P 0.05). The prevalences of FLT3-ITD and FLT3-TKD mutations were 11.5% (9/78) and 3.8% (3/78) respectively, and no one patient has both of the two mutations. Patients with FLT3-ITD mutation had higher white blood cell counts and percentage of in bone marrow blasts (P 0.05). No statistic analysis was performed due to the cases of less FLT3-TKD mutation. C-KIT mutation accounts for 7.7% (6/78). Patients with C-KIT mutation had a higher percentage in abnormal karyotype (P 0.05). It is concluded that the detection of NPM1, FLT3 and C-KIT mutations may contribute to guiding treatment and evaluating prognosis of patients with AML. PMID:23815906

  18. Advances in liquid chromatography-high-resolution mass spectrometry for quantitative and qualitative environmental analysis.

    Science.gov (United States)

    Aceña, Jaume; Stampachiacchiere, Serena; Pérez, Sandra; Barceló, Damià

    2015-08-01

    This review summarizes the advances in environmental analysis by liquid chromatography-high-resolution mass spectrometry (LC-HRMS) during the last decade and discusses different aspects of their application. LC-HRMS has become a powerful tool for simultaneous quantitative and qualitative analysis of organic pollutants, enabling their quantitation and the search for metabolites and transformation products or the detection of unknown compounds. LC-HRMS provides more information than low-resolution (LR) MS for each sample because it can accurately determine the mass of the molecular ion and its fragment ions if it can be used for MS-MS. Another advantage is that the data can be processed using either target analysis, suspect screening, retrospective analysis, or non-target screening. With the growing popularity and acceptance of HRMS analysis, current guidelines for compound confirmation need to be revised for quantitative and qualitative purposes. Furthermore, new commercial software and user-built libraries are required to mine data in an efficient and comprehensive way. The scope of this critical review is not to provide a comprehensive overview of the many studies performed with LC-HRMS in the field of environmental analysis, but to reveal its advantages and limitations using different workflows. PMID:26138893

  19. Mutation analysis of the WFS1 gene in seven Danish Wolfram syndrome families; four new mutations identified

    DEFF Research Database (Denmark)

    Hansen, Lars; Eiberg, Hans Rudolf Lytchoff; Barrett, Timothy;

    2005-01-01

    Wolfram syndrome (WS) is a neuro-degenerative autosomal recessive (AR) disorder (OMIM #222300) caused by mutations in the WFS1 gene on 4p16.1. More than 120 mutations have been identified in WFS1 associated with AR WS, as well as autosomal dominant nonsyndromic low-frequency sensorineural hearing...

  20. Liquid chromatography combined with mass spectrometry for 13C isotopic analysis in life science research.

    Science.gov (United States)

    Godin, Jean-Philippe; Fay, Laurent-Bernard; Hopfgartner, Gérard

    2007-01-01

    Among the different disciplines covered by mass spectrometry, measurement of (13)C/(12)C isotopic ratio crosses a large section of disciplines from a tool revealing the origin of compounds to more recent approaches such as metabolomics and proteomics. Isotope ratio mass spectrometry (IRMS) and molecular mass spectrometry (MS) are the two most mature techniques for (13)C isotopic analysis of compounds, respectively, for high and low-isotopic precision. For the sample introduction, the coupling of gas chromatography (GC) to either IRMS or MS is state of the art technique for targeted isotopic analysis of volatile analytes. However, liquid chromatography (LC) also needs to be considered as a tool for the sample introduction into IRMS or MS for (13)C isotopic analyses of non-volatile analytes at natural abundance as well as for (13)C-labeled compounds. This review presents the past and the current processes used to perform (13)C isotopic analysis in combination with LC. It gives particular attention to the combination of LC with IRMS which started in the 1990's with the moving wire transport, then subsequently moved to the chemical reaction interface (CRI) and was made commercially available in 2004 with the wet chemical oxidation interface (LC-IRMS). The LC-IRMS method development is also discussed in this review, including the possible approaches for increasing selectivity and efficiency, for example, using a 100% aqueous mobile phase for the LC separation. In addition, applications for measuring (13)C isotopic enrichments using atmospheric pressure LC-MS instruments with a quadrupole, a time-of-flight, and an ion trap analyzer are also discussed as well as a LC-ICPMS using a prototype instrument with two quadrupoles. PMID:17853432

  1. Quantitative Analysis of Tetramethylenedisulfotetramine ('Tetramine') Spiked into Beverages by Liquid Chromatography Tandem Mass Spectrometry with Validation by Gas Chromatography Mass Spectrometry

    International Nuclear Information System (INIS)

    Tetramethylenedisulfotetramine, commonly known as tetramine, is a highly neurotoxic rodenticide (human oral LD50 = 0.1 mg/kg) used in hundreds of deliberate food poisoning events in China. Here we describe a method for quantitation of tetramine spiked into beverages, including milk, juice, tea, cola, and water and cleaned up by C8 solid phase extraction and liquid-liquid extraction. Quantitation by high performance liquid chromatography tandem mass spectrometry (LC/MS/MS) was based upon fragmentation of m/z 347 to m/z 268. The method was validated by gas chromatography mass spectrometry (GC/MS) operated in SIM mode for ions m/z 212, 240, and 360. The limit of quantitation was 0.10 (micro)g/mL by LC/MS/MS versus 0.15 (micro)g/mL for GC/MS. Fortifications of the beverages at 2.5 (micro)g/mL and 0.25 (micro)g/mL were recovered ranging from 73-128% by liquid-liquid extraction for GC/MS analysis, 13-96% by SPE and 10-101% by liquid-liquid extraction for LC/MS/MS analysis.

  2. [Analysis of major components in water based stamp pad inks and their imprints by ultra high performance liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry].

    Science.gov (United States)

    Zhang, Qing; Zou, Jixin; Shi, Gaojun; Zhang, Lijuan

    2010-12-01

    Ultra high performance liquid chromatography-mass spectrometry (UHPLC-MS) technology and gas chromatography-mass spectrometry (GC-MS) technology were used to qualitatively analyze the major components in water based stamp pad inks including major colorants and volatile components. After the samples were supersonically extracted and then centrifuged, UHPLC-MS was used to separate and identify the major colorants. A ZORBAX Eclipse Plus Phenyl-Hexyl (50 mm x 4.6 mm, 1.8 microm) column and 15 mmol/L ammonium acetate-acetonitrile were utilized for the separation and negative selected ion monitoring mode (SIM) was set for the MS analysis. An HP-INNOWAX (30 m x 0.25 mm, 0.25 microm) column was employed in the GC-MS analysis with the full-scan mode to determine the volatiles. This study demonstrated that the major colorants in the inks and their imprints were Acid Red R, Eosin Y and Pigment Red 112; and the major volatiles were glycerol, 1,2-propanediol, etc. The method is rapid and accurate. It also demonstrates that the method can meet the requirements for imprint determination in material evidence identification. The work provides a reliable tool for the categorization research in the forensic sciences. PMID:21438364

  3. Quantitative Analysis of Tetramethylenedisulfotetramine ("Tetramine") Spiked into Beverages by Liquid Chromatography Tandem Mass Spectrometry with Validation by Gas Chromatography Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Owens, J; Hok, S; Alcaraz, A; Koester, C

    2008-11-13

    Tetramethylenedisulfotetramine, commonly known as tetramine, is a highly neurotoxic rodenticide (human oral LD{sub 50} = 0.1 mg/kg) used in hundreds of deliberate food poisoning events in China. Here we describe a method for quantitation of tetramine spiked into beverages, including milk, juice, tea, cola, and water and cleaned up by C8 solid phase extraction and liquid-liquid extraction. Quantitation by high performance liquid chromatography tandem mass spectrometry (LC/MS/MS) was based upon fragmentation of m/z 347 to m/z 268. The method was validated by gas chromatography mass spectrometry (GC/MS) operated in SIM mode for ions m/z 212, 240, and 360. The limit of quantitation was 0.10 {micro}g/mL by LC/MS/MS versus 0.15 {micro}g/mL for GC/MS. Fortifications of the beverages at 2.5 {micro}g/mL and 0.25 {micro}g/mL were recovered ranging from 73-128% by liquid-liquid extraction for GC/MS analysis, 13-96% by SPE and 10-101% by liquid-liquid extraction for LC/MS/MS analysis.

  4. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis

    International Nuclear Information System (INIS)

    Carcinogenesis typically involves multiple somatic mutations in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes. Analysis of mutation spectra of the tumor suppressor that is most commonly mutated in human cancers, p53, unexpectedly suggested that somatic evolution of the p53 gene during tumorigenesis is dominated by positive selection for gain of function. This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution. A comprehensive analysis of probable somatic mutations in the sequences of Expressed Sequence Tags (ESTs) from malignant tumors and normal tissues was performed in order to access the prevalence of positive selection in cancer evolution. For each EST, the numbers of synonymous and non-synonymous substitutions were calculated. In order to identify genes with a signature of positive selection in cancers, these numbers were compared to: i) expected numbers and ii) the numbers for the respective genes in the ESTs from normal tissues. We identified 112 genes with a signature of positive selection in cancers, i.e., a significantly elevated ratio of non-synonymous to synonymous substitutions, in tumors as compared to 37 such genes in an approximately equal-sized EST collection from normal tissues. A substantial fraction of the tumor-specific positive-selection candidates have experimentally demonstrated or strongly predicted links to cancer. The results of EST analysis should be interpreted with extreme caution given the noise introduced by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation of EST analysis is that multiple mutations amenable to statistical analysis can be detected only in relatively highly expressed genes. Nevertheless, the present results suggest that positive selection might affect a substantial number of genes during

  5. Mutational analysis of the regulatory region of the srfA operon in Bacillus subtilis.

    OpenAIRE

    Nakano, M M; Zuber, P

    1993-01-01

    Transcription of the Bacillus subtilis srfA operon is dependent on the transcriptional activator ComA. Mutational analysis of the srfA regulatory region suggests that two regions of dyad symmetry upstream of the srfA promoter may function in transcriptional activation by facilitating a cooperative interaction between ComA dimers.

  6. Construction and genetic analysis of mutator insertion mutant population in maize

    Institute of Scientific and Technical Information of China (English)

    LIU Wenting; GAO Youjun; TENG Feng; SHI Qing; ZHENG Yonglian

    2006-01-01

    A total of 26718 M1 plants were obtained by crossing the active mutator transposon donor parents (Q105, WW51, 115F, V26-2 and 919J)with the recipient parents (Hz85,W328 with Bz gene and S-Mo17Rf3Rf3). The phenotypes of M1 plants were observed in the field. M1 plants were self-pollinated to develop the mutator insertion-mutagenized M2 seeds. The transposition frequency of the mutator in the genome was calculated based on the spotted aleurone phenotype of the M2 seeds. The results showed that: (1) the mutation frequency of M1 phenotypes in the field was 0.07 in the population of W328×Mu; (2) the mutation frequency of spotted aleurone seeds on the M2 ears was 0.122 in the population of W328×Mu; (3) five S-cytoplasm male-sterile plants were found among 22500 M1 plants of S-Mo17Rf3Rf3×Mu, with the transposition frequency about 2.2×10-4 per locus. 99 flanking sequences of mutator transposition were amplified by the modified MuTAIL-PCR, and 59 non-redundant sequences with length around 400 bp were obtained.After bioinformatic analysis, 27 sequences of them could be annotated, using non-redundant nucleotide database of maize, rice, and Arabidopsis. 36 sequences of them were located on the genetic map of maize by comparative genomics, and several flanking sequences of mutator insertion were mapped on the single marker locus. Hotspot sequences of mutator transposition were revealed by comparing the homologies between the 9-bp target site duplication of the mutator insertion. The putative functions of 8 flanking sequences of rnutator transposition had identity with the functions of their corresponding marker. The constructed mutator insertion mutant population in maize will facilitate the new gene discovery and functional genomics study in maize.

  7. Subfraction analysis of circulating lipoproteins in a patient with Tangier disease due to a novel ABCA1 mutation.

    Science.gov (United States)

    Murano, Takeyoshi; Yamaguchi, Takashi; Tatsuno, Ichiro; Suzuki, Masayo; Noike, Hirofumi; Takanami, Tarou; Yoshida, Tomoe; Suzuki, Mitsuya; Hashimoto, Ryuya; Maeno, Takatoshi; Terai, Kensuke; Tokuyama, Wataru; Hiruta, Nobuyuki; Schneider, Wolfgang J; Bujo, Hideaki

    2016-01-15

    Tangier disease, characterized by low or absent high-density lipoprotein (HDL), is a rare hereditary lipid storage disorder associated with frequent, but not obligatory, severe premature atherosclerosis due to disturbed reverse cholesterol transport from tissues. The reasons for the heterogeneity in atherogenicity in certain dyslipidemias have not been fully elucidated. Here, using high-performance liquid chromatography with a gel filtration column (HPLC-GFC), we have studied the lipoprotein profile of a 17-year old male patient with Tangier disease who to date has not developed manifest coronary atherosclerosis. The patient was shown to be homozygous for a novel mutation (Leu1097Pro) in the central cytoplasmic region of ATP-binding cassette transporter A1 (ABCA1). Serum total and HDL-cholesterol levels were 59mg/dl and 2mg/dl, respectively. Lipoprotein electrophoretic analyses on agarose and polyacrylamide gels showed the presence of massively abnormal lipoproteins. Further analysis by HPLC-GFC identified significant amounts of lipoproteins in low-density lipoprotein (LDL) subfractions. The lipoprotein particles found in the peak subfraction were smaller than normal LDL, were rich in triglycerides, but poor in cholesterol and phospholipids. These findings in an adolescent Tangier patient suggest that patients in whom these triglyceride-rich, cholesterol- and phospholipid-poor LDL-type particles accumulate over time, would experience an increased propensity for developing atherosclerosis. PMID:26616730

  8. Circulating ultrasound-assisted extraction, countercurrent chromatography, and liquid chromatography for the simultaneous extraction, isolation, and analysis of the constituents of Uncaria tomentosa.

    Science.gov (United States)

    Zhang, Yuchi; Liu, Chunming; Qi, Yanjuan; Li, Sainan; Pan, Yan; Li, Yuchun

    2015-04-01

    A hyphenated automated technique for the online extraction, isolation, analysis, and identification of natural organic compounds was established. Circulating ultrasound-assisted extraction (CUAE) was coupled with countercurrent chromatography (CCC), high performance liquid chromatography (HPLC), and a diode array detector (DAD). This approach was applied to the fractionation and purification of alkaloids from Uncaria tomentosa. A biphasic solvent system of chloroform-methanol-water (6:4:5, v:v:v) was used for the CUAE and CCC separation of compounds from 500 g of U. tomentosa. Two CUAE/CCC/HPLC/DAD modes were established. Either the upper aqueous phase or the lower organic phase of the solvent system could be used as the extraction solvent. The target compounds were extracted by CUAE, and the extract was pumped into a sample loop before being directly injected into the CCC column, or pre-purified using a flash chromatography column before injection. The target compounds were eluted using either the organic or aqueous phase of the solvent system and the fractions were monitored using a UV detector. The target fractions were collected by a sample loop via a six-port valve, and analyzed by HPLC/DAD for purity and structural identification. This system isolated of 8.2mg, 7.4 mg, and 12.9 mg of rhynchophylline, corynoxine, and corynoxine B with HPLC purities of 96.15%, 95.34%, and 95.49%, respectively via the first mode; and isolated 26.6 mg, 24.6 mg, and 45.3mg of rhynchophylline, corynoxine, and corynoxine B with a HPLC purities of 98.22%, 97.18%, and 97.93% via the second mode. PMID:25725954

  9. Analysis of glyphosate residues in cereals using liquid chromatography-mass spectrometry (LC-MS/MS)

    DEFF Research Database (Denmark)

    Granby, Kit; Johannesen, S.; Gabrielsen, Martin Vahl

    2003-01-01

    A fast and specific method for the determination of glyphosate in cereals is described. The method is based on extraction with water by ultrasonication. The samples are cleaned up and separated by high-performance liquid chromatography on a polystyrene-based reverse-phase column (clean-up) in...... monitored m/z 168--> 150 (glyphosate) and 170-->152 (internal standard 2- 13 (CN)-N-15-glyphosate) for quantification. The mean recovery was 85% ( n =32) at spiking levels from 0.03 to 0.33 mg kg(-1) . From 1998 to 2001, from the analysis of about 50 samples per annum, a reduction in the glyphosate residues...... was observed owing to a Danish trade decision not to use grain with glyphosate residues for milling or bread production....

  10. Indirect hydrogen analysis by gas chromatography coupled to mass spectrometry (GC-MS).

    Science.gov (United States)

    Varlet, V; Smith, F; Augsburger, M

    2013-08-01

    Gas chromatography (GC) is an analytical tool very useful to investigate the composition of gaseous mixtures. The different gases are separated by specific columns but, if hydrogen (H2 ) is present in the sample, its detection can be performed by a thermal conductivity detector or a helium ionization detector. Indeed, coupled to GC, no other detector can perform this detection except the expensive atomic emission detector. Based on the detection and analysis of H2 isotopes by low-pressure chemical ionization mass spectrometry (MS), a new method for H2 detection by GC coupled to MS with an electron ionization ion source and a quadrupole analyser is presented. The presence of H2 in a gaseous mixture could easily be put in evidence by the monitoring of the molecular ion of the protonated carrier gas. PMID:23893637

  11. Gas chromatography-mass spectrometry analysis of various organic extracts ofMerremia borneensisfrom Sabah

    Institute of Scientific and Technical Information of China (English)

    M Amzad Hossain; Muhammad Dawood Shah; Mahyar Sakari

    2011-01-01

    Objective:To analyse the chemical composition of different extracts ofMerremia borneensis (M. borneensis) by gas chromatography-mass spectrometry (GC-MS).Methods: The dried leaves powder was extracted with methanol at room temperature by using Soxhlet extractor. Methanol crude extracts ofM. borneensis were extrastel with hexane, chloroform, ethyl acetate and butanol. Results: Qualitative analyses of various organic crude extracts showed that majority of these are flavonoids, terpeniods, alkaloids and glycosides. Most of the identified compounds by GC-MS are biologically important. Further theM. borneensisleaf possesses certain characteristics that can be ascribed to cultivation on a domestic plantation.Conclusions: The suitable extracts for respective compounds can be chosen on the basis of aboveGC-MS analysis. All the major compounds from different extracts are biologically active molecules. Thus the identification of a good number of compounds from various extractsM. borneensis might have some ecological significance.

  12. Diagnosis of propionic acidemia by gas chromatography coupled to mass spectrometry in a case analysis

    International Nuclear Information System (INIS)

    Propionic acidemia is an inherited metabolic disease caused by a deficiency in the propionyl-CoA carboxilase, a biotin-dependent mitochondrial enzyme. The disorder is a clinically heterogeneous disease and one of the most frequently occurring organic acidurias. We report the first Cuban case with a severe form of propionic acidemia followed by acidosis and death. The diagnosis was carried out by gas chromatography coupled to mass spectrometry. Our aim is to highlight the importance of organic acids urine analysis as part of the first laboratory tests in undiagnosed seriously ill children. The definitive diagnosis is important as it serves as a clear guideline to establish a suitable treatment and allows geneticists to provide patients with a proper genetic counseling

  13. Trace Analysis of Boron in Nuclear Graphite by Means of Gas Chromatography

    International Nuclear Information System (INIS)

    No literature is available about the application of gas chromatography in trace analysis of boron in graphite. The following methods of transformation of boron into its volatile compounds are discussed: (a) Ignition of graphite in a stream of oxygen and subsequent transformation of boron oxide into volatile methyl borate which is then analysed on a Dilkens Aerograph H Model 96 gas chromatograph with silicone column and hydrogen as carrier (concentration method). (b) Extraction of boron from the graphite by means of sodium fluoride at 2800oC with simultaneous chlorination and trapping of boron trichloride, which is then analysed (direct method). A home-made gas chromatograph with a thermal conductivity detector and nitrogen as a carrier was used. The column was made of glass with a 20% (wt./wt.) fluorocarbon oil on kieselguhr. Special precautions were taken on account of the sensitivity of boron trichloride to moisture. (author)

  14. Integrating Paper Chromatography with Electrochemical Detection for the Trace Analysis of TNT in Soil

    Directory of Open Access Journals (Sweden)

    Patrick Ryan

    2015-07-01

    Full Text Available We report on the development of an electrochemical probe for the trace analysis of 2,4,6-trinitrotoluene (TNT in soil samples. The probe is a combination of graphite electrodes, filter paper, with ethylene glycol and choline chloride as the solvent/electrolyte. Square wave chromatovoltammograms show the probes have a sensitivity for TNT of 0.75 nA/ng and a limit of detection of 100 ng. In addition, by taking advantage of the inherent paper chromatography step, TNT can be separated in both time and cathodic peak potential from 4-amino-dinitrotolene co-spotted on the probe or in soil samples with the presence of methyl parathion as a possible interferent.

  15. Separation of Caffeine from Beverages and Analysis Using Thin-Layer Chromatography and Gas Chromatography-Mass Spectrometry

    Science.gov (United States)

    Torres y Torres, Janelle L.; Hiley, Shauna L.; Lorimor, Steven P.; Rhoad, Jonathan S.; Caldwell, Benjamin D.; Zweerink, Gerald L.; Ducey, Michael

    2015-01-01

    The Characterization and Analysis of a Product (CAP) project is used to introduce first-semester general chemistry students to chemical instrumentation through the analysis of caffeine-containing beverage products. Some examples of these products have included coffee, tea, and energy drinks. Students perform at least three instrumental experiments…

  16. Establishment of screening techniques for mutant cell and base sequence analysis of its mutation

    International Nuclear Information System (INIS)

    This study aimed at an effective assessment of radiation dose, evaluation for human risk in detail and development of risk reducing techniques. The role of p53 in the mutation inducing mechanism of radiation was investigated in human lymphoblasts. The frequency of gene mutation in p53 mutant cells was more than 30-fold higher than that in the normal cell and most of the mutants were produced through transduction. Cytogenetic analysis revealed that chromosomal translocation occurred frequently in those mutants through heterologous recombination. Abnormalities in p53 were found to increase homologous recombination and reduce its fidelity, resulting to induce LOH-type mutation and chromosomal translocation. The cleavages of double strand DNA induced by radiation are thought to be repaired by such homologous recombination. Therefore, it seemed important to clarify the role of p53 for evaluating the radiation risk. (M.N.)

  17. Genetic mutation analysis of human gastric adenocarcinomas using ion torrent sequencing platform.

    Directory of Open Access Journals (Sweden)

    Zhi Xu

    Full Text Available Gastric cancer is the one of the major causes of cancer-related death, especially in Asia. Gastric adenocarcinoma, the most common type of gastric cancer, is heterogeneous and its incidence and cause varies widely with geographical regions, gender, ethnicity, and diet. Since unique mutations have been observed in individual human cancer samples, identification and characterization of the molecular alterations underlying individual gastric adenocarcinomas is a critical step for developing more effective, personalized therapies. Until recently, identifying genetic mutations on an individual basis by DNA sequencing remained a daunting task. Recent advances in new next-generation DNA sequencing technologies, such as the semiconductor-based Ion Torrent sequencing platform, makes DNA sequencing cheaper, faster, and more reliable. In this study, we aim to identify genetic mutations in the genes which are targeted by drugs in clinical use or are under development in individual human gastric adenocarcinoma samples using Ion Torrent sequencing. We sequenced 737 loci from 45 cancer-related genes in 238 human gastric adenocarcinoma samples using the Ion Torrent Ampliseq Cancer Panel. The sequencing analysis revealed a high occurrence of mutations along the TP53 locus (9.7% in our sample set. Thus, this study indicates the utility of a cost and time efficient tool such as Ion Torrent sequencing to screen cancer mutations for the development of personalized cancer therapy.

  18. Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.

    Science.gov (United States)

    Gatto, Francesco; Schulze, Almut; Nielsen, Jens

    2016-07-19

    Mutations are the basis of the clonal evolution of most cancers. Nevertheless, a systematic analysis of whether mutations are selected in cancer because they lead to the deregulation of specific biological processes independent of the type of cancer is still lacking. In this study, we correlated the genome and transcriptome of 1,082 tumors. We found that nine commonly mutated genes correlated with substantial changes in gene expression, which primarily converged on metabolism. Further network analyses circumscribed the convergence to a network of reactions, termed AraX, that involves the glutathione- and oxygen-mediated metabolism of arachidonic acid and xenobiotics. In an independent cohort of 4,462 samples, all nine mutated genes were consistently correlated with the deregulation of AraX. Among all of the metabolic pathways, AraX deregulation represented the strongest predictor of patient survival. These findings suggest that oncogenic mutations drive a selection process that converges on the deregulation of the AraX network. PMID:27396332

  19. Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics

    Directory of Open Access Journals (Sweden)

    Francesco Gatto

    2016-07-01

    Full Text Available Mutations are the basis of the clonal evolution of most cancers. Nevertheless, a systematic analysis of whether mutations are selected in cancer because they lead to the deregulation of specific biological processes independent of the type of cancer is still lacking. In this study, we correlated the genome and transcriptome of 1,082 tumors. We found that nine commonly mutated genes correlated with substantial changes in gene expression, which primarily converged on metabolism. Further network analyses circumscribed the convergence to a network of reactions, termed AraX, that involves the glutathione- and oxygen-mediated metabolism of arachidonic acid and xenobiotics. In an independent cohort of 4,462 samples, all nine mutated genes were consistently correlated with the deregulation of AraX. Among all of the metabolic pathways, AraX deregulation represented the strongest predictor of patient survival. These findings suggest that oncogenic mutations drive a selection process that converges on the deregulation of the AraX network.

  20. AB036. Analysis of human mitochondrial genome mutations of Vietnamese patients tentatively diagnosed with encephalomyopathy

    Science.gov (United States)

    Nghia, Phan Tuan; Thai, Trinh Hong; Hue, Truong Thi; Van Minh, Nguyen; Khanh, Phung Bao; Hiep, Tran Duc; Anh, Tran Kieu; Loan, Nguyen Thi Hong; Van, Nguyen Thi Hong; Anh, Pham Van; Hung, Cao Vu; Anh, Le Ngoc

    2015-01-01

    Human mitochondrial genome consists of 16,569 bp, and replicates independently from the nuclear genome. Mutations in mitochondrial genome are usually causative factors of various metabolic disorders, especially those of encephalomyopathy. DNA analysis is the most reliable method for detection of mitochondrial genome mutations, and accordingly an excellent diagnostic tool for mitochondrial mutation-related diseases. In this study, 19 different mitochondrial genome mutations including A3243G, A3251G, T3271C and T3291C (MELAS); A8344G, T8356C and G8363A (MERRF); G3460A, G11778A and T14484C (LHON); T8993G/C and T9176G (Leigh); A1555G (deafness) and A4225G, G4298A, T10010C, T14727C, T14728C, T14709C (encephalomyopathy in general) were analyzed using PCR-RFLP in combination with DNA sequencing. In addition, a real-time PCR method using locked nucleic acid (LNA) Taqman probe was set up for heteroplasmy determination. Screening of 283 tentatively diagnosed encephalomyopathy patients revealed 7 cases of A3243G, 1 case of G11778A, 1 case of A1555G, 1 case of A4225G, 1 case G4298A, and 1 case of 6 bp (ACTCCT/CTCCTA) deletion. Using the LNA Taqman probe real-time PCR, the heteroplasmy of some point mutations was determined and the results support a potential relationship between heteroplasmy level and severity of the disease.

  1. Screening of mutations affecting protein stability and dynamics of FGFR1—A simulation analysis

    Directory of Open Access Journals (Sweden)

    C. George Priya Doss

    2012-12-01

    Full Text Available Single amino acid substitutions in Fibroblast Growth Factor Receptor 1 (FGFR1 destabilize protein and have been implicated in several genetic disorders like various forms of cancer, Kallamann syndrome, Pfeiffer syndrome, Jackson Weiss syndrome, etc. In order to gain functional insight into mutation caused by amino acid substitution to protein function and expression, special emphasis was laid on molecular dynamics simulation techniques in combination with in silico tools such as SIFT, PolyPhen 2.0, I-Mutant 3.0 and SNAP. It has been estimated that 68% nsSNPs were predicted to be deleterious by I-Mutant, slightly higher than SIFT (37%, PolyPhen 2.0 (61% and SNAP (58%. From the observed results, P722S mutation was found to be most deleterious by comparing results of all in silico tools. By molecular dynamics approach, we have shown that P722S mutation leads to increase in flexibility, and deviated more from the native structure which was supported by the decrease in the number of hydrogen bonds. In addition, biophysical analysis revealed a clear insight of stability loss due to P722S mutation in FGFR1 protein. Majority of mutations predicted by these in silico tools were in good concordance with the experimental results.

  2. Analysis of phenolic acids as chloroformate derivatives using solid phase microextraction-gas chromatography.

    Science.gov (United States)

    Citová, Ivana; Sladkovský, Radek; Solich, Petr

    2006-07-28

    In the presented study, a simple and original procedure of phenolic acids derivatization treated by ethyl and methyl chloroformate performed in an aqueous media consisting of acetonitrile, water, methanol/ethanol and pyridine has been modified and optimized. Seven phenolic acid standards-caffeic, ferulic, gallic, p-coumaric, protocatechuic, syringic and vanillic were derivatized into corresponding methyl/ethyl esters and subsequently determined by the means of gas chromatography connected to the flame-ionisation detector (FID). Some selected validation parameters as linearity, detection and quantitation limits and peak area repeatability were valued. The total time of gas chromatography (GC) analysis was 24 min for methyl chloroformate and 30 min for ethyl chloroformate derivatization. The more suitable methyl chloroformate derivatization was used for further experiments on the possibility of multiple pre-concentration by the direct solid phase microextraction technique (SPME). For this purpose, polyacrylate (PA), polydimethylsiloxane (PDMS), carboxen/polydimethylsiloxane (CAR/PDMS) and polydimethylsiloxane/divinylbenzene (PDMS/DVB) fibres were tested and the extraction conditions concerning time of extraction, temperature and time of desorption were optimized. The most polar PA fibre gave the best results under optimal extraction conditions (50 min extraction time, 25 degrees C extraction temperature and 10 min desorption time). As a result, the total time of SPME-GC analysis was 74 min and an increase in method sensitivity was reached. The limits of quantitation (LOQ) of p-coumaric, ferulic, syringic and vanillic acid esters after SPME pre-concentration were 0.02, 0.17, 0.2 and 0.2 microg mL(-1), respectively, showing approximately 10 times higher sensitivity in comparison with the original GC method. PMID:17723529

  3. Analysis of pesticides by gas chromatography/multiphoton ionization/mass spectrometry using a femtosecond laser

    International Nuclear Information System (INIS)

    Highlights: → Gas chromatography/multiphoton ionization/time-of-flight mass spectrometry was utilized for analysis. → A standard mixture sample containing 49 pesticides and 4 real samples were measured. → Third-harmonic emission of a Ti:sapphire laser (100 fs) was employed as an ionization source. → Most of the pesticides were softly ionized by the femtosecond laser. → Three pesticides were found, although some of them were not detected by GC/EI/MS-MS. - Abstract: Gas chromatography/multiphoton ionization/time-of-flight mass spectrometry (GC/MPI/TOFMS) was utilized for analysis of a standard mixture sample containing 49 pesticides and 4 real samples using the third-harmonic emission (267 nm) of a femtosecond Ti:sapphire laser (100 fs) as the ionization source. A sample of a standard mixture of n-alkane was also measured for calibration of the retention time indices of the pesticides. Two photons are required for the excitation of n-alkane due to an absorption band located in the far ultraviolet region (140 nm). The n-alkane molecule in the excited state was subsequently ionized either directly or by absorbing another photon because of a high ionization potential. Due to a large excess of energy, the molecular ion was decomposed and formed many fragment ions. Compared to n-alkanes, most of the pesticides were softly ionized by the femtosecond laser; one photon was used for excitation and another was used for the subsequent ionization. The pesticides with no conjugated double bond had a lower ionization efficiency. The present analytical instrument was applied to several samples prepared from a variety of vegetables and a single fruit after pretreatment with solid-phase extraction. Three pesticides were found in these samples, although some of them were not detected by conventional GC/EI/MS-MS due to insufficient sensitivity and selectivity.

  4. Mutation analysis of the NSD1 gene in patients with autism spectrum disorders and macrocephaly

    Directory of Open Access Journals (Sweden)

    Delorme Richard

    2007-11-01

    Full Text Available Abstract Background Sotos syndrome is an overgrowth syndrome characterized by macrocephaly, advanced bone age, characteristic facial features, and learning disabilities, caused by mutations or deletions of the NSD1 gene, located at 5q35. Sotos syndrome has been described in a number of patients with autism spectrum disorders, suggesting that NSD1 could be involved in other cases of autism and macrocephaly. Methods We screened the NSD1 gene for mutations and deletions in 88 patients with autism spectrum disorders and macrocephaly (head circumference 2 standard deviations or more above the mean. Mutation analysis was performed by direct sequencing of all exons and flanking regions. Dosage analysis of NSD1 was carried out using multiplex ligation-dependent probe amplification. Results We identified three missense variants (R604L, S822C and E1499G in one patient each, but none is within a functional domain. In addition, segregation analysis showed that all variants were inherited from healthy parents and in two cases were also present in unaffected siblings, indicating that they are probably nonpathogenic. No partial or whole gene deletions/duplications were observed. Conclusion Our findings suggest that Sotos syndrome is a rare cause of autism spectrum disorders and that screening for NSD1 mutations and deletions in patients with autism and macrocephaly is not warranted in the absence of other features of Sotos syndrome.

  5. DNA microarray analysis of fim mutations in Escherichia coli

    DEFF Research Database (Denmark)

    Schembri, Mark; Ussery, David; Workman, Christopher; Hasman, Henrik; Klemm, Per

    2002-01-01

    we have used DNA microarray analysis to examine the molecular events involved in response to fimbrial gene expression in E. coli K-12. Observed differential expression levels of the fim genes were in good agreement with our current knowledge of the stoichiometry of type I fimbriae. Changes in fim...

  6. Mutation analysis of ATP13A2 in early-onset parkinsonism patients

    Institute of Scientific and Technical Information of China (English)

    Yuping Ning; Hiroyuki Tomiyama; Yuanzhe Li; Manabu Funayama; Hiroyo Yoshino; Shigeto Sato; Yoshikuni Mizuno; Nobutaka Hattori

    2008-01-01

    BACKGROUND: A recent study has found that ATP13A2 is the causative gene for PARK9-linked autosomal recessive early-onset parkinsonism, described previously in Jordanian and Chilean families (Kufor-Rakeb syndrome). OBJECTIVE: To screen eastern Asian patients with early-onset parkinsonism for mutations in ATP13A2 and to describe positron emission tomography (PET) findings of PARK9-linked parkinsonism.DESIGN, TIME AND SETTING: In total, 117 patients were selected from the Department of Neurology, Juntendo University, from February 2003 to October 2006, for this molecular genetics and case-control study.PARTICIPANTS: The patients with parkinsonism consist of two cohorts. Ninety four patients with onset age of less than 30 years were selected for the first cohort. They included 49 males and 44 females, comprising 73 Japanese, 9 Korean, 8 Taiwanese, and 4 Mainland Chinese. Eleven patients had parkinsonism complicated with dementia, 15 patients had family histories of parkinsonism (including 2 families), and 5 patients were from consanguineous parents (including one family). The second cohort of 23 patients was composed of patients with consanguineous parents (n = 15) or who had affected siblings (n = 6) or both (n = 2), but the age at onset ranged from 30 to 50 years.METHODS: In 117 patients with parkinsonism, direct sequencing of ATP13A2 exons 13, 16, and 26, in which mutations had been reported previously, were performed. Sequencing was also performed in all 29 exons, including splice sites, in 28 probands who showed homozygosity at the PARK9 locus by haplotype analysis. Mutation analysis was also performed in 150 normal people. Linkage analysis was performed on all 3 parkinsonism families using short tandem repeat markers flanking the PARK9 locus. For patients who had ATP13A2 mutation, we performed brain MRI and 18F-dopa PET scans.MAIN OUTCOME MEASURES: ATP13A2 DNA sequence, 18F-dopa PET scan and brain MRI findings.RESULTS: A novel F182L mutation in a consanguineous

  7. BRCA1/2 mutation analysis in 41 ovarian cell lines reveals only one functionally deleterious BRCA1 mutation.

    LENUS (Irish Health Repository)

    Stordal, Britta

    2013-06-01

    Mutations in BRCA1\\/2 increase the risk of developing breast and ovarian cancer. Germline BRCA1\\/2 mutations occur in 8.6-13.7% of unselected epithelial ovarian cancers, somatic mutations are also frequent. BRCA1\\/2 mutated or dysfunctional cells may be sensitive to PARP inhibition by synthetic lethality. The aim of this study is to comprehensively characterise the BRCA1\\/2 status of a large panel of ovarian cancer cell lines available to the research community to assist in biomarker studies of novel drugs and in particular of PARP inhibitors. The BRCA1\\/2 genes were sequenced in 41 ovarian cell lines, mRNA expression of BRCA1\\/2 and gene methylation status of BRCA1 was also examined. The cytotoxicity of PARP inhibitors olaparib and veliparib was examined in 20 cell lines. The cell line SNU-251 has a deleterious BRCA1 mutation at 5564G > A, and is the only deleterious BRCA1\\/2 mutant in the panel. Two cell lines (UPN-251 and PEO1) had deleterious mutations as well as additional reversion mutations that restored the protein functionality. Heterozygous mutations in BRCA1\\/2 were relatively common, found in 14.6% of cell lines. BRCA1 was methylated in two cell lines (OVCAR8, A1847) and there was a corresponding decrease in gene expression. The BRCA1 methylated cell lines were more sensitive to PARP inhibition than wild-type cells. The SNU-251 deleterious mutant was more sensitive to PARP inhibition, but only in a long-term exposure to correct for its slow growth rate. Cell lines derived from metastatic disease are significantly more resistant to veliparib (2.0 fold p = 0.03) compared to those derived from primary tumours. Resistance to olaparib and veliparib was correlated Pearsons-R 0.5393, p = 0.0311. The incidence of BRCA1\\/2 deleterious mutations 1\\/41 cell lines derived from 33 different patients (3.0%) is much lower than the population incidence. The reversion mutations and high frequency of heterozygous mutations suggest that there is a selective

  8. Gas chromatography x gas chromatography-time-of-flight mass spectrometry analysis and antibacterial activity of essential oil from Amomum xanthophlebium

    International Nuclear Information System (INIS)

    Essential oils of fresh leaves, stem, rhizomes and whole aromatic plants of Amomum xanthophlebium (Zingiberaceae) were obtained by hydro distillation. Percentage yields of the leaf, stem and whole plant oils were 0.0032, 0.0074 and 0.0021 % whereas the rhizome oil obtained was very little. Chemical components of each oil and their percentages were determined by Gas Chromatography x Gas Chromatography-Time-of-Flight Mass Spectrometry (GCxGC-TOFMS). Analysis of A. xanthophlebium oils showed that they were dominated by terpenes. Main components in the leaves were allo-aromadendrene (3.41 %), (±)-globulol (2.58 %) and rosifoliol (2.55 %); stem, α-terpineol (4.25 %), rosifoliol (2.41 %) and bingpian (2.27 %); rhizomes, viridiflorol (5.72 %), (±)-globulol (5.23 %) and α-cadinol (4.81 %); whole plants, eucalyptol (4.11 %), l-α-terpineol (2.88 %) and rosifoliol (2.82 %). The stem oil of A. xanthophlebium showed antibacterial activity against Gram-negative Escherichia coli and Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) at the minimum inhibitory concentration of 80 mg/ ml. (author)

  9. Analysis of Founder Mutations in Rare Tumors Associated With Hereditary Breast/Ovarian Cancer Reveals a Novel Association of BRCA2 Mutations with Ampulla of Vater Carcinomas.

    Science.gov (United States)

    Pinto, Pedro; Peixoto, Ana; Santos, Catarina; Rocha, Patrícia; Pinto, Carla; Pinheiro, Manuela; Leça, Luís; Martins, Ana Teresa; Ferreira, Verónica; Bartosch, Carla; Teixeira, Manuel R

    2016-01-01

    BRCA1 and BRCA2 mutations are responsible for hereditary breast and ovarian cancer, but they also confer an increased risk for the development of rarer cancers associated with this syndrome, namely, cancer of the pancreas, male breast, peritoneum, and fallopian tube. The objective of this work was to quantify the contribution of the founder mutations BRCA2 c.156_157insAlu and BRCA1 c.3331_3334del for cancer etiology in unselected hospital-based cohorts of Portuguese patients diagnosed with these rarer cancers, by using a strategy that included testing of archival tumor tissue. A total of 102 male breast, 68 pancreatic and 33 peritoneal/fallopian tube carcinoma cases were included in the study. The BRCA2 c.156_157insAlu mutation was observed with a frequency of 7.8% in male breast cancers, 3.0% in peritoneal/fallopian tube cancers, and 1.6% in pancreatic cancers, with estimated total contributions of germline BRCA2 mutations of 14.3%, 5.5%, and 2.8%, respectively. No carriers of the BRCA1 c.3331_3334del mutation were identified. During our study, a patient with an ampulla of Vater carcinoma was incidentally found to carry the BRCA2 c.156_157insAlu mutation, so we decided to test a consecutive series of additional 15 ampullary carcinomas for BRCA1/BRCA2 mutations using a combination of direct founder mutation testing and full gene analysis with next generation sequencing. BRCA2 mutations were observed with a frequency of 14.3% in ampulla of Vater carcinomas. In conclusion, taking into account the implications for both the individuals and their family members, we recommend that patients with these neoplasias should be offered BRCA1/BRCA2 genetic testing and we here show that it is feasible to test for founder mutations in archival tumor tissue. Furthermore, we identified for the first time a high frequency of germline BRCA2 mutations in ampullary cancers. PMID:27532258

  10. Trace analysis of acrylamide by high-performance thin-layer chromatography coupled to mass spectrometry

    OpenAIRE

    Alpmann, Alexander

    2011-01-01

    Planar-chromatography (High-Performance Thin-Layer Chromatography, HPTLC) is a rapid and cost-effective offline separation method. Through advances in the automatization of each step the system reproducibility, from application and development to detection, has been improved. This makes planar-chromatography a highly reliable technique. HPTLC shows a couple of features that make it unique. There is great flexibility concerning application, development and detection that distinguishes HPTLC fr...

  11. Novel C16orf57 mutations in patients with Poikiloderma with Neutropenia: bioinformatic analysis of the protein and predicted effects of all reported mutations

    Directory of Open Access Journals (Sweden)

    Colombo Elisa A

    2012-01-01

    Full Text Available Abstract Background Poikiloderma with Neutropenia (PN is a rare autosomal recessive genodermatosis caused by C16orf57 mutations. To date 17 mutations have been identified in 31 PN patients. Results We characterize six PN patients expanding the clinical phenotype of the syndrome and the mutational repertoire of the gene. We detect the two novel C16orf57 mutations, c.232C>T and c.265+2T>G, as well as the already reported c.179delC, c.531delA and c.693+1G>T mutations. cDNA analysis evidences the presence of aberrant transcripts, and bioinformatic prediction of C16orf57 protein structure gauges the mutations effects on the folded protein chain. Computational analysis of the C16orf57 protein shows two conserved H-X-S/T-X tetrapeptide motifs marking the active site of a two-fold pseudosymmetric structure recalling the 2H phosphoesterase superfamily. Based on this model C16orf57 is likely a 2H-active site enzyme functioning in RNA processing, as a presumptive RNA ligase. According to bioinformatic prediction, all known C16orf57 mutations, including the novel mutations herein described, impair the protein structure by either removing one or both tetrapeptide motifs or by destroying the symmetry of the native folding. Finally, we analyse the geographical distribution of the recurrent mutations that depicts clusters featuring a founder effect. Conclusions In cohorts of patients clinically affected by genodermatoses with overlapping symptoms, the molecular screening of C16orf57 gene seems the proper way to address the correct diagnosis of PN, enabling the syndrome-specific oncosurveillance. The bioinformatic prediction of the C16orf57 protein structure denotes a very basic enzymatic function consistent with a housekeeping function. Detection of aberrant transcripts, also in cells from PN patients carrying early truncated mutations, suggests they might be translatable. Tissue-specific sensitivity to the lack of functionally correct protein accounts for the

  12. Analysis of native human plasma proteins and haemoglobin for the presence of bityrosine by high-performance liquid chromatography

    DEFF Research Database (Denmark)

    Daneshvar, B; Frandsen, H; Dragsted, L O; Knudsen, Lisbeth E.; Autrup, H

    1997-01-01

    fluorescent substance, bityrosine. High-performance liquid chromatography (HPLC) analysis of acid hydrolyzed serum albumin after oxidation with peroxidase/H2O2 or with Cu++/H2O2 showed that bityrosine had been formed whereas oxidation of this protein with Fe(III)/ascorbate did not result in the formation of...

  13. Analysis of polycyclic aromatic hydrocarbons. I. Determination by gas chromatography with glass and fused solica capillary columns

    International Nuclear Information System (INIS)

    A study of the analysis by gas chromatography of aromatic polycyclic hydrocarbons is presented. The separation has been carried out by glass and fused silice capillary column. The limitations and the advantages of the procedure are discussed in terms of separation efficiency, sensitivity and precision. (author). 3 figs., 17 refs

  14. Analysis of polycyclic aromatic hydrocarbons I. Determination by gas chromatography with glass and fused silica capillary columns

    International Nuclear Information System (INIS)

    A study of the analysis by gas chromatography of aromatic polycyclic hydrocarbons is presented. The separation has been carried out by glass and fused silica capillary column. The limitations and the advantages of the procedure are discussed in terms of separation efficiency, sensitivity and precision. (Author) 17 refs

  15. Analysis of human milk oligosaccharides using high-performance anion-exchange chromatography with pulsed amperometric detection

    DEFF Research Database (Denmark)

    Lie, Aleksander; Pedersen, Lars Haastrup

    lacto-N-neotetraose (Galβ1-4GlcNAcβ1-3Galβ1-4Glc), among others. High-performance anion-exchange chromatography (HPAE) with pulsed amperometric detection (PAD) is an analysis method highly suited for carbohydrates. HPAE with alkaline eluents results in retention of neutral carbohydrates depending on the...

  16. DNA microarray analysis of fim mutations in Escherichia coli

    DEFF Research Database (Denmark)

    Schembri, Mark; Ussery, David; Workman, Christopher;

    2002-01-01

    Bacterial adhesion is often mediated by complex polymeric surface structures referred to as fimbriae. Type I fimbriae of Escherichia coli represent the archetypical and best characterised fimbrial system. These adhesive organelles mediate binding to D-mannose and are directly associated with...... we have used DNA microarray analysis to examine the molecular events involved in response to fimbrial gene expression in E. coli K-12. Observed differential expression levels of the fim genes were in good agreement with our current knowledge of the stoichiometry of type I fimbriae. Changes in fim...

  17. Quantitative Analysis of Sphingomyelin by High-Performance Liquid Chromatography after Enzymatic Hydrolysis

    Directory of Open Access Journals (Sweden)

    Seunghyun Lee

    2012-01-01

    Full Text Available Sphingomyelin is the most abundant sphingolipid in mammalian cells and is mostly present in the plasma membrane. A new analytical method using high-performance liquid chromatography (HPLC was developed to quantify sphingomyelin in mouse plasma and tissues, 3T3-L1 cells, rat aortic smooth muscle cells, and HT-29 cells. Sphingomyelin and dihydrosphingomyelin, an internal standard, were separated by high-performance thin-layer chromatography and simultaneously hydrolyzed with sphingolipid ceramide N-deacylase and sphingomyelinase to release sphingosine and dihydrosphingosine, respectively. Sphingomyelin content was measured by HPLC following o-phthalaldehyde derivatization. Sphingomyelin concentrations in 3T3-L1 cells, rat aortic smooth muscle cells, and HT-29 cells were 60.10±0.24, 62.69±0.08, and 58.38±0.37 pmol/μg protein, respectively, whereas those in brain, kidney, and liver of ICR mice were 55.60±0.43, 43.75±0.21, and 22.26±0.14 pmol/μg protein. The sphingomyelin concentration in mouse plasma was 407.40±0.31 μM. The limits of detection and quantification for sphingomyelin were 5 and 20 pmol, respectively, in the HPLC analysis with fluorescence detection. This sensitivity was sufficient for analyzing sphingomyelin in biological samples. In conclusion, this analytical method is a sensitive and specific technique for quantifying sphingomyelin and was successfully applied to diverse biological samples with excellent reproducibility.

  18. Application of high-temperature gas chromatography to the analysis of used frying fats

    Directory of Open Access Journals (Sweden)

    Aguirre, M.

    2010-06-01

    Full Text Available The determination of polar compounds is the most commonly applied technique in the analysis of used frying fats and oils. High-temperature gas chromatography allows for a quantitative determination of oxidized monomeric FAME and dimeric FAME thus giving extra information on oil degradation starting from the fraction of polar compounds. Polar compounds are transesterified and methyl esters are separated in a VF-5ht Ultimetal column (150 °C -held for 5 min- rising at 5 °C min-1 to 370 °C and held for 5 min using methyl tricosanoate as internal standard. Results are compared with those obtained by more complex alternative methodology using high-performance size-exclusion chromatography.

    La determinación de compuestos polares es el método analítico más utilizado en el análisis de los aceites y grasas de fritura. En este estudio se aprovechan las posibilidades actuales de la cromatografía de gases a elevada temperatura que permite cuantificar los dos grupos mayoritarios de ácidos grasos polares como ésteres metílicos: los monómeros oxidados y los dímeros. Con tal fin, la fracción de compuestos polares se tranesterifica y los ésteres metílicos obtenidos se separan en una columna de VF-5ht Ultimetal, usando tricosanoato de metilo como estándar interno, en las siguientes condiciones: 150 °C durante 5 minutos, 5 °C/min hasta 370 °C y 5 minutos a 370 °C. Los resultados se comparan con los obtenidos mediante técnica alternativa más compleja basada en la cromatografía de exclusión por tamaño molecular.

  19. Rapid direct analysis to discriminate geographic origin of extra virgin olive oils by flash gas chromatography electronic nose and chemometrics.

    Science.gov (United States)

    Melucci, Dora; Bendini, Alessandra; Tesini, Federica; Barbieri, Sara; Zappi, Alessandro; Vichi, Stefania; Conte, Lanfranco; Gallina Toschi, Tullia

    2016-08-01

    At present, the geographical origin of extra virgin olive oils can be ensured by documented traceability, although chemical analysis may add information that is useful for possible confirmation. This preliminary study investigated the effectiveness of flash gas chromatography electronic nose and multivariate data analysis to perform rapid screening of commercial extra virgin olive oils characterized by a different geographical origin declared in the label. A comparison with solid phase micro extraction coupled to gas chromatography mass spectrometry was also performed. The new method is suitable to verify the geographic origin of extra virgin olive oils based on principal components analysis and discriminant analysis applied to the volatile profile of the headspace as a fingerprint. The selected variables were suitable in discriminating between "100% Italian" and "non-100% Italian" oils. Partial least squares discriminant analysis also allowed prediction of the degree of membership of unknown samples to the classes examined. PMID:26988501

  20. Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors.

    Science.gov (United States)

    Robbins, Christiane M; Tembe, Waibov A; Baker, Angela; Sinari, Shripad; Moses, Tracy Y; Beckstrom-Sternberg, Stephen; Beckstrom-Sternberg, James; Barrett, Michael; Long, James; Chinnaiyan, Arul; Lowey, James; Suh, Edward; Pearson, John V; Craig, David W; Agus, David B; Pienta, Kenneth J; Carpten, John D

    2011-01-01

    Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of 3508 exons from 577 cancer-related genes using next generation sequencing. Focal homozygous deletions were detected at 8p22, 10q23.31, 13q13.1, 13q14.11, and 13q14.12. Key genes mapping within these deleted regions include PTEN, BRCA2, C13ORF15, and SIAH3. Focal high-level amplifications were detected at 5p13.2-p12, 14q21.1, 7q22.1, and Xq12. Key amplified genes mapping within these regions include SKP2, FOXA1, and AR. Furthermore, targeted mutational analysis of normal-tumor pairs has identified somatic mutations in genes known to be associated with prostate cancer including AR and TP53, but has also revealed novel somatic point mutations in genes including MTOR, BRCA2, ARHGEF12, and CHD5. Finally, in one patient where multiple independent metastatic tumors were available, we show common and divergent somatic alterations that occur at both the copy number and point mutation level, supporting a model for a common clonal progenitor with metastatic tumor-specific divergence. Our study represents a deep genomic analysis of advanced metastatic prostate tumors and has revealed candidate somatic alterations, possibly contributing to lethal prostate cancer. PMID:21147910

  1. Data analysis tool for comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry.

    Science.gov (United States)

    Castillo, Sandra; Mattila, Ismo; Miettinen, Jarkko; Orešič, Matej; Hyötyläinen, Tuulia

    2011-04-15

    Data processing and identification of unknown compounds in comprehensive two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC×GC/TOFMS) analysis is a major challenge, particularly when large sample sets are analyzed. Herein, we present a method for efficient treatment of large data sets produced by GC×GC/TOFMS implemented as a freely available open source software package, Guineu. To handle large data sets and to efficiently utilize all the features available in the vendor software (baseline correction, mass spectral deconvolution, peak picking, integration, library search, and signal-to-noise filtering), data preprocessed by instrument software are used as a starting point for further processing. Our software affords alignment of the data, normalization, data filtering, and utilization of retention indexes in the verification of identification as well as a novel tool for automated group-type identification of the compounds. Herein, different features of the software are studied in detail and the performance of the system is verified by the analysis of a large set of standard samples as well as of a large set of authentic biological samples, including the control samples. The quantitative features of our GC×GC/TOFMS methodology are also studied to further demonstrate the method performance and the experimental results confirm the reliability of the developed procedure. The methodology has already been successfully used for the analysis of several thousand samples in the field of metabolomics. PMID:21434611

  2. Headspace Analysis of Philippine Civet Coffee Beans Using Gas Chromatography-Mass Spectrometry and Electronic Nose

    Science.gov (United States)

    Ongo, E.; Sevilla, F.; Antonelli, A.; Sberveglieri, G.; Montevecchi, G.; Sberveglieri, V.; de Paola, E. L.; Concina, I.; Falasconi, M.

    2011-11-01

    Civet coffee, the most expensive and best coffee in the world, is an economically important export product of the Philippines. With a growing threat of food adulteration and counterfeiting, a need for quality authentication is essential to protect the integrity and strong market value of Philippine civet coffee. At present, there is no internationally accepted method of verifying whether a bean is an authentic civet coffee. This study presented a practical and promising approach to identify and establish the headspace qualitative profile of Philippine civet coffee using electronic nose (E-nose) and gas chromatography-mass spectrometry (GC-MS). E-nose analysis revealed that aroma characteristic is one of the most important quality indicators of civet coffee. The findings were supported by GC-MS analysis. Principal component analysis (PCA) exhibited a clearly separated civet coffees from their control beans. The chromatographic fingerprints indicated that civet coffees differed with their control beans in terms of composition and concentration of individual volatile constituents.

  3. Multiresidue Analysis of Pesticides in Straw Roughage by Liquid Chromatography-Tandem Mass Spectrometry.

    Science.gov (United States)

    Zhang, Zihao; Feng, Mengyuan; Zhu, Kechen; Han, Lijun; Sapozhnikova, Yelena; Lehotay, Steven J

    2016-08-10

    A multiresidue analytical method using a modification of the "quick, easy, cheap, effective, rugged, and safe" (QuEChERS) sample preparation approach combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was established and validated for the rapid determination of 69 pesticides at different levels (1-100 ng/g) in wheat and rice straws. In the quantitative analysis, the recoveries ranged from 70 to 120%, and consistent RSDs ≤ 20% were achieved for most of the target analytes (53 pesticides in wheat straw and 58 in rice straw). Almost all of the analytes achieved good linearity with R(2) > 0.98, and the limit of validation levels (LVLs) for diverse pesticides ranged from 1 to 10 ng/g. Different extraction and cleanup conditions were evaluated in both types of straw, leading to different options. The use of 0.1% formic acid or not in extraction with acetonitrile yielded similar final outcomes, but led to the use of a different sorbent in dispersive solid-phase extraction. Both options are efficient and useful for the multiresidue analysis of targeted pesticides in wheat and rice straw samples. PMID:26881844

  4. A simple ion chromatography method for inorganic anion analysis in edible seaweeds.

    Science.gov (United States)

    Gómez-Ordóñez, Eva; Alonso, Esther; Rupérez, Pilar

    2010-09-15

    A new, simple, fast and sensitive ion chromatography (IC) method, for the simultaneous analysis of fluoride, chloride, nitrite, bromide, nitrate, phosphate and sulphate in edible seaweeds was developed and reported for the first time. The validation of the analytical method was studied in terms of linearity, sensitivity, precision and accuracy. All standard calibration curves showed very good correlation between anion peak area and concentration (r>0.999). Limits of detection and quantitation ranged between 0.002-0.05 mg/L and 0.01-0.1mg/L, respectively and indicated the high sensitivity of the method. Relative standard deviation values of repeatability and inter-day precision for standard anions with the same sample were less than 2%. Anion recoveries ranged from 97 to 113% for chloride and from 87 to 105% for sulphate, respectively and showed the fairly good accuracy of the method. The method was applied to the analysis of inorganic anions in brown and red edible seaweeds. Brown seaweeds were characterized by higher chloride content up to 33.7-36.9%, while red seaweeds were characterized by higher sulphate content (45-57%). Sulphate content in seaweeds is related to the presence of sulphated polysaccharides of biological importance. The method developed was well applicable to mineral anion analysis in edible seaweeds and shows suitability and reliability of use in other food samples of nutritional importance. PMID:20801334

  5. The optimization and validation of sequential injection analysis and sequential injection chromatography methods for some pharmaceuticals

    International Nuclear Information System (INIS)

    The family of flow injection (FI) techniques includes three generations, flow injection analysis (FIA), sequential injection analysis (SIA), and bead injection analysis (BIA). In addition, new versions of SIA, micro-sequential injection-lab-on-valve (μSIA-LOV), and sequential injection chromatography (SIC), have recently been developed. The current study reports the development of four methods for the assay of some pharmaceuticals utilizing flow injection techniques. The methods were validated based on guidelines recommended by the international union of pure and applied chemistry and were then applied to real pharmaceutical samples. The first method was applied for diclofenac assay in various pharmaceutical formulations including tablets, injections and gel. The method was validated and applied to pharmaceutical formulations (tablets, injection and gel). It is recommended to critically optimize effective and interacting conditions using other such optimization tools as response surface and simplex, rather than factorial design that used at initial optimization stage. In the second method a developing oxidation reaction for chlorpromazine by permanganate in acidic media was adopted. Then the method was validated and realized by a British pharmacopoeia methods. It had advantage of high rapidity and was also reagent saving and environmental safety. In the third method, lisinopril (LSP) and hydrochlorothiazide (HCZ) were successfully separated and quantified in tablet formulation using reversed-phase sequential injection liquid chromatography (SIC) coupled with a miniaturized fiber optic spectrometer. The proposed method enjoys outstanding features with respect to analysis time, reagent consumption and safety for the environment. In the fourth method, SIC was exploited for the separation and quantification of sildenafil in tablet formulation. The unique benefits of this method are inexpensive instrumentation, high rapidity, and reagent saving and thus better safety

  6. Analysis of 99mTc-labeled radiopharmaceuticals by high-performance liquid chromatography

    International Nuclear Information System (INIS)

    High-performance liquid chromatography (HPLC) equiped with on line radiometric and optical detectors (i.e. radio-HPLC) have been applied to the radiochemical analysis of commonly-used 99mTc-radio pharma ceuticals with a view point to check the radiochemical purities of the compounds. Chromatographic conditions were determined by examination of the types of column, mobile phase and pH. An aqueous size-exclusion (Shim-pack Diol-300) and reversed-phase column (Zorbax-ODS) were found to be suitable for 99mTc-HSA and the other 99mTc-agents, respectively. The analysis of low molecular weight 99mTc-agents (e.g. 99mTc-DTPA, 99mTc-DMSA, 99mTc-pyrophosphate, 99mTc-phytic acid, 99mTc-MDS, 99mTc-HMDP) were done by reversed-phaseion pairing chromatography using a optimized mobile phase consisted on a mixture of 50 mM phosphate buffer (pH 7.0) and 2 mM TBA (tetra nbutyl) ammonium hydroxide) in 30 % methanol. The mobile phases for analysis of medium molecular weight 99mTc-HSA were consisted of a mixture of 50 mM phosphate buffer (ph 7.0) in 30 % methanol, and a mixtures of 1 % SDS (sodium dodecyl sulfonate) in Tris buffer (pH. 7.0), respectively. It was apparent from the radio-chromatograms obtained from these chromatographic conditions, that impurity of 99mTcO4 was observed in 99mTc-pyrophosphate, 99mTc-phytic acid, 99mTc-MDP, 99mTc-HMDP, and impurities of 99mTc-labeled species and 99mTcO4, were observed in 99mTc-HIDA, 99mTc-HIDA, 99mTc-HSA. The radiochemical impurities of the 99mTc-radiopharmaceuticals were ranged between 90 and 100 %. From these results, radio-HPLC has been shown to be suitable method for analysis of 99mTc-radiopharmaceuticals, with rapidity and excellent precision. (author)

  7. Quantitative chromatography in the analysis of labelled compounds 1. Quantitative paper chromotography of amino acids by A spot comparison technique

    International Nuclear Information System (INIS)

    For the determination of the specific activity of labelled compounds separated by paper sheet chromatography, it was found essential to perfect the quantitative aspect of the paper chromatographic technique. Actually, so far paper chromatography has been used as a separation tool mainly and its use in quantification of the separated materials is by far less studied. In the present work, the quantitative analysis of amino acids by paper sheet chromatography has been carried out by methods, depending on the use of the relative spot area values for correcting the experimental data obtained. The results obtained were good and reproducible. The main advantage of the proposed technique is its extreme simplicity. No complicated equipment of procedures are necessary

  8. Mutational analysis of circulating tumor cells from colorectal cancer patients and correlation with primary tumor tissue.

    Directory of Open Access Journals (Sweden)

    Anna Lyberopoulou

    Full Text Available Circulating tumor cells (CTCs provide a non-invasive accessible source of tumor material from patients with cancer. The cellular heterogeneity within CTC populations is of great clinical importance regarding the increasing number of adjuvant treatment options for patients with metastatic carcinomas, in order to eliminate residual disease. Moreover, the molecular profiling of these rare cells might lead to insight on disease progression and therapeutic strategies than simple CTCs counting. In the present study we investigated the feasibility to detect KRAS, BRAF, CD133 and Plastin3 (PLS3 mutations in an enriched CTCs cell suspension from patients with colorectal cancer, with the hypothesis that these genes` mutations are of great importance regarding the generation of CTCs subpopulations. Subsequently, we compared CTCs mutational status with that of the corresponding primary tumor, in order to access the possibility of tumor cells characterization without biopsy. CTCs were detected and isolated from blood drawn from 52 colorectal cancer (CRC patients using a quantum-dot-labelled magnetic immunoassay method. Mutations were detected by PCR-RFLP or allele-specific PCR and confirmed by direct sequencing. In 52 patients, discordance between primary tumor and CTCs was 5.77% for KRAS, 3.85% for BRAF, 11.54% for CD133 rs3130, 7.69% for CD133 rs2286455 and 11.54% for PLS3 rs6643869 mutations. Our results support that DNA mutational analysis of CTCs may enable non-invasive, specific biomarker diagnostics and expand the scope of personalized medicine for cancer patients.

  9. Rapid liquid chromatography for paralytic shellfish toxin analysis using superficially porous chromatography with AOAC Official Method 2005.06.

    Science.gov (United States)

    Hatfield, Robert G; Turner, Andrew D

    2012-01-01

    The bioaccumulation of paralytic shellfish toxins in mussels, oysters, cockles, hard clams, razors, and king scallops is monitored in England, Scotland, and Wales by AOAC Official Method 2005.06 LC-with fluorescence detection (FLD). One of the commonly perceived disadvantages of using this method is the long turnaround time and low throughput in a busy laboratory environment. The chromatographic analysis of each sample typically utilizes a 15 min cycle time to achieve toxin oxidation product separation and column equilibration prior to subsequent analysis. A standard RP C18 analytical column, used successfully in recent years, achieves good separation with a long column lifetime. The analysis of a 40 sample qualitative screening batch takes approximately 18 h, including blanks, standards, and other QC samples. The availability of superficially porous column technology has offered the potential to reduce analysis time while retaining column performance on existing hardware. In this study, AOAC Official Method 2005.06 with LC-FLD was transferred to two different commercially available superficially porous columns, and the method performance characteristics were evaluated. Both columns separated all toxins adequately with cycle times less than half that of the existing method. Linearity for each toxin was acceptable up to two times the European maximum permitted limit of 800 microg di-HCl saxitoxin equivalent/kg flesh. LOD and LOQ values were substantially improved for the majority of toxins, with gonyautoxin 1&4 and neosaxitoxin showing up to a two- and fourfold improvement, respectively, depending on the column used. Quantification results obtained from parallel analysis of contaminated samples were acceptable on both columns. Comparative screen results gave a slight increase in the occurrence of contaminated samples, which was attributed to the improved detection limit for most toxins. Issues with rapidly increasing back pressure, however, were identified with both

  10. Recent advances in ultra-high performance liquid chromatography for the analysis of traditional chinese medicine

    Science.gov (United States)

    Traditional Chinese medicines (TCMs) have been widely used for the prevention and treatment of various diseases for thousands of years in China. Ultra Performance Liquid Chromatography (UHPLC) is a relatively new technique offering new possibilities in liquid chromatography. This paper reviews recen...

  11. Liquid chromatography analysis of Stevia rebaudiana extract: LC versus LCxLC

    Czech Academy of Sciences Publication Activity Database

    Pól, Jaroslav; Hyötyläinen, T.; Hohnová, B.

    2006 - (Sandra, P.). K*.01 [International Symposium on Capillary Chromatography /29./ and GCxGC Symposium /3./. 29.05.2006-02.06.2006, Riva del Garda] R&D Projects: GA AV ČR KJB4031405 Keywords : comprehensive two-dimensional liquid chromatography Subject RIV: CB - Analytical Chemistry, Separation

  12. Potential of on-line coupling of extraction and chromatography in the analysis of complex samples

    Czech Academy of Sciences Publication Activity Database

    Hyötyläinen, T.; Lüthje, K.; Rautiainen-Rämä, M.; Pól, Jaroslav; Ranta-Aho, O.; Riekkola, M. L.

    Kortrijk: I.O.P.M.S. vzw, 2004 - (Sandra, T.; Sandra, P.), J12 [International Symposium on Capillary Chromatography /27./. Riva del Garda (IT), 31.05.2004-04.06.2004] R&D Projects: GA AV ČR KJB4031405 Institutional research plan: CEZ:AV0Z4031919 Keywords : on-line - extraction * chromatography Subject RIV: CB - Analytical Chemistry, Separation

  13. Analysis of perfluoroalkyl substances in cord blood by turbulent flow chromatography coupled to tandem mass spectrometry

    International Nuclear Information System (INIS)

    A fast on-line analytical method based on turbulent flow chromatography (TFC) in combination with tandem mass spectrometry has been applied for the first time for the analysis of eighteen perfluoroalkyl substances (PFASs), in cord blood. A simple and rapid sample pre-treatment was optimised consisting on protein precipitation of 100 μL of sample with acetonitrile (1:1) followed by centrifugation during 10 min. The method was adapted to be sensitive enough and robust with minimum sample injection volume requirements (20 μL). The optimised methodology presented method limits of detection (MLOD) between 0.031 and 0.76 μg/L, detection capabilities (CCα) in the range between 0.005 and 0.99 μg/L and decision limits (CCβ) ranging from 0.006 to 1.16 μg/L. The recoveries in blank blood were calculated by spiking experiments with a mixture of 18 PFASs and established between 70 and 126% for most of compounds. Isotopic dilution was carried out for quantification of selected analytes. In-house validation of this new approach was carried out according to the requirements in the 2002/657/EC Decision. Finally the good applicability of this new approach was proved by the analysis of 60 cord blood samples from two different Mediterranean cities, Barcelona (Spain) and Heraklion (Greece). Ions perfluorohexanesulfonate (PFHxS) and perfluorooctanesulfonate (PFOS) were found at highest concentration and the more frequently compounds were PFHxS, PFOS and perfluorooctanoic acid (PFOA). The newly developed method proved to be suitable for large-scale epidemiologic studies, and to the data on PFASs exposure during pregnancy. -- Highlights: ► An on-line method has been developed for the analysis of 18 perfluoroalkyl substances. ► The method is based on turbulent flow chromatography tandem mass spectrometry. ► The method was applied in 60 cord blood samples from 2 Mediterranean cities. ► Acidic compounds were more frequently found and the method was proved to be suitable for

  14. Analysis of perfluoroalkyl substances in cord blood by turbulent flow chromatography coupled to tandem mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Llorca, Marta; Perez, Francisca [Department of Environmental Chemistry, IDAEA-CSIC, Barcelona (Spain); Farre, Marinella, E-mail: mfuqam@cid.csic.es [Department of Environmental Chemistry, IDAEA-CSIC, Barcelona (Spain); Agramunt, Silvia [Centre for Research in Environmental Epidemiology (CREAL), Barcelona (Spain); IMIM (Hospital del Mar Research Institute), Barcelona (Spain); Kogevinas, Manolis [Centre for Research in Environmental Epidemiology (CREAL), Barcelona (Spain); IMIM (Hospital del Mar Research Institute), Barcelona (Spain); CIBER Epidemiologia y Salud Publica (CIBERESP), Barcelona (Spain); National School of Public Health, Athens (Greece); Barcelo, Damia [Department of Environmental Chemistry, IDAEA-CSIC, Barcelona (Spain); Catalan Institute for Water Research (ICRA), Girona (Spain); King Saud University, Riyadh (Saudi Arabia)

    2012-09-01

    A fast on-line analytical method based on turbulent flow chromatography (TFC) in combination with tandem mass spectrometry has been applied for the first time for the analysis of eighteen perfluoroalkyl substances (PFASs), in cord blood. A simple and rapid sample pre-treatment was optimised consisting on protein precipitation of 100 {mu}L of sample with acetonitrile (1:1) followed by centrifugation during 10 min. The method was adapted to be sensitive enough and robust with minimum sample injection volume requirements (20 {mu}L). The optimised methodology presented method limits of detection (MLOD) between 0.031 and 0.76 {mu}g/L, detection capabilities (CC{alpha}) in the range between 0.005 and 0.99 {mu}g/L and decision limits (CC{beta}) ranging from 0.006 to 1.16 {mu}g/L. The recoveries in blank blood were calculated by spiking experiments with a mixture of 18 PFASs and established between 70 and 126% for most of compounds. Isotopic dilution was carried out for quantification of selected analytes. In-house validation of this new approach was carried out according to the requirements in the 2002/657/EC Decision. Finally the good applicability of this new approach was proved by the analysis of 60 cord blood samples from two different Mediterranean cities, Barcelona (Spain) and Heraklion (Greece). Ions perfluorohexanesulfonate (PFHxS) and perfluorooctanesulfonate (PFOS) were found at highest concentration and the more frequently compounds were PFHxS, PFOS and perfluorooctanoic acid (PFOA). The newly developed method proved to be suitable for large-scale epidemiologic studies, and to the data on PFASs exposure during pregnancy. -- Highlights: Black-Right-Pointing-Pointer An on-line method has been developed for the analysis of 18 perfluoroalkyl substances. Black-Right-Pointing-Pointer The method is based on turbulent flow chromatography tandem mass spectrometry. Black-Right-Pointing-Pointer The method was applied in 60 cord blood samples from 2 Mediterranean cities

  15. Mutational analysis of hedgehog signaling pathway genes in human malignant mesothelioma.

    Directory of Open Access Journals (Sweden)

    Chuan Bian Lim

    Full Text Available BACKGROUND: The Hedgehog (HH signaling pathway is critical for embryonic development and adult homeostasis. Recent studies have identified regulatory roles for this pathway in certain cancers with mutations in the HH pathway genes. The extent to which mutations of the HH pathway genes are involved in the pathogenesis of malignant mesothelioma (MMe is unknown. METHODOLOGY/PRINCIPAL FINDINGS: Real-time PCR analysis of HH pathway genes PTCH1, GLI1 and GLI2 were performed on 7 human MMe cell lines. Exon sequencing of 13 HH pathway genes was also performed in cell lines and human MMe tumors. In silico programs were used to predict the likelihood that an amino-acid substitution would have a functional effect. GLI1, GLI2 and PTCH1 were highly expressed in MMe cells, indicative of active HH signaling. PTCH1, SMO and SUFU mutations were found in 2 of 11 MMe cell lines examined. A non-synonymous missense SUFU mutation (p.T411M was identified in LO68 cells. In silico characterization of the SUFU mutant suggested that the p.T411M mutation might alter protein function. However, we were unable to demonstrate any functional effect of this mutation on Gli activity. Deletion of exons of the PTCH1 gene was found in JU77 cells, resulting in loss of one of two extracellular loops implicated in HH ligand binding and the intracellular C-terminal domain. A 3-bp insertion (69_70insCTG in SMO, predicting an additional leucine residue in the signal peptide segment of SMO protein was also identified in LO68 cells and a MMe tumour. CONCLUSIONS/SIGNIFICANCE: We identified the first novel mutations in PTCH1, SUFU and SMO associated with MMe. Although HH pathway mutations are relatively rare in MMe, these data suggest a possible role for dysfunctional HH pathway in the pathogenesis of a subgroup of MMe and help rationalize the exploration of HH pathway inhibitors for MMe therapy.

  16. Platelet hexosaminidase a enzyme assay effectively detects carriers missed by targeted DNA mutation analysis.

    Science.gov (United States)

    Nakagawa, Sachiko; Zhan, Jie; Sun, Wei; Ferreira, Jose Carlos; Keiles, Steven; Hambuch, Tina; Kammesheidt, Anja; Mark, Brian L; Schneider, Adele; Gross, Susan; Schreiber-Agus, Nicole

    2012-01-01

    Biochemical testing of hexosaminidase A (HexA) enzyme activity has been available for decades and has the ability to detect almost all Tay-Sachs disease (TSD) carriers, irrespective of ethnic background. This is increasingly important, as the gene pool of those who identify as Ashkenazi Jewish is diversifying. Here we describe the analysis of a cohort of 4,325 individuals arising from large carrier screening programs and tested by the serum and/or platelet HexA enzyme assays and by targeted DNA mutation analysis. Our results continue to support the platelet assay as a highly effective method for TSD carrier screening, with a low inconclusive rate and the ability to detect possible disease-causing mutation carriers that would have been missed by targeted DNA mutation analysis. Sequence analysis performed on one such platelet assay carrier, who had one non-Ashkenazi Jewish parent, identified the amino acid change Thr259Ala (A775G). Based on crystallographic modeling, this change is predicted to be deleterious, as threonine 259 is positioned proximal to the HexA alpha subunit active site and helps to stabilize key residues therein. Accordingly, if individuals are screened for TSD in broad-based programs by targeted molecular testing alone, they must be made aware that there is a more sensitive and inexpensive test available that can identify additional carriers. Alternatively, the enzyme assays can be offered as a first tier test, especially when screening individuals of mixed or non-Jewish ancestry. PMID:23430931

  17. Quantitative and fingerprinting analysis of Atractylodes rhizome based on gas chromatography with flame ionization detection combined with chemometrics.

    Science.gov (United States)

    Liu, Qiutao; Kong, Dandan; Luo, Jiaoyang; Kong, Weijun; Guo, Weiying; Yang, Meihua

    2016-07-01

    This study assessed the feasibility of gas chromatography with flame ionization detection fingerprinting combined with chemometrics for quality analysis of Atractylodes rhizome. We extracted essential oils from 20 Atractylodes lancea and Atractylodes koreana samples by hydrodistillation. The variation in extraction yields (1.33-4.06%) suggested that contents of the essential oils differed between species. The volatile components (atractylon, atractydin, and atractylenolide I, II, and III) were quantified by gas chromatography with flame ionization detection and confirmed by gas chromatography with mass spectrometry, and the results demonstrated that the number and content of volatile components differed between A. lancea and A. koreana. We then calculated the relative peak areas of common components and similarities of samples by comparing the chromatograms of A. lancea and A. koreana extracts. Also, we employed several chemometric techniques, including similarity analysis, hierarchical clustering analysis, principal component analysis, and partial least-squares discriminate analysis, to analyze the samples. Results were consistent across analytical methods and showed that samples could be separated according to species. Five volatile components in the essential oils were quantified to further validate the results of the multivariate statistical analysis. The method is simple, stable, accurate, and reproducible. Our results provide a foundation for quality control analysis of A. lancea and A. koreana. PMID:27133960

  18. Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes

    Directory of Open Access Journals (Sweden)

    Chen Carton W

    2007-08-01

    Full Text Available Abstract Background Most bacterial chromosomes exhibit asymmetry of base composition with respect to leading vs. lagging strands (GC and AT skews. These skews reflect mainly those in protein coding sequences, which are driven by asymmetric mutation pressures during replication and transcription (notably asymmetric cytosine deamination plus subsequent selection for preferred structures, signals, amino acid or codons. The transcription-associated effects but not the replication-associated effects contribute to the overall skews through the uneven distribution of the coding sequences on the leading and lagging strands. Results Analysis of 185 representative bacterial chromosomes showed diverse and characteristic patterns of skews among different clades. The base composition skews in the coding sequences were used to derive quantitatively the effect of replication-driven mutation plus subsequent selection ('replication-associated pressure', RAP, and the effect of transcription-driven mutation plus subsequent selection at translation level ('transcription-associate pressure', TAP. While different clades exhibit distinct patterns of RAP and TAP, RAP is absent or nearly absent in some bacteria, but TAP is present in all. The selection pressure at the translation level is evident in all bacteria based on the analysis of the skews at the three codon positions. Contribution of asymmetric cytosine deamination was found to be weak to TAP in most phyla, and strong to RAP in all the Proteobacteria but weak in most of the Firmicutes. This possibly reflects the differences in their chromosomal replication machineries. A strong negative correlation between TAP and G+C content and between TAP and chromosomal size were also revealed. Conclusion The study reveals the diverse mutation and selection forces associated with replication and transcription in various groups of bacteria that shape the distinct patterns of base composition skews in the chromosomes during

  19. Genetic Analysis and Molecular Mapping of a Rolling Leaf Mutation Gene in Rice

    Institute of Scientific and Technical Information of China (English)

    Ji-Cai Yi; Chu-Xiong Zhuang; Xu-Jie Wang; You-Pei Cao; Yao-Guang Liu; Man-Tong Mei

    2007-01-01

    A rice mutant with rolling leaf, namely y-rl, was obtained from M2 progenies of a native indica rice stable strain Qinghuazhan (QHZ) from mutagenesis of dry seeds by prays.Genetic analysis using the F2 population from a cross between this mutant and QHZ indicated the mutation was controlled by a single recessive gane.In order to map the locus for this mutation,another F2 population with 601 rolling leaf plants was constructed from a cross between y-rl and a japonica cultivar 02428.After primary mapping with SSR (simple sequence repeats) markers, the mutated locus was located at the short arm of chromosome 3, flanked by RM6829 and RM3126.A number of SSR, InDel (insertion/deletion) and SNP (single nucleotide polymorphism) markers within this region were further developed for fine mapping.Finally, two markers, SNP121679 and InDel422395, were identified to be flanked to this locus with genetic distances of 0.08 cM and 0.17 cM respectively, and two SNP markers, SNP75346 and SNP110263, were found to be co-segregated with this locus.These results suggested that this locus was distinguished from all loci for the rolling leaf mutation in rice reported so far, and thus renamed rl10(t).By searching the rice genome database with closely linked markers using BLAST programs, an e-physical map covering rl10(t) locus spanning about a 50 kb region was constructed.Expression analysis of the genes predicted in this region showed that a gene encoding putative flavin-containing monooxygenase (FMO) was silenced in y-rl, thus this is the most likely candidate responsible for the rolling leaf mutation.

  20. Targeted ultradeep next-generation sequencing as a method for KIT D816V mutation analysis in mastocytosis.

    Science.gov (United States)

    Kristensen, Thomas; Broesby-Olsen, Sigurd; Vestergaard, Hanne; Bindslev-Jensen, Carsten; Møller, Michael Boe

    2016-04-01

    Next-generation sequencing (NGS) is becoming increasingly used for diagnostic mutation analysis in myeloid neoplasms and may also represent a feasible technique in mastocytosis. However, detection of the KIT D816V mutation requires a highly sensitive method in most patients due to the typically low mutation levels. In this study, we established an NGS-based KIT mutation analysis and analyzed the sensitivity of D816V detection using the Ion Torrent platform. Eighty-two individual NGS analyses were included in the study. All samples were also analyzed using highly sensitive KIT D816V mutation-specific qPCR. Measurements of the background level in D816V-negative samples supported a cutoff for positivity of 0.2% in three different NGS panels. Clinical samples from patients with SM that tested positive using qPCR with a D816V allele burden >0.2% also tested positive using NGS. Samples that tested positive using qPCR with an allele burden <0.2% tested negative using NGS. We thereby demonstrate that caution should be taken when using the potentially very sensitive NGS technique for KIT D816V mutation analysis in mastocytosis, as many patients with SM have D816V mutation levels below the detection limit of NGS. A dedicated and highly sensitive KIT D816V mutation analysis therefore remains important in mastocytosis diagnostics. PMID:26095448

  1. Identification of Mutation of Glucose-6-Phosphate Dehy-drogenase (G6PD in Iran: Meta- analysis Study

    Directory of Open Access Journals (Sweden)

    Mahmood Moosazadeh

    2013-09-01

    Full Text Available Background: Glucose-6-phosphate dehydrogenase is one of the most common genetic deficiencies, which approximately 400 million people in the world suffer from. According to authors' initial search, numerous studies have been carried out in Iran regarding molecular variants of this enzyme. Thus, this meta-analysis presented a reliable estimation about prevalence of different types of molecular mutations of G6PD Enzyme in Iran.Methods: Keywords "glucose 6 phosphate dehydrogenase or G6PD, Mediterranean or Chatham or Cosenza and mutation, Iran or Iranian and their Persian equivalents" were searched in different databases. Moreover, reference list of the published studies were examined to increase sensitivity and to select more studies. After studying titles and abstracts of retrieved articles, excluding the repeated and unrelated ones, and evaluating quality of articles, documents were selected. Data was analyzed using STATA.Results: After performing systematic review, 22 papers were entered this meta-analysis and 1698 subjects were examined concerning G6PD molecular mutation. In this meta-analysis, prevalence of Mediterranean mutation, Chatham mutation and Cosenza mutation in Iran was estimated 78.2%, 9.1% and 0.5% respectively.Conclusions: This meta-analysis showed that in spite of prevalence of different types of G6PD molecular mutations in center, north, north-west and west of Iran, the most common molecular mutations in people with G6PD deficiency in Iran, like other Mediterranean countries and countries around Persian Gulf, were Mediterranean mutation, Chatham mutation and Cosenza mutation. It is also recommended that future studies may focus on races and regions which haven't been taken into consideration up to now.

  2. Enantiomeric separation in comprehensive two-dimensional gas chromatography with accurate mass analysis.

    Science.gov (United States)

    Chin, Sung-Tong; Nolvachai, Yada; Marriott, Philip J

    2014-11-01

    Chiral comprehensive two-dimensional gas chromatography (eGC×GC) coupled to quadrupole-accurate mass time-of-flight mass spectrometry (QTOFMS) was evaluated for its capability to report the chiral composition of several monoterpenes, namely, α-pinene, β-pinene, and limonene in cardamom oil. Enantiomers in a standard mixture were fully resolved by direct enantiomeric-GC analysis with a 2,3-di-O-methyl-6-t-butylsilyl derivatized β-cyclodextrin phase; however, the (+)-(R)-limonene enantiomer in cardamom oil was overlapped with other background components including cymene and cineole. Verification of (+)-(R)-limonene components based on characteristic ions at m/z 136, 121, and 107 acquired by chiral single-dimension GC-QTOFMS in the alternate MS/MSMS mode of operation was unsuccessful due to similar parent/daughter ions generated by interfering or co-eluting cymene and cineole. Column phases SUPELCOWAX, SLB-IL111, HP-88, and SLB-IL59, were incorporated as the second dimension column ((2)D) in chiral GC×GC analysis; the SLB-IL59 offered the best resolution for the tested monoterpene enantiomers from the matrix background. Enantiomeric ratios for α-pinene, β-pinene, and limonene were determined to be 1.325, 2.703, and 1.040, respectively, in the cardamom oil sample based on relative peak area data. PMID:24420979

  3. Analysis of meat samples for anabolic steroids residues by liquid chromatography/tandem mass spectrometry.

    Science.gov (United States)

    Blasco, Cristina; Van Poucke, Christof; Van Peteghem, Carlos

    2007-06-22

    A rapid, specific and highly sensitive multi-residue method for the determination of anabolic steroid residues in bovine, pork and poultry muscle tissues was developed. The sample preparation involves enzymatic digestion followed by extraction with methanol. The crude extract was cleaned up by solid-phase extraction (SPE) combining C18 and NH2 columns. The detection was carried out by a highly sensitive liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method using both positive and negative ionization modes. Natural and synthetic steroids covering different polarities could be extracted, concentrated and purified using one single method. Mobile phase composition and additives were optimized to achieve the highest sensitivity. The linearity was not good enough for quantitative analysis but the method was well-suited for qualitative confirmation. The method was validated according to the European Commission Decision 2002/657/EC. Decision limits (CCalpha) and detection capabilities (CCbeta) were below 0.5 ng g(-1) for all the compounds in the three types of meat studied. The developed method is suitable for routine analysis in our laboratories. PMID:17459396

  4. Molecular Ionization-Desorption Analysis Source (MIDAS) for Mass Spectrometry: Thin-Layer Chromatography

    Science.gov (United States)

    Winter, Gregory T.; Wilhide, Joshua A.; LaCourse, William R.

    2016-02-01

    Molecular ionization-desorption analysis source (MIDAS), which is a desorption atmospheric pressure chemical ionization (DAPCI) type source, for mass spectrometry has been developed as a multi-functional platform for the direct sampling of surfaces. In this article, its utility for the analysis of thin-layer chromatography (TLC) plates is highlighted. Amino acids, which are difficult to visualize without staining reagents or charring, were detected and identified directly from a TLC plate. To demonstrate the full potential of MIDAS, all active ingredients from an analgesic tablet, separated on a TLC plate, were successfully detected using both positive and negative ion modes. The identity of each of the compounds was confirmed from their mass spectra and compared against standards. Post separation, the chemical signal (blue permanent marker) as reference marks placed at the origin and solvent front were used to calculate retention factor (Rf) values from the resulting ion chromatogram. The quantitative capabilities of the device were exhibited by scanning caffeine spots on a TLC plate of increasing sample amount. A linear curve based on peak are, R2 = 0.994, was generated for seven spots ranging from 50 to 1000 ng of caffeine per spot.

  5. Ultra performance liquid chromatography tandem mass spectrometry performance evaluation for analysis of antibiotics in natural waters.

    Science.gov (United States)

    Tamtam, Fatima; Mercier, Fabien; Eurin, Joëlle; Chevreuil, Marc; Le Bot, Barbara

    2009-03-01

    An ultra performance liquid chromatography electrospray tandem mass spectrometry (UPLC/MS/MS) method was developed and validated for the determination of 17 antibiotics in natural waters in one single extraction and chromatographic procedure. Gradient separation conditions were optimised for 17 compounds belonging to five different antibiotic groups: quinolones (oxolinic acid, nalidixic acid, pipemidic acid, flumequine), fluoroquinolones (enoxacin, ciprofloxacin, norfloxacin, ofloxacin, enrofloxacin, sarafloxacin, danofloxacin, difloxacin, lomefloxacin), sulphonamides (sulphamethoxazole, sulphamethazine), nitro-imidazole (ornidazole) and diaminopyrimidine (trimethoprim). The separation of all compounds, obtained using a 1.7 microm particle size column (100 mm x 2.1 mm), was achieved within 10 min time. Water samples were adjusted to pH 7 and extracted using Oasis hydrophilic-lipophilic balance (HLB) solid phase extraction cartridges. After elution with methanol and concentration, extracts were injected in a C18 column (Acquity UPLC BEH C18) and detected by tandem mass spectrometry. Average recovery from 100 ng L(-1) fortified samples was higher than 70% for most of the compounds, with relative standard deviations below 20%. Performances of the method (recoveries, detection limit, quantification limit and relative standard deviation) and matrix effects were studied, and results obtained showed that method was suitable for routine analysis of antibiotics in surface water. Samples analysis from Seine River (France) confirmed the interest of antibiotic contamination evaluation in that area. PMID:19148627

  6. Quantitative compositional analysis of heparin using exhaustive heparinase digestion and strong anion exchange chromatography

    Directory of Open Access Journals (Sweden)

    Pierre Mourier

    2015-03-01

    Full Text Available Heparin is a linear sulfated polysaccharide widely used therapeutically as an anticoagulant. It is also the starting material for manufacturing low-molecular-weight heparins (LMWH. Quality control of heparin and LMWH is critical to ensure the safety and therapeutic activity of the final product. However due to their complex and heterogeneous structure, orthogonal analytical techniques are needed to characterize the building blocks of heparin. One of the state-of-the-art methods for heparin analysis is based on complete enzymatic digestion using a mixture of heparinases I, II, and III, followed by the separation of the resulting oligosaccharides by liquid chromatography. The European Pharmacopoeia strong anion-exchange chromatographic method, used to quantify 1,6-anhydro derivatives in enoxaparin, is here applied to the analysis of the heparin building blocks. Their quantification, namely the determination of their average w/w percentage in the heparin chain, is obtained after identification of all components including glycoserine derivatives and 3-O sulfated di- and tetrasaccharides. This work therefore provides a comprehensive overview of the building blocks of unfractionated heparin, including those chemically modified by the manufacturing process, either within the polysaccharide chain or at its reducing end.

  7. Morphological, spectral and chromatography analysis and forensic comparison of PET fibers.

    Science.gov (United States)

    Farah, Shady; Tsach, Tsadok; Bentolila, Alfonso; Domb, Abraham J

    2014-06-01

    Poly(ethylene terephthalate) (PET) fiber analysis and comparison by spectral and polymer molecular weight determination was investigated. Plain fibers of PET, a common textile fiber and plastic material was chosen for this study. The fibers were analyzed for morphological (SEM and AFM), spectral (IR and NMR), thermal (DSC) and molecular weight (MS and GPC) differences. Molecular analysis of PET fibers by Gel Permeation Chromatography (GPC) allowed the comparison of fibers that could not be otherwise distinguished with high confidence. Plain PET fibers were dissolved in hexafluoroisopropanol (HFIP) and analyzed by GPC using hexafluoroisopropanol:chloroform 2:98 v/v as eluent. 14 PET fiber samples, collected from various commercial producers, were analyzed for polymer molecular weight by GPC. Distinct differences in the molecular weight of the different fiber samples were found which may have potential use in forensic fiber comparison. PET fibers with average molecular weights between about 20,000 and 70,000 g mol(-1) were determined using fiber concentrations in HFIP as low as 1 μg mL(-1). This GPC analytical method can be applied for exclusively distinguish between PET fibers using 1 μg of fiber. This method can be extended to forensic comparison of other synthetic fibers such as polyamides and acrylics. PMID:24725864

  8. Multiresidue analysis of environmental pollutants in edible vegetable oils by gas chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Zhou, Rui-Ze; Jiang, Jie; Mao, Ting; Zhao, Ya-Song; Lu, Yong

    2016-09-15

    A novel multiresidue determination of polycyclic aromatic hydrocarbons (PAHs), phthalate esters (PAEs) and alkylphenols (APs) in edible vegetable oils was developed. The samples were extracted with hexane-saturated acetonitrile, and after concentration, the extract was directly qualitatively and quantitatively analyzed by gas chromatography-tandem mass spectrometry (GC-MS/MS) with multiple reaction monitoring (MRM) in positive ion mode. The calibration curve displayed good linearity in the range of 2-100μg/L, with correlation coefficients greater than 0.99. The mean recoveries were 70.0-110.8% by analysis of spiked oil, and the relative standard deviations (RSDs) were 2.1-10.2% (n=6), respectively. The limits of detection (LODs) for the 23 PAHs, 17 PAEs and 3 APs were 0.1-1.0μg/kg, 0.1-4.0μg/kg and 1.2-3.0μg/kg, respectively. The established method effectively avoided interference from large amounts of lipids and pigments. It was applied to real sample and shown to be a rapid and reliable alternative for determination and confirmation in routine analysis. PMID:27080878

  9. [Analysis of nine narcotics in urine by microemulsion electrokinetic chromatography-field samplified sample injection].

    Science.gov (United States)

    Zhang, Yu; Li, Qin; Lu, Minghua; Zhang, Lan; Chen, Guonan; Cai, Zongwei

    2011-08-01

    A simple, sensitive and reproducible method using microemulsion electrokinetic chromatography (MEEKC)-field amplified sample injection (FASI) was developed for the analysis of nine narcotics (morphine, codeine, naloxone, heroin, thebaine, cocaine, pethidine, fentanyl and methadone) in urine. In the MEEKC method, sodium dodecyl sulfate (SDS), 1-butanol and ethyl acetate were used as surfactant, co-surfactant and organic solvent, respectively. The effects of the acidity and concentration of borate buffer, SDS, 1-butanol and ethyl acetate contents were investigated. The optimum concentrations (by mass fraction) of microemulsion system were 0.6% SDS, 1.2% 1-butanol, 0.6% ethyl acetate and 97.6% 10 mmol/L Na2B4O7 buffer (pH 9.5). The applied voltage was 25 kV. FASI was coupled with the MEEKC method to increase the sensitivity. Under the optimum conditions, the nine narcotics were baseline separated within 15 min and the detection limits (S/N = 3) were in the range of 0.3 - 8.0 microg/L. The spiked recoveries in urine samples were between 79.4% and 119.9% with the intraday relative standard deviations (RSDs) less than 5.5%. The developed method has been successfully applied to the analysis of methadone in the samples from in vitro metabolism study. PMID:22128745

  10. Analysis of volatile components in Curcuma rhizome by microemulsion electrokinetic chromatography.

    Science.gov (United States)

    Yang, Feng-Qing; Yang, Jing; Zhang, Xue-Mei; Xu, Pan; Xia, Zhi-Ning

    2013-02-01

    Volatile chemicals are a group of very important compounds in natural products. Curcuma rhizome, which contains many bioactive volatile compounds, is a traditional Chinese medicine that has long been used for the treatment of several diseases. In the present study, a microemulsion electrokinetic chromatography (MEEKC) method was developed for the analysis of four volatile components in Curcuma rhizome, including germacrone, furanodiene, curcumenol and curdione. Experimental parameters, including the pH, type and concentrations of background electrolyte, and microemulsion compositions (type and concentrations of surfactant, co-surfactant and oil phase) were intensively investigated. Finally, the primary compounds in the methanol extract of Curcuma rhizome were separated within 30 min using a running buffer composed of 2.31% w/v (80 mmol/L) sodium dodecyl sulfate (SDS), 0.91% w/v (80 mmol/L) 1-octane, 6.95% w/v (937.5 mmol/L) 1-butanol and 1.88% w/v (312.5 mmol/L) propanol in a 5-mM borate buffer (pH 8.1). The contents of the four investigated compounds were determined in the rhizome from C. phaeocaulis. The results showed that the developed MEEKC method provided an alternative tool for the analysis of volatile components, especially those of heat-sensitive compounds from natural products. PMID:22824329

  11. Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

    OpenAIRE

    Koichi Fujie; Hiroyuki Daimon; Yoichi Atsuta; Muhammad Hanif

    2012-01-01

    Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysi...

  12. Comparison of ion chromatography and flow injection analysis methods for monitoring chlorite and chlorate ions in drinking water

    OpenAIRE

    Ledder, Tracey

    1991-01-01

    Up-coming regulations on chlorine dioxide in drinking water treatment require low level measurement of chlorite ion (CI02-) and chlorate ion (CI03-). This research investigated analysis of CI02- and CI03-; in drinking water by flow injection analysis with iodometric detection (FIA) and ion chromatography with conductivity detection (IC). Both the FIA and IC methods were accurate for the determination of CIO2-; and CIO3-; in reagent water. The IC method was accurate in dr...

  13. Gas chromatography mass spectrometry computer analysis of volatile halogenated hydrocarbons in man and his environment--A multimedia environmental study.

    Science.gov (United States)

    Barkley, J; Bunch, J; Bursey, J T; Castillo, N; Cooper, S D; Davis, J M; Erickson, M D; Harris, B S; Kirkpatrick, M; Michael, L C; Parks, S P; Pellizzari, E D; Ray, M; Smith, D; Tomer, K B; Wagner, R; Zweidinger, R A

    1980-04-01

    As part of a study to make a comparative analysis of selected halogenated compounds in man and the environmental media, a quantitative gas chromatography mass spectrometric analysis of the levels of the halogenated compounds found in the breath, blood and urine of an exposed population (Old Love Canal area, Niagara, New York) and their immediate environment (air and water) was undertaken. In addition, levels of halogenated hydrocarbons in air samples taken in the general Buffalo, Niagara Falls area were determined. PMID:7448328

  14. Characterization of Fatty Acid Profile of Argan Oil and Other Edible Vegetable Oils by Gas Chromatography and Discriminant Analysis

    OpenAIRE

    Ascensión Rueda; Isabel Seiquer; Manuel Olalla; Rafael Giménez; Luis Lara; Carmen Cabrera-Vique

    2014-01-01

    Virgin argan oil is an emergent oil that is being introduced into specialized international markets as a healthy and luxury food. In order to compare the fatty acid composition of argan oil with that of the eleven other vegetable edible oils, a combination of gas chromatography as analytical technique and multivariate discriminant analysis was applied. This analysis takes into account the conjoint effect of all the variables analyzed in the discrimination between oils and also shows the contr...

  15. Mutation analysis of COX18 in 29 patients with isolated cytochrome c oxidase deficiency.

    Science.gov (United States)

    Sacconi, Sabrina; Salviati, Leonardo; Trevisson, Eva

    2009-07-01

    Isolated cytochrome c oxidase (COX) deficiency (MIM#220110) is a relatively common biochemical finding in pediatric patients with mitochondrial disorder. It has been associated with different clinical phenotypes ranging from isolated myopathy to severe multisystem disorder. It is a genetically heterogeneous trait, and the most frequent genetic defects affect SURF1 and SCO2, two genes required for COX assembly. However, a significant proportion of patients lacks mutation in these genes and in other known genes that require COX biogenesis. COX18 is a novel COX assembly gene required for membrane insertion of the C-terminal portion of COX subunit II. We have studied 29 pediatric patients with isolated COX deficiency in the skeletal muscle associated with different clinical phenotypes. Mutations in SURF1, SCO2, SCO1, COX10, COX15 and in mitochondrial DNA, had been ruled out earlier. The COX18 gene was analyzed using a PCR-single-stranded conformation polymorphism (PCR-SSCP) protocol, and in 15 patients, the analysis was repeated by direct sequencing. No pathogenic mutations were detected in our cohort of patients indicating that COX18 mutations may be very rare or associated with other phenotypes than isolated COX deficiency in infancy. PMID:19373256

  16. Genetic analysis of suppressors of the PF10 mutation in Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    A mutation at the PF10 locus of the unicellular green alga Chlamydomonas reinhardtii leads to abnormal cell motility. The asymmetric form of the ciliary beat stroke characteristic of wild-type flagella is modified by this mutation to a nearly symmetric beat. We report here that this abnormal motility is a conditional phenotype that depends on light intensity. In the absence of light or under low light intensities, the motility is more severely impaired than at higher light intensities. By UV mutagenesis we obtained 11 intragenic and 70 extragenic strains that show reversion of the pf10 motility phenotype observed in low light. The intragenic events reverted the motility phenotype of the pf10 mutation completely. The extragenic events define at least seven suppressor loci; these map to linkage groups IV, VII, IX, XI, XII and XVII. Suppressor mutations at two of the seven loci (LIS1 and LIS2) require light for their suppressor activity. Forty-eight of the 70 extragenic suppressors were examined in heterozygous diploid cells; 47 of these mutants were recessive to the wild-type allele and one mutant (bop5-1) was dominant to the wild-type allele. Complementation analysis of the 47 recessive mutants showed unusual patterns. Most mutants within a recombinationally defined group failed to complement one another, although there were pairs that showed intra-allelic complementation. Additionally, some of the mutants at each recombinationally defined locus failed to complement mutants at other loci. They define dominant enhancers of one another

  17. Analysis of common mitochondrial DNA mutations by allele-specific oligonucleotide and Southern blot hybridization.

    Science.gov (United States)

    Tang, Sha; Halberg, Michelle C; Floyd, Kristen C; Wang, Jing

    2012-01-01

    Mitochondrial disorders are clinically and genetically heterogeneous. There are a set of recurrent point mutations in the mitochondrial DNA (mtDNA) that are responsible for common mitochondrial diseases, including MELAS (mitochondrial encephalopathy, lactic acidosis, stroke-like episodes), MERRF (myoclonic epilepsy and ragged red fibers), LHON (Leber's hereditary optic neuropathy), NARP (neuropathy, ataxia, retinitis pigmentosa), and Leigh syndrome. Most of the pathogenic mtDNA point mutations are present in the heteroplasmic state, meaning that the wild-type and mutant-containing mtDNA molecules are coexisting. Clinical heterogeneity may be due to the degree of mutant load (heteroplasmy) and distribution of heteroplasmic mutations in affected tissues. Additionally, Kearns-Sayre syndrome and Pearson syndrome are caused by large mtDNA deletions. In this chapter, we describe a multiplex PCR/allele-specific oligonucleotide (ASO) hybridization method for the screening of 13 common point mutations. This method allows the detection of low percentage of mutant heteroplasmy. In addition, a nonradioactive Southern blot hybridization protocol for the analysis of mtDNA large deletions is also described. PMID:22215554

  18. bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis.

    Science.gov (United States)

    Gillet-Markowska, Alexandre; Louvel, Guillaume; Fischer, Gilles

    2015-11-01

    Fluctuation analysis is the standard experimental method for measuring mutation rates in micro-organisms. The appearance of mutants is classically described by a Luria-Delbrück distribution composed of two parameters: the number of mutations per culture (m) and the differential growth rate between mutant and wild-type cells (b). A precise estimation of these two parameters is a prerequisite to the calculation of the mutation rate. Here, we developed bz-rates, a Web tool to calculate mutation rates that provides three useful advances over existing Web tools. First, it allows taking into account b, the differential growth rate between mutant and wild-type cells, in the estimation of m with the generating function. Second, bz-rates allows the user to take into account a deviation from the Luria-Delbrück distribution called z, the plating efficiency, in the estimation of m. Finally, the Web site provides a graphical visualization of the goodness-of-fit between the experimental data and the model. bz-rates is accessible at http://www.lcqb.upmc.fr/bzrates. PMID:26338660

  19. Identification of novel BRCA founder mutations in Middle Eastern breast cancer patients using capture and Sanger sequencing analysis.

    Science.gov (United States)

    Bu, Rong; Siraj, Abdul K; Al-Obaisi, Khadija A S; Beg, Shaham; Al Hazmi, Mohsen; Ajarim, Dahish; Tulbah, Asma; Al-Dayel, Fouad; Al-Kuraya, Khawla S

    2016-09-01

    Ethnic differences of breast cancer genomics have prompted us to investigate the spectra of BRCA1 and BRCA2 mutations in different populations. The prevalence and effect of BRCA 1 and BRCA 2 mutations in Middle Eastern population is not fully explored. To characterize the prevalence of BRCA mutations in Middle Eastern breast cancer patients, BRCA mutation screening was performed in 818 unselected breast cancer patients using Capture and/or Sanger sequencing. 19 short tandem repeat (STR) markers were used for founder mutation analysis. In our study, nine different types of deleterious mutation were identified in 28 (3.4%) cases, 25 (89.3%) cases in BRCA 1 and 3 (10.7%) cases in BRCA 2. Seven recurrent mutations identified accounted for 92.9% (26/28) of all the mutant cases. Haplotype analysis was performed to confirm c.1140 dupG and c.4136_4137delCT mutations as novel putative founder mutation, accounting for 46.4% (13/28) of all BRCA mutant cases and 1.6% (13/818) of all the breast cancer cases, respectively. Moreover, BRCA 1 mutation was significantly associated with BRCA 1 protein expression loss (p = 0.0005). Our finding revealed that a substantial number of BRCA mutations were identified in clinically high risk breast cancer from Middle East region. Identification of the mutation spectrum, prevalence and founder effect in Middle Eastern population facilitates genetic counseling, risk assessment and development of cost-effective screening strategy. PMID:27082205

  20. Mutational analysis of the capsid protein of Leishmania RNA virus LRV1-4.

    OpenAIRE

    Cadd, T L; MacBeth, K; Furlong, D; Patterson, J. L.

    1994-01-01

    The virion of Leishmania RNA virus is predicted to be composed of a 742-amino-acid major capsid protein and a small percentage of capsid-polymerase fusion molecules. Recently, the capsid protein alone was expressed and shown to spontaneously assemble into viruslike particles. Since the major structural protein of the virion shell self-assembles into viruslike particles when expressed in the baculovirus expression system, assembly of the virion can be studied by mutational analysis and express...

  1. The importance of conventional radiography in the mutational analysis of skeletal dysplasias (the TRPV4 mutational family)

    Energy Technology Data Exchange (ETDEWEB)

    Nemec, Stefan F.; Cohn, Daniel H.; Krakow, Deborah; Funari, Vincent A.; Rimoin, David L.; Lachman, Ralph S. [Medical Genetics Institute, Cedars Sinai Medical Center, International Skeletal Dysplasia Registry, Los Angeles, CA (United States)

    2012-01-15

    The spondylo and spondylometaphyseal dysplasias (SMDs) are characterized by vertebral changes and metaphyseal abnormalities of the tubular bones, which produce a phenotypic spectrum of disorders from the mild autosomal-dominant brachyolmia to SMD Kozlowski to autosomal-dominant metatropic dysplasia. Investigations have recently drawn on the similar radiographic features of those conditions to define a new family of skeletal dysplasias caused by mutations in the transient receptor potential cation channel vanilloid 4 (TRPV4). This review demonstrates the significance of radiography in the discovery of a new bone dysplasia family due to mutations in a single gene. (orig.)

  2. Applications of liquid phase chromatographies for the analysis of streams arising at the back end of nuclear fuel cycle

    International Nuclear Information System (INIS)

    India has opted for a closed fuel cycle comprising of reprocessing and recycling technology. The back end of such nuclear fuel cycle involves the reprocessing of spent nuclear fuels for recovery of plutonium and depleted uranium by Purex technology. Wastes arising from the reprocessing plant are classified as high, intermediate and low level wastes (HLW, ILW, LLW). HLW is mixture of over 50 elements present in different chemical forms. The accurate analyses of dissolver solution and HLW are the most challenging but essential tasks for reprocessing plant operations and also for further development of treatment methods. Inductively coupled plasma - atomic emission spectroscopy and atomic absorption spectroscopy techniques are suitable for analysis of metallic anions. Ion chromatography has proven capability to analyse number of cations or anions at ppm or even ppb level in single run. The report reviews the literature regarding the title subject. To assess the technical feasibility of ion chromatography for waste analysis, a simulated PHWR-HLW analogue was prepared. The PHWR-HLW analogue and ground water samples were analysed on DIONEX-DX 500 and Metrohm IC. Results obtained clearly demonstrated the usefulness of ion chromatography as vital analytical tool. HLW and other process or waste streams arising at the back end of nuclear fuel cycle can be analysed for alkali, alkaline earth, rare earth and transition metal cations and important anions. Use of fraction collector along with ion chromatography can enhance it's sensitivity to few Bq/ml for radioactive samples. (author)

  3. IDH1/IDH2 mutations define the prognosis and molecular profiles of patients with gliomas: a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Peng Zou

    Full Text Available BACKGROUND: Isocitrate dehydrogenase isoforms 1 and 2 (IDH1 and IDH2 mutations have received considerable attention since the discovery of their relation with human gliomas. The predictive value of IDH1 and IDH2 mutations in gliomas remains controversial. Here, we present the results of a meta-analysis of the associations between IDH mutations and both progression-free survival (PFS and overall survival (OS in gliomas. The interrelationship between the IDH mutations and MGMT promoter hypermethylation, EGFR amplification, codeletion of chromosomes 1p/19q and TP53 gene mutation were also revealed. METHODOLOGY AND PRINCIPAL FINDINGS: An electronic literature search of public databases (PubMed, Embase databases was performed. In total, 10 articles, including 12 studies in English, with 2,190 total cases were included in the meta-analysis. The IDH mutations were frequent in WHO grade II and III glioma (59.5% and secondary glioblastomas (63.4% and were less frequent in primary glioblastomas (7.13%. Our study provides evidence that IDH mutations are tightly associated with MGMT promoter hypermethylation (P<0.001, 1p/19q codeletion (P<0.001 and TP53 gene mutation (P<0.001 but are mutually exclusive with EGFR amplification (P<0.001. This meta-analysis showed that the combined hazard ratio (HR estimate for overall survival and progression-free survival in patients with IDH mutations was 0.33 (95% CI: 0.25-0.42 and 0.38 (95% CI: 0.21-0.68, compared with glioma patients whose tumours harboured the wild-type IDH. Subgroup analyses based on tumour grade also revealed that the presence of IDH mutations was associated with a better outcome. CONCLUSION: Our study suggests that IDH mutations, which are closely linked to the genomic profile of gliomas, are potential prognostic biomarkers for gliomas.

  4. Mutation analysis of mitogen activated protein kinase 1 gene in Indian cases of 46,XY disorder of sex development

    Directory of Open Access Journals (Sweden)

    Dhanjit Kumar Das

    2013-01-01

    Full Text Available Background: Determination of sex is the result of cascade of molecular events that cause undifferentiated bipotential gonad to develop as a testis or an ovary. A series of genes such as SRY, steroidogenic factor-1 (SF1, AR, SRD5 α, Desert hedgehog (DHH etc., have been reported to have a significant role in development of sex in the fetus and secondary sexual characteristics at the time of puberty. Recently, mitogen activated protein kinase kinase kinase 1 (MAP3K1 gene was found to be associated with 46, XY disorders of sex development (DSD. Aim: The present study is focused to identify mutations in MAP3K1 gene in the cohort of 10 Indian patients with 46,XY DSD including one family with two affected sisters. These patients were already screened for SRY, SF1 and DHH gene, but no mutation was observed in any of these genes. Materials and Methods: The entire coding regions of MAP3K1 were amplified and sequenced using the gene specific primers. Results and Discussions: Sequence analysis of MAP3K1 gene has revealed four variants including one missense, two silent and one deletion mutation. The missense mutation p.D806N was observed in four patients with hypospadias. Two patients showed the presence of silent mutation p.Q1028Q present in exon 14. Another silent mutation p.T428T was observed in a patient with gonadal dysgenesis. We have also observed one deletion mutation p. 942insT present in two patients. The pathogenicity of the missense mutation p.D806N was carried out using in-silico approach. Sequence homology analysis has revealed that the aspartate at 806 was found to be well-conserved across species, indicated the importance of this residue. The score for polyphen analysis of this mutation was found to be 0.999 indicating to be pathogenic mutation. Since, p.D806N mutation was found to be important residue; it might contribute to sexual development. We have reported the presence of mutations/polymorphism in MAP3K1 gene. All the mutations were

  5. Analysis of endocrine disrupters and related compounds in sediments and sewage sludge using on-line turbulent flow chromatography-liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Gorga, Marina; Insa, Sara; Petrovic, Mira; Barceló, Damià

    2014-07-25

    A novel fully automated method based on dual column switching using turbulent flow chromatography followed by liquid chromatography coupled to tandem mass spectrometry (TFC-LC-MS/MS) was applied for the determination of endocrine disruptors (EDCs) and related compounds in sediment and sewage sludge samples. This method allows the unequivocal identification and quantification of the most relevant environmental EDCs such as natural and synthetic estrogens and their conjugates, antimicrobials, parabens, bisphenol A (BPA), alkylphenolic compounds, benzotriazoles, and organophosphorus flame retardants, minimizing time of analysis and alleviating matrix effects. Applying this technique, after the extraction of the target compounds by pressurized liquid extraction (PLE), sediment and sewage sludge extracts were directly injected to the chromatographic system and the analytes were concentrated into the clean-up loading column. Using six-port switching system, the analytes were transferred to the analytical column for subsequent detection by MS-MS (QqQ). In order to optimize this multiplexing system, a comparative study employing six types of TurboFlow™ columns, with different chemical modifications, was performed to achieve the maximum retention of analytes and best elimination of matrix components. Using the optimized protocol low limits of quantification (LOQs) were obtained ranging from 0.0083 to 1.6 ng/g for sediment samples and from 0.10 to 125 ng/g for sewage sludge samples (except for alkylphenol monoethoxylate). The method was used to evaluate the presence and fate of target EDCs in the Ebro River which is the most important river in Spain with intensive agricultural and industrial activities in the basin that contribute to deteriorating soil and water quality. PMID:24909438

  6. Comparative analysis of steroidal saponins in four Dioscoreae herbs by high performance liquid chromatography coupled with mass spectrometry.

    Science.gov (United States)

    Guo, Long; Zeng, Su-Ling; Zhang, Yu; Li, Ping; Liu, E-Hu

    2016-01-01

    Steroidal saponins, which exhibit multiple pharmacological effects, are the major bioactive constituents in herbal medicines from Dioscoreae species. In this study, a sensitive method based on high performance liquid chromatography-mass spectrometry (HPLC-MS) was established and validated for qualitative and quantitative analysis of steroidal saponins in four Dioscoreae herbs including Dioscoreae Nipponica Rhizome (DNR) and Dioscoreae Hypoglaucae Rhizome (DHR), Dioscoreae Spongiosae Rhizome (DSR) and Dioscoreae Rhizome (DR). A total of eleven steroidal saponins were identified by high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-QTOF/MS). Furthermore, seven major steroidal saponins was simultaneous quantified using a high performance liquid chromatography coupled with triple quadrupole mass spectrometry (HPLC-QQQ/MS). The qualitative and quantitative analysis results indicated that the chemical composition of DNR, DHR and DSR samples exhibited a high level of global similarity, while the ingredients in DR varied greatly from the other three herbs. Moreover, principal component analysis (PCA) and hierarchical clustering analysis (HCA) were performed to compare and discriminate the Dioscoreae herbs based on the quantitative data. The results demonstrated the qualitative and quantitative analysis of steroidal saponins based on HPLC-MS is a feasible method for quality control of Dioscoreae herbs. PMID:26344383

  7. A rapid analysis of plasma/serum ethylene and propylene glycol by headspace gas chromatography.

    Science.gov (United States)

    Ehlers, Alexandra; Morris, Cory; Krasowski, Matthew D

    2013-12-01

    A rapid headspace-gas chromatography (HS-GC) method was developed for the analysis of ethylene glycol and propylene glycol in plasma and serum specimens using 1,3-propanediol as the internal standard. The method employed a single-step derivitization using phenylboronic acid, was linear to 200 mg/dL and had a lower limit of quantitation of 1 mg/dL suitable for clinical analyses. The analytical method described allows for laboratories with HS-GC instrumentation to analyze ethanol, methanol, isopropanol, ethylene glycol, and propylene glycol on a single instrument with rapid switch-over from alcohols to glycols analysis. In addition to the novel HS-GC method, a retrospective analysis of patient specimens containing ethylene glycol and propylene glycol was also described. A total of 36 patients ingested ethylene glycol, including 3 patients who presented with two separate admissions for ethylene glycol toxicity. Laboratory studies on presentation to hospital for these patients showed both osmolal and anion gap in 13 patients, osmolal but not anion gap in 13 patients, anion but not osmolal gap in 8 patients, and 1 patient with neither an osmolal nor anion gap. Acidosis on arterial blood gas was present in 13 cases. Only one fatality was seen; this was a patient with initial serum ethylene glycol concentration of 1282 mg/dL who died on third day of hospitalization. Propylene glycol was common in patients being managed for toxic ingestions, and was often attributed to iatrogenic administration of propylene glycol-containing medications such as activated charcoal and intravenous lorazepam. In six patients, propylene glycol contributed to an abnormally high osmolal gap. The common presence of propylene glycol in hospitalized patients emphasizes the importance of being able to identify both ethylene glycol and propylene glycol by chromatographic methods. PMID:23741644

  8. Systematic analysis of glycerol: colourimetric screening and gas chromatography-mass spectrometric confirmation.

    Science.gov (United States)

    Sardela, Vinícius F; Scalco, Fernanda B; Cavalcante, Karina M; Simoni, Ruth E; Silva, Deyvison R; Pereira, Henrique Marcelo G; de Oliveira, Maria Lúcia L Costa; Aquino Neto, Francisco R

    2015-10-01

    Glycerol is a naturally occurring polyol in the human body, essential for several metabolic processes. It is widely used in the food, pharmaceutical, and medical industries and in clinical practice as a plasma volume expander (PVE). Athletes, however, may use glycerol to mask the presence of forbidden substances or to enhance performance, inclusively through hyperhydration achieved by glycerol ingestion with added fluid. These practices are considered doping, and are prohibited by the World Anti-Doping Agency (WADA). Therefore, glycerol was introduced in the prohibited list. Doping through glycerol ingestion can readily be identified by detection of elevated glycerol concentrations in urine. In this paper, a protocol for the fast detection of glycerol in urine is proposed. It consists of a previous visual colourimetric screening, followed by a quantitative/qualitative confirmation analysis by mass spectrometry. The screening procedure involves a reaction in which polyhydric alcohols are oxidized by periodate to formic acid and formaldehyde, which is detected by the addition of a fuchsin solution. For the subsequent qualitative/quantitative confirmation analysis, a gas chromatography-mass spectrometry based approach with a non-deuterated internal standard and a drying step of only 10 min is proposed. The linear correlation was demonstrated within WADA´s threshold range. The calculated RSD were 2.1% for within-day precision and 2.8% for between-day precision. The uncertainty estimation was calculated, and a value of 2.7% was obtained. The procedure may also be used for the analysis of other polyols in urine, as for example the PVE mannitol. PMID:26112364

  9. Metabolomic Analysis of Gingival Crevicular Fluid Using Gas Chromatography/Mass Spectrometry.

    Science.gov (United States)

    Ozeki, Miho; Nozaki, Takenori; Aoki, Jun; Bamba, Takeshi; Jensen, Kirk R; Murakami, Shinya; Toyoda, Michisato

    2016-01-01

    Periodontitis is one of the most prevalent threats to oral health as the most common cause of tooth loss. In order to perform effective treatment, a clinical test that detect sites where disease activity is high and predicts periodontal tissue destruction is strongly desired, however, it is still difficult to prognose the periodontal tissue breakdown on the basis of conventional methods. The aim of this study is to examine the usefulness of gas chromatography/mass spectrometry (GC/MS), which could eventually be used for on-site analysis of metabolites in gingival crevicular fluid (GCF) in order to objectively diagnose periodontitis at a molecular level. GCF samples were collected from two diseased sites (one site with a moderate pocket and another site with a deep pocket) from each patient and from clinically healthy sites of volunteers. Nineteen metabolites were identified using GC/MS. Total ion current chromatograms showed broad differences in metabolite peak patterns between GCF samples obtained from healthy sites, moderate-pocket sites, and deep-pocket sites. The intensity difference of some metabolites was significant at sites with deep pockets compared to healthy sites. Additionally, metabolite intensities at moderate-pocket sites showed an intermediate profile between the severely diseased sites and healthy sites, which suggested that periodontitis progression could be observed with a changing metabolite profile. Principal component analysis confirmed these observations by clearly delineating healthy sites and sites with deep pockets. These results suggest that metabolomic analysis of GCF could be useful for prediction and diagnosis of periodontal disease in a single visit from a patient and provides the groundwork for establishing a new, on-site diagnostic method for periodontitis. PMID:27446770

  10. Metabolomic Analysis of Gingival Crevicular Fluid Using Gas Chromatography/Mass Spectrometry

    Science.gov (United States)

    Ozeki, Miho; Nozaki, Takenori; Aoki, Jun; Bamba, Takeshi; Jensen, Kirk R.; Murakami, Shinya; Toyoda, Michisato

    2016-01-01

    Periodontitis is one of the most prevalent threats to oral health as the most common cause of tooth loss. In order to perform effective treatment, a clinical test that detect sites where disease activity is high and predicts periodontal tissue destruction is strongly desired, however, it is still difficult to prognose the periodontal tissue breakdown on the basis of conventional methods. The aim of this study is to examine the usefulness of gas chromatography/mass spectrometry (GC/MS), which could eventually be used for on-site analysis of metabolites in gingival crevicular fluid (GCF) in order to objectively diagnose periodontitis at a molecular level. GCF samples were collected from two diseased sites (one site with a moderate pocket and another site with a deep pocket) from each patient and from clinically healthy sites of volunteers. Nineteen metabolites were identified using GC/MS. Total ion current chromatograms showed broad differences in metabolite peak patterns between GCF samples obtained from healthy sites, moderate-pocket sites, and deep-pocket sites. The intensity difference of some metabolites was significant at sites with deep pockets compared to healthy sites. Additionally, metabolite intensities at moderate-pocket sites showed an intermediate profile between the severely diseased sites and healthy sites, which suggested that periodontitis progression could be observed with a changing metabolite profile. Principal component analysis confirmed these observations by clearly delineating healthy sites and sites with deep pockets. These results suggest that metabolomic analysis of GCF could be useful for prediction and diagnosis of periodontal disease in a single visit from a patient and provides the groundwork for establishing a new, on-site diagnostic method for periodontitis. PMID:27446770

  11. Advances on the compositional analysis of glycosphingolipids combining thin-layer chromatography with mass spectrometry.

    Science.gov (United States)

    Müthing, Johannes; Distler, Ute

    2010-01-01

    Glycosphingolipids (GSLs), composed of a hydrophilic carbohydrate chain and a lipophilic ceramide anchor, play pivotal roles in countless biological processes, including infectious diseases and the development of cancer. Knowledge of the number and sequence of monosaccharides and their anomeric configuration and linkage type, which make up the principal items of the glyco code of biologically active carbohydrate chains, is essential for exploring the function of GSLs. As part of the investigation of the vertebrate glycome, GSL analysis is undergoing rapid expansion owing to the application of novel biochemical and biophysical technologies. Mass spectrometry (MS) takes part in the network of collaborations to further unravel structural and functional aspects within the fascinating world of GSLs with the ultimate aim to better define their role in human health and disease. However, a single-method analytical MS technique without supporting tools is limited yielding only partial structural information. Because of its superior resolving power, robustness, and easy handling, high-performance thin-layer chromatography (TLC) is widely used as an invaluable tool in GSL analysis. The intention of this review is to give an insight into current advances obtained by coupling supplementary techniques such as TLC and mass spectrometry. A retrospective view of the development of this concept and the recent improvements by merging (1) TLC separation of GSLs, (2) their detection with oligosaccharide-specific proteins, and (3) in situ MS analysis of protein-detected GSLs directly on the TLC plate, are provided. The procedure works on a nanogram scale and was successfully applied to the identification of cancer-associated GSLs in several types of human tumors. The combination of these two supplementary techniques opens new doors by delivering specific structural information of trace quantities of GSLs with only limited investment in sample preparation. PMID:19609886

  12. BRAF mutations in patients with non-small cell lung cancer: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Dong Chen

    Full Text Available BRAF mutations have been well described in non-small cell lung cancer (NSCLC for several years, but the clinical features of patients harboring BRAF mutations are still not well described. We performed a meta-analysis to identify common clinical features in NSCLC patients carrying BRAF mutations.We identified clinical studies that examined the association between BRAF mutations and features of NSCLC within PubMed, Embase and ISI Science Citation Index database up to October 2013. The effect size of clinical features was estimated by odds ratios (ORs with 95% confidence interval (CI for each study, using a fixed-effects or random-effects model.Ten studies with a total of 5599 NSCLC patients were included. There was a 3% (170/5599 BRAF mutation rate. BRAF mutations in NSCLC were significantly associated with adenocarcinomas (ADCs (compared with non-ADCs, OR = 4.96, 95%CI = 2.29-10.75. There were no significant differences in gender, smoking and stage in patients with and without BRAF mutations. The BRAFV600E mutation was more frequent in women than non-BRAFV600E mutations (OR = 0.27, 95%CI = 0.12-0.59, and was closely related to never smokers (OR = 0.14, 95%CI = 0.05-0.42.These findings have important implications for the prediction of the NSCLC sub-types more accurately combined with other genetic changes.

  13. Analysis of low-density lipoprotein receptor gene mutations in a Chinese patient with clinically homozygous familial hypercholesterolemia

    Institute of Scientific and Technical Information of China (English)

    曹守春; 王绿娅; 秦彦文; 蔺洁; 吴邦俊; 刘舒; 潘晓冬; 杜兰平; 陈保生

    2003-01-01

    Objective To screen the point mutation of the low-density lipoprotein receptor (LDL-R) gene in Chinese familial hypercholesterolemia (FH) patients, characterize the relationship between the genotype and the phenotype and discuss the molecular pathological mechanism of FH. Methods A patient with clinical phenotype of homozygous FH and her parents were investigated for mutations in the promoter and all eighteen exons of the LDL-R gene. Screening was carried out using Touch-down PCR and direct DNA sequencing; multiple alignment analysis by DNASIS 2.5 was used to find base alteration, and the LDL-R gene mutation database was searched to identify the alteration. In addition, the apolipoprotein B gene (apo B) was screened for known mutations (R3500Q) that cause familial defective apo B100 (FDB) by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).Results Two new heterozygous mutations in exons 4 and 9 of the LDL-R gene were identified in the proband (C122Y and T383I) as well as her parents. Both of the mutations have not been published in the LDL-R gene mutation database. No mutation of apo B100 (R3500Q) was observed. Conclusion Two new mutations (C112Y and T383I) were found in the LDL-R gene, which may result in FH and may be particularly pathogenetic genotypes in Chinese people.

  14. Analysis of mutation induced by radiation in HPRT gene exon 7/8 of rat smooth muscles cells

    International Nuclear Information System (INIS)

    Objective: To investigate the relationship between radiation dose and HPRT gene locus mutation in rat smooth muscle cells, and provide a molecular basis for prevention of blood vessel restenosis after PTCA. Methods: The smooth muscle cells cultured in vitro were irradiated by radionuclide 188Re with different doses. HPRT gene mutation colonies were selected and isolated by 6-thioguanine. Analysis of mutation in exon 7/8 of HPRT gene were accomplished by polymerase chain reaction and single-strand conformation polymorphism. Results: The HPRT gene mutation frequency of rat smooth muscle cells that were irradiated by radionuclide 188Re ranged from 5.5 x 10-6 to 13 x 10-6. Of 91 HPRT gene mutation colonies, 13 contained exon 7/8 deletion and 15 had point mutation. The exon 7/8 mutation frequency was 30.8%. There was significant relationship between radiation dose and mutation frequency of HPRT gene and exon 7/8. Conclusions: The DNA damage and gene mutation induced by radiation was the basis of proliferation inhibition and apoptosis of smooth muscle cells

  15. Irreversible and reversible reactive chromatography: analytical solutions and moment analysis for rectangular pulse injections.

    Science.gov (United States)

    Bibi, Sameena; Qamar, Shamsul; Seidel-Morgenstern, Andreas

    2015-03-13

    This work is concerned with the analysis of models for linear reactive chromatography describing irreversible A→B and reversible A↔B reactions. In contrast to previously published results rectangular reactant pulses are injected into initially empty or pre-equilibrated columns assuming both Dirichlet and Danckwerts boundary conditions. The models consist of two partial differential equations, accounting for convection, longitudinal dispersion and first order chemical reactions. Due to the effect of involved mechanisms on solute transport, analytical and numerical solutions of the models could be helpful to understand, design and optimize chromatographic reactors. The Laplace transformation is applied to solve the model equations analytically for linear adsorption isotherms. Statistical temporal moments are derived from solutions in the Laplace domain. Analytical results are compared with numerical predictions generated using a high-resolution finite volume scheme for two sets of boundary conditions. Several case studies are carried out to analyze reactive liquid chromatographic processes for a wide range of mass transfer and reaction kinetics. Good agreements in the results validate the correctness of the analytical solutions and accuracy of the proposed numerical algorithm. PMID:25670415

  16. Systematic Optimization of Long Gradient Chromatography Mass Spectrometry for Deep Analysis of Brain Proteome

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hong; Yang, Yanling; Li, Yuxin; Bai, Bing; Wang, Xusheng; Tan, Haiyan; Liu, Tao; Beach, Thomas G.; Peng, Junmun; Wu, Zhiping

    2015-02-06

    Development of high resolution liquid chromatography (LC) is essential for improving the sensitivity and throughput of mass spectrometry (MS)-based proteomics. Here we present systematic optimization of a long gradient LC-MS/MS platform to enhance protein identification from a complex mixture. The platform employed an in-house fabricated, reverse phase column (100 μm x 150 cm) coupled with Q Exactive MS. The column was capable of achieving a peak capacity of approximately 700 in a 720 min gradient of 10-45% acetonitrile. The optimal loading level was about 6 micrograms of peptides, although the column allowed loading as many as 20 micrograms. Gas phase fractionation of peptide ions further increased the number of peptide identification by ~10%. Moreover, the combination of basic pH LC pre-fractionation with the long gradient LC-MS/MS platform enabled the identification of 96,127 peptides and 10,544 proteins at 1% protein false discovery rate in a postmortem brain sample of Alzheimer’s disease. As deep RNA sequencing of the same specimen suggested that ~16,000 genes were expressed, current analysis covered more than 60% of the expressed proteome. Further improvement strategies of the LC/LC-MS/MS platform were also discussed.

  17. Quantitative analysis of mitragynine in human urine by high performance liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Lu, Shijun; Tran, Buu N; Nelsen, Jamie L; Aldous, Kenneth M

    2009-08-15

    Mitragynine is the primary active alkaloid extracted from the leaves of Mitragyna speciosa Korth, a plant that originates in South-East Asia and is commonly known as kratom in Thailand. Kratom has been used for many centuries for their medicinal and psychoactive qualities, which are comparable to that of opiate-based drugs. Kratom abuse can lead to a detectable content of mitragynine residue in urine. Ultra trace amount of mitragynine in human urine was determined by a high performance liquid chromatography coupled to an electrospray tandem mass spectrometry (HPLC-ESI/MS/MS). Mitragynine was extracted by methyl t-butyl ether (MTBE) and separated on a HILIC column. The ESI/MS/MS was accomplished using a triple quadrupole mass spectrometer in positive ion detection and multiple reactions monitoring (MRM) mode. Ajmalicine, a mitragynine's structure analog was selected as internal standard (IS) for method development. Quality control (QC) performed at three levels 0.1, 1 and 5 ng/ml of mitragynine in urine gave mean recoveries of 90, 109, and 98% with average relative standard deviation of 22, 12 and 16%, respectively. The regression linearity of mitragynine calibration ranged from 0.01 to 5.0 ng/ml was achieved with correlation coefficient greater than 0.995. A detection limit of 0.02 ng/ml and high precision data within-day and between days analysis were obtained. PMID:19577523

  18. Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Cajka, Tomas; Fiehn, Oliver

    2014-10-01

    Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics has been a subject of dramatic developments over the past decade. This review focuses on state of the art in LC-MS-based lipidomics, covering all the steps of global lipidomic profiling. On the basis of review of 185 original papers and application notes, we can conclude that typical LC-MS-based lipidomics methods involve: (1) extraction using chloroform/MeOH or MTBE/MeOH protocols, both with addition of internal standards covering each lipid class; (2) separation of lipids using short microbore columns with sub-2-μm or 2.6-2.8-μm (fused-core) particle size with C18 or C8 sorbent with analysis time acquisition using high-resolution MS with capability to MS/MS. Phospholipids (phosphatidylcholines, phosphatidylethanolamines, phosphatidylinositols, phosphatidylserines, phosphatidylglycerols) followed by sphingomyelins, di- and tri-acylglycerols, and ceramides were the most frequently targeted lipid species. PMID:25309011

  19. Determination of extractable organohalogens in apple by neutron activation analysis and gas chromatography

    International Nuclear Information System (INIS)

    In addition to compounds such as dichlorodiphenyl trichloroethanes (DDTs) and polychlorinated biphenyls (PCBs), which originate from by now well-known anthropogenic sources, there is increasing awareness of other halogenated compounds coming from a number of different processes, and probably also from natural source. To provide the reliable results and data for evaluation of hazard of extractable persistent organohalogen (EPOX) to food safety and to further characterize halogenated compounds in fruits, the concentrations of extractable organohalogen (EOX), EPOX, and identified organochlorine compounds including DDTs, hexachlorinated cyclohexanes (HCHs), chlordanes and PCBs in apple samples from Chinese homegrown and imports were determined by neutron activation analysis (NAA) and gas chromatography. The results indicated that the levels of EPOX in apples was in the order of EPOCl >> EPOBr > EPOI, which showed that EPOCl was the major fraction of the EPOX pollutions. Also, most chlorinated compounds in apple samples existed as inorganic species and water-soluble polar compounds, and about 1/10-4/5 of EOX was sulfuric acid-resistant EPOX contaminants. Meanwhile, about more than 94 % of EPOCl in detected specimens cannot be accounted for by DDTs, HCHs, chlordanes and PCBs. Furthermore, the T-test result indicated that the EPOCl levels in apple were significantly higher than those in peeled apple , which stated that people consuming peeled apple will get lesser intakes of EPOCl pollutants than they consume unpeeled apple.

  20. Lipid analysis by thin-layer chromatography--a review of the current state.

    Science.gov (United States)

    Fuchs, Beate; Süss, Rosmarie; Teuber, Kristin; Eibisch, Mandy; Schiller, Jürgen

    2011-05-13

    High-performance thin-layer chromatography (HPTLC) is a widely used, fast and relatively inexpensive method of separating complex mixtures. It is particularly useful for smaller, apolar compounds and offers some advantages over HPLC. This review gives an overview about the special features as well as the problems that have to be considered upon the HPTLC analysis of lipids. The term "lipids" is used here in a broad sense and comprises fatty acids and their derivatives as well as substances related biosynthetically or functionally to these compounds. After a short introduction regarding the stationary phases and the methods how lipids can be visualized on an HPTLC plate, the individual lipid classes will be discussed and the most suitable solvent systems for their separation indicated. The focus will be on lipids that are most abundant in biological systems, i.e. cholesterol and its derivates, glycerides, sphingo- and glycolipids as well as phospholipids. Finally, a nowadays very important topic, the combination between HPTLC and mass spectrometric (MS) detection methods will be discussed. It will be shown that this is a very powerful method to investigate the identities of the HPTLC spots in more detail than by the use of common staining methods. Future aspects of HPTLC in the lipid field will be also discussed. PMID:21167493

  1. Liquid chromatography-tandem mass spectrometry for analysis of intestinal permeability of loperamide in physiological buffer.

    Directory of Open Access Journals (Sweden)

    Miriam S Rubelt

    Full Text Available Analysis of in vitro samples with high salt concentrations represents a major challenge for fast and specific quantification with liquid chromatography-tandem mass spectrometry (LC-MS/MS. To investigate the intestinal permeability of opioids in vitro employing the Ussing chamber technique, we developed and validated a fast, sensitive and selective method based on LC-MS/MS for the determination of loperamide in HEPES-buffered Ringer's solution. Chromatographic separation was achieved with an Atlantis dC18 column, 2.1 mm×20 mm, 3 µm particle size and a gradient consisting of methanol/0.1% formic acid and ammonium acetate. The flow rate was 0.7 ml/min, and the total run time was 3 min. For quantification, two mass transitions for loperamide and a deuterated internal standard (methadone-d(3 were used. The lower limit of loperamide quantification was 0.2 ng/ml. This new LC-MS/MS method can be used for the detection of loperamide in any experimental setup using HEPES-buffered Ringer's solution as a matrix compound.

  2. Liquid chromatography with ultraviolet absorbance detection for the analysis of tetracycline residues in honey.

    Science.gov (United States)

    Viñas, Pilar; Balsalobre, Nuria; López-Erroz, Carmen; Hernández-Córdoba, Manuel

    2004-01-01

    The separation of tetracyclines (TCs) using reversed-phase liquid chromatography (LC) is proposed. The use of an amide-based stationary phase prevents the interaction of tetracyclines with the residual silanol groups and thus avoids the appearance of tailed peaks. Detection was based on using an UV spectrophotometer and gradient elution with acetonitrile-oxalic acid as mobile phase permitted good separation of all the peaks. Specificity was demonstrated by the retention characteristics, UV spectra and peak purity index. Linearity, precision, recovery and sensitivity were satisfactory. The procedure was applied to the analysis of tetracycline residues (tetracycline, oxytetracycline (OTC), chlortetracycline (CTC), doxycycline (DC), minocycline (MINO) and methacycline (MTC)) in honey of different types. Extraction involved using a mild acidic solvent containing EDTA to release protein-bound or sugar-bound tetracyclines. For the clean-up step, solid phase extraction using phenyl cartridges was applied. Detection limits in the honey using the proposed procedure are between 15 and 30 ng g(-1), depending on the tetracycline. PMID:14753778

  3. Analysis of Dyes Extracted from Millimeter-Size Nylon Fibers by Micellar Electrokinetic Chromatography

    International Nuclear Information System (INIS)

    The Learning Objective is to present to the forensic community a potential qualitative/quantitative method for trace-fiber color comparisons using micellar electrokinetic chromatography (MEKC). Developing a means of analyzing extracted dye constituents from millimeter-size nylon fiber samples was the objective of this research initiative. Aside from ascertaining fiber type, color evaluation and source comparison of trace-fiber evidence plays a critical role in forensic-fiber examinations. Literally thousands of dyes exist to date, including both natural and synthetic compounds. Typically a three-color-dye combination is employed to affect a given color on fiber material. The result of this practice leads to a significant number of potential dye combinations capable of producing a similar color and shade. Since a typical forensic fiber sample is 2 mm or less in length, an ideal forensic dye analysis would qualitatively and quantitatively identify the extracted dye constituents from a sample size of 1 mm or smaller. The goal of this research was to develop an analytical method for comparing individual dye constituents from trace-fiber evidence with dyes extracted from a suspected source, while preserving as much of the original evidence as possible

  4. Supercritical fluid chromatography as a method of analysis for the determination of 4-hydroxybenzylglucosinolate degradation products.

    Science.gov (United States)

    Buskov, S; Hasselstrøm, J; Olsen, C E; Sørensen, H; Sørensen, J C; Sørensen, S

    2000-07-01

    In the present study analytical and preparative supercritical fluid chromatography (SFC) were used for investigation of myrosinase catalysed degradation of 4-hydroxybenzylglucosinolate (sinalbin). Sinalbin occurs as a major glucosinolate in seeds of Sinapis alba L., in various mustards and other food products. The degradation products were identified and quantified by analysis based on a developed SFC method using a bare silica column. Determinations comprised transformation products of sinalbin, produced both during degradation of isolated sinalbin, and during autolysis of meal from S. alba seeds. The conditions in the developed SFC method were used as basis for the preparative SFC procedure applied for isolation of the components prior to their identification by nuclear magnetic resonance (NMR) spectroscopy. Myrosinase catalysed sinalbin hydrolysis resulted in the reactive 4-hydroxybenzyl isothiocyanate as an initial product at pH values from 3.5 to 7.5 whereas 4-hydroxybenzyl cyanide was one of the major products at low pH values. 4-Hydroxybenzyl isothiocyanate was found to disappear from the aqueous reaction mixtures in a few hours, as it reacted easily with available nucleophilic reagents. 4-Hydroxybenzyl alcohol was found as the product from reaction with water, and with ascorbic acid, 4-hydroxybenzylascorbigen was produced. PMID:10869674

  5. Qualitative and quantitative analysis of four species of Curcuma rhizomes using twice development thin layer chromatography.

    Science.gov (United States)

    Zhang, J S; Guan, J; Yang, F Q; Liu, H G; Cheng, X J; Li, S P

    2008-11-01

    The rhizomes of Curcuma phaeocaulis, Curcuma kwangsiensis, Curcuma wenyujin and Curcuma longa are used as Ezhu or Jianghuang in traditional Chinese medicine for a long time. Due to their similar morphological characters, it is difficult to distinguish their origins of raw materials used in clinic. In this study, a simple, rapid and reliable twice development TLC method was developed for qualitative and quantitative analysis of the four species of Curcuma rhizomes. The chromatography was performed on silica gel 60F(254) plate with chloroform-methanol-formic acid (80:4:0.8, v/v/v) and petroleum ether-ethyl acetate (90:10, v/v) as mobile phase for twice development. The TLC markers were colorized with 1% vanillin-H(2)SO(4) solution. The four species of Curcuma were easily discriminated based on their characteristic TLC profiles, and simultaneous quantification of eight compounds, including bisdemethoxycurcumin, demethoxycurcumin, curcumine, curcumenol, curcumol, curdione, furanodienone and curzerene, in Curcuma were also performed densitometrically at lambda(scan)=518nm and lambda(reference)=800 nm. The investigated compounds had good linearity (r(2)>0.9905) within test ranges. Therefore, the developed TLC method can be used for quality control of Curcuma rhizomes. PMID:18722068

  6. Analysis of residual toluene in food packaging via headspace extraction method using gas chromatography

    International Nuclear Information System (INIS)

    Polymeric materials are used in many food contact applications as packaging material. The presence of residual toluene in this food packaging material can migrate into food and thus affect the quality of food. In this study, a manual headspace analysis was successfully designed and developed. The determination of residual toluene was carried out with standard addition method and multiple headspace extraction, MHE) method using gas chromatography-flame ionization detector, GC-FID). Identification of toluene was performed by comparison of its retention time with standard toluene and GC-MS. It was found that the suitable heating temperature was 180 degree Celsius with an optimum heating time of 10 minutes. The study also found that the concentration of residual toluene in multicolored sample was higher compared to mono colored sample whereas residual toluene in sample analyzed using standard addition method was higher compared to MHE method. However, comparison with the results obtained from De Paris laboratory, France found that MHE method gave higher accuracy for sample with low analyte concentration. On the other hand, lower accuracy was obtained for sample with high concentration of residual toluene due to systematic errors. Comparison between determination methods showed that MHE method is more precise compared to standard addition method. (author)

  7. Multi-mycotoxin analysis in dairy products by liquid chromatography coupled to quadrupole orbitrap mass spectrometry.

    Science.gov (United States)

    Jia, Wei; Chu, Xiaogang; Ling, Yun; Huang, Junrong; Chang, James

    2014-06-01

    A new analytical method was developed and validated for simultaneous analysis of 58 mycotoxins in dairy products. Response surface methodology was employed to optimize a quick, easy, cheap, effective, rugged, and safe (QuEChERS) sample preparation method. Ultrahigh-performance liquid chromatography and electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC/ESI Q-Orbitrap) was used for the separation and detection of all the analytes. The method was validated by taking into consideration the guidelines specified in Commission Decision 2002/657/EC and 401/2006/EC. The extraction recoveries were in a range of 86.6-113.7%, with coefficient of variation 0.99. The limits of detection for the analytes are in the range 0.001-0.92 μg kg(-1). The repeatability was lower than 6.4%. This method has been successfully applied on screening of mycotoxins in commercial dairy product samples, and it is very useful for fast screening of different food contaminants. PMID:24794937

  8. Mutation analysis of the cathepsin C gene in Indian families with Papillon-Lefèvre syndrome

    Directory of Open Access Journals (Sweden)

    Srivastava Satish

    2003-07-01

    Full Text Available Abstract Background PLS is a rare autosomal recessive disorder characterized by early onset periodontopathia and palmar plantar keratosis. PLS is caused by mutations in the cathepsin C (CTSC gene. Dipeptidyl-peptidase I encoded by the CTSC gene removes dipeptides from the amino-terminus of protein substrates and mainly plays an immune and inflammatory role. Several mutations have been reported in this gene in patients from several ethnic groups. We report here mutation analysis of the CTSC gene in three Indian families with PLS. Methods Peripheral blood samples were obtained from individuals belonging to three Indian families with PLS for genomic DNA isolation. Exon-specific intronic primers were used to amplify DNA samples from individuals. PCR products were subsequently sequenced to detect mutations. PCR-SCCP and ASOH analyses were used to determine if mutations were present in normal control individuals. Results All patients from three families had a classic PLS phenotype, which included palmoplantar keratosis and early-onset severe periodontitis. Sequence analysis of the CTSC gene showed three novel nonsense mutations (viz., p.Q49X, p.Q69X and p.Y304X in homozygous state in affected individuals from these Indian families. Conclusions This study reported three novel nonsense mutations in three Indian families. These novel nonsense mutations are predicted to produce truncated dipeptidyl-peptidase I causing PLS phenotype in these families. A review of the literature along with three novel mutations reported here showed that the total number of mutations in the CTSC gene described to date is 41 with 17 mutations being located in exon 7.

  9. Analysis of esterase isozyme and SSR for mutagenic progenies induced by space mutation in mustard

    International Nuclear Information System (INIS)

    Seeds of five mustard (Brassica juncea Coss) varieties were carried into outer space by 'Shijian No.8' satellite. After five years' consecutive planting and selection, ten relatively stable mutant lines were obtained, which had significant variation in agronomic and economic characters. The mutant lines and their original varieties without space mutation treatment as control were studied by esterase isozyme and SSR analyses. Electrophoresis analysis of esterase isozymes indicated that there were differences between mutant lines and their controls in enzyme types and enzyme activity. Different mustard varieties had different enzymographs, and so did the mutants induced by space mutation, which shows different sensitivity among different mustard varieties. The SSR analysis showed that large differences were found in the SSR loci between mutant lines and their original variety, the variation frequency was between 9.52% and 57.14% with an average frequency of 26.19% for all the mutant lines. Among the mutant SSR loci, about 56.36% showed changes in band number and 43.64% in molecular weight. These results indicated that the ten mutant lines had large genetic difference in phenotype, genomic sequence and gene expression, and the outer space mutation would be an effective method to develop new mustard germplasm and variety. (authors)

  10. Optimization of heteroduplex analysis for the detection of BRCA mutations and SNPs

    Directory of Open Access Journals (Sweden)

    Lucian Negura

    2011-02-01

    Full Text Available BRCA1 and BRCA2 are tumour suppressor genes whose mutant phenotypes predispose to breast and ovarian cancer. Screening for mutations in these genes is now standard practice for hereditary breast and ovarian cancer (HBOC cases in Europe, and permits medical follow-up and genetic counselling adapted to the needs of individuals in such families. Currently, most laboratories performing diagnostic analysis of the BRCA genes use PCR of exons and intron-exon boundaries coupled to a pre-screening step to identify anomalous amplicons. The techniques employed for the detection of mutations and SNPs have evolved over time and vary in sensitivity, specificity and cost-effectiveness. As a variant for pre-screening techniques, we chose the recently developed Surveyor® heteroduplex cleavage method as a sensitive and specific technique to reveal anomalous amplicons of the BRCA genes, using only basic laboratory equipment and agarose gel electrophoresis. Here we present the detection of either mutations or SNPs within the BRCA1 exon 7, using heteroduplex analysis (HA by mismatch-specific endonuclease, confirmed by dideoxy sequencing.

  11. The analysis of aqueous mixtures using liquid chromatography-electrospray mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, S.

    1999-02-12

    The focus of this dissertation is the use of chromatographic methods coupled with electrospray mass spectrometry (ES-MS) for the determination of both organic and inorganic compounds in aqueous solutions. The combination of liquid chromatography (LC) methods and ES-MS offers one of the foremost methods for determining compounds in complex aqueous solutions. In this work, LC-ES-MS methods are devised using ion exclusion chromatography, reversed phase chromatography, and ion exchange chromatography, as well as capillary electrophoresis (CE). For an aqueous sample, these LC-ES-MS and CE-ES-MS techniques require no sample preparation or analyte derivatization, which makes it possible to observe a wide variety of analytes as they exist in solution. The majority of this work focuses on the use of LC-ES-MS for the determination of unknown products and intermediates formed during electrochemical incineration (ECI), an experimental waste remediation process. This report contains a general introduction to the project and the general conclusions. Four chapters have been removed for separate processing. Titles are: Chapter 2: Determination of small carboxylic acids by ion exclusion chromatography with electrospray mass spectrometry; Chapter 3: Electrochemical incineration of benzoquinone in aqueous media using a quaternary metal oxide electrode in the absence of a soluble supporting electrolyte; Chapter 4: The determination of electrochemical incineration products of 4-chlorophenol by liquid chromatography-electrospray mass spectrometry; and Chapter 5: Determination of small carboxylic acids by capillary electrophoresis with electrospray mass spectrometry.

  12. Analysis of morphology, DNA and isozyme of leaf mutation in Brassica napus L

    International Nuclear Information System (INIS)

    This paper aims to study the rule of irradiating effects, provide the effective way of analyzing mutant, and discuss the production application of mutant. By irradiating the 040B of Brassica napus L with . 0Co γ- ray, an obvious leaf mutation (ML) with large leaf area was found. The ML which has been inherited stably after three generations was compared with wide-type (CK) on the morphologic, DNA and isozymic levels. Results showed that S 4 and S17 from RAPD were two molecular markers which can express good polymorphism and have close relationships with leaf mutation sites. And in the analysis of EST and POD between ML and CK, the polymorphisms also proved that many discrepancies exist between ML and CK on the protein level. In addition, the research results in question can be applied to the breeding and genetic research of Brassica napus L

  13. Homozygous beta zero-39 mutation with thalassemia intermedia in northern Sardinia: clinical, hematological and molecular analysis.

    Science.gov (United States)

    Oggiano, L; Dore, F; Pistidda, P; Guiso, L; Manca, L; Masala, B; Pirastu, M; Rosatelli, C; Cao, A; Longinotti, M

    1988-01-01

    In this study, we investigated the clinical and hematological features and carried out alpha- and beta-globin gene analyses in 11 Sardinian adult beta zero-thalassemia homozygotes from Northern Sardinia who were not transfusion-dependent. Oligonucleotide analysis revealed in nine out of 11 patients the nonsense mutation at codon 39, which was associated either with haplotype II or IX (14/16 and 2/16 chromosomes, respectively). Haplotype II was linked to the A gamma T mutation. The G gamma globin level ranged from 50 to 70%. Four out of nine patients (44%) were heterozygous and 3/9 (33%) homozygous for the rightward deletional type of alpha-thalassemia; two (22%) had the normal alpha-gene complement. Patients who were alpha-thalassemia homozygotes (-alpha/-alpha) showed a more balanced globin chain synthesis ratio. This study confirms that alpha-thalassemia may ameliorate the clinical picture of homozygous beta zero-thalassemia. PMID:2905346

  14. Planar chromatography for the hydrocarbon group type analysis of petroleum middle distillates and coal-derived products

    Energy Technology Data Exchange (ETDEWEB)

    Matt, Muriel; Gruber, Rene [Laboratoire de thermodynamique et d' analyses chimiques, Universite de Metz, Ile du Saulcy, UFR SciFA, 57045 cedex 1 Metz (France); Galvez, Eva; Cebolla, Vicente; Membrado, Luis; Vela, Jesus [Instituto de Carboquimica, CSIC, Miguel Luesma Castan 4, 50015 Zaragoza (Spain)

    2002-06-20

    Different methodologies, based on planar chromatography/detection with densitometry, have been used to analyse compound classes (also known as hydrocarbon group type (HGT)) in samples coming from petroleum and coal conversion. The main problem encountered to analyse these samples is the choice of standard: because of the high variability of the signal that is dependent of molecular structure, one pure hydrocarbon does not reflect the response of a mixture. However, a step based on thin layer chromatography at preparative scale has allowed the fractionation of sample to obtain its derived standards. After this, alkanes have been quantified by fluorescence in presence of berberine sulfate and aromatic compounds have been detected by UV after separation by high performance thin layer chromatography (HPTLC) at analytical scale.The feasibility of the planar chromatography has been tested. The quantitative results obtained for different samples are in agreement with those provided using well-established techniques in the petrochemical industry and the coal-derived product (CDP) analysis.

  15. CHD7 mutational analysis and clinical considerations for auditory rehabilitation in deaf patients with CHARGE syndrome.

    Directory of Open Access Journals (Sweden)

    Mee Hyun Song

    Full Text Available BACKGROUND: Otologic manifestations are one of the most consistent findings of CHARGE syndrome found in more than 90%. Since genetic analysis of the CHD7 gene has rarely been performed in previous reports dealing with ear abnormalities, the genotypic spectrum of CHD7 mutations was analyzed in deaf patients with CHARGE syndrome, and the clinical considerations concerning auditory rehabilitation were investigated. METHODS: Nine Korean patients with CHARGE syndrome showing profound hearing loss and semicircular canal aplasia were included. All 38 exons of CHD7 were analyzed by direct sequencing. For splice site variations, in silico and exon-trapping analyses were performed to verify the pathogenicity of nucleotide variations. Clinical features and the outcome of auditory rehabilitation were also analyzed. RESULTS: Eight of 9 patients revealed alterations of the CHD7 gene including 3 frameshift, 2 nonsense, 2 splice site, and 1 missense mutations. Five of 9 patients were clinically diagnosed as atypical CHARGE syndrome but demonstrated various mutations of the CHD7 gene. One familial case showed intra-familial variability. Radiologic findings suggesting cochleovestibular nerve deficiency were identified in most of the patients. Of the 8 patients who underwent cochlear implantation, 5 patients demonstrated favorable outcome. Larger diameter of the cochleovestibular nerve on imaging and absence of severe mental retardation were factors related to better outcome after cochlear implantation rather than the type of CHD7 mutations. Auditory brainstem implantation was performed in two patients who did not benefit from cochlear implantation. CONCLUSIONS: Genetic analysis of the CHD7 gene should be performed in cases with semicircular canal aplasia even when other typical features of CHARGE syndrome are absent. For auditory rehabilitation in CHARGE syndrome, cochlear implantation should be strongly recommended in selected cases with favorable prognostic

  16. High Performance Thin Layer Chromatography method for analysis of 3,4-methylenedioxymethamphetamine in seized tablets

    Directory of Open Access Journals (Sweden)

    Boris E. Duffau

    2015-12-01

    Full Text Available Context: Consumption of synthetic drugs had increased in recent years, used as a recreational drug by young people who presume that consumption of this drug is harmless for health; however clinical studies have shown that this stimulant and its metabolites are toxic. Due to these reasons, chemical analysis of this illicit drug is crucial from the points of view of occupational medicine, toxicology, and law enforcement with the aim of pursuit the traffic of illegal drug. Aims: Implement and fully validate a rapid and simple method for detection and quantitation of MDMA by High-Performance Thin Layer Chromatography in seized samples. Methods: With the implemented method was analyzed 12 positive samples seized by Chilean police, to found the concentration of MDMA in ecstasy tablets. Results: The method was fully validated, the linearity of the method was evaluated by the calibration curve between 51.0 – 510.0 µg/band (R2 0.9977; limit of detection was 12.1 µg per band, and limit of quantitation was 36.8 µg per band. The precision of the method (RSD was lower than 5.0%. Accuracy was evaluated by determination of the percentage of MDMA recovered by the assay (99.13%, and relative Uncertainty was 6.66%. With this method, it was analyzed real seized samples of MDMA, results showed that all samples contained MDMA and concentration was between 18.15 – 59.84 % w/w. Conclusions: The method is selective, sensitive, and specific, with possible application in forensic analysis. To the best of our knowledge, this is the first report about concentration of MDMA in ecstasy pills in Chile.

  17. Analysis of aliphatic carboxylic acids in anaerobic digestion process waters by ion-exclusion chromatography

    Institute of Scientific and Technical Information of China (English)

    Kazuaki ITO; Kazuhiko TANAKA; Jun SAKAMOTO; Kazuya NAGAOKA; Yohichi TAKAYAMA; Takashi KANAHORI; Hiroshi SUNAHARA; Tsuneo HAYASHI; Shinji SATO; Takeshi HIROKAWA

    2012-01-01

    The analysis of seven aliphatic carboxylic acids ( formic,acetic,propionic,iso-butyric,n-butyric,iso-valeric and n-valeric acid) in anaerobic digestion process waters for biogas production was examined by ion-exclusion chromatography with dilute acidic eluents (benzoic acid,perfluorobutyric acid (PFBA) and sulfuric acid) and non-suppressed conductivity/ultraviolet (UV) detection.The columns used were a styrene/divinylbenzene-based strongly acidic cation-exchange resin column ( TSKgel SCX) and a polymethacrylate-based weakly acidic cation-exchange resin column ( TSKgel Super IC-A/C ).Good separation was performed on the TSKgel SCX in shorter retention times.For the TSKgel Super IC-A/C,peak shape of the acids was sharp and symmetrical in spite of longer retention times.In addition,the mutual separation of the acids was good except for iso- and n-butyric acids.The better separation and good detection was achieved by using the two columns (TSKgel SCX and TSKgel Super IC-A/C connected in series),lower concentrations of PFBA and sulfuric acid as eluents,non-suppressed conductivity detection and UV detection at 210 nm.This analysis was applied to anaerobic digestion process waters.The chromatograms with conductivity detection were relatively simpler compared with those of UV detection.The use of two columns with different selectivities for the aliphatic carboxylic acids and the two detection modes was effective for the determination and identification of the analytes in anaerobic digestion process waters containing complex matrices.

  18. Characters of the Plateau of Methanol Increment in Frontal Analysis in Reversed Phase Liquid Chromatography

    Institute of Scientific and Technical Information of China (English)

    GENG,Xin-Du(耿信笃); REGNIER,Fred E(弗莱德 依 瑞格涅尔)

    2002-01-01

    With insulin methanol-water, and the ion-pairing agent, hydrochloric acid and trifiuroacetic acid (TFA), the character of the first plateau (FP) on the elution curve of frontal analysis in reversed phase liquid chromatography (RPLC) was investigated by on-line UV-spectrometry and identified with nuclear magnetic resonance (NMR) spectrometry and mass spectrometry.The proffie of the FP is the same as that of a usual elution curve of methanol in frontal analysis (FA). When the insulin concentration was limited to a certain range, the height of the FP was found to be proportional to the insulin concentration in mobile phase and its length companying to shorten. The FP profile on the intersection of two tangents reflects the components of the microstructure in the depth direction of the bonded stationary phase layer and the desorption dynamics of the displaced components. The displaced methanol was quantitatively determined by NMR and on-line UV spectrometries. TFA with high UV absorbance can not be used as on ionpairing agent for the investigation of the FP in RPLC, but it can be used as a good marker to investigate the complicated transfer process of components in the stationary pdase in RPLC. A stoichiometric displacement process between solute and solvent was proved to be valid in both usual and FA in RPLC. From the point of view of dynamics of mass transfer,the solutes can only contact to the surface of stationary phase in usual RPLC, while solute can penetrate into it in FA of RPLC.The solvation of insulin in methanol and water solution as an example indicating the usage of the FP in the FA was also investigated in this paper.

  19. Perceptual characterization and analysis of aroma mixtures using gas chromatography recomposition-olfactometry.

    Directory of Open Access Journals (Sweden)

    Arielle J Johnson

    Full Text Available This paper describes the design of a new instrumental technique, Gas Chromatography Recomposition-Olfactometry (GC-R, that adapts the reconstitution technique used in flavor chemistry studies by extracting volatiles from a sample by headspace solid-phase microextraction (SPME, separating the extract on a capillary GC column, and recombining individual compounds selectively as they elute off of the column into a mixture for sensory analysis (Figure 1. Using the chromatogram of a mixture as a map, the GC-R instrument allows the operator to "cut apart" and recombine the components of the mixture at will, selecting compounds, peaks, or sections based on retention time to include or exclude in a reconstitution for sensory analysis. Selective recombination is accomplished with the installation of a Deans Switch directly in-line with the column, which directs compounds either to waste or to a cryotrap at the operator's discretion. This enables the creation of, for example, aroma reconstitutions incorporating all of the volatiles in a sample, including instrumentally undetectable compounds as well those present at concentrations below sensory thresholds, thus correcting for the "reconstitution discrepancy" sometimes noted in flavor chemistry studies. Using only flowering lavender (Lavandula angustifola 'Hidcote Blue' as a source for volatiles, we used the instrument to build mixtures of subsets of lavender volatiles in-instrument and characterized their aroma qualities with a sensory panel. We showed evidence of additive, masking, and synergistic effects in these mixtures and of "lavender' aroma character as an emergent property of specific mixtures. This was accomplished without the need for chemical standards, reductive aroma models, or calculation of Odor Activity Values, and is broadly applicable to any aroma or flavor.

  20. Analysis of epinephrine, norepinephrine, and dopamine in urine samples of hospital patients by micellar liquid chromatography.

    Science.gov (United States)

    García Ferrer, Daniel; García García, Aurelio; Peris-Vicente, Juan; Gimeno-Adelantado, José Vicente; Esteve-Romero, Josep

    2015-12-01

    An analytical method based on micellar liquid chromatography was developed to determine the concentration of three catecholamines (epinephrine, norepinephrine, and dopamine) in urine. The detection of these compounds in urine can be useful to diagnose several diseases, related to stress and sympathoadrenal system dysfunction, using a non-invasive collection procedure. The sample pretreatment was a simple dilution in a micellar solution, filtration, and direct injection, thus avoiding time-consuming and tedious extraction steps. Therefore, there is no need to use an internal standard. The three catecholamines were eluted using a C18 column and a mobile phase of 0.055 M sodium dodecyl sulfate-1.5% methanol buffered at pH 3.8 running at 1.5 mL/min under isocratic mode in less than 25 min. The detection was performed by amperometry applying a constant potential of +0.5 V. The procedure was validated following the guidelines of the European Medicines Agency in terms of the following: calibration range (0.09-5 μg/mL), linearity (r(2) > 0.9995), limit of detection (0.02 μg/mL), within- and between-run accuracy (-6.5 to +8.4%) and precision (guide. The method was rapid, easy-to-handle, eco-friendly, and safe and provides reliable quantitative data, and is thus useful for routine analysis. The procedure was applied to the analysis of epinephrine, norepinephrine, and dopamine in urine samples from patients of a local hospital. PMID:26427500

  1. Detection of somatic BRCA1/2 mutations in ovarian cancer - next-generation sequencing analysis of 100 cases.

    Science.gov (United States)

    Koczkowska, Magdalena; Zuk, Monika; Gorczynski, Adam; Ratajska, Magdalena; Lewandowska, Marzena; Biernat, Wojciech; Limon, Janusz; Wasag, Bartosz

    2016-07-01

    The overall prevalence of germline BRCA1/2 mutations is estimated between 11% and 15% of all ovarian cancers. Individuals with germline BRCA1/2 alterations treated with the PARP1 inhibitors (iPARP1) tend to respond better than patients with wild-type BRCA1/2. Additionally, also somatic BRCA1/2 alterations induce the sensitivity to iPARP1. Therefore, the detection of both germline and somatic BRCA1/2 mutations is required for effective iPARP1 treatment. The aim of this study was to identify the frequency and spectrum of germline and somatic BRCA1/2 alterations in a group of Polish patients with ovarian serous carcinoma. In total, 100 formalin-fixed paraffin-embedded (FFPE) ovarian serous carcinoma tissues were enrolled to the study. Mutational analysis of BRCA1/2 genes was performed by using next-generation sequencing. The presence of pathogenic variants was confirmed by Sanger sequencing. In addition, to confirm the germline or somatic status of the mutation, the nonneoplastic tissue was analyzed by bidirectional Sanger sequencing. In total, 27 (28% of patient samples) mutations (20 in BRCA1 and 7 in BRCA2) were identified. For 22 of 27 patients, nonneoplastic cells were available and sequencing revealed the somatic character of two BRCA1 (2/16; 12.5%) and two BRCA2 (2/6; 33%) mutations. Notably, we identified six novel frameshift or nonsense BRCA1/2 mutations. The heterogeneity of the detected mutations confirms the necessity of simultaneous analysis of BRCA1/2 genes in all patients diagnosed with serous ovarian carcinoma. Moreover, the use of tumor tissue for mutational analysis allowed the detection of both somatic and germline BRCA1/2 mutations. PMID:27167707

  2. Radiochemical neutron activation analysis of high pure palladium and platinum by ion exchange chromatography

    International Nuclear Information System (INIS)

    Full text: The palladium and platinum are widely used for jewel manufacture because of their beautiful white color. However the most part of these metals are widely adopted in the world as catalysts. Many works on analytical chemistry of platinum group elements published during last years are devoted to determination of platinum and palladium in other materials. There are no articles on analysis technique of the palladium and platinum purity published during last 20 years. Available publications are very old and are published till 70th of the last century, and implement chemical and spectral methods. At the same time, the palladium and platinum are very suitable for NAA. Therefore the purpose of our research was development of high-sensitivity and multielement techniques of radiochemical neutron activation analysis of a high pure palladium and platinum. Research of nuclear characteristics of palladium and platinum has shown that radioactive nuclides with different yields are formed under the reactor neutrons. 109, 111, 111mPd, 109m, 111Ag, 191,197, 199Pt, 199Au are the most important among them. 109Pd separation factor is equal to 1*105 at palladium analysis, whereas 197Pt and 199Au separation factor is equal to 1*104 at the platinum analysis every other day after irradiation. Palladium and platinum can be separated by precipitation, extraction and ion exchange methods. For separation of radioactive nuclide of the matrix elements from the impurity elements we used ion exchange chromatography system Dowex-1x8 - 1 M HNO3 for palladium and Dowex-1x8 - 0.1 M HNO3 for platinum. At the HNO3 acid concentrations variation from 0,1 M to 1 M more then 25 elements have distribution factors less than 1 and 10 elements have distribution factors 5 while matrix elements have distribution factors higher than 100. It allows an effective separation of these elements from palladium and platinum. Optimum sizes of the chromatographic column and the column effluent volume was obtained

  3. Liquid chromatography-tandem mass spectrometry for the analysis of eicosanoids and related lipids in human biological matrices: a review.

    Science.gov (United States)

    Kortz, Linda; Dorow, Juliane; Ceglarek, Uta

    2014-08-01

    Today, there is an increasing number of liquid chromatography tandem-mass spectrometric (LC-MS/MS) methods for the analysis of eicosanoids and related lipids in biological matrices. An overview of currently applied LC-MS/MS methods is given with attention to sample preparation strategies, chromatographic separation including ultra high performance liquid chromatography (UHPLC) and chiral separation, as well as to mass spectrometric detection using multiple reacting monitoring (MRM). Further, the application in recent clinical research is reviewed with focus on preanalytical aspects prior to LC-MS/MS analysis as well as applications in major diseases of Western civilization including respiratory diseases, diabetes, cancer, liver diseases, atherosclerosis, and neurovascular diseases. PMID:24583205

  4. Analysis of Androgenic Steroids in Environmental Waters by Large-volume Injection Liquid Chromatography Tandem Mass Spectrometry

    OpenAIRE

    Backe, Will J.; Ort, Christoph; Brewer, Alex J.; Field, Jennifer A.

    2011-01-01

    A new method was developed for the analysis of natural and synthetic androgenic steroids and their selected metabolites in aquatic environmental matrices using direct large-volume injection (LVI) high performance liquid chromatography (HPLC) tandem mass spectrometry (MS/MS). Method accuracy ranged from 88 to 108% for analytes with well-matched internal standards. Precision, quantified by relative standard deviation (RSD), was less than 12%. Detection limits for the method ranged from 1.2 to 3...

  5. Capacitively coupled contactless conductivity detection and sequential injection analysis in capillary electrophoresis and capillary electro-chromatography

    OpenAIRE

    Mai, Thanh Duc

    2011-01-01

    This thesis focuses on the applications of capacitively coupled contactless conductivity detection (C4D) in capillary electrophoresis (CE) hybridized with high-performance liquid chromatography (HPLC), i.e. in capillary electrochromatography and pressure-assisted capillary electrophoresis, as well as on the development and applications of an extension of CE-C4D with sequential injection analysis (SIA). At first, the in-house built C4D was used for electro-chromatographic determinations of...

  6. Supercritical Fluid Extraction Directly Coupled with Reversed Phase Liquid Chromatography for Quantitative Analysis of Analytes in Complex Matrices

    OpenAIRE

    Wang, Zhenyu

    2004-01-01

    The purpose of this research was to design a simple, novel interface for on-line coupling of Supercritical Fluid Extraction (SFE) with High Performance Reversed Phase Liquid Chromatography (HP-RPLC), and to explore its ability for quantitative analysis of analytes in different matrices. First, a simple interface was developed via a single one six-port injection valve to connect the SFE and LC systems. A water displacement method was utilized to eliminate decompressed CO2 gas in the solid phas...

  7. Qualitative and Quantitative Analysis of Andrographis paniculata by Rapid Resolution Liquid Chromatography/Time-of-Flight Mass Spectrometry

    OpenAIRE

    Jian-Fei Qin; Zhi-Yuan Jiang; Zhao Jin; Shi-Ping Liu; Yong-Xi Song

    2013-01-01

    A rapid resolution liquid chromatography/time-of-flight tandem mass spectrometry (RRLC-TOF/MS) method was developed for qualitative and quantitative analysis of the major chemical constituents in Andrographis paniculata. Fifteen compounds, including flavonoids and diterpenoid lactones, were unambiguously or tentatively identified in 10 min by comparing their retention times and accurate masses with standards or literature data. The characteristic fragmentation patterns of flavonoids and diter...

  8. Evaluation of Ternary Mobile Phases for the Analysis of Carbonyl Compound Derivatives Using High-Performance Liquid Chromatography

    OpenAIRE

    Duy Xuan Ho; Ki-Hyun Kim

    2011-01-01

    In this study, the feasibility of ternary mobile phases was examined in a high-performance liquid chromatography (HPLC)-based analysis of carbonyl compounds (CCs). To test the performance of different ternary phases, the liquid phase standards containing a 15 aldehyde/ketone-DNPH(o) mix were analyzed through a series of five-point calibration experiments. For this comparison, three types of ternary mobile phases were prepared initially by mixing water (W) with two of the following three organ...

  9. Comprehensive genetic and epigenetic analysis of sporadic meningioma for macro-mutations on 22q and micro-mutations within the NF2 locus

    Directory of Open Access Journals (Sweden)

    Jarbo Caroline

    2007-01-01

    Full Text Available Abstract Background Meningiomas are the most common intracranial neoplasias, representing a clinically and histopathologically heterogeneous group of tumors. The neurofibromatosis type 2 (NF2 tumor suppressor is the only gene known to be frequently involved in early development of meningiomas. The objective of this study was to identify genetic and/or epigenetic factors contributing to the development of these tumors. A large set of sporadic meningiomas were analyzed for presence of 22q macro-mutations using array-CGH in order to identify tumors carrying gene dosage aberrations not encompassing NF2. The NF2 locus was also comprehensively studied for point mutations within coding and conserved non-coding sequences. Furthermore, CpG methylation within the NF2 promoter region was thoroughly analyzed. Results Monosomy 22 was the predominant finding, detected in 47% of meningiomas. Thirteen percent of the tumors contained interstitial/terminal deletions and gains, present singly or in combinations. We defined at least two minimal overlapping regions outside the NF2 locus that are small enough (~550 kb and ~250 kb to allow analysis of a limited number of candidate genes. Bialleinactivationo the NF2 gne was detected in 36% of meningiomas. Among the monosomy 22 cases, no additional NF2 mutations could be identified in 35% (17 out of 49 of tumors. Furthermore, the majority of tumors (9 out of 12 with interstitial/terminal deletions did not have any detectable NF2 mutations. Methylation within the NF2 promoter region was only identified at a single CpG site in one tumor sample. Conclusion We confirmed previous findings of pronounced differences in mutation frequency between different histopathological subtypes. There is a higher frequency of biallelic NF2 inactivation in fibroblastic (52% compared to meningothelial (18% tumors. The presence of macro-mutations on 22q also shows marked differences between fibroblastic (86% and meningothelial (39% subtypes

  10. Trend analysis of performance parameters of pre-packed columns for protein chromatography over a time span of ten years.

    Science.gov (United States)

    Scharl, Theresa; Jungreuthmayer, Christian; Dürauer, Astrid; Schweiger, Susanne; Schröder, Tim; Jungbauer, Alois

    2016-09-23

    Pre-packed small scale chromatography columns are increasingly used for process development, for determination of design space in bioprocess development, and for post-licence process verifications. The packing quality of 30,000 pre-packed columns delivered to customers over a period 10 years has been analyzed by advanced statistical tools. First, the data were extracted and checked for inconsistencies, and then were tabulated and made ready for statistical processing using the programming language Perl (https://www.perl.org/) and the statistical computing environment R (https://www.r-project.org/). Reduced HETP and asymmetry were plotted over time to obtain a trend of packing quality over 10 years. The obtained data were used as a visualized coefficient of variation analysis (VCVA), a process that has often been applied in other industries such as semiconductor manufacturing. A typical fluctuation of reduced HETP was seen. A Tsunami effect in manufacturing, the effect of propagation of manufacturing deviations leading to out-of-specification products, was not observed with these pre-packed columns. Principal component analysis (PCA) showed that all packing materials cluster. Our data analysis showed that the current commercially available chromatography media used for biopharmaceutical manufacturing can be reproducibly and uniformly packed in polymer-based chromatography columns, which are designed for ready-to-use purposes. Although the number of packed columns has quadrupled over one decade the packing quality has remained stable. PMID:27575920

  11. Mutation analysis of the RET gene in individuals with sporadic and familial pheochromocytoma

    Energy Technology Data Exchange (ETDEWEB)

    Iyengar, S.; Sirugo, G.; Bale, A.E. [Yale Univ. School of Medicine, New Haven, CT (United States)] [and others

    1994-09-01

    Pheochromocytoma is common to many familial cancer syndromes including multiple endocrine neoplasia type 2A (MEN2A), von Hippel-Lindau (VHL) and neurofibromatosis (NF). Although sporadic cases of pheochromocytoma have been examined for mutations in exons 10, 11 and 16 of the RET gene, only one case with a mutation in exon 16 has been reported thus far. We are performing systematic examination of exons of the RET gene, which has previously been associated with mutation in both MEN2 A and B, to determine the role RET may play in the etiology of pheochromocytoma. Seventeen cases of sporadic pheochromocytoma and 3 cases of sporadic medullary thyroid carcinoma were obtained from the pathology archives. Histopathology of all specimens was confirmed to be either pheochromocytoma or medullary thyroid carcinoma before DNA was extracted from 0.5{mu} thin sections of paraffin-embedded tissue. DNA from familial pheochromocytoma patients was also available for analysis. All sporadic and familial cases were amplified for exons 2, 6 and 16 of the RET gene. Single strand conformational polymorphism (SSCP) analysis was performed for exons 2 and 6. On finding a variation in the SSCP pattern in the pheochromocytoma kindred we sequenced all the samples for exon 2. A single base pair variation was found, which did not segregate with pheochromocytoma in the family. No variant SSCP patterns have been observed with the exon 6 PCR products thus far. Exon 16 PCR products were subjected to DNA restriction analysis with Fok I. This enzyme detects a single base pair change associated with MEN2 B. With the exception of one sample with sporadic medullary thyroid carcinoma, all samples showed the normal pattern on DNA restriction analysis. Thus we can exclude exons 2 and 6 of the RET gene in the pathogenesis of pheochromocytoma. SSCP analyses with other exons in the RET gene are underway.

  12. UNIFIED THEORETICAL MOMENT EXPRESSIONS FOR ELUTION CHROMATOGRAPHY AND FRONTAL CHROMATOGRAPHY

    Institute of Scientific and Technical Information of China (English)

    YANGGengliang; TAOZuyi

    1992-01-01

    The unified theoretical moment expressions for elution chromatography and frontal chromatography when the sorption process is described by a linear model were derived. The moment expressions derived by previous authors can be obtained from these unified theoretical moment expressions. In this paper, a mathematical analysis has been carried out so as to set up a unified theoretical basis for elution and frontal chromatography.

  13. Utility of MLPA in mutation analysis and carrier detection for Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Prashant K Verma

    2012-01-01

    Full Text Available Context: Multiplex ligation probe amplification (MLPA is a new technique to identify deletions and duplications and can evaluate all 79 exons in dystrophin gene in patients with Duchenne muscular dystrophy (DMD. Being semi-quantitative, MLPA is also effective in detecting duplications and carrier testing of females; both of which cannot be done using multiplex PCR. It has found applications in diagnostics of many genetic disorders. Aim: To study the utility of MLPA in diagnosis and carrier detection for DMD. Materials and Methods: Mutation analysis and carrier detection was done by multiplex PCR and MLPA and the results were compared. Results and Conclusions: We present data showing utility of MLPA in identifying mutations in cases with DMD/BMD. In the present study using MLPA, we identified mutations in additional 5.6% cases of DMD in whom multiplex PCR was not able to detect intragenic deletions. In addition, MLPA also correctly confirmed carrier status of two obligate carriers and revealed carrier status in 6 of 8 mothers of sporadic cases.

  14. Transposition bursts during analysis of secondary mutations in the unstable lines of Drosophila melanogaster

    International Nuclear Information System (INIS)

    The article deals with realization of transposition memory discovered earlier at cut locus and in MDG4. The unstable line cmMR17 ctMRpN17, a derivative of ctMR2 line, was used. It has high frequency of double cm+ct+ revertants and secondary cmMRctMRpN mutants. Such mutant transitions were observed in the line five times. Mutation ctMRpN17 was caused by the insertion at cut locus of MDG4 with another mobile element, jockey. In situ hybridization showed that the transitions from mutational condition to normal are strongly correlated with the excision of MDG4 and jockey from 7B3-4 region of cut locus and their repeated insertion into it. The analysis of distribution of MDG1, MDG2, MDG3, and jockey in the X chromosomes of the revertant larvae and secondary mutants showed that not only transpositions of MDG4 and jockey but also simultaneous multiple migration of all the tested mobile elements take place with their complete stability in the absence of mutational transitions. Therefore, the transposition memory in this system of genetic instability is realized in the process of transposition bursts, but does not lead to isolated repeated transpositions of MDG4

  15. Mutational analysis of PVX TGBp3 links subcellular accumulation and protein turnover

    International Nuclear Information System (INIS)

    Potato virus X (PVX) TGBp3 is required for virus cell-to-cell transport, has an N-terminal transmembrane domain, and a C-terminal cytosolic domain. In the absence of virus infection TGBp3:GFP is seen in the cortical and perinuclear ER. In PVX infected cells the TGBp3:GFP fusion is also seen in the nucleoplasm indicating that events during PVX infection trigger entry into the nucleus. Mutational analysis failed to identify a nuclear targeting domain. Mutations inhibiting TGBp3 association with the ER and inhibiting virus movement did not block TGBp3:GFP in the nucleoplasm. A mutation disrupting the N-terminal transmembrane domain of TGBp3 caused the fusion to accumulate in the nucleus indicating that nuclear import is regulated by ER interactions. Tunicamycin, an ER-stress inducing chemical, caused lower levels of GFP and TGBp3:GFP to accumulate in virus infected protoplasts. MG115 and MG132 were used to demonstrate that wild-type and mutant TGBp3:GFP fusions were degraded by the 26S proteasome. These observations are consistent with an ER-associated protein degradation (ERAD) pathway suggesting that PVX TGBp3, similar to aberrant ER proteins, is translocate to the cytoplasm for degradation. Nuclear accumulation of mutant and wild-type TGBp3:GFP is independent of other PVX proteins and may be another feature of an ERAD pathway

  16. Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations

    International Nuclear Information System (INIS)

    Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and has been used extensively for inducing mutations. In Arabidopsis, two methods for the isolation of genes identified on the basis of mutant phenotypes-genomic subtraction and chromosome walking-either rely on or are greatly facilitated by the availability of these types of mutations. This article gives a detailed characterization of ionizing radiation-induced mutations in plants. The Arabidopsis genes encoding chalcone flavanone isomerase (CHI) and dihydroflavonol 4-reductase (DFR) were cloned and found to correspond to two transparent testa loci. A CHI allele, generated by fast-neutron irradiation, consisted of an inversion within the gene. A 272-bp fragment from 38 centimorgans away on the same chromosome was transferred to one end of this inversion. A DFR allele, induced by x-irradiation, contained two deletions and an inversion of the 2.8-centimorgan intervening region. Sequence analysis of the break points in both mutants indicate that repair of radiation-induced damage involves mechanisms similar or identical to those that mediate the integration of foreign sequences into the genome. The chromosome rearrangements found in these mutants have important implications for the use of ionizing radiation-induced alleles in classical and molecular genetic experiments in plants

  17. Functional and splicing defect analysis of 23 ACVRL1 mutations in a cohort of patients affected by Hereditary Hemorrhagic Telangiectasia.

    Directory of Open Access Journals (Sweden)

    Ferdos Alaa El Din

    Full Text Available Hereditary Hemorrhagic Telangiectasia syndrome (HHT or Rendu-Osler-Weber (ROW syndrome is an autosomal dominant vascular disorder. Two most common forms of HHT, HHT1 and HHT2, have been linked to mutations in the endoglin (ENG and activin receptor-like kinase 1 (ACVRL1or ALK1 genes respectively. This work was designed to examine the pathogenicity of 23 nucleotide variations in ACVRL1 gene detected in more than 400 patients. Among them, 14 missense mutations and one intronic variant were novels, and 8 missense mutations were previously identified with questionable implication in HHT2. The functionality of missense mutations was analyzed in response to BMP9 (specific ligand of ALK1, the maturation of the protein products and their localization were analyzed by western blot and fluorescence microscopy. The splicing impairment of the intronic and of two missense mutations was examined by minigene assay. Functional analysis showed that 18 out of 22 missense mutations were defective. Splicing analysis revealed that one missense mutation (c.733A>G, p.Ile245Val affects the splicing of the harboring exon 6. Similarly, the intronic mutation outside the consensus splicing sites (c.1048+5G>A in intron 7 was seen pathogenic by splicing study. Both mutations induce a frame shift creating a premature stop codon likely resulting in mRNA degradation by NMD surveillance mechanism. Our results confirm the haploinsufficiency model proposed for HHT2. The affected allele of ACVRL1 induces mRNA degradation or the synthesis of a protein lacking the receptor activity. Furthermore, our data demonstrate that functional and splicing analyses together, represent two robust diagnostic tools to be used by geneticists confronted with novel or conflicted ACVRL1 mutations.

  18. ANALYSIS OF CHEMICAL COMPOUNDS OF AGARWOOD OIL FROM DIFFERENT SPECIES BY GAS CHROMATOGRAPHY MASS SPECTROMETRY (GCMS

    Directory of Open Access Journals (Sweden)

    Yumi Zuhanis Has-Yun Hashim

    2014-05-01

    Full Text Available ABSTRACT: Agarwood oil is a highly prized type of oil due to its unique aroma. The oil is extracted from the fragrant resin found in the agarwood tree (trunk.  The unique aroma and quality of agarwood resin and oil are contributed by the presence of certain chemical compounds. In this work, analysis and comparison of the chemical compounds of agarwood oil from A. malaccensis, A. sub-integra and a mixture of both were conducted.  The essential oils were diluted in hexane (5% prior to gas chromatography mass spectrometry (GCMS analysis performed using Agilent GCMS 7890A coupled with MSD quadrupole detector 5975 C.  Separation of analytes by gas chromatography was carried out using a Hewlett Packard HP-5MS silica capillary column (30 m X 0.25 mm X 0.25 mm. A total of 107 compounds were identified from the three samples of agarwood oils. Fifty-five (55 components were identified in A. malaccensis sample which contributes to the largest portion of the total compounds. About 20% of the compounds identified were aromatic and sesquiterpenes which have been revealed to be the main active compounds of agarwood oils which also give the aroma and pleasant odour of agarwood. Different compositions or profile of chemical components were found in agarwood oils from the two different species. Two compounds were commonly identified in all three samples namely 3-phenyl-2-butanone and alpha-cubebene.  Further studies are needed to refine the results which later can be used to assist detection and authentication of agarwood as well as its scientific-based grading. ABSTRAK: Minyak gaharu merupakan sejenis minyak beraroma unik yang mendapat permintaan tinggi dan mahal. Minyak ini diekstrak daripada resin beraroma yang terbentuk di dalam batang pokok gaharu. Keunikan aroma dan kualiti resin dan minyak gaharu ini bergantung kepada kehadiran bahan kimia tertentu. Penyelidikan ini menjurus kepada analisis dan perbandingan bahan-bahan kimia yang terdapat dalam minyak

  19. MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders

    Science.gov (United States)

    Kang, Longli; Zheng, Hong-Xiang; Zhang, Menghan; Yan, Shi; Li, Lei; Liu, Lijun; Liu, Kai; Hu, Kang; Chen, Feng; Ma, Lifeng; Qin, Zhendong; Wang, Yi; Wang, Xiaofeng; Jin, Li

    2016-01-01

    Tibetan highlanders, including Tibetans, Monpas, Lhobas, Dengs and Sherpas, are considered highly adaptive to severe hypoxic environments. Mitochondrial DNA (mtDNA) might be important in hypoxia adaptation given its role in coding core subunits of oxidative phosphorylation. In this study, we employed 549 complete highlander mtDNA sequences (including 432 random samples) to obtain a comprehensive view of highlander mtDNA profile. In the phylogeny of a total of 36,914 sequences, we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya. Through founder analysis, we proposed a three-phase model of colonizing the plateau, i.e., pre-LGM Time (30 kya, 4.68%), post-LGM Paleolithic Time (16.8 kya, 29.31%) and Neolithic Time (after 8 kya, 66.01% in total). We observed that pathogenic mutations occurred far more frequently in 22 highlander-specific lineages (five lineages carrying two pathogenic mutations and six carrying one) than in the 6,857 haplogroups of all the 36,914 sequences (P = 4.87 × 10−8). Furthermore, the number of possible pathogenic mutations carried by highlanders (in average 3.18 ± 1.27) were significantly higher than that in controls (2.82 ± 1.40) (P = 1.89 × 10−4). Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation. PMID:27498855

  20. Counter-current chromatography for oil analysis: retention features and kinetic effects.

    Science.gov (United States)

    Maryutina, Tatyana A; Soin, Alexander V; Katasonova, Olesya N

    2009-05-01

    Application of counter-current chromatography (CCC) for oil analysis has been suggested for the first time. CCC looks very promising as a tool for pre-concentration and isolation of trace elements from oil. Features of stationary phase retention of two-phase liquid systems (oil or oil products-aqueous nitric acid solutions) in CCC have been investigated. The influence of physicochemical properties of crude oil and oil products used as a mobile phase on the volume of stationary phase (acidic aqueous solutions) retained in CCC was studied. Chromatographic behavior of several oil samples was studied. It has been shown that physicochemical properties of test oil influence its chromatographic behavior. Optimal values of density and viscosity (rhocrude oil and oil products that could be analyzed using CCC were estimated. The influence of the column rotational speed and flow rate of mobile phase on the stationary phase retention was also investigated. It is known that kinetic aspects (mass transfer of elements between phases) can play a very important role in selecting an optimal composition of stationary phase for the pre-concentration of elements from oil. The influence of nitric acid concentration in the stationary phase on mass transfer was studied. Kinetic characteristic for trace element recovery has been investigated for the optimization of pre-concentration conditions of trace elements from crude oil and oil products. The extraction recoveries of Zn, Mn, Fe, Ni, V, Cu, Cd, Pb and Ba by CCC in dynamic mode are in the range of 75-95% while they are lower than 35% under batch conditions. PMID:19232415

  1. Liquid chromatography-mass spectrometry analysis of five bisphosphonates in equine urine and plasma.

    Science.gov (United States)

    Wong, April S Y; Ho, Emmie N M; Wan, Terence S M; Lam, Kenneth K H; Stewart, Brian D

    2015-08-15

    Bisphosphonates are used in the management of skeletal disorder in humans and horses, with tiludronic acid being the first licensed veterinary medicine in the treatment of lameness associated with degenerative joint disease. Bisphosphonates are prohibited in horseracing according to Article 6 of the International Agreement on Breeding, Racing and Wagering (published by the International Federation of Horseracing Authorities). In order to control the use of bisphosphonates in equine sports, an effective method to detect the use of bisphosphonates is required. Bisphosphonates are difficult-to-detect drugs due to their hydrophilic properties. The complexity of equine matrices also added to their extraction difficulties. This study describes a method for the simultaneous detection of five bisphosphonates, namely alendronic acid, clodronic acid, ibandronic acid, risedronic acid and tiludronic acid, in equine urine and plasma. Bisphosphonates were first isolated from the sample matrices by solid-phase extractions, followed by methylation with trimethylsilyldiazomethane prior to liquid chromatography - tandem mass spectrometry analysis using selective reaction monitoring in the positive electrospray ionization mode. The five bisphosphonates could be detected at low ppb levels in 0.5mL equine plasma or urine with acceptable precision, fast instrumental turnaround time, and negligible matrix interferences. The method has also been applied to the excretion study of tiludronic acid in plasma and urine collected from a horse having been administered a single dose of tiludronic acid. The applicability and effectiveness of the method was demonstrated by the successful detection and confirmation of the presence of tiludronic acid in an overseas equine urine sample. To our knowledge, this is the first reported method in the successful screening and confirmation of five amino- and non-amino bisphosphonates in equine biological samples. PMID:26143477

  2. Analysis of Some Pesticide Residues in Cauliflower by High Performance Liquid Chromatography

    Directory of Open Access Journals (Sweden)

    Sheheli Islam

    2009-01-01

    Full Text Available Problem statement: Increased use of chemicals on vegetables started gaining momentum and continued its up-trend in Bangladesh. Wide spread use of pesticides in agriculture concern of residue accumulation, which may remain in food and agricultural environment causing concern of human health and risking ecological balance. Attempt made to ensure that their applications were correct and safe and result in no residues in food beyond codex developed maximum residue limits. Approach: This study reported a method based on High Performance Liquid Chromatography (HPLC for determination of pesticide residues used in Cauliflower. Cauliflower sprayed with, 4 different pesticides (diazinon, malathion, chlorpyrifos and cypermethrin at recommended dose and double of recommended dose were analyzed for their residual contents. Samples were collected at same day after application of pesticide. Commercial samples of cauliflowers were collected from different markets of Dhaka city. Reversed-phase HPLC system with UV detection was used for the separation, identification and quantification of all these analytes using acetonitrile-water (70:30, v/v as mobile phase. Results: Limit of detection of 0.02 mg kg-1 was obtained. Calibration curves that constructed for the analytes spiked into samples followed linear relationships with good correlation coefficients (R2>0.990. In the analysis, from vegetables treated with diazinon and chlorpyrifos at recommended and double of recommended doses, residual amounts above respective MRL values were found. Conclusion: Method used permitted the determination of these pesticides in cauliflower at concentration level demanded by current legislation. Attention paid on excess use or abuse of pesticides by judicious application for safety of public health in Bangladesh. Additional data to monitor residues in food and to fill gaps in current knowledge would be helpful in assessing human exposure risks from ingestion of contaminated

  3. Quantitative analysis of antibiotics in aquifer sediments by liquid chromatography coupled to high resolution mass spectrometry.

    Science.gov (United States)

    Tong, Lei; Liu, Hui; Xie, Cong; Li, Minjing

    2016-06-24

    A highly effective analytical method for multi-residue determination of antibiotics in aquifer sediments was first established in this study. Microwave-assisted solvent extraction (MASE) and solid-phase extraction were used for sample pre-concentration and purification, ultra-high performance liquid chromatography coupled to hybrid quadrupole-high resolution Orbitrap mass spectrometry (UHPLC-Q-Orbitrap) was applied for detection. For high resolution mass spectrometry (HRMS), the target compounds were tentatively identified by retention time and accurate mass which was measured with precursor ions in Target-SIM scan, and then confirmed by the monitoring of daughter ion fragments which were generated in dd-MS(2) scan. The results provided good mass accuracy with mass deviations below 2ppm (except norfloxacin with -2.3ppm) for quantitative analysis of the compounds by HRMS. Reasonable recoveries of all analytes were obtained more than 60% (except doxytetracycline) in fortification samples at concentrations higher than 10μgkg(-1). Relative standard deviations of repeatability and inter-day precision were below 21% and 11%. Limits of detection (LOD) ranged from 0.1 to 3.8μgkg(-1), whereas limits of quantification (LOQ) were established between 0.3-9.0μgkg(-1). The method was applied to analyze real aquifer sediment samples in different aquifer depth of 4.0, 7.5, 13.0 and 18.0m. Chlorotetracycline and ofloxacin were observed at relative high concentrations of 53 and 19μgkg(-1) respectively in 18.0m deepness. The exposure to low doses of these compounds in subsurface environment increases concerns on long-term ecological security of underground system. PMID:27215464

  4. Development of Radiochemical Analysis of Uranium Isotopes in Soil Samples with Extraction Chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Myung Ho; Choi, Guk Sik; Cho, Young Hyun; Lee, Chang Woo [KAERI, Daejeon (Korea, Republic of); Lee, Soo Yong [Hanyang Univ., Seoul (Korea, Republic of)

    2001-03-15

    An accurate and rapid analytical technique of uranium isotopes in highly contaminated soil samples was developed and validated by application to the IAEA-Reference samples. For overcoming the demerits of the TBP extraction method, sample materials were decomposited with HNO{sub 3} and HF, and uranium isotopes were purified by an anion exchange resin and a TRU Spec resin. With the extraction chromatography method, the hindrance elements were completely removed from the uranium fraction. The chemical yields with the extraction chromatography method were more 10% higher than those with the TBP extraction method. The concentrations of uranium isotopes in soil samples using the extraction chromatography method were consistent with the reference values reported by the IAEA.

  5. Clinical relevance of sensitive and quantitative STAT3 mutation analysis using next-generation sequencing in T-cell large granular lymphocytic leukemia

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Larsen, Martin; Rewes, Annika; Frederiksen, Henrik; Thomassen, Mads; Møller, Michael Boe

    2014-01-01

    , therefore, represents a promising marker in T-LGL diagnostics. We developed a new quantitative next-generation sequencing assay that allows sensitive analysis of the STAT3 gene. The assay was used to study the utility of STAT3 mutation analysis as a diagnostic tool in T-LGL. The study included 16 T......-LGL patients. A total of 15 mutations, including 2 new mutations (G618R and K658R), were detected in 12 patients (75%), with mutation levels ranging from 2.5% to 45.6% mutation-positive alleles. Next-generation sequencing detected 50% more mutations than Sanger sequencing. Blood samples from 20 healthy blood...... donors all tested negative, thus demonstrating the specificity of the assay. The results also indicated that mutation levels in blood and bone marrow are not systematically different, and next-generation sequencing-based STAT3 mutation analysis represents a sensitive method for monitoring residual...

  6. Mutational analysis of Peroxiredoxin IV: exclusion of a positional candidate for multinodular goitre

    Directory of Open Access Journals (Sweden)

    Bonifazi Emanuela

    2002-07-01

    Full Text Available Abstract Background Multinodular goitre (MNG is a common disorder characterised by an enlargement of the thyroid, occurring as a compensatory response to hormonogenesis impairment. The incidence of MNG is dependent on sex (female:male ratio 5:1 and several reports have documented a genetic basis for the disease. Last year we mapped a MNG locus to chromosome Xp22 in a region containing the peroxiredoxin IV (Prx-IV gene. Since Prx-IV is involved in the removal of H2O2 in thyroid cells, we hypothesize that mutations in Prx-IV gene are involved in pathogenesis of MNG. Methods Four individuals (2 affected, 2 unrelated unaffected were sequenced using automated methods. All individuals were originated from the original three-generation Italian family described in previous studies. A Southern blot analysis using a Prx-IV full-length cDNA as a probe was performed in order to exclude genomic rearrangements and/or intronic mutations. In addition a RT-PCR of PRX-IV was performed in order to investigate expression alterations. Results No causative mutations were found. Two adjacent nucleotide substitutions were detected within introns 1 and 4. These changes were also detected in unaffected individuals, suggesting that they were innocuous polymorphisms. No gross genomic rearrangements and/or restriction fragment alterations were observed on Southern analysis. Finally, using RT-PCR from tissue-specific RNA, no differences of PRX-IV expression-levels were detected between affected and unaffected samples. Conclusions Based on sequence and genomic analysis, Prx-IV is very unlikely to be the MNG2 gene.

  7. The HIVToolbox 2 web system integrates sequence, structure, function and mutation analysis.

    Directory of Open Access Journals (Sweden)

    David P Sargeant

    Full Text Available There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at

  8. Gas chromatography mass spectrometry analysis and in vitro antibacterial activity of essential oil from Trigonella foenum-graecum

    Institute of Scientific and Technical Information of China (English)

    Moniruzzaman; Shahinuzzaman; Ahsanul Haque; Rahima Khatun; Zahira Yaakob

    2015-01-01

    Objective: To evaluate the antibacterial activity of essential oil from Trigonella foenum-graecum seeds powder, and identify the compounds from the extracted oil. Methods: The seeds powder of Trigonella foenum-graecum was subjected to Clevenger extractor. Seven strains of bacteria were used to test antibacterial activity of the extract. The activity against bacteria was tested by disk diffusion method using Whatman No. 1 filter paper. Gas chromatography mass spectrometry analysis was performed with an Agilent7890/5975B-gas chromatography/mass selective detector. Results: The hydrodistillation of seeds powder yielded 0.285%(v/w) of oil. Disk diffu-sion of the oil showed bactericidal activity against both Gram negative and Gram positive bacteria of tasted strains. The inhibition zone ranged from (8 ± 0) mm to (15.0 ± 0.7) mm depending on microbial strains. Gas chromatography mass spectrometry analysis showed 14 different compounds. The total compounds represented 80.96%of the oil. Conclusions: The antibacterial activity is due to the effects of different biological active compounds present in the extract. Identification of the compounds may help to develop new effective antimicrobial agent(s). Further researches on purification, characterization and toxicology of the active compounds are needed.

  9. Analysis of four pentacyclic triterpenoid acids in several bioactive botanicals with gas and liquid chromatography and mass spectrometry detection.

    Science.gov (United States)

    Moldoveanu, Serban C; Scott, Wayne A

    2016-01-01

    Several pentacyclic triterpenoid acids including betulinic, oleanolic, and ursolic acids were reported to have health beneficial properties such as antiviral and anti-inflammatory properties, as well as the capability to inhibit "in vitro" the development of various cancer cell types. For this reason betulinic, oleanolic, and ursolic acids are used as neutraceuticals. For the analysis of the pentacyclic triterpenoid acids in complex plant materials, an improved scheme was developed, involving a qualitative screening using silylation and gas chromatography with mass spectrometry analysis, followed by quantitation using a novel liquid chromatography with tandem mass spectrometry procedure. The use of the two methods provides more reliable information regarding the plant materials with unknown composition. Besides betulinic, oleanolic, and ursolic acids that were analyzed, by this procedure a fourth pentacyclic triterpenoid acid was identified and quantitated that was not previously reported to be present in plants. This acid has been identified as 3β-3-hydroxy-lupa-18,20(29)-dien-28-oic acid. The newly identified acid has a structure as a derivative of lupane, although lupane with a double bond in the 18-position was not previously reported as present in plants. The new liquid chromatography with tandem mass spectrometry procedure developed for this study offers a very low limit of quantitation, excellent precision, and robustness. Rosemary was found to contain the largest levels of pentacyclic triterpenoid acids among all the analyzed botanicals. PMID:26549610

  10. Analysis of glyphosate residues in cereals using liquid chromatography-mass spectrometry (LC-MS/MS)

    DEFF Research Database (Denmark)

    Granby, Kit; Johannesen, S.; Gabrielsen, Martin Vahl

    2003-01-01

    A fast and specific method for the determination of glyphosate in cereals is described. The method is based on extraction with water by ultrasonication. The samples are cleaned up and separated by high-performance liquid chromatography on a polystyrene-based reverse-phase column (clean-up) in...... series with an ion chromatography column (separation) using NaHCO3 as eluent. A micro-membrane suppressor was inserted after the separator column to remove the Na + ions before detection by electrospray ionization mass spectrometry in the negative-ion mode. In MS/MS, mode the following transitions were...

  11. Analysis of hydrosoluble organic chelating agents. Potentialities of capillary electrophoresis and ionic chromatography

    International Nuclear Information System (INIS)

    Capillary electrophoresis and ion exchange chromatography are good techniques for the determination of organic chelating agents as mono or poly-carboxylates. Ion exchange chromatography allows to obtain very high sensitivities (a few μg/L). Capillary electrophoresis generates practically none analytical waste; this technique is then very interesting for nuclear industry. This microanalysis technique has been here carried out for the determination of organic chelating agents in leaching water of an old waste for which an important release rate of radio-toxic metals had been found. Thus, formate and especially acetate ions have been correlated with this unusual behaviour

  12. Gas and liquid chromatography with inductively coupled plasma mass spectrometry detection for environmental speciation analysis — advances and limitations

    Science.gov (United States)

    Szpunar, Joanna; McSheehy, Shona; Połeć, Kasia; Vacchina, Véronique; Mounicou, Sandra; Rodriguez, Isaac; Łobiński, Ryszard

    2000-07-01

    Recent advances in the coupling of gas chromatography (GC) and high performance liquid chromatography (HPLC) with inductively coupled plasma mass spectrometry (ICP MS) and their role in trace element speciation analysis of environmental materials are presented. The discussion is illustrated with three research examples concerning the following topics: (i) development and coupling of multicapillary microcolumn GC with ICP MS for speciation of organotin in sediment and biological tissue samples; (ii) speciation of arsenic in marine algae by size-exclusion-anion-exchange HPLC-ICP MS; and (iii) speciation of cadmium in plant cell cultures by size-exclusion HPLC-ICP MS. Particular attention is paid to the problem of signal identification in ICP MS chromatograms; the potential of electrospray MS/MS for this purpose is highlighted.

  13. Separation of Berberine Hydrochloride and Tetrahydropalmatine and Their Quantitative Analysis with Thin Layer Chromatography Involved with Ionic Liquids

    Directory of Open Access Journals (Sweden)

    Jing Lu

    2015-01-01

    Full Text Available [BMIM]OH was used in mobile and stationary phase of thin layer chromatography (TLC to analyze berberine hydrochloride and tetrahydropalmatine for the first time. Supported imidazole ionic liquid with hydroxide ion on silica gel (SiO2·Im+·OH− was synthesized through simple procedure and characterized by Fourier transform infrared spectroscopy (FT-IR, elemental analysis, and scanning electron microscope (SEM. Moreover, on the plates prepared by SiO2·Im+·OH−, the contents of the above alkaloids in the Chinese patent medicine (CPM of “Stomacheasy” capsule were successfully determined by TLC scanner. The key conditions and chromatographic behaviors were also investigated in detail. According to similar ways, ionic liquids (ILs also can be used in other planar chromatographies in two modes. This study is expected to be helpful in expanding the application of IL and its bonded silica gel in TLC separation field.

  14. Genome Analysis of a Transmissible Lineage of Pseudomonas aeruginosa Reveals Pathoadaptive Mutations and Distinct Evolutionary Paths of Hypermutators

    DEFF Research Database (Denmark)

    Marvig, Rasmus Lykke; Johansen, Helle Krogh; Molin, Søren;

    2013-01-01

    . Here we perform a retrospective study of the DK2 clone type of P. aeruginosa isolated from Danish patients suffering from cystic fibrosis (CF), and analyze the genomes of 55 bacterial isolates collected from 21 infected individuals over 38 years. Our phylogenetic analysis of 8,530 mutations in the DK2...... likelihood to acquire mutations and identify two homopolymer-containing genes preferentially mutated in hypermutators. This homopolymer facilitated differential mutagenesis provides a novel genome-wide perspective on the different evolutionary trajectories of hypermutators, which may help explain their...

  15. Structure of the SLC7A7 Gene and Mutational Analysis of Patients Affected by Lysinuric Protein Intolerance

    OpenAIRE

    Sperandeo, Maria Pia; Bassi, Maria Teresa; Riboni, Mirko; Parenti, Giancarlo; Buoninconti, Anna; Manzoni, Marta; Incerti, Barbara; Larocca, Maria Rosaria; Di Rocco, Maja; Strisciuglio, Pietro; Dianzani, Irma; Parini, Rossella; Candito, Miranda; Endo, Fumio; Ballabio, Andrea

    1999-01-01

    Lysinuric protein intolerance (LPI) is a rare autosomal recessive defect of cationic amino acid transport caused by mutations in the SLC7A7 gene. We report the genomic structure of the gene and the results of the mutational analysis in Italian, Tunisian, and Japanese patients. The SLC7A7 gene consists of 10 exons; sequences of all of the exon-intron boundaries are reported here. All of the mutant alleles were characterized and eight novel mutations were detected, including two missense mutati...

  16. Knowledge-based analysis of functional impacts of mutations in microRNA seed regions

    Indian Academy of Sciences (India)

    Anindya Bhattacharya; Yan Cui

    2015-10-01

    MicroRNAs are a class of important post-transcriptional regulators. Genetic and somatic mutations in miRNAs, especially those in the seed regions, have profound and broad impacts on gene expression and physiological and pathological processes. Over 500 SNPs were mapped to the miRNA seeds, which are located at position 2–8 of the mature miRNA sequences. We found that the central positions of the miRNA seeds contain fewer genetic variants and therefore are more evolutionary conserved than the peripheral positions in the seeds. We developed a knowledge-based method to analyse the functional impacts of mutations in miRNA seed regions. We computed the gene ontology-based similarity score GOSS and the GOSS percentile score for all 517 SNPs in miRNA seeds. In addition to the annotation of SNPs for their functional effects, in the present article we also present a detailed analysis pipeline for finding the key functional changes for seed SNPs. We performed a detailed gene ontology graph-based analysis of enriched functional categories for miRNA target gene sets. In the analysis of a SNP in the seed region of hsa-miR-96 we found that two key biological processes for progressive hearing loss `Neurotrophin TRK receptor signaling pathway' and `Epidermal growth factor receptor signaling pathway' were significantly and differentially enriched by the two sets of allele-specific target genes of miRNA hsa-miR-96.

  17. Genome analysis of a transmissible lineage of pseudomonas aeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators.

    Directory of Open Access Journals (Sweden)

    Rasmus Lykke Marvig

    Full Text Available Genome sequencing of bacterial pathogens has advanced our understanding of their evolution, epidemiology, and response to antibiotic therapy. However, we still have only a limited knowledge of the molecular changes in in vivo evolving bacterial populations in relation to long-term, chronic infections. For example, it remains unclear what genes are mutated to facilitate the establishment of long-term existence in the human host environment, and in which way acquisition of a hypermutator phenotype with enhanced rates of spontaneous mutations influences the evolutionary trajectory of the pathogen. Here we perform a retrospective study of the DK2 clone type of P. aeruginosa isolated from Danish patients suffering from cystic fibrosis (CF, and analyze the genomes of 55 bacterial isolates collected from 21 infected individuals over 38 years. Our phylogenetic analysis of 8,530 mutations in the DK2 genomes shows that the ancestral DK2 clone type spread among CF patients through several independent transmission events. Subsequent to transmission, sub-lineages evolved independently for years in separate hosts, creating a unique possibility to study parallel evolution and identification of genes targeted by mutations to optimize pathogen fitness (pathoadaptive mutations. These genes were related to antibiotic resistance, the cell envelope, or regulatory functions, and we find that the prevalence of pathoadaptive mutations correlates with evolutionary success of co-evolving sub-lineages. The long-term co-existence of both normal and hypermutator populations enabled comparative investigations of the mutation dynamics in homopolymeric sequences in which hypermutators are particularly prone to mutations. We find a positive exponential correlation between the length of the homopolymer and its likelihood to acquire mutations and identify two homopolymer-containing genes preferentially mutated in hypermutators. This homopolymer facilitated differential

  18. Analysis of Y chromosome microdeletions and CFTR gene mutations as genetic markers of infertility in Serbian men

    Directory of Open Access Journals (Sweden)

    Dinić Jelena

    2007-01-01

    Full Text Available Background/Aim. Impaired fertility of a male partner is the main cause of infertility in up to one half of all infertile couples. At the genetic level, male infertility can be caused by chromosome aberrations or gene mutations. The presence and types of Y chromosome microdeletions and cystic fybrosis transmembrane conductance regulator (CFTR gene mutations as genetic cause of male infertility was tested in Serbian men. The aim of this study was to analyze CFTR gene mutations and Y chromosome microdelations as potential causes of male infertility in Serbian patients, as well as to test the hypothesis that CFTR mutations in infertile men are predominantly located in the several last exons of the gene. Methods. This study has encompassed 33 men with oligo- or azoospermia. The screening for Y chromosome microdeletions in the azoospermia factor (AZF region was performed by multiplex PCR analysis. The screening of the CFTR gene was performed by denaturing gradient gel electrophoresis (DGGE method. Results. Deletions on Y chromosome were detected in four patients, predominantly in AZFc region (four of total six deletions. Mutations in the CFTR gene were detected on eight out of 66 analyzed chromosomes of infertile men. The most common mutation was F508del (six of total eight mutations. Conclusion. This study confirmed that both Y chromosome microdeletions and CFTR gene mutations played important role in etiology of male infertility in Serbian infertile men. Genetic testing for Y chromosome microdeletions and CFTR gene mutations has been introduced in routine diagnostics and offered to couples undergoing assisted reproduction techniques. Considering that both the type of Y chromosome microdeletion and the type of CFTR mutation have a prognostic value, it is recommended that AZF and CFTR genotyping should not only be performed in patients with reduced sperm quality before undergoing assisted reproduction, but also for the purpose of preimplantation and

  19. Advancement and application of gas chromatography isotope ratio mass spectrometry techniques for atmospheric trace gas analysis

    Science.gov (United States)

    Giebel, Brian M.

    2011-12-01

    The use of gas chromatography isotope ratio mass spectrometry (GC-IRMS) for compound specific stable isotope analysis is an underutilized technique because of the complexity of the instrumentation and high analytical costs. However stable isotopic data, when coupled with concentration measurements, can provide additional information on a compounds production, transformation, loss, and cycling within the biosphere and atmosphere. A GC-IRMS system was developed to accurately and precisely measure delta13C values for numerous oxygenated volatile organic compounds having natural and anthropogenic sources. The OVOCs include methanol, ethanol, acetone, methyl ethyl ketone, 2-pentanone, and 3-pentanone. Guided by the requirements for analysis of trace components in air, the GC-IRMS system was developed with the goals of increasing sensitivity, reducing dead-volume and peak band broadening, optimizing combustion and water removal, and decreasing the split ratio to the IRMS. The technique relied on a two-stage preconcentration system, a low-volume capillary reactor and water trap, and a balanced reference gas delivery system. Measurements were performed on samples collected from two distinct sources (i.e. biogenic and vehicle emissions) and ambient air collected from downtown Miami and Everglades National Park. However, the instrumentation and the method have the capability to analyze a variety of source and ambient samples. The measured isotopic signatures that were obtained from source and ambient samples provide a new isotopic constraint for atmospheric chemists and can serve as a new way to evaluate their models and budgets for many OVOCs. In almost all cases, OVOCs emitted from fuel combustion were enriched in 13C when compared to the natural emissions of plants. This was particularly true for ethanol gas emitted in vehicle exhaust, which was observed to have a uniquely enriched isotopic signature that was attributed to ethanol's corn origin and use as an alternative

  20. Spectrum of mutations in sarcoglycan genes in the Mumbai region of western India: High prevalence of 525del T

    Directory of Open Access Journals (Sweden)

    Khadilkar Satish

    2009-01-01

    Full Text Available Background : While the clinical and immunocytochemical features of sarcoglycanopathies have been reported from India, genetic aspects have not been studied. There is large variation in the sarcoglycan mutations among the studied populations. Aim : To study the spectrum of mutations in sarcoglycan genes (SG. Materials and Methods : Patients fulfilling Bushby′s criteria for limb girdle muscular dystrophy were prospectively analyzed. Patients gave their medical history and underwent a clinical examination, serum creatine kinase estimation, electrophysiology, muscle biopsy with immunostaining for alpha, beta, gamma, and delta subunits and mutational analysis using denaturing high pressure liquid chromatography and direct sequencing. Results : Mutations in SG accounted for 26.4% of the cohort of limb girdle muscular dystrophy. The mean age of these 18 patients was 22.5 years. Generally, proximal weakness affected the flexor and adductor compartments of the lower and upper limbs. The clinical profile of various mutations was indistinguishable from each other. Gamma SG mutations were most common, seen in 8 patients, followed by delta SG mutation in 5 patients and alpha mutation in 4 patients, while only 1 patient had mutation in the beta sarcoglycan gene. The most prevalent mutation in the gamma SG gene was 525del T. This is of interest as the mutation has been known to exist only in specific populations. Conclusion : This study, the first mutational analysis of Indian patients with sarcoglycanopathies suggests gamma SG mutations were the most common and the most prevalent mutation in the gamma SG gene was 525del T.

  1. Electrochemical detection coupled with high-performance liquid chromatography in pharmaceutical and biomedical analysis: a mini review.

    Science.gov (United States)

    Wang, Chengyin; Xu, Jianyun; Zhou, Guiyou; Qu, Qishu; Yang, Gongjun; Hu, Xiaoya

    2007-08-01

    Recent advances in electrochemical detection techniques coupled with high-performance liquid chromatography (HPLC-ECD) in pharmaceutical and biomedical analysis are reviewed. ECD classification and modes including common amperometric, coulometric, conductimetric, and potentiometric detector, are outlined and the some typical examples of determinations in pharmaceutical and biomedical analysis are described. The electrochemical detection system can offer superior merits over other detectors commonly used with HPLC. These techniques have great potential owing to their prominent characteristics in high-throughput screening procedures of drugs in various matrices. Fundamental 67 references from last 5 years related with a field are cited in this review. PMID:17979637

  2. Mutation analysis of the ERCC4/FANCQ gene in hereditary breast cancer.

    Directory of Open Access Journals (Sweden)

    Sandra Kohlhase

    Full Text Available The ERCC4 protein forms a structure-specific endonuclease involved in the DNA damage response. Different cancer syndromes such as a subtype of Xeroderma pigmentosum, XPF, and recently a subtype of Fanconi Anemia, FA-Q, have been attributed to biallelic ERCC4 gene mutations. To investigate whether monoallelic ERCC4 gene defects play some role in the inherited component of breast cancer susceptibility, we sequenced the whole ERCC4 coding region and flanking untranslated portions in a series of 101 Byelorussian and German breast cancer patients selected for familial disease (set 1, n = 63 or for the presence of the rs1800067 risk haplotype (set 2, n = 38. This study confirmed six known and one novel exonic variants, including four missense substitutions but no truncating mutation. Missense substitution p.R415Q (rs1800067, a previously postulated breast cancer susceptibility allele, was subsequently screened for in a total of 3,698 breast cancer cases and 2,868 controls from Germany, Belarus or Russia. The Gln415 allele appeared protective against breast cancer in the German series, with the strongest effect for ductal histology (OR 0.67; 95%CI 0.49; 0.92; p = 0.003, but this association was not confirmed in the other two series, with the combined analysis yielding an overall Mantel-Haenszel OR of 0.94 (95% CI 0.81; 1.08. There was no significant effect of p.R415Q on breast cancer survival in the German patient series. The other three detected ERCC4 missense mutations included two known rare variants as well as a novel substitution, p.E17V, that we identified on a p.R415Q haplotype background. The p.E17V mutation is predicted to be probably damaging but was present in just one heterozygous patient. We conclude that the contribution of ERCC4/FANCQ coding mutations to hereditary breast cancer in Central and Eastern Europe is likely to be small.

  3. Proteomic Analysis of the Low Mutation Rate of Diploid Male Gametes Induced by Colchicine in Ginkgo biloba L.

    OpenAIRE

    Yang, Nina; Sun, Yuhan; Wang, Yaru; Long, Cui; Li, Yingyue; Li, Yun

    2013-01-01

    Colchicine treatment of G. biloba microsporocytes results in a low mutation rate in the diploid (2n) male gamete. The mutation rate is significantly lower as compared to other tree species and impedes the breeding of new economic varieties. Proteomic analysis was done to identify the proteins that influence the process of 2n gamete formation in G. biloba. The microsporangia of G. biloba were treated with colchicine solution for 48 h and the proteins were analyzed using 2-D gel electrophoresis...

  4. Molecular analysis of point mutations in a barley genome exposed to MNU and gamma rays

    Energy Technology Data Exchange (ETDEWEB)

    Kurowska, Marzena, E-mail: mkurowsk@us.edu.pl [Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice (Poland); Labocha-Pawlowska, Anna; Gnizda, Dominika; Maluszynski, Miroslaw; Szarejko, Iwona [Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice (Poland)

    2012-10-15

    We present studies aimed at determining the types and frequencies of mutations induced in the barley genome after treatment with chemical (N-methyl-N-nitrosourea, MNU) and physical (gamma rays) mutagens. We created M{sub 2} populations of a doubled haploid line and used them for the analysis of mutations in targeted DNA sequences and over an entire barley genome using TILLING (Targeting Induced Local Lesions in Genomes) and AFLP (Amplified Fragment Length Polymorphism) technique, respectively. Based on the TILLING analysis of the total DNA sequence of 4,537,117 bp in the MNU population, the average mutation density was estimated as 1/504 kb. Only one nucleotide change was found after an analysis of 3,207,444 bp derived from the highest dose of gamma rays applied. MNU was clearly a more efficient mutagen than gamma rays in inducing point mutations in barley. The majority (63.6%) of the MNU-induced nucleotide changes were transitions, with a similar number of G > A and C > T substitutions. The similar share of G > A and C > T transitions indicates a lack of bias in the repair of O{sup 6}-methylguanine lesions between DNA strands. There was, however, a strong specificity of the nucleotide surrounding the O{sup 6}-meG at the -1 position. Purines formed 81% of nucleotides observed at the -1 site. Scanning the barley genome with AFLP markers revealed ca. a three times higher level of AFLP polymorphism in MNU-treated as compared to the gamma-irradiated population. In order to check whether AFLP markers can really scan the whole barley genome for mutagen-induced polymorphism, 114 different AFLP products, were cloned and sequenced. 94% of bands were heterogenic, with some bands containing up to 8 different amplicons. The polymorphic AFLP products were characterised in terms of their similarity to the records deposited in a GenBank database. The types of sequences present in the polymorphic bands reflected the organisation of the barley genome.

  5. Molecular analysis of point mutations in a barley genome exposed to MNU and gamma rays

    International Nuclear Information System (INIS)

    We present studies aimed at determining the types and frequencies of mutations induced in the barley genome after treatment with chemical (N-methyl-N-nitrosourea, MNU) and physical (gamma rays) mutagens. We created M2 populations of a doubled haploid line and used them for the analysis of mutations in targeted DNA sequences and over an entire barley genome using TILLING (Targeting Induced Local Lesions in Genomes) and AFLP (Amplified Fragment Length Polymorphism) technique, respectively. Based on the TILLING analysis of the total DNA sequence of 4,537,117 bp in the MNU population, the average mutation density was estimated as 1/504 kb. Only one nucleotide change was found after an analysis of 3,207,444 bp derived from the highest dose of gamma rays applied. MNU was clearly a more efficient mutagen than gamma rays in inducing point mutations in barley. The majority (63.6%) of the MNU-induced nucleotide changes were transitions, with a similar number of G > A and C > T substitutions. The similar share of G > A and C > T transitions indicates a lack of bias in the repair of O6-methylguanine lesions between DNA strands. There was, however, a strong specificity of the nucleotide surrounding the O6-meG at the −1 position. Purines formed 81% of nucleotides observed at the −1 site. Scanning the barley genome with AFLP markers revealed ca. a three times higher level of AFLP polymorphism in MNU-treated as compared to the gamma-irradiated population. In order to check whether AFLP markers can really scan the whole barley genome for mutagen-induced polymorphism, 114 different AFLP products, were cloned and sequenced. 94% of bands were heterogenic, with some bands containing up to 8 different amplicons. The polymorphic AFLP products were characterised in terms of their similarity to the records deposited in a GenBank database. The types of sequences present in the polymorphic bands reflected the organisation of the barley genome.

  6. Cancer mutation screening: Comparison of high-resolution melt analysis between two platforms.

    Science.gov (United States)

    Ebili, Henry O; Ilyas, Mohammad

    2015-01-01

    High-resolution melt analysis (HRMA) is a cheap and reliable post-polymerase chain reaction (PCR) cancer mutation screening technique, which is fast gaining clinical relevance. The HRMA capabilities of the LightScanner (Idaho Technology) have been severally studied. However, the ABI 7500 HRM has not been tested against the purpose-built HRM instrument such as the LightScanner. DNA from formalin-fixed, paraffin-embedded gastric cancer, colorectal cancer, and normal tissue as well as from colorectal cancer cell lines were amplified at exons 2, 3, and 4 of KRAS, and at exons 11 and 15 of BRAF in the ABI 7500 fast real-time PCR machine and subjected to melting both on the ABI and on the LightScanner. HRMA data were analysed with the ABI HRM software v2.0.1 and the LightScanner Call-IT 2.5. We tested the ABI 7500 HRM for internal precision, accuracy, sensitivity, and specificity at mutation screening relative to the LightScanner, using crude percentage concordance, kappa statistics, and the area under the receiver operator characteristics (AUROC) curve on SPSS version 19. The results show that the ABI 7500 HRMA has a high internal precision, and excellent concordance, sensitivity, and specificity at mutation screening compared with the LightScanner. However, in contrast to the LightScanner HRM software analysis, the ABI HRM software v.2.0.1, cannot distinguish real from certain pseudovariations in PCR amplicons that are sometimes brought about by the artefacts of the melting process. In conclusion, the ABI HRM has a comparable performance level with the LightScanner, although in certain respects mentioned previously, the LightScanner has an edge over the ABI. PMID:25932046

  7. Predicting the effect of missense mutations on protein function: analysis with Bayesian networks

    Directory of Open Access Journals (Sweden)

    Care Matthew A

    2006-09-01

    Full Text Available Abstract Background A number of methods that use both protein structural and evolutionary information are available to predict the functional consequences of missense mutations. However, many of these methods break down if either one of the two types of data are missing. Furthermore, there is a lack of rigorous assessment of how important the different factors are to prediction. Results Here we use Bayesian networks to predict whether or not a missense mutation will affect the function of the protein. Bayesian networks provide a concise representation for inferring models from data, and are known to generalise well to new data. More importantly, they can handle the noisy, incomplete and uncertain nature of biological data. Our Bayesian network achieved comparable performance with previous machine learning methods. The predictive performance of learned model structures was no better than a naïve Bayes classifier. However, analysis of the posterior distribution of model structures allows biologically meaningful interpretation of relationships between the input variables. Conclusion The ability of the Bayesian network to make predictions when only structural or evolutionary data was observed allowed us to conclude that structural information is a significantly better predictor of the functional consequences of a missense mutation than evolutionary information, for the dataset used. Analysis of the posterior distribution of model structures revealed that the top three strongest connections with the class node all involved structural nodes. With this in mind, we derived a simplified Bayesian network that used just these three structural descriptors, with comparable performance to that of an all node network.

  8. Analysis of Currently Available Analgesic Tablets by Modern Liquid Chromatography: An Undergraduate Laboratory Introduction to HPLC.

    Science.gov (United States)

    Kagel, R. A.; Farwell, S. O.

    1983-01-01

    Background information, procedures, and results, are provided for an undergraduate experiment in which analgesic tablets are analyzed using liquid chromatography. The experiment, an improved, modified version of the Waters Associates Inc. experiment, is simple to prepare, requiring little glassware and minimal sample manipulation by students. (JN)

  9. Analysis of Peppermint Leaf and Spearmint Leaf Extracts by Thin-Layer Chromatography

    Science.gov (United States)

    Pelter, Libbie S. W.; Amico, Andrea; Gordon, Natalie; Martin, Chylah; Sandifer, Dessalyn; Pelter, Michael W.

    2008-01-01

    In this inquiry-based activity, the usefulness of thin-layer chromatography (TLC) to visualize the difference between spearmint and peppermint is explored. The experiment may be used in any class where TLC is discussed from high school to college. We have used this activity with science majors in an organic chemistry laboratory, with non-science…

  10. Gas Chromatography/mass Spectrometry Analysis of Exhaled Leukotrienes in Asthmatic Patients

    Czech Academy of Sciences Publication Activity Database

    Čáp, P.; Chládek, J.; Pehal, F.; Malý, Marek; Petrů, V.; Barnes, P.J.; Montuschi, P.

    2004-01-01

    Roč. 59, č. 6 (2004), s. 465-470. ISSN 0040-6376 Source of funding: V - iné verejné zdroje Keywords : asthma * breath condensate * gas chromatography/mass spectrometry * leukotrienes Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 5.040, year: 2004

  11. Simultaneous analysis of small organic acids and humic acids using high performance size exclusion chromatography

    NARCIS (Netherlands)

    Qin, X.P.; Liu, F.; Wang, G.C.; Weng, L.P.

    2012-01-01

    An accurate and fast method for simultaneous determination of small organic acids and much larger humic acids was developed using high performance size exclusion chromatography. Two small organic acids, i.e. salicylic acid and 2,3-dihydroxybenzoic acid, and one purified humic acid material were used

  12. Analysis of organochlorine compounds in effluents from bleacheries by neutron activation analysis and gas chromatography/mass spectrometry

    International Nuclear Information System (INIS)

    Effluents from chlorine bleacheries in a sulfite and a sulfate paper plant have been investigated. The total amounts of nonpolar and phenolic organohalogenated compounds have been determined by neutron activation analysis. In the sulfate plant nonpolar (cyclohexane extractable) and phenolic (butyl acetate extractable) chlorinated compounds are present in concentrations of 0.36 and 1.7 ppm, respectively. In the sulfite plant both chlorinated and brominated compounds are present in average concentrations of 0.67 ppm Cl and 0.06 ppm Br for nonpolar compounds and 1.1 ppm Cl and 0.1 ppm Br for phenolic compounds. The occurrence of organobromine compounds in the sulfite plant is due to the use of seawater in the first chlorination step. The effluents have also been analysed by gas chromatography/mass spectrometry, and a number of halogenated aromatic hydrocarbons have been identified. These include chloro-p-methylisopropylbenzene (2 isomers), dichloro-p-methylisopropylbenzene (2 isomers), bromo-p-methylisopropylbenzene, chloro-p-methylisopropenylbenzene (2 isomers) and dichloro-p-methylisopropenylbenzene (2 isomers). These compounds are presumably formed by substitution reactions of the parent molecules which are formed by the cooking of the terpenes naturally present in wood. (author)

  13. Advances in Application of Chromatography and Chromatography- Mass Spectrometry in Analysis of Traditional Chinese Medicine%色谱及色谱-质谱联用技术在中药分析中的应用进展

    Institute of Scientific and Technical Information of China (English)

    张晶; 杨海龙; 臧恒昌

    2013-01-01

    The advances in the application of chromatography and chromatography- mass spectrometry in the analysis of traditional Chinese medicine (TCM) are reviewed in this paper. Characteristics, range of application and research status of each method are elaborated, which aim to provide reference for TCM researchers.%  对色谱及其质谱联用技术在中药领域的应用进展做一综述,阐述了各方法的特点、应用范围及研究现状,旨在为中药研究工作者提供参考依据。

  14. Mutational analysis of root characters in food plants. Proceedings of a final research coordination meeting

    International Nuclear Information System (INIS)

    Efficient exploration for water and nutrient uptake from the soil is achieved by adaptation of root architecture, plasticity of root construction, specialized root structures, root physiological responses and beneficial relationships with microorganisms. Roots may also serve as storage organs for carbohydrates and as perennial structures that last for many years. Historically, the genetic analysis of root traits has been neglected, largely because of the difficulty in accessing this below ground organ. Consequently, few characterised root mutants of crop plants are available. The scarcity of root mutants has resulted in the inability to evaluate specific root traits in breeding programmes. This Coordinated Research Project (CRP) on Mutational Analysis of Root Characters in Annual Food Plants Related to Plant Performance was initiated in 1999, with the objective of assisting Member States in the application of mutation techniques and related biotechnologies to generate and utilise mutants for the identification of root properties and genes for improving productivity and sustainability of crop plants. Mutational analysis results obtained over the five year life span of the CRP have shown that changes in root architecture are correlated with crop plant response to stress. Some of the major outputs of the CRP have been the development and genetic analysis of new germplasm and populations in various crops and the development of new methods for phenotyping root architecture. Furthermore, mutants for root traits have been used in the production of new cultivars suitable for stressed environments and new specific root mutations provided a means to identify genes important for root traits. Moreover, new research collaborations have been formed and a consortium, 'Crops Root Research', was established (http://www.crop-roots.org), which extends the collaborative scientific network created by this CRP. Plant research is entering a new era that will permit the use of functional

  15. Targeted ultradeep next-generation sequencing as a method for KIT D816V mutation analysis in mastocytosis

    DEFF Research Database (Denmark)

    Kielsgaard Kristensen, Thomas; Broesby-Olsen, Sigurd; Vestergaard, Hanne;

    2016-01-01

    mutation levels. In this study, we established an NGS-based KIT mutation analysis and analyzed the sensitivity of D816V detection using the Ion Torrent platform. Eighty-two individual NGS analyses were included in the study. All samples were also analyzed using highly sensitive KIT D816V mutation...

  16. Quantitative analysis of arbutin and hydroquinone in strawberry tree (Arbutus unedo L., Ericaceae) leaves by gas chromatography-mass spectrometry.

    Science.gov (United States)

    Jurica, Karlo; Karačonji, Irena Brčić; Šegan, Sandra; Opsenica, Dušanka Milojković; Kremer, Dario

    2015-09-01

    The phenolic glycoside arbutin and its metabolite with uroantiseptic activity hydroquinone occur naturally in the leaves of various medicinal plants and spices. In this study, an extraction procedure coupled with gas chromatography-mass spectrometry (GC-MS) was developed to determine arbutin and hydroquinone content in strawberry tree (Arbutus unedo L., Ericaceae) leaves. The method showed good linearity (R2>0.9987) in the tested concentration range (0.5-200 μg mL(-1)), as well as good precision (RSDarbutin and hydroquinone, respectively). The results obtained by the validated GC-MS method corresponded well to those obtained by high performance liquid chromatography (HPLC) method. The proposed method was then applied for determining arbutin and hydroquinone content in methanolic leaf extracts. The amount of arbutin in the leaves collected on the island of Koločep (6.82 mg g(-1) dry weight) was found to be higher (tpaired=43.57, tc=2.92) in comparison to the amount of arbutin in the leaves collected on the island of Mali Lošinj (2.75 mg g(-1) dry weight). Hydroquinone was not detected in any of the samples. The analytical features of the proposed GC-MS method demonstrated that arbutin and hydroquinone could be determined alternatively by gas chromatography. Due to its wide concentration range, the method could also be suitable for arbutin and hydroquinone analysis in leaves of other plant families (Rosaceae, Lamiaceae, etc.). PMID:26444340

  17. FBN1 mutation in Chinese patients with Marfan syndrome and its gene diagnosis using haplotype linkage analysis

    Institute of Scientific and Technical Information of China (English)

    王冰; 胡冬煦; 夏家辉; 李崎; 杨进福; 吕国华

    2003-01-01

    Objectives To analyze the FBN1 mutations in Chinese patients with Marfan syndrome (MFS) and to make a genetic diagnosis based on haplotype linkage analysis for MFS. Methods Nine MFS families (17 patients) were analyzed with single strand conformation polymorphism (SSCP) and sequencing. Four primers were designed for the flanking sequences of FBN1 gene and used for haplotype-segregation analysis of MFS (B).Conclusion The combination of mutation detection and chromosome haplotype analysis can provide better evidence for a genetic diagnosis of MFS.

  18. Immunohistochemical Determination of p53 Protein Overexpression for Predicting p53 Gene Mutations in Hepatocellular Carcinoma: A Meta-Analysis

    Science.gov (United States)

    Deng, Miao; Liu, Dechun; Ma, Qingyong; Feng, Xiaoshan

    2016-01-01

    Background Whether increased expression of the tumor suppressor protein p53 indicates a p53 gene mutation in hepatocellular carcinoma (HCC) remains unclear. We conducted a meta-analysis to determine whether p53 protein overexpression detected by immunohistochemistry (IHC) offers a diagnostic prediction for p53 gene mutations in HCC patients. Methods Systematic literature searches were conducted with an end date of December 2015. A meta-analysis was performed to estimate the diagnostic accuracy of IHC-determined p53 protein overexpression in the prediction of p53 gene mutations in HCC. Sensitivity, subgroup, and publication bias analyses were also conducted. Results Thirty-six studies were included in the meta-analysis. The results showed that the overall sensitivity and specificity for IHC-determined p53 overexpression in the diagnostic prediction of p53 mutations in HCC were 0.83 (95% CI: 0.80–0.86) and 0.74 (95% CI: 0.71–0.76), respectively. The summary positive likelihood ratio (PLR) and negative likelihood ratio (NLR) were 2.65 (95% CI: 2.21–3.18) and 0.36 (95% CI: 0.26–0.50), respectively. The diagnostic odds ratio (DOR) of IHC-determined p53 overexpression in predicting p53 mutations ranged from 0.56 to 105.00 (pooled, 9.77; 95% CI: 6.35–15.02), with significant heterogeneity between the included studies (I2 = 40.7%, P = 0.0067). Moreover, subgroup and sensitivity analyses did not alter the results of the meta-analysis. However, potential publication bias was present in the current meta-analysis. Conclusion The upregulation of the tumor suppressor protein p53 was indeed linked to p53 gene mutations. IHC determination of p53 overexpression can predict p53 gene mutations in HCC patients. PMID:27428001

  19. Multiclass mycotoxin analysis in food, environmental and biological matrices with chromatography/mass spectrometry.

    Science.gov (United States)

    Capriotti, Anna Laura; Caruso, Giuseppe; Cavaliere, Chiara; Foglia, Patrizia; Samperi, Roberto; Laganà, Aldo

    2012-01-01

    Mold metabolites that can elicit deleterious effects on other organisms are classified as mycotoxins. Human exposure to mycotoxins occurs mostly through the intake of contaminated agricultural products or residues due to carry over or metabolite products in foods of animal origin such as milk and eggs, but can also occur by dermal contact and inhalation. Mycotoxins contained in moldy foods, but also in damp interiors, can cause diseases in humans and animals. Nephropathy, various types of cancer, alimentary toxic aleukia, hepatic diseases, various hemorrhagic syndromes, and immune and neurological disorders are the most common diseases that can be related to mycotoxicosis. The absence or presence of mold infestation and its propagation are seldom correlated with mycotoxin presence. Mycotoxins must be determined directly, and suitable analytical methods are necessary. Hundreds of mycotoxins have been recognized, but only for a few of them, and in a restricted number of utilities, a maximum acceptable level has been regulated by law. However, mycotoxins seldom develop alone; more often various types and/or classes form in the same substrate. The co-occurrence might render the individual mycotoxin tolerance dose irrelevant, and therefore the mere presence of multiple mycotoxins should be considered a risk factor. The advantage of chromatography/mass spectrometry (MS) is that many compounds can be determined and confirmed in one analysis. This review illustrates the state-of-the-art of mycotoxin MS-based analytical methods for multiclass, multianalyte determination in all the matrices in which they appear. A chapter is devoted to the history of the long-standing coexistence and interaction among humans, domestic animals and mycotoxicosis, and the history of the discovery of mycotoxins. Quality assurance, although this topic relates to analytical chemistry in general, has been also examined for mycotoxin analysis as a preliminary to the systematic literature excursus

  20. Intra-familiar discordant PKU phenotype explained by mutation analysis in three pedigrees.

    Science.gov (United States)

    Trunzo, Roberta; Santacroce, Rosa; D'Andrea, Giovanna; Longo, Vittoria; De Girolamo, Giuseppe; Dimatteo, Claudia; Leccese, Angelica; Lillo, Vincenza; Papadia, Francesco; Margaglione, Maurizio

    2014-02-01

    Classical phenylketonuria (PKU) and mild hyperphenylalaninemia (MHP) are two phenotypes of phenylalanine hydroxylase (PAH) deficiency with different degrees of severity. We have analyzed three families in which classical PKU, MHP and a normal phenotype occurred within each family due to the different combinations of three mutations segregating within the family. Indeed, sequence PAH analysis revealed three different alleles segregating in each family. This report suggests that when discordant phenotypes occur in a family, complete analysis of the PAH gene may be performed in order to support the diagnosis and assist in accurate genetic counseling and patient management. We further support the marked heterogeneity of hyperphenylalaninemia primarily due to allelic heterogeneity at the PAH locus. PMID:24296287

  1. Application Of Dexamethasone Analysis Procedure In Pharmaceutical Product And Food Samples By Using The Liquid Chromatography Mass Spectrometry (LC-MS)

    International Nuclear Information System (INIS)

    The high pressure liquid chromatography mass spectrometry method for determination of dexamethasone has been studied. The authors have some results in found the optimal conditions in high pressure liquid chromatography mass spectrometry system for applications analysis of dexamethasone such as flow rate 0.5 ml/minute, the rate of mobile phase ACN: 0.1% HCOOH (80:20), injection volume was 20 μl. Besides, the authors analyzed a number of experimental samples with recovery range 84-96%. These initial results give the high pressure liquid chromatography mass spectrometry in operation. (author)

  2. Mutational and haplotype analysis of the {alpha}{sub 1} subunit of the glycine receptor in hyperekplexia patients

    Energy Technology Data Exchange (ETDEWEB)

    Shiang, R.; Zhu, Y.Z.; Wasmuth, J.J. [Univ. of California, Irivne, CA (United States)] [and others

    1994-09-01

    Familial hyperekplexia or Startle disease (STHE) is a rare autosomal dominant neurologic disorder manifested by marked muscular hypertonia in infants and exaggerated startle response that persists throughout the lifetime of the patient. This disorder is caused by mutations in the {alpha}{sub 1} subunit of the receptor for the inhibitory neurotransmitter glycine (GLRA1). Previously, we have reported three mutations, two of which change arginine 271 (Arg 271) to uncharged amino acids and a third which changes a tyrosine at amino acid 279 to a cysteine. The most common mutation, detected in three of six original families, is a G to A transition mutation at Arg 271. Four new STHE patients have been screened and were found to have the most common Arg 271 mutation. Three of the new patients have a clear family history while family information on the fourth patient was unavailable. Four possible sporadic cases of STHE have been screened by DGGE in all exons of the GLRA1 gene and no mutations have been detected. These sporadic cases may represent defects from other causes. A new three-allele dinucleotide repeat polymorphism at the GLRA1 locus has been detected. Haplotype analysis of two polymorphisms at the GLRA1 locus and CA-repeat polymorphism, D5S119, suggests that the most common mutation arose at least two and most likely three independent times. Thus, it appears that at least five independent GLRA1 mutation events (two of which are identical) have occurred in ten STHE families. The fact that these mutations affect only two amino acids suggests that the dominant STHE phenotype can only be caused by abnormalities in a highly restricted region of GLRA1.

  3. Selected AGXT gene mutations analysis provides a genetic diagnosis in 28% of Tunisian patients with primary hyperoxaluria

    Directory of Open Access Journals (Sweden)

    Achour Abdellatif

    2011-05-01

    Full Text Available Abstract Background Primary hyperoxaluria type I (PH1 is a rare genetic disorder characterized by allelic and clinical heterogeneity. Four mutations (G170R, 33_34insC, I244T and F152I account for more than 50% of PH1 alleles and form the basis for diagnostic genetic screening for PH1. We aimed to analyze the prevalence of these specific mutations causing PH1, and to provide an accurate tool for diagnosis of presymptomatic patients as well as for prenatal diagnosis in the affected families. Methods Polymerase chain reaction/Restriction Fragment Length Polymorphism, were used to detect the four mutations in the AGXT gene in DNA samples from 57 patients belonging to 40 families. Results Two mutations causing PH1 were detected in 24 patients (42.1%, with a predominance of the I244T mutation (68% of patients and 33_34insC (in the remaining 32%. In 92% of cases, mutated alleles were in homozygous state. The presented clinical features were similar for the two mutations. The age of onset was heterogeneous with a higher frequency of the pediatric age. In 58.3% of cases, the presentation corresponded to advanced renal disease which occurred early ( Conclusion Limited mutation analysis can provide a useful first line investigation for PH1. I244T and 33_34insC presented 28.2% of identified mutations causing disease in our cohort. This identification could provide an accurate tool for prenatal diagnosis in the affected families, for genetic counselling and for detection of presymptomatic individuals.

  4. Thin-layer chromatography and colorimetric analysis of multi-component explosive mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Pagoria, Philip F.; Mitchell, Alexander R.; Whipple, Richard E.; Carman, M. Leslie

    2014-08-26

    A thin-layer chromatography method for detection and identification of common military and peroxide explosives in samples includes the steps of provide a reverse-phase thin-layer chromatography plate; prepare the plate by marking spots on which to deposit the samples by touching the plate with a marker; spot one micro liter of a first standard onto one of the spots, spot one micro liter of a second standard onto another of the spots, and spot samples onto other of spots producing a spotted plate; add eluent to a developing chamber; add the spotted plate to the developing chamber; remove the spotted plate from the developing chamber producing a developed plate; place the developed plate in an ultraviolet light box; add a visualization agent to a dip tank; dip the developed plate in the dip tank and remove the developed plate quickly; and detect explosives by viewing said developed plate.

  5. Analysis of oak tannins by liquid chromatography-electrospray ionisation mass spectrometry.

    Science.gov (United States)

    Mämmelä, P; Savolainen, H; Lindroos, L; Kangas, J; Vartiainen, T

    2000-09-01

    Extractable tannins were analysed by liquid chromatography-electrospray ionisation mass spectrometry in two oak species, North American white oak (Quercus alba) and European red oak (Quercus robur). They mainly included various glucose gallic and ellagic acid esters. The structures were partially determined, and they included grandinin/roburin E, castalagin/vescalagin, gallic acid, valoneic acid bilactone, monogalloyl glucose, digalloyl glucose, trigalloyl glucose, ellagic acid rhamnose, quercitrin and ellagic acid. PMID:10999626

  6. Analysis of Volatile Compounds of Malaysian Tualang (Koompassia Excelsa) Honey Using Gas Chromatography Mass Spectrometry

    OpenAIRE

    Nurul Syazana, MS; Gan, SH; Halim, AS; Shah, Nurul Syazana Mohamad; Gan, Siew Hua; Sukari, Halim Ahmad

    2012-01-01

    The constituents of honey's volatile compounds depend on the nectar source and differ depending on the place of origin. To date, the volatile constituents of Tualang honey have never been investigated. The objective of this study was to analyze the volatile compounds in local Malaysian Tualang honey. A continuous extraction of Tualang honey using five organic solvents was carried out starting from non-polar to polar solvents and the extracted samples were analysed using gas chromatography-mas...

  7. High-performance liquid chromatography analysis of plant saponins: An update 2005-2010

    OpenAIRE

    Jagmohan S Negi; Pramod Singh; Geeta Joshi Nee Pant; Rawat, M. S. M.

    2011-01-01

    Saponins are widely distributed in plant kingdom. In view of their wide range of biological activities and occurrence as complex mixtures, saponins have been purified and separated by high-performance liquid chromatography using reverse-phase columns at lower wavelength. Mostly, saponins are not detected by ultraviolet detector due to lack of chromophores. Electrospray ionization mass spectrometry, diode array detector , evaporative light scattering detection, and charged aerosols have been u...

  8. Quantitative analysis of cytokinins in plants by liquid chromatography single-quadrupole mass spectrometry

    Czech Academy of Sciences Publication Activity Database

    Novák, Ondřej; Tarkowski, Petr; Tarkowská, Danuše; Doležal, Karel; Lenobel, René; Strnad, Miroslav

    2003-01-01

    Roč. 480, č. 2 (2003), s. 207ů218. ISSN 0003-2670 R&D Projects: GA ČR GA522/01/0275 Grant ostatní: Volkswagen Stiftung(DE) I/76 865 Institutional research plan: CEZ:AV0Z5038910; CEZ:MSM 153100008 Keywords : Liquid chromatography mass spectrometry * Cytokinins Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.210, year: 2003

  9. Gas Chromatography/Electron Ionization Mass Spectrometric Analysis of Oligomeric Polyethylene Glycol Mono Alkyl Ethers

    OpenAIRE

    Adebayo O. Onigbinde; Burnaby Munson; Bamidele M.W. Amos-tautua

    2013-01-01

    Polyethylene Glycol Monoalkyl Ethers, CxH2x+1 (OC2H4)n OH, (PEGMAE), are polar compounds like Polyethylene Glycols (PEG) and they undergo microbial degradation which produces toxic substances that are potentially dangerous to the environment. Therefore, the purpose of this study is to carry out proper identification and characterization of these compounds. The Electron Ionization (EI) and Chemical Ionization (CI) spectra of various PEGMAE were obtained by Gas Chromatography/Mass Spectrometry ...

  10. Perchloroethylene Analysis by Chemical Oxidation and Determination of Intermediate Products by Gas Chromatography, Mass Spectrometry

    OpenAIRE

    Sadeghi, M. (PhD; Naddafi, K. (PhD; Nabizadeh, R. (PhD

    2014-01-01

    Background and Objective: Perchloroethylene (PCE) is a chlorinated hydrocarbon used as a solvent in many industrial processes. In contaminated water and soil a great deal of PCE is found. This study aimed to determine the rate of decomposition of PCE occurred after advanced oxidation. Material and Methods: In this descriptive-analytic study conducted (2011) in public health faculty of Tehran University of medical sciences, gas chromatographic was used to measure PCE and gas chromatography - m...

  11. Epidermal Growth Factor Receptor (EGFR) mutation analysis, gene expression profiling and EGFR protein expression in primary prostate cancer

    International Nuclear Information System (INIS)

    Activating mutations of the epidermal growth factor receptor (EGFR) confer sensitivity to the tyrosine kinase inhibitors (TKi), gefitinib and erlotinib. We analysed EGFR expression, EGFR mutation status and gene expression profiles of prostate cancer (PC) to supply a rationale for EGFR targeted therapies in this disease. Mutational analysis of EGFR TK domain (exons from 18 to 21) and immunohistochemistry for EGFR were performed on tumour tissues derived from radical prostatectomy from 100 PC patients. Gene expression profiling using oligo-microarrays was also carried out in 51 of the PC samples. EGFR protein overexpression (EGFRhigh) was found in 36% of the tumour samples, and mutations were found in 13% of samples. Patients with EGFRhigh tumours experienced a significantly increased risk of biochemical relapse (hazard ratio-HR 2.52, p=0.02) compared with patients with tumours expressing low levels of EGFR (EGFRlow). Microarray analysis did not reveal any differences in gene expression between EGFRhigh and EGFRlow tumours. Conversely, in EGFRhigh tumours, we were able to identify a 79 gene signature distinguishing mutated from non-mutated tumours. Additionally, 29 genes were found to be differentially expressed between mutated/EGFRhigh (n=3) and mutated/EGFRlow tumours (n=5). Four of the down-regulated genes, U19/EAF2, ABCC4, KLK3 and ANXA3 and one of the up-regulated genes, FOXC1, are involved in PC progression. Based on our findings, we hypothesize that accurate definition of the EGFR status could improve prognostic stratification and we suggest a possible role for EGFR-directed therapies in PC patients. Having been generated in a relatively small sample of patients, our results warrant confirmation in larger series

  12. The prognostic value of BRAF mutation in colorectal cancer and melanoma: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Gholamreza Safaee Ardekani

    Full Text Available BACKGROUND: Mutation of BRAF is a predominant event in cancers with poor prognosis such as melanoma and colorectal cancer. BRAF mutation leads to a constitutive activation of mitogen activated protein kinase pathway which is essential for cell proliferation and tumor progression. Despite tremendous efforts made to target BRAF for cancer treatment, the correlation between BRAF mutation and patient survival is still a matter of controversy. METHODS/PRINCIPAL FINDINGS: Clinical studies on the correlation between BRAF mutation and patient survival were retrieved from MEDLINE and EMBASE databases between June 2002 and December 2011. One hundred twenty relevant full text studies were categorized based on study design and cancer type. Publication bias was evaluated for each category and pooled hazard ratio (HR with 95% confidence interval (CI was calculated using random or fixed effect meta-analysis based on the percentage of heterogeneity. Twenty six studies on colorectal cancer (11,773 patients and four studies on melanoma (674 patients were included in our final meta-analysis. The average prevalence of BRAF mutation was 9.6% in colorectal cancer, and 47.8% in melanoma reports. We found that BRAF mutation increases the risk of mortality in colorectal cancer patients for more than two times; HR = 2.25 (95% CI, 1.82-2.83. In addition, we revealed that BRAF mutation also increases the risk of mortality in melanoma patients by 1.7 times (95% CI, 1.37-2.12. CONCLUSIONS: We revealed that BRAF mutation is an absolute risk factor for patient survival in colorectal cancer and melanoma.

  13. Methods of analysis-Determination of pesticides in sediment using gas chromatography/mass spectrometry

    Science.gov (United States)

    Hladik, Michelle L.; McWayne, Megan M.

    2012-01-01

    A method for the determination of 119 pesticides in environmental sediment samples is described. The method was developed by the U.S. Geological Survey (USGS) in support of the National Water Quality Assessment (NAWQA) Program. The pesticides included in this method were chosen through prior prioritization. Herbicides, insecticides, and fungicides along with degradates are included in this method and span a variety of chemical classes including, but not limited to, chloroacetanilides, organochlorines, organophosphates, pyrethroids, triazines, and triazoles. Sediment samples are extracted by using an accelerated solvent extraction system (ASE®, and the compounds of interest are separated from co-extracted matrix interferences (including sulfur) by passing the extracts through high performance liquid chromatography (HPLC) with gel-permeation chromatography (GPC) along with the use of either stacked graphitized carbon and alumina solid-phase extraction (SPE) cartridges or packed Florisil®. Chromatographic separation, detection, and quantification of the pesticides from the sediment-sample extracts are done by using gas chromatography with mass spectrometry (GC/MS). Recoveries in test sediment samples fortified at 10 micrograms per kilogram (μg/kg) dry weight ranged from 75 to 102 percent; relative standard deviations ranged from 3 to 13 percent. Method detection limits (MDLs), calculated by using U.S. Environmental Protection Agency procedures (40 CFR 136, Appendix B), ranged from 0.6 to 3.4 μg/kg dry weight.

  14. Analysis of benzene, toluene, ethylbenzene and xylenes in soils by headspace and gas chromatography/flame ionization detector

    Directory of Open Access Journals (Sweden)

    Jurandir Pereira Pinto

    2006-02-01

    Full Text Available The constituents of gasoline: benzene, toluene, ethylbenzene and xylenes (BTEX are frequently found in soils due to leaks in fuel storage tanks and they present chronic toxicity. In this work it was developed and validated a methodology of BTEX analysis in soil by gas chromatography/ flame ionization detector and static headspace. The recovery of BTEX in soil samples was evaluated using soils with different textures (sandy and loamy. The analysis method showed good resolution, in a low time of analysis (less than 30 minutes. Limits of quantification of 0.05 mg Kg¯¹ soil for benzene, toluene, ethylbenzene and xylenes are below the guiding values that range from 0.15 to 95 mg Kg¯¹ soil, established to determine soil quality. It was verified that the methodology enables the use of this method for BTEX analysis of soil samples for passive environmental identification of gas stations.

  15. Analysis of benomyl by liquid chromatography/time-of-flight mass spectrometer and its occurrence in the environment

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Yong Chan; Kim, Kee D. [Sangji Univ., Wonju (Korea, Republic of); Kim, Nack Joo [Seoul National Univ., Seoul (Korea, Republic of)

    2002-03-01

    Benomyl, one of the known endocrine disrupting chemicals, was analyzed to understand the fate in the nature. Water, sediment and biota samples are acidified to hydrolyze benomyl into carbendazim then followed by extraction and concentration. The concentrations of carbendazim in the samples were determined by liquid chromatography/time-of-flight mass spectrometer. Analysis data showed that certain amount of carbendazim was accumulated in sediment. On the contrary, no sign of accumulation in biota was observed probably due to the increased degradation rate in vivo. It is , however, that no one can claim carbendazim is not harmful to biota, since carbendazim may give a negative effect against organisms at the point of intaking.

  16. Air quality status in Kinshasa as determined by instrumental neutron activation analysis, atomic absorption spectrometry and ion-exchange chromatography

    International Nuclear Information System (INIS)

    Three independent analytical techniques - instrumental neutron activation analysis. Atomic absorption spectrometry and ion-exchange chromatography - were applied to airborne particulate collected on filters and to atmospheric acid gases collected in carbonate buffer solutions. 20 trace elements and 7 acid gases and acid aerosols were determined. Results were compared with those observed elsewhere and showed that air pollution is low in Kinshasa and does not give rise to anxieties. The main known sources of pollutants are: vehicle exhaust and aeolian process on stripped soils. (author). 13 refs, 2 figs, 6 tabs

  17. Comparative analysis of charged particle-induced autosomal mutations in murine cells and tissues

    Science.gov (United States)

    Kronenberg, Amy; Gauny, Stacey; Turker, Mitchell; Dan, Cristian; Kwoh, Ely

    exposed to 2 Gy of Fe ions. Mutant spectra were analyzed via PCR using a series of heterozygous markers along mouse chromosome 8. Cytotoxicity assays were performed immediately after Fe ion exposure of cells from two primary clones. Cells irradiated in vitro demonstrated a dose-dependent decrement in cloning efficiency with no evidence of a shoulder. The results demonstrate the two clones behave similarly (unpaired t-test, p>0.3) with a D0 of 84.3 cGy for the combined data set. Mutation data were obtained using cells from one of the primary clones. In three experiments, we observed a linear dose-response for Aprt mutation with an induced mutant frzction of 1.06 x 10-3 /Gy. Kidney epithelial cells irradiated in vivo and incubated for 2-4 months in situ prior to harvest also showed an exponential reduction of cloning efficiency. Cells harvested 8-10 months postirradiation showed evidence of recovery for doses up to 1.5 Gy, but there was no improvement in cloning efficiency for kidney cells exposed to 2 Gy Fe ions in vivo evaluated at the late time point. Results for Aprt mutation induction in vivo indicated considerable inter-animal variation within each dose group (0, 1.0, 1.5 and 2 Gy). Fe ion exposures were mutagenic to the kidney, even at the lowest dose (p<0.01). A comparison of the mutant frequency results at the two harvest times indicates that the dose response did not vary with incubation time in vivo. Analysis of the pooled data from the 2-4 months harvests and the 8-10 month harvests indicated an increase in mutant frequency of 1.49 fold per Gy (p=0.01, CI 1.11-2.01). Molecular analysis of Aprtdeficient cells collected after a 2 Gy exposure to Fe ions in vitro showed an increased proportion of mutants arising via interstitial deletion or mitotic recombination, with an indication of an increase in chromosome loss. Similar results have been obtained for Aprt mutants isolated from mice exposed to 2 Gy of Fe ions, as compared with mutants collected from sham

  18. Rapid detection of most frequent Slovenian germ-line mutations in BRCA1 gene using real-time PCR and melting curve analysis

    International Nuclear Information System (INIS)

    Background. Detection of inherited mutations in cancer susceptibility genes is of great importance in some types of cancers including the colorectal cancer (mutations of APC gene in familial adenomatous polyposis - FAP, mutations in mismatch repair genes in hereditary nonpolyposis colorectal cancer - HNPCC), malignant melanoma (mutations in CDKN2A and CDK4 genes) and breast cancer (mutations in BRCA1 and BRCA2 genes). Methods. This article presents the technical data for the detection of five mutations in BRCA1 gene in breast cancer patients and their relatives. The mutations - 1806C>T, 300T>G, 300T>A, 310G>A, 5382insC - were determined by the real-time PCR and the melting curve analysis. Results and conclusion. In comparison to direct sequencing, this method proved to be sensitive and rapid enough for the routine daily determination of mutations in DNA isolated from the peripheral blood. (author)

  19. Gas Chromatography.

    Science.gov (United States)

    Karasek, Francis W.; And Others

    1984-01-01

    This review covers fundamental developments in gas chromatography during 1982 and 1983. Literature is considered under these headings: columns; liguid phases; solid supports; sorption processes and solvents; open tubular column gas chromatography; instrumentation; high-resolution columns and applications; other techniques; qualitative and…

  20. Analysis of Whiskey by Dispersive Liquid-Liquid Microextraction Coupled with Gas Chromatography/Mass Spectrometry: An Upper Division Analytical Chemistry Experiment Guided by Green Chemistry

    Science.gov (United States)

    Owens, Janel E.; Zimmerman, Laura B.; Gardner, Michael A.; Lowe, Luis E.

    2016-01-01

    Analysis of whiskey samples prepared by a green microextraction technique, dispersive liquid-liquid microextraction (DLLME), before analysis by a qualitative gas chromatography-mass spectrometry (GC/MS) method, is described as a laboratory experiment for an upper division instrumental methods of analysis laboratory course. Here, aroma compounds in…

  1. Functional analysis of HNPCC-related missense mutations in MSH2

    DEFF Research Database (Denmark)

    Lützen, Anne; de Wind, Niels; Georgijevic, Dubravka; Nielsen, Finn Cilius; Rasmussen, Lene Juel

    Hereditary nonpolyposis colorectal cancer (HNPCC) is associated with germline mutations in the human DNA mismatch repair (MMR) genes, most frequently MSH2 and MLH1. The majority of HNPCC mutations cause truncations and thus loss of function of the affected polypeptide. However, a significant...... proportion of MMR mutations found in HNPCC patients are single amino acid substitutions and the functional consequences of many of these mutations in DNA repair are unclear. We have examined the consequences of seven MSH2 missense mutations found in HNPCC families by testing the MSH2 mutant proteins in...

  2. Analysis of P53 Mutation and Invasion Front Grading in Oral Squamous Cell Carcinomas

    Institute of Scientific and Technical Information of China (English)

    唐三保; 徐东选; 周彬

    2010-01-01

    We examined P53 mutation and invasion front grading (IFG) in 30 cases of oral squamous cell carcinomas (OSCCs). The association of P53 mutation and IFG scores with clinicopa-thological parameters was evaluated. P53 mutation existed in exon 5-8 in 15 out of the 30 OSCCs (50%). The incidence of P53 mutation was not associated with age, gender, N value and TNM stage. However, there was a significant correlation between P53 mutation and T value (P=0.046). There were no statistically significant correlations amo...

  3. Gas chromatography in space

    Science.gov (United States)

    Akapo, S. O.; Dimandja, J. M.; Kojiro, D. R.; Valentin, J. R.; Carle, G. C.

    1999-01-01

    Gas chromatography has proven to be a very useful analytical technique for in situ analysis of extraterrestrial environments as demonstrated by its successful operation on spacecraft missions to Mars and Venus. The technique is also one of the six scientific instruments aboard the Huygens probe to explore Titan's atmosphere and surface. A review of gas chromatography in previous space missions and some recent developments in the current environment of fiscal constraints and payload size limitations are presented.

  4. Mutation Analysis in the BRCA1 Gene in Chinese Breast Cancer Families

    Institute of Scientific and Technical Information of China (English)

    WUZhengyan; ZHENLinlin; FANPing

    2003-01-01

    Objective: To study the mutation of BRCA1 gene in Chinese breast cancer families. Methods:Fifteen families were selected, involving 41 members, consisting of 23 breast cancer patients. Using poly-merase chain reaction and single stranded conformation polymorphism (PCR-SSCP), and subsequent DNA sequencing, the mutation of BRCA1 genes were analyzed. Results: Four mutations were found in all fam-ilies, and the proportion of mutation was 26.7% (4/15) in breast cancer families. One of the 4 mutations was 2228 insC, resulting in chain termination at codon 711. The remaining 3 mutations were 1884A→T and 3232A→G, resulting in single amino acid change respectively. Conclusion: BRCA1 is a breast cancer susceptibility gene. The relatively low proportion and frequency of BRCA1 mutations in our study hints additional BRCA genes existed.

  5. Mutation analysis of codons 345 and 347 of rhodopsin gene in Indian retinitis pigmentosa patients

    Indian Academy of Sciences (India)

    Madhurima Dikshit; Rakhi Agarwal

    2001-08-01

    More than 100 mutations have been reported till date in the rhodopsin gene in patients with retinitis pigmentosa. The present study was undertaken to detect the reported rhodopsin gene point mutations in Indian retinitis pigmentosa patients. We looked for presence or absence of codon 345 and 347 mutations in exon 5 of the gene using the technique of allele-specific polymerase chain reaction by designing primers for each mutation. We have examined 100 patients from 76 families irrespective of genetic categories. Surprisingly, in our sample the very widely reported highly frequent mutations of codon 347 (P → S/A/R/Q/L/T) were absent while the codon 345 mutation V → M was seen in three cases in one family (autosomal dominant form) and in one sporadic case (total two families). This is the first report on codon 345 and 347 mutation in Indian retinitis pigmentosa subjects.

  6. Molecular analysis of heavy ion induced mutations in the budding yeast

    International Nuclear Information System (INIS)

    This study is intended to elucidate the molecular mechanism of the mutagenesis caused by High-linear energy transfer (LET) ion beam. The frequency of DNA double stranded breaks (DSBs) was estimated by agarose gel electrophoresis. Moreover, the mutation sites of ura3 mutants were determined by DNA sequencing. The yeast cells were irradiated with carbon ions (12C5+; 290 MeV) with the dose 50 to 200 Gy. Carbon ion beam was generated from synchrotron in HIMAC. The carbon ion beams at 100 Gy generate mutations 10.3 - fold more than spontaneous mutation. The mutation frequency increased consistently with LET. This result indicates the high LET ion beam is more mutagenic than low LET ion beam. The remarkable feature of yeast mutations induced by carbon ions was that the mutation sites were localized near the linker regions of nucleosomes, whereas mutations induced by gamma-ray irradiation were located uniformly throughout the gene. (author)

  7. Confirmatory and quantitative analysis using experimental design for the extraction and liquid chromatography-UV, liquid chromatography-mass spectrometry and liquid chromatography-mass spectrometry/mass spectrometry determination of quinolones in turkey muscle.

    Science.gov (United States)

    Clemente, M; Hermo, M P; Barrón, D; Barbosa, J

    2006-12-01

    The aim of this work is to established methods for determination of quinolones (ciprofloxacin, danofloxacin, enrofloxacin, difloxacin and flumequine), regulated by European Union, and sarafloxacin in turkey muscle. An experimental design has been applied for the optimization of the factors that influence the extraction of quinolones from turkey muscle in order to determine the experimental conditions for their extraction with high recoveries. Liquid chromatography with ultraviolet detection (LC-UV), liquid chromatography-mass spectrometry (LC-MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS) have been used for the simultaneous quantification of quinolones antibiotics in turkey muscle. The proposed methods have been validated according to the Food Drugs Administration guideline and presents the limit of quantification below the maximum residue limits established by the European Union for quinolones in turkey muscle. The methods developed have been applied to quantification of enrofloxacin and its main metabolite ciprofloxacin in samples of turkey muscle obtained from animals treated with enrofloxacin. PMID:17027811

  8. Analysis of Parkinson disease patients from Portugal for mutations in SNCA, PRKN, PINK1 and LRRK2

    Directory of Open Access Journals (Sweden)

    Calado Ana

    2008-01-01

    Full Text Available Abstract Background Mutations in the genes PRKN and LRRK2 are the most frequent known genetic lesions among Parkinson's disease patients. We have previously reported that in the Portuguese population the LRRK2 c.6055G > A; p.G2019S mutation has one of the highest frequencies in Europe. Methods Here, we follow up on those results, screening not only LRRK2, but also PRKN, SNCA and PINK1 in a cohort of early-onset and late-onset familial Portuguese Parkinson disease patients. This series comprises 66 patients selected from a consecutive series of 132 patients. This selection was made in order to include only early onset patients (age at onset below 50 years or late-onset patients with a positive family history (at least one affected relative. All genes were sequenced bi-directionally, and, additionally, SNCA, PRKN and PINK1 were subjected to gene dosage analysis. Results We found mutations both in LRRK2 and PRKN, while the remaining genes yielded no mutations. Seven of the studied patients showed pathogenic mutations, in homozygosity or compound heterozygosity for PRKN, and heterozygosity for LRRK2. Conclusion Mutations are common in Portuguese patients with Parkinson's disease, and these results clearly have implications not only for the genetic diagnosis, but also for the genetic counseling of these patients.

  9. The analysis of some CFTR gene mutations in a small group of cf patients from southern part of Romania

    Directory of Open Access Journals (Sweden)

    Lucian GAVRILA

    2009-05-01

    Full Text Available Cystic fibrosis is the most common hereditary disease in European descendant populations, with prevalencedepending on ethnic groups studied. In contrast to other European countries, there is little information regarding the frequency ofCFTR mutations for the Southern part of Romania. The aim of this study was to test the presence of nine CFTR mutations in CFpatients from the Southern part of Romania, using complementary analysis methods. We investigated a group of unrelated CFpatients (n=19 and, when possible, their voluntary parents (n=15. We observed that the most frequently worldwide CF mutation,delta F508, was present in 17 of our patients (89.5% in homozygous (n=7 or heterozygous (n=10 condition and absent in 2 cases(10.5%. This mutation was also detected in ten parents, seven of them (100% have homozygous children and three (37.5%have heterozygous children for delta F508 mutation. None of the G542X, S549N, G551D, R553X, R560T, S1255X, W1282X andN1303K mutations have been detected in the samples from patients or parents. Our results are partially similar with those reportedin neighbouring countries where the delta F508 is the most common mutation detected and the frequency of R560T, S549N, G551D andS1255X mutations is near zero. The enlargement of this study could give a better result regarding the spectrum of CFTR mutationsin Romanian patients with CF.

  10. c-Met Mutational Analysis in the Sema and Juxtamembrane Domains in Small-Cell-Lung-Cancer

    Science.gov (United States)

    de Aguirre, Itziar; Salvatierra, Alejandro; Font, Albert; Mate, Jose Luis; Perez, Maria; Botia, Monica; Taron, Miquel; Rosell, Rafael

    2006-01-01

    Background: c-Met mutations play a critical role in the development and progression of primary tumors and metastases. Activation of the HGF/SF-c-Met pathway determines a poor prognosis in non-small-cell and small-cell lung cancer (SCLC) patients. Missense mutations of c-Met have been identified in SCLC patients located in the juxtamembrane (JM) and in the Sema domain. To determine the role of the c-Met pathway in SCLC, we have investigated the presence of c-Met mutations in SCLC patients. Patients and methods: Forty-four tumor tissue samples from SCLC patients were obtained with bronchoscopy before beginning treatment. Analysis of c-Met mutations was performed in exon 2 and exon 14. Results: Of the 44 patients included in this study, 23 were classified as limited disease and were treated with sequential or concurrent chemotherapy and thoracic radiotherapy. Twenty-one patients with extensive disease received chemotherapy alone, the majority with cisplatin or carboplatin plus etoposide. The median survival was 14 months (95% CI: 9.4 to 18.5 months) and the 2- and 5-year survival rates were 24% and 15%, respectively. Previously identified missense mutations E168D, R988C and T1010I in c-Met were not found in our study. However, novel mutations were identified, including T995I in the juxtamembrane domain (T995I) and a mutation which does not change amino acid in codon 178 in the Sema domain. Conclusion: In SCLC patients, the presence of mutations in c-Met gene is a rare event. Other genetic alterations involved in the HGF/SF-c-Met pathway should be assessed to define the role of this signaling pathway in SCLC. PMID:23662036

  11. Performance Comparison of FSA Red & Apriori Algorithm’s in Mutation Analysis

    Directory of Open Access Journals (Sweden)

    Mayilvaganan M

    2014-11-01

    Full Text Available In this paper the attempt has been made to analyze the DNA gene cancer dataset with RBC ,WBC and platelet cancer data set. The basic idea behind this proposed method is comparing the 3 large nucleotide DNA dataset with with Bloom filter and discovering the matched subsequence. To validate the proposed algorithm, association and classification rule based on the FSA red algorithm with bloom filters and apriori algorithm using hierarchical clustering are compared using data mining technique. Here this algorithm is applied to find no of sequence occurrences and mutation analysis for the 3 nucleotide DNA gene dataset. In order to evaluate the proposed methodology, Comparisons are made based on the Execution time and memory efficiency in finding frequent patterns. The extracted rules and analyzed results are graphically demonstrated. The performance is analyzed based on the different no of instances and confidence in DNA sequence data set.

  12. Genetic analysis of jumbled spine and ribs (Jsr) mutation affecting the vertebral development in mice.

    Science.gov (United States)

    Okano, Shinya; Asano, Atsushi; Kon, Yasuhiro; Miyoshi, Hiroyuki; Watanabe, Tomomasa

    2002-10-01

    The jumbled spine and ribs (Jsr) mouse was derived from a spontaneous mutation. As the phenotype, a shortened trunk and kinky tail are characteristic Jsr traits. In this study, on high resolution mapping it was found that Lunatic fringe (Lfng) mapped at the same position as Jsr. Lfng was identified as the candidate gene for Jsr, but sequence analysis of this gene revealed no substitution in the coding region of cDNA. Therefore, we adopted the strategy of positional cloning for Jsr using a mouse bacterial artificial chromosome (BAC) library. A BAC contig was constructed from three BAC clones showing positive signals of Lfng and 11MMHAP75FRD8.seq near the Jsr locus on chromosome 5. Based on the genetic mapping of both T7 and sp6 ends of a clone of BAC382-O-7 (BAC382), the Jsr gene was considered to exist in BAC382 and to be positioned near the sp6 side. PMID:12392169

  13. Comparative analysis of charged particle-induced autosomal mutations in murine cells and tissues

    Science.gov (United States)

    Kronenberg, Amy; Gauny, Stacey; Turker, Mitchell; Dan, Cristian; Kwoh, Ely

    exposed to 2 Gy of Fe ions. Mutant spectra were analyzed via PCR using a series of heterozygous markers along mouse chromosome 8. Cytotoxicity assays were performed immediately after Fe ion exposure of cells from two primary clones. Cells irradiated in vitro demonstrated a dose-dependent decrement in cloning efficiency with no evidence of a shoulder. The results demonstrate the two clones behave similarly (unpaired t-test, p>0.3) with a D0 of 84.3 cGy for the combined data set. Mutation data were obtained using cells from one of the primary clones. In three experiments, we observed a linear dose-response for Aprt mutation with an induced mutant frzction of 1.06 x 10-3 /Gy. Kidney epithelial cells irradiated in vivo and incubated for 2-4 months in situ prior to harvest also showed an exponential reduction of cloning efficiency. Cells harvested 8-10 months postirradiation showed evidence of recovery for doses up to 1.5 Gy, but there was no improvement in cloning efficiency for kidney cells exposed to 2 Gy Fe ions in vivo evaluated at the late time point. Results for Aprt mutation induction in vivo indicated considerable inter-animal variation within each dose group (0, 1.0, 1.5 and 2 Gy). Fe ion exposures were mutagenic to the kidney, even at the lowest dose (pvivo. Analysis of the pooled data from the 2-4 months harvests and the 8-10 month harvests indicated an increase in mutant frequency of 1.49 fold per Gy (p=0.01, CI 1.11-2.01). Molecular analysis of Aprtdeficient cells collected after a 2 Gy exposure to Fe ions in vitro showed an increased proportion of mutants arising via interstitial deletion or mitotic recombination, with an indication of an increase in chromosome loss. Similar results have been obtained for Aprt mutants isolated from mice exposed to 2 Gy of Fe ions, as compared with mutants collected from sham-irradiated mice. Taken together, the results to date demonstrate that Fe ions are mutagenic to

  14. Developments in suppressor technology for inorganic ion analysis by ion chromatography using conductivity detection.

    Science.gov (United States)

    Hadda, Paul R; Jackson, Peter E; Shaw, Matthew J

    2003-06-01

    A review is presented detailing the development and use of suppression devices for the conductimetric detection of inorganic ions by ion chromatography (IC). An overview of the general response equation for conductivity detection is also given. Topics of discussion include the role and function of suppressors, the development of early suppressors including packed column and membrane devices from 1975 to 1990 and the subsequent progression towards present day commercially available suppressors and recent innovations. Post-suppression devices for signal enhancement are also discussed. PMID:12877197

  15. Advances in Micro-Ultrahigh-Preformance Liquid Chromatography-Mass Spectrometry in Residue and Contaminant Analysis

    OpenAIRE

    Gerssen, A.; Mol, J.G.J.; Blokland, M. H.

    2014-01-01

    Advances in nano-ultrahigh-performance liquid chromatography (nUHPLC) and "plug-and-play" micro-UHPLC (µUHPLC) for the detection of veterinary drugs and steroids in porcine meat and urine respectively are described. Recent developments in "plug-and-play" µUHPLC devices offer several advantages compared to earlier micro-LC systems. As well as the ease of use, solvent consumption can be reduced by more than 95% and the amount of sample required can be reduced 10-fold. In addition, the performan...

  16. Headspace gas chromatography-flame ionization detector method for organic solvent residue analysis in dietary supplements.

    Science.gov (United States)

    Jeong, Mijeong Lee; Zahn, Michael; Trinh, Thao; Jia, Qi; Ma, Wenwen

    2006-01-01

    An analytical method has been developed for the identification and quantification of 20 organic solvent residues in dietary supplements. The method utilizes a headspace sampler interfaced with gas chromatography and flame ionization detection. With split injection (5:1) and a DB-624 column, most of the organic solvents are separated in 9 min. The method has been validated and was found to be relatively simple and fast, and it can be applied to most common organic solvent residues. With the mass detector, the method was able to identify organic solvents beyond the 20 standards tested. PMID:17225592

  17. Analysis of Essential Oil in Jerusalem Artichoke (Helianthus tuberosus L.) Leaves and Tubers by Gas Chromatography-Mass Spectrometry

    Science.gov (United States)

    Helmi, Zead; Al Azzam, Khaldun Mohammad; Tsymbalista, Yuliya; Ghazleh, Refat Abo; Shaibah, Hassan; Aboul-Enein, Hassan

    2014-01-01

    Purpose: To investigate, for the first time, the chemical composition of essential oil of the tubers and leaves of Jerusalem artichoke (Helianthus tuberosus L.), a species of sunflower native to eastern North America, growing in Ukraine. Methods: A hydrodistillation apparatus was used for the extraction of volatile components and then it was analysed by gas chromatography equipped with a split-splitless injector (split ratio, 1:50) and flame ionization detector (FID). The oil was analyzed under linear temperature programming applied at 4°C/min from 50°C - 340°C. Temperatures of the injector and FID detector were maintained at 280°C and 300°C, respectively. The chemical analysis of the oil was carried out using gas chromatography coupled to mass spectrometry (GC-MS), to determine the chemical composition of the volatile fraction. Results: The essential oils content ranged from 0.00019 to 0.03486 and 0.00011 to 0.00205 (g/100g), in leaves and tubers, respectively. The qualitative and quantitative analysis led to the identification of 17 components in both species samples. The major component found in leaves and tubers was (-)-β-bisabolene with 70.7% and 63.1%, respectively. Conclusion: Essential oil profile of Jerusalem artichoke species showed significant differences between leaves and tubers species. Additionally, the leaves of Jerusalem artichoke are a promising source of natural β-bisabolene. PMID:25671184

  18. Analysis of neonicotinoids by gas chromatography coupled to nuclide 63Ni - Electron Capture Detector - GC/ECD

    International Nuclear Information System (INIS)

    Recently, several reports have been published discussing reduction in bee population which polymerizes cultures around the world this phenomenon is known as Colony Collapse Disorder (CCD). The phenomenon describes the lack of worker honeybees in the colony despite having pups and food. The causes of this problem are unknown but there are studies that claim that reduction of population of bees is linked to poisoning through insecticides specifically neonicotinoids. Among this type of pesticide are imidacloprid (C9H10ClN5O2), clothianidin (C6H8ClN5O2S) and thiamethoxam (C8H10ClN5O3S). This paper presents the analysis of neonicotinoids - clothianidin, imidacloprid and thiamethoxam - by the technique of gas chromatography coupled to nuclide 63Ni electron capture detector (GC/ECD). The electron capture detector (ECD) is a gas chromatography detector that has been used for the detection of organic halogens, nitriles, nitrates and organometallic compounds. The ECD detector ionizes the analytes by the beta particles from the nuclide sources 63Ni within carrier gas N2. The electrons produced in this process are collected and create a current that are amplified and generates a chromatographic peak. Methodology and details of the analysis are present in this work. (author)

  19. Application of integrated comprehensive/multidimensional gas chromatography with mass spectrometry and olfactometry for aroma analysis in wine and coffee.

    Science.gov (United States)

    Chin, Sung-Tong; Eyres, Graham T; Marriott, Philip J

    2015-10-15

    Component coelution in chromatographic analysis complicates identification and attribution of individual odour-active volatile molecules in complex multi-component samples. An integrated system incorporating comprehensive two-dimensional gas chromatography (GC × GC) and multidimensional gas chromatography (MDGC), with flame ionisation, olfactometry and mass spectrometry detection was developed to circumvent data correlation across different systems. Identification of potent odorants in Shiraz wine and the headspace of ground coffee are demonstrated as selected applications. Multiple solid-phase microextraction (SPME) sampling with GC-O located odour-active regions; GC × GC established the complexity of odour-active regions; MDGC provided high-resolution separation for each region; simultaneous 'O' and MS detection completed the analysis for target resolved peaks. Seven odour regions in Shiraz were analysed with MDGC-O/MS detection, revealing 11 odour volatiles through matching of mass spectrometry and retention indices from both separating dimensions, including acetic acid; octen-3-ol; ethyl octanoate; methyl-2-oxo-nonanoate; butanoic acid, 2-methylbutanoic acid, and 3-methylbutanoic acid; 3-(methylthio)-1-propanol; hexanoic acid; β-damascenone; and ethyl-3-phenylpropanoate. A capsicum odour in ground coffee was identified as 2-methoxy-3-isobutylpyrazine with a 5-fold increase in S/N of the odorant when acquired using a 6-time cumulative SPME sampling approach. PMID:25952879

  20. Size exclusion chromatography: an improved method to harvest Corynebacterium glutamicum cells for the analysis of cytosolic metabolites.

    Science.gov (United States)

    Persicke, Marcus; Plassmeier, Jens; Neuweger, Heiko; Rückert, Christian; Pühler, Alfred; Kalinowski, Jörn

    2011-07-10

    The efficient separation of Corynebacterium glutamicum cells from culture medium by size exclusion chromatography (SEC) is presented. Residue analysis demonstrated that this method effectively depletes extracellular compounds. For evaluation, SEC was compared with the common methods cold methanol treatment, fast centrifugation and fast filtration. For this purpose, samples of C. glutamicum cells from fermenter cultures were harvested and subjected to a metabolome analysis. In particular, the wild type strain C. glutamicum ATCC13032 and the lysine production strain C. glutamicum DM1730 were grown in a minimal or in a complex medium. Comparison of metabolite pool sizes after harvesting C. glutamicum cells by the methods mentioned above by gas chromatography coupled to mass spectrometry (GC-MS) revealed that SEC is the most suitable method when intracellular metabolite pools are to be measured during growth in complex media or in the presence of significant amounts of secreted metabolites. In contrast to the other methods tested, the SEC method turned out to be fast and able to remove extracellular compounds almost completely. PMID:20817050

  1. An Ultra-Trace Analysis Technique for SF6 Using Gas Chromatography with Negative Ion Chemical Ionization Mass Spectrometry.

    Science.gov (United States)

    Jong, Edmund C; Macek, Paul V; Perera, Inoka E; Luxbacher, Kray D; McNair, Harold M

    2015-07-01

    Sulfur hexafluoride (SF6) is widely used as a tracer gas because of its detectability at low concentrations. This attribute of SF6 allows the quantification of both small-scale flows, such as leakage, and large-scale flows, such as atmospheric currents. SF6's high detection sensitivity also facilitates greater usage efficiency and lower operating cost for tracer deployments by reducing quantity requirements. The detectability of SF6 is produced by its high molecular electronegativity. This property provides a high potential for negative ion formation through electron capture thus naturally translating to selective detection using negative ion chemical ionization mass spectrometry (NCI-MS). This paper investigates the potential of using gas chromatography (GC) with NCI-MS for the detection of SF6. The experimental parameters for an ultra-trace SF6 detection method utilizing minimal customizations of the analytical instrument are detailed. A method for the detection of parts per trillion (ppt) level concentrations of SF6 for the purpose of underground ventilation tracer gas analysis was successfully developed in this study. The method utilized a Shimadzu gas chromatography with negative ion chemical ionization mass spectrometry system equipped with an Agilent J&W HP-porous layer open tubular column coated with an alumina oxide (Al2O3) S column. The method detection limit (MDL) analysis as defined by the Environmental Protection Agency of the tracer data showed the method MDL to be 5.2 ppt. PMID:25452581

  2. Analysis of neonicotinoids by gas chromatography coupled to nuclide {sup 63}Ni - Electron Capture Detector - GC/ECD

    Energy Technology Data Exchange (ETDEWEB)

    Amaral, Priscila O.; Leao, Claudio; Redigolo, Marcelo M.; Crepaldi, Caike; Bustillos, Oscar V., E-mail: priscilaoamaral@gmail.com, E-mail: claudio.leao@usp.br, E-mail: marceloredigolo@gmail.com, E-mail: caike1995@gmail.com, E-mail: ovega@ipen.bremails [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2015-07-01

    Recently, several reports have been published discussing reduction in bee population which polymerizes cultures around the world this phenomenon is known as Colony Collapse Disorder (CCD). The phenomenon describes the lack of worker honeybees in the colony despite having pups and food. The causes of this problem are unknown but there are studies that claim that reduction of population of bees is linked to poisoning through insecticides specifically neonicotinoids. Among this type of pesticide are imidacloprid (C{sub 9}H{sub 10}ClN{sub 5}O{sub 2}), clothianidin (C{sub 6}H{sub 8}ClN{sub 5}O{sub 2}S) and thiamethoxam (C{sub 8}H{sub 10}ClN{sub 5}O{sub 3}S). This paper presents the analysis of neonicotinoids - clothianidin, imidacloprid and thiamethoxam - by the technique of gas chromatography coupled to nuclide {sup 63}Ni electron capture detector (GC/ECD). The electron capture detector (ECD) is a gas chromatography detector that has been used for the detection of organic halogens, nitriles, nitrates and organometallic compounds. The ECD detector ionizes the analytes by the beta particles from the nuclide sources {sup 63}Ni within carrier gas N{sub 2}. The electrons produced in this process are collected and create a current that are amplified and generates a chromatographic peak. Methodology and details of the analysis are present in this work. (author)

  3. Computational analysis of the R85C and R85H epilepsy mutations in Na+ channel beta1 subunits.

    Science.gov (United States)

    Thomas, E A; Xu, R; Petrou, S

    2007-07-29

    Mutations in Na+ channels cause a variety of epilepsy syndromes. Analysis of these mutations shows a range of simultaneous functional consequences, each of which may increase or decrease membrane excitability, making it difficult to predict the combined effect on neuron firing. This may be addressed by building mathematical models of Na+ channel gating and using them in neuron models to predict responses to natural stimuli. The R85C and R85H mutations of the beta1 subunit cause generalized epilepsy syndromes in humans, and an experimental study showed that these mutations shift steady-state activation in the negative direction, which predicts increased excitability, and shift fast inactivation in the negative direction, which predicts decreased excitability. In addition, the R85C also shifts slow inactivation in the negative direction. To predict changes in neuron excitability resulting from these contradictory effects we built Na+ channel models based on our earlier data and on new measurements of the rate of slow inactivation over a range of potentials. Use of these Na+ channel models in simple neuron models revealed that both mutations cause an increase in excitability but the R85H mutation was more excitable. This is due to differences in steady-state slow inactivation and to subtle differences in fast kinetics captured by the model fitting process. To understand the effect of changes in different gating processes and to provide a simple guide for interpreting changes caused by mutations, we performed a sensitivity analysis. Using the wild-type model we shifted each activation curve by +/-5 mV or altered gating rates up or down by 20%. Excitability was most sensitive to changes in voltage dependence of activation, followed by voltage dependence of inactivation and then slow inactivation. By contrast, excitability was relatively insensitive to gating rates. PMID:17604911

  4. MEFV Gene Profile in Northwest of Iran, Twelve Common MEFV Gene Mutations Analysis in 216 Patients with Familial Mediterranean Fever

    Directory of Open Access Journals (Sweden)

    Farhad Salehzadeh

    2015-01-01

    Full Text Available Familial Mediterranean Fever (FMF is a hereditary autoinflammatory disease with autosomal recessive inheritance pattern often seen around the Mediterranean Sea. It is characterized by recurrent episodes of fever and polyserositis and rash. Recently, MEFV gene analysis determines the definitive diagnosis of FMF. In this study, we analyzed 12 MEFV gene mutations in more than 200 FMF patients, previously diagnosed by Tel-Hashomer clinical criteria, in northwest of Iran, located in the proximity of the Mediterranean Sea. In the northwest of Iran (Ardabil, 216 patients with FMF diagnosis, based on Tel-Hashomer criteria, referred to the genetic laboratory to be tested for the following mutations; P369S, F479L, M680I(G/C, M680I(G/A, I692del, M694V, M694I, K695R, V726A, A744S, R761H, E148Q. All patients were screened for MEFV gene mutations by a reverse hybridization assay (FMF Strip Assay, Vienna lab, Vienna, Austria according to manufacturer’s instructions. Among these FMF patients, no mutation was detected in 51 (23/62% patients, but 165 (76/38% patients had one or two mutations, 33 patients (15/28% homozygous, 86 patients (39/81% compound heterozygous and 46 patients (21/29% were heterozygous. The most common mutations were M694V (23/61%, V726A (11/11% and E148Q (9/95% respectively. MEFV gene mutations showed similarities and dissimilarities in different ethnic groups, while it is common among Arabs and Armenians genotype. Since common 12 MEFV gene analysis could not detect up to 50% of our patients, who had FMF on the basis of clinical Tel-Hashomer criteria, clinical criteria is still the best way in the diagnosis of FMF in this area.

  5. Qualitative and Quantitative Analysis of Volatile Components of Zhengtian Pills Using Gas Chromatography Mass Spectrometry and Ultra-High Performance Liquid Chromatography

    Science.gov (United States)

    Liu, Cui-ting; Zhang, Min; Yan, Ping; Liu, Hai-chan; Liu, Xing-yun; Zhan, Ruo-ting

    2016-01-01

    Zhengtian pills (ZTPs) are traditional Chinese medicine (TCM) which have been commonly used to treat headaches. Volatile components of ZTPs extracted by ethyl acetate with an ultrasonic method were analyzed by gas chromatography mass spectrometry (GC-MS). Twenty-two components were identified, accounting for 78.884% of the total components of volatile oil. The three main volatile components including protocatechuic acid, ferulic acid, and ligustilide were simultaneously determined using ultra-high performance liquid chromatography coupled with diode array detection (UHPLC-DAD). Baseline separation was achieved on an XB-C18 column with linear gradient elution of methanol-0.2% acetic acid aqueous solution. The UHPLC-DAD method provided good linearity (R2 ≥ 0.9992), precision (RSD protocatechuic acid, ferulic acid, and ligustilide, in 13 batches of ZTPs, which is suitable for discrimination and quality assessment of ZTPs. PMID:26904360

  6. rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations

    OpenAIRE

    Ponomarenko, Julia V.; Merkulova, Tatyana I.; Gennady V Vasiliev; Levashova, Zoya B.; Orlova, Galina V.; Lavryushev, Sergey V.; Fokin, Oleg N.; Ponomarenko, Mikhail P.; Frolov, Anatoly S.; Sarai, Akinori

    2001-01-01

    rSNP_Guide is a novel curated database system for analysis of transcription factor (TF) binding to target sequences in regulatory gene regions altered by mutations. It accumulates experimental data on naturally occurring site variants in regulatory gene regions and site-directed mutations. This database system also contains the web tools for SNP analysis, i.e., active applet applying weight matrices to predict the regulatory site candidates altered by a mutation. T...

  7. Analysis of ochratoxin A in pig tissues using high pressure liquid chromatography (HPLC) and liquid chromatography tandem mass spectrometry (LC/MS/MS) as confirmative methods

    OpenAIRE

    Milićević Dragan R.; Jurić Verica B.; Stefanović Srđan M.; Vesković-Moračanin Slavica M.; Janković Saša I.

    2009-01-01

    Two different analytical methods for the determination and confirmation of ochratoxin A (OTA) in blood serum, kidney and liver of pigs have been compared. Sample clean-up was based on liquid-liquid phase extraction. The detection of OTA was accomplished with high-performance liquid chromatography (HPLC) combined either with fluorescence detection (FL) or electro spray ionization (ESI+) tandem mass spectrometry (MS-MS). Comparative method evaluation was based on the investigation of 82 samples...

  8. Genetic diagnosis of Duchenne/Becker muscular dystrophy using next-generation sequencing: validation analysis of DMD mutations.

    Science.gov (United States)

    Okubo, Mariko; Minami, Narihiro; Goto, Kanako; Goto, Yuichi; Noguchi, Satoru; Mitsuhashi, Satomi; Nishino, Ichizo

    2016-06-01

    Duchenne and Becker muscular dystrophies (DMD/BMD) are the most common inherited neuromuscular disease. The genetic diagnosis is not easily made because of the large size of the dystrophin gene, complex mutational spectrum and high number of tests patients undergo for diagnosis. Multiplex ligation-dependent probe amplification (MLPA) has been used as the initial diagnostic test of choice. Although MLPA can diagnose 70% of DMD/BMD patients having deletions/duplications, the remaining 30% of patients with small mutations require further analysis, such as Sanger sequencing. We applied a high-throughput method using Ion Torrent next-generation sequencing technology and diagnosed 92% of patients with DMD/BMD in a single analysis. We designed a multiplex primer pool for DMD and sequenced 67 cases having different mutations: 37 with deletions/duplications and 30 with small mutations or short insertions/deletions in DMD, using an Ion PGM sequencer. The results were compared with those from MLPA or Sanger sequencing. All deletions were detected. In contrast, 50% of duplications were correctly identified compared with the MLPA method. Small insertions in consecutive bases could not be detected. We estimated that Ion Torrent sequencing could diagnose ~92% of DMD/BMD patients according to the mutational spectrum of our cohort. Our results clearly indicate that this method is suitable for routine clinical practice providing novel insights into comprehensive genetic information for future molecular therapy. PMID:26911353

  9. Residual on column host cell protein analysis during lifetime studies of protein A chromatography.

    Science.gov (United States)

    Lintern, Katherine; Pathak, Mili; Smales, C Mark; Howland, Kevin; Rathore, Anurag; Bracewell, Daniel G

    2016-08-26

    Capacity reduction in protein A affinity chromatography with extended cycling during therapeutic antibody manufacture is well documented. Identification of which residual proteins remain from previous cycles during the lifetime of these adsorbent materials is required to understand their role in this ageing process, but represents a significant metrological challenge. Scanning electron microscopy (SEM) and liquid chromatography mass spectrometry (LC-MS/MS) are combined to detect and map this phenomenon of protein carry-over. We show that there is a morphological change at the surface of the agarose resin, revealing deposits on the polymer fibres increasing with cycle number. The amount of residual host cell proteins (HCPs) by LC-MS/MS present on the resin is shown to increase 10-fold between 50 and 100 cycles. During this same period the functional class of the predominant HCPs associated with the resin increased in diversity, with number of proteins identified increasing 5-fold. This ageing is observed in the context of the product quality of the eluate HCP and protein A leachate concentration remaining constant with cycle number. PMID:27473513

  10. An application of high performance liquid chromatography to analysis of lipids in archaeological samples.

    Science.gov (United States)

    Passi, S; Rothschild-Boros, M C; Fasella, P; Nazzaro-Porro, M; Whitehouse, D

    1981-07-01

    Five samples from three different types of 1500-year-old Mediterranean amphorae, as well as from a contemporary oil lamp found in the same deposit, were analyzed for the presence of lipid residues. Each sample of finely ground amphorae powder weighed 1-2 g. The abundance of interfering secondary products makes thin-layer chromatography (TLC) an essential step of the procedure. The fractionation of the extract into its various lipid components by means of TLC was followed by quantitative recovery of the triglyceride (TG) and free fatty acid (FFA) fractions from the plates and by the measurement of their components by high performance liquid chromatography (HPLC) after esterification. The minimum detectable level is 1 ng. The amphorae samples revealed a more abundant FFA fraction than a TG fraction, which is the reverse of what we know about the composition of fresh oil. Despite the considerable age of the amphorae and their preservation under non-ideal conditions, the lipid residues have retained certain identifiable characteristics that enable one to make valid suggestions as to the type of commodity originally transported in the amphorae. The results of these experiments yield important information that enables the biochemist to observe an aging process irreproducible in the laboratory and provides the archaeologist with previously unavailable information about trade 15 centuries ago. PMID:7026710

  11. Comprehensive sample analysis using high performance liquid chromatography with multi-detection

    International Nuclear Information System (INIS)

    Graphical abstract: -- Highlights: •Detection selectivity was assessed with 6 detection modes. •Natural samples show great diversity in detection selectivity. •Complex samples require evaluation using a multifaceted approach to detection. •23/30 known compounds (detected by MS) detected by chemiluminescence, DPPH and UV. -- Abstract: Herein we assess the separation space offered by a liquid chromatography system with an optimised uni-dimensional separation for the determination of the key chemical entities in the highly complex matrix of a tobacco leaf extract. Multiple modes of detection, including UV–visible absorbance, chemiluminescence (acidic potassium permanganate, manganese(IV), and tris(2,2′-bipyridine)ruthenium(III)), mass spectrometry and DPPH radical scavenging were used in an attempt to systematically reduce the data complexity of the sample whilst obtaining a greater degree of molecule-specific information. A large amount of chemical data was obtained, but several limitations in the ability to assign detector responses to particular compounds, even with the aid of complementary detection systems, were observed. Thirty-three compounds were detected via MS on the tobacco extract and 12 out of 32 compounds gave a peak height ratio (PHR) greater than 0.33 on one or more detectors. This paper serves as a case study of these limitations, illustrating why multidimensional chromatography is an important consideration when developing a comprehensive chemical detection system

  12. Comprehensive sample analysis using high performance liquid chromatography with multi-detection

    Energy Technology Data Exchange (ETDEWEB)

    Pravadali, Sercan [Australian Centre for Research on Separation Sciences (ACROSS), School of Science and Health, University of Western Sydney (Parramatta), NSW 1797 (Australia); Bassanese, Danielle N.; Conlan, Xavier A.; Francis, Paul S.; Smith, Zoe M.; Terry, Jessica M. [Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Victoria 3216 (Australia); Shalliker, R. Andrew, E-mail: R.Shalliker@uws.edu.au [Australian Centre for Research on Separation Sciences (ACROSS), School of Science and Health, University of Western Sydney (Parramatta), NSW 1797 (Australia)

    2013-11-25

    Graphical abstract: -- Highlights: •Detection selectivity was assessed with 6 detection modes. •Natural samples show great diversity in detection selectivity. •Complex samples require evaluation using a multifaceted approach to detection. •23/30 known compounds (detected by MS) detected by chemiluminescence, DPPH and UV. -- Abstract: Herein we assess the separation space offered by a liquid chromatography system with an optimised uni-dimensional separation for the determination of the key chemical entities in the highly complex matrix of a tobacco leaf extract. Multiple modes of detection, including UV–visible absorbance, chemiluminescence (acidic potassium permanganate, manganese(IV), and tris(2,2′-bipyridine)ruthenium(III)), mass spectrometry and DPPH radical scavenging were used in an attempt to systematically reduce the data complexity of the sample whilst obtaining a greater degree of molecule-specific information. A large amount of chemical data was obtained, but several limitations in the ability to assign detector responses to particular compounds, even with the aid of complementary detection systems, were observed. Thirty-three compounds were detected via MS on the tobacco extract and 12 out of 32 compounds gave a peak height ratio (PHR) greater than 0.33 on one or more detectors. This paper serves as a case study of these limitations, illustrating why multidimensional chromatography is an important consideration when developing a comprehensive chemical detection system.

  13. Comprehensive sample analysis using high performance liquid chromatography with multi-detection.

    Science.gov (United States)

    Pravadali, Sercan; Bassanese, Danielle N; Conlan, Xavier A; Francis, Paul S; Smith, Zoe M; Terry, Jessica M; Shalliker, R Andrew

    2013-11-25

    Herein we assess the separation space offered by a liquid chromatography system with an optimised uni-dimensional separation for the determination of the key chemical entities in the highly complex matrix of a tobacco leaf extract. Multiple modes of detection, including UV-visible absorbance, chemiluminescence (acidic potassium permanganate, manganese(IV), and tris(2,2'-bipyridine)ruthenium(III)), mass spectrometry and DPPH radical scavenging were used in an attempt to systematically reduce the data complexity of the sample whilst obtaining a greater degree of molecule-specific information. A large amount of chemical data was obtained, but several limitations in the ability to assign detector responses to particular compounds, even with the aid of complementary detection systems, were observed. Thirty-three compounds were detected via MS on the tobacco extract and 12 out of 32 compounds gave a peak height ratio (PHR) greater than 0.33 on one or more detectors. This paper serves as a case study of these limitations, illustrating why multidimensional chromatography is an important consideration when developing a comprehensive chemical detection system. PMID:24216214

  14. Use of CT-guided fine needle aspiration biopsy in epidermal growth factor receptor mutation analysis in patients with advanced lung cancer

    Energy Technology Data Exchange (ETDEWEB)

    Zhuang, Yi-Ping; Wang, Hai-Yan; Zhang, Jin; Feng, Yong (Dept. of Radiology, Jiangsu Cancer Inst. and Hospital, Nanjing, Jiangsu (China)), email: yipingzhuang2010@sina.com; Shi, Mei-Qi (Dept. of Chemotherapy, Jiangsu Cancer Inst. and Hospital, Nanjing, Jiangsu (China))

    2011-12-15

    Background. The safety of using a cutting needle when performing a core-needle biopsy is of major concern, in particular for small lung tumors or tumors near the hilum. Purpose. To investigate the usefulness of CT-guided fine needle aspiration biopsy (FNAB) of the lung in obtaining tumor tissue for epidermal growth factor receptor (EGFR) mutation analysis in advanced lung cancer patients. Material and Methods. Forty-three patients with stage IIIB-IV lung cancer were enrolled. In all patients, CT-guided FNAB was performed using an 18-gauge or 20-gauge Chiba aspiration needle for histology diagnosis and EGFR mutation analysis. Complications associated with CT-guided FNAB were observed, and the specimen mutational assessments were recorded. Results. The obtained tumor samples ranged from 0.5-1.5 cm in length and were adequate for histological and DNA analyses in all patients. No patient had a pneumothorax or hemoptysis. Minor needle tract bleeding appeared in eight patients. Mutation analysis was satisfactorily demonstrated in 23 mutations and 20 non-mutations. Ten and 13 mutations were identified by 18-gauge and 20-gauge needle biopsies, respectively. EFGR mutations, including 12 cases of EGFR exon 19 deletion and 11 cases of exon 21 point mutation, were present in 21 patients with adenocarcinomas, one with squamous cell carcinoma, and one with undifferentiated carcinoma. Conclusion. CT-guided FNAB is a feasible and safe technique for obtaining lung tumor tissues for EGFR gene mutation analysis

  15. Use of CT-guided fine needle aspiration biopsy in epidermal growth factor receptor mutation analysis in patients with advanced lung cancer

    International Nuclear Information System (INIS)

    Background. The safety of using a cutting needle when performing a core-needle biopsy is of major concern, in particular for small lung tumors or tumors near the hilum. Purpose. To investigate the usefulness of CT-guided fine needle aspiration biopsy (FNAB) of the lung in obtaining tumor tissue for epidermal growth factor receptor (EGFR) mutation analysis in advanced lung cancer patients. Material and Methods. Forty-three patients with stage IIIB-IV lung cancer were enrolled. In all patients, CT-guided FNAB was performed using an 18-gauge or 20-gauge Chiba aspiration needle for histology diagnosis and EGFR mutation analysis. Complications associated with CT-guided FNAB were observed, and the specimen mutational assessments were recorded. Results. The obtained tumor samples ranged from 0.5-1.5 cm in length and were adequate for histological and DNA analyses in all patients. No patient had a pneumothorax or hemoptysis. Minor needle tract bleeding appeared in eight patients. Mutation analysis was satisfactorily demonstrated in 23 mutations and 20 non-mutations. Ten and 13 mutations were identified by 18-gauge and 20-gauge needle biopsies, respectively. EFGR mutations, including 12 cases of EGFR exon 19 deletion and 11 cases of exon 21 point mutation, were present in 21 patients with adenocarcinomas, one with squamous cell carcinoma, and one with undifferentiated carcinoma. Conclusion. CT-guided FNAB is a feasible and safe technique for obtaining lung tumor tissues for EGFR gene mutation analysis

  16. Different headspace solid phase microextraction--gas chromatography/mass spectrometry approaches to haloanisoles analysis in wine.

    Science.gov (United States)

    Jeleń, Henryk H; Dziadas, Mariusz; Majcher, Małgorzata

    2013-10-25

    Three approaches in determination of six haloanisoles (2,4,6-trichloroanisole, 2,3,4-trichloroanisole, 2,3,6-trichloroanisole, tetrachloroanisole, pentachloroanisole and 2,4,6-tribromoanisole) in wine were compared. Comprehensive gas chromatography - time of flight mass spectrometry (GC×GC-ToF-MS) was described for the first time for this application and compared to gas chromatography-tandem mass spectrometry (GC-MS/MS) using triple quadrupole instrument. These techniques were compared with "standard" analytical approach using GC-MS(SIM). SPME method was developed and used for all separation methods (DVB/PDMS fiber, 70 °C, 30%NaCl, 20 min extraction). Extraction dependence on matrix was discussed using model wines with different ethanol contents (8%, 12%, and 18%) as well as water and different wines (dry white, dry red and sweet liqueur), with the lowest sensitivities obtained for highest ethanol contents in model wine and for liqueur wine. Limits of detection for GC×GC-ToF-MS method were 0.09-2.92 ng/L depending on the examined compound and matrix (compared to 0.1-13.3 ng/L obtained using GC/MS(SIM)). For GC-MS/MS method lower detection limits were achieved than for the GC×GC method (0.01-0.1 ng/L), however comprehensive gas chromatography-mass spectrometry provides full spectral information on analyzed compounds. Both methods had limits of detection far below odor thresholds of haloanisoles in wine, good linearity up to 2000 ng/L tested and good precision, what makes them suitable for analysis of these compounds in low ppt levels. PMID:23932370

  17. Tumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomes.

    Science.gov (United States)

    Wilmott, James S; Field, Matthew A; Johansson, Peter A; Kakavand, Hojabr; Shang, Ping; De Paoli-Iseppi, Ricardo; Vilain, Ricardo E; Pupo, Gulietta M; Tembe, Varsha; Jakrot, Valerie; Shang, Catherine A; Cebon, Jonathan; Shackleton, Mark; Fitzgerald, Anna; Thompson, John F; Hayward, Nicholas K; Mann, Graham J; Scolyer, Richard A

    2015-12-01

    Whole genome sequencing (WGS) of cancer patients' tumours offers the most comprehensive method of identifying both novel and known clinically-actionable genomic targets. However, the practicalities of performing WGS on clinical samples are poorly defined.This study was designed to test sample preparation, sequencing specifications and bioinformatic algorithms for their effect on accuracy and cost-efficiency in a large WGS analysis of human melanoma samples.WGS was performed on melanoma cell lines (n = 15) and melanoma fresh frozen tumours (n = 222). The appropriate level of coverage and the optimal mutation detection algorithm for the project pipeline were determined.An incremental increase in sequencing coverage from 36X to 132X in melanoma tissue samples and 30X to 103X for cell lines only resulted in a small increase (1-2%) in the number of mutations detected, and the quality scores of the additional mutations indicated a low probability that the mutations were real. The results suggest that 60X coverage for melanoma tissue and 40X for melanoma cell lines empower the detection of 98-99% of informative single nucleotide variants (SNVs), a sensitivity level at which clinical decision making or landscape research projects can be carried out with a high degree of confidence in the results. Likewise the bioinformatic mutation analysis methodology strongly influenced the number and quality of SNVs detected. Detecting mutations in the blood genomes separate to the tumour genomes generated 41% more SNVs than if the blood and melanoma tissue genomes were analysed simultaneously. Therefore, simultaneous analysis should be employed on matched melanoma tissue and blood genomes to reduce errors in mutation detection.This study provided valuable insights into the accuracy of SNV with WGS at various coverage levels in human clinical cancer specimens. Additionally, we investigated the accuracy of the publicly available mutation detection algorithms to detect cancer

  18. Germline mutational analysis in negative hereditary breast cancer families by MALDI-TOF mass spectrometry

    OpenAIRE

    Graña, B.; Fachal, L; Darder, E.; Balmaña, J.; Ramón Y Cajal, T.; Blanco, I.; A. Torres; Lázaro, C; Diez, O; Alonso, C; Santamariña, M; Velasco, A.; Teulé, A; Lasa, A; Blanco, A.

    2011-01-01

    Biallelic inactivation of gene causes the rare autosomal recessive disorder Ataxia-telangiectasia (A-T). Female relatives of A-T patients have a two-fold higher risk of developing breast cancer (BC) compared with the general population. mutation carrier identification is laborious and expensive, therefore, a more rapid and directed strategy for mutation profiling is needed. We designed a case-control study to determine the prevalence of 32 known mutations causing A-T in Spanish population in ...

  19. Analysis of microsatellite instability in stool DNA of patients with colorectal cancer using denaturing high performance liquid chromatography

    Institute of Scientific and Technical Information of China (English)

    Seok-Byung Lim; Yong Shin; Sang-Geun Jang; Jae-Hyun Park; Jae-Gahb Park; Seung-Yong Jeong; Il-Jin Kim; Dae Yong Kim; Kyung Hae Jung; Hee Jin Chang; Hyo Seong Choi; Dae Kyung Sohn; Hio Chung Kang

    2006-01-01

    AIM: To evaluate the usefulness of denaturing high performance liquid chromatography (DHPLC) for analyzing microsatellite instability (MSI) status in stool DNA of patients with colorectal cancer.METHODS: A total of 80 cancer tissues from patients with primary sporadic colorectal tumor (proximal cancer:27, distal cancer: 53) and matched stool (which were employed for comparison with the tissues) were analyzed for MSI status in BAT 26. DNA samples extracted from stool were evaluated by nested polymerase chain reaction (PCR) and DHPLC for MSI analysis.RESULTS: Six cases (7.5%) of MSI were identified in BAT 26 from 80 cancer tissues. All the stool DNA samples from patients whose cancer tissue showed MSI also displayed MSI in BAT 26.CONCLUSION: As MSI is one of the established fecal DNA markers to screen colorectal cancer, we propose to use DHPLC for the MSI analysis in fecal DNA.

  20. Comparative analysis of conjugated bile acids in human serum using high-performance liquid chromatography and capillary electrophoresis.

    Science.gov (United States)

    Lee, B L; New, A L; Ong, C N

    1997-12-19

    This paper describes the analysis of conjugated bile acids in human serum using reversed-phase high-performance liquid chromatography (HPLC) and micellar electrokinetic capillary electrophoresis (CE). Samples of healthy subjects and patients with different hepatic diseases were pretreated with a simple preparation procedure using a solid-phase extraction technique. The optimal analytical conditions of both chromatographic methods were investigated for the convenience and reliability for routine analysis. Both HPLC and CE methods were found to be reliable and compatible. The recoveries of nine bile acid conjugates using both methods were generally >85% and reproducibility >90%. The day-to-day variation of retention time was limit of the HPLC method (1 nmol/ml) was five times more sensitive than that of the CE method, the CE method was considered to be more time and cost effective. PMID:9518169

  1. The Analysis of Orange Oil and the Aqueous Solubility of d-Limonene. Two Complementary Gas Chromatography Experiments

    Science.gov (United States)

    Williams, Kathryn R.; Pierce, Russell E.

    1998-02-01

    The monoterpene d-limonene is determined by gas chromatography using anisole as the internal standard. Unknowns for the orange oil analysis are prepared by diluting commercially available Valencia oil with n-hexane (ca. 2% oil by weight). Students determine the d-limonene content from the GC results and divide by the known d-limonene content of Valencia oil (95.03 %) to obtain the wt% oil in the unknown. In the experiment, students determine the concentration of d--limonene in the head-space vapors above aqueous samples containing varying amounts of d--limonene. The concentration in the vapor levels off at the solubility limit. At the University of Florida, the experiments are performed in the beginning analytical (orange oil analysis) and physical chemistry (solubility determination) laboratories, but they are also applicable to other laboratory courses.

  2. Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers.

    Science.gov (United States)

    Yoo, Seong-Keun; Lee, Seungbok; Kim, Su-Jin; Jee, Hyeon-Gun; Kim, Byoung-Ae; Cho, Hyesun; Song, Young Shin; Cho, Sun Wook; Won, Jae-Kyung; Shin, Jong-Yeon; Park, Do Joon; Kim, Jong-Il; Lee, Kyu Eun; Park, Young Joo; Seo, Jeong-Sun

    2016-08-01

    Follicular thyroid carcinoma (FTC) and benign follicular adenoma (FA) are indistinguishable by preoperative diagnosis due to their similar histological features. Here we report the first RNA sequencing study of these tumors, with data for 30 minimally invasive FTCs (miFTCs) and 25 FAs. We also compared 77 classical papillary thyroid carcinomas (cPTCs) and 48 follicular variant of PTCs (FVPTCs) to observe the differences in their molecular properties. Mutations in H/K/NRAS, DICER1, EIF1AX, IDH1, PTEN, SOS1, and SPOP were identified in miFTC or FA. We identified a low frequency of fusion genes in miFTC (only one, PAX8-PPARG), but a high frequency of that in PTC (17.60%). The frequencies of BRAFV600E and H/K/NRAS mutations were substantially different in miFTC and cPTC, and those of FVPTC were intermediate between miFTC and cPTC. Gene expression analysis demonstrated three molecular subtypes regardless of their histological features, including Non-BRAF-Non-RAS (NBNR), as well as BRAF-like and RAS-like. The novel molecular subtype, NBNR, was associated with DICER1, EIF1AX, IDH1, PTEN, SOS1, SPOP, and PAX8-PPARG. The transcriptome of miFTC or encapsulated FVPTC was indistinguishable from that of FA, providing a molecular explanation for the similarly indolent behavior of these tumors. We identified upregulation of genes that are related to mitochondrial biogenesis including ESRRA and PPARGC1A in oncocytic follicular thyroid neoplasm. Arm-level copy number variations were correlated to histological and molecular characteristics. These results expanded the current molecular understanding of thyroid cancer and may lead to new diagnostic and therapeutic approaches to the disease. PMID:27494611

  3. Genetic mutation analysis at early stages of cell line development using next generation sequencing.

    Science.gov (United States)

    Wright, Chapman; Groot, Joost; Swahn, Samantha; McLaughlin, Helen; Liu, Mei; Xu, Chongfeng; Sun, Chao; Zheng, Eric; Estes, Scott

    2016-05-01

    A central goal for most biopharmaceutical companies is to reduce the development timeline to reach clinical proof of concept. This objective requires the development of tools that ensure the quality of biotherapeutic material destined for the clinic. Recent advances in high throughput protein analytics provide confidence in our ability to assess productivity and product quality attributes at early stages of cell line development. However, one quality attribute has, until recently, been absent from the standard battery of analytical tests facilitating informed choices early in cell line selection: genetic sequence confirmation. Techniques historically used for mutation analysis, such as detailed mass spectrometry, have limitations on the sample number and turnaround times making it less attractive at early stages. Thus, we explored the utility of Next-Generation Sequencing (NGS) as a solution to address these limitations. Amplicon sequencing is one such NGS technique that is robust, rapid, sensitive, and amenable to multiplexing, all of which are essential attributes for our purposes. Here we report a NGS method based upon amplicon sequencing that has been successfully incorporated into our cell line development workflow alongside other high-throughput protein analytical assays. The NGS method has demonstrated its value by identifying at least one Chinese hamster ovary (CHO) clone expressing a variant form of the biotherapeutic in each of the four clinical programs in which it has been utilized. We believe this sequence confirmation method is essential to safely accelerating the time to clinical proof of concept of biotherapeutics, and guard against delays related to sequence mutations. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:813-817, 2016. PMID:27004436

  4. High-throughput mutational analysis of TOR1A in primary dystonia

    OpenAIRE

    Xiao, Jianfeng; Bastian, Robert W; Perlmutter, Joel. S.; Racette, Brad A.; Tabbal, Samer D; Karimi, Morvarid; Paniello, Randal C; Blitzer, Andrew; Batish, Sat Dev; Wszolek, Zbigniew K; Uitti, Ryan J.; Hedera, Peter; Truong, Daniel D.; Frei, Karen P; Pfeiffer, Ronald F

    2009-01-01

    Background: Although the c.904_906delGAG mutation in Exon 5 of TOR1A typically manifests as early-onset generalized dystonia, DYT1 dystonia is genetically and clinically heterogeneous. Recently, another Exon 5 mutation (c.863G>A) has been associated with early-onset generalized dystonia and some ΔGAG mutation carriers present with late-onset focal dystonia. The aim of this study was to identify TOR1A Exon 5 mutations in a large cohort of subjects with mainly non-generalized primary dystonia. ...

  5. High-throughput mutational analysis of TOR1A in primary dystonia

    OpenAIRE

    Truong Daniel D; Tarsy Daniel; Simon David K; Hedera Peter; Uitti Ryan J; Wszolek Zbigniew K; Batish Sat; Blitzer Andrew; Paniello Randal C; Karimi Morvarid; Tabbal Samer D; Racette Brad A; Perlmutter Joel S; Bastian Robert W; Xiao Jianfeng

    2009-01-01

    Abstract Background Although the c.904_906delGAG mutation in Exon 5 of TOR1A typically manifests as early-onset generalized dystonia, DYT1 dystonia is genetically and clinically heterogeneous. Recently, another Exon 5 mutation (c.863G>A) has been associated with early-onset generalized dystonia and some ΔGAG mutation carriers present with late-onset focal dystonia. The aim of this study was to identify TOR1A Exon 5 mutations in a large cohort of subjects with mainly non-generalized primary dy...

  6. Mutational analysis of divalent metal ion binding in the active site of class II α-mannosidase from sulfolobus solfataricus

    DEFF Research Database (Denmark)

    Hansen, Dennis K.; Webb, Helen; Nielsen, Jonas Willum; Winther, Jakob R.; Willemoes, Martin; Harris, Pernille

    2015-01-01

    Mutational analysis of Sulfolobus solfataricus class II α-mannosidase was focused on side chains that interact with the hydroxyls of the-1 mannosyl of the substrate (Asp-534) or form ligands to the active site divalent metal ion (His-228 and His-533) judged from crystal structures of homologous...

  7. Mutation analysis of SLC26A4 for Pendred syndrome and nonsyndromic hearing loss by high-resolution melting

    DEFF Research Database (Denmark)

    Chen, Neng; Tranebjærg, Lisbeth; Rendtorff, Nanna Dahl; Schrijver, Iris

    2011-01-01

    Pendred syndrome and DFNB4 (autosomal recessive nonsyndromic congenital deafness, locus 4) are associated with autosomal recessive congenital sensorineural hearing loss and mutations in the SLC26A4 gene. Extensive allelic heterogeneity, however, necessitates analysis of all exons and splice sites...

  8. Modification on labeling technique and chromatography mobile phase in the preparation and radiochemical analysis of 135Sm-EDTMP

    International Nuclear Information System (INIS)

    Modification on labeling technique and chromatography mobile phase in the preparation and radiochemical analysis of 153Sm-EDTMP. Preparation of 135Sm-EDTMP. Preparation of 153Sm-EDTMP for the therapy of metastatic bone cencer is carried out in CDRR-BATAN based on the reaction of 153SmCl3 solution with EDTMP in phosphate buffer. Some disadvantages appear from the routine procedure, e.g. relatively lengthy radiochemical analysis, relatively low and fluctuative radioactivity yields, and potentially high radiation exposure and contamination risk to the operator and the working area. The present work is aimed at solving those problems. Radiochemical analysis using Whatman I-paper chromatography was performed in a variety of mobile phases consisting of one, two and three components, while the labeling technique was modified by changing the solvent for the EDTMP and by changing the reactant mixing procedure. It was proven that the of NH4OH 25% - H2O mixture (1 : 9, v/v) as the chromatographic solvent gave faster migration rate better chromatographic behaviour as compared to other mobile phases used in this experiment, including that is used in the routine procedure. The migration distance of 14 cm and 10 cm gave no significant difference on the radiochemical analysis results. The labeling technique by gradual addition of EDTMP in NaOH (pH 9 - 10) into 135SmCl3 solution gave higher radioactivity yield and technically produced lower radiation exponsure and radioactive contamination risk as compared to the routine procedure. The proposed procedure is also better than the EDTMP labeling technique in acetic salt solution. The labeling efficiency achieved was highr than 98%, and therefore do not require any purification step. In general, the results of the present experiment gave good prospect to increase the efficiency and safety in the routine preparation process of 135Sm-EDTMP

  9. Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects

    Directory of Open Access Journals (Sweden)

    Tuch Brian B

    2008-06-01

    Full Text Available Abstract Background The patterns of mutation vary both within and across genomes. It has been shown for a few mammals that mutation rates vary within the genome, while for unknown reasons, the sensu stricto yeasts have uniform rates instead. The generality of these observations has been unknown. Here we examine silent site substitutions in a more expansive set (20 mammals, 27 fungi, 4 insects to determine why some genomes demonstrate this mosaic distribution and why others are uniform. Results We applied several intragene and intergene correlation tests to measure regional substitution patterns. Assuming that silent sites are a reasonable approximation to neutrally mutating sequence, our results show that all multicellular eukaryotes exhibit mutational heterogeneity. In striking contrast, all fungi are mutationally uniform – with the exception of three Candida species: C. albicans, C. dubliniensis, and C. tropicalis. We speculate that aspects of replication timing may be responsible for distinguishing these species. Our analysis also reveals classes of genes whose silent sites behave anomalously with respect to the mutational background in many species, indicating prevalent selective pressures. Genes associated with nucleotide binding or gene regulation have consistently low silent substitution rates in every mammalian species, as well as multiple fungi. On the other hand, receptor genes repeatedly exhibit high silent substitution rates, suggesting they have been influenced by diversifying selection. Conclusion Our findings provide a framework for understanding the regional mutational properties of eukaryotes, revealing a sharp difference between fungi and multicellular species. They also elucidate common selective pressures acting on eukaryotic silent sites, with frequent evidence for both purifying and diversifying selection.

  10. Novel molecularly-imprinted solid-phase microextraction fiber coupled with gas chromatography for analysis of furan.

    Science.gov (United States)

    Hashemi-Moghaddam, Hamid; Ahmadifard, Mojtaba

    2016-04-01

    This study combined a molecularly-imprinted polymer with headspace solid-phase microextraction (HS-SPME). Preparation of molecularly-imprinted polymer is not effective for volatile compounds. To overcome this limitation, pyrrole was chosen as a template for the preparation of the furan-imprinted polymer. The holes in the synthesized polymer were suitable for furan adsorption because the chemical structure of pyrrole is similar to that of furan. The extraction properties of the fiber to furan were examined using an HS-SPME device coupled with gas chromatography-flame ionization detection (GC-FID) and gas chromatography-mass spectrometry (GC-MS). The effects of the extraction parameters of exposure time, sampling temperature, and salt concentration on extraction efficiency were studied. Satisfactory reproducibility was obtained for extractions from spiked water samples at RSDdetection limit for furan was 0.042 ng ml(-1). The fabricated fiber was successfully applied for headspace extraction of furan from tap water and canned tuna as shown by GC-MS analysis. PMID:26838393

  11. Gas Chromatography Analysis with Olfactometric Detection (GC-O as a Useful Methodology for Chemical Characterization of Odorous Compounds

    Directory of Open Access Journals (Sweden)

    Magda Brattoli

    2013-12-01

    Full Text Available The gas chromatography-olfactometry (GC-O technique couples traditional gas chromatographic analysis with sensory detection in order to study complex mixtures of odorous substances and to identify odor active compounds. The GC-O technique is already widely used for the evaluation of food aromas and its application in environmental fields is increasing, thus moving the odor emission assessment from the solely olfactometric evaluations to the characterization of the volatile components responsible for odor nuisance. The aim of this paper is to describe the state of the art of gas chromatography-olfactometry methodology, considering the different approaches regarding the operational conditions and the different methods for evaluating the olfactometric detection of odor compounds. The potentials of GC-O are described highlighting the improvements in this methodology relative to other conventional approaches used for odor detection, such as sensoristic, sensorial and the traditional gas chromatographic methods. The paper also provides an examination of the different fields of application of the GC-O, principally related to fragrances and food aromas, odor nuisance produced by anthropic activities and odorous compounds emitted by materials and medical applications.

  12. Analysis of paralytic shellfish toxins, potential chemical threat agents, in food using hydrophilic interaction liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Jansson, Daniel; Åstot, Crister

    2015-10-23

    A novel method for determining paralytic shellfish toxin (PST) profiles in food was developed using a combination of silica and strong cation exchange (SCX) solid phase extraction (SPE) coupled to hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS). Besides the risk for natural contamination of seafood and drinking water, PSTs also pose potent threats through intentional contamination of food, due to their high toxicity and the wide distributions of toxin-producing algae. The new preparation method aim to maintain the samples' original toxin profiles by avoiding conditions known to induce interconversion or degradation of the PSTs. The method was evaluated for PST extraction from water, milk, orange juice, apple purée, baby food, and blue mussels (Mytilus edulis). The extracts were found to produce reproducible retention times in HILIC-MS/MS analysis. When an authentic toxic mussel sample was analyzed using the novel method, saxitoxin and gonyautoxin-3 were identified, in agreement with data acquired using the Lawrence pre-column oxidation high-performance liquid chromatography-fluorescence detection (HPLC-FLD) method. Overall recoveries of the PSTs from tested foods by the novel method ranged from 36% to 111%. PMID:26404910

  13. Analysis of lipids by gas-liquid chromatography and complementary methods in four strains of Aedes aegypti mosquitoes.

    Science.gov (United States)

    Miller, S; Novak, R J

    1985-01-01

    Fatty acid composition of total lipids, neutral lipids and phospholipids of strains of Aedes aegypti were determined. The fatty acid composition of the strains differed quantitatively with regard to the relative percentage of commonly occurring fatty acids. Gas-liquid chromatography of fatty acid methyl esters showed 18:1 (oleic or elaidic) to be the predominant fatty acid. The fatty acid was identified as oleic by argentation thin-layer chromatography. A modified colorimetric method was used to determine tissue-free fatty acids. The lipids were predominantly triacylglycerol with lesser amounts of free fatty acids and decreasing amount of sterol ester, sterol, monoacylglycerol, diacylglycerol and hydrocarbons. The data show considerable lipid differences between the Caribbean strains (Les Cayes, Haiti, and San Juan, Puerto Rico) and the Jakarta (Indonesia) strain. The Shimba Hills (Kenya) strain was more similar to Jakarta than to the Caribbean strains. The results obtained with the different strains are discussed in relation to the established oral susceptibility to Dengue 1 and Dengue 2, yellow fever, and genetic analysis by isoenzyme studies. PMID:4017543

  14. High-throughput analysis of 19 endogenous androgenic steroids by ultra-performance convergence chromatography tandem mass spectrometry.

    Science.gov (United States)

    Quanson, Jonathan L; Stander, Marietjie A; Pretorius, Elzette; Jenkinson, Carl; Taylor, Angela E; Storbeck, Karl-Heinz

    2016-09-15

    11-Oxygenated steroids such as 11-ketotestosterone and 11-ketodihydrotestosterone have recently been shown to play a putative role in the development and progression of castration resistant prostate cancer. In this study we report on the development of a high throughput ultra-performance convergence chromatography tandem mass spectrometry (UPC(2)-MS/MS) method for the analysis of thirteen 11-oxygenated and six canonical C19 steroids isolated from a cell culture matrix. Using an Acquity UPC(2) BEH 2-EP column we found that UPC(2) resulted in superior selectivity, increased chromatographic efficiency and a scattered elution order when compared to conventional reverse phase ultra-performance liquid chromatography (UPLC). Furthermore, there was a significant improvement in sensitivity (5-50 times). The lower limits of quantification ranged between 0.01-10ngmL(-1), while the upper limit of quantification was 100ngmL(-1) for all steroids. Accuracy, precision, intra-day variation, recovery, matrix effects and process efficiency were all evaluated and found to be within acceptable limits. Taken together we show that the increased power of UPC(2)-MS/MS allows the analyst to complete in vitro assays at biologically relevant concentrations for the first time and in so doing determine the routes of steroid metabolism which is vital for studies of androgen responsive cancers, such as prostate cancer, and could highlight new mechanisms of disease progression and new targets for cancer therapy. PMID:27479683

  15. Quantitative analysis of polymeric procyanidins (Tannins) from grape (Vitis vinifera) seeds by reverse phase high-performance liquid chromatography.

    Science.gov (United States)

    Peng, Z; Hayasaka, Y; Iland, P G; Sefton, M; Høj, P; Waters, E J

    2001-01-01

    A reverse phase C(18) HPLC method with potential for high automated throughput has been developed for the quantitative analysis of polymeric procyanidins (tannins) in grape seed extracts. Chromatography gave rise to 13 distinct UV-absorbing peaks with good baseline separation. The UV-absorbing peak eluting last is distinct and therefore easily quantified. Biochemical analyses including ultrafiltration, protein precipitation, and Sephadex LH20 chromatography combined with electrospray mass spectrometric analyses establish that this peak predominantly contains polymeric procyanidins. The polymers, which appear to be galloylated to various degrees and seem to fragment in a characteristic manner during electrospray mass spectrometry, are well separated from catechins and procyanidin oligomers of up to 4 units. The recovery of polymeric grape seed tannins with this HPLC method was 86%, which is similar to the 89% recovery achieved with commercial quebracho tannins. The concentration of tannins in seeds from ripe Vitis vinifera cv. Shiraz grapes ranged from 1360 to 2830 mg/kg of berries. PMID:11170555

  16. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss

    OpenAIRE

    Gross, Andrew M.; Ryan K. Orosco; Shen, John P.; Egloff, Ann Marie; Carter, Hannah; Hofree, Matan; Choueiri, Michel; Charles S. Coffey; Lippman, Scott M.; Hayes, D. Neil; Cohen, Ezra E.; Grandis, Jennifer R.; Nguyen, Quyen T.; Ideker, Trey

    2014-01-01

    Head and neck squamous cell carcinoma (HNSCC) is characterized by aggressive behavior with a propensity for metastasis and recurrence. Here we report a comprehensive analysis of the molecular and clinical features of HNSCC that govern patient survival. We find that TP53 mutation is frequently accompanied by loss of chromosome 3p, and that the combination of both events associates with a surprising decrease in survival rates (1.9 years versus >5 years for TP53 mutation alone). The TP53-3p inte...

  17. ANALYSIS OF PENTACHLOROPHENOL IN WATER BY PURGE AND TRAP CONCENTRATOR COUPLED TO GAS CHROMATOGRAPHY

    Institute of Scientific and Technical Information of China (English)

    HuixiaLan; YuancaiChen; ZhonghaoChen

    2004-01-01

    It is convenient and time saving to analyze pentachlorophenol (PCP) in water by purge and trap concentrator coupled to gas chromatography that avoids employing a great deal of organic solvent. In this paper, the appropriate purge and trap conditions of PCP are determined: the trapped sorbent is TenaxGC; the purge gas is pure nitrogen and purge flow is 40ml/min; the purge time is 30min. A series of standard PCP water samples 5, 10, 50, 100, 200, 400, 800, 1000ppb are analyzed in order to obtain standard curve, and the linear regressive equation obtained is Y=109.65X-687.72, which correlation coefficient r is 0.9949. The precision of the method is determined with 0.5ppb PCP water sample, and the standard deviation measured is 3%. The detection limit for PCP is 0.2ppb.

  18. ANALYSIS OF PENTACHLOROPHENOL IN WATER BY PURGE AND TRAP CONCENTRATOR COUPLED TOGAS CHROMATOGRAPHY

    Institute of Scientific and Technical Information of China (English)

    Huixia Lan; Yuancai Chen; Zhonghao Chen

    2004-01-01

    It is convenient and time saving to analyze pentachlorophenol (PCP) in water by purge and trap concentrator coupled to gas chromatography that avoids employing a great deal of organic solvent: In this paper, the appropriate purge and trap conditions of PCP are determined: the trapped sorbent is TenaxGC; the purge gas is pure nitrogen and purge flow is 40ml/min; the purge time is 30min. A series of standard PCP water samples 5, 10, 50, 100, 200,400, 800, 1000ppb are analyzed in order to obtain standard curve, and the linear regressive equation obtained is Y=109.65X-687.72, which correlation coefficient r is 0.9949. The precision of the method is determined with 0.5ppb PCP water sample, and the standard deviation measured is 3%. The detection limit for PCP is 0.2ppb.

  19. [Analysis of chlorogenic acid in sunflower cake by thin-layer chromatography].

    Science.gov (United States)

    Zhu, Y; Zhang, S S; Zhang, X L; Chen, J

    2001-01-01

    The analytical method of chlorogenic acid in sunflower cake by thin-layer chromatography(TLC) was developed. With 36% acetic acid as mobile phase and on the polyamide film plate, the Rf value of chlorogenic acid was 0.61. The calibration curve was linear in the range of 0.05 microgram-0.6 microgram of chlorogenic acid with the detection limit of 0.025 microgram and the average recovery of 97.53%. The inter-plate accuracy of chlorogenic acid was 2.57%. With 70% ethyl alcohol as extracting solvent and 30 min of extraction time, the amount of chlorogenic acid in the extract, the residue amount of chlorogenic acid in the sunflower cake and the extraction rate were determined and calculated by applying this method. The optimal time of extraction was found. PMID:12541854

  20. [Analysis of cracking gas compressor fouling by pyrolysis gas chromatography-mass spectrometry].

    Science.gov (United States)

    Hu, Yunfeng; Fang, Fei; Wei, Tao; Liu, Shuqing; Jiang, Guangshen; Cai, Jun

    2013-06-01

    The fouling from the different sections of the cracked gas compressor in Daqing Petrochemical Corporation was analyzed by pyrolysis gas chromatography-mass spectrometry (Py/GC-MS). All the samples were cracked in RJ-1 tube furnace cracker at the cracking temperature of 500 degrees C, and separated with a 60 m DB-1 capillary column. An electron impact ionization (EI) source was used with the ionizing voltage of 70 eV. The results showed the formation of fouling was closely related with cyclopentadiene which accounted for about 50% of the cracking products. Other components detected were 1-butylene, propylene, methane and n-butane. This Py/GC-MS method can be used as an effective approach to analyze the causes of fouling in the petrochemical plants. PMID:24063202

  1. Analysis of N-nitrosodiethylamine by ion chromatography coupled with UV photolysis pretreatment

    Directory of Open Access Journals (Sweden)

    Xueli Li

    2016-04-01

    Full Text Available Nitrosamines such as N-nitrosodiethylamine (NDEA are commonly detected by spectrophotometry after photolysis and Griess reaction (PG in food industries for lower cost. Results of this research indicate that NDEA decays rapidly under UV irradiation, and concentrations of the generated NO2− and NO3− ions vary with photolysis conditions. Thus, the measurement of the PG method may be inconsistent because it is based on the amount of photoproduced NO2−. In addition, more errors may be present in the PG method since NO3− cannot be measured colorimetrically using Griess reagent. In this work, the sum of the concentrations of photoproduced NO2− and NO3− was found to be equivalent to the initial NDEA before photolysis, and a photolysis–ion chromatography method was validated, which may serve as a feasible and accurate method to determine nitrosamines.

  2. Affinity chromatography and capillary electrophoresis for analysis of the yeast ribosomal proteins

    Directory of Open Access Journals (Sweden)

    Miriam S. Goyder

    2012-04-01

    Full Text Available We present a top down separation platform for yeast ribosomalproteins using affinity chromatography and capillary electrophoresiswhich is designed to allow deposition of proteins ontoa substrate. FLAG tagged ribosomes were affinity purified, andrRNA acid precipitation was performed on the ribosomes followedby capillary electrophoresis to separate the ribosomalproteins. Over 26 peaks were detected with excellent reproducibility(<0.5% RSD migration time. This is the first reportedseparation of eukaryotic ribosomal proteins using capillaryelectrophoresis. The two stages in this workflow, affinity chromatographyand capillary electrophoresis, share the advantagesthat they are fast, flexible and have small sample requirementsin comparison to more commonly used techniques. This methodis a remarkably quick route from cell to separation that hasthe potential to be coupled to high throughput readout platformsfor studies of the ribosomal proteome. [BMB reports2012; 45(4: 233-238

  3. Analysis of lipophilic pigments from a phototrophic microbial mat community by high performance liquid chromatography

    Science.gov (United States)

    Palmisano, A. C.; Cronin, S. E.; Des Marais, D. J.

    1988-01-01

    As assay for lipophilic pigments in phototrophic microbial mat communities using reverse phase-high performance liquid chromatography was developed which allows the separation of 15 carotenoids and chloropigments in a single 30 min program. Lipophilic pigments in a laminated mat from a commercial salina near Laguna Guerrero Negro, Baja California Sur, Mexico reflected their source organisms. Myxoxanthophyll, echinenone, canthaxanthin, and zeaxanthin were derived from cyanobacteria; chlorophyll c, and fucoxanthin from diatoms; chlorophyll a from cyanobacteria and diatoms; bacteriochlorophylls a and c, bacteriophaeophytin a, and gamma-carotene from Chloroflexus spp.; and beta-carotene from a variety of phototrophs. Sensitivity of detection was 0.6-6.1 ng for carotenoids and 1.7-12 ng for most chloropigments. This assay represents a significant improvement over previous analyses of lipophilic pigments in microbial mats and promises to have a wider application to other types of phototrophic communities.

  4. A micro gas chromatography column with a micro thermal conductivity detector for volatile organic compound analysis

    Science.gov (United States)

    Sun, J. H.; Cui, D. F.; Chen, X.; Zhang, L. L.; Cai, H. Y.; Li, H.

    2013-02-01

    In this paper, a micro gas chromatography (μGC) system contained a μGC column and a micro thermal conductivity detector (μTCD) was proposed. In order to reduce the volume of the system, some micro heaters were integrated on the surface and backside of the GC column, which could provide a robust temperature programming capability and rapidly increase the temperature of the μGC column. In addition, a silicon-glass μTCD with four-thermistor thermal conductivity cells that can offer significant advantages over previously reported designs including low dead volume, good thermal isolation, and elimination of the thermal noise was proposed in this paper. Experimental results have indicated that the μGC system with a detection limit of several ppm concentration levels separated and detected the benzene, toluene, and styrene in less than 3 min, and the μGC system also exhibited a good linear response in the test range.

  5. Trace analysis of chloramphenicol residues in eggs, milk, and meat: comparison of gas chromatography radioimmunoassay

    International Nuclear Information System (INIS)

    A radioimmunological assay (RIA) to detect chloramphenicol (CAP) residues in eggs, milk, and meat is described. For tissues and other edible products of chloramphenicol-treated animals (chickens, cows, and pigs), the limit of detection is about 200 ng/kg. Residue levels above 1 μg/kg can easily be quantitated. When highly specific antisera produced in sheep were used, cross-reactivity was insignificant except for metabolites deviating from the parent compound in the acyl side chain only. Thiamphenicol fails to bind to the antisera; hence, it does not interfere with the assay. In the procedure described, the role of cleanup is merely to remove lipids. Thus, skim milk can be analyzed following appropriate dilution without cleanup. The results obtained by RIA were confirmed by gas chromatography with electron capture detection. The new RIA allows rapid, sensitive, and specific screening of large numbers of samples

  6. Restricted-access media development for direct analysis of drugs in biofluids using capillary liquid chromatography.

    Science.gov (United States)

    Jarmalaviciene, Reda; Kornysova, Olga; Bendokas, Vidmantas; Westerlund, Douglas; Buszewski, Boguslaw; Maruska, Audrius

    2008-07-01

    In analytical sciences the design of novel materials and stationary phases for the sample preparation and separation of analytes from biological fluids is needed. In this work we present different strategies for modification of stationary phases to produce tailored solutions for the analytical problem. In this context a novel shielded polymeric reversed-phase monolithic material was prepared in the presence of different numbers of reactive groups and concentrations of the coating polymer. Chromatographic experiments were performed using benzoic acid propyl ester in order to characterize the hydrophobicity and efficiency of the different restricted-access continuous beds prepared. Inverse size-exclusion chromatography was used for investigation of the pore structure properties of the beds. Capillary columns were applied for nanochromatography of biological fluids containing a mixture of nitrazepamum and medazepamum. PMID:18392755

  7. Liquid chromatography/coordination ion spray-mass spectrometry for the analysis of rubber vulcanization products.

    Science.gov (United States)

    Hayen, Heiko; Alvarez-Grima, M Montserrat; Debnath, Subhas C; Noordermeer, Jacques W M; Karst, Uwe

    2004-02-15

    Liquid chromatography/coordination ion spray-mass spectrometry has been used for the identification of reaction products in a model rubber vulcanization process. After LC separation using reversed-phase conditions, AgBF(4) in acetonitrile was added, and strong signals were observed for silica-rubber coupling agents and products of the reaction between these and alkenes. The method performs best for substances containing sulfur chains with chain lengths between two and eight sulfur atoms, but sulfur-free compounds containing triethoxysilyl groups were detected as well. For the latter, the postcolumn addition of NaBF(4) proved to be a suitable alternative. Besides the coupling agents, various reaction products, including sulfur-chain bridged alkenes were identified. PMID:14961739

  8. CEBPA mutations in patients with de novo acute myeloid leukemia: data analysis in a Chinese population

    Directory of Open Access Journals (Sweden)

    Su L

    2016-06-01

    Full Text Available Long Su, SuJun Gao, XiaoLiang Liu, YeHui Tan, Lu Wang, Wei Li Cancer Center, The First Hospital, Jilin University, Changchun, People’s Republic of China Background: This study was aimed to explore the clinical characteristics and prognoses of acute myeloid leukemia (AML patients with CEBPA mutations. Patients and methods: Three hundred and forty-five patients with de novo AML were retrospectively analyzed with regard to CEBPA mutations, clinical characteristics, therapeutic responses, and long-term outcomes. Results: CEBPA mutations were detected in 59 patients (17.10%, with 47 cases harboring double mutations and 12 cases harboring single mutations. In those with a normal karyotype (NK, 44 cases (25.29% were detected with CEBPA mutations. The following characteristics were observed in CEBPA-mutated patients: most (66.10% of them were M1 or M2; they presented with higher peripheral white blood cell counts (23.71 [12.6, 60.02] ×109/L versus 7.34 [2.38, 26.63] ×109/L; u=4.944, P<0.001 and higher hemoglobin levels (89.64±23.05 g/L versus 75.65±23.65 g/L; t=4.156, P<0.001 than those observed in patients without the mutation; and the expression of CD7 and HLA-DR was higher, whereas that of CD34 and CD56 was lower in patients with the mutation than in those without the mutation. Compared with those without the mutation, patients with CEBPA mutations had a superior complete remission rate (75.0% versus 56.54%; χ2=6.185, P=0.013 and superior overall survival (P=0.034. Conclusion: The frequency of CEBPA mutations may be higher in Chinese patients with AML than has been reported in populations of western countries, and the presence of CEBPA mutations is an indication of favorable prognoses for these patients. Keywords: acute myeloid leukemia, CEBPA mutations, immunophenotype, complete remission, long-term prognoses

  9. Genome wide SNP comparative analysis between EGFR and KRAS mutated NSCLC and characterization of two models of oncogenic cooperation in non-small cell lung carcinoma

    Directory of Open Access Journals (Sweden)

    Tremblay-Gravel Maxime

    2008-06-01

    Full Text Available Abstract Background Lung cancer with EGFR mutation was shown to be a specific clinical entity. In order to better understand the biology behind this disease we used a genome wide characterization of loss of heterozygosity and amplification by Single Nucleotide Polymorphism (SNP Array analysis to point out chromosome segments linked to EGFR mutations. To do so, we compared genetic profiles between EGFR mutated adenocarcinomas (ADC and KRAS mutated ADC from 24 women with localized lung cancer. Results Patterns of alterations were different between EGFR and KRAS mutated tumors and specific chromosomes alterations were linked to the EGFR mutated group. Indeed chromosome regions 14q21.3 (p = 0.027, 7p21.3-p21.2 (p = 0.032, 7p21.3 (p = 0.042 and 7p21.2-7p15.3 (p = 0.043 were found significantly amplified in EGFR mutated tumors. Within those regions 3 genes are of special interest ITGB8, HDAC9 and TWIST1. Moreover, homozygous deletions at CDKN2A and LOH at RB1 were identified in EGFR mutated tumors. We therefore tested the existence of a link between EGFR mutation, CDKN2A homozygous deletion and cyclin amplification in a larger series of tumors. Indeed, in a series of non-small-cell lung carcinoma (n = 98 we showed that homozygous deletions at CDKN2A were linked to EGFR mutations and absence of smoking whereas cyclin amplifications (CCNE1 and CCND1 were associated to TP53 mutations and smoking habit. Conclusion All together, our results show that genome wide patterns of alteration differ between EGFR and KRAS mutated lung ADC, describe two models of oncogenic cooperation involving either EGFR mutation and CDKN2A deletion or cyclin amplification and TP53 inactivating mutations and identified new chromosome regions at 7p and 14q associated to EGFR mutations in lung cancer.

  10. Quantitative Analysis of [11C]-Erlotinib PET Demonstrates Specific Binding for Activating Mutations of the EGFR Kinase Domain

    Directory of Open Access Journals (Sweden)

    J. Ryan Petrulli

    2013-12-01

    Full Text Available Activating mutations of the epidermal growth factor receptor (EGFR occur in multiple tumor types, including non-small cell lung cancer (NSCLC and malignant glioma, and have become targets for therapeutic intervention. The determination of EGFR mutation status using a noninvasive, molecular imaging approach has the potential for clinical utility. In this study, we investigated [11C]-erlotinib positron emission tomography (PET imaging as a tool to identify activating mutations of EGFR in both glioma and NSCLC xenografts. Radiotracer specific binding was determined for high and low specific activity (SA [11C]-erlotinib PET scans in mice bearing synchronous human cancer xenografts with different EGFR expression profiles (PC9, HCC827, U87, U87 ΔEGFR, and SW620. Although xenograft immunohistochemistry demonstrated constitutive EGFR phosphorylation, PET scan analysis using the Simplified Reference Tissue Model showed that only kinase domain mutant NSCLC (HCC827 and PC9 had significantly greater binding potentials in high versus low SA scans. Xenografts with undetectable EGFR expression (SW620, possessing wild-type EGFR (U87, and expressing an activating extracellular domain mutation (U87 ΔEGFR were indistinguishable under both high and low SA scan conditions. The results suggest that [11C]-erlotinib is a promising radiotracer that could provide a novel clinical methodology for assessing EGFR and erlotinib interactions in patients with tumors that harbor EGFR-activating kinase domain mutations.

  11. Genetic mutation analysis in Japanese patients with non-syndromic congenital heart disease.

    Science.gov (United States)

    Yoshida, Akiko; Morisaki, Hiroko; Nakaji, Mai; Kitano, Masataka; Kim, Ki-Sung; Sagawa, Koichi; Ishikawa, Shiro; Satokata, Ichiro; Mitani, Yoshihide; Kato, Hitoshi; Hamaoka, Kenji; Echigo, Shigeyuki; Shiraishi, Isao; Morisaki, Takayuki

    2016-02-01

    Congenital heart disease (CHD) is the most common birth defect occurring in humans and some transcriptional factors have been identified as causative. However, additional mutation analysis of these genes is necessary to develop effective diagnostic and medical treatment methods. We conducted sequence analysis of the coding regions of NKX2.5, GATA4, TBX1, TBX5, TBX20, CFC1 and ZIC3 in 111 Japanese patients with non-syndromic CHD and 9 of their relatives. All patient samples were also analyzed by multiplex ligation-dependent probe amplification using probes involved in chromosome deletion related to CHD. Five novel variations of TBX5, GATA4 and TBX20 were detected in 6 of the patients, whereas none were found in 200 controls. The TBX5 variation p.Pro108Thr, located in the T-box domain, was identified in a patient with tricuspid atresia, an exon-intron boundary variation of GATA4 (IVS4+5G>A) was detected in a Tetralogy of Fallot patient and an 8p23 microdeletion was detected in one patient with atrioventricular septal defect and psychomotor delay. A total of seven non-synonymous polymorphisms were found in the patients and controls. Accumulation of novel variations of genes involving the cardiac development may be required for better understanding of CHD. PMID:26490186

  12. Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants

    Directory of Open Access Journals (Sweden)

    Dina A. Ghoraba

    2015-02-01

    Full Text Available Methylmalonic aciduria (MMA is an autosomal recessive disorder of methylmalonate and cobalamin (cbl; vitamin B12 metabolism. It is an inborn error of organic acid metabolism which commonly results from a defect in the gene encoding the methylmalonyl-CoA mutase (MCM apoenzyme. Here we report the results of mutation study of exon 2 of the methylmalonyl CoA mutase (MUT gene, coding MCM residues from 1 to 128, in ten unrelated Egyptian families affected with methylmalonic aciduria. Patients were presented with a wide-anion gap metabolic acidosis. The diagnosis has established by the measurement of C3 (propionylcarnitine and C3:C2 (propionylcarnitine/acetylcarnitine in blood by using liquid chromatography–tandem mass spectrometry (LC/MS–MS and was confirmed by the detection of an abnormally elevated level of methylmalonic acid in urine by using gas chromatography–mass spectrometry (GC/MS and isocratic cation exchange high-performance liquid-chromatography (HPLC. Direct sequencing of gDNA of the MUT gene exon 2 has revealed a total of 26 allelic variants: ten of which were intronic, eight were located upstream to the exon 2 coding region, four were novel modifications predicted to affect the splicing region, three were novel mutations within the coding region: c.15G>A (p.K5K, c.165C>A (p.N55K and c.7del (p.R3EfsX14, as well as the previously reported mutation c.323G>A (p.R108H.

  13. Analysis of libraries of 'Micro-Tom' tomato mutations induced by heavy-ion bombardment

    International Nuclear Information System (INIS)

    Fruit setting, development, and ripening are complex, genetically programmed processes. Identifying the factors that control these processes is important for understanding the mechanisms of reproductive development. We induced mutations in the tomato cultivar 'Micro-Tom' by irradiation with accelerated heavy ions (HII), recently established as an effective method for inducing mutations in plants, and constructed mutation libraries. 'Micro-Tom' showed lower sensitivities to higher HII doses. The survival rate of 'Micro-Tom' was about 50% with both ions. Screening 6,814 M1 plants, we found various mutations, including those affecting the sizes of plants, leaves, or fruit, and one conferring a broccoli-like inflorescence. This M1 mutant resembles tomato anantha mutant,in which the development of floral primordia is blocked before organogenesis. Because we could not obtain seeds from this mutant, inheritance and segregation of the trait are unknown, but anantha was reported, caused by a recessive mutation. The isolation of monogenic homozygous recessive mutants in the M1 generation has not commonly been described in other mutational studies using many plant species, although our group isolated such mutants in sweet pepper by M1 plant selection in HII mutational studies. To date, we have visually phenotyped 1,175 M2 families (five sibs per line) in the field, and found 262 plants differing from the wild type in one or more characteristics. These results suggest that such mutation libraries could be powerful tools to explain the reproductive development of plants. (author)

  14. [Mutational analysis of the MECP2 gene by direct sequencing in Hungarian patients with Rett syndrome

    NARCIS (Netherlands)

    Karteszi, J.; Hollody, K.; Bene, J.; Morava, E.; Hadzsiev, K.; Czako, M.; Melegh, B.; Kosztolanyi, G.Y.

    2004-01-01

    INTRODUCTION: Rett syndrome is an X-linked neurodevelopmental disorder characterized by loss of acquired skills and stereotypical hand movements. Mutations in the gene encoding methyl-CpG-binding protein 2 have been identified as cause of Rett syndrome in 1999. AIM: The authors initialized mutation

  15. Fifteen novel FBN1 mutations causing Marfan syndrome detected by heteroduplex analysis of genomic amplicons

    Energy Technology Data Exchange (ETDEWEB)

    Nijbroek, G.; Sood, S.; McIntosh, I. [John Hopkins Univ. School of Medicine, Baltimore, MD (United States)] [and others

    1995-07-01

    Mutations in the gene encoding fibrillin-1 (FBN1), a component of the extracellular microfibril, cause the Marfan syndrome (MFS). This statement is supported by the observations that the classic Marfan phenotype cosegregates with intragenic and/or flanking marker alleles in all families tested and that a significant number of FBN1 mutations have been identified in affected individuals. We have now devised a method to screen the entire coding sequence and flanking splice junctions of FBN1. On completion for a panel of nine probands with classic MFS, six new mutations were identified that accounted for disease in seven (78%) of nine patients. Nine additional new mutations have been characterized in the early stages of a larger screening project. These 15 mutations were equally distributed throughout the gene and, with one exception, were specific to single families. One-third of mutations created premature termination codons, and 6 of 15 substituted residues with putative significance for calcium finding to epidermal growth factor (EGF)-like domains. Mutations causing severe and rapidly progressive disease that presents in the neonatal period can occur in a larger region of the gene than previously demonstrated, and the nature of the mutation is as important a determinant as its location, in predisposing to this phenotype. 56 refs., 5 figs., 3 tabs.

  16. Analysis of mutations in the cystic fibrosis transmembrane regulator (CFTR gene in patients with obstructive azoospermia

    Directory of Open Access Journals (Sweden)

    Andrea L.F. Bernardino

    2003-01-01

    Full Text Available Congenital bilateral absence of the vas deferens (CBAVD accounts for 1%-2% of sterility in men. A high incidence of mutations, as well as the involvement of the 5T variant of the T tract length in intron 8 of the cystic fibrosis conductance regulator (CFTR gene, have been previously described in males with CBAVD. Herein we report the screening for mutations and for the 5T variant of the CFTR gene in 17 patients with CBAVD and three others with non-CABVD obstructive azoospermia. In the CBAVD group, three patients (15% were compound heterozygotes for mutations, and five patients (25% had a mutation in one allele and the 5T variant in the other; the 5T variant was also present in two other patients, one of them being homozygous. The most frequent mutation was DF508, present on five chromosomes (12.5%. A novel missense mutation (A399D was detected in a Japanese CBVAD patient. Our results yield further evidence for a strong association between male obstructive azoospermia caused by CBAVD and mutation/5T variant in the CFTR gene. The search for CFTR mutations in such patients is thus recommended for genetic counseling of couples who undergo assisted fertilization due to CBAVD.

  17. Mutation analysis of breast cancer gene BRCA among breast cancer Jordanian females

    International Nuclear Information System (INIS)

    To screen mutations of the tumor suppressor breast cancer susceptibility gene 1 (BRCA1) within 3 exons among Jordanian breast cancer females. A total of 135 Jordanian breast cancer females were genetically analyzed by denaturing gradient electrophoresis (DGGE) for mutation detection in 3 BRCA1 exons (2, 11 and 20) between 2000-2002 in Al-Basheer Hospital, Amman, Jordan. Of the studied patients 50 had a family history of breast cancer, 28 had a family history of cancer other than breast cancer, and 57 had no family history of any cancer. Five germline mutations were detected among breast cancer females with a family history of breast cancers (one in exon 2 and 4 mutations in exon 11). Another germline mutation (within exon 11) was detected among breast cancer females with family history of cancer other than breast cancer, and no mutation was detected among breast cancer females with no family history of any cancer or among normal control females. Screening mutations within exon 2, exon 11 and exon 20 showed that most screened mutations were within BRCA1 exon 11 among breast cancer Jordanian families with a family history of breast cancer. (author)

  18. Genetic diagnosis of Liddle's syndrome by mutation analysis of SCNN1B and SCNN1G in a Chinese family

    Institute of Scientific and Technical Information of China (English)

    WANG Lin-ping; FAN Xiao-han; JIANG Xiong-jing; ZHANG Hui-min; HUI Ru-tai; GAO Ling-gen; ZHOU Xian-liang; WU Hai-ying; ZHANG Lin; WEN Dan; LI Yue-hua; LIU Ya-xin; TIAN Tao

    2012-01-01

    Background Liddle's syndrome is a rare autosomal-dominant monogenic form of salt-sensitive hypertension.This study aimed to screen the gene mutation in β and y subunits of the epithelial sodium channel (ENaC) of a Chinese family with Liddle's syndrome,an autosomal dominant form of hypertension.Methods DNA samples from the proband with early-onset,treatment-resistant hypertension and suppressed plasma renin activity were initially screened for mutations in the C-terminal exons of the ENaC β or Y subunit genes,usingamplification by polymerase chain reaction and direct DNA sequencing.We also screened the C-terminus of SCNN1B and SCNN1G in family members,and screened for the mutation in 150 controls.Results Genetic analysis of the β ENaC gene revealed a missense mutation of CCC to TCC at codon 616 in the proband,her mother and her grandmother.One hundred and fifty randomly selected controls had not the mutation,indicating that this is not a common genetic polymorphism.There was no mutation of the Y ENaC gene in any of the individuals examined.Conclusions Through direct DNA sequencing analysis,we established the diagnosis of Liddle's syndrome for the proband and her families,and provided tailored therapies to this abnormality.These results provide further evidence that Pro616Ser is a critical amino acid that has a key role in the inhibition of sodium channel activity.

  19. Genetic study of autosomal dominant progressive external ophthalmoplegia and familial myasthenia gravis : linkage analysis, candidate gene cloning and mutation detection

    OpenAIRE

    Li, Fang-Yuan

    2001-01-01

    Identification of genes responsible for familial human diseases is a major task of medical genetics. In this process, linkage analysis, candidate gene screening and mutation detection are the three major steps (Paper I-VI). The purpose of this study was to elucidate the genetic backgrounds of autosomal dominant progressive external ophthalmoplegia (adPEO) and familial inyasthenia gravis (FMG). The methods applied in this study for linkage analysis and repeat expansion we...

  20. KRAS mutation analysis in ovarian samples using a high sensitivity biochip assay

    Directory of Open Access Journals (Sweden)

    Reinthaller Alexander

    2009-04-01

    Full Text Available Abstract Background Mutations in the KRAS gene are one of the most frequent genetic abnormalities in ovarian carcinoma. They are of renewed interest as new epidermal growth factor receptor (EGFR-targeted therapies are being investigated for use in ovarian carcinoma. As KRAS mutations are associated with poor response and resistance to EGFR-targeting drugs, this study was conducted to obtain more information on the spectrum of KRAS mutations in ovarian carcinoma. Methods The presence of KRAS mutations in codon 12 and 13 was analyzed in frozen and formalin-fixed paraffin-embedded (FFPE tissue with a low density biochip platform. 381 malignant (29 borderline malignancy, 270 primary carcinomas, and 82 recurrent carcinomas and 22 benign tissue samples from a total of 394 patients were examined. KRAS mutational status of each sample was correlated with dignity, FIGO stage, grade, histology, and survival. Results KRAS mutations were found in 60 (15% samples with 58 samples deriving from malignant tissue and 2 samples deriving from benign tissue. In 55 (92% samples codon 12 was found to be mutated. Frozen and FFPE samples concurred with respect to KRAS mutation status. Conclusion KRAS mutation is a common event in ovarian cancer primarily in carcinomas of lower grade, lower FIGO stage, and mucinous histotype. The KRAS mutational status is no prognostic factor for patients treated with standard therapy. However, in line with experience from colorectal cancer and non-small-cell-lung cancer (NSCLC, it may be important for prediction of response to EGFR-targeted therapies.

  1. Precise Detection of IDH1/2 and BRAF Hotspot Mutations in Clinical Glioma Tissues by a Differential Calculus Analysis of High-Resolution Melting Data.

    Science.gov (United States)

    Hatae, Ryusuke; Hata, Nobuhiro; Yoshimoto, Koji; Kuga, Daisuke; Akagi, Yojiro; Murata, Hideki; Suzuki, Satoshi O; Mizoguchi, Masahiro; Iihara, Koji

    2016-01-01

    High resolution melting (HRM) is a simple and rapid method for screening mutations. It offers various advantages for clinical diagnostic applications. Conventional HRM analysis often yields equivocal results, especially for surgically obtained tissues. We attempted to improve HRM analyses for more effective applications to clinical diagnostics. HRM analyses were performed for IDH1R132 and IDH2R172 mutations in 192 clinical glioma samples in duplicate and these results were compared with sequencing results. BRAFV600E mutations were analyzed in 52 additional brain tumor samples. The melting profiles were used for differential calculus analyses. Negative second derivative plots revealed additional peaks derived from heteroduplexes in PCR products that contained mutations; this enabled unequivocal visual discrimination of the mutations. We further developed a numerical expression, the HRM-mutation index (MI), to quantify the heteroduplex-derived peak of the mutational curves. Using this expression, all IDH1 mutation statuses matched those ascertained by sequencing, with the exception of three samples. These discordant results were all derived from the misinterpretation of sequencing data. The effectiveness of our approach was further validated by analyses of IDH2R172 and BRAFV600E mutations. The present analytical method enabled an unequivocal and objective HRM analysis and is suitable for reliable mutation scanning in surgically obtained glioma tissues. This approach could facilitate molecular diagnostics in clinical environments. PMID:27529619

  2. Analysis of radioactive mixed hazardous wastes using derivatization gas chromatography/mass spectrometry(GC/MS) and liquid chromatography(LC)

    International Nuclear Information System (INIS)

    At the Hanford site in southeastern Washington, 24 of the 177 high-level waste tanks are being watched closely because of the possibility that flammable gas mixtures may be produced from the mixed wastes contained in the storage tanks. One tank in particular, Tank 241-SY-101 (Tank 101-SY), has exhibited episodic releases of flammable gas mixtures since its final filling in the late 1970s. It has been postulated that the organic compounds present in the waste may be precursors to the production of hydrogen. Six samples of core segments from Tank 101-SY, obtained during the window E core sampling, have been analyzed for organic constituents using derivatization gas chromatography/mass spectrometry (GC/MS), liquid chromatography (LC), and LC/MS. Four of the samples were from the upper region, or convective layer, of the tank and two were from the lower, nonconvective layer. The combined techniques of derivatization GC/MS and LC have accounted for approximately 71 to 93% of the total organic carbon depending on the sample. In addition, normal paraffin hydrocarbon (C12-C15) was detected in the convective layer samples

  3. Analysis of organics in waste from tank 101-SY using derivatization gas chromatography/mass spectrometry (GC/MS) and liquid chromatography (LC)

    International Nuclear Information System (INIS)

    Twenty-three of the 177 high-level waste storage tanks at the Hanford Site in southeastern Washington are being watched closely because of the possibility that flammable gas mixtures may be produced from the mixed wastes contained in the storage tanks. One tank in particular, Tank 241-SY-101 (Tank 101-SY), has exhibited episodic releases of flammable gas mixtures since its final filling in the late 1970s. It has been postulated that the organic compounds present in the waste may be precursors to the production of hydrogen. Six samples of core segments from Tank 101-SY, obtained during the window E core sampling, have been analyzed for organic constituents using derivatization gas chromatography/mass spectrometry (GC/MS), liquid chromatography (LC), and LC/MS. Four of the samples were from the upper region, or convective layer, of the tank and two were from the lower, nonconvective layer. The combined techniques of derivatization GC/MS and LC have accounted for approximately 71 to 93% of the total organic carbon (TOC) depending on the sample

  4. Impact of gas chromatography and mass spectrometry combined with gas chromatography and olfactometry for the sex differentiation of Baccharis articulata by the analysis of volatile compounds.

    Science.gov (United States)

    Minteguiaga, Manuel; Umpiérrez, Noelia; Fariña, Laura; Falcão, Manuel A; Xavier, Vanessa B; Cassel, Eduardo; Dellacassa, Eduardo

    2015-09-01

    The Baccharis genus has more than 400 species of aromatic plants. However, only approximately 50 species have been studied in oil composition to date. From these studies, very few take into consideration differences between male and female plants, which is a significant and distinctive factor in Baccharis in the Asteraceae family. Baccharis articulata is a common shrub that grows wild in south Brazil, northern and central Argentina, Bolivia, Paraguay and Uruguay. It is considered to be a medicinal plant and is employed in traditional medicine. We report B. articulata male and female volatile composition obtained by simultaneous distillation-extraction technique and analyzed by gas chromatography with mass spectrometry. Also, an assessment of aromatic differences between volatile extracts was evaluated by gas chromatography with olfactometry. The results show a very similar chemical composition between male and female extracts, with a high proportion of terpene compounds of which β-pinene, limonene and germacrene D are the main components. Despite the chemical similarity, great differences in aromatic profile were found: male plant samples exhibited the strongest odorants in number and intensity of aromatic attributes. These differences explain field observations which indicate differences between male and female flower aroma, and might be of ecological significance in the attraction of pollinating insects. PMID:26140379

  5. Pesticide analysis at ppt concentration levels: coupling nano-liquid chromatography with dielectric barrier discharge ionization-mass spectrometry.

    Science.gov (United States)

    Mirabelli, Mario F; Wolf, Jan-Christoph; Zenobi, Renato

    2016-05-01

    We report the coupling of nano-liquid chromatography (nano-LC) with an ambient dielectric barrier discharge ionization (DBDI)-based source. Detection and quantification were carried out by high-resolution mass spectrometry (MS), using an LTQ-Orbitrap in full scan mode. Despite the fact that nano-LC systems are rarely used in food analysis, this coupling was demonstrated to deliver extremely high sensitivity in pesticide analysis, with limits of detection (LODs) as low as 10 pg/mL. In all cases, the limits of quantification (LOQs) were compliant with the current EU regulation. An excellent signal linearity over up to four orders of magnitude was also observed. Therefore, this method can easily compete with conventional GC-(EI)-MS or LC-ESI-MS/MS methods and in some cases outperform them. The method was successfully tested for food sample analysis, with apples and baby food, extracted using the QuEChERS approach. Our results demonstrate an outstanding sensitivity (at femtogram level) and reproducibility of the nano-LC-DBDI coupling, capable of improving routine pesticide analysis. To the best of our knowledge, this is the most sensitive and reproducible plasma-MS-based method for pesticide analysis reported to date. PMID:26898206

  6. Analysis of 10 systemic pesticide residues in various baby foods using liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Yang, Angel; Abd El-Aty, A M; Park, Jong-Hyouk; Goudah, Ayman; Rahman, Md Musfiqur; Do, Jung-Ah; Choi, Ok-Ja; Shim, Jae-Han

    2014-06-01

    Ten systemic pesticides, comprising methomyl, thiamethoxam, acetamiprid, carbofuran, fosthiazate, metalaxyl, azoxystrobin, diethofencarb, propiconazole, and difenoconazole, were detected in 13 baby foods (cereals, boiled potatoes, fruit and milk) using QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) for sample preparation and liquid chromatography tandem mass spectrometry for analysis. The matrix-matched calibration curves showed good linearity with determination coefficients (R(2) ) >0.992. The limits of detection and quantitation were 0.0015-0.003 and 0.005-0.01 mg/kg, respectively. The mean recoveries of three different concentrations ranged from 69.2 to 127.1% with relative standard deviations pesticide residues. This method is suitable for the identification and quantification of systemic pesticides with matrix-matched standards in various baby foods. PMID:24861738

  7. Direct analysis of volatile fatty acids in marine sediment porewater by two-dimensional ion chromatography-mass spectrometry

    DEFF Research Database (Denmark)

    Glombitza, Clemens; Pedersen, Jeanette; Røy, Hans;

    2014-01-01

    ion monitoring mode. No sample pretreatment is required and statistically determined detection limits are below 25 ppb (μg L–1). The method can also be used without the online coupling to a mass spectrometer. In the latter case, quantification of the VFAs can be done by the conductivity detector......Volatile fatty acids (VFAs) are key intermediates in the microbial food web. However, the analysis of low concentrations of VFAs in marine porewater is hampered by interference from high concentrations of inorganic ions. Published methods often use sample pretreatment, including distillation...... by two-dimensional ion chromatography-mass spectrometry (2D IC-MS). The first chromatographic dimension is used to separate the VFAs from the inorganic ions whereas the second dimension separates the individual VFAs. Quantification and identification are achieved by online mass spectrometry in selected...

  8. Comparative analysis of different plant oils by high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry.

    Science.gov (United States)

    Jakab, Annamaria; Héberger, Károly; Forgács, Esther

    2002-11-01

    Different vegetable oil samples (almond, avocado, corngerm, grapeseed, linseed, olive, peanut, pumpkin seed, soybean, sunflower, walnut, wheatgerm) were analyzed using high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry. A gradient elution technique was applied using acetone-acetonitrile eluent systems on an ODS column (Purospher, RP-18e, 125 x 4 mm, 5 microm). Identification of triacylglycerols (TAGs) was based on the pseudomolecular ion [M+1]+ and the diacylglycerol fragments. The positional isomers of triacylglycerol were identified from the relative intensities of the [M-RCO2]+ fragments. Linear discriminant analysis (LDA) as a common multivariate mathematical-statistical calculation was successfully used to distinguish the oils based on their TAG composition. LDA showed that 97.6% of the samples were classified correctly. PMID:12462617

  9. Ultra performance liquid chromatography analysis to study the changes in the carotenoid profile of commercial monovarietal fruit juices.

    Science.gov (United States)

    Delpino-Rius, Antoni; Eras, Jordi; Marsol-Vall, Alexis; Vilaró, Francisca; Balcells, Mercè; Canela-Garayoa, Ramon

    2014-02-28

    We have developed an analytical method that allows the simultaneous determination of epoxycarotenoids, hydroxycarotenoids and carotenes in monovarietal fresh homemade and industrially processed fruit products. Analyses were carried out using ultra performance liquid chromatography (UPLC). The extraction method was optimized using methanol as the first extraction solvent for lyophilized samples followed by a saponification step. Recoveries ranged between 75% and 104% depending on the compound. Repeatability was better than 10% for all compounds (%RSD, n=3). The chromatographic analysis takes less than 17min. In this short period, up to 27 carotenoids were identified in apple, peach and pear products. The developed method allowed us to differentiate juice from six varieties of apple by their carotenoid profile. Moreover, the methodology allows us to differentiate the carotenoid profiles from commercial juices and homemade fresh peach and pear juices, as well as to study the rearrangements of 5,6- to 5,8-epoxycarotenoids. PMID:24503121

  10. Wheat gluten amino acid analysis by high-performance anion-exchange chromatography with integrated pulsed amperometric detection.

    Science.gov (United States)

    Rombouts, Ine; Lagrain, Bert; Lamberts, Lieve; Celus, Inge; Brijs, Kristof; Delcour, Jan A

    2012-01-01

    This chapter describes an accurate and user-friendly method for determining amino acid composition of wheat gluten proteins and their gliadin and glutenin fractions. The method consists of hydrolysis of the peptide bonds in 6.0 M hydrochloric acid solution at 110°C for 24 h, followed by evaporation of the acid and separation of the free amino acids by high-performance anion-exchange chromatography with integrated pulsed amperometric detection. In contrast to conventional methods, the analysis requires neither pre- or postcolumn derivatization, nor a time-consuming oxidation or derivatization step prior to hydrolysis. Correction factors account for incomplete release of Val and Ile even after hydrolysis for 24 h, and for losses of Ser during evaporation. Gradient conditions including an extra eluent allow multiple sequential sample analyses without risk of Glu accumulation on the anion-exchange column which otherwise would result from high Gln levels in gluten proteins. PMID:22125156

  11. Fourier transform-infrared spectroscopy and Gas chromatography-mass spectroscopy: Reliable techniques for analysis of Parthenium mediated vermicompost

    Science.gov (United States)

    Rajiv, P.; Rajeshwari, Sivaraj; Venckatesh, Rajendran

    2013-12-01

    Fourier transform infrared spectroscopy (FT-IR) and Gas chromatography-mass spectroscopy have been carried out to investigate the chemical composition of Parthenium mediated vermicompost. Four different concentrations of Parthenium and cow dung mixtures were vermicomposted using the earthworms (Eudrilus eugeniae). FT-IR spectra reveal the absence of Parthenin toxin (sesquiterpene lactone) and phenols in vermicompost which was obtained from high concentration of cow dung mixed treatments. GC-MS analysis shows no phenolic compounds and predominant level of intermediate metabolites such as 4,8,12,16-Tetramethylheptadecan-4-olide (7.61%), 2-Pentadecanone, 6,10,14-trimethyl- (5.29%) and Methyl 16-methyl-heptadecanoate (4.69%) during the vermicomposting process. Spectral results indicated that Parthenin toxin and phenols can be eradicated via vermicomposting if mixed with appropriate quantity of cow dung.

  12. Panax ginseng Adventitious Root Suspension Culture: Protocol for Biomass Production and Analysis of Ginsenosides by High Pressure Liquid Chromatography.

    Science.gov (United States)

    Murthy, Hosakatte Niranjana; Paek, Kee Yoeup

    2016-01-01

    Panax ginseng C.A. Meyer (Korean ginseng) is a popular herbal medicine. It has been used in Chinese and Oriental medicines since thousands of years. Ginseng products are generally used as a tonic and an adaptogen to resist the adverse influence of a wide range of physical, chemical and biological factors, and to restore homeostasis. Ginsenosides or ginseng saponins are the principal active ingredients of ginseng. Since ginseng cultivation process is very slow and needs specific environment for field cultivation, cell and tissue cultures are sought as alternatives for the production of ginseng biomass and bioactive compounds. In this chapter, we focus on methods of induction of adventitious roots from ginseng roots, establishment of adventitious root suspension cultures using bioreactors, procedures for processing of adventitious roots, and analysis of ginsenosides by high pressure liquid chromatography. PMID:27108314

  13. Evaluation of supercritical fluid extraction/gas chromatography/matrix isolation-infrared spectrometry for analysis of organic compounds

    International Nuclear Information System (INIS)

    Analysis of soil samples for organic compounds typically first requires Soxhlet extraction or sonication. These processes are time consuming and generate large amounts of waste solvent. Supercritical fluid extraction (SFE), which uses a supercritical fluid such as carbon dioxide, has recently been shown to extract organic compounds from soil samples in good yields. Moreover, SFE does not generate waste solvent and can be performed rapidly. Gas Chromatography/Matrix Isolation-Infrared Spectrometry (GC/MI-IR) has been used in our laboratories for determining organic compounds present in extracts from various matrices. The authors have interfaced an SFE extraction apparatus to GC/MI-IR instruments. In this paper the utility of SPE/GC/MI-IR instrumentation is discussed

  14. Isolation of individual fatty acids in sediments using preparative capillary gas chromatography (PCGC) for radiocarbon analysis at NIES-TERRA

    International Nuclear Information System (INIS)

    Compound-specific radiocarbon analysis (CSRA) of individual fatty acids (140-1190 μg C) in an estuarine sediment sample collected from Tokyo Bay was carried out using a recently developed preparative capillary gas chromatography (PCGC) system and accelerator mass spectrometry (AMS). The results showed that the estimated 14C ages of four components greatly varied from modern age (combined iso and anteiso C15:0, C16:0) to 17 000 years BP (C22:0), while a bulk-phase 14C age of organic matter is 5000 years BP. The 14C ages of the fatty acids derived from phytoplankton and bacteria are much younger than that of the bulk phase. On the other hand, the fatty acid originated from terrestrial higher plants (C22:0) shows an older 14C age of 17 000 years BP

  15. Waardenburg syndrome (WS): the analysis of a single family with a WS1 mutation showing linkage to RFLP markers on human chromosome 2q.

    OpenAIRE

    Asher, J H; Morell, R; Friedman, T B

    1991-01-01

    Waardenburg syndrome type I (WS1; MIM 19350) is caused by a pleiotropic, autosomal dominant mutation with variable penetrance and expressivity. Of individuals with this mutation, 20%-25% are hearing impaired. A multilocus linkage analysis of RFLP data from a single WS1 family with 11 affected individuals indicates that the WS1 mutation in this family is linked to the following four marker loci located on the long arm of chromosome 2: ALPP (alkaline phosphatase, placental), FN1 (fibronectin 1)...

  16. Paraffin-embedded tissue is less accurate than frozen section analysis for determining VHL mutational status in sporadic renal cell carcinoma.

    OpenAIRE

    Verhoest, Grégory; Patard, Jean-Jacques; Fergelot, Patricia; Jouan, Florence; Zerrouki, Salim; Dréano, Stéphane; Mottier, Stéphanie; Rioux-Leclercq, Nathalie; Denis, Marc,

    2012-01-01

    International audience INTRODUCTION: Literature controversies exist regarding the prognostic value of VHL mutations. The objective was to compare paraffin-embedded and frozen section specimens for VHL mutations detection and to evaluate the reliability of DNA analysis in formalin-fixed tissues. METHODS: Seventy-six patients with clear cell renal cell carcinoma (RCC) previously assessed for VHL status from frozen samples were included. Seventy-three tumor samples were known to be mutated fo...

  17. β-tubulin mutations in ovarian cancer using single strand conformation analysis – risk of false positive results from paraffin embedded tissues

    OpenAIRE

    Green, Henrik; Rosenberg, Per; Söderkvist, Peter; Horvath, György; Peterson, Curt

    2006-01-01

    Mutations in the β-tubulin gene have been proposed as a resistance mechanism to paclitaxel. We therefore investigated the presence of mutations in the β-tubulin M40 gene in 40 ovarian tumours (16 paraffin-embedded and 24 freshly frozen) selected for good or poor response to chemotherapy with paclitaxel or non-tubulin-affecting regimens. The presence of mutations was investigated using single strand conformation analysis followed by sequencing of the products with altered mobility. No sequence...

  18. Environmental analysis of alcohol ethoxylates and nonylphenol ethoxylate metabolites by ultra-performance liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Lara-Martín, Pablo A; González-Mazo, Eduardo; Brownawell, Bruce J

    2012-03-01

    Surfactants and their metabolites can be found in aquatic environments at relatively high concentrations compared with other micropollutants due in part to the exceptionally large volumes produced every year. We have focused our attention here on the most widely used nonionic surfactants, alcohol ethoxylates (AEOs), and on nonylphenol ethoxylate (NPEO) degradation products (short-chain nonylphenol ethoxylates, NP1-3EO, nonylphenol, NP, and nonylphenol ethoxycarboxylates, NP1-2EC), which are endocrine-disrupting compounds. Our main objective in this work was to develop a methodology aimed at the extraction, isolation, and improved analysis of these analytes in environmental samples at trace levels. Extraction recoveries of target compounds were determined for sediment samples after ultrasonic extraction and purification using HLB or C18 solid-phase extraction minicolumns. Recovery percentages were usually between 61 and 102% but were lower for longer AEO ethoxymers. Identification and quantification of target compounds was carried out using a novel ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS-MS) approach, a combination that provides higher sensitivity and faster analysis than prior methods using conventional high-performance liquid chromatography-mass spectrometry. Limits of detection were usually below 0.5 ng/g, being higher for monoethoxylate species (>5 ng/g) because of poor ionization. The method was used for analyzing surface sediment samples collected at Jamaica Bay (NY) in 2008. The highest values (28,500 ng/g for NP, 4,200 ng/g for NP1-3EO, 22,400 ng/g for NP1-2EC, and 1,500 ng/g for AEOs) were found in a sampling station from a restricted water circulation area that is heavily impacted by wastewater discharges. PMID:22002557

  19. Mutation analysis of CACNA1S and SCN4A in patients with hypokalemic periodic paralysis.

    Science.gov (United States)

    Wang, Xiao-Ying; Ren, Bing-Wen; Yong, Zeng-Hua; Xu, Hong-Yan; Fu, Qiu-Xia; Yao, He-Bin

    2015-10-01

    Mutations in CACNA1S (calcium channel, voltage‑dependent, L type, alpha 1S subunit) and SCN4A (sodium channel, voltage‑gated, type IV, alpha subunit) are associated with hypokalemic periodic paralysis (HPP). The aim of the current study was to investigate CACNA1S and SCN4A mutations in patients with HPP. Mutations in CACNA1S and SCN4A were detected in three familial hypokalemic periodic paralysis (FHPP) pedigrees and in two thyrotoxic hypokalemic periodic paralysis (THPP) pedigrees using polymerase chain reaction, DNA sequencing and sequence alignment with GenBank data. A single base mutation from cytosine to guanine at site 1582 was identified in exon 11 of CACNA1S in one FHPP pedigree, resulting in an arginine to glycine (R528G) substitution. A single base mutation from thymine to cytosine at site 2012 was identified in exon 12 of SCN4A in one THPP pedigree, resulting in a phenylalanine to serine (F671S) substitution. No mutations in CACNA1S or SCN4A were identified in the remaining three pedigrees. The present study indicated that CACNA1S and SCN4A mutations are relatively rare in patients with HPP, and further studies are required to determine whether these mutation‑associated substitutions are representative of patients with HPP. PMID:26252573

  20. Analysis of Frankincense in Archaeological Samples by Gas Chromatography-Mass Spectrometry

    International Nuclear Information System (INIS)

    Four archaeological samples, unearthed from Qana in Yemen were analysed by analytical technique, currently applied in the field of petroleum geochemistry, and by gas chromatography coupled with a mass spectrometer (GC-MS). Sample no 1286 comes from a burned warehouse and samples no 964, 963 and 962 from the central sanctuary. These specimens were probably exposed to a heating source. In each case olibanum resin was identified according to the presence of their chemical markers corresponding to α-, β-boswellic and lupeolic acids (3α-hydroxy-olean-12-en-24-oic, 3α-hydroxy-urs-12-en-24-oic and 3α-hydroxy-lup-20(29)en-24-oic acids) and their respective O-acetyled derivatives (3α- O-acetyl -olean-12-en-24-oic, 3α-O-acetyl-urs-12-en-24-oic and 3α-O-acetyl-lup-20(29)-en-24-oic acids). Concerning the thermal degradation state of samples, the GC-MS results are in agreement with the geochemical ones. Sample no 1286 and 964 correspond to ageing incense which has not undergone any heating action and are consequently relatively well preserved. Lastly, samples no 963 and 962 are thermally degraded resins and their gross composition data permits to conclude that sample no 963 is only partially burnt while sample no 962 has been much more degraded