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Sample records for two-hybrid assays confirmed

  1. Estrogenic/Antiestrogenic Activities of Polycyclic Aromatic Hydrocarbons and Their Monohydroxylated Derivatives by Yeast Two-Hybrid Assay

    OpenAIRE

    Hayakawa, Kazuichi; Onoda, Yu; Tachikawa, Chihiro; Hosoi, Shinzo; Yoshita, Morio; Chung, Sang Woon; Kizu, Ryoichi; Toriba, Akira; Kameda, Takayuki; Tang, Ning

    2007-01-01

    Estrogenic/antiestrogenic activities of 14 polycyclic aromatic hydrocarbons (PAHs) and 63 monohydroxylated PAHs (OHPAHs) having 2 to 6 rings were evaluated by yeast two-hybrid assay expressing human estrogen receptor α. Relative effective potencies of estrogenic and antiestrogenic activities were calculated as the inverse values of the relative concentration of the test compound that gave the same activities of E2 and 4-hydroxytamoxifen, respectively. PAHs did not show any estrogenic/antiestr...

  2. Determination of estrogen receptor {beta}-mediated estrogenic potencies of hydroxylated PCBS by a yeast two-hybrid assay

    Energy Technology Data Exchange (ETDEWEB)

    Kuroki, H.; Kumate, M.; Nakaoka, H.; Yonekura, S. [Daiichi Coll. of Pharmaceutical Sciences, Fukuoka (Japan); Nishikawa, J.; Nishihara, T. [Osaka Univ., Osaka (Japan)

    2004-09-15

    Several environmental phenolic chemicals such as Nonylphenol and Bisphenol A (BPA) have been previously shown to possess estrogenic properties. In the previous paper, we have investigated the estrogenic activity of a series of hydroxylated PCBs (OH-PCBs) by a yeast two-hybrid assay (estrogen receptor{alpha} (ER{alpha}) -TIF2), in which the expression of estrogenic activity is based on the interaction of chemicals with ER{alpha}, and demonstrated that 4'-OH-CB30 and 4'-OH-CB61 are more estrogenic than BPA, one of the environmental estrogens. We have showed that one chlorine substitution adjacent to 4-OH at 3- or 5-position significantly reduces the ER{alpha}-mediated estrogenic activity of 4-OH-PCBs. Thus, 4'-OH-CB25 and 4-OH-CB56 showed a very weak estrogenicity. We have also showed that 4-OH-PCBs with two chlorine substitutions adjacent to 4-OH at 3- and 5-position such as 4'-OH-CB79 (hydroxylated metabolite of CB77) and persistent 4-OH-PCBs retained in human blood (4-OH-CB107, 4-OH-CB146 and 4-OH-CB187) have no ER{alpha}-mediated estrogenic activity. ER is known to have two subtypes, namely ER{alpha} and ER{beta} and it is reported that ligand, some agonist and antagonist have a different binding affinity for ER{alpha} and ER{beta}. However, there is limited information on ER{beta}-mediated endocrine disrupting potency. In this study, we examined the ER{beta}-mediated estrogenic activity of a series of OH-PCBs, including environmentally relevant 4-OH-PCBs by a yeast two-hybrid assay (ER{beta}-TIF2).

  3. Microfluidic assay without blocking for rapid HIV screening and confirmation.

    Science.gov (United States)

    Song, Lusheng; Zhang, Yi; Wang, Wenjun; Ma, Liying; Liu, Yong; Hao, Yanlin; Shao, Yiming; Zhang, Wei; Jiang, Xingyu

    2012-08-01

    The essential step for HIV spreading limitation is the screening tests. However, there are multiple disadvantages in current screening assays which need further confirmation test. Herein we developed a rapid HIV assay combining screening and confirmation test by using the microfluidic network assay. Meanwhile, the assay is accelerated by bypassing the step of blocking. We call this method as microfluidic assay without blocking (MAWB). Both the limit of detection and reagent incubation time of MAWB are determined by screening of one model protein pair: ovalbumin and its antibody. The assay time is accelerated about 25% while the limit of detection (LOD) is well kept. Formatting the method in for both HIV screening (testing 8 HIV-related samples) and confirmation (assaying 6 kinds of HIV antibodies of each sample) within 30 min was successful. Fast HIV screening and confirmation of 20 plasma samples were also demonstrated by this method. MAWB improved the assay speed while keeping the LOD of conventional ELISA. Meanwhile, both the accuracy and throughput of MAWB were well improved, which made it an excellent candidate for a quick HIV test for both screening and confirmation. Methods like this one will find wide applications in clinical diagnosis and biochemical analysis based on the interactions between pairs of molecules.

  4. Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

    Energy Technology Data Exchange (ETDEWEB)

    Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

    2011-09-10

    Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.

  5. Screening of agonistic activities against four nuclear receptors in wastewater treatment plants in Japan using a yeast two-hybrid assay

    Institute of Scientific and Technical Information of China (English)

    Daisuke Inoue; Koki Nakama; Kazuko Sawada; Taro Watanabe; Hisae Matsui; Kazunari Sei; Tsuyoshi Nakanishi; Michihiko Ike

    2011-01-01

    To assess the potential endocrine disruptive effects through multiple nuclear receptors (NRs), especially non-steroidal NRs, in municipal wastewater, we examined the agonistic activities on four NRs (estrogen receptor c, thyroid hormone receptor α, retinoic acid receptor α and retinoid X receptor α) of untreated and treated wastewater from municipal wastewater treatment plants (WWTPs) in Japan using a yeast two-hybrid assay.Investigation of the infiuent and effluent of seven WWTPs revealed that agonistic activities against steroidal and non-steroidal NRs were always detected in the infiuents and partially remained in the effluents.Further investigation of four WWTPs employing conventional activated sludge, pseudo-anoxic-oxic, anoxic-oxic and anaerobic-anoxic-oxic processes revealed that the ability to reduce the agonistic activity against each of the four NRs varies depending on the treatment process.These results indicated that municipal wastewater in Japan commonly contains endocrine disrupting chemicals that exert agonistic activities on steroidal and non-steroidal NRs, and that some of these chemicals are released into the natural aquatic environment.Although the results obtained in yeast assays suggested that measured levels of non-steroidal NR agonists in the effluent of WWTPs were not likely to cause any biological effect, further study is required to assess their possible risks in detail.

  6. Design of a multiplex PCR assay for the simultaneous detection and confirmation of Neisseria gonorrhoeae.

    LENUS (Irish Health Repository)

    O'Callaghan, Isabelle

    2010-05-01

    To improve the detection of Neisseria gonorrhoeae by designing a multiplex PCR assay using two N gonorrhoeae-specific genes as targets, thereby providing detection and confirmation of a positive result simultaneously.

  7. Atypical myopathy in Denmark confirmed with the aTRAQ assay

    DEFF Research Database (Denmark)

    Høffer, Sofie Esbjørn; Votion, Dominique-Marie; Anderberg, Marie

    2016-01-01

    was to confirm cases in this country and to use a new diagnostic technique (aTRAQ assay). Seven out of 8 samples from clinically highly suspicious cases were positive for hypoglycin A, and all had multiple acyl-CoA dehydrogenase deficiency, which confirms that the disease is also present in Denmark. Hypoglycin...

  8. Measuring dabigatran with the dilute Russell viper venom confirm assay in an anticoagulation clinic population.

    Science.gov (United States)

    McGlasson, David L; Fritsma, George A

    2016-01-01

    The dabigatran dose-response is predictable; however, it is necessary to measure plasma levels in a variety of clinical conditions. We evaluated a novel dabigatran measure - the 'dilute Russell viper venom confirm (DRVVC) assay' - against current developmental assays and a reference method. We measured plasma dabigatran and compared results from the Stago Sta-Clot DRVVC assay, Stago Ecarin Chromogenic Assay, Biophen Hemoclot Thrombin Inhibitor, and liquid chromatography tandem mass spectrometry. We obtained dabigatran calibrators and controls from Biophen, and performed the coagulation assays using a Stago STA-R Evolution coagulometer. Liquid chromatography tandem mass spectrometry method specimens were performed on an AB Sciex instrument at LabCorp. We enrolled 97 anticoagulation clinic patients (mean age 76 years) who were taking 150 mg dabigatran twice daily. All had creatinine clearances above 30 ml/min; patients were not excluded for concurrent medications or health issues. Citrated blood specimens were processed immediately, and stored at -70°C. We did not correlate collection time with medication time. We employed descriptive statistics, analysis of variance, and the Bland-Altman difference plot to assess the data. The range for all assays was 11.6-917 ng/ml. Analysis of variance generated a P value of 0.1 and Bland-Altman differences were all below 4.0% compared with DRVVC. The DRVVC measures dabigatran with validity comparable to other methods.

  9. Imported intraocular gnathostomiasis with subretinal tracks confirmed by western blot assay.

    Science.gov (United States)

    Yang, Ji Ho; Kim, Moosang; Kim, Eung Suk; Na, Byoung-Kuk; Yu, Seung-Young; Kwak, Hyung-Woo

    2012-03-01

    We report a case of intraocular gnathostomiasis diagnosed by western blot assay in a patient with subretinal tracks. A 15-year-old male patient complained of blurred vision in the right eye, lasting for 2 weeks. Eight months earlier, he had traveled to Vietnam for 1 week and ate raw wild boar meat and lobster. His best-corrected visual acuity was 20/20 in both eyes and anterior chamber examination revealed no abnormalities. Fundus examination showed subretinal tracks in the right eye. Fluorescein angiography and indocyanine green angiography showed linear hyperfluorescence of the subretinal lesion observed on fundus in the right eye. Ultrasound examination revealed no abnormalities. Blood tests indicated mild eosinophilia (7.5%), and there was no abnormality found by systemic examinations. Two years later, the patient visited our department again for ophthalmologic evaluation. Visual acuity remained 20/20 in both eyes and the subretinal tracks in the right eye had not changed since the previous examination. Serologic examination was performed to provide a more accurate diagnosis, and the patient's serum reacted strongly to the Gnathostoma nipponicum antigen by western blot assay, which led to a diagnosis of intraocular gnathostomiasis. This is the first reported case of intraocular gnathostomiasis with subretinal tracks confirmed serologically using western blot in Korea.

  10. Yeast two-hybrid screen.

    Science.gov (United States)

    Makuch, Lauren

    2014-01-01

    Yeast two-hybrid is a method for screening large numbers of gene products (encoded by cDNA libraries) for their ability to interact with a protein of interest. This system can also be used for characterizing and manipulating candidate protein: protein interactions. Interactions between proteins are monitored by the growth of yeast plated on selective media.

  11. Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections.

    Science.gov (United States)

    Corman, V M; Müller, M A; Costabel, U; Timm, J; Binger, T; Meyer, B; Kreher, P; Lattwein, E; Eschbach-Bludau, M; Nitsche, A; Bleicker, T; Landt, O; Schweiger, B; Drexler, J F; Osterhaus, A D; Haagmans, B L; Dittmer, U; Bonin, F; Wolff, T; Drosten, C

    2012-12-06

    We present a rigorously validated and highly sensitive confirmatory real-time RT-PCR assay (1A assay) that can be used in combination with the previously reported upE assay. Two additional RT-PCR assays for sequencing are described, targeting the RdRp gene (RdRpSeq assay) and N gene (NSeq assay), where an insertion/deletion polymorphism might exist among different hCoV-EMC strains. Finally, a simplified and biologically safe protocol for detection of antibody response by immunofluorescence microscopy was developed using convalescent patient serum.

  12. Antioxidant and anti-inflammatory assays confirm bioactive compounds in Ajwa date fruit.

    Science.gov (United States)

    Zhang, Chuan-Rui; Aldosari, Saleh A; Vidyasagar, Polana S P V; Nair, Karun M; Nair, Muraleedharan G

    2013-06-19

    Ajwa, a variety of date palm Phoenix dactylifera L., produces the most expensive date fruits. Percentages of seed, moisture, fructose, glucose, soluble protein, and fiber in Ajwa dates were 13.24, 6.21, 39.06, 26.35, 1.33, and 11.01, respectively. The ethyl acetate, methanolic, and water extracts of Ajwa dates, active at 250 μg/mL in the MTT assay, inhibited lipid peroxidation (LPO) by 88, 70, and 91% at 250 μg/mL and cyclooxygenase enzymes COX-1 by 30, 31, and 32% and COX-2 by 59, 48, and 45% at 100 μg/mL, respectively. Bioactivity-guided purifications afforded compounds 1-7, in addition to phthalates and fatty acids. Compounds 1-3 showed activity at 100 μg/mL in the MTT assay; inhibited COX-1 enzyme by 59, 48, amd 50% and COX-2 enzyme by 60, 40, amd 39% at 50 μg/mL; and inhibited LPO by 95, 58, amd 66% at 100 μg/mL, respectively. The soluble protein fraction was also very active in both antioxidant and anti-inflammatory assays.

  13. Concurrent Reactivation of Herpes Simplex and Varicella Zoster Viruses Confirmed by the Loop-Mediated Isothermal Amplification Assay

    Directory of Open Access Journals (Sweden)

    Tsukane Kobayashi

    2014-01-01

    Full Text Available Concurrent reactivation of herpes simplex and varicella zoster viruses is rare. Here, we describe the case of an elderly patient with herpes labialis and herpes zoster manifesting as a right-side facial eruption with vesicles and crusting. The loop-mediated isothermal amplification (LAMP assay demonstrated the presence of both herpes simplex virus type 1 and varicella zoster virus in swab samples taken from the face, which was confirmed by real-time PCR, suggesting concurrent reactivation of both viruses. The use of the LAMP assay in the present case indicates its usefulness in the diagnosis of atypical herpes infections.

  14. Herpes simplex encephalitis: MRI findings in two cases confirmed by polymerase chain reaction assay

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J.W.; Kim, I.O.; Kim, W.S.; Yeon, K.M. [Dept. of Radiology and the Institute of Radiation Medicine, Seoul National University Hospital, Seoul (Korea); Lee, H.-J.; Hwang, Y.S. [Dept. of Paediatrics, Seoul National University College of Medicine, Seoul (Korea)

    2001-09-01

    Herpes simplex virus (HSV) type I causes a fulminant necrotising meningoencephalitis distinguished from other encephalitides by its focal and often haemorrhagic nature. Specific antiviral therapy with acyclovir can significantly improve the prognosis. We present MRI findings of two cases of herpes simplex encephalitis (HSE) confirmed by PCR analysis, focusing on the serial changes after acyclovir therapy: gyral swelling, high signal intensity on T2-weighted images in the subfrontal region, temporal lobe and insula in the initial stage, then regional extension with enhancement and haemorrhage despite appropriate acyclovir therapy, and finally encephalomalacia and brain atrophy. (orig.)

  15. The identification of carbapenemase types in Enterobacteriaceae by using molecular assay and phenotyping confirmation tests.

    Science.gov (United States)

    Genc, Ozlem; Aksu, Evrim; Gulcan, Aynur

    2016-06-01

    In this study, we aimed to identify the molecular carbapenemase types of the Enterobacteriaceae isolates and to evaluate the performance of manually prepared and commercially available combination disc methods and the modified Hodge test. One hundred and forty carbapenemase producing isolates and 45 isolates as control group were included in our study. The Xpert CARBA-R test was used as the molecular method. Antibiotic susceptibility tests were performed using combined discs, manually prepared with APBA (3-aminophenyl boronic acid), DPA (dipicolinic acid), EDTA (Ethylene diamine tetra acetic acid), cloxacillin supplements and Mastdiscs Combi-D70C that includes four antibiotic discs with specific inhibitors and temocillin discs. The modified Hodge test was performed on all isolates. OXA-48 gene was identified in 129 isolates , the NDM gene was identified in 10 isolates and VIM in one isolate. Thirty inaccurate results (30/185, 16%) were detected by using the manually prepared confirmation test. The sensitivity and specificity of this test were identified respectively 85% and 73%. Also, the sensitivity and specificity of the Mastdiscs Combi-D70C were identified as 100%. Negative results were detected in 3 NDM isolates with the use of a modified Hodge test. Sensitivity and specificity were calculated for the modified Hodge test respectively 97% and 100%. Finally, molecular methods provide results rapidly but they are not always easily accessible. The modified Hodge test can be used only for screening as a first step test and is not one of the tests that can identify the type of the carbapenemase. When carbapenem-resistant Enterobacteriaceae are detected, a commercial kit like Mastdiscs Combi-D70 may be preferred instead of the manually prepared phenotypic verification tests. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Interaction of the heterotrimeric G protein alpha subunit SSG-1 of Sporothrix schenckii with proteins related to stress response and fungal pathogenicity using a yeast two-hybrid assay

    Directory of Open Access Journals (Sweden)

    González-Méndez Ricardo

    2010-12-01

    Full Text Available Abstract Background Important biological processes require selective and orderly protein-protein interactions at every level of the signalling cascades. G proteins are a family of heterotrimeric GTPases that effect eukaryotic signal transduction through the coupling of cell surface receptors to cytoplasmic effector proteins. They have been associated with growth and pathogenicity in many fungi through gene knock-out studies. In Sporothrix schenckii, a pathogenic, dimorphic fungus, we previously identified a pertussis sensitive G alpha subunit, SSG-1. In this work we inquire into its interactions with other proteins. Results Using the yeast two-hybrid technique, we identified protein-protein interactions between SSG-1 and other important cellular proteins. The interactions were corroborated using co-immuneprecipitation. Using these techniques we identified a Fe/Mn superoxide dismutase (SOD, a glyceraldehyde-3-P dehydrogenase (GAPDH and two ion transport proteins, a siderophore-iron transporter belonging to the Major Facilitator Superfamily (MFS and a divalent-cation transporter of the Nramp (natural resistance-associated macrophage protein family as interacting with SSG-1. The cDNA's encoding these proteins were sequenced and bioinformatic macromolecular sequence analyses were used for the correct classification and functional assignment. Conclusions This study constitutes the first report of the interaction of a fungal G alpha inhibitory subunit with SOD, GAPDH, and two metal ion transporters. The identification of such important proteins as partners of a G alpha subunit in this fungus suggests possible mechanisms through which this G protein can affect pathogenicity and survival under conditions of environmental stress or inside the human host. The two ion transporters identified in this work are the first to be reported in S. schenckii and the first time they are identified as interacting with fungal G protein alpha subunits. The association

  17. LA PROTEÍNA PTHB DE Xanthomonas axonopodis pv. Manihotis ES AUTOACTIVA EN ENSAYOS DE DOBLE HÍBRIDO The PthB Protein from Xanthomonas axonopodis pv. Manihotis is an Autoactive in Yeast Two-Hybrid Assays

    Directory of Open Access Journals (Sweden)

    JULIANA GIL

    the yeast two hybrid expression vector pLAW10, generating a fusion protein with the Binding Domain (BD of the transcription factor GAL4. In this work, PthB was cloned in a translational fusion with Gal4-BD (DNA Binding Domain. After transforming this construct into a yeast strain, autoactivation of the reporter genes was observed, even at the highest concentrations of 3-AT. The deletion of the first, second or both NLS and the AAD did not eliminate the ability of autoactivation of PthB. These results show the impossibility of using PthB to screen a cassava cDNA library to identify the proteins interacting with PthB.

  18. All major prion types recognised by a multiplex immunofluorometric assay for disease screening and confirmation in sheep

    NARCIS (Netherlands)

    Tang, Y.; gielbert, A.; Jacobs, J.G.; Baron, T.; Andreoletti, O.; Langeveld, J.P.M.; Sauer, M.J.

    2012-01-01

    Prion diseases or transmissible spongiform encephalopathies (TSEs) in small ruminants are presented in many forms: classical scrapie, Nor98/atypical scrapie, CH1641 scrapie and bovine spongiform encephalopathy (BSE). We previously described a multiplex immunofluorometric assay (mIFMA), based on a be

  19. CONFIRMATIONAL IDENTIFICATION OF ESCHERICHIA COLI, A COMPARISON OF GENOTYPIC AND PHENOTYPIC ASSAYS FOR GLUTAMATE DECARBOXYLASE AND B-D-GLUCURONIDASE

    Science.gov (United States)

    Genotypic and phenotypic assays for glutamate decarboxylase (GAD) and B-D-glucuronidase (GUD) were compared for their abilities to detect various strains of Escherichia coli and to discriminate among other bacterial species. Test strains included nonpathogenic E.coli, three major...

  20. Confirmation of positive antibody screens by solid-phase red cell adherence assay using a tube technique method with polyethylene glycol enhancement.

    Science.gov (United States)

    Gammon, R R; Lake, M; Velasquez, N; Prichard, A

    2001-01-01

    Our blood bank routinely screens donors for antibodies using a solid-phase red cell adherence (SPRCA) assay. Positive results are then confirmed using a tube technique with polyethylene glycol (PEG) enhancement due to reported higher specificity than with SPRCA. Over a 5-month period, 49,084 donor serum or plasma samples were tested using the SPRCA assay. Further identification of positive samples was performed using a PEG enhancement method. Testing was performed with strict adherence to the manufacturers' inserts. Of 49,084 samples, 313 (0.64%) were positive by the SPRCA assay. Of these, 99 (31.6%) samples remained positive when tested with PEG enhancement. The remaining 214 (68.4%) were negative, giving specificity for the SPRCA assay of 99.6 percent (48,985/ 49,199). We report a high specificity for antibody screening using the SPRCA assay. However, it is cost effective to perform a confirmatory tube test with PEG enhancement because 214 SPRCA assay samples were interpreted as having a negative antibody screen, thus allowing the release of valuable blood components for transfusion.

  1. Direct enzyme assay evidence confirms aldehyde reductase function of Ydr541cp and Ygl039wp from Saccharomyces cerevisiae.

    Science.gov (United States)

    Moon, Jaewoong; Liu, Z Lewis

    2015-04-01

    The aldehyde reductase gene ARI1 is a recently characterized member of an intermediate subfamily within the short-chain dehydrogenase/reductase (SDR) superfamily that clarified mechanisms of in situ detoxification of 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde by Saccharomyces cerevisiae. Uncharacterized open reading frames (ORFs) are common among tolerant candidate genes identified for lignocellulose-to-advanced biofuels conversion. This study presents partially purified proteins of two ORFs, YDR541C and YGL039W, and direct enzyme assay evidence against aldehyde-inhibitory compounds commonly encountered during lignocellulosic biomass fermentation processes. Each of the partially purified proteins encoded by these ORFs showed a molecular mass of approximately 38 kDa, similar to Ari1p, a protein encoded by aldehyde reductase gene. Both proteins demonstrated strong aldehyde reduction activities toward 14 aldehyde substrates, with high levels of reduction activity for Ydr541cp toward both aromatic and aliphatic aldehydes. While Ydr541cp was observed to have a significantly higher specific enzyme activity at 20 U/mg using co-factor NADPH, Ygl039wp displayed a NADH preference at 25 U/mg in reduction of butylaldehyde. Amino acid sequence analysis identified a characteristic catalytic triad, Ser, Tyr and Lys; a conserved catalytic motif of Tyr-X-X-X-Lys; and a cofactor-binding sequence motif, Gly-X-X-Gly-X-X-Ala, near the N-terminus that are shared by Ydr541cp, Ygl039wp, Yol151wp/GRE2 and Ari1p. Findings of aldehyde reductase genes contribute to the yeast gene annotation and aids development of the next-generation biocatalyst for advanced biofuels production.

  2. Cytochrome C oxidase Ⅲ interacts with hepatitis B virus X protein in vivo by yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    Dan Li; Xiao-Zhong Wang; Jie-Ping Yu; Zhi-Xin Chen; Yue-Hong Huang; Qi-Min Tao

    2004-01-01

    AIM: To screen and identify the proteins which interact with hepatitis B virus (HBV) X protein in hepatocytes by yeast two-hybrid system and to explore the effects of X protein in the development of hepatocellular carcinoma (HCC).METHODS: With HBV X gene amplified by polymerase chain reaction (PCR), HBV X bait plasmid, named pAS2-1-X, was constructed by yeast-two hybridization system3 and verified by auto-sequencing assay. pAS2-1-X was transformed into the yeast AH109, and X-BD fusion protein expressed in the yeast cells was detected by Western blotting. The yeast cells cotransformed with pAS2-1-X and normal human liver cDNA library were grown in selective SC/-trp-leu-his-ade medium. The second screen was performed with β-gal activity detection, and false positive clones were eliminated by segregation analysis, true positive clones were amplified,sequenced and analyzed with bioinformatics. Mating experiment was peformed to confirm the binding of putative proteins to X protein in the yeast cells.RESULTS: Bait plasmid pAS2-1-X was successfully constructed and pAS2-1-X correctly expressed BD-X fusion protein in yeast AH109. One hundred and three clones grew in the selective SC/-trp-leu-his-ade medium, and only one clone passed through β-gal activity detection and segregation analysis. The inserted cDNA fragment showed high homology with Homo sapiens cytochrome C oxidase Ⅲ(COXIII). Furthermore, mating experiment identified that the binding of COXIII to X protein was specific.CONCLUSION: COXIII protein is a novel protein that can interact with X protein in vivo by yeast two-hybrid system,and may contribute to the development of HCC through the interaction with X protein.

  3. Molecular detection and confirmation of Neisseria gonorrhoeae in urogenital and extragenital specimens using the Abbott CT/NG RealTime assay and an in-house assay targeting the porA pseudogene.

    LENUS (Irish Health Repository)

    Walsh, A

    2011-04-01

    Culture for detection of Neisseria gonorrhoeae (NG) is being replaced by molecular assays, but difficulties are observed with false positive and negatives results, especially for extragenital samples. This study evaluates the Abbott CT\\/NG Real-Time assay and a real-time porA pseudogene assay. Samples (n = 600) from a mixed prevalence Irish population include 164 male urines with corresponding urethral swabs, 58 endocervical swabs, 173 male pharyngeal swabs, 205 male rectal swabs, 36 NG clinical isolates and 26 commensal Neisseria species isolates. There was a 100% concordance between the Abbott CT\\/NG Real-Time and the porA assay. The positivity rate was 1.2%, 1.7%, 8.1% and 5.8% for FVU\\/urethral swabs, endocervical, pharyngeal and rectal swabs, respectively. These results were compared to culture and discrepancies were found with nine pharyngeal and three rectal swabs. Seven of the 12 discrepant positive samples were sequenced and were confirmed "true positives". The sensitivity and specificity of the molecular assays was 100%. The sensitivity of the culture-based testing was 100% for urogenital samples but 36% and 75% for pharyngeal and rectal swabs, respectively. The combined Abbott CT\\/NG and porA assays provide a valuable alternative to culture and also generate a significant increase in the diagnosis of pharyngeal and rectal NG infection.

  4. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast.

    Science.gov (United States)

    James, P; Halladay, J; Craig, E A

    1996-12-01

    The two-hybrid system is a powerful technique for detecting protein-protein interactions that utilizes the well-developed molecular genetics of the yeast Saccharomyces cerevisiae. However, the full potential of this technique has not been realized due to limitations imposed by the components available for use in the system. These limitations include unwieldy plasmid vectors, incomplete or poorly designed two-hybrid libraries, and host strains that result in the selection of large numbers of false positives. We have used a novel multienzyme approach to generate a set of highly representative genomic libraries from S. cerevisiae. In addition, a unique host strain was created that contains three easily assayed reporter genes, each under the control of a different inducible promoter. This host strain is extremely sensitive to weak interactions and eliminates nearly all false positives using simple plate assays. Improved vectors were also constructed that simplify the construction of the gene fusions necessary for the two-hybrid system. Our analysis indicates that the libraries and host strain provide significant improvements in both the number of interacting clones identified and the efficiency of two-hybrid selections.

  5. The Multispot rapid HIV-1/HIV-2 differentiation assay is comparable with the Western blot and an immunofluorescence assay at confirming HIV infection in a prospective study in three regions of the United States.

    Science.gov (United States)

    Pandori, Mark W; Westheimer, Emily; Gay, Cindy; Moss, Nicholas; Fu, Jie; Hightow-Weidman, Lisa B; Craw, Jason; Hall, Laura; Giancotti, Francesca R; Mak, Mae Ling; Madayag, Carmela; Tsoi, Benjamin; Louie, Brian; Patel, Pragna; Owen, S Michele; Peters, Philip J

    2013-12-01

    A new HIV diagnostic algorithm has been proposed which replaces the use of the HIV-1 Western blot and HIV-1 immunofluorescence assays (IFA) as the supplemental test with an HIV-1/HIV-2 antibody differentiation assay. To compare an FDA-approved HIV-1/HIV-2 antibody differentiation test (Multispot) as a confirmatory test with the HIV-1 Western blot and IFA. Participants were screened with an HIV-1/HIV-2 combination Antigen/Antibody (Ag/Ab) screening assay. Specimens with repeatedly reactive results were tested with Multispot and either Western blot or IFA. Specimens with discordant screening and confirmatory results were resolved with HIV-1 RNA testing. Individuals (37,876) were screened for HIV infection and 654 (1.7%) had a repeatedly reactive Ag/Ab assay result. On Multispot, 554 (84.7%) were HIV-1 reactive, 0 (0%) were HIV-2 reactive, 1 (0.2%) was reactive for both HIV-1 and HIV-2 (undifferentiated), 9 (1.4%) were HIV-1 indeterminate, and 90 (13.8%) were non-reactive. HIV-1 RNA was detected in 47/90 Multispot non-reactive (52.2%) specimens. Among specimens confirmed to have HIV infection (true positives), Multispot and Western blot detected HIV-1 antibody in a similar proportion of cases (93.7% vs. 94.4% respectively) while Multispot and IFA also detected HIV-1 antibody in a similar proportion of cases (84.5% vs. 83.4% respectively). In this study, Multispot confirmed HIV infections at a similar proportion to Western blot and IFA. Multispot, Western blot, and IFA, however, did not confirm all of the reactive Ag/Ab assay results and underscores the importance of HIV NAT testing to resolve discordant screening and confirmatory results. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  6. Detection of AmpC Beta-Lactamase in Escherichia coli: Comparison of Three Phenotypic Confirmation Assays and Genetic Analysis▿†

    OpenAIRE

    Peter-Getzlaff, S; Polsfuss, S; Poledica, M.; Hombach, M.; Giger, J.; Böttger, E C; Zbinden, R.; Bloemberg, G. V.

    2011-01-01

    Two mechanisms account for AmpC activity in Escherichia coli, namely, mutations in the ampC promoter and attenuator regions resulting in ampC overexpression and acquisition of plasmid-carried ampC genes. In this study, we analyzed 51 clinical E. coli isolates with reduced susceptibility to amoxicillin-clavulanic acid, piperacillin-tazobactam, or extended-spectrum cephalosporins for the presence of AmpC production. Three phenotypic AmpC confirmation assays (cefoxitin-cloxacillin disk diffusion...

  7. Isolation and characterization of a human apoptosis-inducing gene with yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    齐兵; 齐义鹏; Masuo; Yutsudo; 刘青珍

    2000-01-01

    asy gene is a novel apoptosis-inducing gene, but its mechanism is unclear. To investigate the mechanism of asy inducing apoptosis, a novel gene encoding ASY interacting protein (asyip) is isolated from human lung cell line (WI-38) cDNA library with yeast two-hybrid system. The asyip gene is constitutively expressed as two mRNA transcripts with the size of 1.8 and 2.7 kb in various human tissues at different levels. Sequence analysis of full-length cDNA reveals that the two alternative transcripts of asyip gene contain common 5’ end and different 3’ end, and share a common open reading frame encoding a polypeptide of 236 amino acids. Two protein kinase C phosphorylation sites and two casein kinase II phosphorylation sites are found in ASYIP amino acid sequence. Two highly hydrophobic regions encoding potentially two transmembrane domains are present. The ASYIP protein contains a C-terminal endoplasmic reticulum retrieval signal (Lys-Lys-Lys-Ala-Glu). Immunoprecipitation assay confirmed the interaction of

  8. Isolation and characterization of a human apoptosis-inducing gene with yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    asy gene is a novel apoptosis-inducing gene,but its mechanism is unclear.To investigate the mechanism of asy inducing apoptosis,a novel gene encoding ASY interacting protein (asyip) is isolated from human lung cell line (WI-38) cDNA library with yeast two-hybrid system.The asyip gene is constitutively expressed as two mRNA transcripts with the size of 1.8 and 2.7 kb in various human tissues at different levels.Sequence analysis of full-length cDNA reveals that the two alternative transcripts of asyip gene contain common 5' end and different 3' end,and share a common open reading frame encoding a polypeptide of 236 amino acids.Two protein kinase C phosphorylation sites and two casein kinase II phosphorylation sites are found in ASYIP amino acid sequence.Two highly hydrophobic regions encoding potentially two transmembrane domains are present.The ASYIP protein contains a C-terminal endoplasmic reticulum retrieval signal (Lys-Lys-Lys-Ala-Glu).Immunoprecipitation assay confirmed the interaction of ASY and ASYIP in mammalian cells.Compared with asy gene,overexpression of asyip gene can inhibit growth of tumor cell Saos2 and induce cell apoptosis with a low efficiency.

  9. Lab-on-a-chip-based PCR-RFLP assay for the confirmed detection of short-length feline DNA in food.

    Science.gov (United States)

    Ali, Md Eaqub; Al Amin, Md; Hamid, Sharifah Bee Abd; Hossain, M A Motalib; Mustafa, Shuhaimi

    2015-01-01

    Wider availability but lack of legal market trades has given feline meat a high potential for use as an adulterant in common meat and meat products. However, mixing of feline meat or its derivatives in food is a sensitive issue, since it is a taboo in most countries and prohibited in certain religions such as Islam and Judaism. Cat meat also has potential for contamination with of severe acute respiratory syndrome, anthrax and hepatitis, and its consumption might lead to an allergic reaction. We developed a very short-amplicon-length (69 bp) PCR assay, authenticated the amplified PCR products by AluI-restriction digestion followed by its separation and detection on a lab-on-a-chip-based automated electrophoretic system, and proved its superiority over the existing long-amplicon-based assays. Although it has been assumed that longer DNA targets are susceptible to breakdown under compromised states, scientific evidence for this hypothesis has been rarely documented. Strong evidence showed that shorter targets are more stable than the longer ones. We confirmed feline-specificity by cross-challenging the primers against 10 different species of terrestrial, aquatic and plant origins in the presence of a 141-bp site of an 18S rRNA gene as a universal eukaryotic control. RFLP analysis separated 43- and 26-bp fragments of AluI-digest in both the gel-image and electropherograms, confirming the original products. The tested detection limit was 0.01% (w/w) feline meat in binary and ternary admixed as well as meatball matrices. Shorter target, better stability and higher sensitivity mean such an assay would be valid for feline identification even in degraded specimens.

  10. Yeast two-hybrid screening for proteins that interact with α1-adrenergic receptors

    Institute of Scientific and Technical Information of China (English)

    TanZHANG; QiXU; Feng-rongCHEN; Qi-deHAN; You-yiZHANG

    2004-01-01

    AIM: To find novel proteins that may bind to α1A-adrenergic receptor (α1A-AR) and investigate their interactions with the other two α1-AR subtypes (α1B-AR and α1D-AR) with an expectation to provide new leads for the function study of the receptors. METHODS: Yeast two-hybrid assay was performed to screen a human brain cDNA library using the C terminus of α1A-AR (α1A-AR-CT) as bait. X-Gal assay and o-nitrophenyl-beta-D-galactopyranoside (ONPG) assay were subsequently conducted to further qualitatively or quantitatively confirm the interactions between receptors and the three identified proteins. RESULTS: (1) Selection medium screening identified segments of bone morphogenetic protein-1 (BMP-1), active Bcr-related protein (Abr), and filamin-C as binding partners of α1A-AR-CT in yeast cells respectively. Besides, protein segments of BMP-1 and Abr could only specifically interact with α1A-AR-CT while filamin-C segment interacted with all three α1-AR subtypes. (2) In X-Gal assay, the cotransformants of α1A-AR-CT and BMP-1 segments turned strong blue at about 30 min while other positive transformants only developed weak blue at about 5-6 h. (3) In ONPG assay, interaction (shown in β-galactosidase activity) between α1A-AR-CT and BMP-1 segments was about 30 times stronger than that of control (P<0.01), while other positive interactions were only about 2-5 times as strong as those of controls (P<0.05). CONCLUSION: In yeast cells BMP-1, Abr and/or filamin-C could interact with three α1-AR subtypes, among which, interaction between BMP-1 and α1A-AR was the strongest while other interactions between proteins and receptors were relatively weak.

  11. Yeast two-hybrid screening for proteins that interact with α1-adrenergic receptors

    Institute of Scientific and Technical Information of China (English)

    Tan ZHANG; Qi XU; Feng-rong CHEN; Qi-de HAN; You-yi ZHANG

    2004-01-01

    AIM: To find novel proteins that may bind to α1A-adrenergic receptor (α1A-AR) and investigate their interactions with the other two α1-AR subtypes (α1B-AR and α1D-AR) with an expectation to provide new leads for the function study of the receptors. METHODS: Yeast two-hybrid assay was performed to screen a human brain cDNA library using the C terminus of α1A-AR (α1A-AR-CT) as bait. X-Gal assay and o-nitrophenyl-beta-D-galactopyranoside(ONPG) assay were subsequently conducted to further qualitatively or quantitatively confirm the interactions between receptors and the three identified proteins. RESULTS: (1) Selection medium screening identified segments of bone morphogenetic protein-1 (BMP-1), active Bcr-related protein (Abr), and filamin-C as binding partners ofα1A-AR-CT in yeast cells respectively. Besides, protein segments of BMP-1 and Abr could only specifically interact with α1A-AR-CT while filamin-C segment interacted with all three α1-AR subtypes. (2) In X-Gal assay, the cotransformants of α1A-AR-CT and BMP-1 segments turned strong blue at about 30 min while other positive transformants only developed weak blue at about 5-6 h. (3) In ONPG assay, interaction (shown in β-galactosidase activity) between α1A-AR-CT and BMP-1 segments was about 30 times stronger than that of control (P<0.01),while other positive interactions were only about 2-5 times as strong as those of controls (P<0.05). CONCLUSION:In yeast cells BMP-1, Abr and/or filamin-C could interact with three α1-AR subtypes, among which, interaction between BMP-1 and α1A-AR was the strongest while other interactions between proteins and receptors were relatively weak.

  12. Characterization of single chain antibody targets through yeast two hybrid

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    Vielemeyer Ole

    2010-08-01

    Full Text Available Abstract Background Due to their unique ability to bind their targets with high fidelity, antibodies are used widely not only in biomedical research, but also in many clinical applications. Recombinant antibodies, including single chain variable fragments (scFv, are gaining momentum because they allow powerful in vitro selection and manipulation without loss of function. Regardless of the ultimate application or type of antibody used, precise understanding of the interaction between the antibody's binding site and its specific target epitope(s is of great importance. However, such data is frequently difficult to obtain. Results We describe an approach that allows detailed characterization of a given antibody's target(s using the yeast two-hybrid system. Several recombinant scFv were used as bait and screened against highly complex cDNA libraries. Systematic sequencing of all retained clones and statistical analysis allowed efficient ranking of the prey fragments. Multiple alignment of the obtained cDNA fragments provided a selected interacting domain (SID, efficiently narrowing the epitope-containing region. Interactions between antibodies and their respective targets were characterized for several scFv. For AA2 and ROF7, two conformation-specific sensors that exclusively bind the activated forms of the small GTPases Rab6 and Rab1 respectively, only fragments expressing the entire target protein's core region were retained. This strongly suggested interaction with a non-linear epitope. For two other scFv, TA10 and SF9, which recognize the large proteins giantin and non-muscle myosin IIA, respectively, precise antibody-binding regions within the target were defined. Finally, for some antibodies, secondary targets within and across species could be revealed. Conclusions Our method, utilizing the yeast two-hybrid technology and scFv as bait, is a simple yet powerful approach for the detailed characterization of antibody targets. It allows precise

  13. Yeast Two-Hybrid: State of the Art

    Directory of Open Access Journals (Sweden)

    Van Criekinge Wim

    1999-01-01

    Full Text Available Genome projects are approaching completion and are saturating sequence databases. This paper discusses the role of the two-hybrid system as a generator of hypotheses. Apart from this rather exhaustive, financially and labour intensive procedure, more refined functional studies can be undertaken. Indeed, by making hybrids of two-hybrid systems, customised approaches can be developed in order to attack specific function-related problems. For example, one could set-up a "differential" screen by combining a forward and a reverse approach in a three-hybrid set-up. Another very interesting project is the use of peptide libraries in two-hybrid approaches. This could enable the identification of peptides with very high specificity comparable to "real" antibodies. With the technology available, the only limitation is imagination.

  14. The bacterial two-hybrid system uncovers the involvement of acetylation in regulating of Lrp activity in Salmonella Typhimurium

    Directory of Open Access Journals (Sweden)

    Ran Qin

    2016-11-01

    Full Text Available Nε-lysine acetylation is an abundant and important Post-translational modification in bacteria. We used the bacterial two-hybrid system to screen the genome library of the Salmonella Typhimurium to identify potential proteins involved in acetyltransferase Pat - or deacetylase CobB-mediated acetylation. Then, the in vitro (deacetylation assays were used to validate the potential targets, such as STM14_1074, NrdF, RhaR. Lrp, a leucine-responsive regulatory protein and global regulator, was shown to interact with Pat. We further demonstrate that Lrp could be acetylated by Pat and deacetylated by NAD+-dependent CobB in vitro. Specifically, the conserved lysine residue 36 (K36 in helix-turn-helix (HTH DNA-binding domain of Lrp was acetylated. Acetylation of K36 impaired the function of Lrp through altering the affinity with the target promoter. The mutation of K36 in chromosome mimicking acetylation enhanced the transcriptional level of itself and attenuated the mRNA levels of Lrp-regulated genes including fimA, which was confirmed by yeast agglutination assay. These findings demonstrate that the acetylation regulates the DNA-binding activity of Lrp, suggesting that acetylation modification of transcription factors is a conserved regulatory manner to modulate gene expression in bacteria and eukaryotes.

  15. The Bacterial Two-Hybrid System Uncovers the Involvement of Acetylation in Regulating of Lrp Activity in Salmonella Typhimurium

    Science.gov (United States)

    Qin, Ran; Sang, Yu; Ren, Jie; Zhang, Qiufen; Li, Shuxian; Cui, Zhongli; Yao, Yu-Feng

    2016-01-01

    N𝜀-lysine acetylation is an abundant and important Post-translational modification in bacteria. We used the bacterial two-hybrid system to screen the genome library of the Salmonella Typhimurium to identify potential proteins involved in acetyltransferase Pat – or deacetylase CobB-mediated acetylation. Then, the in vitro (de)acetylation assays were used to validate the potential targets, such as STM14_1074, NrdF, RhaR. Lrp, a leucine-responsive regulatory protein and global regulator, was shown to interact with Pat. We further demonstrate that Lrp could be acetylated by Pat and deacetylated by NAD+-dependent CobB in vitro. Specifically, the conserved lysine residue 36 (K36) in helix-turn-helix (HTH) DNA-binding domain of Lrp was acetylated. Acetylation of K36 impaired the function of Lrp through altering the affinity with the target promoter. The mutation of K36 in chromosome mimicking acetylation enhanced the transcriptional level of itself and attenuated the mRNA levels of Lrp-regulated genes including fimA, which was confirmed by yeast agglutination assay. These findings demonstrate that the acetylation regulates the DNA-binding activity of Lrp, suggesting that acetylation modification of transcription factors is a conserved regulatory manner to modulate gene expression in bacteria and eukaryotes. PMID:27909434

  16. Media composition influences yeast one- and two-hybrid results

    Directory of Open Access Journals (Sweden)

    Gonzalez Kim L

    2011-08-01

    Full Text Available Abstract Although yeast two-hybrid experiments are commonly used to identify protein interactions, the frequent occurrence of false negatives and false positives hampers data interpretation. Using both yeast one-hybrid and two-hybrid experiments, we have identified potential sources of these problems: the media preparation protocol and the source of the yeast nitrogen base may not only impact signal range but also effect whether a result appears positive or negative. While altering media preparation may optimize signal differences for individual experiments, media preparation must be reported in detail to replicate studies and accurately compare results from different experiments.

  17. Using the Two-Hybrid Screen in the Classroom Laboratory

    OpenAIRE

    Odom, Daniel P.; Grossel, Martha J

    2002-01-01

    The National Science Foundation and others have made compelling arguments that research be incorporated into the learning of undergraduates. In response to these arguments, a two-hybrid research project was incorporated into a molecular biology course that contained both a lecture section and a laboratory section. The course was designed around specific goals for educational outcomes, including introducing research to a wide range of students, teaching students experimental design and data an...

  18. Molecular epidemiological study on pre-X region of hepatitis B virus and identification of hepatocyte proteins interacting with whole-X protein by yeast two-hybrid

    Institute of Scientific and Technical Information of China (English)

    Qian Yang; Jun Cheng; Jing Dong; Jian Zhang; Shu-Lin Zhang

    2005-01-01

    AIM: To identify the pre-X region in hepatitis B virus (HBV)genome and to study the relationship between the genotype and the pre-X region. To investigate the biological function of whole-X (pre-X plus X) protein, we performed yeast two-hybrid to screen proteins in liver interacting with whole-X protein.METHODS: The pre-X region of HBV was amplified by polymerase chain reaction (PCR) method, and was cloned to pGEM Teasy vector. After the target region was sequenced, Vector 8.0 software was used to analyze the sequences. The whole-X bait plasmid was constructed by using yeast two-hybrid system 3. Yeast strain AH109 was transformed. After expression of the whole-X protein in AH109 yeast strains was proved, yeast two-hybrid screening was performed by mating AH109 with Y187 containing liver cDNA library plasmid. The mated yeast was plated on quadruple dropout medium and assayed for α-gal activity. The interaction between whole-X protein and the protein obtained from positive colonies was further confirmed by repeating yeast two-hybrid. After extracting and sequencing of plasmid from blue colonies, we carried out analysis by bioinformatics. RESULTS: After sequencing, 27 of 45 clones (60%) were found encoding the pre-X peptide. Eighteen of twenty-seven clones (66.7%) of pre-X coding sequences were found from genotype C. Five positive colonies that interacted with whole-X protein were obtained and sequenced; namely, fetuin B, UDP glycosyltransferase 1 family-polypeptide A9, mannose-P-dolichol utilization defect 1, fibrinogen-B beta polypeptide, transmembrane 4 superfamily member 4CD81 (TM4SF4).CONCLUSION: The pre-X gene exists in HBV genome.Genes of proteins interacting with whole-X protein in hepatocytes were successfully cloned. These results brought some new clues for studying the biological functions of whole-X protein.

  19. Molecular confirmation of t(6;11)(p21;q12) renal cell carcinoma in archival paraffin-embedded material using a break-apart TFEB FISH assay expands its clinicopathologic spectrum.

    Science.gov (United States)

    Argani, Pedram; Yonescu, Raluca; Morsberger, Laura; Morris, Kerry; Netto, George J; Smith, Nathan; Gonzalez, Nilda; Illei, Peter B; Ladanyi, Marc; Griffin, Constance A

    2012-10-01

    A subset of renal cell carcinomas (RCCs) is characterized by t(6;11)(p21;q12), which results in fusion of the untranslated Alpha (MALAT1) gene to the TFEB gene. Only 21 genetically confirmed cases of t(6;11) RCCs have been reported. This neoplasm typically demonstrates a distinctive biphasic morphology, comprising larger epithelioid cells and smaller cells clustered around basement membrane material; however, the full spectrum of its morphologic appearances is not known. The t(6;11) RCCs differ from most conventional RCCs in that they consistently express melanocytic immunohistochemical (IHC) markers such as HMB45 and Melan A and the cysteine protease cathepsin K but are often negative for epithelial markers such as cytokeratins. TFEB IHC has been proven to be useful to confirm the diagnosis of t(6;11) RCCs in archival material, because native TFEB is upregulated through promoter substitution by the gene fusion. However, IHC is highly fixation dependent and has been proven to be particularly difficult for TFEB. A validated fluorescence in situ hybridization (FISH) assay for molecular confirmation of the t(6;11) RCC in archival formalin-fixed, paraffin-embedded material has not been previously reported. We report herein the development of a break-apart TFEB FISH assay for the diagnosis of t(6;11)(p21;q12) RCCs. We validated the assay on 4 genetically confirmed cases and 76 relevant expected negative control cases and used the assay to report 8 new cases that expand the clinicopathologic spectrum of t(6;11) RCCs. An additional previously reported TFEB IHC-positive case was confirmed by TFEB FISH in 46-year-old archival material. In conclusion, TFEB FISH is a robust, clinically validated assay that can confirm the diagnosis of t(6;11) RCC in archival material and should allow a more comprehensive clinicopathologic delineation of this recently recognized neoplastic entity.

  20. Precision and recall estimates for two-hybrid screens.

    Science.gov (United States)

    Huang, Hailiang; Bader, Joel S

    2009-02-01

    Yeast two-hybrid screens are an important method to map pairwise protein interactions. This method can generate spurious interactions (false discoveries), and true interactions can be missed (false negatives). Previously, we reported a capture-recapture estimator for bait-specific precision and recall. Here, we present an improved method that better accounts for heterogeneity in bait-specific error rates. For yeast, worm and fly screens, we estimate the overall false discovery rates (FDRs) to be 9.9%, 13.2% and 17.0% and the false negative rates (FNRs) to be 51%, 42% and 28%. Bait-specific FDRs and the estimated protein degrees are then used to identify protein categories that yield more (or fewer) false positive interactions and more (or fewer) interaction partners. While membrane proteins have been suggested to have elevated FDRs, the current analysis suggests that intrinsic membrane proteins may actually have reduced FDRs. Hydrophobicity is positively correlated with decreased error rates and fewer interaction partners. These methods will be useful for future two-hybrid screens, which could use ultra-high-throughput sequencing for deeper sampling of interacting bait-prey pairs. All software (C source) and datasets are available as supplemental files and at http://www.baderzone.org under the Lesser GPL v. 3 license.

  1. Yeast Two-Hybrid, a Powerful Tool for Systems Biology

    Directory of Open Access Journals (Sweden)

    Uwe Schlattner

    2009-06-01

    Full Text Available A key property of complex biological systems is the presence of interaction networks formed by its different components, primarily proteins. These are crucial for all levels of cellular function, including architecture, metabolism and signalling, as well as the availability of cellular energy. Very stable, but also rather transient and dynamic protein-protein interactions generate new system properties at the level of multiprotein complexes, cellular compartments or the entire cell. Thus, interactomics is expected to largely contribute to emerging fields like systems biology or systems bioenergetics. The more recent technological development of high-throughput methods for interactomics research will dramatically increase our knowledge of protein interaction networks. The two most frequently used methods are yeast two-hybrid (Y2H screening, a well established genetic in vivo approach, and affinity purification of complexes followed by mass spectrometry analysis, an emerging biochemical in vitro technique. So far, a majority of published interactions have been detected using an Y2H screen. However, with the massive application of this method, also some limitations have become apparent. This review provides an overview on available yeast two-hybrid methods, in particular focusing on more recent approaches. These allow detection of protein interactions in their native environment, as e.g. in the cytosol or bound to a membrane, by using cytosolic signalling cascades or split protein constructs. Strengths and weaknesses of these genetic methods are discussed and some guidelines for verification of detected protein-protein interactions are provided.

  2. Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes

    Directory of Open Access Journals (Sweden)

    Saint Christopher P

    2007-03-01

    Full Text Available Abstract Background DNA melting curve analysis using double-stranded DNA-specific dyes such as SYTO9 produce complex and reproducible melting profiles, resulting in the detection of multiple melting peaks from a single amplicon and allowing the discrimination of different species. We compare the melting curves of several Naegleria and Cryptosporidium amplicons generated in vitro with in silico DNA melting simulations using the programs POLAND and MELTSIM., then test the utility of these programs for assay design using a genetic marker for toxin production in cyanobacteria. Results The SYTO9 melting curve profiles of three species of Naegleria and two species of Cryptosporidium were similar to POLAND and MELTSIM melting simulations, excepting some differences in the relative peak heights and the absolute melting temperatures of these peaks. MELTSIM and POLAND were used to screen sequences from a putative toxin gene in two different species of cyanobacteria and identify regions exhibiting diagnostic melting profiles. For one of these diagnostic regions the POLAND and MELTSIM melting simulations were observed to be different, with POLAND more accurately predicting the melting curve generated in vitro. Upon further investigation of this region with MELTSIM, inconsistencies between the melting simulation for forward and reverse complement sequences were observed. The assay was used to accurately type twenty seven cyanobacterial DNA extracts in vitro. Conclusion Whilst neither POLAND nor MELTSIM simulation programs were capable of exactly predicting DNA dissociation in the presence of an intercalating dye, the programs were successfully used as tools to identify regions where melting curve differences could be exploited for diagnostic melting curve assay design. Refinements in the simulation parameters would be required to account for the effect of the intercalating dye and salt concentrations used in real-time PCR. The agreement between the melting

  3. [Identification of C(2)M interacting proteins by yeast two-hybrid screening].

    Science.gov (United States)

    Shanshan, Yue; Laixin, Xia

    2015-11-01

    The synaptonemal complex (SC) is a huge structure which assembles between the homologous chromosomes during meiotic prophase I. Drosophila germ cell-specific nucleoprotein C(2)M clustering at chromosomes can induce SC formation. To further study the molecular function and mechanism of C(2)M in meiosis, we constructed a bait vector for C(2)M and used the yeast two-hybrid system to identify C(2)M interacting proteins. Forty interacting proteins were obtained, including many DNA and histone binding proteins, ATP synthases and transcription factors. Gene silencing assays in Drosophila showed that two genes, wech and Psf1, may delay the disappearance of SC. These results indicate that Wech and Psf1 may form a complex with C(2)M to participate in the formation or stabilization of the SC complex.

  4. Use of rapid HIV assays as supplemental tests in specimens with repeatedly reactive screening immunoassay results not confirmed by HIV-1 Western blot.

    Science.gov (United States)

    Wesolowski, Laura G; Delaney, Kevin P; Meyer, William A; Blatt, Amy J; Bennett, Berry; Chavez, Pollyanna; Granade, Timothy C; Owen, Michele

    2013-09-01

    An alternate HIV testing algorithm has been proposed which includes a fourth-generation immunoassay followed by an HIV-1/HIV-2 antibody differentiation supplemental test for reactive specimens and a nucleic acid test (NAT) for specimens with discordant results. To evaluate the performance of five rapid tests (Alere Clearview, Bio-Rad Multispot, OraSure OraQuick, MedMira Reveal, and Trinity Biotech Unigold) as the supplemental antibody assay in the algorithm. A total of 3273 serum and plasma specimens that were third-generation immunoassay repeatedly reactive and Western blot (WB) negative or indeterminate were tested with rapid tests and NAT. Specimens were classified by NAT: (1) HIV-1 infected (NAT-reactive; n=184, 5.6%), (2) HIV-status unknown (NAT nonreactive; n=3078, 94.2%) or by Multispot, (3) HIV-2 positive (n=5), and (4) HIV-1 and HIV-2 positive (n=6). Excluding HIV-2 positive specimens, we calculated the proportion of reactive rapid tests among specimens with reactive and nonreactive NAT. The proportion of infected specimens with reactive rapid test results and negative or indeterminate WB ranged from 30.4% (56) to 47.8% (88) depending on the rapid test. From 1% to 2% of NAT-negative specimens had reactive rapid test results. In these diagnostically challenging specimens, all rapid tests identified infections that were missed by the Western blot, but only Multispot could differentiate HIV-1 from HIV-2. Regardless of which rapid test is used as a supplemental test in the alternative algorithm, false-positive algorithm results (i.e., reactive screening and rapid test in uninfected person) may occur, which will need to be resolved during the baseline medical evaluation. Published by Elsevier B.V.

  5. Evaluation and Comparison of Enzyme Immunoassay (Eia and Acid Fast Staining with Confirmation by Immunofluorescent Antibody Assay for Detection of Cryptosporidium Species in Infants and Young Children.

    Directory of Open Access Journals (Sweden)

    D Dorostcar Moghaddam

    2005-01-01

    Full Text Available Introduction: Cryptosporidiosis is prevalent world wide, causing a variety of problems ranging from acute, self-limiting diarrhea to fatal cases in immunocompromised persons, particulary those with acquired immunodeficiency (AIDS. Diagnosis of Cryptosporidium is made by identification of oocysts in stool specimens. The detection is most commonly made by the acid-fast staining method followed by microscopic examination which has low specificity and sensitivity. Material and Methods: In the present study, we evaluated diagnostic utility of a commercially available enzyme immunoassay (EIA, which detects Cryptosporidium-Specific antigen (CSA in 204 unprocessed stool specimens obtained from patients less than 3 years of age. Results: When compared with the routine screening procedure applied in this field study (screening by acid-fast staining and microscopy after concentration of positive results by IFA, both sensitivity and specificity were 98%. Of the 139 specimens negative by microscopy, 13 (9.3% were positive by EIA, 11 of which were confirmed by inhibition with antibody to Cryptosporidia-specific antigen. Conclusion: The EIA is an important tool for identifying Cryptosporidium in fecal specimens in field studies since it is sensitive, specific, simple to use and unaffected by the presence of a preservative.

  6. New classes of mind bomb-interacting proteins identified from yeast two-hybrid screens.

    Science.gov (United States)

    Tseng, Li-Chuan; Zhang, Chengjin; Cheng, Chun-Mei; Xu, Haoying; Hsu, Chia-Hao; Jiang, Yun-Jin

    2014-01-01

    Notch signaling pathway defines an evolutionarily conserved mechanism in cell-fate determination in a broad spectrum of developmental processes through local cell interactions. mind bomb (mib) encodes an E3 ubiquitin ligase that is involved in Notch activation through Delta ubiquitylation and internalization. To further dissect the function of Mib, two yeast two-hybrid screens for zebrafish Mib/Mib2-binding proteins with different strategies have been performed. 81 putative interesting proteins were discovered and classified into six groups: ubiquitin proteasome pathway, cytoskeleton, trafficking, replication/transcription/translation factors, cell signaling and others. Confirmed by coimmunoprecipitation (Co-IP), Mib interacted with four tested proteins: ubiquitin specific protease 1 (Usp1), ubiquitin specific protease 9 (Usp9), tumor-necrosis-factor-receptor-associated factor (TRAF)-binding domain (Trabid)/zinc finger, RAN-binding domain containing 1 (Zranb1) and hypoxia-inducible factor 1, alpha subunit inhibitor (Hif1an)/factor inhibiting HIF 1 (Fih-1). Usp1, Usp9, Trabid and Fih-1 also bound to zebrafish Mib2, a Mib homolog with similar structural domains and functions. Both Mib and Mib2 can ubiquitylate Trabid and Fih-1, indicating a potential regulating role of Mib and Mib2 on Trabid and Fih-1 and, furthermore, the possible involvement of Notch signaling in hypoxia-regulated differentiation, tumorigenesis and NF-κB pathway. Finally, functions of confirmed Mib/Mib2-interacting proteins are collated, summarized and hypothesized, which depicts a regulating network beyond Notch signaling.

  7. Calcium/calmodulin kinase1 and its relation to thermotolerance and HSP90 in Sporothrix schenckii: an RNAi and yeast two-hybrid study

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    Gonzalez-Mendez Ricardo

    2011-07-01

    Full Text Available Abstract Background Sporothrix schenckii is a pathogenic dimorphic fungus of worldwide distribution. It grows in the saprophytic form with hyaline, regularly septated hyphae and pyriform conidia at 25°C and as the yeast or parasitic form at 35°C. Previously, we characterized a calcium/calmodulin kinase in this fungus. Inhibitors of this kinase were observed to inhibit the yeast cell cycle in S. schenckii. Results The presence of RNA interference (RNAi mechanism in this fungus was confirmed by the identification of a Dicer-1 homologue in S. schenckii DNA. RNAi technology was used to corroborate the role of calcium/calmodulin kinase I in S. schenckii dimorphism. Yeast cells were transformed with the pSilent-Dual2G (pSD2G plasmid w/wo inserts of the coding region of the calcium/calmodulin kinase I (sscmk1 gene. Transformants were selected at 35°C using resistance to geneticin. Following transfer to liquid medium at 35°C, RNAi transformants developed as abnormal mycelium clumps and not as yeast cells as would be expected. The level of sscmk1 gene expression in RNAi transformants at 35°C was less than that of cells transformed with the empty pSD2G at this same temperature. Yeast two-hybrid analysis of proteins that interact with SSCMK1 identified a homologue of heat shock protein 90 (HSP90 as interacting with this kinase. Growth of the fungus similar to that of the RNAi transformants was observed in medium with geldanamycin (GdA, 10 μM, an inhibitor of HSP90. Conclusions Using the RNAi technology we silenced the expression of sscmk1 gene in this fungus. RNAi transformants were unable to grow as yeast cells at 35°C showing decreased tolerance to this temperature. The interaction of SSCMK1 with HSP90, observed using the yeast two-hybrid assay suggests that this kinase is involved in thermotolerance through its interaction with HSP90. SSCMK1 interacted with the C terminal domain of HSP90 where effector proteins and co-chaperones interact. These

  8. Screening of the interacting proteins with NifA in Azospirillum brasilense Sp7 by the yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    CHEN Sanfeng; GUAN Yu; TU Ran; SUN Wengai; LI Jilun

    2005-01-01

    NifA in Azospirillum brasilense plays a key role in regulating the synthesis and activity of nitrogenase in response to ammonia and oxygen available. In this work we used the yeast two-hybrid system to identify the proteins that interact with NifA. The nifA gene was fused to the yeast two-hybrid vector pGBD-C2, and three A. brasilense Sp7 genomic libraries for use in yeast two-hybrid studies were constructed. Screening of the libraries identified four clones encoding proteins that interact with NifA. The confirmation of the interactions of each gene product of the four clones and NifA were carried out by exchanging the vectors for nifA and the four clones and by mutageneses of the four clones with shift reading frame experiments in yeast two-hybrid studies. DNA sequence analyses showed that two clones encode proteins containing PAS domains that play an important role in signal transduction. One clone has high similarity with the fhuE gene of Escherichia coli, whose gene product is involved in iron uptake and transportation, and the other clone encodes an unknown protein.

  9. Generation of high-affinity fully human anti-interleukin-8 antibodies from its cDNA by two-hybrid screening and affinity maturation in yeast.

    Science.gov (United States)

    Ding, Ling; Azam, Mark; Lin, Yu-Huei; Sheridan, James; Wei, Shuanghong; Gupta, Gigi; Singh, Rakesh K; Pauling, Michelle H; Chu, Waihei; Tran, Antares; Yu, Nai-Xuan; Hu, Jiefeng; Wang, Wei; Long, Hao; Xiang, Dong; Zhu, Li; Hua, Shao-Bing

    2010-10-01

    We have developed a technology for rapidly generating novel and fully human antibodies by simply using the antigen DNA. A human single-chain variable fragment (scFv) antibody library was constructed in a yeast two-hybrid vector with high complexity. After cloning cDNA encoding the mature sequence of human interleukin-8 (hIL8) into the yeast two-hybrid system vector, we have screened the human scFv antibody library and obtained three distinct scFv clones that could specifically bind to hIL8. One clone was chosen for further improvement by a novel affinity maturation process using the error-prone PCR of the scFv sequence followed by additional rounds of yeast two-hybrid screening. The scFv antibodies of both primary and affinity-matured scFv clones were expressed in E. coli. All purified scFvs showed specific binding to hIL8 in reciprocal coimmunoprecipitation and ELISA assays. All scFvs, as well as a fully human IgG antibody converted from one of the scFv clones and expressed in the mammalian cells, were able to effectively inhibit hIL8 in neutrophil chemotaxis assays. The technology described can generate fully human antibodies with high efficiency and low cost.

  10. Interaction of CSFV E2 protein with swine host factors as detected by yeast two-hybrid system.

    Directory of Open Access Journals (Sweden)

    Douglas P Gladue

    Full Text Available E2 is one of the envelope glycoproteins of pestiviruses, including classical swine fever virus (CSFV and bovine viral diarrhea virus (BVDV. E2 is involved in several critical functions, including virus entry into target cells, induction of a protective immune response and virulence in swine. However, there is no information regarding any host binding partners for the E2 proteins. Here, we utilized the yeast two-hybrid system and identified fifty-seven host proteins as positive binding partners which bound E2 from both CSFV and BVDV with the exception of two proteins that were found to be positive for binding only to CSFV E2. Alanine scanning of CSFV E2 demonstrated that the binding sites for these cellular proteins on E2 are likely non-linear binding sites. The possible roles of the identified host proteins are discussed as the results presented here will be important for future studies to elucidate mechanisms of host protein-virus interactions during pestivirus infection. However, due to the limitations of the yeast two hybrid system, the proteins identified is not exhaustive and each interaction identified needs to be confirmed by independent experimental approaches in the context of virus-infected cells before any definitive conclusion can be drawn on relevance for the virus life cycle.

  11. 电化学发光法进行HBsAg阳性确认的可行性及应用研究%Feasibility and application of HBsAg positive confirmation by electrochemiluminescence assay in blood screening

    Institute of Scientific and Technical Information of China (English)

    邓雪莲; 陈辉; 王新梅; 臧亮; 王东; 高慧卉; 邹亚轩; 周璐; 梁晓华

    2016-01-01

    Objective To evaluate the feasibility of HBsAg positive confirmation by electrochemiluminescence assay (ECL) in blood screening and to investigate the gray area setting of HBsAg ELISA and an alternative method of HBsAg positive confirmation,and to simplify the algorithm of donor reentry.Method As the supplementary test,HBsAg ECL was adopted to retest samples of HBsAg reactive (ELISA) in blood screening and those HBsAg ECL reactive were confirmed by neutralization test (ECL).HBsAg positive was confirmed by combination of nucleic acid test (NAT),ECL and ELISA and blood donor follow-up.Neutralization test (ECL) and HBsAg (ECL) were compared for detecting HBV DNA positive among samples that were HBsAg reactive to both of two ELISA kits (S/CO≥ 1).The detection efficiency of HBsAg positive confirmed in different detection processes supplemented with HBsAg ECL were analyzed with sensitivity (SEN) and positive predictive value (PPV),as well as grey area setting.The S/CO value distributions of HBsAg false reactive and HBsAg positive were analyzed for each ELISA kit.Results Among 821 HBsAg reactive excluded from 192 065 samples collected in Dalian Blood Center between January 1st,2013 and June 30th,2015,about 160 HBsAg positive were confirmed by combination tests and blood donor follow-up.The ability of HBsAg (ECL) in detecting HBV DNA positive among samples that were HBsAg reactive to both of two ELISA kits (S/CO ≥ 1) was significandy higher than that of neutralization test (ECL) (P < 0.05).The PPV of different detection processes in detecting HBsAg positive confirmed was increased to 92.6%-99.2% by HBsAg (ECL) supplementary test (P =0).There was significant difference between S/CO value distributions of HBsAg false reactive and of the HBsAg positive confirmed for each ELISA kit.The plateau regions of SEN and PPV for two ELISA kits were observed when gray area setting was decreased.The SEN and PPV for ELISA1 were already in plateau regions when S/CO≤ 1,and S

  12. An improved yeast two-hybrid approach for detection of interacting proteins

    Institute of Scientific and Technical Information of China (English)

    Wan Bingbing; Shi Yan; Huo Keke

    2006-01-01

    Yeast two-hybrid approach is popularly used nowadays as an important technical method in the field of studying protein-protein interactions.Although yeast two-hybrid system is obviously advantageous in searching interacting proteins and setting up the network of proteins interaction.not all of proteins can use routine yeast two-hybrid method to search interacting proteins.Many important proteins,such as some nucleoprotein transcriptional factor,carry out the regular method and construct the bait-BD vector to screen the library containing AD vector.However,it usually results in failures because it contains the activate domain and can self-activate the reporter gene.In this study,we changed the research strategy,fused the bait gene(FOXA3)with the AD vector to screen the library containing BD vector,so that we constructed a two-hybrid library containing BD vector and Can bypass the interference of self-activation.And we used this two-hybrid library to screen FOXA3.a hepatocyte nuclear factor,and found out an interacting protein:complement component C3.

  13. Subunit orientation in the Escherichia coli enterobactin biosynthetic EntA-EntE complex revealed by a two-hybrid approach.

    Science.gov (United States)

    Pakarian, Paknoosh; Pawelek, Peter D

    2016-08-01

    The siderophore enterobactin is synthesized by the enzymes EntA-F and EntH in the Escherichia coli cytoplasm. We previously reported in vitro evidence of an interaction between tetrameric EntA and monomeric EntE. Here we used bacterial adenylate cyclase two-hybrid (BACTH) assays to demonstrate that the E. coli EntA-EntE interaction occurs intracellularly. Furthermore, to obtain information on subunit orientation in the EntA-EntE complex, we fused BACTH reporter fragments T18 and T25 to EntA and EntE in both N-terminal and C-terminal orientations. To validate functionality of our fusion proteins, we performed Chrome Azurol S (CAS) assays using E. coli entE(-) and entA(-) knockout strains transformed with our BACTH constructs. We found that transformants expressing N-terminal and C-terminal T18/T25 fusions to EntE exhibited CAS signals, indicating that these constructs could rescue the entE(-) phenotype. While expression of EntA with N-terminal T18/T25 fusions exhibited CAS signals, C-terminal fusions did not, presumably due to disruption of the EntA tetramer in vivo. Bacterial growth assays supported our CAS findings. Co-transformation of functional T18/T25 fusions into cya(-)E. coli BTH101 cells resulted in positive BACTH signals only when T18/T25 fragments were fused to the N-termini of both EntA and EntE. Co-expression of N-terminally fused EntA with C-terminally fused EntE resulted in no detectable BACTH signal. Analysis of protein expression by Western blotting confirmed that the loss of BACTH signal was not due to impaired expression of fusion proteins. Based on our results, we propose that the N-termini of EntA and EntE are proximal in the intracellular complex, while the EntA N-terminus and EntE C-terminus are distal. A protein-protein docking simulation using SwarmDock was in agreement with our experimental observations.

  14. Yeast Two-Hybrid Screening for Proteins that Interact with the Extracellular Domain of Amyloid Precursor Protein.

    Science.gov (United States)

    Yu, You; Li, Yinan; Zhang, Yan

    2016-04-01

    Alzheimer's disease (AD) is a neurodegenerative disorder in which amyloid β plaques are a pathological characteristic. Little is known about the physiological functions of amyloid β precursor protein (APP). Based on its structure as a type I transmembrane protein, it has been proposed that APP might be a receptor, but so far, no ligand has been reported. In the present study, 9 proteins binding to the extracellular domain of APP were identified using a yeast two-hybrid system. After confirming the interactions in the mammalian system, mutated PLP1, members of the FLRT protein family, and KCTD16 were shown to interact with APP. These proteins have been reported to be involved in Pelizaeus-Merzbacher disease (PMD) and axon guidance. Therefore, our results shed light on the mechanisms of physiological function of APP in AD, PMD, and axon guidance.

  15. Androgen receptor coregulator ARA267-α interacts with death receptor-6 revealed by the yeast two-hybrid

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    ARA267-αis a newly identified androgen receptor coactivator.In order to further elucidate its precise role in cells,using the ARA267- α fragment containing four PHD and one SET conserved domains as bait we revealed an ARA267-α-PHD-SET-interacting protein,death receptor-6(DR6),in the yeast two-hybrid screening.DR6 is the member of TNF receptor family and has a death domain in its intracellular cytoplasmic portion(DR6cp)to mediate the cell apoptosis.The interaction between ARA267-α-PHD-SET and DR6cp was confirmed in vitro and in vivo.Our finding implied that androgen signaling pathway might cross talk with apoptosis signaling pathway through the interaction between ARA267-α and DR6.

  16. Mapping the interactions of dengue virus NS1 protein with human liver proteins using a yeast two-hybrid system: identification of C1q as an interacting partner.

    Directory of Open Access Journals (Sweden)

    Emiliana M Silva

    Full Text Available Dengue constitutes a global health concern. The clinical manifestation of this disease varies from mild febrile illness to severe hemorrhage and/or fatal hypovolemic shock. Flavivirus nonstructural protein 1 (NS1 is a secreted glycoprotein that is displayed on the surface of infected cells but is absent in viral particles. NS1 accumulates at high levels in the plasma of dengue virus (DENV-infected patients, and previous reports highlight its involvement in immune evasion, dengue severity, liver dysfunction and pathogenesis. In the present study, we performed a yeast two-hybrid screen to search for DENV2 NS1-interacting partners using a human liver cDNA library. We identified fifty genes, including human complement component 1 (C1q, which was confirmed by coimmunoprecipitation, ELISA and immunofluorescence assays, revealing for the first time the direct binding of this protein to NS1. Furthermore, the majority of the identified genes encode proteins that are secreted into the plasma of patients, and most of these proteins are classified as acute-phase proteins (APPs, such as plasminogen, haptoglobin, hemopexin, α-2-HS-glycoprotein, retinol binding protein 4, transferrin, and C4. The results presented here confirm the direct interaction of DENV NS1 with a key protein of the complement system and suggest a role for this complement protein in the pathogenesis of DENV infection.

  17. Construction and Identification of a Yeast Two-Hybrid Bait Vector and Its Effect on the Growth of Yeast Cells and the Self-Activating Function of Reporter Genes for Screening of HPV18 E6-Interacting Protein

    Institute of Scientific and Technical Information of China (English)

    梅泉; 李双; 刘萍; 奚玲; 王世宣; 孟玉菡; 刘杰; 杨欣慰; 卢运萍; 汪辉

    2010-01-01

    By using a yeast two-hybrid system,a yeast two-hybrid bait vector was constructed and identified for screening of the HPV18 E6-interacting proteins,and its effects on the growth of yeast cells and the activation of reporter genes were investigated.Total mRNA extracted from Hela cells was reversely transcribed into cDNA.Fragment of HPV18 E6 cDNA was amplified using RT-PCR and directly ligated to the pGBKT7 vector.The recombinant plasmid was confirmed by restriction endonuclease analysis and DNA sequencing.Th...

  18. Interaction of hTCF4 by yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    To investigate the interaction of hTCF4, the yeast two-hybrid system has been used for testing the interaction of mutants of hTCF4 with themselves. Mutants of hTCF4 (hTCF4Ⅰ) and hTCF4Ⅱ) have been obtained by polymerase chain reaction (PCR). Bait (hTCF4Ⅰ-pDBLeu and hTCF4Ⅱ-pDBLeu) and prey (hTCF4Ⅰ-pPC86 and hTCF4Ⅱ-pPC86) have been constructed by DNA recombination for yeast two-hybrid. Interaction of hTCF4Ⅱ with itself is found in the reverse yeast two-hybrid system (GIBCOBRL Co.). However, no interactions are found in hTCF4Ⅱ with hTCF4Ⅰand in hTCF4Ⅰ with hTCF4Ⅰ. These results suggest that hTCF4 could interact with itself to form homodimer or homocopolymer and perform the transcriptional activating function through LZ or HLH motifs in nucleus of renal cell carcinoma.

  19. Isolation of Cronobacter spp. (formerly Enterobacter sakazakii from infant food, herbs and environmental samples and the subsequent identification and confirmation of the isolates using biochemical, chromogenic assays, PCR and 16S rRNA sequencing

    Directory of Open Access Journals (Sweden)

    Samara Nawal A

    2009-10-01

    Full Text Available Abstract Background Cronobacter spp. (formerly Enterobacter sakazakii, are a group of Gram-negative pathogens that have been implicated as causative agents of meningitis and necrotizing enterocolitis in infants. The pathogens are linked to infant formula; however, they have also been isolated from a wide range of foods and environmental samples. Results In this study, 233 samples of food, infant formula and environment were screened for the presence of Cronobacter spp. in an attempt to find its source. Twenty nine strains were isolated from samples of spices, herbs, infant foods, and dust obtained from household vacuum cleaners. Among the 76 samples of infant food, infant formula, milk powder and non-milk dairy products tested, only one sample of infant food contained Cronobacter spp. (1.4%. The other Cronobacter spp. isolates recovered include two from household vacuum dust, and 26 from 67 samples of herbs and spices. Among the food categories analyzed, herbs and spices harbored the highest number of isolates, indicating plants as a possible reservoir of this pathogen. Initial screening with API 20E test strips yielded 42 presumptive isolates. Further characterization using 3 chromogenic media (α-MUG, DFI and EsPM and 8 sets of PCR primers detecting ITS (internal transcribed spacer sequences, 16S rRNA, zpx, gluA, gluB, OmpA genes followed by nucleotide sequencing of some PCR amplicons did not confirm the identity of all the isolates as none of the methods proved to be free of both false positives or false negatives. The final confirmation step was done by 16S rRNA sequence analysis identifying only 29 of the 42 isolates as Cronobacter spp. Conclusion Our studies showed that Cronobacter spp. are highly diverse and share many phenotypic traits with other Enterobacteriaceae members highlighting the need to use several methods to confirm the identity of this pathogen. None of the biochemical, chromogenic or PCR primers proved to be a reliable

  20. pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis

    Directory of Open Access Journals (Sweden)

    de Chassey Benoît

    2009-10-01

    Full Text Available Abstract Background High-throughput screening of protein-protein interactions opens new systems biology perspectives for the comprehensive understanding of cell physiology in normal and pathological conditions. In this context, yeast two-hybrid system appears as a promising approach to efficiently reconstruct protein interaction networks at the proteome-wide scale. This protein interaction screening method generates a large amount of raw sequence data, i.e. the ISTs (Interaction Sequence Tags, which urgently need appropriate tools for their systematic and standardised analysis. Findings We develop pISTil, a bioinformatics pipeline combined with a user-friendly web-interface: (i to establish a standardised system to analyse and to annotate ISTs generated by two-hybrid technologies with high performance and flexibility and (ii to provide high-quality protein-protein interaction datasets for systems-level approach. This pipeline has been validated on a large dataset comprising more than 11.000 ISTs. As a case study, a detailed analysis of ISTs obtained from yeast two-hybrid screens of Hepatitis C Virus proteins against human cDNA libraries is also provided. Conclusion We have developed pISTil, an open source pipeline made of a collection of several applications governed by a Perl script. The pISTil pipeline is intended to laboratories, with IT-expertise in system administration, scripting and database management, willing to automatically process large amount of ISTs data for accurate reconstruction of protein interaction networks in a systems biology perspective. pISTil is publicly available for download at http://sourceforge.net/projects/pistil.

  1. Screening of FOXP3-interacted proteins by yeast two-hybrid technique

    Institute of Scientific and Technical Information of China (English)

    Zhou Lina; Wu Jun; Luo Gaoxing; He Weifeng; Chen Xiwei; Bo Ganping; Yuan Shunzong; Zhang Xiaorong; Hu Xiaohong

    2008-01-01

    Objective: To screen the proteins interacting with the Treg specification factor forkhead box protein P3 (FOXP3) by yeast two-hybrid system. Methods: Human FOXP3 gene was amplified by nest RT-PCR from peripheral blood mononuclear cells (PBMC) and inserted into plasmid pGBKT7 to construct the bait vector, then the self-activation and toxicity of the bait vector in host yeast strain AH109 were observed. Thereafter, a human liver cDNA library was screened by the bait vector. The positive clones were selected out by nutrient-deficient culture and back-hybridizing. The sequences from the candidate positive clones were blasted and analyzed by bioinformatics methods. Results: The constructed bait vector encoding FOXP3 was found no self-activation and toxicity in yeast AH109. Three proteins which interacted with FOXP3, including tumor protein D52, splicing factor 3b subunit 1 and hypothetical protein, were identified. Conclusion: Three new candidate proteins interacting with FOXP3 are selected out by this yeast two-hybrid system and library, which may facilitate the further study of FOXP3 in Treg.

  2. CERN confirms LHC schedule

    CERN Multimedia

    2003-01-01

    The CERN Council held its 125th session on 20 June. Highlights of the meeting included confirmation that the LHC is on schedule for a 2007 start-up, and the announcement of a new organizational structure in 2004.

  3. Detection of Leishmania infantum in naturally infected Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) and Canis familiaris in Misiones, Argentina: the first report of a PCR-RFLP and sequencing-based confirmation assay.

    Science.gov (United States)

    Acardi, Soraya Alejandra; Liotta, Domingo Javier; Santini, María Soledad; Romagosa, Carlo Mariano; Salomón, Oscar Daniel

    2010-09-01

    In this study, a genotypification of Leishmania was performed using polimerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing techniques to identify species of Leishmania parasites in phlebotomine sand flies and dogs naturally infected. Between January-February of 2009, CDC light traps were used to collect insect samples from 13 capture sites in the municipality of Posadas, which is located in the province of Misiones of Argentina. Sand flies identified as Lutzomyia longipalpis were grouped into 28 separate pools for molecular biological analysis. Canine samples were taken from lymph node aspirates of two symptomatic stray animals that had been positively diagnosed with canine visceral leishmaniasis. One vector pool of 10 sand flies (1 out of the 28 pools tested) and both of the canine samples tested positively for Leishmania infantum by PCR and RFLP analysis. PCR products were confirmed by sequencing and showed a maximum identity with L. infantum. Given that infection was detected in one out of the 28 pools and that at least one infected insect was infected, it was possible to infer an infection rate at least of 0.47% for Lu. longipalpis among the analyzed samples. These results contribute to incriminate Lu. longipalpis as the vector of L. infantum in the municipality of Posadas, where cases of the disease in humans and dogs have been reported since 2005.

  4. Use of PCR-based assays for the detection of the adventitious agent porcine circovirus type 1 (PCV1) in vaccines, and for confirming the identity of cell substrates and viruses used in vaccine production.

    Science.gov (United States)

    Kumar, Deepak; Beach, Nathan M; Meng, Xiang-Jin; Hegde, Nagendra R

    2012-01-01

    Safety and quality are important issues for vaccines. Whereas reversion to virulence poses a safety risk with live attenuated vaccines, the potential for the presence of adventitious agents is also an issue of vaccine quality. The recent detection or porcine circovirus type 1 (PCV1) in human vaccines has further highlighted the importance of quality control in vaccine production. The purpose of this study was to use a novel conventional PCR to detect PCV1, and subsequently screen materials used in the manufacture of vaccines at Bharat Biotech International Limited, India. The genome or gene fragments of PCV1 were not detected in any of the vaccines and materials tested, including the live attenuated rotavirus vaccine candidate ROTAVAC(®). Further, the identity of the cells and the viruses used as starting materials in the manufacture of these vaccines was confirmed by species-specific PCR or virus-specific RT-PCR, and no cross-contamination was detected in any case. The methods can be applied for regular in-house quality control screening of raw materials and seeds/banks, as well as formulated vaccines.

  5. Repository performance confirmation.

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, Francis D.

    2011-09-01

    Repository performance confirmation links the technical bases of repository science and societal acceptance. This paper explores the myriad aspects of what has been labeled performance confirmation in U.S. programs, which involves monitoring as a collection of distinct activities combining technical and social significance in radioactive waste management. This paper is divided into four parts: (1) A distinction is drawn between performance confirmation monitoring and other testing and monitoring objectives; (2) A case study illustrates confirmation activities integrated within a long-term testing and monitoring strategy for Yucca Mountain; (3) A case study reviews compliance monitoring developed and implemented for the Waste Isolation Pilot Plant; and (4) An approach for developing, evaluating and implementing the next generation of performance confirmation monitoring is presented. International interest in repository monitoring is exhibited by the European Commission Seventh Framework Programme 'Monitoring Developments for Safe Repository Operation and Staged Closure' (MoDeRn) Project. The MoDeRn partners are considering the role of monitoring in a phased approach to the geological disposal of radioactive waste. As repository plans advance in different countries, the need to consider monitoring strategies within a controlled framework has become more apparent. The MoDeRn project pulls together technical and societal experts to assimilate a common understanding of a process that could be followed to develop a monitoring program. A fundamental consideration is the differentiation of confirmation monitoring from the many other testing and monitoring activities. Recently, the license application for Yucca Mountain provided a case study including a technical process for meeting regulatory requirements to confirm repository performance as well as considerations related to the preservation of retrievability. The performance confirmation plan developed as part

  6. Screening of genes for proteins interacting with the PS1TP5 protein of hepatitis B virus: probing a human leukocyte cDNA library using the yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jian-kang; ZHAO Long-feng; CHENG Jun; GUO Jiang; LUN Yong-zhi; HONG Yuan

    2006-01-01

    Background The hepatitis B virus (HBV) genome includes S, C, P and X regions. The S region is divided into four subregions of pre-pre-S, pre-S1, pre-S2 and S. PS1TP5 (human gene 5 transactivated by pre-S1 protein of HBV) is a novel target gene transactivated by the pre-S1 protein that has been screened with a suppression subtractive hybridization technique in our laboratory (GenBank accession: AY427953). In order to investigate the biological function of the PS1TP5 protein, we performed a yeast two-hybrid system 3 to screen proteins from a human leukocyte cDNA library interacting with the PS 1TP5 protein.Methods The reverse transcription polymerase chain reaction (RT-PCR) was performed to amplify the gene of PS1TP5 from the mRNA of HepG2 cells and the gene was then cloned into the pGEM-T vector. After being sequenced and analyzed with Vector NTI 9.1 and NCBI BLAST software, the target gene of PS1TP5 was cut from the pGEM-T vector and cloned into a yeast expression plasmid pGBKT7, then "bait" plasmid pGBKT7-PS 1TP5 was transformed into the yeast strain AH109. The yeast protein was isolated and analyzed with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting hybridization.After expression of the pGBKT7-PS1TP5 fusion protein in the AH109 yeast strain was accomplished, a yeast two-hybrid screening was performed by mating AH 109 with Y 187 containing a leukocyte cDNA library plasmid.The mated yeast was plated on quadruple dropout medium and assayed for α-gal activity. The interaction between the PS1TP5 protein and the proteins obtained from positive colonies was further confirmed by repeating the yeast two-hybrid screen. After extracting and sequencing of plasmids from blue colonies we carried out a bioinformatic analysis.Results Forty true positive colonies were selected and sequenced, full length sequences were obtained and we searched for homologous DNA sequences from GenBank. Among the 40 positive colonies, 23 coding genes

  7. Screening for cardiac HERG potassium channel interacting proteins using the yeast two-hybrid technique.

    Science.gov (United States)

    Ma, Qingyan; Yu, Hong; Lin, Jijin; Sun, Yifan; Shen, Xinyuan; Ren, Li

    2014-02-01

    The human ERG protein (HERG or Kv 11.1) encoded by the human ether-a-go-go-related gene (herg) is the pore-forming subunit of the cardiac delayed rectifier potassium current (IKr) responsible for action potential (AP) repolarization. Mutations in HERG lead to long-QT syndrome, a major cause of arrhythmias. Protein-protein interactions are fundamental for ion channel trafficking, membrane localization, and functional modulation. To identify proteins involved in the regulation of the HERG channel, we conducted a yeast two-hybrid screen of a human heart cDNA library using the C-terminus or N-terminus of HERG as bait. Fifteen proteins were identified as HERG amino terminal (HERG-NT)-interacting proteins, including Caveolin-1 (a membrane scaffold protein with multiple interacting partners, including G-proteins, kinases and NOS), the zinc finger protein, FHL2 and PTPN12 (a non-receptor tyrosine phosphatase). Eight HERG carboxylic terminal (HERG-CT)-interacting proteins were also identified, including the NF-κB-interacting protein myotrophin, We have identified multiple potential interacting proteins that may regulate cardiac IKr through cytoskeletal interactions, G-protein modulation, phosphorylation and downstream second messenger and transcription cascades. These findings provide further insight into dynamic modulation of HERG under physiological conditions and arrhythmogenesis.

  8. Screening of BRD7 interacting proteins by yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    余鹰; 朱诗国; 张必成; 周鸣; 李小玲; 李桂源

    2002-01-01

    BRD7 gene is low or undetectably expressed in nasopharyngeal carcinoma tissue (NPC) and can obviously suppress the growth of NPC cell line HNE1. In this study, the proteins that interacted with BRD7 coding protein were screened by yeast two-hybrid system. The complete reading frame of BRD7 gene was subcloned into pAS2 vector (BRD7-BD). Then the human embryo brain cDNA library was screened by BRD7-BD bait. Eleven positive clones were obtained from 4.8×106 transformed clones. By sequencing directly, 6 interacting proteins of BRD7 coding protein were isolated (Bromodomain-containing 3 protein (BRD3), Bromodomain-containing 2 protein (BRD2), IκB kinase-beta, KIAA1375 protein, interleukin 7 and adaptor-related protein complex 3δ-1 subunit). These results suggest BRD7 protein might form heterogenous dimer or triplex polymer with BRD2 and/or BRD3 to participate in transcriptional regulation.

  9. Using yeast two-hybrid system to detect interactions of ATP synthase subunits from Spinacia oleracea

    Institute of Scientific and Technical Information of China (English)

    石晓冰; 魏家绵; 沈允钢

    2000-01-01

    Subunit interactions among the chloroplast ATP synthase subunits were studied using the yeast two-hybrid system. Various pairwise combinations of genes encoding a, p, y, 8 and e subunits of Spinach ATP synthase fused to the binding domain or activation domain of GAL4 DNA were introduced into yeast and then expression of a reporter gene encoding p-galactosidase was detected. Of all the combinations, that of y and e subunit genes showed the highest level of reporter gene expression, while those of a and p, a and e, p and e and p and 8 induced stable and significant reporter gene expression. The combination of 8 and e as well as that of 8 and y induced weak and unstable reporter gene expression. However, combinations of a and y, p and y and a and 8 did not induce reporter gene expression. These results suggested that specific and strong interactions between y and e, a and p, a and e, p and e and p and 8 subunits, and weak and transient interactions between 8 and e and 8 and y subunits occurred in the yeast

  10. CONFIRMATION OF CIRCUMSTELLAR PHOSPHINE

    Energy Technology Data Exchange (ETDEWEB)

    Agúndez, M.; Cernicharo, J. [Instituto de Ciencia de Materiales de Madrid, CSIC, C/ Sor Juana Inés de la Cruz 3, E-28049 Cantoblanco (Spain); Decin, L. [Sterrenkundig Instituut Anton Pannekoek, University of Amsterdam, Science Park 904, NL-1098 Amsterdam (Netherlands); Encrenaz, P. [LERMA, Observatoire de Paris, 61 Av. de l' Observatoire, F-75014 Paris (France); Teyssier, D. [European Space Astronomy Centre, Urb. Villafranca del Castillo, P.O. Box 50727, E-28080 Madrid (Spain)

    2014-08-01

    Phosphine (PH{sub 3}) was tentatively identified a few years ago in the carbon star envelopes IRC +10216 and CRL 2688 from observations of an emission line at 266.9 GHz attributable to the J = 1-0 rotational transition. We report the detection of the J = 2-1 rotational transition of PH{sub 3} in IRC +10216 using the HIFI instrument on board Herschel, which definitively confirms the identification of PH{sub 3}. Radiative transfer calculations indicate that infrared pumping in excited vibrational states plays an important role in the excitation of PH{sub 3} in the envelope of IRC +10216, and that the observed lines are consistent with phosphine being formed anywhere between the star and 100 R {sub *} from the star, with an abundance of 10{sup –8} relative to H{sub 2}. The detection of PH{sub 3} challenges chemical models, none of which offer a satisfactory formation scenario. Although PH{sub 3} holds just 2% of the total available phosphorus in IRC +10216, it is, together with HCP, one of the major gas phase carriers of phosphorus in the inner circumstellar layers, suggesting that it could also be an important phosphorus species in other astronomical environments. This is the first unambiguous detection of PH{sub 3} outside the solar system, and is a further step toward a better understanding of the chemistry of phosphorus in space.

  11. Confirmation of circumstellar phosphine

    CERN Document Server

    Agundez, M; Decin, L; Encrenaz, P; Teyssier, D

    2014-01-01

    Phosphine (PH3) was tentatively identified a few years ago in the carbon star envelopes IRC+10216 and CRL2688 from observations of an emission line at 266.9 GHz attributable to the J=1-0 rotational transition. We report the detection of the J=2-1 rotational transition of PH3 in IRC+10216 using the HIFI instrument on board Herschel, which definitively confirms the identification of PH3. Radiative transfer calculations indicate that infrared pumping to excited vibrational states plays an important role in the excitation of PH3 in the envelope of IRC+10216, and that the observed lines are consistent with phosphine being formed anywhere between the star and 100 R* from the star, with an abundance of 1e-8 relative to H2. The detection of PH3 challenges chemical models, none of which offers a satisfactory formation scenario. Although PH3 locks just 2 % of the total available phosphorus in IRC+10216, it is together with HCP, one of the major gas phase carriers of phosphorus in the inner circumstellar layers, suggest...

  12. Identification of two proteins that interact with the Erp virulence factor from Mycobacterium tuberculosis by using the bacterial two-hybrid system

    Directory of Open Access Journals (Sweden)

    Cataldi Angel A

    2009-01-01

    Full Text Available Abstract Background The exported repetitive protein (erp gene encodes a secreted 36-kDa protein with a central domain containing several proline-glycine-leucine-threonine-serine (PGLTS repeats. It has been demonstrated that erp is a virulence-associated factor since the disruption of this gene impairs the growth of Mycobacterium bovis and Mycobacterium tuberculosis in mice. Results In order to elucidate the function of Erp we searched for Erp-binding proteins from M. tuberculosis by using a bacterial two-hybrid system. Our results indicate that Erp interacts specifically with two putative membrane proteins, Rv1417 and Rv2617c. Further analysis revealed that the latter two interact with each other, indicating that Rv1417, Rv2617c and Erp are connected through multiple interactions. While Rv1417 is disseminated in several Actinomycetales genera, orthologues of Rv2617c are exclusively present in members of the M. tuberculosis complex (MTC. The central and amino-terminal regions of Erp were determined to be involved in the interaction with Rv1417 and Rv2627c. Erp forms from Mycobacterium smegmatis and Mycobacterium leprae were not able to interact with Rv2617c in two-hybrid assays. Immunolocalization experiments showed that Rv1417 and Rv2617c are found on the cell membrane and Erp on the bacterial cell wall. Finally, comparative genomics and expression studies revealed a possible role of Rv1417 in riboflavin metabolism. Conclusion We identified interactive partners of Erp, an M. tuberculosis protein involved in virulence, which will be the focus of future investigation to decipher the function of the Erp family protein.

  13. 酵母双杂交筛选与单剪接型2.2 kb乙型肝炎病毒剪接特异性新蛋白相互作用的肝细胞蛋白%Yeast two-hybrid system screening liver cell proteins interacting with the novel protein encoded by the 2.2 kb singly spliced variant of hepatitis B virus genome

    Institute of Scientific and Technical Information of China (English)

    陈婉南; 陈金烟; 黄清玲; 林建银; 林旭

    2010-01-01

    目的 筛选与单剪接型2.2 kb乙型肝炎病毒(HBV)剪接特异性新蛋白相互作用的肝细胞蛋白.方法 PCR扩增单剪接型2.2 kb HBV剪接特异性新基因TPss并克隆于诱饵载体pGBKT7,在证实TPss蛋白不具有自激活作用的前提下,以酵母双杂交系统筛查与TPss蛋白相互作用的肝细胞蛋白,进而通过哺乳动物细胞双杂交实验验证候选肝细胞蛋白与TPss蛋白在Huh7和HepG2肝细胞中的相互作用.结果 构建酵母双杂交诱饵载体pGBKT7-TPss,Western blot显示其在酵母中表达TPss蛋白.酵母双杂交筛选及哺乳动物细胞双杂交证实TPss蛋白可与4种肝细胞蛋白相互作用,即组织蛋白酶B、微粒体环氧化物水解酶、组织蛋白酶D与纤维蛋白原γ链.结论 TPss可与多种肝细胞蛋白相互作用.%Objective To screen the liver cell proteins interacting with the novel protein encoded by the 2.2 kb singly spliced variant of hepatitis B virus genome. Methods The splicing-specific gene TPss generated by the 2.2 kb singly spliced variant of HBV genome was amplified by PCR and cloned into the bait vector pGBKT7. After exclusion of self-activatian capacities of TPss protein, a two-hybrid library screening was performed using a pre-transformed human liver cDNA library to screen the liver cell proteins interacting with TPss. Mammalian two-hybrid assay was also done to further confirm the interactions between the bait and prey proteins in Huh7 and HepG2 hepatacytes. Results TPss gene with the size of 336 bp was successfully amplified and cloned, and the TPss protein expressed well in AHI09 yeast cells. Four liver cell proteins interacting with TPss, i. e. , cathepsin B, epoxide hydrolase 1, cathepsin D and fibrinogen gamma chain, were screened by yeast two-hybrid assay and further confirmed by mammalian two-hybrid assay. Conclusion TPss could interact with liver cell proteins.

  14. Degradation of Acid Orange 7 Dye in Two Hybrid Plasma Discharge Reactors

    Institute of Scientific and Technical Information of China (English)

    SHEN Yongjun; LEI Lecheng; ZHANG Xingwang; DING Jiandong

    2014-01-01

    To get an optimized pulsed electrical plasma discharge reactor and to increase the energy utilization efficiency in the removal of pollutants,two hybrid plasma discharge reactors were designed and optimized.The reactors were compared via the discharge characteristics,energy transfer efficiency,the yields of the active species and the energy utilization in dye wastewater degradation.The results showed that under the same AC input power,the characteristics of the discharge waveform of the point-to-plate reactor were better.Under the same AC input power,the two reactors both had almost the same peak voltage of 22 kV.The peak current of the point-to-plate reactor was 146 A,while that of the wire-to-cylinder reactor was only 48.8 A.The peak powers of the point-to-plate reactor and the wire-to-cylinder reactor were 1.38 MW and 1.01 MW,respectively.The energy per pulse of the point-to-plate reactor was 0.2221 J,which was about 29.4% higher than that of the wire-to-cylinder reactor (0.1716 J).To remove 50% Acid Orange 7 (AO7),the energy utilizations of the point-to-plate reactor and the wireto-cylinder reactor were 1.02×10-9 mol/L and 0.61×10-9 mol/L,respectively.In the point-to-plate reactor,the concentration of hydrogen peroxide in pure water was 3.6 mmol/L after 40 min of discharge,which was higher than that of the wire-to-cylinder reactor (2.5 mmol/L).The concentration of liquid phase ozone in the point-to-plate reactor (5.7×10-2 mmol/L) was about 26.7% higher than that in the wire-to-cylinder reactor (4.5× 10-2 mmol/L).The analysis results of the variance showed that the type of reactor and reaction time had significant impacts on the yields of the hydrogen peroxide and ozone.The main degradation intermediates of AO7 identified by gas chromatography and mass spectrometry (GCMS) were acetic acid,maleic anhydride,pbenzoquinone,phenol,benzoic acid,phthalic anhydride,coumarin and 2-naphthol.Proposed degradation pathways were elucidated in light of the analyzed

  15. Yeast Protein–Protein Interaction Assays and Screens

    NARCIS (Netherlands)

    Folter, de S.; Immink, G.H.

    2011-01-01

    Most transcription factors fulfill their role in protein complexes. As a consequence, information about their interaction capacity sheds light on a protein’s function and the molecular mechanism underlying this activity. The yeast two-hybrid GAL4 (Y2H) assay is a powerful method to unravel and ident

  16. Screening of proteins that interact with human thrombopoietin receptor c-Mpl using yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    赵新燕[1; 冯丽冰[2; 周伟国[3; 戴卫列[4; 李昌本[5; 赵寿元[6

    2000-01-01

    Thrombopoietin (TPO) is the major cytokine involved in platelet production and exerts its effects via the receptor c-Mpl. The yeast two-hybrid system has been used to screen the proteins interacting with c-Mpl. First, the cDNA fragment of c-Mpl intracellular domain was cloned into two-hybrid vector pAS2, and the resulting plasmid is designated as pASMM. Then a human placenta cDNA library was screened using the pASMM as a target plasmid. Seven positive clones were isolated from 150 000 independent transformants. Sequence analysis of one of the positive clones demonstrates that a part of coding sequence of vimentin from 611 bp to 3’ end and flanking non-translation region was obtained. Therefore, there is an interaction between vimentin and TPO receptor. The results suggest that cytoskeletal protein may play an important role in TPO signal transduction pathway.

  17. Screening of proteins that interact with human thrombopoietin receptor c-Mpl using yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Thrombopoietin(TPO) is the major cytokine involved in platelet production and exerts its effects via the receptor c-Mpl.The yeast two-hybrid system has been used to screen the proteins interacting with c-Mpl.First,the cDNA fragment of c-Mpl intracellular domain was cloned into two-hybrid vector pAS2,and the resulting plasmid is designated as pASMM.Then a human placenta cDNA library was screened using the pASMM as a target plasmid.Seven positive clones were isolated from 150 000 independent transformants.Sequence analysis of one of the positive clones demonstrates that a part of coding sequence of vimentin from 611 bp to 3'end and flanking non-translation region was obtained.Therefore,there is an interaction between vimentin and TPO receptor.The results suggest that cytoskeletal protein may play an important role in TPO signal transduction pathway.

  18. Identification of the specificity of isolated phage display single-chain antibodies using yeast two-hybrid screens

    DEFF Research Database (Denmark)

    Rasmussen, Nicolaj; Ditzel, Henrik

    2009-01-01

    A method is described for the identification of the antigen recognised by an scFv isolated from an antibody phage display library using selection against a complex mixture of proteins (e.g. intact cells, purified cell surface membranes, and tissue sections). The method takes advantage of a yeast ...... two-hybrid system that additionally allows for reorganization of post-translational modifications to the bait and target proteins. This technique is therefore especially useful for identifying surface-expressed antigens....

  19. A yeast two-hybrid screen for SYP-3 interactors identifies SYP-4, a component required for synaptonemal complex assembly and chiasma formation in Caenorhabditis elegans meiosis.

    Directory of Open Access Journals (Sweden)

    Sarit Smolikov

    2009-10-01

    Full Text Available The proper assembly of the synaptonemal complex (SC between homologs is critical to ensure accurate meiotic chromosome segregation. The SC is a meiotic tripartite structure present from yeast to humans, comprised of proteins assembled along the axes of the chromosomes and central region (CR proteins that bridge the two chromosome axes. Here we identify SYP-4 as a novel structural component of the SC in Caenorhabditis elegans. SYP-4 interacts in a yeast two-hybrid assay with SYP-3, one of components of the CR of the SC, and is localized at the interface between homologs during meiosis. SYP-4 is essential for the localization of SYP-1, SYP-2, and SYP-3 CR proteins onto chromosomes, thereby playing a crucial role in the stabilization of pairing interactions between homologous chromosomes. In the absence of SYP-4, the levels of recombination intermediates, as indicated by RAD-51 foci, are elevated in mid-prophase nuclei, and crossover recombination events are significantly reduced. The lack of chiasmata observed in syp-4 mutants supports the elevated levels of chromosome nondisjunction manifested in high embryonic lethality. Altogether our findings place SYP-4 as a central player in SC formation and broaden our understanding of the structure of the SC and its assembly.

  20. Generation of intracellular single-chain antibodies directed against polypeptide GalNAc-transferase using a yeast two-hybrid system.

    Science.gov (United States)

    Ma, Li; Koyota, Souichi; Myoen, Yu; Yamashita, Tetsuro; Yatabe, Naoki; Koizumi, Yukio; Aosasa, Masayoshi; Nishimichi, Norihisa; Matsuda, Haruo; Sugiyama, Toshihiro

    2012-02-24

    Mucin-type O-glycosylation is initiated by a large number of UDP-GalNAc: polypeptide N-acetylgalactosaminyltransferases (GalNAc-T). Although extensive in vitro studies using synthetic peptides as substrates suggest that most GalNAc-Ts exhibit overlapping substrate specificities, many studies have shown that individual GalNAc-Ts play an important role in both animals and humans. Further investigations of the functions of individual GalNAc-Ts including in vivo substrate proteins and O-glycosylation sites are necessary. In this study, we attempted to generate single-chain variable fragment (scFv) antibodies to bind to GalNAc-T1, T2, T3, and T4 using a yeast two-hybrid system for screening a naive chicken scFv library. Several different scFvs were isolated against a single target GalNAc-T isoform specifically under expressed in yeast and were confirmed to be expressed in mammalian cells and to retain binding activity inside the cells. Generation of these specific antibodies provides an opportunity to modify and exploit antibodies for specific applications in investigations of GalNAc-T functions.

  1. Detección de Cryptosporidium spp. en terneras de lecherías de la Región Metropolitana mediante Ziehl Neelsen y confirmada por inmunocromatografía y ensayo molecular Detection of Cryptosporidium spp. in calves by using a acid fast method and confirmed by immunochromatographic and molecular assays

    Directory of Open Access Journals (Sweden)

    P Muñoz

    2011-01-01

    , Cryptosporidium can cause great economic losses in systems that involve the raising of cattle by producing various degrees of diarrhea, particularly in calves that are less than 30 days of age. The main objective of this study was the detection of Cryptosporidium spp. oocysts in faecal samples of diarrheic calves of less than one month of age from two milk farms in the Metropolitan Region of Chile. For the first time in the country, an immunochromatographic and a molecular assay were used to confirm the microscopical observation of Cryptosporidium spp. oocysts in the bovine samples studied. A total of 205 fecal samples were stained with acid-fast method (Ziehl Neelsen, ZN and 102 (49.8% were found to have parasite oocysts. From these ZN positive samples, 58 were randomly selected and were all confirmed positive by the immunochromatographic test (IC. Conversely, 10 ZN negative samples were all negative by using IC test. A genus-specific molecular assay (18S ribosomal RNA PCR was designed and carried out in the study of the 58 ZN/IC positive and the 10 ZN/IC negative faecal samples for the detection of Cryptosporidium spp. 37 (64% samples were confirmed positive by this genus-specific PCR assay while all the 10 ZN/IC negative samples yielded no amplification. Detection limit of the genus-specific PCR was compared with the ZN staining method. Fewer parasites were detected by PCR (10(4 oocysts/mL when compared to ZN (2 x 10(4 oocysts/mL. The results showed that cryptosporidiosis continues to be a parasitic infection of high frequency in dairy farm cattle in the Metropolitan Region. The ZN stain method is extremely operator dependent, but this disadvantage can be reduced by combining ZN with the IC test. Further studies are needed to improve the yield of the genus-specific PCR method as a diagnostic tool for bovine Cryptosporidium. Molecular tests also contribute to define the veterinary epidemiology of this parasitic infection in a specific geographical area.

  2. Effects of in vitro ozone treatment on proteolysis of purified rubisco from two hybrid poplar clones. [Populus maximowizii x trichocarpa

    Energy Technology Data Exchange (ETDEWEB)

    Landry, L.G.; Pell, E.J. (Pennsylvania State Univ., University Park (USA))

    1989-04-01

    Plants exposed to ozone (O{sub 3}) exhibited symptoms of premature senescence, including early decline in quantity of rubisco. O{sub 3}-induced oxidation may cause changes in protein conformation of rubisco, resulting in enhanced proteolysis. To test this hypothesis, rubisco was purified from two hybrid clones of Populus maximowizii x trichocarpa, clones 388 and 245, and treated in vitro with O{sub 3} or air. Rubisco was then challenged with bromelain, papain, chymotrypsin, carboxypeptidase A, or endoproteinase Glu-C and percent degradation measured by SDS-PAGE and densitometric scanning of the gels. Degree of rubisco sensitivity to oxidation may be related to available sulfhydryl (SH) groups on the protein. The number of SH groups in native and denatured rubisco was measured for purified rubisco of both clones by DTNB titration method. The relationship between sensitivity to proteolysis and number and availability of SH groups is discussed.

  3. Exploring Protein Interactions on a Minimal Type II Polyketide Synthase Using a Yeast Two-Hybrid System

    Directory of Open Access Journals (Sweden)

    Gaetano Castaldo

    2005-01-01

    Full Text Available Interactions between proteins that form the ’minimal’ type II polyketide synthase in the doxorubicin producing biosynthetic pathway from Streptomyces peucetius were investigated using a yeast two-hybrid system (Y2H. Proteins that function as the so called ’chain length factor’ (DpsB and putative transacylase (DpsD were found to interact with the ketosynthase subunit (DpsA, which can also interact with itself. On the basis of these results we propose a head-to-tail homodimeric structure, which is consistent with previously published in vivo mutagenesis studies. No interactions were found between the acyl-carrier protein (DpsG and any of the other constituents of the complex, however, transient interactions, not detectable using the Y2H system, cannot be discounted and warrant further investigation.

  4. Enzyme assays.

    Science.gov (United States)

    Reymond, Jean-Louis; Fluxà, Viviana S; Maillard, Noélie

    2009-01-07

    Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.

  5. Opinion Dynamics with Confirmation Bias

    CERN Document Server

    Allahverdyan, A E

    2014-01-01

    Background: Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. Methodology/Principal Findings: We formulate a (non-Bayesian) model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect|when consecutively exposed to two opinions, the preferenc...

  6. Performance Confirmation Data Aquisition System

    Energy Technology Data Exchange (ETDEWEB)

    D.W. Markman

    2000-10-27

    The purpose of this analysis is to identify and analyze concepts for the acquisition of data in support of the Performance Confirmation (PC) program at the potential subsurface nuclear waste repository at Yucca Mountain. The scope and primary objectives of this analysis are to: (1) Review the criteria for design as presented in the Performance Confirmation Data Acquisition/Monitoring System Description Document, by way of the Input Transmittal, Performance Confirmation Input Criteria (CRWMS M&O 1999c). (2) Identify and describe existing and potential new trends in data acquisition system software and hardware that would support the PC plan. The data acquisition software and hardware will support the field instruments and equipment that will be installed for the observation and perimeter drift borehole monitoring, and in-situ monitoring within the emplacement drifts. The exhaust air monitoring requirements will be supported by a data communication network interface with the ventilation monitoring system database. (3) Identify the concepts and features that a data acquisition system should have in order to support the PC process and its activities. (4) Based on PC monitoring needs and available technologies, further develop concepts of a potential data acquisition system network in support of the PC program and the Site Recommendation and License Application.

  7. Opinion dynamics with confirmation bias.

    Science.gov (United States)

    Allahverdyan, Armen E; Galstyan, Aram

    2014-01-01

    Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. We formulate a (non-Bayesian) model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect-when consecutively exposed to two opinions, the preference is given to the last opinion (recency) or the first opinion (primacy) -and relates recency to confirmation bias. Finally, we study the model in the case of repeated persuasion and analyze its convergence properties. The standard Bayesian approach to probabilistic opinion revision is inadequate for describing the observed phenomenology of persuasion process. The simple non-Bayesian model proposed here does agree with this phenomenology and is capable of reproducing a spectrum of effects observed in psychology: primacy-recency phenomenon, boomerang effect and cognitive dissonance. We point out several limitations of the model that should motivate its future development.

  8. Opinion dynamics with confirmation bias.

    Directory of Open Access Journals (Sweden)

    Armen E Allahverdyan

    Full Text Available Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science.We formulate a (non-Bayesian model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect-when consecutively exposed to two opinions, the preference is given to the last opinion (recency or the first opinion (primacy -and relates recency to confirmation bias. Finally, we study the model in the case of repeated persuasion and analyze its convergence properties.The standard Bayesian approach to probabilistic opinion revision is inadequate for describing the observed phenomenology of persuasion process. The simple non-Bayesian model proposed here does agree with this phenomenology and is capable of reproducing a spectrum of effects observed in psychology: primacy-recency phenomenon, boomerang effect and cognitive dissonance. We point out several limitations of the model that should motivate its future development.

  9. Opinion Dynamics with Confirmation Bias

    Science.gov (United States)

    Allahverdyan, Armen E.; Galstyan, Aram

    2014-01-01

    Background Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. Methodology/Principal Findings We formulate a (non-Bayesian) model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect–when consecutively exposed to two opinions, the preference is given to the last opinion (recency) or the first opinion (primacy) –and relates recency to confirmation bias. Finally, we study the model in the case of repeated persuasion and analyze its convergence properties. Conclusions The standard Bayesian approach to probabilistic opinion revision is inadequate for describing the observed phenomenology of persuasion process. The simple non-Bayesian model proposed here does agree with this phenomenology and is capable of reproducing a spectrum of effects observed in psychology: primacy-recency phenomenon, boomerang effect and cognitive dissonance. We point out several limitations of the model that should motivate its future development. PMID:25007078

  10. Model confirmation in climate economics.

    Science.gov (United States)

    Millner, Antony; McDermott, Thomas K J

    2016-08-01

    Benefit-cost integrated assessment models (BC-IAMs) inform climate policy debates by quantifying the trade-offs between alternative greenhouse gas abatement options. They achieve this by coupling simplified models of the climate system to models of the global economy and the costs and benefits of climate policy. Although these models have provided valuable qualitative insights into the sensitivity of policy trade-offs to different ethical and empirical assumptions, they are increasingly being used to inform the selection of policies in the real world. To the extent that BC-IAMs are used as inputs to policy selection, our confidence in their quantitative outputs must depend on the empirical validity of their modeling assumptions. We have a degree of confidence in climate models both because they have been tested on historical data in hindcasting experiments and because the physical principles they are based on have been empirically confirmed in closely related applications. By contrast, the economic components of BC-IAMs often rely on untestable scenarios, or on structural models that are comparatively untested on relevant time scales. Where possible, an approach to model confirmation similar to that used in climate science could help to build confidence in the economic components of BC-IAMs, or focus attention on which components might need refinement for policy applications. We illustrate the potential benefits of model confirmation exercises by performing a long-run hindcasting experiment with one of the leading BC-IAMs. We show that its model of long-run economic growth-one of its most important economic components-had questionable predictive power over the 20th century.

  11. Confirmation of shutdown cooling effects

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Kotaro, E-mail: ksato@nelted.co.jp; Tabuchi, Masato; Sugimura, Naoki; Tatsumi, Masahiro [Nuclear Engineering, Limited, 1-3-7 Tosabori Nishi-ku, Osaka-shi, Osaka 550-0001 (Japan)

    2015-12-31

    After the Fukushima accidents, all nuclear power plants in Japan have gradually stopped their operations and have long periods of shutdown. During those periods, reactivity of fuels continues to change significantly especially for high-burnup UO{sub 2} fuels and MOX fuels due to radioactive decays. It is necessary to consider these isotopic changes precisely, to predict neutronics characteristics accurately. In this paper, shutdown cooling (SDC) effects of UO{sub 2} and MOX fuels that have unusual operation histories are confirmed by the advanced lattice code, AEGIS. The calculation results show that the effects need to be considered even after nuclear power plants come back to normal operation.

  12. Screening for proteins interacting with MCM7 in human lung cancer library using yeast two hybrid system

    Directory of Open Access Journals (Sweden)

    Yuchen HAN

    2008-08-01

    Full Text Available Background and objective MCM7 is a subunit of the MCM complex that plays a key role in DNA replication initiation. But little is known about its interaction proteins. In this study yeast two hybrid screening was used to identify the MCM7 interacting proteins. Methods Yeast expression vector containing human full length MCM7-pGBKT7 plasmid was constructed, and with a library of cDNAs from human lung cancer-pACT2 plasmid was transformed into yeast strain AH109, and was electively grew in X-a-gal auxotrophy medium SD/-Trp-Leu-His-Ade, and the blue colonies were picked up, the plasmid of the yeast colonies was extracted , and transformed into E. Coli to extract DNA and performed sequence analysis. Results Eleven proteins were identified which could specifically interact with MCM7 proteins, among these five were cytoskeleton proteins, six were enzymes, kinases and related receptors. Conclusion The investigation provides functional clues for further exploration of MCM7 gene.

  13. Screening of hepatocyte proteins binding to NS5ABP37 protein by yeast-two hybrid system

    Institute of Scientific and Technical Information of China (English)

    Lei Zhang; Qing-yong Ma; Xian-kui Meng; Kang Li; Jun Cheng

    2009-01-01

    Objective To investigate the biological function of NS5ABP37 and to look for proteins interacting with NS5ABP37 protein in hepatocytes. Methods We constructed bait plasmid expressing NS5ABP37 protein of hepatitis C virus (HCV) by cloning the gene of NS5ABP37 protein into pGBKT7, then the recombinant plasmid DNA was transformed into yeast AH109 (α type). The transformed yeast AH109 was mated with yeast Y187 (α type) containing liver cDNA library plasmid in 2×YPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) containing X-α-gal for selection and screening. After extracting and sequencing of plasmids from positive (blue) colonies, we made a sequence analysis by bioinformatics. Results We screened twenty-five proteins binding to NS5ABP37, including Homo sapiens cyclin Ⅰ (CCNI) gene, Homo sapiens matrix metallopeptidase 25 (MMP25) and Homo sapiens talin 1. Conclusion The yeast-two hybrid system is an effective method for identifying hepatocyte proteins interacting with NS5ABP37 of HCV. And the biological function of NS5ABP37 may be associated with glycometabolism, lipid metabolism and apoptosis.

  14. The GacS-GacA two-component regulatory system of Pseudomonas fluorescens: a bacterial two-hybrid analysis.

    Science.gov (United States)

    Workentine, Matthew L; Chang, Limei; Ceri, Howard; Turner, Raymond J

    2009-03-01

    The two-component regulatory system comprised of the sensor kinase, GacS, and its response regulator, GacA, is involved in regulation of secondary metabolism and many other aspects of bacterial physiology. Although it is known that the sensor kinases RetS and LadS feed into the GacS/GacA system, the mechanism through which this occurs is unknown, as are the protein-protein interactions in this system. To characterize and define these interactions, we utilized a bacterial two-hybrid system to study the interactions of GacS and GacA from Pseudomonas fluorescens CHA0. Domains of GacA and GacS, identified through bioinformatics, were subcloned and their ability to interact in vivo was investigated. We found that the entire GacA molecule is required for GacA to interact with itself or GacS. Furthermore, the HisKA/HATPase/REC domains of GacS together are responsible for GacS interacting with GacA, while the HAMP domain of GacS is responsible for GacS interacting with itself. In addition, homologs of Pseudomonas aeruginosa hybrid sensor kinases, RetS and LadS, were identified in P. fluorescens, and shown to interact with GacS, but not GacA.

  15. Modeling confirmation bias and polarization

    CERN Document Server

    Del Vicario, Michela; Caldarelli, Guido; Stanley, H Eugene; Quattrociocchi, Walter

    2016-01-01

    Online users tend to select claims that adhere to their system of beliefs and to ignore dissenting information. Confirmation bias, indeed, plays a pivotal role in viral phenomena. Furthermore, the wide availability of content on the web fosters the aggregation of likeminded people where debates tend to enforce group polarization. Such a configuration might alter the public debate and thus the formation of the public opinion. In this paper we provide a mathematical model to study online social debates and the related polarization dynamics. We assume the basic updating rule of the Bounded Confidence Model (BCM) and we develop two variations a) the Rewire with Bounded Confidence Model (RBCM), in which discordant links are broken until convergence is reached; and b) the Unbounded Confidence Model, under which the interaction among discordant pairs of users is allowed even with a negative feedback, either with the rewiring step (RUCM) or without it (UCM). From numerical simulations we find that the new models (UCM...

  16. Analysis of the protein-protein interactions between the human acidic ribosomal P-proteins: evaluation by the two hybrid system

    DEFF Research Database (Denmark)

    Tchórzewski, M; Boldyreff, B; Issinger, O

    2000-01-01

    on the function of these proteins, we are the first to have precisely analyzed mutual interactions among human P-proteins, employing the two hybrid system. The human acidic ribosomal P-proteins, (P1 or P2,) were fused to the GAL4 binding domain (BD) as well as the activation domain (AD), and analyzed in yeast...

  17. 利用酵母双杂交系统筛选与人巨细胞病毒皮层蛋白pUL23相互作用的病毒编码蛋白%Screening of Human Cytomegalovirus Tegument Protein pUL23 Interacting Partner via Yeast Two-hybrid System

    Institute of Scientific and Technical Information of China (English)

    肖静; 李弘剑; 胡嘉淼; 肖小平; 员月明; 刘明亮; 曾宝娟; 李婧惠; 周天鸿; 冉艳红

    2011-01-01

    人巨细胞病毒(HCMV)UL23基因编码病毒皮层蛋白,该基因缺失时,病毒在人包皮成纤维细胞(HEF)中的繁殖速度加快.为进一步阐述HCMV UL23基因编码产物pUL23的功能及调控机制,采用鸟枪法构建了融合于GAL4活性区域的HCMV Towne株基因组随机表达文库.利用酵母双杂交技术,以pGBKT7-UL23为诱饵质粒,从构建的HCMV基因组表达文库中筛选到与pUL23相互作用的病毒编码蛋白pUL24.GST-pull down实验和免疫共沉淀实验进一步确认两种病毒蛋白之间的相互作用.结果表明,构建的HCMV基因组表达文库能够用于GAL40酵母双杂交系统筛选与诱饵蛋白相互作用的病毒自身编码蛋白.病毒蛋白pUL23和pUL24之间具有相互作用,这为进一步阐述pUL23在HCMV感染过程中的功能提供依据.该研究为揭示HCMV病毒感染机制奠定了基础.%Human cytomegalovirus(HCMV) UL23 gene codes a tegument protein pUL23, and the UL23 deletion HCMV mutant exhibited enhanced growth in HFF cells. In order to provide an effective tool for further study of the function and regulatory mechanism of HCMV pUL23, a random genomic library of HCMV strains Towne fused to the GAL4 activation domain was constructed by shot-gun method. Using this library, we performed yeast two-hybrid screening with a bait plasmid encoding a fusion of the GAL4 DNA binding domain (GAL4-BD) with the UL23 open reading frame. One of the interacting clones corresponds to HCMV protein pUL24. GST-pull down and co-immunoprecipitation assays confirmed the interaction between these two vial proteins. These results demonstrated that the viral genomic library could be applied to GAL4 yeast two-hybrid assay for screening HCMV proteins which interact with the bait protein. And the interaction between HCMV proteins pUL23 and pUL24 will be further characterized to elucidate the functions of pUL23 during HCMV infection. It was laid a foundation for further study of the infection mechanism of

  18. Modeling confirmation bias and polarization

    Science.gov (United States)

    Del Vicario, Michela; Scala, Antonio; Caldarelli, Guido; Stanley, H. Eugene; Quattrociocchi, Walter

    2017-01-01

    Online users tend to select claims that adhere to their system of beliefs and to ignore dissenting information. Confirmation bias, indeed, plays a pivotal role in viral phenomena. Furthermore, the wide availability of content on the web fosters the aggregation of likeminded people where debates tend to enforce group polarization. Such a configuration might alter the public debate and thus the formation of the public opinion. In this paper we provide a mathematical model to study online social debates and the related polarization dynamics. We assume the basic updating rule of the Bounded Confidence Model (BCM) and we develop two variations a) the Rewire with Bounded Confidence Model (RBCM), in which discordant links are broken until convergence is reached; and b) the Unbounded Confidence Model, under which the interaction among discordant pairs of users is allowed even with a negative feedback, either with the rewiring step (RUCM) or without it (UCM). From numerical simulations we find that the new models (UCM and RUCM), unlike the BCM, are able to explain the coexistence of two stable final opinions, often observed in reality. Lastly, we present a mean field approximation of the newly introduced models. PMID:28074874

  19. Modeling confirmation bias and polarization

    Science.gov (United States)

    Del Vicario, Michela; Scala, Antonio; Caldarelli, Guido; Stanley, H. Eugene; Quattrociocchi, Walter

    2017-01-01

    Online users tend to select claims that adhere to their system of beliefs and to ignore dissenting information. Confirmation bias, indeed, plays a pivotal role in viral phenomena. Furthermore, the wide availability of content on the web fosters the aggregation of likeminded people where debates tend to enforce group polarization. Such a configuration might alter the public debate and thus the formation of the public opinion. In this paper we provide a mathematical model to study online social debates and the related polarization dynamics. We assume the basic updating rule of the Bounded Confidence Model (BCM) and we develop two variations a) the Rewire with Bounded Confidence Model (RBCM), in which discordant links are broken until convergence is reached; and b) the Unbounded Confidence Model, under which the interaction among discordant pairs of users is allowed even with a negative feedback, either with the rewiring step (RUCM) or without it (UCM). From numerical simulations we find that the new models (UCM and RUCM), unlike the BCM, are able to explain the coexistence of two stable final opinions, often observed in reality. Lastly, we present a mean field approximation of the newly introduced models.

  20. Performance confirmation data acquisition system

    Energy Technology Data Exchange (ETDEWEB)

    McAffee, D.A.; Raczka, N.T. [Yucca Mountain Project, Las Vegas, NV (United States)

    1997-12-31

    As part of the Viability Assessment (VA) work, this QAP-3-9 document presents and evaluates a comprehensive set of viable concepts for collecting Performance Confirmation (PC) related data. The concepts include: monitoring subsurface repository air temperatures, humidity levels and gaseous emissions via the subsurface ventilation systems, and monitoring the repository geo-technical parameters and rock mass from bore-holes located along the perimeter main drifts and throughout a series of human-rated Observation Drifts to be located in a plane 25 meters above the plane of the emplacement drifts. A key element of this document is the development and analysis of a purposed multi-purpose Remote Inspection Gantry that would provide direct, real-time visual, thermal, and radiological monitoring of conditions inside operational emplacement drifts and close-up observations of in-situ Waste Packages. Preliminary finite-element analyses are presented that indicate the technological feasibility of operating an inspection gantry inside the operational emplacement drifts for short inspection missions lasting 2--3 hours. Overall reliability, availability, and maintainability of the PC data collection concepts are discussed. Preliminary concepts for PC data collection network are also provided.

  1. Identification of interacting proteins with aryl hydrocarbon receptor in scallop Chlamys farreri by yeast two hybrid screening.

    Science.gov (United States)

    Cai, Yuefeng; Pan, Luqing; Miao, Jingjing; Liu, Tong

    2016-11-01

    The aryl hydrocarbon receptor (AhR) belongs to the basic-helix-loop helix (bHLH) Per-Arnt-Sim (PAS) family of transcription factors. AhR has been known primarily for its role in the regulation of several drug and xenobiotic metabolizing enzymes, as well as the mediation of the toxicity of certain xenobiotics, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Although the AhR is well-studied as a mediator of the toxicity of certain xenobiotics in marine bivalves, the normal physiological function remains unknown. In order to explore the function of the AhR, the bait protein expression plasmid pGBKT7-CfAhR and the cDNA library of gill from Chlamys farreri were constructed. By yeast two hybrid system, after multiple screening with the high screening rate medium, rotary verification, sequencing and bioinformatics analysis, the interactions of the CfAhR with receptor for activated protein kinase C 1 (RACK1), thyroid peroxidase-like protein (TPO), Toll-like receptor 4(TLR 4), androglobin-like, store-operated Ca(2+) entry (SocE), ADP/ATP carrier protein, cytochrome b, thioesterase, actin, ferritin subunit 1, poly-ubiquitin, short-chain collagen C4-like and one hypothetical protein in gill cells were identified. This study suggests that the CfAhR played fundamental roles in immune system homeostasis, oxidative stress response, and in grow and development of C. farreri. The elucidation of these protein interactions is of much importance both in understanding the normal physiological function of AhR, and as potential targets for further research on protein function in AhR interactions.

  2. Flavivirus NS3 and NS5 proteins interaction network: a high-throughput yeast two-hybrid screen

    Directory of Open Access Journals (Sweden)

    Canard Bruno

    2011-10-01

    Full Text Available Abstract Background The genus Flavivirus encompasses more than 50 distinct species of arthropod-borne viruses, including several major human pathogens, such as West Nile virus, yellow fever virus, Japanese encephalitis virus and the four serotypes of dengue viruses (DENV type 1-4. Each year, flaviviruses cause more than 100 million infections worldwide, some of which lead to life-threatening conditions such as encephalitis or haemorrhagic fever. Among the viral proteins, NS3 and NS5 proteins constitute the major enzymatic components of the viral replication complex and are essential to the flavivirus life cycle. Results We report here the results of a high-throughput yeast two-hybrid screen to identify the interactions between human host proteins and the flavivirus NS3 and NS5 proteins. Using our screen results and literature curation, we performed a global analysis of the NS3 and NS5 cellular targets based on functional annotation with the Gene Ontology features. We finally created the first flavivirus NS3 and NS5 proteins interaction network and analysed the topological features of this network. Our proteome mapping screen identified 108 human proteins interacting with NS3 or NS5 proteins or both. The global analysis of the cellular targets revealed the enrichment of host proteins involved in RNA binding, transcription regulation, vesicular transport or innate immune response regulation. Conclusions We proposed that the selective disruption of these newly identified host/virus interactions could represent a novel and attractive therapeutic strategy in treating flavivirus infections. Our virus-host interaction map provides a basis to unravel fundamental processes about flavivirus subversion of the host replication machinery and/or immune defence strategy.

  3. Spatial variability of soil carbon and nitrogen in two hybrid poplar-hay crop systems in southern Quebec, Canada

    Science.gov (United States)

    Winans, K. S.

    2013-12-01

    Canadian agricultural operations contribute approximately 8% of national GHG emissions each year, mainly from fertilizers, enteric fermentation, and manure management (Environment Canada, 2010). With improved management of cropland and forests, it is possible to mitigate GHG emissions through carbon (C) sequestration while enhancing soil and crop productivity. Tree-based intercropped (TBI) systems, consisting of a fast-growing woody species such as poplar (Populus spp.) planted in widely-spaced rows with crops cultivated between tree rows, were one of the technologies prioritized for investigation by the Agreement for the Agricultural Greenhouse Gases Program (AAGGP), because fast growing trees can be a sink for atmospheric carbon-dioxide (CO2) as well as a long-term source of farm income (Montagnini and Nair, 2004). However, there are relatively few estimates of the C sequestration in the trees or due to tree inputs (e.g., fine root turnover, litterfall that gets incorporated into SOC), and hybrid poplars grow exponentially in the first 8-10 years after planting. With the current study, our objectives were (1) to evaluate spatial variation in soil C and nitrogen (N) storage, CO2 and nitrogen oxide (N20), and tree and crop productivity for two hybrid poplar-hay intercrop systems at year 9, comparing TBI vs. non-TBI systems, and (2) to evaluate TBI systems in the current context of C trading markets, which value C sequestration in trees, unharvested crop components, and soils of TBI systems. The study results will provide meaningful measures that indicate changes due to TBI systems in the short-term and in the long-term, in terms of GHG mitigation, enhanced soil and crop productivity, as well as the expected economic returns in TBI systems.

  4. Screening of hepatocyte proteins binding to complete S protein of hepatitis B virus by yeast-two hybrid system

    Institute of Scientific and Technical Information of China (English)

    Gui-Qin Bai; Jun Cheng; Shu-Lin Zhang; Yan-Ping Huang; Lin Wang; Yan Liu; Shu-Mei Lin

    2005-01-01

    AIM: To investigate the biological function of complete S protein and to look for proteins interacting with complete S protein in hepatocytes.METHODS: We constructed bait plasmid expressing complete S protein of HBV by cloning the gene of complete S protein into pGBKT7, then the recombinant plasmid DNA was transformed into yeast AH109 (a type). The transformed yeast AH109 was mated with yeast Y187 (α type) containing liver cDNA library plasmid in 2xYPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium (SD/Trp-Leu-His-Ade) containing X-α-gal for selection and screening. After extracting and sequencing of plasmids from positive (blue) colonies, we underwent sequence analysis by bioinformatics.RESULTS: Nineteen colonies were selected and sequenced.Among them, five colonies were Homo sapiens solute carrier family 25, member 23 (SLC25A23), one was Homo sapiens calreticulin, one was human serum albumin (ALB)gene, one was Homo sapiens metallothionein 2A, two were Homo sapiens betaine-homocysteine methyltransferase,three were Homo sapiensNa+ and H+ coupled amino acid transport system N, one was Homo sapiens CD81 antigen (target of anti-proliferative antibody 1) (CD81), three were Homo sapiens diazepam binding inhibitor, two colonies were new genes with unknown function.CONCLUSION: The yeast-two hybrid system is an effective method for identifying hepatocyte proteins interacting with complete S protein of HBV. The complete S protein may bind to different proteins i.e., its multiple functions in vivo.

  5. Separation and confirmation of showers

    Science.gov (United States)

    Neslušan, L.; Hajduková, M.

    2017-01-01

    Aims: Using IAU MDC photographic, IAU MDC CAMS video, SonotaCo video, and EDMOND video databases, we aim to separate all provable annual meteor showers from each of these databases. We intend to reveal the problems inherent in this procedure and answer the question whether the databases are complete and the methods of separation used are reliable. We aim to evaluate the statistical significance of each separated shower. In this respect, we intend to give a list of reliably separated showers rather than a list of the maximum possible number of showers. Methods: To separate the showers, we simultaneously used two methods. The use of two methods enables us to compare their results, and this can indicate the reliability of the methods. To evaluate the statistical significance, we suggest a new method based on the ideas of the break-point method. Results: We give a compilation of the showers from all four databases using both methods. Using the first (second) method, we separated 107 (133) showers, which are in at least one of the databases used. These relatively low numbers are a consequence of discarding any candidate shower with a poor statistical significance. Most of the separated showers were identified as meteor showers from the IAU MDC list of all showers. Many of them were identified as several of the showers in the list. This proves that many showers have been named multiple times with different names. Conclusions: At present, a prevailing share of existing annual showers can be found in the data and confirmed when we use a combination of results from large databases. However, to gain a complete list of showers, we need more-complete meteor databases than the most extensive databases currently are. We also still need a more sophisticated method to separate showers and evaluate their statistical significance. Tables A.1 and A.2 are also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc

  6. 猪瘟病毒酵母双杂交 pGBK T7-NS3诱饵载体的构建与鉴定%Construction and Identification of CSFV pGBKT7-NS3 Bait Vector in Yeast Two-hybrid System

    Institute of Scientific and Technical Information of China (English)

    宋江伟; 田宏; 吴锦艳; 陈妍; 尚佑军; 刘湘涛

    2014-01-01

    The NS3 gene of classical swine fever virus was amplified by RT-PCR and confirmed by sequen-cing and enzyme digestion .The NS3 gene was then subcloned into pGBKT7 to construct the bait vector ac-cording to the reading frame .The reconstructed bait vector pGBKT7-NS3 was transformed into Y2H Gold yeast strain ,its self-activation and toxic effect were tested by the phenotype assay .The expression of pG-BKT7-NS3 was analysed by Western blot .As a result ,the successfully reconstructed bait vector pGBKT7-NS3 would not self-activitate the reporter gene and had no toxic effect to the yeast ,which laid the founda-tion for using yeast two-hybrid assay to screen interaction proteins .%利用 RT-PCR技术扩增获得猪瘟病毒NS3基因片段,将其克隆至酵母双杂交系统诱饵载体pGBKT7中,经酶切,测序验证其正确插入后,将重组诱饵质粒转化酵母菌Y2H Gold ,检测其在酵母中毒性和自我激活作用,并利用Western blot分析诱饵载体在酵母中的转化情况。结果表明,pGBKT7-NS3诱饵载体在Y2H Gold酵母细胞中可以表达,此载体在酵母细胞Y2H Gold中无毒性和自我激活能力,研究结果为使用酵母双杂交技术筛选相互作用蛋白奠定了基础。

  7. Characterization of L1 ORF1p self-interaction and cellular localization using a mammalian two-hybrid system.

    Directory of Open Access Journals (Sweden)

    Mark Sokolowski

    Full Text Available Long INterspersed Element-1 (LINE-1, L1 is an active retrotransposon that mobilizes using a ribonucleoprotein particle (RNP intermediate composed of the full-length bicistronic L1 mRNA and the two proteins (ORF1p and ORF2p encoded by that mRNA. ORF1p and ORF2p demonstrate cis-preference for their encoding mRNA. Previous studies of ORF1p, purified from bacterial and insect cells demonstrated that this protein forms trimers in vitro. While valuable for understanding ORF1p function, these in vitro approaches do not provide any information on ORF1p self-interaction in the context of mammalian cells. We used a mammalian two-hybrid (M2H system in order to study L1 ORF1p self-interaction in human and mouse cells. We demonstrate that the M2H system successfully detects human and mouse ORF1p self-interactions in transiently transfected mammalian cells. We also generated mouse and human ORF1p-specific antibodies to characterize the expression of ORF1p fusion proteins used in the M2H system. Using these antibodies, we demonstrate that ORF1p interaction in trans leads to the formation of heterodimers that are expected to produce a positive signal in the M2H system. Although the role for L1 ORF1p cis-preference in L1 mobilization is established, the impact of ability of ORF1pto interact in trans on the L1 replication cycle is not known. Furthermore, western blot analysis of ORF1p generated by a full-length L1, wild type ORF1, or a codon-optimized ORF1 expression vector is detected in the nucleus. In contrast, the addition of a tag to the N-terminus of the mouse and human ORF1 proteins can significantly alter the subcellular localization in a tag-specific manner. These data support that nuclear localization of ORF1p may contribute to L1 (and potentially the SINE Alu RNP nuclear access in the host cell.

  8. Angiogenesis Assays.

    Science.gov (United States)

    Nambiar, Dhanya K; Kujur, Praveen K; Singh, Rana P

    2016-01-01

    Neoangiogenesis constitutes one of the first steps of tumor progression beyond a critical size of tumor growth, which supplies a dormant mass of cancerous cells with the required nutrient supply and gaseous exchange through blood vessels essentially needed for their sustained and aggressive growth. In order to understand any biological process, it becomes imperative that we use models, which could mimic the actual biological system as closely as possible. Hence, finding the most appropriate model is always a vital part of any experimental design. Angiogenesis research has also been much affected due to lack of simple, reliable, and relevant models which could be easily quantitated. The angiogenesis models have been used extensively for studying the action of various molecules for agonist or antagonistic behaviour and associated mechanisms. Here, we have described two protocols or models which have been popularly utilized for studying angiogenic parameters. Rat aortic ring assay tends to bridge the gap between in vitro and in vivo models. The chorioallantoic membrane (CAM) assay is one of the most utilized in vivo model system for angiogenesis-related studies. The CAM is highly vascularized tissue of the avian embryo and serves as a good model to study the effects of various test compounds on neoangiogenesis.

  9. Method for Confirming Cytoplasmic Delivery of RNA Aptamers

    Science.gov (United States)

    Dickey, David D; Dassie, Justin P; Giangrande, Paloma H

    2016-01-01

    RNA aptamers are single-stranded RNA oligos that represent a powerful emerging technology with potential for treating numerous diseases. More recently, cell-targeted RNA aptamers have been developed for delivering RNA interference (RNAi) modulators (siRNAs and miRNAs) to specific diseased cells (e.g., cancer cells or HIV infected cells) in vitro and in vivo. However, despite initial promising reports, the broad application of this aptamer delivery technology awaits the development of methods that can verify and confirm delivery of aptamers to the cytoplasm of target cells where the RNAi machinery resides. We recently developed a functional assay (RIP assay) to confirm cellular uptake and subsequent cytoplasmic release of an RNA aptamer which binds to a cell surface receptor expressed on prostate cancer cells (PSMA). To assess cytoplasmic delivery, the aptamer was chemically conjugated to saporin, a ribosome inactivating protein toxin that is toxic to cells only when delivered to the cytoplasm (where it inhibits the ribosome) by a cell-targeting ligand (e.g., aptamer). Here, we describe the chemistry used to conjugate the aptamer to saporin and discuss a gel-based method to verify conjugation efficiency. We also detail an in vitro functional assay to confirm that the aptamer retains function following conjugation to saporin and describe a cellular assay to measure aptamer-mediated saporin-induced cytotoxicity. PMID:26472453

  10. Cloning of C-Terminal of Opioid μ-Receptor and Construction of Its Expression Plasmid for Yeast Two Hybrid System

    Institute of Scientific and Technical Information of China (English)

    YANHui; GONGZe-hui

    2004-01-01

    Aim: To obtain the C-terminal DNA and construct the expression plasmid in yeast two-hybrid. Methods: About 177bp DNA fragment was amplified from the complete sequence of ( receptor by PCR. After being sequenced, the C-terminal fragment was ligased into EcoR I-BamH I site of pGBKT7 vector to form recombinants. The recombinant plasmid

  11. The yeast two hybrid system in a screen for proteins interacting with axolotl (Ambystoma mexicanum) Msx1 during early limb regeneration.

    Science.gov (United States)

    Abuqarn, Mehtap; Allmeling, Christina; Amshoff, Inga; Menger, Bjoern; Nasser, Inas; Vogt, Peter M; Reimers, Kerstin

    2011-07-01

    Urodele amphibians are exceptional in their ability to regenerate complex body structures such as limbs. Limb regeneration depends on a process called dedifferentiation. Under an inductive wound epidermis terminally differentiated cells transform to pluripotent progenitor cells that coordinately proliferate and eventually redifferentiate to form the new appendage. Recent studies have developed molecular models integrating a set of genes that might have important functions in the control of regenerative cellular plasticity. Among them is Msx1, which induced dedifferentiation in mammalian myotubes in vitro. Herein, we screened for interaction partners of axolotl Msx1 using a yeast two hybrid system. A two hybrid cDNA library of 5-day-old wound epidermis and underlying tissue containing more than 2×10⁶ cDNAs was constructed and used in the screen. 34 resulting cDNA clones were isolated and sequenced. We then compared sequences of the isolated clones to annotated EST contigs of the Salamander EST database (BLASTn) to identify presumptive orthologs. We subsequently searched all no-hit clone sequences against non redundant NCBI sequence databases using BLASTx. It is the first time, that the yeast two hybrid system was adapted to the axolotl animal model and successfully used in a screen for proteins interacting with Msx1 in the context of amphibian limb regeneration.

  12. Assessment of two hybrid van der Waals density functionals for covalent and non-covalent binding of molecules

    Science.gov (United States)

    Berland, Kristian; Jiao, Yang; Lee, Jung-Hoon; Rangel, Tonatiuh; Neaton, Jeffrey B.; Hyldgaard, Per

    2017-06-01

    Two hybrid van der Waals density functionals (vdW-DFs) are developed using 25% Fock exchange with (i) the consistent-exchange vdW-DF-cx functional [K. Berland and P. Hyldgaard, Phys. Rev. B 89, 035412 (2014)] and (ii) with the vdW-DF2 functional [K. Lee et al., Phys. Rev. B 82, 081101 (2010)]. The ability to describe covalent and non-covalent binding properties of molecules is assessed. For properties related to covalent binding, atomization energies (G2-1 set), molecular reaction energies (G2RC set), and ionization energies (G21IP set) are benchmarked against experimental reference values. We find that hybrid-vdW-DF-cx yields results that are rather similar to those of the standard non-empirical hybrid PBE0 [C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999)], with mean average deviations (MADs) of 4.9 and 5.0 kcal/mol for the G2-1 set, respectively. In this comparison, experimental reference values are used, back corrected by wavefunction-based quantum-chemistry calculations of zero-point energies. Hybrid vdW-DF2 follows somewhat different trends, showing on average significantly larger deviations from the reference energies, with a MAD of 14.5 kcal/mol for the G2-1 set. Non-covalent binding properties of molecules are assessed using the S22 benchmark set of non-covalently bonded dimers and the X40 set of dimers of small halogenated molecules, using wavefunction-based quantum chemistry results as references. For the S22 set, hybrid-vdW-DF-cx performs better than standard vdW-DF-cx for the mostly hydrogen-bonded systems, with MAD dropping from 0.6 to 0.3 kcal/mol, but worse for purely dispersion-bonded systems, with MAD increasing from 0.2 to 0.6 kcal/mol. Hybrid-vdW-DF2 offers a slight improvement over standard vdW-DF2. Similar trends are found for the X40 set, with hybrid-vdW-DF-cx performing particularly well for binding energies involving the strongly polar hydrogen halides, but poorly for systems with tiny binding energies. Our study of the X40 set

  13. Design and selection of a camelid single-chain antibody yeast two-hybrid library produced de novo for the cap protein of porcine circovirus type 2 (PCV2.

    Directory of Open Access Journals (Sweden)

    Xiangjing Fu

    Full Text Available Nanobodies (or variable domain of the heavy chain of the heavy-chain antibodies, VHHs are single-domain antigen-binding fragments derived from camelid heavy chain antibodies. Their comparatively small size, monomeric behavior, high stability, high solubility, and ability to bind epitopes inaccessible to conventional antibodies make them especially suitable for many therapeutic and biotechnological applications. In this paper, for the first time, we created the immunized Camelus Bactrianus VHH yeast two-hybrid (Y2H library according to the Clontech Mate & Plate library construction system. The transformation efficiency and titer of the VHH Y2H library were 7.26×10(6 cfu/3 µg and 2×10(9 cfu/ml, which met the demand for Y2H library screening. Using as an example the porcine circovirus type 2 (PCV2 Cap protein as bait, we screened 21 positive Cap-specific VHH sequences. Among these sequences, 7 of 9 randomly selected clones were strongly positive as indicated by enzyme-linked immunosorbent assay, either using PCV2 viral lysis or purified Cap protein as coated antigen. Additionally, the immunocytochemistry results further indicated that the screened VHHs could specifically detected PCV2 in the infected cells. All this suggests the feasibility of in vivo VHH throughput screening based on Y2H strategy.

  14. Yeast Two-Hybrid Studies on Interaction of Proteins Involved in Regulation of Nitrogen Fixation in the Phototrophic Bacterium Rhodobacter capsulatus

    OpenAIRE

    Pawlowski, Alice; Riedel, Kai-Uwe; Klipp, Werner; Dreiskemper, Petra; Groß, Silke; Bierhoff, Holger; Drepper, Thomas; Masepohl, Bernd

    2003-01-01

    Rhodobacter capsulatus contains two PII-like proteins, GlnB and GlnK, which play central roles in controlling the synthesis and activity of nitrogenase in response to ammonium availability. Here we used the yeast two-hybrid system to probe interactions between these PII-like proteins and proteins known to be involved in regulating nitrogen fixation. Analysis of defined protein pairs demonstrated the following interactions: GlnB-NtrB, GlnB-NifA1, GlnB-NifA2, GlnB-DraT, GlnK-NifA1, GlnK-NifA2, ...

  15. Progress on Application of Yeast Two-hybrid Technique%酵母双杂交技术应用进展

    Institute of Scientific and Technical Information of China (English)

    王婷; 葛怀娜; 郭宏

    2015-01-01

    Yeast two-hybrid system is one of the most powerful and widely used method to detect protein-protein interaction in living cells.Yeast two-hybrid technique is cost-effective, easy to operate, can reach the whole-genome level, and identify the interaction between different varieties.Compared with the traditional detected method, it has obvious advantages and has been applied in more and more fields.In this paper, the yeast two-hybrid technology principle and application were reviewed, including the applications on discovering new protein and proteins’new function, setting up the protein linkage map, studing of human genome DNA library, screening target for drug, and so on.The paper was expected to provide reference for the application of yeast two-hybrid system.%酵母双杂交技术是鉴定蛋白互作最有效和最广泛的分子生物学技术。该技术能直接作用于活细胞,检测细胞内蛋白质互作,具有成本低、易操作、可达到全基因组水平、能进行品种间的互作鉴定等诸多优点。较之传统的检测方法有明显优势,已在越来越多的领域得到应用。对酵母双杂交的技术原理以及应用进行了综述,介绍了该技术在发现新蛋白质、探究蛋白质功能、建立基因组蛋白连锁图、研究人类DNA文库和筛选药物作用位点等方面的重要应用,以期为该技术的广泛应用提供参考。

  16. The establishment of a library screening method based on yeast two-hybrid system and its use to determine the potential interactions of liver proteins in ayu, Plecoglossus altivelis.

    Science.gov (United States)

    Shi, Y H; Chen, J; Li, C H; Yang, H Y; Lu, X J

    2011-01-01

    Knowledge of specific protein-protein interaction (PPI) is an important component in understanding biological processes and regulatory mechanisms. A library to library screening method (LLS) was established based on yeast two-hybrid (YTH) system in this research, and applied to study the PPIs in ayu liver. In total, 23 out of 55 interaction pairs were found positive through phenotypic identification, with a positive rate of 41.8%. Of the 11 unique PPIs, 9 interactions including FGB/FGG, CaM/Spna2, C9/Apo-AI-1, α₂M/Ft, RPL10/RPL5, C8α/C9, FGG/Apo-AI-1, LECT2/Tf, and Apo-AI-2/C9 were previously reported. The other two PPIs including FGG/CLR and Wap65/C3 are novel, and in vitro co-immunoprecipitation (co-IP) experiments further confirmed these interactions. FGG/CLR interaction might play a role in regulating the inflammatory response. The interaction between Wap65 and C3 hints that Wap65 might function through the complement activation pathways when microbial infection occurs.

  17. Identification of novel protein-protein interactions of Yersinia pestis type III secretion system by yeast two hybrid system.

    Directory of Open Access Journals (Sweden)

    Huiying Yang

    Full Text Available Type III secretion system (T3SS of the plague bacterium Y. pestis encodes a syringe-like structure consisting of more than 20 proteins, which can inject virulence effectors into host cells to modulate the cellular functions. Here in this report, interactions among the possible components in T3SS of Yersinia pestis were identified using yeast mating technique. A total of 57 genes, including all the pCD1-encoded genes except those involved in plasmid replication and partition, pseudogenes, and the putative transposase genes, were subjected to yeast mating analysis. 21 pairs of interaction proteins were identified, among which 9 pairs had been previously reported and 12 novel pairs were identified in this study. Six of them were tested by GST pull down assay, and interaction pairs of YscG-SycD, YscG-TyeA, YscI-YscF, and YopN-YpCD1.09c were successfully validated, suggesting that these interactions might play potential roles in function of Yersinia T3SS. Several potential new interactions among T3SS components could help to understand the assembly and regulation of Yersinia T3SS.

  18. A set of host proteins interacting with papaya ringspot virus NIa-Pro protein identified in a yeast two-hybrid system.

    Science.gov (United States)

    Gao, L; Shen, W T; Yan, P; Tuo, D C; Li, X Y; Zhou, P

    2012-01-01

    The protein-protein interactions between viral and host proteins play an essential role in plant virus infection and host defense. The potyviral nuclear inclusion protein a protease (NIa-Pro) is involved in various steps of viral infection. In this study, the host proteins interacting with papaya ringspot virus (PRSV) NIa-Pro were screened in a Carica papaya L. plant cDNA library using a Sos recruitment two-hybrid system (SRS). We confirmed that the full-length EIF3G, FBPA1, FK506BP, GTPBP, MSRB1, and MTL from papaya can interact specifically with PRSV NIa-Pro in yeast, respectively. These proteins fufill important functions in plant protein translation, biotic and abiotic stress, energy metabolism and signal transduction. In this paper, we discuss possible functions of interactions between these host proteins and NIa-Pro in PRSV infection and their role in host defense. Sos recruitment two-hybrid system; papaya ringspot virus; NIa-Pro; protein-protein interaction.

  19. Homomeric and heteromeric interactions between wild-type and mutant phenylalanine hydroxylase subunits: evaluation of two-hybrid approaches for functional analysis of mutations causing hyperphenylalaninemia.

    Science.gov (United States)

    Waters, P J; Scriver, C R; Parniak, M A

    2001-07-01

    Phenylketonuria (PKU) is caused by mutations in the phenylalanine hydroxylase gene (PAH), while mutations in genes encoding the two enzymes (dihydropteridine reductase, DHPR, and pterin-4-alpha-carbinolamine dehydratase, PCD) required for recycling of its cofactor, tetrahydrobiopterin (BH(4)), cause other rarer disease forms of hyperphenylalaninemia. We have applied a yeast two-hybrid method, in which protein--protein interactions are measured by four reporter gene constructs, to the analysis of six PKU-associated PAH missense mutations (F39L, K42I, L48S, I65T, A104D, and R157N). By studying homomeric interactions between mutant PAH subunits, we show that this system is capable of detecting quite subtle aberrations in PAH oligomerization caused by missense mutations and that the observed results generally correlate with the severity of the mutation as determined by other expression systems. The mutant PAH subunits are also shown in this system to be able to interact with wild-type PAH subunits, pointing to an explanation for apparent dominant negative effects previously observed in obligate heterozygotes for PKU mutations. Based on our findings, the applications and limitations of two-hybrid approaches in understanding mechanisms by which PAH missense mutations exert their pathogenic effects are discussed. We have also used this technique to demonstrate homomeric interactions between wild-type DHPR subunits and between wild-type PCD subunits. These data provide a basis for functional studies on HPA-associated mutations affecting these enzymes.

  20. Falsification or Confirmation: From Logic to Psychology

    CERN Document Server

    Lukyanenko, Roman

    2015-01-01

    Corroboration or confirmation is a prominent philosophical debate of the 20th century. Many philosophers have been involved in this debate most notably the proponents of confirmation led by Hempel and its most powerful criticism by the falsificationists led by Popper. In both cases however the debates were primarily based on the arguments from logic. In this paper we review these debates and suggest that a different perspective on falsification versus confirmation can be taken by grounding arguments in cognitive psychology.

  1. A split-ubiquitin yeast two-hybrid screen to examine the substrate specificity of atToc159 and atToc132, two Arabidopsis chloroplast preprotein import receptors.

    Directory of Open Access Journals (Sweden)

    Siddhartha Dutta

    Full Text Available Post-translational import of nucleus-encoded chloroplast pre-proteins is critical for chloroplast biogenesis, and the Toc159 family of proteins serve as receptors for the process. Toc159 shares with other members of the family (e.g. Toc132, homologous GTPase (G- and Membrane (M- domains, but a highly dissimilar N-terminal acidic (A- domain. Although there is good evidence that atToc159 and atToc132 from Arabidopsis mediate the initial sorting step, preferentially recognizing photosynthetic and non-photosynthetic preproteins, respectively, relatively few chloroplast preproteins have been assigned as substrates for particular members of the Toc159 family, which has limited the proof for the hypothesis. The current study expands the number of known preprotein substrates for members of the Arabidopsis Toc159 receptor family using a split-ubiquitin membrane-based yeast two-hybrid system using the atToc159 G-domain (Toc159G, atToc132 G-domain (Toc132G and atToc132 A- plus G-domains (Toc132AG as baits. cDNA library screening with all three baits followed by pairwise interaction assays involving the 81 chloroplast preproteins identified show that although G-domains of the Toc159 family are sufficient for preprotein recognition, they alone do not confer specificity for preprotein subclasses. The presence of the A-domain fused to atToc132G (Toc132AG not only positively influences its specificity for non-photosynthetic preproteins, but also negatively regulates the ability of this receptor to interact with a subset of photosynthetic preproteins. Our study not only substantiates the fact that atToc132 can serve as a receptor by directly binding to chloroplast preproteins but also proposes the existence of subsets of preproteins with different but overlapping affinities for more than one member of the Toc159 receptor family.

  2. Genetic variation in dieback resistance in Fraxinus excelsior confirmed by progeny inoculation assay

    DEFF Research Database (Denmark)

    Lobo, Albin; McKinney, Lea Vig; Hansen, Jon Kehlet;

    2015-01-01

    Ash dieback caused by the pathogenic fungus Hymenoscyphus fraxineus [previously known as H. pseudoalbidus (sexual stage) and Chalara fraxinea (asexual stage)] is a widespread problem in Europe. Here, we assess crown damage from natural infection and necrosis development following artificial contr...... of heritable resistance and indicates that a bioassay based on controlled inoculations has the potential of becoming a fast and cost-effective tool for estimation of dieback susceptibility in breeding programmes for resistance in ash trees....

  3. Associations of UBE2I with RAD52, UBL1, p53, and RAD51 proteins in a yeast two-hybrid system

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Zhiyuan; Pardington-Purtymun, P.E.; Comeaux, J.C. [Los Alamos National Labs., NM (United States)] [and others

    1996-10-15

    The yeast RAD52-dependent pathway is involved in DNA recombination and double-strand break repair. Yeast ubiquitin-conjugating enzyme UBC9 participates in S- and M-phase cyclin degradation and mitotic control. Using the human RAD52 protein as the bait in a yeast two-hybrid system, we have identified a human homolog of yeast UBC9, designated UBE2I, that interacts with RAD52, RAD51, p53, and a ubiquitin-like protein UBL1. These interactions are UBE2I-specific, since another DNA repair-related ubiquitin-conjugating enzyme, RAD6 (UBC2), does not interact with these proteins. The interaction of UBE2I with RAD52 is mediated by RAD52`s self-association region. These results suggest that the RAD52-dependent processes, cell cycle control, p53-mediated pathway(s), and ubiquitination interact through human UBE2I. 22 refs., 3 figs.

  4. Screening proteins that interact with mutant superoxide dismutase 1 from familial amyotrophic lateral sclerosis using a yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    Guisheng Chen; Xu Peng; Shugui Shi; Lusi Li; Kangning Chen; Ju Hu; Zhenhua Zhou; Jun Wu; Gaoxing Luo; Shunzong Yuan

    2011-01-01

    The present study screened a human fetal brain cDNA library to find the proteins that interact with mutant superoxide dismutase 1 (SOD1) using a yeast two-hybrid system. Using BLAST software, 15 real proteins which interacted with mutant SOD1 were obtained, including 8 known proteins (protein tyrosine-phosphatase non-receptor type 2, TBC1D4, protein kinase family, splicing factor, arginine/serine-rich 2, SRC protein tyrosine kinase Fyn, β-sarcoglycan; glycine receptor α2, microtubule associated protein/microtubule affinity-regulating kinase 1, ferritin H chain), and 7 unknown proteins. Results demonstrated interaction of mutant SOD1 with microtubule associated protein/microtubule affinity-regulating kinase 1 and β-sarcoglycan.

  5. Use of bacterial two-hybrid system to investigate the molecular interaction between the regulators NifA and NifL of Enterobacter cloacae

    Institute of Scientific and Technical Information of China (English)

    廖贡献; 俞冠翘; 沈善炯; 朱家璧

    2002-01-01

    Expression of the nitrogen fixation (nif ) genes is tightly regulated by two proteins NifA and NifL in the (-subdivision of the proteobacteria. NifA is a transcriptional activator, which can be inactivated by NifL in the presence of oxygen or excess fixed nitrogen. A direct interaction between E. cloacae NifL and NifA was detected using the bacterial two-hybrid system. This interaction was accelerated in the presence of fixed nitrogen, while oxygen had no effect. NifL proteins, with their C-terminus being deleted, completely lost the ability to interact with NifA. The data suggest that the C-terminal domain of NifL acts as a sensor of the nitrogen status of the cell and mediates interaction with NifA.

  6. Longer Addiction Treatment Is Better, Study Confirms

    Science.gov (United States)

    ... https://medlineplus.gov/news/fullstory_163911.html Longer Addiction Treatment Is Better, Study Confirms Success rate goes up ... 3, 2017 (HealthDay News) -- The longer patients receive treatment for addiction, the greater their chances of success, a new ...

  7. Molecular confirmation of Lassa fever imported into Ghana

    Directory of Open Access Journals (Sweden)

    Joseph H.K. Bonney

    2016-02-01

    Full Text Available Background: Recent reports have shown an expansion of Lassa virus from the area where it was first isolated in Nigeria to other areas of West Africa. Two Ghanaian soldiers on a United Nations peacekeeping mission in Liberia were taken ill with viral haemorrhagic fever syndrome following the death of a sick colleague and were referred to a military hospital in Accra, Ghana, in May 2013. Blood samples from the soldiers and five asymptomatic close contacts were subjected to laboratory investigations.Objective: We report the results of these investigations to highlight the importance of molecular diagnostic applications and the need for heightened awareness about Lassa fever in West Africa.Methods: We used molecular assays on sera from the two patients to identify the causativeorganism. Upon detection of positive signals for Lassa virus ribonucleic material by two differentpolymerase chain reaction assays, sequencing and phylogenetic analyses were performed.Results: The presence of Lassa virus in the soldiers’ blood samples was shown by L-gene segment homology to be the Macenta and las803792 strains previously isolated in Liberia, with close relationships then confirmed by phylogenetic tree construction. The five asymptomatic close contacts were negative for Lassa virus.Conclusions: The Lassa virus strains identified in the two Ghanaian soldiers had molecular epidemiological links to strains from Liberia. Lassa virus was probably responsible for the outbreak of viral haemorrhagic fever in the military camp. These data confirm Lassa fever endemicity in West Africa.

  8. A New Way to Confirm Planet Candidates

    Science.gov (United States)

    Kohler, Susanna

    2016-05-01

    What was the big deal behind the Kepler news conference yesterday? Its not just that the number of confirmed planets found by Kepler has more than doubled (though thats certainly exciting news!). Whats especially interesting is the way in which these new planets were confirmed.Number of planet discoveries by year since 1995, including previous non-Kepler discoveries (blue), previous Kepler discoveries (light blue) and the newly validated Kepler planets (orange). [NASA Ames/W. Stenzel; Princeton University/T. Morton]No Need for Follow-UpBefore Kepler, the way we confirmed planet candidates was with follow-up observations. The candidate could be validated either by directly imaging (which is rare) or obtaining a large number radial-velocity measurements of the wobble of the planets host star due to the planets orbit. But once Kepler started producing planet candidates, these approaches to validation became less feasible. A lot of Kepler candidates are small and orbit faint stars, making follow-up observations difficult or impossible.This problem is what inspired the development of whats known as probabilistic validation, an analysis technique that involves assessing the likelihood that the candidates signal is caused by various false-positive scenarios. Using this technique allows astronomers to estimate the likelihood of a candidate signal being a true planet detection; if that likelihood is high enough, the planet candidate can be confirmed without the need for follow-up observations.A breakdown of the catalog of Kepler Objects of Interest. Just over half had previously been identified as false positives or confirmed as candidates. 1284 are newly validated, and another 455 have FPP of1090%. [Morton et al. 2016]Probabilistic validation has been used in the past to confirm individual planet candidates in Kepler data, but now Timothy Morton (Princeton University) and collaborators have taken this to a new level: they developed the first code thats designed to do fully

  9. Confirmed and Potential Sources of Legionella Reviewed.

    Science.gov (United States)

    van Heijnsbergen, Eri; Schalk, Johanna A C; Euser, Sjoerd M; Brandsema, Petra S; den Boer, Jeroen W; de Roda Husman, Ana Maria

    2015-04-21

    Legionella bacteria are ubiquitous in natural matrices and man-made systems. However, it is not always clear if these reservoirs can act as source of infection resulting in cases of Legionnaires' disease. This review provides an overview of reservoirs of Legionella reported in the literature, other than drinking water distribution systems. Levels of evidence were developed to discriminate between potential and confirmed sources of Legionella. A total of 17 systems and matrices could be classified as confirmed sources of Legionella. Many other man-made systems or natural matrices were not classified as a confirmed source, since either no patients were linked to these reservoirs or the supporting evidence was weak. However, these systems or matrices could play an important role in the transmission of infectious Legionella bacteria; they might not yet be considered in source investigations, resulting in an underestimation of their importance. To optimize source investigations it is important to have knowledge about all the (potential) sources of Legionella. Further research is needed to unravel what the contribution is of each confirmed source, and possibly also potential sources, to the LD disease burden.

  10. The composition of Io - a late confirmation

    CERN Document Server

    Celebonovic, V

    1996-01-01

    Nine years ago,working within the framework of theoretical dense matter physics,the present author has determined the chemical composition of the Galileian satellites of Jupiter.A few months ago,in the flyby of the GA- LILEO spaceprobe,some of the theoretical predictions were confirmed.

  11. Confirmation via Analogue Simulation: A Bayesian Analysis

    CERN Document Server

    Dardashti, Radin; Thebault, Karim P Y; Winsberg, Eric

    2016-01-01

    Analogue simulation is a novel mode of scientific inference found increasingly within modern physics, and yet all but neglected in the philosophical literature. Experiments conducted upon a table-top 'source system' are taken to provide insight into features of an inaccessible 'target system', based upon a syntactic isomorphism between the relevant modelling frameworks. An important example is the use of acoustic 'dumb hole' systems to simulate gravitational black holes. In a recent paper it was argued that there exists circumstances in which confirmation via analogue simulation can obtain; in particular when the robustness of the isomorphism is established via universality arguments. The current paper supports these claims via an analysis in terms of Bayesian confirmation theory.

  12. Diffuse panbronchiolitis with histopathological confirmation among Chinese

    Institute of Scientific and Technical Information of China (English)

    谢广顺; 李龙芸; 刘鸿瑞; 张伟宏; 朱元珏

    2004-01-01

    Background Diffuse panbronchiolitis (DPB) was originally and is still primarily reported in Japan, rarely in other countries. As macrolide therapy is effective for this disease with once dismal prognosis, familiarity with its clinical features is urgently needed, especially for clinicians outside Japan. The objectives of this study were to investigate the clinical features of DPB in a Chinese population and propose diagnostic procedures that will lead to increased awareness of this treatable disease among clinicians, ultimately allowing for more rapid diagnosis. Methods After a literature review, the clinical features of DPB were histopathologically confirmed in a series of 9 cases either by open lung biopsy or video-assisted thoracic surgical biopsy, resulting in the largest series of confirmed DPB cases in a non-Japanese population. Here, the cases are retrospectively described and diagnostic procedures are discussed.Conclusions Although its clinical features may vary with disease course and ethnic populations, most cases of DPB can be diagnosed or suggested according to clinical diagnostic criteria. However, underdiagnosis as a result of unfamiliarity with its clinical features and diagnostic criteria prevails. If difficulty in diagnosis arises, the diagnosis should be based on clinicopathological features and the exclusion of other diseases. Few cases can be confirmed by transbronchial biopsies; in these cases, either an open-lung biopsy or a video-assisted thoracic surgical lung biopsy should be recommended.

  13. Screening for Novel Binding Proteins Interacting with Human Papillomavirus Type 18 E6 Oncogene in the Hela cDNA Library by Yeast Two-Hybrid System

    Institute of Scientific and Technical Information of China (English)

    Shuang LI; Ping LIU; Ling XI; Xuefeng JIANG; Jianfeng ZHOU; Shixuan WANG; Li MENG; Yunping LU; Ding Ma

    2008-01-01

    To screen for novel binding proteins interacting with high-risk HPV 18 E6 oncogene, the strain AH109 was transformed with pGBKT7-HPV18 E6 plasmid, and subsequent transference was utilized to screen for interacting proteins with HPV 18 E6 in human Hela cDNA library. HPVl8 E6 mRNA was expressed in yeast and there was no self-activation and toxicity in AH109. Seven proteins that interacted with HPV18 E6, including transmembrane protein 87B, phosphonoformate im- muno-associated protein 5, vimentin, KM-HN-1 protein, dedicator of cytokinesis 7, vaccinia related kinase 2 and a hypothetical protein, were identified. It was suggested that yeast two-hybrid system is an efficient for screening interacting proteins. The high-risk HPV 18 E6 oncogene may interact with the proteins, which may be associated with signal transduction and transeriptional control, epithelial cell invasion and migration, as well as humoral and cellular immune etc. This investigation provides functional clues for further exploration of potential oncogenesis targets for cancer biotherapy.

  14. MOR is not enough: identification of novel mu-opioid receptor interacting proteins using traditional and modified membrane yeast two-hybrid screens.

    Science.gov (United States)

    Petko, Jessica; Justice-Bitner, Stephanie; Jin, Jay; Wong, Victoria; Kittanakom, Saranya; Ferraro, Thomas N; Stagljar, Igor; Levenson, Robert

    2013-01-01

    The mu-opioid receptor (MOR) is the G-protein coupled receptor primarily responsible for mediating the analgesic and rewarding properties of opioid agonist drugs such as morphine, fentanyl, and heroin. We have utilized a combination of traditional and modified membrane yeast two-hybrid screening methods to identify a cohort of novel MOR interacting proteins (MORIPs). The interaction between the MOR and a subset of MORIPs was validated in pulldown, co-immunoprecipitation, and co-localization studies using HEK293 cells stably expressing the MOR as well as rodent brain. Additionally, a subset of MORIPs was found capable of interaction with the delta and kappa opioid receptors, suggesting that they may represent general opioid receptor interacting proteins (ORIPS). Expression of several MORIPs was altered in specific mouse brain regions after chronic treatment with morphine, suggesting that these proteins may play a role in response to opioid agonist drugs. Based on the known function of these newly identified MORIPs, the interactions forming the MOR signalplex are hypothesized to be important for MOR signaling and intracellular trafficking. Understanding the molecular complexity of MOR/MORIP interactions provides a conceptual framework for defining the cellular mechanisms of MOR signaling in brain and may be critical for determining the physiological basis of opioid tolerance and addiction.

  15. A yeast two-hybrid screen reveals a strong interaction between the Legionella chaperonin Hsp60 and the host cell small heat shock protein Hsp10.

    Science.gov (United States)

    Nasrallah, Gheyath K

    2015-06-01

    L. pneumophila is an intracellular bacterium that replicates inside a membrane-bound vacuole called Legionella-containing vacuole (LCV), where it plentifully liberates its HtpB chaperonin. From LCV, HtpB reaches the host cell cytoplasm, where it interacts with SAMDC, a cytoplasmic protein required for synthesis of host polyamines that are important for intracellular growth of L. pneumophila. Additionally, cytoplasmic expression of HtpB in S. cerevisiae induces pseudohyphal growth, and in mammalian cells recruits mitochondria to LCV, and modifies actin microfilaments organization. This led us to hypothesize here that HtpB recruits a protein(s) from eukaryotic cells that is involved in the emergence of the aforementioned phenotypes. To identify this protein, a commercially available HeLa cDNA library was screened using a yeast two-hybrid system. Approximately 5×10(6) yeast clones carrying HeLa cDNA library plasmid were screened. Twenty-one positive clones were identified. DNA sequence analysis revealed that all of these positive clones encoded the mammalian small heat shock protein Hsp10. Based on the fact that chaperonions are required to interact with co-chaperonins to function properly in protein folding, we believe that HtpB recruits the host cell Hsp10 to appropriately interact with SAMDC and to induce the multifunction phenotypes deemed important in L. pneumophila pathogenesis.

  16. Systematic two-hybrid and comparative proteomic analyses reveal novel yeast pre-mRNA splicing factors connected to Prp19.

    Directory of Open Access Journals (Sweden)

    Liping Ren

    Full Text Available Prp19 is the founding member of the NineTeen Complex, or NTC, which is a spliceosomal subcomplex essential for spliceosome activation. To define Prp19 connectivity and dynamic protein interactions within the spliceosome, we systematically queried the Saccharomyces cerevisiae proteome for Prp19 WD40 domain interaction partners by two-hybrid analysis. We report that in addition to S. cerevisiae Cwc2, the splicing factor Prp17 binds directly to the Prp19 WD40 domain in a 1:1 ratio. Prp17 binds simultaneously with Cwc2 indicating that it is part of the core NTC complex. We also find that the previously uncharacterized protein Urn1 (Dre4 in Schizosaccharomyces pombe directly interacts with Prp19, and that Dre4 is conditionally required for pre-mRNA splicing in S. pombe. S. pombe Dre4 and S. cerevisiae Urn1 co-purify U2, U5, and U6 snRNAs and multiple splicing factors, and dre4Δ and urn1Δ strains display numerous negative genetic interactions with known splicing mutants. The S. pombe Prp19-containing Dre4 complex co-purifies three previously uncharacterized proteins that participate in pre-mRNA splicing, likely before spliceosome activation. Our multi-faceted approach has revealed new low abundance splicing factors connected to NTC function, provides evidence for distinct Prp19 containing complexes, and underscores the role of the Prp19 WD40 domain as a splicing scaffold.

  17. Polymerase chain reaction assay for avian polyomavirus.

    OpenAIRE

    Phalen, D.N.; Wilson, V G; Graham, D L

    1991-01-01

    A polymerase chain reaction assay was developed for detection of budgerigar fledgling disease virus (BFDV). The assay used a single set of primers complementary to sequences located in the putative coding region for the BFDV VP1 gene. The observed amplification product had the expected size of 550 bp and was confirmed to derive from BFDV DNA by its restriction digestion pattern. This assay was specific for BFDV and highly sensitive, being able to detect as few as 20 copies of the virus. By us...

  18. Troubleshooting Requests e-mail Confirmation

    CERN Multimedia

    TS Department

    2004-01-01

    In an ongoing effort to improve quality of the repair requests, a new e-mail confirmation automatic system will be implemented starting from the 21st October. All repair requests transmitted to the TCR (72201) or the FM Helpdesk (77777) will be confirmed in an e-mail to the requestor, provided that the latter has a valid e-mail address in the HR database. The e-mail will contain a reference number, a brief description of the problem, the location and a contact where more information can be obtained. A second e-mail will be sent when the processing of the repair request is finished. We hope that this initiative will improve the transparency and quality of our service. Helpdesk Troubleshooting Requests (reminder) We remind you that all the repair requests and other communication concerning the CERN machine buildings have to be transmitted to the TCR via 72201, whereas the ones concerning tertiary buildings are handled directly by the FM helpdesk under the phone number 77777, i.e. problems on systems and equ...

  19. [Cutaneous gnathostomiasis, first confirmed case in Colombia].

    Science.gov (United States)

    Jurado, Leonardo F; Palacios, Diana M; López, Rocío; Baldión, Margarita; Matijasevic, Eugenio

    2015-01-01

    Gnathostomiasis is a parasitic zoonosis caused by some species of helminthes belonging to the genus Gnathostoma . It has a wide clinical presentation and its diagnosis is a challenge. Tropical and subtropical countries are endemic, and its transmission is associated with eating raw or undercooked meat from fresh water animals. Increasing global tourism and consuming exotic foods have produced a noticeable rise in cases of the disease in the last decades. However, in our country, there has not been any confirmed case of gnathostomiasis previously reported. We present the case of a 63-year-old Colombian man with an international travel history, who presented with gastrointestinal symptoms. During the hospital stay, he developed a cutaneous lesion on the upper right abdominal quadrant, where later, a larva was found. A morphological study allowed us to identify it as Gnathostoma spinigerum . As such, this is the first report of an imported case of gnathostomiasis confirmed in Colombia. This article describes the principles, etiology, pathogenic cycle and treatment of this disease with special considerations to our patient´s particular features.

  20. Microbead agglutination based assays

    KAUST Repository

    Kodzius, Rimantas

    2013-01-21

    We report a simple and rapid room temperature assay for point-of-care (POC) testing that is based on specific agglutination. Agglutination tests are based on aggregation of microbeads in the presence of a specific analyte thus enabling the macroscopic observation. Such tests are most often used to explore antibody-antigen reactions. Agglutination has been used for protein assays using a biotin/streptavidin system as well as a hybridization based assay. The agglutination systems are prone to selftermination of the linking analyte, prone to active site saturation and loss of agglomeration at high analyte concentrations. We investigated the molecular target/ligand interaction, explaining the common agglutination problems related to analyte self-termination, linkage of the analyte to the same bead instead of different microbeads. We classified the agglutination process into three kinds of assays: a two- component assay, a three-component assay and a stepped three- component assay. Although we compared these three kinds of assays for recognizing DNA and protein molecules, the assay can be used for virtually any molecule, including ions and metabolites. In total, the optimized assay permits detecting analytes with high sensitivity in a short time, 5 min, at room temperature. Such a system is appropriate for POC testing.

  1. Colorimetric protein assay techniques.

    Science.gov (United States)

    Sapan, C V; Lundblad, R L; Price, N C

    1999-04-01

    There has been an increase in the number of colorimetric assay techniques for the determination of protein concentration over the past 20 years. This has resulted in a perceived increase in sensitivity and accuracy with the advent of new techniques. The present review considers these advances with emphasis on the potential use of such technologies in the assay of biopharmaceuticals. The techniques reviewed include Coomassie Blue G-250 dye binding (the Bradford assay), the Lowry assay, the bicinchoninic acid assay and the biuret assay. It is shown that each assay has advantages and disadvantages relative to sensitivity, ease of performance, acceptance in the literature, accuracy and reproducibility/coefficient of variation/laboratory-to-laboratory variation. A comparison of the use of several assays with the same sample population is presented. It is suggested that the most critical issue in the use of a chromogenic protein assay for the characterization of a biopharmaceutical is the selection of a standard for the calibration of the assay; it is crucial that the standard be representative of the sample. If it is not possible to match the standard with the sample from the perspective of protein composition, then it is preferable to use an assay that is not sensitive to the composition of the protein such as a micro-Kjeldahl technique, quantitative amino acid analysis or the biuret assay. In a complex mixture it might be inappropriate to focus on a general method of protein determination and much more informative to use specific methods relating to the protein(s) of particular interest, using either specific assays or antibody-based methods. The key point is that whatever method is adopted as the 'gold standard' for a given protein, this method needs to be used routinely for calibration.

  2. Screening of cellular proteins that interact with the classical swine fever virus non-structural protein 5A by yeast two-hybrid analysis

    Indian Academy of Sciences (India)

    Chengcheng Zhang; Lei He; Kai Kang; Heng Chen; Lei Xu; Yanming Zhang

    2014-03-01

    Classical swine fever virus (CSFV), the pathogen of classical swine fever (CSF), causes severe hemorrhagic fever and vascular necrosis in domestic pigs and wild boar. A large number of evidence has proven that non-structural 5A (NS5A) is not only a very important part of viral replication complex, but also can regulate host cell’s function; however, the underlying mechanisms remain poorly understood. In the current study, aiming to find more clues in understanding the molecular mechanisms of CSFV NS5A’s function, the yeast two-hybrid (Y2H) system was adopted to screen for CSFV NS5A interactive proteins in the cDNA library of the swine umbilical vein endothelial cell (SUVEC). Alignment with the NCBI database revealed 16 interactive proteins: DDX5, PSMC3, NAV1, PHF5A, GNB2L1, CSDE1, HSPA8, BRMS1, PPP2R3C, AIP, TMED10, POLR1C, TMEM70, METAP2, CHORDC1 and COPS6. These proteins are mostly related to gene transcription, protein folding, protein degradation and metabolism. The interactions detected by the Y2H system should be considered as preliminary results. Since identifying novel pathways and host targets, which play essential roles during infection, may provide potential targets for therapeutic development. The finding of proteins obtained from the SUVEC cDNA library that interact with the CSFV NS5A protein provide valuable information for better understanding the interactions between this viral protein and the host target proteins.

  3. Can weak lensing surveys confirm BICEP2 ?

    CERN Document Server

    Chisari, Nora Elisa; Schmidt, Fabian

    2014-01-01

    The detection of B-modes in the Cosmic Microwave Background (CMB) polarization by the BICEP2 experiment, if interpreted as evidence for a primordial gravitational wave background, has enormous ramifications for cosmology and physics. It is crucial to test this hypothesis with independent measurements. A gravitational wave background leads to B-modes in galaxy shape correlations (shear) both through lensing and tidal alignment effects. Since the systematics and foregrounds of galaxy shapes and CMB polarization are entirely different, a detection of a cross-correlation between the two observables would provide conclusive proof for the existence of a primordial gravitational wave background. We find that upcoming weak lensing surveys will be able to detect the cross-correlation between B-modes of the CMB and galaxy shapes. However, this detection is not sufficient to confirm or falsify the hypothesis of a primordial origin for CMB B-mode polarization.

  4. Efficacy of ibandronate: a long term confirmation.

    Science.gov (United States)

    Di Munno, Ombretta; Delle Sedie, Andrea

    2010-01-01

    Data deriving from randomized clinical trials, observational studies and meta-analyses, including treatment regimens unlicensed for use in clinical practice, clearly support that 150 mg once-monthly oral and 3 mg quarterly i.v. doses of ibandronate are associated with efficacy, safety and tolerability; notably both these marketed regimens, which largely correspond to ACE ≥10.8 mg, may in addition provide a significant efficacy on non-vertebral and clinical fracture (Fx) efficacy. The MOBILE and the DIVA LTE studies confirmed a sustained efficacy of monthly oral and quarterly i.v. regimens respectively, over 5 years. Furthermore, improved adherence rates with monthly ibandronate, deriving from studies evaluating large prescription databases, promise to enhance fracture protection and decrease the social and economic burden of postmenopausal osteoporosis.

  5. Automatic earthquake confirmation for early warning system

    Science.gov (United States)

    Kuyuk, H. S.; Colombelli, S.; Zollo, A.; Allen, R. M.; Erdik, M. O.

    2015-07-01

    Earthquake early warning studies are shifting real-time seismology in earthquake science. They provide methods to rapidly assess earthquakes to predict damaging ground shaking. Preventing false alarms from these systems is key. Here we developed a simple, robust algorithm, Authorizing GRound shaking for Earthquake Early warning Systems (AGREEs), to reduce falsely issued alarms. This is a network threshold-based algorithm, which differs from existing approaches based on apparent velocity of P and S waves. AGREEs is designed to function as an external module to support existing earthquake early warning systems (EEWSs) and filters out the false events, by evaluating actual shaking near the epicenter. Our retrospective analyses of the 2009 L'Aquila and 2012 Emilia earthquakes show that AGREEs could help an EEWS by confirming the epicentral intensity. Furthermore, AGREEs is able to effectively identify three false events due to a storm, a teleseismic earthquake, and broken sensors in Irpinia Seismic Network, Italy.

  6. Spectroscopic Confirmation of the Pisces Overdensity

    CERN Document Server

    Kollmeier, Juna A; Shectman, Stephen; Thompson, Ian B; Preston, George W; Simon, Joshua D; Crane, Jeffrey D; Ivezić, Željko; Sesar, Branimir

    2009-01-01

    We present spectroscopic confirmation of the "Pisces Overdensity", also known as "Structure J", a photometric overdensity of RR Lyrae stars discovered by the Sloan Digital Sky Survey (SDSS) at an estimated photometric distance of ~85kpc. We measure radial velocities for 8 RR Lyrae stars within Pisces. We find that 5 of the 8 stars have heliocentric radial velocities within a narrow range of -87 km/s < v < -67 km/s, suggesting that the photometric overdensity is mainly due to a physically associated system, probably a dwarf galaxy or a disrupted galaxy. Two of the remaining 3 stars differ from one another by only 9 km/s, but it would be premature to identify them as a second system.

  7. Fishing TaSC Interacting Protein in Wheat Using Split Ubiquitin Yeast Two Hybrid System%利用分裂泛素酵母双杂交技术钓取小麦TaSC互作蛋白质

    Institute of Scientific and Technical Information of China (English)

    蔺芳芳; 杨旭; 武小翠; 刘晓梅; 葛荣朝; 赵宝存

    2013-01-01

      TaSC (Triticum asetivum L. salt-tolerance related gene, GenBank 登录号为 AY956330)是从小麦耐盐突变体RH8706-49中克隆的高盐诱导表达的耐盐相关基因.以该基因编码的蛋白质TaSC为诱饵,运用分裂泛素酵母双杂交技术从小麦 cDNA 表达文库中钓取互作蛋白质,筛选到一个编码小麦未知功能蛋白质的基因(GenBank 登录号为AK336035),命名为TaSCIP1(TaSC interaction protein 1).双分子荧光互补(BiFC)实验证实TaSCIP1与TaSC存在互作.该互作蛋白的分离有利于进一步研究TaSC基因的耐盐机制.%The TaSC (Triticum asetivum L. salt-tolerance related gene, GenBank accession number AY956330) has been cloned from wheat salt tolerant mutant RH 8706-49, which is induced by high salinity. To fish interacting proteins of this gene, we used TaSC protein as bait to hybrid with the wheat cDNA expression library using the split ubiquitin yeast two hybrid system in this experiment. A novel wheat gene (GenBank accession number AK336035) encoding a protein with unknown function was isolated, which was designated TaSCIP1 (TaSC interaction protein 1). Bimolecular fluorescence complementation (BiFC) experiment con-firmed the interaction between proteins TaSCIP1 and TaSC. The separation of TaSC-interacting protein is beneficial to disclose the mechanism of salt tolerance gene TaSC.

  8. Absolute nuclear material assay

    Science.gov (United States)

    Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

    2012-05-15

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  9. TANK 50 BATCH 0 SALTSTONE FORMULATION CONFIRMATION

    Energy Technology Data Exchange (ETDEWEB)

    Langton, C.

    2006-06-05

    Savannah River National Laboratory (SRNL) personnel were requested to confirm the Tank 50 Batch 0 grout formulation per Technical Task Request, SSF-TTR-2006-0001 (task 1 of 2) [1]. Earlier Batch 0 formulation testing used a Tank 50 sample collected in September 2005 and is described elsewhere [2]. The current testing was performed using a sample of Tank 50 waste collected in May 2006. This work was performed according to the Technical Task and Quality Assurance Plan (TT/QAP), WSRC-RP-2006-00594 [3]. The salt solution collected from Tank 50 in May 2006 contained approximately 3 weight percent more solids than the sample collected in September 2005. The insoluble solids took longer to settle in the new sample which was interpreted as indicating finer particles in the current sample. The saltstone formulation developed for the September 2005 Tank 50 Batch 0 sample was confirmed for the May 2006 sample with one minor exception. Saltstone prepared with the Tank 50 sample collected in May 2006 required 1.5 times more Daratard 17 set retarding admixture than the saltstone prepared with the September In addition, a sample prepared with lower shear mixing (stirring with a spatula) had a higher plastic viscosity (57 cP) than samples made with higher shear mixing in a blender (23cP). The static gel times of the saltstone slurries made with low shear mixing were also shorter ({approx}32 minutes) than those for comparable samples made in the blender ({approx}47 minutes). The addition of the various waste streams (ETP, HEU-HCAN, and GPE-HCAN) to Tank 50 from September 2005 to May 2006 has increased the amount of set retarder, Daratard 17, required for processing saltstone slurries through the Saltstone facility. If these streams are continued to be added to Tank 50, the quantity of admixtures required to maintain the same processing conditions for the Saltstone facility will probably change and additional testing is recommended to reconfirm the Tank 50 Saltstone formulation.

  10. Observational Confirmations of Spiral Density Wave Theory

    Science.gov (United States)

    Kennefick, Julia D.; Kennefick, Daniel; Shameer Abdeen, Mohamed; Berrier, Joel; Davis, Benjamin; Fusco, Michael; Pour Imani, Hamed; Shields, Doug; DMS, SINGS

    2017-01-01

    Using two techniques to reliably and accurately measure the pitch angles of spiral arms in late-type galaxies, we have compared pitch angles to directly measured black hole masses in local galaxies and demonstrated a strong correlation between them. Using the relation thus established we have developed a pitch angle distribution function of a statistically complete volume limited sample of nearby galaxies and developed a central black hole mass function for nearby spiral galaxies.We have further shown that density wave theory leads us to a three-way correlation between bulge mass, pitch angle, and disk gas density, and have used data from the Galaxy Disk Mass Survey to confirm this possible fundamental plane. Density wave theory also predicts that the pitch angle of spiral arms should change with observed waveband as each waveband is sampling a different stage in stellar population formation and evolution. We present evidence that this is indeed the case using a sample of galaxies from the Spitzer Infrared Nearby Galaxy Survey. Furthermore, the evolved spiral arms cross at the galaxy co-rotation radius. This gives a new method for determining the co-rotation radius of spiral galaxies that is found to agree with those found using previous methods.

  11. Manned in Situ Confirmation of Lunar Ice

    Science.gov (United States)

    Gerené, S. P. B.; Hummeling, R. W. J.; Ockels, W. J.

    A study is performed to investigate the feasibility of a manned expedition to the Moon using the European Ariane-5 launcher. The primary objective of this lunar mission is to confirm the presence of water at the South-Pole craters. It is believed that these permanently shadowed craters contain water in the form of ice. Secondary objective is to perform lunar surface science and making a first step towards a lunar outpost. Early results show that a minimum of two Ariane-5 launches is required. In this `two Ariane' scenario the first launch will bring a Lunar Landing Vehicle (LLV) into low lunar orbit. The second will launch two astronauts in a Crew Transfer Vehicle into a rendez- vous trajectory with the LLV. Arrived at the Moon, the astronauts will enter the LLV, undock from the CTV and land at the designated site located near the rim of the South-Pole Shackleton crater. The transfer strategy for both spacecraft will be the so-called direct transfer, taking about four days. At arrival the LLV will start mapping the landing site at a ground resolution of one meter. As a consequence of the polar orbit, the CTV has to arrive fourteen days later and surface operations can take about twelve days, accumulating in a total mission-duration of 36 days. 32 days for the CTV and 22 days for the LLV. In case a `two Ariane' flight does not posses sufficient capabilities also a `three Ariane' scenario is developed, in which the LLV is split-up into two stages and launched separately. These two will dock at the Moon forming a descent stage and an ascent stage. The third launch will be a CTV. During surface operations, astronauts will set up a solar power unit, install the sample retrieval system and carry out surface science. Samples of the crater floor will be retrieved by means of a probe or robot guided along a cable suspended over the crater rim. Also, this paper shows the way in which European astronauts can be brought to the Moon for other future missions, like the

  12. The Yeast Split-Ubiquitin Membrane Protein Two-Hybrid Screen Identifies BAP31 as a Regulator of the Turnover of Endoplasmic Reticulum-Associated Protein Tyrosine Phosphatase-Like B

    OpenAIRE

    Wang, Bing; Pelletier, Jerry; Massaad, Michel J.; Herscovics, Annette; Shore, Gordon C

    2004-01-01

    In the past decade, traditional yeast two-hybrid techniques have identified a plethora of interactions among soluble proteins operating within diverse cellular pathways. The discovery of associations between membrane proteins by genetic approaches, on the other hand, is less well established due to technical limitations. Recently, a split-ubiquitin system was developed to overcome this barrier, but so far, this system has been limited to the analysis of known membrane protein interactions. He...

  13. Cell viability assays: introduction.

    Science.gov (United States)

    Stoddart, Martin J

    2011-01-01

    The measurement of cell viability plays a fundamental role in all forms of cell culture. Sometimes it is the main purpose of the experiment, such as in toxicity assays. Alternatively, cell viability can be used to -correlate cell behaviour to cell number, providing a more accurate picture of, for example, anabolic -activity. There are wide arrays of cell viability methods which range from the most routine trypan blue dye exclusion assay to highly complex analysis of individual cells, such as using RAMAN microscopy. The cost, speed, and complexity of equipment required will all play a role in determining the assay used. This chapter aims to provide an overview of many of the assays available today.

  14. Tube-Forming Assays.

    Science.gov (United States)

    Brown, Ryan M; Meah, Christopher J; Heath, Victoria L; Styles, Iain B; Bicknell, Roy

    2016-01-01

    Angiogenesis involves the generation of new blood vessels from the existing vasculature and is dependent on many growth factors and signaling events. In vivo angiogenesis is dynamic and complex, meaning assays are commonly utilized to explore specific targets for research into this area. Tube-forming assays offer an excellent overview of the molecular processes in angiogenesis. The Matrigel tube forming assay is a simple-to-implement but powerful tool for identifying biomolecules involved in angiogenesis. A detailed experimental protocol on the implementation of the assay is described in conjunction with an in-depth review of methods that can be applied to the analysis of the tube formation. In addition, an ImageJ plug-in is presented which allows automatic quantification of tube images reducing analysis times while removing user bias and subjectivity.

  15. Transgenic Animal Mutation Assays

    Institute of Scientific and Technical Information of China (English)

    Tao Chen; Ph.D.D.A.B.T.

    2005-01-01

    @@ The novel transgenic mouse and rat mutation assays have provided a tool for analyzing in vivo mutation in any tissue, thus permitting the direct comparison of cancer incidence with mutant frequency.

  16. Assays for thrombopoietin

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, T.P.

    1977-01-01

    In summary, thrombopoietin levels have been determined indirectly by measuring thrombocytopoiesis in assay animals (platelet counting, measurement of isotope incorporation into newly formed platelets, changes in platelet sizes, or alterations in number and size of megakaryocytes) and by use of an immunoassay. Although much work remains, it seems clear at the present time that isotopic uptake into platelets of specially prepared assay mice (rebound-thrombocytosis) is superior to the other techniques now available for the measurement of thrombopoietin. However, the ideal assay for TSF which is specific, rapid, and inexpensive is yet to be developed. An immunoassay is in the development stage, but will require additional work before it can be utilized for the routine assay of TSF.

  17. New Rapid Spore Assay

    Science.gov (United States)

    Kminek, Gerhard; Conley, Catharine

    2012-07-01

    The presentation will detail approved Planetary Protection specifications for the Rapid Spore Assay for spacecraft components and subsystems. Outlined will be the research and studies on which the specifications were based. The research, funded by ESA and NASA/JPL, was conducted over a period of two years and was followed by limited cleanroom studies to assess the feasibility of this assay during spacecraft assembly.

  18. Confirmation of antiphospholipid antibody positivity: a year’s results in a cohort of 113 patients

    Directory of Open Access Journals (Sweden)

    A. Ruffatti

    2011-06-01

    Full Text Available Objective: To evaluate the confirmation rate of antiphospholipid antibodies (aPL, to analyze their behaviour at confirmation time, and to study the clinical value of their confirmation. Methods: Blood samples from 380 subjects, enrolled in this study from June 1, 2007 to May 31, 2008, were tested for anti-cardiolipin (aCL and anti-beta2glycoprotein (aβ2GPI antibodies using an ELISA method and for Lupus anticoagulant (LA using a series of clotting tests. The samples of the 113 subjects resulting positive at the first testing time were assayed again to confirm antiphospholipid positivity. Results: aPL positivity was confirmed in 67 out of the 113 subjects (59.3%. Medium-high antibody levels of all, except IgM aCL, aPL/ELISA had a significantly higher confirmation rate with respect to that in subjects with low levels. The confirmation rate in the category I antibody patients (multiple positivity was higher than that in the category II antibody subjects (single positivity. LA positivity was confirmed only when it was associated to other aPL. The cut-off of 40 GPL produced a confirmation rate equal to that resulting from a 99th percentile cut-off. Confirmation of aPL positivity made it possible for us to confirm the diagnosis of antiphospholipid syndrome (APS in 8 out of the 113 subjects originally resulting positive (7,1%. APS clinical features were vascular thrombosis in 4 of these and pregnancy morbidity in the other 4. Conclusions: Our data emphasize aPL positivity confirmation selectivity, and medium-high antibody levels and category I antibodies (multiple positivity had the best confirmation rates.

  19. Virological confirmation of suspected dengue in a Phase 2 Latin American vaccine trial: Implications for vaccine efficacy evaluation

    Directory of Open Access Journals (Sweden)

    Mark Boaz

    2014-01-01

    Full Text Available The CYD tetravalent dengue vaccine candidate is being evaluated for protective efficacy against symptomatic dengue in Phase 3 efficacy trials. The laboratory test algorithm to confirm dengue cases was evaluated prior to Phase 3 trials. During a Phase 2 trial in Latin America a dengue epidemic occurred in the study countries. A total of 72 suspected dengue cases were reported and assessed: virological confirmation comprised qRT-PCR methods and a commercial ELISA kit for NS1 protein (Bio-Rad. The qRT-PCR included a screening assay targeting a conserved dengue region of the 3′-UTR (dengue screen assay followed by 4 individual serotype assays targeting the conserved dengue NS5 genomic region (WT dengue qRT-PCR assays. The NS1 and WT dengue qRT-PCR were endpoint assays for protocol virological confirmation (PVC. Of the 72 suspected cases, 14 were PVC. However, a unique pattern of dengue qRT-PCR results were observed in 5 suspected cases from Honduras: the dengue screen qRT-PCR assay was positive but WT dengue qRT-PCR and NS1 Ag ELISA were negative. To investigate these observations, additional molecular methods were applied: a SYBR® Green-based RT-PCR assay, sequencing assays directed at the genome regions covered by the WT dengue qRT-PCR, and a modified commercial dengue RT-PCR test (Simplexa™ Dengue, Focus Diagnostics. The exploratory data confirmed these additional cases as dengue and indicated the serotype 2 WT dengue qRT-PCR assay was unable to detect a circulating Latin American strain (DENV-2/NI/BID-V608/2006 due to a sequence variation in the isolate. The Simplexa Dengue RT-PCR test was able to detect and serotype dengue. Based on these findings an updated molecular test algorithm for the virological confirmation of dengue cases was developed and implemented in the Phase 3 efficacy trials.

  20. Confirmed identification and toxin profiling of Campylobacter jejuni using a thermostabilized multiplex PCR formulation.

    Science.gov (United States)

    Ramachandran, Nitya; Ramlal, Shylaja; Batra, Harsh Vardhan

    2017-07-01

    Cytolethal distending toxin (CDT) producing Campylobacter jejuni species are one of the leading causes of human gastroenteritis worldwide. The main intent of the study was to develop a multiplex PCR assay for the confirmed identification and toxin profiling of C. jejuni. The genes targeted were rpo B as genus specific, hip O for species; cdt A, cdt B, cdt C encoding respective subunit proteins of CDT with Internal Amplification Control (IAC). To enhance its application as a pre-mixed ready-to-use format, the master mix of developed mPCR was dried by lyophilization and stability was assessed. Thermostabilized reagents showed stability of 1.5 months at room-temperature and upto six months at 4 °C without any loss of functionality. The assay was evaluated on a number of presumptive Campylobacter isolates along with biochemical tests. Results obtained indicated the accurate identification of C. jejuni by developed mPCR format in contrast to misconception associated with biochemical assays. The assay was also tested on spiked samples for its real-time utility. Altogether, the room-temperature storable and ready-to- use mPCR format developed in this study could be preferred for rapid detection and confirmed identification of toxigenic strains of C. jejuni in place of conventional biochemical assays. © 2017 APMIS. Published by John Wiley & Sons Ltd.

  1. Against vaccine assay secrecy.

    Science.gov (United States)

    Herder, Matthew; Hatchette, Todd F; Halperin, Scott A; Langley, Joanne M

    2015-01-01

    Increasing the transparency of the evidence base behind health interventions such as pharmaceuticals, biologics, and medical devices, has become a major point of critique, conflict, and policy focus in recent years. Yet the lack of publicly available information regarding the immunogenicity assays upon which many important, widely used vaccines are based has received no attention to date. In this paper we draw attention to this critical public health problem by reporting on our efforts to secure vaccine assay information in respect of 10 vaccines through Canada's access to information law. We argue, under Canadian law, that the public health interest in having access to the methods for these laboratory procedures should override claims by vaccine manufacturers and regulators that this information is proprietary; and, we call upon several actors to take steps to ensure greater transparency with respect to vaccine assays, including regulators, private firms, researchers, research institutions, research funders, and journal editors.

  2. Against vaccine assay secrecy

    Science.gov (United States)

    Herder, Matthew; Hatchette, Todd F; Halperin, Scott A; Langley, Joanne M

    2015-01-01

    Increasing the transparency of the evidence base behind health interventions such as pharmaceuticals, biologics, and medical devices, has become a major point of critique, conflict, and policy focus in recent years. Yet the lack of publicly available information regarding the immunogenicity assays upon which many important, widely used vaccines are based has received no attention to date. In this paper we draw attention to this critical public health problem by reporting on our efforts to secure vaccine assay information in respect of 10 vaccines through Canada's access to information law. We argue, under Canadian law, that the public health interest in having access to the methods for these laboratory procedures should override claims by vaccine manufacturers and regulators that this information is proprietary; and, we call upon several actors to take steps to ensure greater transparency with respect to vaccine assays, including regulators, private firms, researchers, research institutions, research funders, and journal editors. PMID:25826194

  3. Rover waste assay system

    Energy Technology Data Exchange (ETDEWEB)

    Akers, D.W.; Stoots, C.M.; Kraft, N.C.; Marts, D.J. [Idaho National Engineering Lab., Idaho Falls, ID (United States)

    1997-11-01

    The Rover Waste Assay System (RWAS) is a nondestructive assay system designed for the rapid assay of highly-enriched {sup 235}U contaminated piping, tank sections, and debris from the Rover nuclear rocket fuel processing facility at the Idaho Chemical Processing Plant. A scanning system translates a NaI(Tl) detector/collimator system over the structural components where both relative and calibrated measurements for {sup 137}Cs are made. Uranium-235 concentrations are in operation and is sufficiently automated that most functions are performed by the computer system. These functions include system calibration, problem identification, collimator control, data analysis, and reporting. Calibration of the system was done through a combination of measurements on calibration standards and benchmarked modeling. A description of the system is presented along with the methods and uncertainties associated with the calibration and analysis of the system for components from the Rover facility. 4 refs., 2 figs., 4 tabs.

  4. CTL ELISPOT assay.

    Science.gov (United States)

    Ranieri, Elena; Popescu, Iulia; Gigante, Margherita

    2014-01-01

    Enzyme-linked immune absorbent spot (Elispot) is a quantitative method for measuring relevant parameters of T cell activation. The sensitivity of Elispot allows the detection of low-frequency antigen-specific T cells that secrete cytokines and effector molecules, such as granzyme B and perforin. Cytotoxic T cell (CTL) studies have taken advantage with this high-throughput technology by providing insights into quantity and immune kinetics. Accuracy, sensitivity, reproducibility, and robustness of Elispot resulted in a wide range of applications in research as well as in diagnostic field. Actually, CTL monitoring by Elispot is a gold standard for the evaluation of antigen-specific T cell immunity in clinical trials and vaccine candidates where the ability to detect rare antigen-specific T cells is of relevance for immune diagnostic. The most utilized Elispot assay is the interferon-gamma (IFN-γ) test, a marker for CD8(+) CTL activation, but Elispot can also be used to distinguish different subsets of activated T cells by using other cytokines such as T-helper (Th) 1-type cells (characterized by the production of IFN-γ, IL-2, IL-6, IL-12, IL-21, and TNF-α), Th2 (producing cytokines like IL-4, IL-5, IL-10, and IL-13), and Th17 (IL-17) cells. The reliability of Elispot-generated data, by the evaluation of T cell frequency recognizing individual antigen/peptide, is the core of this method currently applied widely to investigate specific immune responses in cancer, infections, allergies, and autoimmune diseases. The Elispot assay is competing with other methods measuring single-cell cytokine production, e.g., intracellular cytokine by FACS or Miltenyi cytokine secretion assay. Other types of lymphocyte frequency and function assays include limiting dilution assay (LDA), cytotoxic T cell assay (CTL), and tetramer staining. Compared with respect to sensitivity the Elispot assay is outranking other methods to define frequency of antigen-specific lymphocytes. The method

  5. Assays for calcitonin receptors

    Energy Technology Data Exchange (ETDEWEB)

    Teitelbaum, A.P.; Nissenson, R.A.; Arnaud, C.D.

    1985-01-01

    The assays for calcitonin receptors described focus on their use in the study of the well-established target organs for calcitonin, bone and kidney. The radioligand used in virtually all calcitonin binding studies is /sup 125/I-labelled salmon calcitonin. The lack of methionine residues in this peptide permits the use of chloramine-T for the iodination reaction. Binding assays are described for intact bone, skeletal plasma membranes, renal plasma membranes, and primary kidney cell cultures of rats. Studies on calcitonin metabolism in laboratory animals and regulation of calcitonin receptors are reviewed.

  6. New oligosaccharyltransferase assay method.

    Science.gov (United States)

    Kohda, Daisuke; Yamada, Masaki; Igura, Mayumi; Kamishikiryo, Jun; Maenaka, Katsumi

    2007-11-01

    We developed a new in vitro assay for oligosaccharyltransferase (OST), which catalyzes the transfer of preassembled oligosaccharides on lipid carriers onto asparagine residues in polypeptide chains. The asparagine residues reside in the sequon, Asn-X-Thr/Ser, where X can be any amino acid residue except Pro. We demonstrate the potency of our assay using the OST from yeast. In our method, polyacrylamide gel electrophoresis is used to separate the glycopeptide products from the peptide substrates. The substrate peptide is fluorescently labeled and the formation of glycopeptides is analyzed by fluorescence gel imaging. Two in vitro OST assay methods are now widely used, but both the methods depend on previous knowledge of the oligosaccharide moiety: One method uses lectin binding as the separation mechanism and the other method uses biosynthetically or chemoenzymatically synthesized lipid-linked oligosaccharides as donors. N-linked protein glycosylation is found in all three domains of life, but little is known about the N-glycosylation in Archaea. Thus, our new assay, which does not require a priori knowledge of the oligosaccharides, will be useful in such cases. Indeed, we have detected the OST activity in the membrane fraction from a hyperthermophilic archaeon, Pyrococcus furiosus.

  7. Hyaluronic Acid Assays

    DEFF Research Database (Denmark)

    Itenov, Theis S; Kirkby, Nikolai S; Bestle, Morten H

    2015-01-01

    BACKGROUD: Hyaluronic acid (HA) is proposed as a marker of functional liver capacity. The aim of the present study was to compare a new turbidimetric assay for measuring HA with the current standard method. METHODS: HA was measured by a particle-enhanced turbidimetric immunoassay (PETIA) and enzyme...

  8. Instrument for assaying radiation

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, Jody Rustyn; Farfan, Eduardo B.

    2016-03-22

    An instrument for assaying radiation includes a flat panel detector having a first side opposed to a second side. A collimated aperture covers at least a portion of the first side of the flat panel detector. At least one of a display screen or a radiation shield may cover at least a portion of the second side of the flat panel detector.

  9. The interaction between LHBs and homo sapiens pancreatic elastase 2A protein using mammalian two-hybrid%哺乳动物双杂交技术验证HBV表面抗原大蛋白与胰腺弹性蛋白酶2A的相互作用

    Institute of Scientific and Technical Information of China (English)

    刘文祥; 张楠; 汪涛; 侯鹏

    2013-01-01

    目的 验证乙型肝炎病毒(hepatitis B virus,HBV)表面抗原大蛋白(hepatitis B virus large surface protein,LHBs)与人胰腺弹性蛋白酶2A(elastase 2A)蛋白在细胞内是否存在明确的相互作用关系.方法 构建真核表达质粒pACT-Elastase 2A,设立阳性对照组、实验组、阴性对照组和空细胞组,用哺乳动物双杂交技术验证LHBs与人胰腺Elastase 2A蛋白之间的相互作用.结果 实验组与3个阴性对照组之间,均数都存在统计学差异(其P值分别为0.031、0.006和0.007).结论 哺乳动物双杂交技术证实了LHBs与人胰腺Elastase 2A蛋白在Capan2细胞内存在相互作用关系.%Objective To validate the intra-cellular interaction between LHBs and homo sapiens elastase 2A protein.Methods At first,we constructed eukaryotic expression vector pACT-Elastase 2A and confirmed the interaction between LHBs and homo sapiens elastase 2A protein by mammalian two-hybrid experiment.We set up positive control group,experimental group,negative control group and empty cell group.Results We constructed successfully eukaryotic expression vector pACT-Elastase 2A.The results of mammalian two-hybrid experiment showed that there were significant difference in means between experimental group and negative controls(experimental group vs group 1:P =0.031 ;experimental group vs group 2:P =0.006 ;experimental group vs group3:P =0.007).There were significantly statistics difference between experimental group and each negative control group.Conclusions LHBs can directly interact with homo sapiens elastase 2A protein in intra-cell.

  10. The corneal pocket assay.

    Science.gov (United States)

    Ziche, Marina; Morbidelli, Lucia

    2015-01-01

    The cornea in most species is physiologically avascular, and thus this assay allows the measurement of newly formed vessels. The continuous monitoring of neovascular growth in the same animal allows the evaluation of drugs acting as suppressors or stimulators of angiogenesis. Under anesthesia a micropocket is produced in the cornea thickness and the angiogenesis stimulus (tumor tissue, cell suspension, growth factor) is placed into the pocket in order to induce vascular outgrowth from the limbal capillaries. Neovascular development and progression can be modified by the presence of locally released or applied inhibitory factors or by systemic treatments. In this chapter the experimental details of the avascular cornea assay, the technical challenges, and advantages and disadvantages in different species are discussed. Protocols for local drug treatment and tissue sampling for histology and pharmacokinetic profile are reported.

  11. Kinetic Tetrazolium Microtiter Assay

    Science.gov (United States)

    Pierson, Duane L.; Stowe, Raymond; Koenig, David

    1993-01-01

    Kinetic tetrazolium microtiter assay (KTMA) involves use of tetrazolium salts and Triton X-100 (or equivalent), nontoxic, in vitro color developer solubilizing colored metabolite formazan without injuring or killing metabolizing cells. Provides for continuous measurement of metabolism and makes possible to determine rate of action of antimicrobial agent in real time as well as determines effective inhibitory concentrations. Used to monitor growth after addition of stimulatory compounds. Provides for kinetic determination of efficacy of biocide, greatly increasing reliability and precision of results. Also used to determine relative effectiveness of antimicrobial agent as function of time. Capability of generating results on day of test extremely important in treatment of water and waste, disinfection of hospital rooms, and in pharmaceutical, agricultural, and food-processing industries. Assay also used in many aspects of cell biology.

  12. B cell helper assays.

    Science.gov (United States)

    Abrignani, Sergio; Tonti, Elena; Casorati, Giulia; Dellabona, Paolo

    2009-01-01

    Activation, proliferation and differentiation of naïve B lymphocytes into memory B cells and plasma cells requires engagement of the B cell receptor (BCR) coupled to T-cell help (1, 2). T cells deliver help in cognate fashion when they are activated upon recognition of specific MHC-peptide complexes presented by B cells. T cells can also deliver help in a non-cognate or bystander fashion, when they do not find specific MHC-peptide complexes on B cells and are activated by alternative mechanisms. T-cell dependent activation of B cells can be studied in vitro by experimental models called "B cell helper assays" that are based on the co-culture of B cells with activated T cells. These assays allow to decipher the molecular bases for productive T-dependent B cell responses. We show here examples of B cell helper assays in vitro, which can be reproduced with any subset of T lymphocytes that displays the appropriate helper signals.

  13. Confirmation and Disconfirmation in Nurse/Physician Communication.

    Science.gov (United States)

    Garvin, Bonnie J.; Kennedy, Carol W.

    1986-01-01

    In an attempt to better understand the quality of interprofessional relationships, research used a confirmation/disconfirmation framework to analyze communication in nurse-physician dyads. Results indicated that nurses and physicians were primarily confirming in their interaction. (SRT)

  14. Molecular Confirmation of Trypanosoma evansi and Babesia bigemina in Cattle from Lower Egypt

    Directory of Open Access Journals (Sweden)

    Mahmoud M. Elhaig, Abdelfattah Selim, Mohamed M. Mahmoud and Eman K El-Gayar

    2016-11-01

    Full Text Available Trypanosomosis and babesiosis are economically important vector-borne diseases for animal health and productivity in developing countries. In Egypt, molecular epidemiological surveys on such diseases are scarce. In the present study, we examined 475 healthy and 25 clinically diagnosed cattle from three provinces in Lower Egypt, for Trypanosoma (T. and Babesia (B. infections using an ITS1 PCR assay that confirmed Trypanosoma species presence and an 18S rRNA assay that detected B. bigemina. Results confirmed Trypanosoma spp. and B. bigemina presence in 30.4% and 11% individuals, respectively, with eight animals (1.6% being co-infected with both hemoparasites. Subsequent type-specific PCRs revealed that all Trypanosoma PCR positive samples corresponded to T. evansi and that none of the animals harboured T. brucei gambiense or T. brucei rhodesiense. Nucleotide sequencing of the variable surface glycoprotein revealed the T. evansi cattle strain to be most closely related (99% nucleotide sequence identity to strains previously detected in dromedary camels in Egypt, while the 18S rRNA gene phylogeny confirmed the presence of a unique B. bigemina haplotype closely related to strains from Turkey and Brazil. Statistically significant differences in PCR prevalence were noted with respect to gender, clinical status and locality. These results confirm the presence of high numbers of carrier animals and signal the need for expanded surveillance and control efforts.

  15. 42 CFR 32.87 - Confirmation of diagnosis.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Confirmation of diagnosis. 32.87 Section 32.87... Hansen's Disease § 32.87 Confirmation of diagnosis. At the earliest practicable date, after the arrival... the medical staff shall confirm or disprove the diagnosis of Hansen's disease. If the diagnosis...

  16. Linking feeding inhibition with reproductive impairment in Gammarus confirms the ecological relevance of feeding assays in environmental monitoring.

    Science.gov (United States)

    Coulaud, Romain; Geffard, Olivier; Vigneron, Amandine; Quéau, Hervé; François, Adeline; Chaumot, Arnaud

    2015-05-01

    The in situ feeding bioassay in Gammarus fossarum is recognized as a reliable tool for monitoring the toxicity of freshwater contamination. However, whether recorded feeding inhibitions can potentially provoke population-level adverse outcomes remains an open question. In the present study, the authors present an experimental study in G. fossarum, which contributes to the quantitative description of the links between feeding inhibitions and impacts on female reproductive performance. The authors studied the impacts of food deprivation on reproductive endpoints (i.e., fecundity, fertility, molt cycle) during 2 successive molting cycles. Among the main results, the authors found that food deprivation triggered a slowdown of the molting process and a reduction in fertility but no alteration to embryonic development. These reproductive impairments appeared for feeding inhibition values usually recorded in monitoring programs of environmental pollution. Using a population model translating Gammarus life-history, the authors predicted that the observed reproductive alterations predict a strong degradation of population dynamics. The present study underlines the importance of feeding inhibition in population-level risk assessment and discusses how establishing upscaling schemes based on quantitative mechanistic links between impacts at different levels of biological organization can be applied in environmental monitoring to propose an ecotoxicological assessment of water quality, which would be sensitive, specific, and ecologically relevant. © 2015 SETAC.

  17. Growth cone collapse assay.

    Science.gov (United States)

    Cook, Geoffrey M W; Jareonsettasin, Prem; Keynes, Roger J

    2014-01-01

    The growth cone collapse assay has proved invaluable in detecting and purifying axonal repellents. Glycoproteins/proteins present in detergent extracts of biological tissues are incorporated into liposomes, added to growth cones in culture and changes in morphology are then assessed. Alternatively purified or recombinant molecules in aqueous solution may be added directly to the cultures. In both cases after a defined period of time (up to 1 h), the cultures are fixed and then assessed by inverted phase contrast microscopy for the percentage of growth cones showing a collapsed profile with loss of flattened morphology, filopodia, and lamellipodia.

  18. FLUIDICS DEVICE FOR ASSAY

    DEFF Research Database (Denmark)

    2007-01-01

    The present invention relates to a device for use in performing assays on standard laboratory solid supports whereon chemical entities are attached. The invention furthermore relates to the use of such a device and a kit comprising such a device. The device according to the present invention is a......, when operatively connected, one or more chambers (21) comprising the chemical entities (41), the inlet(s) (5) and outlet(s) (6) and chambers (21) being in fluid connection. The device further comprise means for providing differing chemical conditions in each chamber (21)....

  19. Radon assay for SNO+

    Energy Technology Data Exchange (ETDEWEB)

    Rumleskie, Janet [Laurentian University, Greater Sudbury, Ontario (Canada)

    2015-12-31

    The SNO+ experiment will study neutrinos while located 6,800 feet below the surface of the earth at SNOLAB. Though shielded from surface backgrounds, emanation of radon radioisotopes from the surrounding rock leads to back-grounds. The characteristic decay of radon and its daughters allows for an alpha detection technique to count the amount of Rn-222 atoms collected. Traps can collect Rn-222 from various positions and materials, including an assay skid that will collect Rn-222 from the organic liquid scintillator used to detect interactions within SNO+.

  20. Gene expression and yeast two-hybrid studies of transcription factors mediating drought stress response in root tissues of chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Abirami eRamalingam

    2015-12-01

    Full Text Available Drought stress has been one of the serious constraints affecting chickpea productivity to a great extent. Genomic assisted breeding in chickpea has been effective in providing a yield advantage of up to 24 %, thus having a potential to accelerate breeding precisely and efficiently. In order to do so, understanding the molecular mechanisms for drought tolerance and identification of candidate genes are crucial. Transcription factors (TFs have important roles in the regulation of plant stress related genes. In this context, quantitative real time-PCR (qRT-PCR was used to study the differential gene expression of selected TFs, identified from large-scale gene expression analysis, in contrasting drought responsive genotypes. Root tissues of ICC 4958 (tolerant, ICC 1882 (sensitive, JG 11 (elite and JG 11+ (introgression line were used for the study. Subsequently, a candidate single repeat MYB gene (1R-MYB that was remarkably induced in the drought tolerant genotypes under drought stress was cloned and subjected to Y2H analysis by screening a root cDNA library. The protein-protein interaction study identified three interacting peptides, a galactinol-sucrose galactosyltransferase 2, a CBL (Calcineurin B-like-interacting serine/threonine-protein kinase 25 and an ABA responsive 17-like, which were confirmed by the co-transformation of candidate plasmids in yeast. These findings provide preliminary insights into the ability of 1R-MYB TF to co-regulate drought tolerance mechanism in chickpea roots.

  1. Assessment of plaque assay methods for alphaviruses.

    Science.gov (United States)

    Juarez, Diana; Long, Kanya C; Aguilar, Patricia; Kochel, Tadeusz J; Halsey, Eric S

    2013-01-01

    Viruses from the Alphavirus genus are responsible for numerous arboviral diseases impacting human health throughout the world. Confirmation of acute alphavirus infection is based on viral isolation, identification of viral RNA, or a fourfold or greater increase in antibody titers between acute and convalescent samples. In convalescence, the specificity of antibodies to an alphavirus may be confirmed by plaque reduction neutralization test. To identify the best method for alphavirus and neutralizing antibody recognition, the standard solid method using a cell monolayer overlay with 0.4% agarose and the semisolid method using a cell suspension overlay with 0.6% carboxymethyl cellulose (CMC) overlay were evaluated. Mayaro virus, Una virus, Venezuelan equine encephalitis virus (VEEV), and Western equine encephalitis virus (WEEV) were selected to be tested by both methods. The results indicate that the solid method showed consistently greater sensitivity than the semisolid method. Also, a "semisolid-variant method" using a 0.6% CMC overlay on a cell monolayer was assayed for virus titration. This method provided the same sensitivity as the solid method for VEEV and also had greater sensitivity for WEEV titration. Modifications in plaque assay conditions affect significantly results and therefore evaluation of the performance of each new assay is needed.

  2. RAS - Screens & Assays - Drug Discovery

    Science.gov (United States)

    The RAS Drug Discovery group aims to develop assays that will reveal aspects of RAS biology upon which cancer cells depend. Successful assay formats are made available for high-throughput screening programs to yield potentially effective drug compounds.

  3. Development of the performance confirmation program at YUCCA mountain, nevada

    Science.gov (United States)

    LeCain, G.D.; Barr, D.; Weaver, D.; Snell, R.; Goodin, S.W.; Hansen, F.D.

    2006-01-01

    The Yucca Mountain Performance Confirmation program consists of tests, monitoring activities, experiments, and analyses to evaluate the adequacy of assumptions, data, and analyses that form the basis of the conceptual and numerical models of flow and transport associated with a proposed radioactive waste repository at Yucca Mountain, Nevada. The Performance Confirmation program uses an eight-stage risk-informed, performance-based approach. Selection of the Performance Confirmation activities for inclusion in the Performance Confirmation program was done using a risk-informed performance-based decision analysis. The result of this analysis was a Performance Confirmation base portfolio that consists of 20 activities. The 20 Performance Confirmation activities include geologic, hydrologie, and construction/engineering testing. Some of the activities began during site characterization, and others will begin during construction, or post emplacement, and continue until repository closure.

  4. Development of the Performance Confirmation Program at Yucca Mountain, Nevada

    Energy Technology Data Exchange (ETDEWEB)

    G.D. LeCain; R. Snell; D. Barr; S.W. Goodin; D. Weaver; F.D. Hansen

    2006-03-17

    The Yucca Mountain Performance Confirmation program consists of tests, monitoring activities, experiments, and analyses to evaluate the adequacy of assumptions, data, and analyses that form the basis of the conceptual and numerical models of flow and transport associated with a proposed radioactive waste repository at Yucca Mountain, Nevada. The Performance Confirmation program uses an eight-stage risk-informed, performance-based approach. Selection of the Performance Confirmation activities (a parameter and a test method) for inclusion in the Performance Confirmation program was done using a risk-informed performance-based decision analysis. The result of this analysis and review was a Performance Confirmation base portfolio that consists of 20 activities. The 20 Performance Confirmation activities include geologic, hydrologic, and construction/engineering testing. Several of the activities were initiated during site characterization and are ongoing. Others activities will commence during construction and/or post emplacement and will continue until repository closure.

  5. Cry1Ab protein quantification in leaves, stems and grains, and effectiveness to control Spodoptera frugiperda and Helicoverpa zea on two hybrids of genetically modified corn

    Directory of Open Access Journals (Sweden)

    Geraldo Balieiro Neto

    2013-01-01

    Full Text Available A study was carried out to evaluate the infestation and associated damages to the presence of the Spodoptera frugiperda and Helicoverpa zea caterpillars, in two genetically modified (GM corn, Dekalb DKB390 and Agroceres AG8088, expressing the cry1Ab protein. For this objective, an split-splot design with two factors (hybrid x gene was carried out. Negative controls were made with the same corn hybrids without the gene cry1Ab (NoGM. The concentration of the protein Cry1Ab was determined by the ELISA (enzyme linked immuno sorbent assay technique in previously dehydrated stems, leaves and grains of GM corns. Caterpillars sampling of S. frugiperda and associated damage survey were accomplished at 15, 22, 29, 36 and 42 days after the sowing, according to a damage scale with 5 levels (0- pest absence to 5- dead plant. Countings of H. zea caterpillars and associated damage were assessed at 57, 71, 78 and 85 days after the sowing, according to a damage scale with 4 levels (0-pest absence curse to 4-gallery in the corn cob minor than 3cm. Sampled caterpillars were divided in two groups, smaller or equal to 15mm and bigger than 15mm. No insecticide application was accomplished in the GM blocks while NoGM blocks were sprayed with deltametrina (2,8%, 42 days after the sowing. The infestation level and associated damage due to S. frugiperda presence was significantly smaller (p < 0,05 in the GM corns in comparison to NoGM corns. Nevertheless, the number and associated damage of S. frugiperda caterpillars, smaller than 15 mm, were superior in the GM DKB390 corn when compared to the GM AG8088 corn. Differences were not observed in the S. frugiperda infestation and associated damage between GM corns and between NoGM corns. On average, the concentration of Cry1Ab protein was significantly superior in leaves and stems in comparison to the grain and, usually, superior in the GM AG8088 corn comparatively to GM DKB390 corn. No differences were found on level damages

  6. Bacterial assays for recombinagens.

    Science.gov (United States)

    Hoffmann, G R

    1992-12-01

    Two principal strategies have been used for studying recombinagenic effects of chemicals and radiation in bacteria: (1) measurement of homologous recombination involving defined alleles in a partially diploid strain, and (2) measurement of the formation and loss of genetic duplications in the bacterial chromosome. In the former category, most methods involve one allele in the bacterial chromosome and another in a plasmid, but it is also possible to detect recombination between two chromosomal alleles or between two extrachromosomal alleles. This review summarizes methods that use each of these approaches for detecting recombination and tabulates data on agents that have been found to be recombinagenic in bacteria. The assays are discussed with respect to their effectiveness in testing for recombinagens and their potential for elucidating mechanisms underlying recombinagenic effects.

  7. The confirmation of the interaction between HBV large protein and homo sapiens pancreatic CDK5RAP3 protein using mammalian two-hybrid experiment%哺乳动物双杂交技术验证HBV表面抗原大蛋白与人胰腺CDK5RAP3蛋白间的相互作用

    Institute of Scientific and Technical Information of China (English)

    巩雪俐; 张丽; 张建龙; 张锦前

    2010-01-01

    目的 验证HBV表面抗原大蛋白(LHBs)与人胰腺CDK5RAP3蛋白在细胞内是否存在相互作用关系,为进一步研究HBV影响糖、脂代谢机制奠定研究基础.方法 构建真核表达质粒pACT-CDK5RAP3,哺乳动物双杂交技术验证LHBs与人胰腺CDK5RAP3蛋白之间的相互作用.结果 实验组和各阴性对照组差别均有统计学意义(P<0.05).结论 LHBs与人胰腺CDK5RAP3蛋白在细胞内存在相互作用关系,且单独转染后没有自身激活作用.

  8. Experimental confirmation of a new reversed butterfly-shaped attractor

    Institute of Scientific and Technical Information of China (English)

    Liu Ling; Su Yan-Chen; Liu Chong-Xin

    2007-01-01

    This paper reports a new reverse butterfly-shaped chaotic attractor and its experimental confirmation. Some basic dynamical properties, and chaotic behaviours of this new reverse butterfly attractor are studied. Simulation results support brief theoretical derivations. Furthermore, the system is experimentally confirmed by a simple electronic circuit.

  9. 17 CFR 1.33 - Monthly and confirmation statements.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 1 2010-04-01 2010-04-01 false Monthly and confirmation statements. 1.33 Section 1.33 Commodity and Securities Exchanges COMMODITY FUTURES TRADING COMMISSION GENERAL REGULATIONS UNDER THE COMMODITY EXCHANGE ACT Recordkeeping § 1.33 Monthly and confirmation statements. (a...

  10. Identification of calcium/calmodulin-binding receptor-like kinase GsCBRLK-interactive proteins using yeast two-hybrid system%酵母双杂交筛选与GsCBRLK相互作用的蛋白质

    Institute of Scientific and Technical Information of China (English)

    杨姗姗; 孙晓丽; 于洋; 才华; 纪巍; 柏锡; 朱延明

    2013-01-01

    GsCBRLK(calcium/calmodulin-binding receptor-like kinase from Glycine soja)在ABA及盐胁迫诱导的钙离子信号通路中起到关键的调节作用.为深入研究GsCBRLK蛋白的作用机制,文章采用膜酵母双杂交系统,以GsCBRLK为诱饵蛋白,筛选与其相互作用的蛋白质.通过构建野生大豆盐胁迫条件下的cDNA文库、膜酵母双杂交系统筛选、复筛、回转验证、生物信息学分析以及酵母体内互作验证等手段,最终获得2个(SNARE和14-3-3蛋白)与GsCBRLK诱饵蛋白相互作用的蛋白质.%GsCBRLK (calcium/calmodulin-binding receptor-like kinase from Glycine soja) links ABA (abscisic acid)-and salt-induced calcium/calmodulin signal in plant cells. In order to study the molecular mechanismes of GsCBLRK, the salt-treated Glycine soja cDNA library was screened with pB73-STE-CBRLK as bait plasmid using yeast two hybrid system. Two positive clones (SNARE and 14-3-3 protein) were identified by constructing cDNA library of wild soybean under salt treatment, membrane system yeast two hybrid screening, multiple screen, rotary validation, bioinformatic analysis and interaction identification in yeast.

  11. Herbicide resistance screening assay.

    Science.gov (United States)

    Peterson, Joan M

    2009-01-01

    Herbicide resistance screening is a method that can be used not only to determine presence of the enzyme, phosphinothricin acetyltransferase, encoded by either the Bar or the Pat gene in transgenic maize, but also to assess the inheritance ratio of those genes in a segregating population. Herbicide screening can also be used to study linkage of a transgene of interest that was cotransformed with the herbicide resistance marker gene. By combining the herbicide screen assay with a PCR-based screen of leaf tissue DNA for the presence of both the Bar or the Pat gene marker and a cotransformed transgene of interest from the same seedling tissue and maintaining that seedling identity, the researcher can identify linkage or the possible breakdown in linkage of the marker gene and the transgene of interest. Further, the occurrence of "DNA silencing" can be evaluated if an individual seedling that was susceptible to the applied herbicide nonetheless gave PCR data that indicated presence of the gene responsible for herbicide resistance. Similarly, "DNA silencing" of the gene of interest may be investigated if the seeds can be screened and scored for that phenotypic trait in a nondestructive manner prior to planting.

  12. Primary ovary choriocarcinoma: individual DNA polymorphic analysis as a strategy to confirm diagnosis and treatment

    Directory of Open Access Journals (Sweden)

    Fernando Nalesso

    2013-04-01

    Full Text Available Primary choriocarcinoma of the ovary is rare. Furthermore, this tumor can arise from gestational tissue or pure germ cells of the ovary, with the latter resulting in non-gestational choriocarcinoma. While the clinical characteristics and histology of both tumor types are identical, differentiation of these tumors is necessary for effective treatment. One strategy for the differentiation of these tumors types is to assay for the presence of paternal DNA. Accordingly, in the present case, a patient with primary choriocarcinoma of the ovary with a non-gestational origin was confirmed by DNA analysis. The patient subsequently exhibited an excellent response to chemotherapy, and following surgery, achieved complete remission. A pathological analysis of surgical specimens further confirmed the absence of tumor.

  13. Disagreement between Human Papillomavirus Assays

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Preisler, Sarah; Ejegod, Ditte Møller

    2014-01-01

    assays. Positive agreement between the assays was measured as the conditional probability that the results of all compared assays were positive given that at least one assay returned a positive result. Of all 5,064 samples, 1,679 (33.2%) tested positive on at least one of the assays. Among these, 41......We aimed to determine the disagreement in primary cervical screening between four human papillomavirus assays: Hybrid Capture 2, cobas, CLART, and APTIMA. Material from 5,064 SurePath samples of women participating in routine cervical screening in Copenhagen, Denmark, was tested with the four......% tested positive on all four. Agreement was lower in women aged ≥ 30 years (30%, vs. 49% at samples (29%, vs. 38% in follow-up samples), and in women with concurrent normal cytology (22%, vs. 68% with abnormal cytology). Among primary screening samples from women aged 30...

  14. CERN confirms goal of 2007 start-up for LHC

    CERN Multimedia

    2005-01-01

    Speaking at the 131st session of CERN Council on 17 December 2004, the Director-General, Robert Aymar, confirmed that the top priority is to maintain the goal of starting up the Large Hadron Collider (LHC) in 2007.

  15. Confirming psychogenic nonepileptic seizures with video-EEG: sex matters.

    Science.gov (United States)

    Noe, Katherine H; Grade, Madeline; Stonnington, Cynthia M; Driver-Dunckley, Erika; Locke, Dona E C

    2012-03-01

    The influence of gender on psychogenic nonepileptic seizures (PNES) diagnosis was examined retrospectively in 439 subjects undergoing video-EEG (vEEG) for spell classification, of whom 142 women and 42 men had confirmed PNES. The epileptologist's predicted diagnosis was correct in 72% overall. Confirmed epilepsy was correctly predicted in 94% men and 88% women. In contrast, confirmed PNES was accurately predicted in 86% women versus 61% men (p=0.003). Sex-based differences in likelihood of an indeterminate admission were not observed for predicted epilepsy or physiologic events, but were for predicted PNES (39% men, 12% women, p=0.0002). More frequent failure to record spells in men than women with predicted PNES was not explained by spell frequency, duration of monitoring, age, medication use, or personality profile. PNES are not only less common in men, but also more challenging to recognize in the clinic, and even when suspected more difficult to confirm with vEEG.

  16. NIH study confirms risk factors for male breast cancer

    Science.gov (United States)

    Pooled data from studies of about 2,400 men with breast cancer and 52,000 men without breast cancer confirmed that risk factors for male breast cancer include obesity, a rare genetic condition called Klinefelter syndrome, and gynecomastia.

  17. Theory-led confirmation bias and experimental persona

    Science.gov (United States)

    Allen, Michael

    2011-04-01

    Questionnaire and interview findings from a survey of three Year 8 (ages 12-13 years) science practical lessons (n = 52) demonstrate how pupils' data collection and inference making were sometimes biased by desires to confirm a personal theory. A variety of behaviours are described where learners knowingly rejected anomalies, manipulated apparatus, invented results or carried out other improper operations to either collect data which they believed were scientifically correct, or achieve social conformity. It is proposed that confirmation bias was a consequence of the degree to which individuals were laden by theory, and driven by this, experimenters assumed one of three different personas: becoming right answer confirmers; good scientists; or indifferent spectators. These personas have parallels with historical instances of scientific behaviour. Implications of a continued teacher-tolerance of pupil confirmation bias include the promotion of unscientific experimenting, and the persistence of unchallenged science misconceptions. Solutions are offered in the way of practical strategies that might reduce experimenters' theory-ladeness.

  18. Consumer satisfaction and confirmation of habits of comprehension

    DEFF Research Database (Denmark)

    Sørensen, Bent; Andersen, Christian; Andersen, Morten Purup

    2014-01-01

    The purpose of this article is twofold: First, within a Peircean framework it shall be demonstrated how there is a relation between the compositional structure of certain types of print advertisements and their bringing about inductive comprehension, and how the consumer can be understood...... as a bundle of habits. It is the assumption that advertising that supports an inductive effect particularly appeals to the cognitive tendency of habit formation in the consumer. Second, it is asked whether advertisements that predominantly invite inductive processes of comprehension also influence...... the formation of consumer satisfaction; the perspective is that of the confirmation paradigm within advertisement research. Inductive advertisements support cognitive habit formation through confirmation, and the confirmation paradigm explains exactly consumer satisfaction with reference to confirmation. Hence...

  19. Imaging Study Confirms Brain Differences in People with ADHD

    Science.gov (United States)

    ... Imaging Study Confirms Brain Differences in People With ADHD Attention-deficit/hyperactivity should be considered a brain ... Researchers who pinpointed brain differences in people with attention-deficit/hyperactivity disorder (ADHD) say their findings show the condition should ...

  20. Screening of novel proteins that interact with FLA8-C terminal from Dunaliella salina using yeast two-hybrid system%与杜氏盐藻驱动蛋白Ⅱ动力亚基C端相互作用的新蛋白的酵母双杂交筛选

    Institute of Scientific and Technical Information of China (English)

    李靓; 崔柳青; 王瑞莉; 毛丽红; 韩康; 柴丹丹; 薛乐勋

    2013-01-01

    目的:用酵母双杂交的方法筛选与杜氏盐藻驱动蛋白Ⅱ动力亚基(FLA8)C端相互作用的蛋白.方法:设计特异性引物(上下游分别引入EcoRⅠ和BamHⅠ酶切位点),扩增FLA8 C端(433个氨基酸)cDNA,与穿梭载体pGBKT7连接以构建诱饵表达载体,然后转化酵母菌株Y187和AH109,Western blot法检测诱饵蛋白在转化酵母菌株内的表达.通过自激活实验和毒性实验检测诱饵表达载体是否适合利用酵母双杂交的方法筛选相互作用蛋白.转化诱饵质粒的酵母菌株Y187与AH109(文库菌)杂交,待三叶形合子形成后用营养缺陷型培养基和α-半乳糖苷酶活性实验筛选阳性克隆,并对阳性克隆进行测序.结果:成功构建了pGBKT7-FLA8-C双杂交诱饵载体;经检测该载体的表达产物对Y187和AH109均无自激活和毒性作用,可用于酵母双杂交实验;杂交后筛选得到2个阳性克隆,测序结果显示为鞭毛结合蛋白107(FAP107)和含蛋白结合结构域的预测蛋白.结论:成功筛选得到了与杜氏盐藻驱动蛋白Ⅱ动力亚基C端相互作用的蛋白,分别为FAP107和预测蛋白.%Aim : To isolate proteins that interact with C-Lerminal region oi FLA8 which is the motor subunit of kinesin II from Dunaliella salina. Methods:The coding sequences of FLA8-C( 433 aa )was cloned into the pGBKT7 as bait and transformed into Y187 and AH109 yeast strains,and then the transcriptional activation and toxicity were tested. Yeast two-hybrid method was performed to screen the Dunaliella salina cDNA expression library. The positive clones were screened by auxotroph culture and assayed for α-galactosidase activity according the manufacturer s instructions. The cDNA fragments of prey proteins from positive colonies were detected by colony PCR. Results :The results showed that the FLA8-C is suitable for two-hybrid library screening. Sequence analysis on positive colonies showed that they were flagellar associated protein 107( FAP107 )and

  1. Polymerase chain reaction assay for avian polyomavirus.

    Science.gov (United States)

    Phalen, D N; Wilson, V G; Graham, D L

    1991-05-01

    A polymerase chain reaction assay was developed for detection of budgerigar fledgling disease virus (BFDV). The assay used a single set of primers complementary to sequences located in the putative coding region for the BFDV VP1 gene. The observed amplification product had the expected size of 550 bp and was confirmed to derive from BFDV DNA by its restriction digestion pattern. This assay was specific for BFDV and highly sensitive, being able to detect as few as 20 copies of the virus. By using the polymerase chain reaction, BFDV was detected in adult, nestling, and embryo budgerigar (Melopsitticus undulatus) tissue DNAs and in sera from adult and nestling budgerigars. These results suggest the possibility of persistent infections in adult birds and lend further support to previously described evidence of possible in ovo transmission. BFDV was also detected in chicken embryo fibroblast cell cultures and chicken eggs inoculated with the virus. A 550-bp product with identical restriction enzyme sites was amplified from a suspected polyomavirus isolated from a peach-faced lovebird (Agapornis pesonata) and from tissue DNA from a Hahn's macaw (Ara nobilis) and a sun conure (Aratinga solstitialis) with histological lesions suggestive of polyomavirus infection. These fragments also hybridized with a BFDV-derived probe, proving that they were derived from a polyomavirus very similar, if not identical, to BFDV.

  2. Diagnostic Certified Assay: Neuromuscular and Cardiac Assessments

    Directory of Open Access Journals (Sweden)

    Rea Valaperta

    2013-01-01

    Full Text Available The expansion of the specific trinucleotide sequence, [CTG], is the molecular pathological mechanism responsible for the clinical manifestations of DM1. Many studies have described different molecular genetic techniques to detect DM1, but as yet there is no data on the analytical performances of techniques used so far in this disease. We therefore developed and validated a molecular method, “Myotonic Dystrophy SB kit,” to better characterize our DM1 population. 113 patients were examined: 20 DM1-positive, 11 DM1/DM2-negative, and13 DM1-negative/DM2-positive, who had a previous molecular diagnosis, while 69 were new cases. This assay correctly identified 113/113 patients, and all were confirmed by different homemade assays. Comparative analysis revealed that the sensitivity and the specificity of the new kit were very high (>99%. Same results were obtained using several extraction procedures and different concentrations of DNA. The distribution of pathologic alleles showed a prevalence of the “classical” form, while of the 96 nonexpanded alleles 19 different allelic types were observed. Cardiac and neuromuscular parameters were used to clinically characterize our patients and support the new genetic analysis. Our findings suggest that this assay appears to be a very robust and reliable molecular test, showing high reproducibility and giving an unambiguous interpretation of results.

  3. Preliminary Analysis of Remote Monitoring & Robotic Concepts for Performance Confirmation

    Energy Technology Data Exchange (ETDEWEB)

    D.A. McAffee

    1997-02-18

    As defined in 10 CFR Part 60.2, Performance Confirmation is the ''program of tests, experiments and analyses which is conducted to evaluate the accuracy and adequacy of the information used to determine with reasonable assurance that the performance objectives for the period after permanent closure will be met''. The overall Performance Confirmation program begins during site characterization and continues up to repository closure. The main purpose of this document is to develop, explore and analyze initial concepts for using remotely operated and robotic systems in gathering repository performance information during Performance Confirmation. This analysis focuses primarily on possible Performance Confirmation related applications within the emplacement drifts after waste packages have been emplaced (post-emplacement) and before permanent closure of the repository (preclosure). This will be a period of time lasting approximately 100 years and basically coincides with the Caretaker phase of the project. This analysis also examines, to a lesser extent, some applications related to Caretaker operations. A previous report examined remote handling and robotic technologies that could be employed during the waste package emplacement phase of the project (Reference 5.1). This analysis is being prepared to provide an early investigation of possible design concepts and technical challenges associated with developing remote systems for monitoring and inspecting activities during Performance Confirmation. The writing of this analysis preceded formal development of Performance Confirmation functional requirements and program plans and therefore examines, in part, the fundamental Performance Confirmation monitoring needs and operating conditions. The scope and primary objectives of this analysis are to: (1) Describe the operating environment and conditions expected in the emplacement drifts during the preclosure period. (Presented in Section 7.2). (2

  4. Reverse phase liquid chromatographic determination and confirmation of aflatoxin M1 in cheese.

    Science.gov (United States)

    Hisada, K; Terada, H; Yamamoto, K; Tsubouchi, H; Sakabe, Y

    1984-01-01

    A systematic method is proposed for determination and confirmation of aflatoxin M1 in cheese by liquid chromatography (LC). A sample of cheese is extracted with chloroform, cleaned up on 2 silica gel columns followed by a Sep-Pak C18 cartridge, and chromatographed on a 5 microns octadecyl silica column with fluorometric detection. The sample extract or standard is treated with n-hexane-trifluoroacetic acid (TFA) (4 + 1) for 30 min at 40 degrees C. Analysis by LC with TFA-treatment of the extract provides quantitative data. Multiple assays of 5 samples of Gouda cheese spiked with aflatoxin M1 at levels of 0.5, 0.1, and 0.05 ng/g showed average recoveries of 93.2, 91.6, and 92.4%, with coefficients of variation of 2.63, 3.97, and 4.52%, respectively. Assay of 5 naturally contaminated cheeses resulted in 0.051-0.448 ng/g of aflatoxin M1. Limit of quantitation is about 0.01 ng/g. The identity of aflatoxin M1 is confirmed by treating aflatoxin M1 or the M2a derivative with TFA-methanol (or ethanol) (3 + 1). The TFA-methanol reaction products of M2a could be detected quantitatively.

  5. Colorimetric Assay Of Naproxen Tablets by Derivatization Using 4 ...

    African Journals Online (AJOL)

    (BP) UV spectrophotometric method but combined the advantages of speed and ... The assay methods employed aromatic ring ... 6051, Spectronic Analytical Instruments, ... A 5 µg/ml standard test solution of naproxen and ... Validation of method: Calibration lines using .... temperature (100 oC) in addition to confirming.

  6. Construction and evaluation of yeast two-hybrid cDNA library of Diaphorina citri (Hemiptera: Psyllidae)%柑橘木虱酵母双杂交cDNA文库的构建及评价

    Institute of Scientific and Technical Information of China (English)

    马晓芳; 陈国庆; 张学潮; 徐海君

    2013-01-01

    In order to study the interacting proteins between the Asian citrus psyllid ( Diaphorina citri) and Candidatus Liberibacter asiaticus ( CLas) which is the pathogenic bacterium causing Huanglongbing, yeast two-hybrid cDNA library of D. citri was constructed using the Switching Mechanism at 5' End of the RNA Transcript (SMART) technique. The total RNA was isolated from the citrus psyllid adults bred in the laboratory and subjected to reverse transcription, and the double-strand cDNAs ( ds cDNAs) were synthesized. The ds cDNAs were ligated with homologous adapter and purified by the chromatography column. By using homologous recombination reaction, the ds cDNAs were transformed into the Y187 competent cell with the library plasmid pGADT7-Rec to construct yeast two-hybrid cDNA library. Detection of the library indicated that it contained more than 106 independent clones, the titer of the amplified library was 2. 23 × 10 cfu/mL, and the average size of inserts was above 750 bp in the cDNA library. These results demonstrate that the library meets the requirements of the standard cDNA library. Moreover, two membrane proteins, ORF420 and ORF3420, from ( CLas) were used as bait proteins to screen the interacting proteins in the library, but no positive clone was screened in the tests. The yeast two-hybrid cDNA library of D. citri will be useful for the research on the interaction between insect vectors and C. Liberibacter asiaticus in the future.%为了探索研究柑橘木虱Diaphorina citri与柑橘黄龙病(Huanglongbing,HLB)病原菌的相互作用蛋白,本研究运用RNA转录中5 '末端转换机制(Switching Mechanism at 5'End of the RNA Transcript,SMART)技术构建了柑橘木虱的酵母双杂交cDNA文库.以实验室饲养的柑橘木虱为材料,提取总RNA,经反转录后合成ds cDNA,两端添加同源重组序列,并用层析柱纯化;ds cDNA与文库质粒pGADT7-Rec在酵母Y187感受态细胞内发生同源重组,柑橘木虱cDNA重组到文库质粒

  7. Screening for the Interaction Proteins of SOC1 from Phyllostachys violascens Using Yeast Two-Hybrid System%利用酵母双杂交系统筛选雷竹 SOC1相互作用蛋白

    Institute of Scientific and Technical Information of China (English)

    潘现飞; 施泉; 林新春; 徐英武; 曹友志

    2016-01-01

    This work aims to study the target proteins of suppressor of overexpression of constans1(SOC1)in flowering way of Phyllostachys violaceus and to explore the action mechanism of SOC1. The pGBKT7-PvSOC1 vector was constructed as the bait protein,then the cDNA library of P. violascens flowering was established using SMART technology,and the interaction proteins with SOC1 were screened by yeast two-hybrid system as well as analyzed and identified. The results showed that the cDNA library for yeast two-hybrid was constructed successfully,the conversion rate of the library was about 3.0×106 converters per μg pGADT7-Rec,and the capacity of the library was up to 7.5×106 cfu/mL and the insert fragments were distributed from 0.25 kb to 2 kb. The protein interacted with the bait protein PvSOC1 was screened through the yeast two-hybrid technology. The screened target protein was identified as a protein kinase containing plentiful leucine which amino acid sequence was very conservative in different species,and had the highest affinity with rice.%在雷竹(Phyllostachys violascens)中找到 SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1(SOC1)在开花途径中的作用靶标,进一步探索 SOC1的作用机制。构建 pGBKT7-PvSOC1诱饵表达载体,通过 SMART 技术构建开花时期的雷竹 cDNA文库,酵母双杂交筛选与 SOC1互作的蛋白,并对其进行分析鉴定。结果显示,成功构建了可用于酵母双杂交的 cDNA 文库,文库的转化率为每微克 pGADT7-Rec 3.0×106转化子,文库滴度为7.5×106 cfu/mL,插入片段主要在250-2000 bp 之间。通过酵母双杂交实验得到与诱饵蛋白 PvSOC1相互作用的蛋白,筛选到的靶标蛋白经鉴定是一个富含亮氨酸的蛋白激酶,特征氨基酸序列在不同物种中非常保守,与水稻中的同源蛋白亲缘性最高。

  8. Practical assay issues with the PERT/PBRT assay: a highly sensitive reverse transcriptase assay.

    Science.gov (United States)

    Chang, A; Dusing, S

    2006-01-01

    Product safety testing for retroviruses can be achieved by a panel of screening assays, including electron microscopy, viral gene specific PCRs, virus propagation, and detection of reverse transciptase activity. The application of PCR-based reverse transcriptase assays (PERT) that are approximately a million-fold more sensitive than conventional nucleotide incorporation assays in the testing of biologicals is described. Use of PERT assays can be applied to three areas: (i) screening for adventitious retrovirus contamination; (ii) detecting and quantifying endogenous viral particle load and (iii) monitoring levels of infectious retrovirus generation in cell lines that contain endogenous retroviruses.

  9. 玉米弯孢叶斑病菌酵母双杂交cDNA文库的构建及评价%Construction and characterization of yeast two hybrid cDNA library of Curvularia lunata

    Institute of Scientific and Technical Information of China (English)

    荆晶; 刘铜; 陈捷

    2012-01-01

    由新月弯孢[Curvularia lunata (Wakker)Boed]引起的玉米弯孢叶斑病是我国玉米生产区的一种重要性叶斑病,曾在20世纪90年代给我国玉米生产造成较大损失.目前对该病原菌致病类型鉴定与致病相关基因、病害发生规律、综合防治等方面均有较好的研究基础[1],并且在前期的研究中发现该病菌调控毒素形成的相关基因与色素合成相关基因在表达上存在某种关联性[2],由于这2个基因均为致病相关基因,因此研究两基因表达的蛋白的关联性对于全面揭示病菌致病机理和调控网络具有重要意义.%BD SMART technique and LD-PCR were applied to synthesize double strand cDNA(ds cDNA). The ds cDNA and pGADT7-Rec were transfered into competent yeast cell to construct yeast two-hybrid cDNA library of Curvularia lunata by homologous recombination method. The results showed that library capacitance was 2.46×105 and transformation rate was 2.13×105/μg pGADT7-Rec. The plaque titer of the library was 2.5×108 pfu/mL and the recombination frequency was 88. 24%. The length of inserted cDNA fragment was ranged from 0.4 kb to 3 kb in average. This is the first time to use BD SMART technique to construct yeast two-hybrid cDNA library of C. lunata by homologous recombination.

  10. From Antenna to Assay

    Science.gov (United States)

    Moore, Evan G.; Samuel, Amanda P. S.; Raymond, Kenneth N.

    2009-01-01

    Conspectus Ligand-sensitized, luminescent lanthanide(III) complexes are of considerable importance because their unique photophysical properties (microsecond to millisecond lifetimes, characteristic and narrow emission bands, and large Stokes shifts) make them well suited as labels in fluorescence-based bioassays. The long-lived emission of lanthanide(III) cations can be temporally resolved from scattered light and background fluorescence to vastly enhance measurement sensitivity. One challenge in this field is the design of sensitizing ligands that provide highly emissive complexes with sufficient stability and aqueous solubility for practical applications. In this Account, we give an overview of some of the general properties of the trivalent lanthanides and follow with a summary of advances made in our laboratory in the development of highly luminescent Tb(III) and Eu(III) complexes for applications in biotechnology. A focus of our research has been the optimization of these compounds as potential commercial agents for use in Homogeneous Time-Resolved Fluorescence (HTRF) technology. Our approach involves developing high-stability octadentate Tb(III) and Eu(III) complexes that rely on all-oxygen donor atoms and using multi-chromophore chelates to increase molar absorptivity; earlier examples utilized a single pendant chromophore (that is, a single “antenna”). Ligands based on 2-hydroxyisophthalamide (IAM) provide exceptionally emissive Tb(III) complexes with quantum yield values up to ∼60% that are stable at the nanomolar concentrations required for commercial assays. Through synthetic modification of the IAM chromophore and time-dependent density functional theory (TD-DFT) calculations, we have developed a method to predict absorption and emission properties of these chromophores as a tool to guide ligand design. Additionally, we have investigated chiral IAM ligands that yield Tb(III) complexes possessing both high quantum yield values and strong

  11. Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease-Towards a Point-of-Care Test.

    Directory of Open Access Journals (Sweden)

    Marcus Beissner

    2015-11-01

    Full Text Available As the major burden of Buruli ulcer disease (BUD occurs in remote rural areas, development of point-of-care (POC tests is considered a research priority to bring diagnostic services closer to the patients. Loop-mediated isothermal amplification (LAMP, a simple, robust and cost-effective technology, has been selected as a promising POC test candidate. Three BUD-specific LAMP assays are available to date, but various technical challenges still hamper decentralized application. To overcome the requirement of cold-chains for transport and storage of reagents, the aim of this study was to establish a dry-reagent-based LAMP assay (DRB-LAMP employing lyophilized reagents.Following the design of an IS2404 based conventional LAMP (cLAMP assay suitable to apply lyophilized reagents, a lyophylization protocol for the DRB-LAMP format was developed. Clinical performance of cLAMP was validated through testing of 140 clinical samples from 91 suspected BUD cases by routine assays, i.e. IS2404 dry-reagent-based (DRB PCR, conventional IS2404 PCR (cPCR, IS2404 qPCR, compared to cLAMP. Whereas qPCR rendered an additional 10% of confirmed cases and samples respectively, case confirmation and positivity rates of DRB-PCR or cPCR (64.84% and 56.43%; 100% concordant results in both assays and cLAMP (62.64% and 52.86% were comparable and there was no significant difference between the sensitivity of the assays (DRB PCR and cPCR, 86.76%; cLAMP, 83.82%. Likewise, sensitivity of cLAMP (95.83% and DRB-LAMP (91.67% were comparable as determined on a set of 24 samples tested positive in all routine assays.Both LAMP formats constitute equivalent alternatives to conventional PCR techniques. Provided the envisaged availability of field friendly DNA extraction formats, both assays are suitable for decentralized laboratory confirmation of BUD, whereby DRB-LAMP scores with the additional advantage of not requiring cold-chains. As validation of the assays was conducted in a third

  12. Racial athletic stereotype confirmation in college football recruiting.

    Science.gov (United States)

    Thomas, Grant; Good, Jessica J; Gross, Alexi R

    2015-01-01

    The present study tested real-world racial stereotype use in the context of college athletic recruiting. Stereotype confirmation suggests that observers use stereotypes as hypotheses and interpret relevant evidence in a biased way that confirms their stereotypes. Shifting standards suggest that the evaluative standard to which we hold a target changes as a function of their group membership. We examined whether stereotype confirmation and shifting standards effects would be seen in college football coaches during recruiting. College football coaches evaluated a Black or White player on several attributes and made both zero- and non-zero-sum allocations. Results suggested that coaches used the evidence presented to develop biased subjective evaluations of the players based on race while still maintaining equivalent objective evaluations. Coaches also allocated greater overall resources to the Black recruit than the White recruit.

  13. 酵母双杂交诱饵表达载体pGBKT7-cide-3的构建、鉴定以及毒性、自激活效应的检测%Construction, identification and transformation of "bait plasmid" containing human cide-3 gene in yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    闵婕; 李青; 马楠; 康艳霞; 李娜

    2013-01-01

    Objective;To construct a bait vector containing human cide -3 gene in yeast two -hybrid system in order to screen the human liver cDNA library. Methods; The fragment including all exons of cide -3 gene was amplified by RT-PCR and was inserted into the multiple cloning sites of the shuttle vector pGBKT7. After confirmation with restricted endonuclease digestion and sequence analysis,by using PEG/LiAC method,the plasmid pGBKT7 - cide -3 was transformed into yeast AH109. The plasmid and protein isolated from the positive yeast AH109 clone was tested its expression,toxicity and transcriptional activation. Results:The human cide -3 cDNA was amplified. The restrictive endonuclease digestion and DNA sequencing proved that the plasmid pGBKT7 - cide - 3 was obtained. The yeast AH109 clone transformed with pGBKT7 - cide - 3 was screened out by the SD/ - Trp nutritional media. Sequence analysis revealed that the fragment was correctly inserted into pGBKT7 with a right reading frame and its expression in yeast was verified. Conclusion; The bait plasmid pGBKT7 -cide -3 constructed expresses correctly,and can not activate the transcription of reporter gene alone in yeast two - hybrid system.%目的:构建并转化酵母双杂交体系中“诱饵”载体pGBKT7-cide-3以便用于人肝cDNA文库的筛选.方法:用RT-PCR方法从人肝细胞株QZG中扩增cide-3基因全外显子片段,并定向克隆入细菌-酵母穿梭表达质粒pGBKT7中;用PEG/LiAC法将pGBKT7-cide-3转化感受态酵母菌AH109.提取转化酵母菌的质粒DNA和总蛋白进行鉴定.同时检测表达产物对报告基因的激活作用及对酵母株AH109的毒性.结果:成功扩增出人cide-3 cDNA片段,限制性内切酶酶切和DNA测序证实获得正确的重组质粒pGBKT7-cide-3;获得可在色氨酸缺陷培养基(SD/-Trp)上生长含pGBKT7-cide-3的酵母菌克隆.鉴定表明pG-BKT7-cide-3已转化入酵母菌AH109,无自主激活报告基因的能力及对酵母的生长无毒性.结

  14. 人星状病毒非结构蛋白酵母双杂交诱饵表达载体构建及酵母转化子特性鉴定%Construction of Yeast Two-Hybrid Bait Vector of HAstV Non-Struc-tural Protein and Characterization of Yeast Transformants

    Institute of Scientific and Technical Information of China (English)

    李攀; 崔成成; 杨思达; 黄芬; 曾韦锟; 井申荣

    2014-01-01

    Objective To construct a yeast two-hybrid bait vector of non-structure protein 1a/3 (nsP1a/3) of human astrovirus (HAstV), and to characterize the yeast transformants after elec-trotransformation of the recombinant plasmid into the yeast competent cells .Methods The coding sequence of HAstV nsP 1 a/3 obtained by PCR was inserted into the modified plasmid pGST 7.The re-combinant vector nsP1a/3-pGBST7 confirmed by DNA sequencing was transformed into the Y 2 HGo-ld yeast competent cells .The cytotoxicity of the expression products of the recombiant plasmid nsP1a/3-pGBST7 and the autoactivation of the report gene in yeast transformants were exam-ined.Results The sequencing of the nsP 1 a/3-pGBST7 vector showed that the recombinant bait plasmid was successfully constructed and the open reading frame of nsP 1a/3 insert was correct.After electrotransformation, it was found that the expression products of the nsP 1a/3-pGBST7 vector had no cytotoxicity to yeast transformants and also they did not activate the report gene .Conclusion The yeast two-hybrid bait vector of HAstV nsP 1 a/3 was successfully constructed , which laid a foun-dation for further studying the interaction of HAstV nsP 1 a/3 with target proteins and the replication mechanism of HAstV in host cells .%目的:构建人星状病毒非结构蛋白3( non-structure protein 1a/3, nsP1a/3)基因酵母双杂交诱饵重组质粒,电转化酵母感受态细胞后鉴定酵母转化子特性。方法聚合酶链反应扩增人星状病毒nsP1a/3编码的基因序列,定向插入到穿梭表达载体pGBKT7改造后的pGBST7中,测序确定无误后将其电转化到Y2HGold酵母感受态细胞中,对细胞特性即nsP1a/3-pGBST7诱饵质粒表达产物的毒性和报告基因自激活作用进行鉴定。结果测序结果表明诱饵重组质粒构建正确,阅读框无误。电转化酵母后,其表达产物对酵母细胞无毒性作用,对报告基因亦无激活作用。结论成功构建了

  15. Apnoea testing to confirm brain death in clinical practice.

    Science.gov (United States)

    van Donselaar, C A; Meerwaldt, J D; van Gijn, J

    1986-09-01

    In six patients an apnoea test was carried out to confirm brain death according to a protocol recommended in the USA. After ten minutes' apnoea the pCO2 did not reach the target value of 7.98 kPa (60 mm Hg) in any of these patients. This was caused by the low initial value and the slow increase of the pCO2. Moreover, we could not confirm the belief that the necessary duration of the apnoea test can be predicted by assuming a rise of the pCO2 of 0.33 kPa (2.5 mm Hg) per minute.

  16. Apnoea testing to confirm brain death in clinical practice.

    Science.gov (United States)

    van Donselaar, C A; Meerwaldt, J D; van Gijn, J

    1986-01-01

    In six patients an apnoea test was carried out to confirm brain death according to a protocol recommended in the USA. After ten minutes' apnoea the pCO2 did not reach the target value of 7.98 kPa (60 mm Hg) in any of these patients. This was caused by the low initial value and the slow increase of the pCO2. Moreover, we could not confirm the belief that the necessary duration of the apnoea test can be predicted by assuming a rise of the pCO2 of 0.33 kPa (2.5 mm Hg) per minute. PMID:3093640

  17. Apnoea testing to confirm brain death in clinical practice.

    OpenAIRE

    van Donselaar, C. A.; Meerwaldt, J D; van Gijn, J

    1986-01-01

    In six patients an apnoea test was carried out to confirm brain death according to a protocol recommended in the USA. After ten minutes' apnoea the pCO2 did not reach the target value of 7.98 kPa (60 mm Hg) in any of these patients. This was caused by the low initial value and the slow increase of the pCO2. Moreover, we could not confirm the belief that the necessary duration of the apnoea test can be predicted by assuming a rise of the pCO2 of 0.33 kPa (2.5 mm Hg) per minute.

  18. Rapid GC-MS confirmation of amphetamines in urine by extractive acylation.

    Science.gov (United States)

    Marais, Adriaan A S; Laurens, Johannes B

    2009-01-10

    Amphetamine and related derivatives are widely abused central- and psychostimulants. Detection of certain derivatives, such as methcathinone, by commonly available immunoassay screening techniques is insufficient. Multi-analyte confirmations for amphetamine type stimulants are therefore required, but traditional gas chromatography-mass spectrometry methods necessitate lengthy analytical procedures with prolonged sample turn-around times. A validated rapid GC-MS assay for urinary confirmation of amphetamine, methamphetamine, methcathinone, ephedrine, norephedrine, methylenedioxyamphetamine, methylenedioxymethamphetamine, methylenedioxyethylamphetamine and N-methyl-1-(3,4 methylenedioxyphenyl)-2-butanamine is reported. The method entailed in situ derivatization of urine specimens by extractive acylation with pentafluoropropionic anhydride, followed by rapid chromatography on a microbore capillary column. Analytes were separated in less than 3 min and quantified simultaneously by selected-ion monitoring using stable isotope substituted internal standards. The total instrument cycle-time was 6 min per sample. The limits of detection were between 1.5 ng/mL and 6.25 ng/mL for the various analytes. Intermediate precision and accuracy were in the range of 6.3-13.8% and 90.5-107.3% for the respective analytes at the lower limit of quantitation, and between 5.8-12.6% and 95.4-103.1% for the high control. Long-term storage of methcathinone positive specimens at -20 degrees C proved insufficient stability of this analyte. The proposed assay is precise and accurate for confirmation of amphetamine and derivatives in urine. The complementary approach of extractive-derivatization and fast GC-MS analysis is especially applicable in routine clinical settings where reduced sample turn-around times are required. Further investigation of cathinone as a possible metabolite of methcathinone is warranted, based on results from analyzed authentic urine samples.

  19. Transporter assays and assay ontologies: useful tools for drug discovery.

    Science.gov (United States)

    Zdrazil, Barbara; Chichester, Christine; Zander Balderud, Linda; Engkvist, Ola; Gaulton, Anna; Overington, John P

    2014-06-01

    Transport proteins represent an eminent class of drug targets and ADMET (absorption, distribution, metabolism, excretion, toxicity) associated genes. There exists a large number of distinct activity assays for transport proteins, depending on not only the measurement needed (e.g. transport activity, strength of ligand–protein interaction), but also due to heterogeneous assay setups used by different research groups. Efforts to systematically organize this (divergent) bioassay data have large potential impact in Public-Private partnership and conventional commercial drug discovery. In this short review, we highlight some of the frequently used high-throughput assays for transport proteins, and we discuss emerging assay ontologies and their application to this field. Focusing on human P-glycoprotein (Multidrug resistance protein 1; gene name: ABCB1, MDR1), we exemplify how annotation of bioassay data per target class could improve and add to existing ontologies, and we propose to include an additional layer of metadata supporting data fusion across different bioassays.

  20. Confirmation of the absolute configuration of (−)-aurantioclavine

    KAUST Repository

    Behenna, Douglas C.

    2011-04-01

    We confirm our previous assignment of the absolute configuration of (-)-aurantioclavine as 7R by crystallographically characterizing an advanced 3-bromoindole intermediate reported in our previous synthesis. This analysis also provides additional support for our model of enantioinduction in the palladium(II)-catalyzed oxidative kinetic resolution of secondary alcohols. © 2010 Elsevier Ltd. All rights reserved.

  1. Ticks Carrying Lyme Disease Confirmed in Eastern National Parks

    Science.gov (United States)

    ... html Ticks Carrying Lyme Disease Confirmed in Eastern National Parks U.S. National Park Service and CDC advise using insect repellents on ... Planning a hiking trip in an eastern U.S. national park? Better pack tick repellent -- a new study found ...

  2. Theory-Led Confirmation Bias and Experimental Persona

    Science.gov (United States)

    Allen, Michael

    2011-01-01

    Questionnaire and interview findings from a survey of three Year 8 (ages 12-13 years) science practical lessons (n = 52) demonstrate how pupils' data collection and inference making were sometimes biased by desires to confirm a personal theory. A variety of behaviours are described where learners knowingly rejected anomalies, manipulated…

  3. Confirmation and justification. A commentary on Shogenji's measure

    NARCIS (Netherlands)

    Atkinson, David

    2012-01-01

    So far no known measure of confirmation of a hypothesis by evidence has satisfied a minimal requirement concerning thresholds of acceptance. In contrast, Shogenji's new measure of justification (Shogenji, Synthese, this number 2009) does the trick. As we show, it is ordinally equivalent to the most

  4. Objectivity in confirmation: post hoc monsters and novel predictions.

    Science.gov (United States)

    Votsis, Ioannis

    2014-03-01

    The aim of this paper is to put in place some cornerstones in the foundations for an objective theory of confirmation by considering lessons from the failures of predictivism. Discussion begins with a widely accepted challenge, to find out what is needed in addition to the right kind of inferential-semantical relations between hypothesis and evidence to have a complete account of confirmation, one that gives a definitive answer to the question whether hypotheses branded as "post hoc monsters" can be confirmed. The predictivist view is then presented as a way to meet this challenge. Particular attention is paid to Worrall's version of predictivism, as it appears to be the most sophisticated of the lot. It is argued that, despite its faults, his view turns our heads in the right direction by attempting to remove contingent considerations from confirmational matters. The demand to remove such considerations becomes the first of four cornerstones. Each cornerstone is put in place with the aim to steer clear of the sort of failures that plague various kinds of predictivism. In the process, it becomes obvious that the original challenge is wrongheaded and in need of revision. The paper ends with just such a revision.

  5. The influence of stimulus valence on confirmation bias in children

    NARCIS (Netherlands)

    Dibbets, Pauline; Meesters, Cor

    2016-01-01

    BACKGROUND AND OBJECTIVES: The aim of the present study was to replicate our previous study and to further examine the relation between fear and positive and negative confirmation bias in children. METHODS: Fifty-three non-clinical children (9-13 years) were shown pictures of a kindly-perceived (quo

  6. Confirmation of Solar-Like Oscillations in eta Bootis

    CERN Document Server

    Kjeldsen, H; Baldry, I K; Frandsen, S; Bruntt, H; Grundahl, F; Lang, K; Butler, R P; Fischer, D A; Marcy, G W; Misch, A A; Vogt, S S

    2002-01-01

    We report observations of the G0 subgiant eta Boo made in 1998, in Balmer-line equivalent width with the 2.5-m Nordic Optical Telescope and in velocity with the 24-inch Lick CAT. In both data sets we see an excess in the power spectrum, with oscillation frequencies that confirm the earlier observations by Kjeldsen et al. (1995).

  7. The yeast split-ubiquitin membrane protein two-hybrid screen identifies BAP31 as a regulator of the turnover of endoplasmic reticulum-associated protein tyrosine phosphatase-like B.

    Science.gov (United States)

    Wang, Bing; Pelletier, Jerry; Massaad, Michel J; Herscovics, Annette; Shore, Gordon C

    2004-04-01

    In the past decade, traditional yeast two-hybrid techniques have identified a plethora of interactions among soluble proteins operating within diverse cellular pathways. The discovery of associations between membrane proteins by genetic approaches, on the other hand, is less well established due to technical limitations. Recently, a split-ubiquitin system was developed to overcome this barrier, but so far, this system has been limited to the analysis of known membrane protein interactions. Here, we constructed unique split-ubiquitin-linked cDNA libraries and provide details for implementing this system to screen for binding partners of a bait protein, in this case BAP31. BAP31 is a resident integral protein of the endoplasmic reticulum, where it operates as a chaperone or cargo receptor and regulator of apoptosis. Here we describe a novel human member of the protein tyrosine phosphatase-like B (PTPLB) family, an integral protein of the endoplasmic reticulum membrane with four membrane-spanning alpha helices, as a BAP31-interacting protein. PTPLB turns over rapidly through degradation by the proteasome system. Comparisons of mouse cells with a deletion of Bap31 or reconstituted with human BAP31 indicate that BAP31 is required to maintain PTPLB, consistent with a chaperone or quality control function for BAP31 in the endoplasmic reticulum membrane.

  8. The screening of functional proteins interacting with IrrE by the yeast two-hybrid system%利用酵母双杂交系统筛选IrrE相互作用蛋白

    Institute of Scientific and Technical Information of China (English)

    田霞; 代其林; 龚元亚; 孙英坤; 谢琳; 杨娟; 王劲

    2012-01-01

    IrrE was constructed as the bait protein and then interacted with functional proteins from the Arabidopsis cDNA library by yeast two-hybrid system. The result showed that there was one interacting protein from all the positive clones which had high identity (as high identical to 98%) with the LEA14 protein (Late Embryogenesis Abundant protein 14) encoded by Arabidopsis thaliana gene Atlg01470. It was inferred that IrrE protein may play an important role in improving the tolerance to salt stress in trans-gene plants.%本研究通过酵母双杂交技术,构建了IrrE蛋白为诱饵载体,从拟南芥cDNA文库中筛选与IrrE诱饵蛋白相互作用的功能蛋白.研究结果表明,在所获得的阳性克隆中,发现了一个与拟南芥基因Atlg01470所编码的蛋白有较高同源性的蛋白,即LEA14蛋白(晚期胚胎发育富集蛋白),同源性高达98%.推测IrrE转录因子在提高植物耐盐性的过程中起了重要作用.

  9. A simultaneous disulfide bond cleavage, N,S-bialkylation/N-protonation and self-assembly reaction: syntheses, structures and properties of two hybrid iodoargentates with thiazolyl-based heterocycles.

    Science.gov (United States)

    Liu, Guang-Ning; Li, Ke; Fan, Qing-Shun; Sun, Hui; Li, Xin-Yu; Han, Xiao-Nan; Li, Yu; Zhang, Zhen-Wei; Li, Cuncheng

    2016-12-21

    Solvothermal reactions of AgI with the vulcanization accelerator 2,2'-dibenzothiazolyl disulfide and hydroiodic acid in alcohols afford two hybrid iodoargentates with one-dimensional structures, namely (Et2mbt)[Ag2I3] (1, Hmbt = 2-mercaptobenzothiazole) and {(Hmbt)[AgI]}n (2). The syntheses of both 1 and 2 involve unprecedented multiple in situ reactions. Specifically, a simultaneous disulfide bond cleavage, N and S donor atoms bialkylation, and self-assembly reaction lead to 1 that contains a discrete N,S-biethylated cation (Et2mbt)(+) and a rare inorganic (Ag2I3)(-) anionic chain, while a simultaneous disulfide bond cleavage, N-protonation and self-assembly reaction affords 2 which features zwitterionic Hmbt molecules coordinating with the opposite side Ag atoms of a neutral inorganic (AgI)n chain via forming Ag-S coordination bonds. The simultaneous alkylation on a thiazolyl-N donor and a thiol-S donor atom for a thiazolyl-based heterocycle using inexpensive alcohols and haloids under solvothermal conditions instead of traditional two-step organic synthesis was found for the first time. The two compounds have band gaps of 2.95 eV for 1, and 2.78 eV for 2 exhibiting an observed blue shift compared with bulk AgI. Also, 1 and 2 can be used as effective heterogeneous photocatalysts for methyl orange dye treatment under UV light irradiation.

  10. Laboratory confirmation of rubella infection in suspected measles cases.

    Science.gov (United States)

    Vaidya, Sunil R; Raut, Chandrashekhar G; Jadhav, Santoshkumar M

    2016-10-01

    As a part of measles outbreak based surveillance undertaken by the World Health Organization India, suspected measles cases were referred for the laboratory diagnosis at National Institute of Virology (NIV) Pune and NIV Unit Bengaluru. Altogether, 4,592 serum samples were referred during 2010-2015 from the States of Karnataka (n = 1,173), Kerala (n = 559), and Maharashtra (n = 2,860). Initially, serum samples were tested in measles IgM antibody EIA and samples with measles negative and equivocal results (n = 1,954) were subjected to rubella IgM antibody detection. Overall, 62.9% (2,889/4,592) samples were laboratory confirmed measles, 27.7% (542/1,954) were laboratory confirmed rubella and remaining 25.2% (1,161/4,592) were negative for measles and rubella. The measles vaccination status was available for 1,206 cases. Among the vaccinated individuals, 50.7% (612/1,206) were laboratory confirmed measles. The contribution of laboratory confirmed measles was 493 (40.8%) from Maharashtra, 90 (7.5%) from Karnataka, and 29 (2.4%) from Kerala. Since, 1/3rd of suspected measles cases were laboratory confirmed rubella, an urgent attention needed to build rubella surveillance in India. Additional efforts are required to rule out other exanthematous disease including Dengue and Chikungunya in measles and rubella negatives. J. Med. Virol. 88:1685-1689, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  11. Overview of NRC's Regulatory Perspective on Performance Confirmation

    Science.gov (United States)

    Fedors, R. W.; Pohle, J. A.

    2007-12-01

    Regulations governing the disposal of high-level radioactive waste at 10 CFR Part 63, Subpart F, require the implementation of a Performance Confirmation Program for a geologic repository at Yucca Mountain, Nevada. The goals of the Performance Confirmation Program are to confirm that the (i) actual subsurface conditions and potential changes in these conditions during construction and waste emplacement operations are within the limits assumed during the licensing review, and (ii) natural and engineered barriers are functioning as intended and anticipated. For a license application for construction authorization, only a plan is required by the regulations. Proposed activities might include (i) monitoring the repository environment, both engineered and natural components, (ii) field and laboratory investigations under more controlled conditions to better understand processes, and (iii) scientific and programmatic evaluation of the data to support operational decisionmaking and guide adaptive design alterations. NRC review of vadose zone monitoring methods revealed limitations in current technological solutions such that many presently available hydro-environmental sensors would likely not be suitable for long- term, deep-subsurface, fractured rock monitoring activities, particularly with respect to the temperatures and radiation environment that will occur near or within waste emplacement drifts. Sensor deployment strategies will also have to be developed considering the repository environment. Thus, achieving the goals of the performance confirmation program could be affected by limits on sensor capabilities or on an as yet to be proposed sensor deployment strategy. A performance confirmation program implemented over a lengthy operational period allows for future evolution and development of sensors and strategies to further advance the collection of information relevant to processes important for performance of the potential repository at Yucca Mountain. The NRC

  12. Confirming the Lanchestrian linear-logarithmic model of attrition

    Energy Technology Data Exchange (ETDEWEB)

    Hartley, D.S. III.

    1990-12-01

    This paper is the fourth in a series of reports on the breakthrough research in historical validation of attrition in conflict. Significant defense policy decisions, including weapons acquisition and arms reduction, are based in part on models of conflict. Most of these models are driven by their attrition algorithms, usually forms of the Lanchester square and linear laws. None of these algorithms have been validated. The results of this paper confirm the results of earlier papers, using a large database of historical results. The homogeneous linear-logarithmic Lanchestrian attrition model is validated to the extent possible with current initial and final force size data and is consistent with the Iwo Jima data. A particular differential linear-logarithmic model is described that fits the data very well. A version of Helmbold's victory predicting parameter is also confirmed, with an associated probability function. The implications of these findings are potentially far-reaching. Two-sided daily attrition data on a large number of battles is needed to absolutely confirm these results. Such a confirmation will require that numerous computer conflict models containing square and linear law based attrition algorithms be reexamined. It is conceivable that complex mixed, heterogeneous, square plus linear law algorithms may produce the same results as a homogeneous mixed linear-logarithmic law algorithm; however, such an occurrence is by no means assured. Even without such absolute confirmation, the results of this research allow the analysis of combat data for the effects of training, weather, leadership, and other human factors, unencumbered by the force size effects.

  13. MICROBIOLOGICAL ASSAY FOR VITAMIN B

    OpenAIRE

    Bishnoi Kapil*, , ,; Kataria Mahesh; Singhal Vipin; Gupta Deepika

    2012-01-01

    Micronutrients added to foods are analyzed using various procedures depending on their nature and properties. The microbiological assays are better than chemical method because any suitable change in vitamin molecule which may not be detected by chemical method will be revealed by change in microbial activity. The microbiological assay of vitamins is based upon the comparison of the stimulation of growth of bacteria by measured concentration of vitamin with that produced by known concentratio...

  14. Evaluation of environmental genotoxicity by comet assay in Columba livia.

    Science.gov (United States)

    González-Acevedo, Anahi; García-Salas, Juan A; Gosálvez, Jaime; Fernández, José Luis; Dávila-Rodríguez, Martha I; Cerda-Flores, Ricardo M; Méndez-López, Luis F; Cortés-Gutiérrez, Elva I

    2016-01-01

    The concentrations of recognized or suspected genotoxic and carcinogenic agents found in the air of large cities and, in particular, developing countries, have raised concerns about the potential for chronic health effects in the populations exposed to them. The biomonitoring of environmental genotoxicity requires the selection of representative organisms as "sentinels," as well as the development of suitable and sensitive assays, such as those aimed at assessing DNA damage. The aim of this study was to evaluate DNA damage levels in erythrocytes from Columba livia living in the metropolitan area of Monterrey, Mexico, compared with control animals via comet assay, and to confirm the results via Micronuclei test (MN) and DNA breakage detection-fluorescence in situ hybridization (DBD-FISH). Our results showed a significant increase in DNA migration in animals from the area assayed compared with that observed in control animals sampled in non-contaminated areas. These results were confirmed by MN test and DBD-FISH. In conclusion, these observations confirm that the examination of erythrocytes from Columba livia via alkaline comet assay provides a sensitive and reliable end point for the detection of environmental genotoxicants.

  15. Confirming the Lanchestrian linear-logarithmic model of attrition

    Energy Technology Data Exchange (ETDEWEB)

    Hartley, D.S. III.

    1990-12-01

    This paper is the fourth in a series of reports on the breakthrough research in historical validation of attrition in conflict. Significant defense policy decisions, including weapons acquisition and arms reduction, are based in part on models of conflict. Most of these models are driven by their attrition algorithms, usually forms of the Lanchester square and linear laws. None of these algorithms have been validated. The results of this paper confirm the results of earlier papers, using a large database of historical results. The homogeneous linear-logarithmic Lanchestrian attrition model is validated to the extent possible with current initial and final force size data and is consistent with the Iwo Jima data. A particular differential linear-logarithmic model is described that fits the data very well. A version of Helmbold's victory predicting parameter is also confirmed, with an associated probability function. 37 refs., 73 figs., 68 tabs.

  16. Caldwell Ranch Exploration and Confirmation Project, Northwest Geysers, CA

    Energy Technology Data Exchange (ETDEWEB)

    Walters, Mark A.

    2013-04-25

    The purpose of the Caldwell Ranch Exploration and Confirmation Project was to drill, test, and confirm the present economic viability of the undeveloped geothermal reservoir in the 870 acre Caldwell Ranch area of the Northwest Geysers that included the CCPA No.1 steam field. All of the drilling, logging, and sampling challenges were met. Three abandoned wells, Prati 5, Prati 14 and Prati 38 were re-opened and recompleted to nominal depths of 10,000 feet in 2010. Two of the wells required sidetracking. The flow tests indicated Prati 5 Sidetrack 1 (P-5 St1), Prati 14 (P-14) and Prati 38 Sidetrack 2 (P-38 St2) were collectively capable of initially producing an equivalent of 12 megawatts (MWe) of steam using a conversion rate of 19,000 pounds of steam/hour

  17. Theory of chaotic orbital variations confirmed by Cretaceous geological evidence.

    Science.gov (United States)

    Ma, Chao; Meyers, Stephen R; Sageman, Bradley B

    2017-02-22

    Variations in the Earth's orbit and spin vector are a primary control on insolation and climate; their recognition in the geological record has revolutionized our understanding of palaeoclimate dynamics, and has catalysed improvements in the accuracy and precision of the geological timescale. Yet the secular evolution of the planetary orbits beyond 50 million years ago remains highly uncertain, and the chaotic dynamical nature of the Solar System predicted by theoretical models has yet to be rigorously confirmed by well constrained (radioisotopically calibrated and anchored) geological data. Here we present geological evidence for a chaotic resonance transition associated with interactions between the orbits of Mars and the Earth, using an integrated radioisotopic and astronomical timescale from the Cretaceous Western Interior Basin of what is now North America. This analysis confirms the predicted chaotic dynamical behaviour of the Solar System, and provides a constraint for refining numerical solutions for insolation, which will enable a more precise and accurate geological timescale to be produced.

  18. Cardiac MRI-confirmed mesalamine-induced myocarditis.

    Science.gov (United States)

    Baker, William L; Saulsberry, Whitney J; Elliott, Kaitlyn; Parker, Matthew W

    2015-09-04

    A 38-year-old Caucasian man with a medical history significant for inflammatory bowel disease (IBD) and mesalamine use presented to the emergency department with stabbing, pleuritic, substernal chest pain over the previous 2 days. Findings of leucocytosis, elevated cardiac enzymes and inflammatory markers, T-wave or ST-segment abnormalities and left ventricular systolic dysfunction suggested mesalamine-induced myocarditis. However, a cardiac MRI confirmed the diagnosis. Signs and symptoms improved within days of withdrawal of mesalamine, and initiation of corticosteroids and follow-up studies within the next year were unremarkable. Importantly, the diagnosis of mesalamine-induced myocarditis confirmed via cardiac MRI is a step rarely performed in published cases.

  19. An Anonymous Voting Scheme based on Confirmation Numbers

    Science.gov (United States)

    Alam, Kazi Md. Rokibul; Tamura, Shinsuke; Taniguchi, Shuji; Yanase, Tatsuro

    This paper proposes a new electronic voting (e-voting) scheme that fulfills all the security requirements of e-voting i.e. privacy, accuracy, universal verifiability, fairness, receipt-freeness, incoercibility, dispute-freeness, robustness, practicality and scalability; usually some of which are found to be traded. When compared with other existing schemes, this scheme requires much more simple computations and weaker assumptions about trustworthiness of individual election authorities. The key mechanism is the one that uses confirmation numbers involved in individual votes to make votes verifiable while disabling all entities including voters themselves to know the linkages between voters and their votes. Many existing e-voting schemes extensively deploy zero-knowledge proof (ZKP) to achieve verifiability. However, ZKP is expensive and complicated. The confirmation numbers attain the verifiability requirement in a much more simple and intuitive way, then the scheme becomes scalable and practical.

  20. Repeated use of request for confirmation in atypical interaction

    Science.gov (United States)

    Rasmussen, Gitte

    2016-01-01

    ABSTRACT This study investigates a specific method for making possible the participation of participants with cognitive and communicative impairments in social face-to-face interaction. Non-impaired co-participants design close-ended questions that project who the next speaker is, i.e. the impaired co-participant. The questions also project what kind of response amongst alternatives the impaired co-participant is supposed to produce. Upon answers to these questions, the non-impaired co-participant requests the impaired participant to confirm the answer twice. Using conversation analytic (CA) methods, the study scrutinises what is achieved by requesting a confirmation of the provided answer – repeatedly so. The study argues that the practice may put the (deficit) competence of the participant with impairments in focus if the initial close-ended question works to establish an understanding of a prior action by the participant with impairments. PMID:27610755

  1. Histopathology confirms white-nose syndrome in bats in Europe

    Science.gov (United States)

    Pikula, J.; Bandouchova, H.; Novotny, L.; Meteyer, C.U.; Zukal, J.; Irwin, N.R.; Zima, J.; Martinkova, N.

    2012-01-01

    White-nose syndrome, associated with the fungal skin infection geomycosis, caused regional population collapse in bats in North America. Our results, based on histopathology, show the presence of white-nose syndrome in Europe. Dermatohistopathology on two bats (Myotis myotis) found dead in March 2010 with geomycosis in the Czech Republic had characteristics resembling Geomyces destructans infection in bats confirmed with white-nose syndrome in US hibernacula. In addition, a live M. myotis, biopsied for histopathology during hibernation in April 2011, had typical fungal infection with cupping erosion and invasion of muzzle skin diagnostic for white-nose syndrome and conidiospores identical to G. destructans that were genetically confirmed as G. destructans. ?? Wildlife Disease Association 2012.

  2. Theory of chaotic orbital variations confirmed by Cretaceous geological evidence

    Science.gov (United States)

    Ma, Chao; Meyers, Stephen R.; Sageman, Bradley B.

    2017-02-01

    Variations in the Earth’s orbit and spin vector are a primary control on insolation and climate; their recognition in the geological record has revolutionized our understanding of palaeoclimate dynamics, and has catalysed improvements in the accuracy and precision of the geological timescale. Yet the secular evolution of the planetary orbits beyond 50 million years ago remains highly uncertain, and the chaotic dynamical nature of the Solar System predicted by theoretical models has yet to be rigorously confirmed by well constrained (radioisotopically calibrated and anchored) geological data. Here we present geological evidence for a chaotic resonance transition associated with interactions between the orbits of Mars and the Earth, using an integrated radioisotopic and astronomical timescale from the Cretaceous Western Interior Basin of what is now North America. This analysis confirms the predicted chaotic dynamical behaviour of the Solar System, and provides a constraint for refining numerical solutions for insolation, which will enable a more precise and accurate geological timescale to be produced.

  3. [Implantable loop recorder of the Confirm family (St. Jude Medical)].

    Science.gov (United States)

    Pujdak, Krzysztof

    2016-12-01

    St. Jude Medical produces the implantable loop recorder (ILR) Confirm AF DM2102 which offers subcutaneous electrodes on both sides of the device, a specific sensing algorithm and extensive storage capacity for up to 147 episodes. The reliability of detection of atrial fibrillation (AF) has been evaluated in the DETECT-AF study. The device is MR-conditional and allows patients an interrogation at home. The data are transferred to the follow-up centre via telephone by the patient activator, although this process is currently rather complex and slow. Therefore, remote monitoring of the Confirm AF DM2102 is rarely an option for elderly patients. St. Jude medical announced the introduction of a new, substantially smaller ILR using more modern technology by the end of 2016.

  4. Hindsight and confirmation biases in an exercise in telepathy.

    Science.gov (United States)

    Rudski, Jeffrey M

    2002-12-01

    Belief in the paranormal or claims of paranormal experiences may be, at least in part, associated with systematic cognitive biases. 48 undergraduate college students engaged in an exercise in telepathy in which the color of cards was 'sent' to them by the experimenter under two conditions. In a Hindsight-possible condition, participants recorded whether their choice was correct following the revelation of the color. In the Control condition participants committed to a particular response by writing it down before receiving feedback, thus eliminating ability to alter retrospectively what 'was known all along'. Consistent with a hindsight bias, participants performed significantly better under the Hindsight-possible condition. Moreover, a statisically significant correlation was found between paranormal belief assessed on Tobacyk's 1988 Revised Paranormal Belief Scale in the Hindsight-possible but not in the Control condition, suggesting a confirmation bias. Results are discussed in terms of interactions between hindsight and confirmation biases and how they might relate to paranormal beliefs.

  5. Earthquake Model Confirms Traffic Jams Caused by Tiredness

    CERN Document Server

    Jarai-Szabo, Ferenc

    2011-01-01

    A simple one-dimensional spring-block model elaborated for the idealized single-lane highway traffic reveals the causes for the emergence of traffic jams. Based on the stop-time statistics of one car in the row, an order parameter is defined and studied. By extensive computer simulations, the parameter space of the model is explored, analyzed and interpreted. Existence of a free a and congested flow phases is confirmed and the transition between them is analyzed.

  6. Quantitative CrAssphage PCR Assays for Human Fecal ...

    Science.gov (United States)

    Environmental waters are monitored for fecal pollution to protect public health and water resources. Traditionally, general fecal indicator bacteria are used; however, they cannot distinguish human fecal waste from pollution from other animals. Recently, a novel bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in and closely associated with human fecal waste. To confirm bioinformatic predictions, 384 primer sets were designed along the length of the crAssphage genome. Based upon initial screening, two novel crAssphage qPCR assays (CPQ_056 and CPQ_064) were designed and evaluated in reference fecal samples and water matrices. The assays exhibited high specificities (98.6%) when tested against a large animal fecal reference library and were highly abundant in raw sewage and sewage impacted water samples. In addition, CPQ_056 and CPQ_064 assay performance was compared to HF183/BacR287 and HumM2 methods in paired experiments. Findings confirm viral crAssphage qPCR assays perform at a similar level to well established bacterial human-associated fecal source identification technologies. These new viral based assays could become important water quality management and research tools. To inform the public.

  7. Optimization of Regression Models of Experimental Data Using Confirmation Points

    Science.gov (United States)

    Ulbrich, N.

    2010-01-01

    A new search metric is discussed that may be used to better assess the predictive capability of different math term combinations during the optimization of a regression model of experimental data. The new search metric can be determined for each tested math term combination if the given experimental data set is split into two subsets. The first subset consists of data points that are only used to determine the coefficients of the regression model. The second subset consists of confirmation points that are exclusively used to test the regression model. The new search metric value is assigned after comparing two values that describe the quality of the fit of each subset. The first value is the standard deviation of the PRESS residuals of the data points. The second value is the standard deviation of the response residuals of the confirmation points. The greater of the two values is used as the new search metric value. This choice guarantees that both standard deviations are always less or equal to the value that is used during the optimization. Experimental data from the calibration of a wind tunnel strain-gage balance is used to illustrate the application of the new search metric. The new search metric ultimately generates an optimized regression model that was already tested at regression model independent confirmation points before it is ever used to predict an unknown response from a set of regressors.

  8. Clinical confirmation of trichothecene mycotoxicosis in patient urine.

    Science.gov (United States)

    Croft, William A; Jastromski, Bonnie M; Croft, Amanda L; Peters, Henry A

    2002-07-01

    The investigations of four Cases involving mold-contaminated buildings and human reaction to exposure, documents tests of extracted urine containing trichothecene mycotoxins confirming exposure and the diagnosis of mycotoxicosis in humans. In each of four Cases, the urine demonstrated antibiotic activity, sulfuric acid charring, and protein release. Urine was extracted using ethyl acetate 40V/60V[EA]. Extracted mycotoxin spotted on (TLC) displayed color and a range of (rf) between 0.2-0.6 using various solvents. Extract was re-suspended using 50% ethanol V/V to inject mycotoxins into weanling female Sprague-Dawley rats. Degeneration and necrosis of the rat's tissue followed. Koch's Postulates conditions were fulfilled by isolation of the causative agent, the trichothecene mycotoxins and the reproduction of disease. Examination of human tissue within the urine extraction group confirms Koch's Postulates and comparative pathology confirms inhalation Mycotoxicosis, with severe necrosis of the central nervous system and severe scarring within the lungs. Extraction of mycotoxins from human patient urine is a very useful confirmatory test to demonstrate exposure and identify mycotoxicosis. Low concentrations (6%) of sodium hypochlorite were ineffective against the activity of trichothecene mycotoxin. The severity or stages of disease directly correlates the level of exposure or poisoning (Patent Pending).

  9. Correlation between the genotoxicity endpoints measured by two different genotoxicity assays: comet assay and CBMN assay

    Directory of Open Access Journals (Sweden)

    Carina Ladeira

    2015-06-01

    The results concerning of positive findings by micronuclei and non significant ones by comet assay, are corroborated by Deng et al. (2005 study performed in workers occupationally exposed to methotrexate, also a cytostatic drug. According to Cavallo et al. (2009, the comet assay seems to be more suitable for the prompt evaluation of the genotoxic effects, for instance, of polycyclic aromatic hydrocarbons mixtures containing volatile substances, whereas the micronucleus test seems more appropriate to evaluate the effects of exposure to antineoplastic agents. However, there are studies that observed an increase in both the comet assay and the micronucleus test in nurses handling antineoplastic drugs, although statistical significance was only seen in the comet assay, quite the opposite of our results (Maluf & Erdtmann, 2000; Laffon et al. 2005.

  10. [Comparison of the clinical performance of the ECLusys HIV combi assay with the Lumipulse f and HISCL 2000-i HIV-1/2 ab screening assays].

    Science.gov (United States)

    Sugiura, Aya; Iwahara, Kunihiro; Suga, Yasuyuki; Uchiyama, Sachinori; Maekawa, Masato

    2012-04-01

    We compared the ECLusys HIV combi assay (ECL HIV Ag/Ab) to the Lumipulse Forte (LPf HIV 1/2 Ab) and HISCL (HIS HIV 1/2 Ab) assays. In a dilution sensitivity test using dilution panels of WHO HIV antibody international reference panel (HIV-1 Subtype A, B, C, E, HIV-1 Group O, HIV-2) and HIV-1/2 Ab CE marked material(HIV-1, HIV-2) parent specimens, the ECL assay enabled detection at a higher level of sensitivity than either the LPf assay or the HIS assay for all dilution panels. In an early detection test in the early phase of infection in which a BBI HIV seroconversion panel was used, the ECL assay enabled detection 7 days after initial blood sample collection, whereas the LPf and HIS assays enabled detection after 27 days. In a specificity test using high RF positive specimens (n=33), pregnancy specimens (n=35), cytomegalovirus antibody positive specimens (n=36), and high M protein positive specimens (n=21) that were confirmed negative for HIV-1/2 antibodies by the LPf assay, negative results were obtained for all specimens on both the ECL assay and the HIS assay. In a correlation test using routinely collected clinical specimens (n=121), including positive stock specimens, the ECL and HIS assays demonstrated the highest agreement rate 98.3%. The above results confirmed that the fourth-generation reagent ECL assay, which simultaneously detects both HIV-1/2 antibodies and p24 antigens, is both highly sensitive and specific, and is a suitable assay for use in routine testing.

  11. Use of laminar flow patterning for miniaturised biochemical assays

    DEFF Research Database (Denmark)

    Regenberg, Birgitte; Krühne, Ulrich; Beyer, M.

    2004-01-01

    Laminar flow in microfluidic chambers was used to construct low (one dimensional) density arrays suitable for miniaturized biochemical assays. By varying the ratio of flows of two guiding streams flanking a sample stream, precise focusing and positioning of the latter was achieved, and reactive...... species carried in the sample stream were deposited on functionalized chip surfaces as discrete 50 mm wide lanes. Using different model systems we have confirmed the method's suitability for qualitative screening and quantification tasks in receptor-ligand assays, recording biotin......-streptavidin interactions, DNA-hybridization and DNA-triplex formation. The system is simple, fast, reproducible, flexible, and has small sample requirements....

  12. Anticonvulsant hypersensitivity syndrome to lamotrigine confirmed by lymphocyte stimulation in vitro

    Directory of Open Access Journals (Sweden)

    Karande Sunil

    2006-02-01

    Full Text Available Anticonvulsant hypersensitivity syndrome (AHS developing to lamotrigine, a non-aromatic anticonvulsant, has rarely been reported. We present a two-year-old boy with refractory epilepsy on valproic acid and lamotrigine therapy who developed fever and a maculopapular itchy rash. Blood investigations detected lymphocytosis and thrombocytopenia. With a presumptive diagnosis of AHS, lamotrigine was discontinued. The fever and rash resolved over the next three days and the child was discharged on valproic acid and clobazam. The diagnosis was confirmed by in vitro lymphocyte toxicity assay, which not only demonstrated increased cell death following exposure to lamotrigine, but also to the three first-line aromatic anticonvulsants: phenytoin, phenobarbital and carbamazepine. The potential of first-line aromatic anticonvulsants to cause AHS should be remembered in a patient who has developed AHS on exposure to lamotrigine. Timely recognition of this rare but potentially fatal drug reaction is important.

  13. Screening of proteins interacting with HSPC016 by yeast two-hybridization technique%用酵母双杂交技术筛选与HSPC016相互作用的蛋白

    Institute of Scientific and Technical Information of China (English)

    宋志强; 孙丽华; 郝飞

    2011-01-01

    目的 采用酵母双杂交技术筛选毛乳头细胞中与造血干细胞(hematopoietic stem/progenitor cells,HSPC)分化相关基因HSPC016相互作用的蛋白,了解其参与调控毛乳头细胞凝集性生长的分子机制.方法 应用酵母双杂交系统,将构建的pGBKT7-HSPC016诱饵质粒与含原代人毛乳头细胞cDNA文库质粒的酵母Y187进行配合,筛选与HSPC016相互作用的蛋白,通过回复性杂交试验验证其可靠性,并对阳性克隆进行测序和生物信息学分析.结果 筛选出4个与HSPC016有相互作用的蛋白,包括转录因子叉头框蛋白O1(forkhead box O1,FOXO1)、丝裂原活化蛋白激酶11、磷酸次黄苷酸激酶3调节亚单位3(PIK3R3)、肝X受体,它们均与细胞内能量代谢、转录调节相关.结论 HSPC016可能通过参与细胞内活性氧水平调节,并与细胞内参与能量和转录调节的相关信号分子相互作用,调节毛乳头细胞的凝集性生长状态.%Objective To screen and identify proteins interacting with hematopoietic stem/progenitor cell differentiation-related gene HSPC016, and to explore the molecular mechanism involved in the regulation by HSPC016 on the aggregative behavior of dermal papilla cells. Methods By using yeast two-hybridization,HSPC016 gene was sub-cloned into pGBKT7 to construct the bait plasmid (named as pGBKT7-HSPC016) in yeast AH109. The cDNA yeast expression library of human dermal papillae cells in yeast Y187 was screened with the bait plasmid and the proteins interacting with HSPC016 were identified. Yeast two-hybridization retransformation experiment was conducted to exclude the false positive clones and verify the interactions, then,the positive clones were sequenced and analyzed by using bioinformatic methods. Results The bait plasmid pGBKT7-HSPC016 was constructed successfully and there was no self-activation in or toxicity against yeast AH 109. Four proteins,including forkhead family of transcription factors (FOXO 1 ), mitogen

  14. Construction of Yeast Two-hybrid cDNA Library of Verticillium dahliae%大丽轮枝菌酵母双杂交 cDNA 文库的构建

    Institute of Scientific and Technical Information of China (English)

    康静敏; 刘坤; 刘严; 张怡; 李成伟; 谭光轩

    2015-01-01

    为了分离克隆与植物互作的大丽轮枝菌致病相关蛋白基因,利用 SMART 技术构建了大丽轮枝菌酵母双杂交 cDNA 文库。结果表明,构建的文库滴度为5.2×107 cfu/mL,库容为3.9×107 cfu;文库 cDNA 插入片段长度主要分布在0.5~2.0 kb,平均为1 kb;文库重组率为96%。表明文库质量较好,为筛选与植物互作的大丽轮枝菌致病蛋白基因奠定了基础。%To seek out the V. dahliae proteins involved in the interaction of plant with V. dahliae,a yeast two-hybrid library of V. dahliae was constructed using SMART technique. Results showed that the titer of cDNA library was 5. 2 × 107 cfu/mL,the library contained 3. 9 × 107 cfu independent clones,the size distribution of insert frag-ments ranged from 0. 5 -2. 0 kb,and the recombination rate was about 96%. These data demonstrated that the li-brary could meet the requirements of standard cDNA library,which laid a foundation for screening the interaction proteins from V. dahliae.

  15. 肝细胞生成素在睾丸组织中的相互作用蛋白%Identification of Hepatopoietin Interacting Proteins in Human Testis by Yeast Two-hybrid System

    Institute of Scientific and Technical Information of China (English)

    陈筱潇; 李勇; 邱宗荫; 贺福初

    2004-01-01

    Hepatopoietin (HPO) has diverse functions in the regulation of cell growth and differentiation. Its high level expression in testis suggests that HPO may have important role for testicular physiological functions. Using HPO as "bait", a yeast two-hybrid library screen of human testis was performed. By screening and selecting the positive colonies, retesting interactions in yeast, amplifying the AD/library inserts, sequencing and sequence comparing, four HPO-interacting proteins were identified: NADH dehydrogenase 1, Na+/K+ ATPase beta-3 subunit (ATP1β3), phospholipase C delta 1 and epididymal secretory protein. The significance of identification of these proteins may provide mechanistic insight into the biologic role of HPO in testis.%肝细胞生成素(HPO)具有复杂的生理功能,在睾丸中的高表达提示其在生殖活动中的重要性,而不仅局限于肝再生.构建了酵母表达载体pGBKT7-HPO,采用酵母双杂交系统,以HPO为诱饵蛋白,从人睾丸cDNA文库中寻找能够与HPO相互作用的蛋白质.经过筛选、验证阳性克隆,并进行PCR、测序和序列比对,得到4种相互作用蛋白质:NADH脱氢酶1、钠/钾ATP酶β3亚基、磷脂酶C δ1以及附睾分泌蛋白.提示HPO可能参与了细胞的蛋白质合成,能量代谢等.通过对候选蛋白的研究,为探讨HPO对睾丸组织细胞功能的调节机制提供了重要的线索.

  16. Failure to Confirm the Macrophage Electrophoretic Mobility Test in Cancer

    Science.gov (United States)

    Forrester, J. A.; Dando, P. M.; Smith, W. J.; Turberville, C.

    1977-01-01

    A series of patients with a variety of histopathologically confirmed cancers have been examined using the MOD-MEM test as described by Pritchard et al. (1973). Despite the closest possible adherence to the experimental protocols recommended by these authors, no positive reactions to the test were observed in this series: neither were we able to demonstrate the release of a “macrophage-slowing factor” by a panel of normal donors when challenged with tubercle PPD. We conclude that the test has no present application to the diagnosis of cancer.

  17. The Problem of Confirmation in the Everett Interpretation

    CERN Document Server

    Adlam, Emily

    2015-01-01

    I argue that the Oxford school Everett interpretation is internally incoherent, because we cannot claim that in an Everettian universe the kinds of reasoning we have used to arrive at our beliefs about quantum mechanics would lead us to form true beliefs. I show that in an Everettian context, the experimental evidence that we have available could not provide empirical confirmation for quantum mechanics, and moreover that we would not even be able to establish reference to the theoretical entities of quantum mechanics. I then consider a range of existing Everettian approaches to the probability problem and show that they do not succeed in overcoming this incoherence.

  18. Barcoded microchips for biomolecular assays.

    Science.gov (United States)

    Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu

    2015-01-20

    Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

  19. Radioreceptor assay method for insulin

    Energy Technology Data Exchange (ETDEWEB)

    Mori, K.F.; Wood, R.J. (Bureau of Drug Research, Health and Welfare Canada, Ottawa, Ontario. Health Protection Branch)

    1984-01-01

    A sensitive practical radioreceptor assay method for pharmaceutical insulin products has been developed with partially purified rat liver plasma membranes and the optimal conditions under which the best overall assay performance is obtainable have been defined. Intra- and inter-assay variations of the method averaged 7.3 and 12.2% of the man, respectively, when expressed as the coefficient of variation. Potency estimates of an insulin product obtained with the proposed method correlated well with those determined by the mouse convulsion bioassay method. Liver membranes prepared according to the method could be stored for up to ten weeks at 4/sup 0/C and for 6 months or more at -18/sup 0/C without losing insulin-binding ability.

  20. Catapult current sheet relaxation model confirmed by THEMIS observations

    Science.gov (United States)

    Machida, S.; Miyashita, Y.; Ieda, A.; Nose, M.; Angelopoulos, V.; McFadden, J. P.

    2014-12-01

    In this study, we show the result of superposed epoch analysis on the THEMIS probe data during the period from November, 2007 to April, 2009 by setting the origin of time axis to the substorm onset determined by Nishimura with THEMIS all sky imager (THEMS/ASI) data (http://www.atmos.ucla.edu/~toshi/files/paper/Toshi_THEMIS_GBO_list_distribution.xls). We confirmed the presence of earthward flows which can be associated with north-south auroral streamers during the substorm growth phase. At around X = -12 Earth radii (Re), the northward magnetic field and its elevation angle decreased markedly approximately 4 min before substorm onset. A northward magnetic-field increase associated with pre-onset earthward flows was found at around X = -17Re. This variation indicates the occurrence of the local depolarization. Interestingly, in the region earthwards of X = -18Re, earthward flows in the central plasma sheet (CPS) reduced significantly about 3min before substorm onset. However, the earthward flows enhanced again at t = -60 sec in the region around X = -14 Re, and they moved toward the Earth. At t = 0, the dipolarization of the magnetic field started at X ~ -10 Re, and simultaneously the magnetic reconnection started at X ~ -20 Re. Synthesizing these results, we can confirm the validity of our catapult current sheet relaxation model.

  1. Structural confirmation of oligosaccharides newly isolated from sugar beet molasses

    Directory of Open Access Journals (Sweden)

    Abe Tatsuya

    2012-08-01

    Full Text Available Abstract Background Sugar beet molasses is a viscous by-product of the processing of sugar beets into sugar. The molasses is known to contain sucrose and raffinose, a typical trisaccharide, with a well-established structure. Although sugar beet molasses contains various other oligosaccharides as well, the structures of those oligosaccharides have not been examined in detail. The purpose of this study was isolation and structural confirmation of these other oligosaccharides found in sugar beet molasses. Results Four oligosaccharides were newly isolated from sugar beet molasses using high-performance liquid chromatography (HPLC and carbon-Celite column chromatography. Structural confirmation of the saccharides was provided by methylation analysis, matrix-assisted laser desorption/ionaization time of flight mass spectrometry (MALDI-TOF-MS, and nuclear magnetic resonance (NMR measurements. Conclusion The following oligosaccharides were identified in sugar beet molasses: β-D-galactopyranosyl-(1- > 6-β-D-fructofuranosyl-(2 1-α-D-glucopyranoside (named β-planteose, α-D-galactopyranosyl-(1- > 1-β-D-fructofuranosyl-(2 1-α-D-glucopyranoside (named1-planteose, α-D-glucopyranosyl-(1- > 6-α-D-glucopyranosyl-(1 2-β-D-fructofuranoside (theanderose, and β-D-glucopyranosyl-(1- > 3-α-D-glucopyranosyl-(1 2-β-D-fructofuranoside (laminaribiofructose. 1-planteose and laminaribiofructose were isolated from natural sources for the first time.

  2. Development of a high-throughput replicon assay for the identification of respiratory syncytial virus inhibitors.

    Science.gov (United States)

    Tiong-Yip, Choi-Lai; Plant, Helen; Sharpe, Paul; Fan, Jun; Rich, Kirsty; Gorseth, Elise; Yu, Qin

    2014-01-01

    Respiratory syncytial virus (RSV) drug discovery has been hindered by the lack of good chemistry starting points and would benefit from robust and convenient assays for high-throughput screening (HTS). In this paper, we present the development and optimization of a 384-well RSV replicon assay that enabled HTS for RSV replication inhibitors with a low bio-containment requirement. The established replicon assay was successfully implemented for high-throughput screening. A validation screen was performed which demonstrated high assay performance and reproducibility. Assay quality was further confirmed via demonstration of appropriate pharmacology for different classes of RSV replication tool inhibitors. RSV replicon and cytotoxicity assays were further developed into a multiplexed format that measured both inhibition of viral replication and cytotoxicity from the same well. This provided a time and cost efficient approach to support lead optimization. In summary, we have developed a robust RSV replicon assay to help expedite the discovery of novel RSV therapeutics.

  3. [Comparison of the clinical performance of the ECLusys HBsAg II assay with the Lumipulse f and HISCL 2000-i HBsAg screening assays].

    Science.gov (United States)

    Sugiura, Aya; Iwahara, Kunihiro; Suga, Yasuyuki; Uchiyama, Sachinori; Maekawa, Masato

    2012-02-01

    We compared the ECLusys HBsAgII (ECL HBsAg) assay to the Lumipulse Forte (LPf HBsAg) and HISCL (HIS HBsAg) assays. Measurement of dilution panels for which the WHO HBsAg international reference panel was the parent specimen revealed that the ECL and HIS assays enabled detection to a theoretical level of 0.04 IU/mL, whereas the LPf assay enabled detection to a level of 0.08 IU/mL. In a specificity test using high RF positive specimens (n = 33), pregnancy specimens (n = 35), cytomegalovirus antibody positive specimens (n = 36), and high M protein positive specimens (n = 21) that were confirmed negative for HBsAg by the LPf assay, negative results were obtained for all specimens on the HIS assay, but the ECL assay yielded a positive result for one of the high RF positive specimens. This individual was suggested on further testing to be an HBV carrier who was strongly positive for HBc antibody. In HBsAg mutants detection test, the detection rate was 92.3% with the ECL assay and 69.2% with the HIS assay. In a correlation test using routinely collected clinical specimens (n = 155), including positive stock specimens, aside from the one case where the LPf assay gave a negative result but both the ECL and HIS assays gave positive results, all of the results were consistent for all specimens. The above results confirmed that the ECL assay is both highly sensitive and specific, and also enables a high rate of HBsAg mutant detection.

  4. Confirmation of a new conserved linear epitope of Lyssavirus nucleoprotein.

    Science.gov (United States)

    Xinjun, Lv; Xuejun, Ma; Lihua, Wang; Hao, Li; Xinxin, Shen; Pengcheng, Yu; Qing, Tang; Guodong, Liang

    2012-05-01

    Bioinformatics analysis was used to predict potential epitopes of Lyssavirus nucleoprotein and highlighted some distinct differences in the quantity and localization of the epitopes disclosed by epitope analysis of monoclonal antibodies against Lyssavirus nucleoprotein. Bioinformatics analysis showed that the domain containing residues 152-164 of Lyssavirus nucleoprotein was a conserved linear epitope that had not been reported previously. Immunization of two rabbits with the corresponding synthetic peptide conjugated to the Keyhole Limpe hemocyanin (KLH) macromolecule resulted in a titer of anti-peptide antibody above 1:200,000 in rabbit sera as detected by indirect enzyme-linked immunosorbent assay (ELISA). Western blot analysis demonstrated that the anti-peptide antibody recognized denatured Lyssavirus nucleoprotein in sodium dodecylsulfonate-polyacrylate gel electrophoresis (SDS-PAGE). Affinity chromatography purification and FITC-labeling of the anti-peptide antibody in rabbit sera was performed. FITC-labeled anti-peptide antibody could recognize Lyssavirus nucleoprotein in BSR cells and canine brain tissues even at a 1:200 dilution. Residues 152-164 of Lyssavirus nucleoprotein were verified as a conserved linear epitope in Lyssavirus. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Confirmation of the Y(4260) Resonance Production in ISR

    CERN Document Server

    He, Q; Muramatsu, H; Park, C S; Thorndike, E H; Yang, F; Coan, T E; Gao, Y S; Artuso, M; Blusk, S; Butt, J; Li, J; Menaa, N; Mountain, R; Nisar, S; Randrianarivony, K; Sia, R; Skwarnicki, T; Stone, S; Wang, J C; Zhang, K; Csorna, S E; Bonvicini, G; Cinabro, D; Dubrovin, M; Lincoln, A; Asner, D M; Edwards, K W; Briere, R A; Chen, J; Ferguson, T; Tatishvili, G T; Vogel, H; Watkins, M E; Rosner, J L; Adam, N E; Alexander, J P; Berkelman, K; Cassel, D G; Duboscq, J E; Ecklund, K M; Ehrlich, R; Fields, L; Galik, R S; Gibbons, L; Gray, R; Gray, S W; Hartill, D L; Hertz, D; Jones, C D; Kandaswamy, J; Kreinick, D L; Kuznetsov, V E; Mahlke-Krüger, H; Onyisi, P U E; Patterson, J R; Peterson, D; Pivarski, J; Riley, D; Ryd, A; Sadoff, A J; Schwarthoff, H; Shi, X; Stroiney, S; Sun, W M; Wilksen, T; Weinberger, M; Athar, S B; Patel, R; Potlia, V; Yelton, J; Rubin, P; Cawlfield, C; Eisenstein, B I; Karliner, I; Kim, D; Lowrey, N; Naik, P; Sedlack, C; Selen, M; White, E J; Wiss, J; Mitchell, R E; Shepherd, M R; Besson, D; Pedlar, T K; Cronin-Hennessy, D; Gao, K Y; Hietala, J; Kubota, Y; Klein, T; Lang, B W; Poling, R; Scott, A W; Smith, A; Zweber, P; Dobbs, S; Metreveli, Z V; Seth, K K; Tomaradze, A G; Ernst, J; Severini, H; Dytman, S A; Love, W; Savinov, V; Aquines, O; Li, Z; López, A; Mehrabyan, S S; Méndez, H; Ramírez, J; Huang, G S; Miller, D H; Pavlunin, V; Sanghi, B; Shipsey, I P; Xin, B; Adams, G S; Anderson, M; Cummings, J P; Danko, I; Napolitano, J; al., et

    2006-01-01

    Using 13.3 fb^-1 of e+e- collision data taken in the Upsilon(1S-4S) region with the CLEO III detector at the CESR collider, a search has been made for the new resonance Y(4260) recently reported by the BaBar Collaboration. The production of Y(4260) in initial state radiation (ISR), and its decay into pi+pi-J/psi are confirmed. A good quality fit to our data is obtained with a single resonance. We determine M(Y(4260))=(4284+17-16(stat)+-4(syst)) MeV/c^2, Gamma(Y(4260))=(73+39-25(stat)+-5(syst)) MeV/c^2, and Gamma_ee(Y(4260))xBr(Y(4260)->pi+pi-J/psi)=(8.9+3.9-3.1(stat)+-1.9(syst)) eV/c^2.

  6. Improved statistical confirmation of margins for setpoints and transients

    Energy Technology Data Exchange (ETDEWEB)

    Nutt, W.T. [Framatome ANP Richland, INC., WA (United States)

    2001-07-01

    Framatome ANP Richland, Inc. has developed an integrated, automated, statistical methodology for Pressurized Water Reactors (PWRs). Margins for transients and calculated trips are confirmed using several new applications of probability theory. The methods used for combining statistics reduces the conservatisms inherent in conventional methods and avoids the numerical limitations and time constraints imposed by Monte Carlo techniques. The new methodology represents the state of the art in the treatment of uncertainties for reactor protection systems. It all but eliminates concerns with the calculated trips for PWRs and by improving the margin for all transients will allow for far more aggressive peaking limits and fuel management schemes. The automated nature of the bulk of this process saves Framatome ANP time and effort, minimizes the potential for errors and makes the analysis for all cycles and plants consistent. The enhanced margins remove analytical limitations from the customer and allow for more economical operation of the plant. (authors)

  7. Model-independent confirmation of the $Z(4430)^-$ state

    CERN Document Server

    Aaij, Roel; Adinolfi, Marco; Affolder, Anthony; Ajaltouni, Ziad; Albrecht, Johannes; Alessio, Federico; Alexander, Michael; Ali, Suvayu; Alkhazov, Georgy; Alvarez Cartelle, Paula; Alves Jr, Antonio; Amato, Sandra; Amerio, Silvia; Amhis, Yasmine; An, Liupan; Anderlini, Lucio; Anderson, Jonathan; Andreassen, Rolf; Andreotti, Mirco; Andrews, Jason; Appleby, Robert; Aquines Gutierrez, Osvaldo; Archilli, Flavio; Artamonov, Alexander; Artuso, Marina; Aslanides, Elie; Auriemma, Giulio; Baalouch, Marouen; Bachmann, Sebastian; Back, John; Badalov, Alexey; Balagura, Vladislav; Baldini, Wander; Barlow, Roger; Barschel, Colin; Barsuk, Sergey; Barter, William; Batozskaya, Varvara; Bauer, Thomas; Bay, Aurelio; Beaucourt, Leo; Beddow, John; Bedeschi, Franco; Bediaga, Ignacio; Belogurov, Sergey; Belous, Konstantin; Belyaev, Ivan; Ben-Haim, Eli; Bencivenni, Giovanni; Benson, Sean; Benton, Jack; Berezhnoy, Alexander; Bernet, Roland; Bettler, Marc-Olivier; van Beuzekom, Martinus; Bien, Alexander; Bifani, Simone; Bird, Thomas; Bizzeti, Andrea; Bjørnstad, Pål Marius; Blake, Thomas; Blanc, Frédéric; Blouw, Johan; Blusk, Steven; Bocci, Valerio; Bondar, Alexander; Bondar, Nikolay; Bonivento, Walter; Borghi, Silvia; Borgia, Alessandra; Borsato, Martino; Bowcock, Themistocles; Bowen, Espen Eie; Bozzi, Concezio; Brambach, Tobias; van den Brand, Johannes; Bressieux, Joël; Brett, David; Britsch, Markward; Britton, Thomas; Brodzicka, Jolanta; Brook, Nicholas; Brown, Henry; Bursche, Albert; Busetto, Giovanni; Buytaert, Jan; Cadeddu, Sandro; Calabrese, Roberto; Calvi, Marta; Calvo Gomez, Miriam; Camboni, Alessandro; Campana, Pierluigi; Campora Perez, Daniel; Carbone, Angelo; Carboni, Giovanni; Cardinale, Roberta; Cardini, Alessandro; Carranza-Mejia, Hector; Carson, Laurence; Carvalho Akiba, Kazuyoshi; Casse, Gianluigi; Cassina, Lorenzo; Castillo Garcia, Lucia; Cattaneo, Marco; Cauet, Christophe; Cenci, Riccardo; Charles, Matthew; Charpentier, Philippe; Chen, Shanzhen; Cheung, Shu-Faye; Chiapolini, Nicola; Chrzaszcz, Marcin; Ciba, Krzystof; Cid Vidal, Xabier; Ciezarek, Gregory; Clarke, Peter; Clemencic, Marco; Cliff, Harry; Closier, Joel; Coco, Victor; Cogan, Julien; Cogneras, Eric; Collins, Paula; Comerma-Montells, Albert; Contu, Andrea; Cook, Andrew; Coombes, Matthew; Coquereau, Samuel; Corti, Gloria; Corvo, Marco; Counts, Ian; Couturier, Benjamin; Cowan, Greig; Craik, Daniel Charles; Cruz Torres, Melissa Maria; Cunliffe, Samuel; Currie, Robert; D'Ambrosio, Carmelo; Dalseno, Jeremy; David, Pascal; David, Pieter; Davis, Adam; De Bruyn, Kristof; De Capua, Stefano; De Cian, Michel; De Miranda, Jussara; De Paula, Leandro; De Silva, Weeraddana; De Simone, Patrizia; Decamp, Daniel; Deckenhoff, Mirko; Del Buono, Luigi; Déléage, Nicolas; Derkach, Denis; Deschamps, Olivier; Dettori, Francesco; Di Canto, Angelo; Dijkstra, Hans; Donleavy, Stephanie; Dordei, Francesca; Dorigo, Mirco; Dosil Suárez, Alvaro; Dossett, David; Dovbnya, Anatoliy; Dujany, Giulio; Dupertuis, Frederic; Durante, Paolo; Dzhelyadin, Rustem; Dziurda, Agnieszka; Dzyuba, Alexey; Easo, Sajan; Egede, Ulrik; Egorychev, Victor; Eidelman, Semen; Eisenhardt, Stephan; Eitschberger, Ulrich; Ekelhof, Robert; Eklund, Lars; El Rifai, Ibrahim; Elsasser, Christian; Ely, Scott; Esen, Sevda; Evans, Timothy; Falabella, Antonio; Färber, Christian; Farinelli, Chiara; Farley, Nathanael; Farry, Stephen; Ferguson, Dianne; Fernandez Albor, Victor; Ferreira Rodrigues, Fernando; Ferro-Luzzi, Massimiliano; Filippov, Sergey; Fiore, Marco; Fiorini, Massimiliano; Firlej, Miroslaw; Fitzpatrick, Conor; Fiutowski, Tomasz; Fontana, Marianna; Fontanelli, Flavio; Forty, Roger; Francisco, Oscar; Frank, Markus; Frei, Christoph; Frosini, Maddalena; Fu, Jinlin; Furfaro, Emiliano; Gallas Torreira, Abraham; Galli, Domenico; Gallorini, Stefano; Gambetta, Silvia; Gandelman, Miriam; Gandini, Paolo; Gao, Yuanning; Garofoli, Justin; Garra Tico, Jordi; Garrido, Lluis; Gaspar, Clara; Gauld, Rhorry; Gavardi, Laura; Gersabeck, Evelina; Gersabeck, Marco; Gershon, Timothy; Ghez, Philippe; Gianelle, Alessio; Giani', Sebastiana; Gibson, Valerie; Giubega, Lavinia-Helena; Gligorov, Vladimir; Göbel, Carla; Golubkov, Dmitry; Golutvin, Andrey; Gomes, Alvaro; Gordon, Hamish; Gotti, Claudio; Grabalosa Gándara, Marc; Graciani Diaz, Ricardo; Granado Cardoso, Luis Alberto; Graugés, Eugeni; Graziani, Giacomo; Grecu, Alexandru; Greening, Edward; Gregson, Sam; Griffith, Peter; Grillo, Lucia; Grünberg, Oliver; Gui, Bin; Gushchin, Evgeny; Guz, Yury; Gys, Thierry; Hadjivasiliou, Christos; Haefeli, Guido; Haen, Christophe; Haines, Susan; Hall, Samuel; Hamilton, Brian; Hampson, Thomas; Han, Xiaoxue; Hansmann-Menzemer, Stephanie; Harnew, Neville; Harnew, Samuel; Harrison, Jonathan; Hartmann, Thomas; He, Jibo; Head, Timothy; Heijne, Veerle; Hennessy, Karol; Henrard, Pierre; Henry, Louis; Hernando Morata, Jose Angel; van Herwijnen, Eric; Heß, Miriam; Hicheur, Adlène; Hill, Donal; Hoballah, Mostafa; Hombach, Christoph; Hulsbergen, Wouter; Hunt, Philip; Hussain, Nazim; Hutchcroft, David; Hynds, Daniel; Idzik, Marek; Ilten, Philip; Jacobsson, Richard; Jaeger, Andreas; Jalocha, Pawel; Jans, Eddy; Jaton, Pierre; Jawahery, Abolhassan; Jezabek, Marek; Jing, Fanfan; John, Malcolm; Johnson, Daniel; Jones, Christopher; Joram, Christian; Jost, Beat; Jurik, Nathan; Kaballo, Michael; Kandybei, Sergii; Kanso, Walaa; Karacson, Matthias; Karbach, Moritz; Kelsey, Matthew; Kenyon, Ian; Ketel, Tjeerd; Khanji, Basem; Khurewathanakul, Chitsanu; Klaver, Suzanne; Kochebina, Olga; Kolpin, Michael; Komarov, Ilya; Koopman, Rose; Koppenburg, Patrick; Korolev, Mikhail; Kozlinskiy, Alexandr; Kravchuk, Leonid; Kreplin, Katharina; Kreps, Michal; Krocker, Georg; Krokovny, Pavel; Kruse, Florian; Kucharczyk, Marcin; Kudryavtsev, Vasily; Kurek, Krzysztof; Kvaratskheliya, Tengiz; La Thi, Viet Nga; Lacarrere, Daniel; Lafferty, George; Lai, Adriano; Lambert, Dean; Lambert, Robert W; Lanciotti, Elisa; Lanfranchi, Gaia; Langenbruch, Christoph; Langhans, Benedikt; Latham, Thomas; Lazzeroni, Cristina; Le Gac, Renaud; van Leerdam, Jeroen; Lees, Jean-Pierre; Lefèvre, Regis; Leflat, Alexander; Lefrançois, Jacques; Leo, Sabato; Leroy, Olivier; Lesiak, Tadeusz; Leverington, Blake; Li, Yiming; Liles, Myfanwy; Lindner, Rolf; Linn, Christian; Lionetto, Federica; Liu, Bo; Liu, Guoming; Lohn, Stefan; Longstaff, Iain; Lopes, Jose; Lopez-March, Neus; Lowdon, Peter; Lu, Haiting; Lucchesi, Donatella; Luo, Haofei; Lupato, Anna; Luppi, Eleonora; Lupton, Oliver; Machefert, Frederic; Machikhiliyan, Irina V; Maciuc, Florin; Maev, Oleg; Malde, Sneha; Manca, Giulia; Mancinelli, Giampiero; Manzali, Matteo; Maratas, Jan; Marchand, Jean François; Marconi, Umberto; Marin Benito, Carla; Marino, Pietro; Märki, Raphael; Marks, Jörg; Martellotti, Giuseppe; Martens, Aurelien; Martín Sánchez, Alexandra; Martinelli, Maurizio; Martinez Santos, Diego; Martinez Vidal, Fernando; Martins Tostes, Danielle; Massafferri, André; Matev, Rosen; Mathe, Zoltan; Matteuzzi, Clara; Mazurov, Alexander; McCann, Michael; McCarthy, James; McNab, Andrew; McNulty, Ronan; McSkelly, Ben; Meadows, Brian; Meier, Frank; Meissner, Marco; Merk, Marcel; Milanes, Diego Alejandro; Minard, Marie-Noelle; Moggi, Niccolò; Molina Rodriguez, Josue; Monteil, Stephane; Moran, Dermot; Morandin, Mauro; Morawski, Piotr; Mordà, Alessandro; Morello, Michael Joseph; Moron, Jakub; Morris, Adam Benjamin; Mountain, Raymond; Muheim, Franz; Müller, Katharina; Muresan, Raluca; Mussini, Manuel; Muster, Bastien; Naik, Paras; Nakada, Tatsuya; Nandakumar, Raja; Nasteva, Irina; Needham, Matthew; Neri, Nicola; Neubert, Sebastian; Neufeld, Niko; Neuner, Max; Nguyen, Anh Duc; Nguyen, Thi-Dung; Nguyen-Mau, Chung; Nicol, Michelle; Niess, Valentin; Niet, Ramon; Nikitin, Nikolay; Nikodem, Thomas; Novoselov, Alexey; Oblakowska-Mucha, Agnieszka; Obraztsov, Vladimir; Oggero, Serena; Ogilvy, Stephen; Okhrimenko, Oleksandr; Oldeman, Rudolf; Onderwater, Gerco; Orlandea, Marius; Otalora Goicochea, Juan Martin; Owen, Patrick; Oyanguren, Maria Arantza; Pal, Bilas Kanti; Palano, Antimo; Palombo, Fernando; Palutan, Matteo; Panman, Jacob; Papanestis, Antonios; Pappagallo, Marco; Parkes, Christopher; Parkinson, Christopher John; Passaleva, Giovanni; Patel, Girish; Patel, Mitesh; Patrignani, Claudia; Pazos Alvarez, Antonio; Pearce, Alex; Pellegrino, Antonio; Pepe Altarelli, Monica; Perazzini, Stefano; Perez Trigo, Eliseo; Perret, Pascal; Perrin-Terrin, Mathieu; Pescatore, Luca; Pesen, Erhan; Petridis, Konstantin; Petrolini, Alessandro; Picatoste Olloqui, Eduardo; Pietrzyk, Boleslaw; Pilař, Tomas; Pinci, Davide; Pistone, Alessandro; Playfer, Stephen; Plo Casasus, Maximo; Polci, Francesco; Poluektov, Anton; Polycarpo, Erica; Popov, Alexander; Popov, Dmitry; Popovici, Bogdan; Potterat, Cédric; Powell, Andrew; Prisciandaro, Jessica; Pritchard, Adrian; Prouve, Claire; Pugatch, Valery; Puig Navarro, Albert; Punzi, Giovanni; Qian, Wenbin; Rachwal, Bartolomiej; Rademacker, Jonas; Rakotomiaramanana, Barinjaka; Rama, Matteo; Rangel, Murilo; Raniuk, Iurii; Rauschmayr, Nathalie; Raven, Gerhard; Reichert, Stefanie; Reid, Matthew; dos Reis, Alberto; Ricciardi, Stefania; Richards, Alexander; Rihl, Mariana; Rinnert, Kurt; Rives Molina, Vincente; Roa Romero, Diego; Robbe, Patrick; Rodrigues, Ana Barbara; Rodrigues, Eduardo; Rodriguez Perez, Pablo; Roiser, Stefan; Romanovsky, Vladimir; Romero Vidal, Antonio; Rotondo, Marcello; Rouvinet, Julien; Ruf, Thomas; Ruffini, Fabrizio; Ruiz, Hugo; Ruiz Valls, Pablo; Sabatino, Giovanni; Saborido Silva, Juan Jose; Sagidova, Naylya; Sail, Paul; Saitta, Biagio; Salustino Guimaraes, Valdir; Sanchez Mayordomo, Carlos; Sanmartin Sedes, Brais; Santacesaria, Roberta; Santamarina Rios, Cibran; Santovetti, Emanuele; Sapunov, Matvey; Sarti, Alessio; Satriano, Celestina; Satta, Alessia; Savrie, Mauro; Savrina, Darya; Schiller, Manuel; Schindler, Heinrich; Schlupp, Maximilian; Schmelling, Michael; Schmidt, Burkhard; Schneider, Olivier; Schopper, Andreas; Schune, Marie Helene; Schwemmer, Rainer; Sciascia, Barbara; Sciubba, Adalberto; Seco, Marcos; Semennikov, Alexander; Senderowska, Katarzyna; Sepp, Indrek; Serra, Nicola; Serrano, Justine; Sestini, Lorenzo; Seyfert, Paul; Shapkin, Mikhail; Shapoval, Illya; Shcheglov, Yury; Shears, Tara; Shekhtman, Lev; Shevchenko, Vladimir; Shires, Alexander; Silva Coutinho, Rafael; Simi, Gabriele; Sirendi, Marek; Skidmore, Nicola; Skwarnicki, Tomasz; Smith, Anthony; Smith, Edmund; Smith, Eluned; Smith, Jackson; Smith, Mark; Snoek, Hella; Sokoloff, Michael; Soler, Paul; Soomro, Fatima; Souza, Daniel; Souza De Paula, Bruno; Spaan, Bernhard; Sparkes, Ailsa; Spinella, Franco; Spradlin, Patrick; Stagni, Federico; Stahl, Sascha; Steinkamp, Olaf; Stenyakin, Oleg; Stevenson, Scott; Stoica, Sabin; Stone, Sheldon; Storaci, Barbara; Stracka, Simone; Straticiuc, Mihai; Straumann, Ulrich; Stroili, Roberto; Subbiah, Vijay Kartik; Sun, Liang; Sutcliffe, William; Swientek, Krzysztof; Swientek, Stefan; Syropoulos, Vasileios; Szczekowski, Marek; Szczypka, Paul; Szilard, Daniela; Szumlak, Tomasz; T'Jampens, Stephane; Teklishyn, Maksym; Tellarini, Giulia; Teubert, Frederic; Thomas, Christopher; Thomas, Eric; van Tilburg, Jeroen; Tisserand, Vincent; Tobin, Mark; Tolk, Siim; Tomassetti, Luca; Tonelli, Diego; Topp-Joergensen, Stig; Torr, Nicholas; Tournefier, Edwige; Tourneur, Stephane; Tran, Minh Tâm; Tresch, Marco; Tsaregorodtsev, Andrei; Tsopelas, Panagiotis; Tuning, Niels; Ubeda Garcia, Mario; Ukleja, Artur; Ustyuzhanin, Andrey; Uwer, Ulrich; Vagnoni, Vincenzo; Valenti, Giovanni; Vallier, Alexis; Vazquez Gomez, Ricardo; Vazquez Regueiro, Pablo; Vázquez Sierra, Carlos; Vecchi, Stefania; Velthuis, Jaap; Veltri, Michele; Veneziano, Giovanni; Vesterinen, Mika; Viaud, Benoit; Vieira, Daniel; Vieites Diaz, Maria; Vilasis-Cardona, Xavier; Vollhardt, Achim; Volyanskyy, Dmytro; Voong, David; Vorobyev, Alexey; Vorobyev, Vitaly; Voß, Christian; Voss, Helge; de Vries, Jacco; Waldi, Roland; Wallace, Charlotte; Wallace, Ronan; Walsh, John; Wandernoth, Sebastian; Wang, Jianchun; Ward, David; Watson, Nigel; Websdale, David; Whitehead, Mark; Wicht, Jean; Wiedner, Dirk; Wilkinson, Guy; Williams, Matthew; Williams, Mike; Wilson, Fergus; Wimberley, Jack; Wishahi, Julian; Wislicki, Wojciech; Witek, Mariusz; Wormser, Guy; Wotton, Stephen; Wright, Simon; Wu, Suzhi; Wyllie, Kenneth; Xie, Yuehong; Xing, Zhou; Xu, Zhirui; Yang, Zhenwei; Yuan, Xuhao; Yushchenko, Oleg; Zangoli, Maria; Zavertyaev, Mikhail; Zhang, Feng; Zhang, Liming; Zhang, Wen Chao; Zhang, Yanxi; Zhelezov, Alexey; Zhokhov, Anatoly; Zhong, Liang; Zvyagin, Alexander

    2015-01-01

    The decay $B^0\\to \\psi(2S) K^+\\pi^-$ is analyzed using $\\rm 3~fb^{-1}$ of $pp$ collision data collected with the LHCb detector. A model-independent description of the $\\psi(2S) \\pi$ mass spectrum is obtained, using as input the $K\\pi$ mass spectrum and angular distribution derived directly from data, without requiring a theoretical description of resonance shapes or their interference. The hypothesis that the $\\psi(2S)\\pi$ mass spectrum can be described in terms of $K\\pi$ reflections alone is rejected with more than 8$\\sigma$ significance. This provides confirmation, in a model-independent way, of the need for an additional resonant component in the mass region of the $Z(4430)^-$ exotic state.

  8. The first confirmed case of Diphyllobothrium latum in Brazil

    Directory of Open Access Journals (Sweden)

    FLN Santos

    2005-10-01

    Full Text Available Diphyllobothriasis is an infection of the small intestine by the broad tapeworm Diphyllobothrium sp. The associated symptomatology is nonspecific, but megaloblastic anemia is a well-described complication. Although the infection is common in temperate regions, descriptions in South America have so far been limited to Chile, Peru, and a few cases in Argentina. This paper presents the first confirmed Brazilian case of diphyllobothriasis. A 29-years-old woman living in Salvador (state of Bahia apparently acquired the infection from eating sushi. The diagnosis was based on fecal examination that revealed a large quantity of operculated eggs. A single dose of praziquantel (600 mg was sufficient to cure the infection.

  9. Molecular confirmation of an adenovirus in brushtail possums (Trichosurus vulpecula).

    Science.gov (United States)

    Thomson, Darelle; Meers, Joanne; Harrach, Balázs

    2002-02-26

    Partial genome characterisation of a non-cultivable marsupial adenovirus is described. Adenovirus-like particles were found by electron microscopy (EM) in the intestinal contents of brushtail possums (Trichosurus vulpecula) in New Zealand. Using degenerate PCR primers complementary to the most conserved genome regions of adenoviruses, the complete nucleotide sequence of the penton base gene, and partial nucleotide sequences of the DNA polymerase, hexon, and pVII genes were obtained. Phylogenetic analysis of the penton base gene strongly suggested that the brushtail possum adenovirus (candidate PoAdV-1) belongs to the recently proposed genus Atadenovirus. Sequence analysis of the PCR products amplified from the intestinal contents of brushtail possums originating from different geographical regions of New Zealand identified a single genotype. This is the first report of molecular confirmation of an adenovirus in a marsupial.

  10. A Photometrically and Spectroscopically Confirmed Population of Passive Spiral Galaxies

    CERN Document Server

    Fraser-McKelvie, Amelia; Pimbblet, Kevin A; Dolley, Tim; Crossett, Jacob P; Bonne, Nicolas J

    2016-01-01

    We have identified a population of passive spiral galaxies from photometry and integral field spectroscopy. We selected z<0.035 spiral galaxies that have WISE colours consistent with little mid-infrared emission from warm dust. Matched aperture photometry of 51 spiral galaxies in ultraviolet, optical and mid-infrared show these galaxies have colours consistent with passive galaxies. Six galaxies form a spectroscopic pilot study and were observed using the Wide-Field Spectrograph (WiFeS) to check for signs of nebular emission from star formation. We see no evidence of substantial nebular emission found in previous red spiral samples. These six galaxies possess absorption-line spectra with 4000\\AA\\ breaks consistent with an average luminosity-weighted age of 2.3 Gyr. Our photometric and IFU spectroscopic observations confirm the existence of a population of local passive spiral galaxies, implying that transformation into early-type morphologies is not required for the quenching of star formation.

  11. Exploring nurses' confirmed expectations regarding health IT: a phenomenological study.

    Science.gov (United States)

    Zadvinskis, Inga M; Chipps, Esther; Yen, Po-Yin

    2014-02-01

    Health information technology (IT) benefits both patients and providers with respect to health care quality and perceived usefulness. Although existing research provides a preliminary understanding of nurses' perception of health IT, perceptions do not guide actions. This phenomenological study explored nurses' perceptions regarding electronic health records and bar code medication administration four months post implementation on a medical-surgical unit in an academic medical center. Ten staff nurses (8 females and 2 males) participated. We categorized the results into five themes from personal-level to organizational-level confirmed expectations: (1) nurses' interaction with computer, (2) nursing performance regarding task accomplishment, (3) unit-specific teamwork, (4) interdisciplinary teamwork, and (5) quality of care. We discovered that effective health IT must be congruent with nursing expectations. IT professionals, nursing and organizational leaders may use findings to structure an environment supportive of effective health IT in nursing practice.

  12. Capabilities for identification and confirmation of bacterial biological agents

    Directory of Open Access Journals (Sweden)

    Diana M. Popescu

    2016-12-01

    Full Text Available Military Medical Service is able for detection, identification and confirmation of biological agents; it is part of medical protection against CBRN weapons. We are specialized capabilities for in vitro tests, under construction, the maximum containment laboratory designed for work with Risk Group Microorganisms. An efficient primary containment system must be in place, consisting of one or a combination of the following: Class III safety cabinet laboratory, passage of two doors, suit laboratory, controlled access, controlled air system. Negative pressure in the facility, supply and exhaust air must be HEPA-filtered, decontamination of effluents, sterilization of waste and materials, airlock entry ports for specimens, materials and animals must be provided etc. Complementary is an Animal facility for in vivo tests. This is suitable for work with animals that are deliberately inoculated with microorganisms in Risk Group.

  13. Experimenter Confirmation Bias and the Correction of Science Misconceptions

    Science.gov (United States)

    Allen, Michael; Coole, Hilary

    2012-06-01

    This paper describes a randomised educational experiment ( n = 47) that examined two different teaching methods and compared their effectiveness at correcting one science misconception using a sample of trainee primary school teachers. The treatment was designed to promote engagement with the scientific concept by eliciting emotional responses from learners that were triggered by their own confirmation biases. The treatment group showed superior learning gains to control at post-test immediately after the lesson, although benefits had dissipated after 6 weeks. Findings are discussed with reference to the conceptual change paradigm and to the importance of feeling emotion during a learning experience, having implications for the teaching of pedagogies to adults that have been previously shown to be successful with children.

  14. Confirmation of prenatal diagnosis of sex chromosome mosaicism.

    Science.gov (United States)

    McFadden, D E; Kalousek, D K

    1989-04-01

    Prenatal diagnosis of mosaicism causes problems in interpretation and in genetic counselling. Part of the difficulty with any prenatal diagnosis of mosaicism is interpretation of results without knowing the exact origin, embryonic or extraembryonic, of the abnormal cell line. To confuse the issue in cases of prenatal diagnosis of 45,X/46,XY mosaicism is the recent demonstration that a diagnosis of 45,X/46,XY made prenatally is not necessarily associated with the same phenotype as when diagnosed postnatally. We present two cases of prenatal diagnosis of sex chromosome mosaicism (45,X/46,XY and 45,X/47,XYY). Posttermination examination of the phenotypically normal male fetuses and their placentas established that the placenta was the most likely source of the 45,X cell line. An approach to confirming the prenatal diagnosis of sex chromosome mosaicism and establishing its origin utilizing detailed cytogenetic examination of both fetus and placenta is suggested.

  15. Validity of quasilinear theory: refutations and new numerical confirmation

    Energy Technology Data Exchange (ETDEWEB)

    Besse, Nicolas; Bertrand, Pierre [UMR 7198 CNRS-Nancy Universites, Universite Henri Poincare, Bd des Aiguillettes, BP 70239, FR-54506 Vandoeuvre-les-Nancy Cedex (France); Elskens, Yves; Escande, D F, E-mail: nicolas.besse@iecn.u-nancy.fr, E-mail: yves.elskens@univ-provence.fr, E-mail: dominique.escande@univ-provence.fr [UMR 6633 CNRS-Universite de Provence, Faculte de St Jerome, Case 321, Av. Normandie Niemen, FR-13397 Marseille Cedex 20 (France)

    2011-02-15

    The validity of quasilinear (QL) theory describing the weak warm beam-plasma instability has been a controversial topic for several decades. This issue is tackled anew, both analytically and by numerical simulations which benefit from the power of modern computers and from the development in the last decade of Vlasov codes endowed with both accuracy and weak numerical diffusion. Self-consistent numerical simulations within the Vlasov-wave description show that QL theory remains valid in the strong chaotic diffusion regime. However, there is a non-QL regime before saturation, which confirms previous analytical work and numerical simulation, but contradicts another analytical work. We show analytically the absence of mode coupling in the saturation regime of the instability where a plateau is present in the tail of the particle distribution function. This invalidates several analytical works trying to prove or to contradict the validity of QL theory in the strongly nonlinear regime of the weak warm beam-plasma instability.

  16. Confirmation of some formulas related to spin coherence time

    CERN Document Server

    Orlov, Yuri

    2015-01-01

    This paper considers two sets of formulas related to a Spin Coherence Time (SCT) case with only vertical oscillations in a purely electric ring, the first derived by the author for the field index m > 0 and the second by Ivan Koop for the field index m = 0. I argue that a continuous transition can exist from one set to the other (contrary to appearances), and assume that a necessary condition for the transition is that both sets of formulas follow from the same equation. I demonstrate that they do follow when one takes into account that the first set of formulas holds only for times much larger than the period of the vertical oscillations. This demonstration confirms the correctness of the formulas and the equation.

  17. Neuroimaging findings in children with retinopathy-confirmed cerebral malaria

    Energy Technology Data Exchange (ETDEWEB)

    Potchen, Michael J. [Michigan State University, Department of Radiology, 184 Radiology Building, East Lansing, MI 48824-1303 (United States)], E-mail: mjp@rad.msu.edu; Birbeck, Gretchen L. [Michigan State University, International Neurologic and Psychiatric Epidemiology Program, 324 West Fee Hall, East Lansing, MI 48824 (United States)], E-mail: Gretchen.Birbeck@ht.msu.edu; DeMarco, J. Kevin [Michigan State University, Department of Radiology, 184 Radiology Building, East Lansing, MI 48824-1303 (United States)], E-mail: jkd@rad.msu.edu; Kampondeni, Sam D. [University of Malawi, Department of Radiology, Queen Elizabeth Central Hospital, Blantyre (Malawi)], E-mail: kamponde@msu.edu; Beare, Nicholas [St. Paul' s Eye Unit, Royal Liverpool University Hospital, Prescot Street, Liverpool L7 8XP (United Kingdom)], E-mail: nbeare@btinternet.com; Molyneux, Malcolm E. [Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine (Malawi); School of Tropical Medicine, University of Liverpool, Liverpool (United Kingdom)], E-mail: mmolyneux999@google.com; Taylor, Terrie E. [Michigan State University, College of Osteopathic Medicine, B309-B West Fee Hall, East Lansing, MI 48824 (United States); University of Malawi, College of Medicine, Blantyre Malaria Project, Blantyre (Malawi)], E-mail: taylort@msu.edu

    2010-04-15

    Purpose: To describe brain CT findings in retinopathy-confirmed, paediatric cerebral malaria. Materials and methods: In this outcomes study of paediatric cerebral malaria, a subset of children with protracted coma during initial presentation was scanned acutely. Survivors experiencing adverse neurological outcomes also underwent a head CT. All children had ophthalmological examination to confirm the presence of the retinopathy specific for cerebral malaria. Independent interpretation of CT images was provided by two neuroradiologists. Results: Acute brain CT findings in three children included diffuse oedema with obstructive hydrocephalus (2), acute cerebral infarctions in multiple large vessel distributions with secondary oedema and herniation (1), and oedema of thalamic grey matter (1). One child who was reportedly normal prior to admission had parenchymal atrophy suggestive of pre-existing CNS injury. Among 56 survivors (9-84 months old), 15 had adverse neurologic outcomes-11/15 had a follow-up head CT, 3/15 died and 1/15 refused CT. Follow-up head CTs obtained 7-18 months after the acute infection revealed focal and multifocal lobar atrophy correlating to regions affected by focal seizures during the acute infection (5/11). Other findings were communicating hydrocephalus (2/11), vermian atrophy (1/11) and normal studies (3/11). Conclusions: The identification of pre-existing imaging abnormalities in acute cerebral malaria suggests that population-based studies are required to establish the rate and nature of incidental imaging abnormalities in Malawi. Children with focal seizures during acute cerebral malaria developed focal cortical atrophy in these regions at follow-up. Longitudinal studies are needed to further elucidate mechanisms of CNS injury and death in this common fatal disease.

  18. Chromosome aberration assays in Allium

    Energy Technology Data Exchange (ETDEWEB)

    Grant, W.F.

    1982-01-01

    The common onion (Allium cepa) is an excellent plant for the assay of chromosome aberrations after chemical treatment. Other species of Allium (A. cepa var. proliferum, A. carinatum, A. fistulosum and A. sativum) have also been used but to a much lesser extent. Protocols have been given for using root tips from either bulbs or seeds of Allium cepa to study the cytological end-points, such as chromosome breaks and exchanges, which follow the testing of chemicals in somatic cells. It is considered that both mitotic and meiotic end-points should be used to a greater extent in assaying the cytogenetic effects of a chemical. From a literature survey, 148 chemicals are tabulated that have been assayed in 164 Allium tests for their clastogenic effect. Of the 164 assays which have been carried out, 75 are reported as giving a positive reaction, 49 positive and with a dose response, 1 positive and temperature-related, 9 borderline positive, and 30 negative; 76% of the chemicals gave a definite positive response. It is proposed that the Allium test be included among those tests routinely used for assessing chromosomal damage induced by chemicals.

  19. Specific detection and confirmation of Campylobacter jejuni by DNA hybridization and PCR.

    Science.gov (United States)

    Ng, L K; Kingombe, C I; Yan, W; Taylor, D E; Hiratsuka, K; Malik, N; Garcia, M M

    1997-11-01

    Conventional detection and confirmation methods for Campylobacter jejuni are lengthy and tedious. A rapid hybridization protocol in which a 1,475-bp chromogen-labelled DNA probe (pDT1720) and Campylobacter strains filtered and grown on 0.22-micron-pore-size hydrophobic grid membrane filters (HGMFs) are used was developed. Among the environmental and clinical isolates of C. jejuni, Campylobacter coli, Campylobacter jejuni subsp. doylei, Campylobacter lari, and Arcobacter nitrofigilis and a panel of 310 unrelated bacterial strains tested, only C. jejuni and C. jejuni subsp. doylei isolates hybridized with the probe under stringent conditions. The specificity of the probe was confirmed when the protocol was applied to spiked skim milk and chicken rinse samples. Based on the nucleotide sequence of pDT1720, a pair of oligonucleotide primers was designed for PCR amplification of DNA from Campylobacter spp. and other food pathogens grown overnight in selective Mueller-Hinton broth with cefoperazone and growth supplements. All C. jejuni strains tested, including DNase-producing strains and C. jejuni subsp. doylei, produced a specific 402-bp amplicon, as confirmed by restriction and Southern blot analysis. The detection range of the assay was as low as 3 CFU per PCR to as high as 10(5) CFU per PCR for pure cultures. Overnight enrichment of chicken rinse samples spiked initially with as little as approximately 10 CFU/ml produced amplicons after the PCR. No amplicon was detected with any of the other bacterial strains tested or from the chicken background microflora. Since C. jejuni is responsible for 99% of Campylobacter contamination in poultry, PCR and HGMF hybridization were performed on naturally contaminated chicken rinse samples, and the results were compared with the results of conventional cultural isolation on Preston agar. All samples confirmed to be culture positive for C. jejuni were also identified by DNA hybridization and PCR amplification, thus confirming that

  20. Evaluation of carbapenemase screening and confirmation tests with Enterobacteriaceae and development of a practical diagnostic algorithm.

    Science.gov (United States)

    Maurer, Florian P; Castelberg, Claudio; Quiblier, Chantal; Bloemberg, Guido V; Hombach, Michael

    2015-01-01

    Reliable identification of carbapenemase-producing members of the family Enterobacteriaceae is necessary to limit their spread. This study aimed to develop a diagnostic flow chart using phenotypic screening and confirmation tests that is suitable for implementation in different types of clinical laboratories. A total of 334 clinical Enterobacteriaceae isolates genetically characterized with respect to carbapenemase, extended-spectrum β-lactamase (ESBL), and AmpC genes were analyzed. A total of 142/334 isolates (42.2%) were suspected of carbapenemase production, i.e., intermediate or resistant to ertapenem (ETP) and/or meropenem (MEM) and/or imipenem (IPM) according to EUCAST clinical breakpoints (CBPs). A group of 193/334 isolates (57.8%) showing susceptibility to ETP, MEM, and IPM was considered the negative-control group in this study. CLSI and EUCAST carbapenem CBPs and the new EUCAST MEM screening cutoff were evaluated as screening parameters. ETP, MEM, and IPM with or without aminophenylboronic acid (APBA) or EDTA combined-disk tests (CDTs) and the Carba NP-II test were evaluated as confirmation assays. EUCAST temocillin cutoffs were evaluated for OXA-48 detection. The EUCAST MEM screening cutoff (carbapenemase confirmation. ETP and MEM EDTA CDTs showed 100% sensitivity and specificity for class B carbapenemases. Temocillin zone diameters/MIC testing on MH-CLX was highly specific for OXA-48 producers. The overall sensitivity, specificity, positive predictive value, and negative predictive value of the Carba NP-II test were 78.9, 100, 100, and 98.7%, respectively. Combining the EUCAST MEM carbapenemase screening cutoff (carbapenemase detection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. 应用酵母双杂交技术筛选猪Calsarcin-2蛋白结合蛋白%Screening of Proteins Interacting with Porcine Calsarcin-2 by Yeast Two-hybrid Techniques

    Institute of Scientific and Technical Information of China (English)

    辛磊磊; 朱文娟; 杨锷; 陈大雷; 张宁波; 唐中林; 杨述林; 李奎

    2011-01-01

    Calsarcins是钙调磷酸酶肌小节特异性结合蛋白家族,本实验旨在研究Calsarcin-2(CS2)在猪骨骼肌纤维形成和信号通路调控中的功能.应用酵母双杂交方法筛选猪骨骼肌组织中CS2蛋白结合蛋白,从猪骨骼肌文库中筛选出180个阳性克隆,经分析得到12个相互作用的蛋白,研究发现骨骼肌α-肌动蛋白1(ACTA1),肌联蛋白(TTN)及钙调素1(CALM1)为CS2互作蛋白.ACTA1参与肌肉收缩过程,TTN调节肌小节动力传导及Z线装配,CALM1参与钙离子信号传导.结果表明,CS2在维持Z线结构稳定和参与钙离子信号传导方面起重要作用.%To elucidate the function of calsarcin-2 (CS2) in the formation of skeletal muscle fiber and signaling pathway regulation, we used yeast two-hybrid approach to look for CS2 interacting proteins. The porcine skeletal library screen gave 180 positive interactions, in which 12 interacting proteins were obtained. Bioinformation analysis found that actin alpha l(ACTAl), titin(TTN) and calmodulin 1 (CALM 1) were CS2 interaction partners. ACTA1 involved in the process of muscle contraction, TTN regulated the dynamics conduction of sarcomere and Z disc assembly, CALM 1 paticipated in calcium signal transduction. These results indicate that CS2 is implicated in the transduction of calcium signals and maintaining the structure of Z disc.

  2. Sensibilidad in vitro de micobacterias a dos péptidos sintéticos híbridos con actividad antimicrobiana In-vitro activity of two hybrid synthetic peptides having antimicrobial activity against mycobacteria

    Directory of Open Access Journals (Sweden)

    E. Zerbini

    2006-12-01

    Full Text Available El aumento de aislamientos clínicos de Mycobacterium tuberculosis resistentes a las drogas esenciales y de casos de micobacteriosis diseminadas debidas al complejo Mycobacterium avium hacen necesario investigar nuevos agentes antimicobacterianos. Los péptidos antimicrobianos son un nuevo grupo de antibióticos que poseen un mecanismo de acción particular. Algunos de ellos, como la cecropina y la melitina, han sido aislados de insectos y han demostrado buena actividad in vitro contra bacterias gram positivas y gram negativas. Híbridos sintéticos de esos péptidos han presentado mayor actividad que los péptidos individuales. En este trabajo se evaluó la actividad in vitro de dos péptidos híbridos sintéticos de melitina y cecropina contra M. tuberculosis, complejo M. avium, Mycobacterium fortuitum y Mycobacterium smegmatis. Se determinó la concentración inhibitoria mínima empleando la técnica de macrodilución en caldo. Luego se estableció la concentración bactericida mínima en medio Lowenstein Jensen. Los péptidos evaluados mostraron ser activos in vitro contra M. smegmatis, mientras que no presentaron ninguna actividad contra las otras micobacterias estudiadas.The increase in both Mycobacterium tuberculosis human clinical isolates resistant to the essential drugs and cases of disseminated micobacteriosis due to Mycobacterium avium Complex, underlines the need to investigate new antimicobacterial agents. The antimicrobial peptides are a new group of active antibiotics with a particular mechanism of action. Some of them, like cecropin and melittin, isolated from insects, have demonstrated good in vitro activity against Gram-positive and Gram-negative bacteria. Synthetic hybrids of those peptides have been more active than individual peptides. In this study, the in vitro activity of two hybrid synthetic peptides from melittin and cecropin against M. tuberculosis, M. avium Complex, Mycobacterium fortuitum and Mycobacterium smegmatis

  3. Hunting for Novel Protein Factors in G-protein Pathway with Yeast Two-hybrid System%应用酵母双杂交研究G蛋白通路中的蛋白因子

    Institute of Scientific and Technical Information of China (English)

    鲁宁; 李旌军; 黄秉仁

    2001-01-01

    Objective To explore the protein factors that could interact with Gβ subunit within the G protein sig nal transducing pathway. Methods The highly sensitive protein-protein interaction system——Yeast Two-hybrid System was applied to screen the human cDNA library with constructed “Bite plasmid” contain ing Gβ subunit gene fragment. And then the faulse positive test was adapted. Results Three positive gene fragments were obtained. One codes for “Actin bundling protein”. The other two are new ones and their GeneBank accession numbers are AF288405 and AF288406 respectively. Conclusions It is the first time to find that among human brain tissue, Gβ subunit becomes a structural or functional unit interacts with actin bundling protein and the other two unknown protein factors to activate the following pathway. This re sult may be important to understand the relationship between the actin cytoskeleton and G proteins.%目的探寻G蛋白信号传导途径中与Gβ亚基相互作用的下游蛋白因子,揭示G蛋白信号传导通路的机制。方法采用敏感性较高的酵母双杂交体系,构建含Gβ亚基基因的饵质粒筛选人脑cDNA文库。结果获得了肌动蛋白集束调控蛋白(actin bundling protein)的编码基因和两个新基因片段,GeneBank登录号分别为AF288405(427 bp)及AF288406(2832 bp)。结论提示在人脑组织中Gβ亚基作为结构和功能单位可能通过与actin bundling protein 及另两种未知的蛋白因子间的相互作用而介导了信号的传导,对于揭示G蛋白信号传递通路与actin细胞骨架之间的关系起重要的提示作用

  4. Increased retention of functional fusions to toxic genes in new two-hybrid libraries of the E. coli strain MG1655 and B. subtilis strain 168 genomes, prepared without passaging through E. coli

    Directory of Open Access Journals (Sweden)

    Projan Steve

    2003-09-01

    Full Text Available Abstract Background Cloning of genes in expression libraries, such as the yeast two-hybrid system (Y2H, is based on the assumption that the loss of target genes is minimal, or at worst, managable. However, the expression of genes or gene fragments that are capable of interacting with E. coli or yeast gene products in these systems has been shown to be growth inhibitory, and therefore these clones are underrepresented (or completely lost in the amplified library. Results Analysis of candidate genes as Y2H fusion constructs has shown that, while stable in E. coli and yeast for genetic studies, they are rapidly lost in growth conditions for genomic libraries. This includes the rapid loss of a fragment of the E. coli cell division gene ftsZ which encodes the binding site for ZipA and FtsA. Expression of this clone causes slower growth in E. coli. This clone is also rapidly lost in yeast, when expressed from a GAL1 promoter, relative to a vector control, but is stable when the promoter is repressed. We have demonstrated in this report that the construction of libraries for the E. coli and B. subtilis genomes without passaging through E. coli is practical, but the number of transformants is less than for libraries cloned using E. coli as a host. Analysis of several clones in the libraries that are strongly growth inhibitory in E. coli include genes for many essential cellular processes, such as transcription, translation, cell division, and transport. Conclusion Expression of Y2H clones capable of interacting with E. coli and yeast targets are rapidly lost, causing a loss of complexity. The strategy for preparing Y2H libraries described here allows the retention of genes that are toxic when inappropriately expressed in E. coli, or yeast, including many genes that represent potential antibacterial targets. While these methods are generally applicable to the generation of Y2H libraries from any source, including mammalian and plant genomes, the

  5. Chromatographic assessment of two hybrid monoliths prepared via epoxy-amine ring-opening polymerization and methacrylate-based free radical polymerization using methacrylate epoxy cyclosiloxane as functional monomer.

    Science.gov (United States)

    Wang, Hongwei; Ou, Junjie; Lin, Hui; Liu, Zhongshan; Huang, Guang; Dong, Jing; Zou, Hanfa

    2014-11-07

    Two kinds of hybrid monolithic columns were prepared by using methacrylate epoxy cyclosiloxane (epoxy-MA) as functional monomer, containing three epoxy moieties and one methacrylate group. One column was in situ fabricated by ring-opening polymerization of epoxy-MA and 1,10-diaminodecane (DAD) using a porogenic system consisting of isopropanol (IPA), H2O and ethanol at 65°C for 12h. The other was prepared by free radical polymerization of epoxy-MA and ethylene dimethacrylate (EDMA) using 1-propanol and 1,4-butanediol as the porogenic solvents at 60°C for 12h. Two hybrid monoliths were investigated on the morphology and chromatographic assessment. Although two kinds of monolithic columns were prepared with epoxy-MA, their morphologies looked rather different. It could be found that the epoxy-MA-DAD monolith possessed higher column efficiencies (25,000-34,000plates/m) for the separation of alkylbenzenes than the epoxy-MA-EDMA monolith (12,000-13,000plates/m) in reversed-phase nano-liquid chromatography (nano-LC). Depending on the remaining epoxy or methacrylate groups on the surface of two pristine monoliths, the epoxy-MA-EDMA monolith could be easily modified with 1-octadecylamine (ODA) via ring-opening reaction, while the epoxy-MA-DAD monolith could be modified with stearyl methacrylate (SMA) via free radical reaction. The chromatographic performance for the separation of alkylbenzenes on SMA-modified epoxy-MA-DAD monolith was remarkably improved (42,000-54,000 plates/m) when compared with that on pristine epoxy-MA-DAD monolith, while it was not obviously enhanced on ODA-modified epoxy-MA-EDMA monolith when compared with that on pristine epoxy-MA-EDMA monolith. The enhancement of the column efficiency of epoxy-MA-DAD monolith after modification might be ascribed to the decreased mass-transfer resistence. The two kinds of hybrid monoliths were also applied for separations of six phenols and seven basic compounds in nano-LC. Copyright © 2014 Elsevier B.V. All

  6. Study on a rooting inducing culture system for plantlets of two hybrid Rhododendron%两种杜鹃杂交种不定芽生根的培养基配方

    Institute of Scientific and Technical Information of China (English)

    吴影倩; 耿兴敏; 罗凤霞

    2013-01-01

    以杜鹃杂交种R.simsii×R.mucronatum和R.pulchrum×R.mucronatum组培苗的不定芽为外植体,对基本培养基和蔗糖浓度采用单因子设计,对生长素种类和活性炭采用正交试验,对适宜的生根培养基配方进行了探讨.结果表明:不同的杂交组合适宜不定芽生根的培养基类型、蔗糖浓度及激素组合都有所不同.R.simsii×R.mucronatum的适宜生根培养基为1/2 WPM+ 20 g/L蔗糖+3g/L AC,R.pulchrum×R.mucronatum的合适生根培养基为WPM+ 10 g/L蔗糖+2 mg/L IBA.适宜的移栽基质均为V泥炭∶V蛭石∶V珍珠岩=1∶1∶1.%To optimize a micro propagation of hybrid Rhododendron and improve the efficiency of Rhododendron breeding,In vitro shoots were used as the explants to establish a rooting system for two hybrid Rhododendron(R.simsii × R.mucronatum and R.pulchrum × R.mucronatum).Single factor experiments were used in basic medium and sucrose concentration,orthogonal test was applied to the type of auxin and activated carbon,select the appropriate culture conditions.The results showed that the optimal rooting medium was 1/2 WPM +20 g/L sucrose +3 g/L AC for R.simsii ×R.mucronatum and the optimal rooting medium was WPM + 10 g/L sucrose + 2 mg/L IBA for R.pulchrum × R.mucronatum.Optimal transplanting medium were peat∶ vermiculite∶ perlite =1 ∶ 1 ∶ 1.

  7. Comet assay to assess the genotoxicity of Persian walnut (Juglans regia L.) husks with statistical evaluation.

    Science.gov (United States)

    Petriccione, Milena; Ciniglia, Claudia

    2012-07-01

    The aim of this study was to confirm the utility of the Comet assay as a genotoxicity screening test for evaluating the impact of walnut husk aqueous extract. Phytotoxicity assays using diluted and undiluted walnut husk aqueous extracts were performed on young roots of Raphanus sativus (radish), and the Comet assay was used to evaluate DNA integrity in isolated radish radicle nuclei. The results reveal a dose-dependent accumulation of DNA damage in radish radicles treated with walnut husks water extract and that the Kolmogorov-Smirnov test combined with Johnson SB distribution was the best approach for describing Comet assay data.

  8. Managing a duopolistic water market with confirmed proposals. An experiment

    Directory of Open Access Journals (Sweden)

    García-Gallego, Aurora

    2012-03-01

    Full Text Available We report results from experimental water markets in which owners of two different sources of water supply water to households and farmers. The final water quality consumed by each type of consumer is determined through mixing of qualities from two different resources. We compare the standard duopolistic market structure with an alternative market clearing mechanism inspired by games with confirmed strategies (which have been shown to yield collusive outcomes. As in the static case, complex dynamic markets operating under a confirmed proposals protocol yield less efficient outcomes because coordination among independent suppliers has the usual effects of restricting output and increasing prices to the users. Our results suggest that, when market mechanisms are used to allocate water to its users, the rule of thumb used by competition authorities can also serve as a guide towards water market regulation.

    Se presentan resultados de un experimento con mercados acuíferos en el que los propietarios de agua de distinta calidad la ofrecen a hogares y agricultores. La calidad finalmente consumida por cada tipo de consumidor se determina a partir de una mezcla de las dos calidades. Se compara el duopolio estándar con una forma alternativa de cerrar el mercado que está inspirada en los juegos con propuestas confirmadas, que consiguen resultados relativamente más colusivos. Como en el caso estático, los mercados dinámicos y complejos que operan bajo un protocolo de propuestas confirmadas son menos eficientes porque la coordinación entre oferentes independientes tiene los efectos de restringir el output y de provocar un crecimiento de los precios. Nuestros resultados sugieren que cuando los mecanismos de mercado se utilizan para distribuir el agua a sus usuarios, la regla utilizada por parte de las autoridades de la competencia puede servir también como guía para la regulación de los mercados acuíferos.

  9. 21 CFR 225.158 - Laboratory assays.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Laboratory assays. 225.158 Section 225.158 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS... Laboratory assays. Where the results of laboratory assays of drug components, including assays by State...

  10. Confirmed rare copy number variants implicate novel genes in schizophrenia.

    Science.gov (United States)

    Tam, Gloria W C; van de Lagemaat, Louie N; Redon, Richard; Strathdee, Karen E; Croning, Mike D R; Malloy, Mary P; Muir, Walter J; Pickard, Ben S; Deary, Ian J; Blackwood, Douglas H R; Carter, Nigel P; Grant, Seth G N

    2010-04-01

    Understanding how cognitive processes including learning, memory, decision making and ideation are encoded by the genome is a key question in biology. Identification of sets of genes underlying human mental disorders is a path towards this objective. Schizophrenia is a common disease with cognitive symptoms, high heritability and complex genetics. We have identified genes involved with schizophrenia by measuring differences in DNA copy number across the entire genome in 91 schizophrenia cases and 92 controls in the Scottish population. Our data reproduce rare and common variants observed in public domain data from >3000 schizophrenia cases, confirming known disease loci as well as identifying novel loci. We found copy number variants in PDE10A (phosphodiesterase 10A), CYFIP1 [cytoplasmic FMR1 (Fragile X mental retardation 1)-interacting protein 1], K(+) channel genes KCNE1 and KCNE2, the Down's syndrome critical region 1 gene RCAN1 (regulator of calcineurin 1), cell-recognition protein CHL1 (cell adhesion molecule with homology with L1CAM), the transcription factor SP4 (specificity protein 4) and histone deacetylase HDAC9, among others (see http://www.genes2cognition.org/SCZ-CNV). Integrating the function of these many genes into a coherent model of schizophrenia and cognition is a major unanswered challenge.

  11. Gluten Psychosis: Confirmation of a New Clinical Entity

    Directory of Open Access Journals (Sweden)

    Elena Lionetti

    2015-07-01

    Full Text Available Non-celiac gluten sensitivity (NCGS is a syndrome diagnosed in patients with symptoms that respond to removal of gluten from the diet, after celiac disease and wheat allergy have been excluded. NCGS has been related to neuro-psychiatric disorders, such as autism, schizophrenia and depression. A singular report of NCGS presenting with hallucinations has been described in an adult patient. We report a pediatric case of a psychotic disorder clearly related to NCGS and investigate the causes by a review of literature. The pathogenesis of neuro-psychiatric manifestations of NCGS is unclear. It has been hypothesized that: (a a “leaky gut” allows some gluten peptides to cross the intestinal membrane and the blood brain barrier, affecting the endogenous opiate system and neurotransmission; or (b gluten peptides may set up an innate immune response in the brain similar to that described in the gut mucosa, causing exposure from neuronal cells of a transglutaminase primarily expressed in the brain. The present case-report confirms that psychosis may be a manifestation of NCGS, and may also involve children; the diagnosis is difficult with many cases remaining undiagnosed. Well-designed prospective studies are needed to establish the real role of gluten as a triggering factor in neuro-psychiatric disorders.

  12. Gluten Psychosis: Confirmation of a New Clinical Entity.

    Science.gov (United States)

    Lionetti, Elena; Leonardi, Salvatore; Franzonello, Chiara; Mancardi, Margherita; Ruggieri, Martino; Catassi, Carlo

    2015-07-08

    Non-celiac gluten sensitivity (NCGS) is a syndrome diagnosed in patients with symptoms that respond to removal of gluten from the diet, after celiac disease and wheat allergy have been excluded. NCGS has been related to neuro-psychiatric disorders, such as autism, schizophrenia and depression. A singular report of NCGS presenting with hallucinations has been described in an adult patient. We report a pediatric case of a psychotic disorder clearly related to NCGS and investigate the causes by a review of literature. The pathogenesis of neuro-psychiatric manifestations of NCGS is unclear. It has been hypothesized that: (a) a "leaky gut" allows some gluten peptides to cross the intestinal membrane and the blood brain barrier, affecting the endogenous opiate system and neurotransmission; or (b) gluten peptides may set up an innate immune response in the brain similar to that described in the gut mucosa, causing exposure from neuronal cells of a transglutaminase primarily expressed in the brain. The present case-report confirms that psychosis may be a manifestation of NCGS, and may also involve children; the diagnosis is difficult with many cases remaining undiagnosed. Well-designed prospective studies are needed to establish the real role of gluten as a triggering factor in neuro-psychiatric disorders.

  13. Anaplasma phagocytophilum in Danish sheep: confirmation by DNA sequencing

    Directory of Open Access Journals (Sweden)

    Thamsborg Stig M

    2009-12-01

    Full Text Available Abstract Background The presence of Anaplasma phagocytophilum, an Ixodes ricinus transmitted bacterium, was investigated in two flocks of Danish grazing lambs. Direct PCR detection was performed on DNA extracted from blood and serum with subsequent confirmation by DNA sequencing. Methods 31 samples obtained from clinically normal lambs in 2000 from Fussingø, Jutland and 12 samples from ten lambs and two ewes from a clinical outbreak at Feddet, Zealand in 2006 were included in the study. Some of the animals from Feddet had shown clinical signs of polyarthritis and general unthriftiness prior to sampling. DNA extraction was optimized from blood and serum and detection achieved by a 16S rRNA targeted PCR with verification of the product by DNA sequencing. Results Five DNA extracts were found positive by PCR, including two samples from 2000 and three from 2006. For both series of samples the product was verified as A. phagocytophilum by DNA sequencing. Conclusions A. phagocytophilum was detected by molecular methods for the first time in Danish grazing lambs during the two seasons investigated (2000 and 2006.

  14. Spectroscopic Confirmation of a Protocluster at z=3.786

    CERN Document Server

    Dey, Arjun; Reddy, Naveen; Cooper, Michael; Inami, Hanae; Hong, Sungryong; Gonzalez, Anthony H; Jannuzi, Buell T

    2016-01-01

    We present new observations of the field containing the z=3.786 protocluster, PC217.96+32.3. We confirm that it is one of the largest and most overdense high-redshift structures known. Such structures are rare even in the largest cosmological simulations. We used the Mayall/MOSAIC1.1 imaging camera to image a 1.2x0.6 deg area (~150x75 comoving Mpc) surrounding the protocluster's core and discovered 165 candidate Lyman Alpha emitting galaxies (LAEs) and 788 candidate Lyman Break galaxies (LBGs). There are at least 2 overdense regions traced by the LAEs, the largest of which shows an areal overdensity in its core (i.e., within a radius of 2.5 comoving Mpc) of 14+/-7 relative to the average LAE spatial density in the imaged field. Further, the average LAE spatial density in the imaged field is twice that derived by other field LAE surveys. Spectroscopy with Keck/DEIMOS yielded redshifts for 164 galaxies (79 LAEs and 85 LBGs); 65 lie at a redshift of 3.785+/-0.010. The velocity dispersion of galaxies near the cor...

  15. Synthesis gas demonstration plant program, Phase I. Site confirmation report

    Energy Technology Data Exchange (ETDEWEB)

    1978-12-01

    With few reservations, the Baskett, Kentucky site exhibits the necessary characteristics to suggest compatibility with the proposed Synthesis Gas Demonstration Plant Project. An evaluation of a broad range of technical disciplinary criteria in consideration of presently available information indicated generally favorable conditions or, at least, conditions which could be feasibly accommodated in project design. The proximity of the Baskett site to market areas and sources of raw materials as well as a variety of transportation facilities suggests an overall favorable impact on Project economic feasibility. Two aspects of environmental engineering, however, have been identified as areas where the completion or continuation of current studies are required before removing all conditions on site suitability. The first aspect involves the current contradictory status of existing land use and planning ordinances in the site area. Additional investigation of the legality of, and local attitudes toward, these present plans is warranted. Secondly, terrestrial and aquatic surveys of plant and animal life species in the site area must be completed on a seasonal basis to confirm the preliminary conclusion that no exclusionary conditions exist.

  16. Confirming and Improving Ross Variable Star RV Del

    Science.gov (United States)

    Linder, Tyler R.; Sanchez, Rick; Palser, Sage; Schultze, Kendra; Kenney, Jessica; Thompson, Briana; DeCoster, Richard; Mills, Frank; Osborn, Wayne; Hoette, Vivian L.; Skynet Junior Scholars; Stone Edge Observatory

    2017-01-01

    RV Del is an intrinsic pulsating variable star in the constellation Delphinus, discovered by Ross (1926). The AAVSO list RV Del as a RRAB type of variable star. RV Del has been found to have a magnitude that varies from 12.9 - 14.2 and a period of 11.9553 hours.The purpose of our research of RV Del is to confirm and improve previous results as well as explore different methods to engage middle school students in the scientific method and astronomy. The SKYNET network of telescopes allows students to request images from a group of international research class telescopes. The telescope request process allows students first-hand experience in astronomy while the data analysis allows students to understand advance software systems to produce publishable results. Data is being gathered using the SKYNET network and Stone Edge Observatory to gather photometry of RV Del and create a new light curve. Findings will be presented the January 2017 AAS.

  17. Suzaku Confirms NGC~3660 is an Unabsorbed Seyfert 2

    CERN Document Server

    Rivers, E; Bianchi, S; Matt, G; Nandra, K; Ueda, Y

    2016-01-01

    An enigmatic group of objects, unabsorbed Seyfert 2s may have intrinsically weak broad line regions, obscuration in the line of sight to the BLR but not to the X-ray corona, or so much obscuration that the X-ray continuum is completely suppressed and the observed spectrum is actually scattered into the line of sight from nearby material. NGC 3660 has been shown to have weak broad optical/near infrared lines, no obscuration in the soft X-ray band, and no indication of "changing look" behavior. The only previous hard X-ray detection of this source by Beppo-SAX seemed to indicate that the source might harbor a heavily obscured nucleus. However, our analysis of a long-look Suzaku observation of this source shows that this is not the case, and that this source has a typical power law X-ray continuum with normal reflection and no obscuration. We conclude that NGC 3660 is confirmed to have no unidentified obscuration and that the anomolously high Beppo-SAX measurement must be due to source confusion or similar, bein...

  18. Confirming theoretical pay constructs of a variable pay scheme

    Directory of Open Access Journals (Sweden)

    Sibangilizwe Ncube

    2013-01-01

    Full Text Available Orientation: Return on the investment in variable pay programmes remains controversial because their cost versus contribution cannot be empirically justified. Research purpose: This study validates the findings of the model developed by De Swardt on the factors related to successful variable pay programmes.Motivation for the study: Many organisations blindly implement variable pay programmes without any means to assess the impact these programmes have on the company’s performance. This study was necessary to validate the findings of an existing instrument that validates the contribution of variable pay schemes.Research design, approach and method: The study was conducted using quantitative research. A total of 300 completed questionnaires from a non-purposive sample of 3000 participants in schemes across all South African industries were returned and analysed.Main findings: Using exploratory and confirmatory factor analysis, it was found that the validation instrument developed by De Swardt is still largely valid in evaluating variable pay schemes. The differences between the study and the model were reported.Practical/managerial implications: The study confirmed the robustness of an existing model that enables practitioners to empirically validate the use of variable pay plans. This model assists in the design and implementation of variable pay programmes that meet critical success factors.Contribution/value-add: The study contributed to the development of a measurement instrument that will assess whether a variable pay plan contributes to an organisation’s success.

  19. Chandra Confirmation of a Pulsar Wind Nebula in DA 495

    CERN Document Server

    Arzoumanian, Z; Landecker, T L; Kothes, R; Camilo, F

    2008-01-01

    As part of a multiwavelength study of the unusual radio supernova remnant DA 495, we present observations made with the Chandra X-ray Observatory. Imaging and spectroscopic analysis confirms the previously detected X-ray source at the heart of the annular radio nebula, establishing the radiative properties of two key emission components: a soft unresolved source with a blackbody temperature of 1 MK consistent with a neutron star, surrounded by a nonthermal nebula 40'' in diameter exhibiting a power-law spectrum with photon index Gamma = 1.6+/-0.3, typical of a pulsar wind nebula. The implied spin-down luminosity of the neutron star, assuming a conversion efficiency to nebular flux appropriate to Vela-like pulsars, is ~10^{35} ergs/s, again typical of objects a few tens of kyr old. Morphologically, the nebular flux is slightly enhanced along a direction, in projection on the sky, independently demonstrated to be of significance in radio polarization observations; we argue that this represents the orientation o...

  20. Confirmation of Two Hot Jupiters from K2 Campaign 4

    CERN Document Server

    Johnson, Marshall C; Fridlund, Malcolm; Csizmadia, Szilard; Endl, Michael; Cabrera, Juan; Cochran, William D; Deeg, Hans J; Grziwa, Sascha; Ramírez, Ivan; Hatzes, Artie P; Eigmüller, Philipp; Barragán, Oscar; Erikson, Anders; Guenther, Eike W; Korth, Judith; Kuutma, Teet; Nespral, David; Pätzold, Martin; Palle, Enric; Prieto-Arranz, Jorge; Rauer, Heike; Saario, Joonas

    2016-01-01

    We confirm the planetary nature of two transiting hot Jupiters discovered by the Kepler spacecraft's K2 extended mission in its Campaign 4, using precise radial velocity measurements from FIES@NOT, HARPS-N@TNG, and the coud\\'e spectrograph on the McDonald Observatory 2.7 m telescope. EPIC 211089792 b transits a K1V star with a period of $3.2589263\\pm0.0000015$ days; its orbit is slightly eccentric ($e=0.086_{-0.025}^{+0.035}$). It has a radius of $R_P=0.998_{-0.066}^{+0.072}$ $R_J$ and a mass of $M_P=0.613_{-0.027}^{+0.028}$ $M_J$. Its host star exhibits significant rotational variability, and we measure a rotation period of $P_{\\mathrm{rot}}=10.777 \\pm 0.031$ days. EPIC 210957318 b transits a G6V star with a period of $4.098503\\pm0.000011$ days. It has a radius of $R_P=1.039_{-0.051}^{+0.050}$ $R_J$ and a mass of $M_P=0.579_{-0.027}^{+0.028}$ $M_J$. The star has a low metallicity for a hot Jupiter host, $[\\mathrm{Fe}/\\mathrm{H}]=-0.15 \\pm 0.05$.

  1. Chandra Confirmation of a Pulsar Wind Nebula in DA 495

    Science.gov (United States)

    Arzoumanian, Z.; Safi-Harb, S.; Landecker, T.L.; Kothes, R.; Camilo, F.

    2008-01-01

    As part of a multiwavelength study of the unusual radio supernova remnant DA 495, we present observations made with the Chandra X-ray Observatory. Imaging and spectroscopic analysis confirms the previously detected X-ray source at the heart of the annular radio nebula, establishing the radiative properties of two key emission components: a soft unresolved source with a blackbody temperature of 1 MK consistent with a neutron star, surrounded by a nontherma1 nebula 40" in diameter exhibiting a power-law spectrum with photon index Gamma = 1.63, typical of a pulsar wind nebula. Morphologically, the nebula appears to be slightly extended along a direction, in projection on the sky, previously demonstrated to be of significance in radio and ASCA observations; we argue that this represents the orientation of the pulsar spin axis. At smaller scales, a narrow X-ray feature is seen extending out 5" from the point source, but energetic arguments suggest that it is not the resolved termination shock of the pulsar wind against the ambient medium. Finally, we argue based on synchrotron lifetimes in the nebular magnetic field that DA 495 represents the first example of a pulsar wind nebula in which electromagnetic flux makes up a significant part, together with particle flux, of the neutron star's wind.

  2. 利用酵母双杂交筛选与苹果褪绿叶斑病毒CP互作的寄主因子%Screening of the Host Factors Interacting with CP ofApple chlorotic leaf spot virusby Yeast Two-Hybrid System

    Institute of Scientific and Technical Information of China (English)

    何乙坤; 钟敏; 胡同乐; 王树桐; 段豪; 丁丽; 王亚南; 曹克强

    2014-01-01

    Objective] The objective of this study is to screen the host factors interacting with coat protein (CP) ofApple chlorotic leaf spot virus (ACLSV) by yeast two-hybrid system and analyze their function in the interaction between host and virus by the method of bioinformatics.[Method] Firstly, the bait vector of pGBKT7-CP was constructed and transformed into Y2H gold. The growth of the transformed yeast was assayed on the culture plate of SD/-Trp, SD/-Trp/-His and SD/-Trp/-Ade-X-α-Gal to make clear the self-activating effect of pGBKT7-CP. The plasmids of pGBKT7-CPand pGBKT7 were transformed intoY2H gold, the OD 600 of which was tested by ultraviolet spectrophotometer at different stages. The effect of pGBKT7-CP on the yeast was analyzed. Secondly, the interactive proteins of CP were screened from cDNA library ofMalus sylvestris cv. R12740-7A constructed early by yeast two-hybrid sequencing transformation. At last, the positive clones were selected from the culture plate of SD/-Ade/-His/-Leu/-Trp/X-α-Gal and sequenced. BLAST analysis was made for the host factors in the GenBank and the function in the interaction between host and virus was deduced based on gene annotation.[Result] The bait vector of pGBKT7-CP was constructed. The transformed yeast Y2H gold was able to grow on the plate of SD/-Trp, but not able to grow on the plate of SD/-Trp/-His and SD/-Trp/-Ade-X-α-Gal, which implied that the recombined plasmid had no ability to activate the reporter gene of His and Ade.The growth of pGBKT7-CPand the control was similar, which predicated that the recombined plasmid had no virulence to the yeast. Sixty-nine interactive factors were obtained, which were divided into 10 types of proteins based on their functions, including transcription factor activity, carbon fixation activity, cellular iron ion homeostasis, defense response, hydrolase activity, oxidase activity, oxidoreductase activity, photosystem II assembly and protein binding activity. Eight host genes (Malus3

  3. Comet Assay in Cancer Chemoprevention.

    Science.gov (United States)

    Santoro, Raffaela; Ferraiuolo, Maria; Morgano, Gian Paolo; Muti, Paola; Strano, Sabrina

    2016-01-01

    The comet assay can be useful in monitoring DNA damage in single cells caused by exposure to genotoxic agents, such as those causing air, water, and soil pollution (e.g., pesticides, dioxins, electromagnetic fields) and chemo- and radiotherapy in cancer patients, or in the assessment of genoprotective effects of chemopreventive molecules. Therefore, it has particular importance in the fields of pharmacology and toxicology, and in both environmental and human biomonitoring. It allows the detection of single strand breaks as well as double-strand breaks and can be used in both normal and cancer cells. Here we describe the alkali method for comet assay, which allows to detect both single- and double-strand DNA breaks.

  4. The skin-blanching assay.

    Science.gov (United States)

    Smit, P; Neumann, H A M; Thio, H B

    2012-10-01

    The skin-blanching assay is used for the determination and bioequivalence of dermatologic glucocorticoids (GCs). The exact mechanism of the production of blanching is not fully understood, but it is considered that local vasoconstriction of the skin microvasculature and the consequent blood-flow reduction cause this phenomenon. Several factors influence skin blanching, including drug concentration, duration of application, nature of vehicle, occlusion, posture and location. The intensity of vasoconstriction can be measured in several ways: visual or quantitative methods, such as reflectance spectroscopy, thermography, laser Doppler velocimetry and chromametry. In literature, contradicting results in the correlation of the skin-blanching assay with different tests to determine GC sensitivity have been reported, limiting its clinical usefulness.

  5. Development of a colorimetric assay for rapid quantitative measurement of clavulanic acid in microbial samples.

    Science.gov (United States)

    Dai, Xida; Xiang, Sihai; Li, Jia; Gao, Qiang; Yang, Keqian

    2012-02-01

    We developed a colorimetric assay to quantify clavulanic acid (CA) in culture broth of Streptomyces clavuligerus, to facilitate screening of a large number of S. clavuligerus mutants. The assay is based on a β-lactamase-catalyzed reaction, in which the yellow substrate nitrocefin (λ (max)=390 nm) is converted to a red product (λ (max)=486 nm). Since CA can irreversibly inhibit β-lactamase activity, the level of CA in a sample can be measured as a function of the A (390)/A (486) ratio in the assay mixture. The sensitivity and detection window of the assay were determined to be 50 μg L(-1) and 50 μg L(-1) to 10 mg L(-1), respectively. The reliability of the assay was confirmed by comparing assay results with those obtained by HPLC. The assay was used to screen a pool of 65 S. clavuligerus mutants and was reliable for identifying CA over-producing mutants. Therefore, the assay saves time and labor in large-scale mutant screening and evaluation tasks. The detection window and the reliability of this assay are markedly better than those of previously reported CA assays. This assay method is suitable for high throughput screening of microbial samples and allows direct visual observation of CA levels on agar plates.

  6. Bioluminescence assay for cell viability.

    Science.gov (United States)

    Lomakina, G Yu; Modestova, Yu A; Ugarova, N N

    2015-06-01

    Theoretical aspects of the adenosine triphosphate bioluminescence assay based on the use of the firefly luciferin-luciferase system are considered, as well as its application for assessing cell viability in microbiology, sanitation, medicine, and ecology. Various approaches for the analysis of individual or mixed cultures of microorganisms are presented, and capabilities of the method for investigation of biological processes in live cells including necrosis, apoptosis, as well as for investigation of the dynamics of metabolism are described.

  7. Protein binding assay for hyaluronate

    Energy Technology Data Exchange (ETDEWEB)

    Lacy, B.E.; Underhill, C.B.

    1986-11-01

    A relatively quick and simple assay for hyaluronate was developed using the specific binding protein, hyaluronectin. The hyaluronectin was obtained by homogenizing the brains of Sprague-Dawley rats, and then centrifuging the homogenate. The resulting supernatant was used as a source of crude hyaluronectin. In the binding assay, the hyaluronectin was mixed with (/sup 3/H)hyaluronate, followed by an equal volume of saturated (NH/sub 4/)/sub 2/SO/sub 4/, which precipitated the hyaluronectin and any (/sup 3/H)hyaluronate associated with it, but left free (/sup 3/H)hyaluronate in solution. The mixture was then centrifuged, and the amount of bound (/sup 3/H)hyaluronate in the precipitate was determined. Using this assay, the authors found that hyaluronectin specifically bound hyaluronate, since other glycosaminoglycans failed to compete for the binding protein. In addition, the interaction between hyaluronectin and hyaluronate was of relatively high affinity, and the size of the hyaluronate did not appear to substantially alter the amount of binding. To determine the amount of hyaluronate in an unknown sample, they used a competition assay in which the binding of a set amount of (/sup 3/H)hyaluronate was blocked by the addition of unlabeled hyaluronate. By comparing the degree of competition of the unknown samples with that of known amounts of hyaluronate, it was possible to determine the amount of hyaluronate in the unknowns. They have found that this method is sensitive to 1 ..mu..g or less of hyaluronate, and is unaffected by the presence of proteins.

  8. Comparison of three diagnostic methods to confirm Helicobacter pylori infection

    Directory of Open Access Journals (Sweden)

    Opavski Nataša

    2007-01-01

    Full Text Available Introduction: Helicobacter pylori induces gastric inflammation in host and such gastritis increases the risk of gastric and duodenal ulceration as well as adenocarcinoma. Because peptic ulcer disease is the major cause of morbidity, accurate diagnosis of H. pylori infection is very important. Unfortunately, there is no gold standard among diagnostic tests for Helicobacter infections. If gastroscopy is performed, histopathology and urease test are the most often used. Still, culturing of this bacterium is essential for drug susceptibility testing and analysis of virulence factors. Objective The aim of this study was to compare three diagnostic procedures - histopathology, urease test and culture, which are used to verify H. pylori infection. Method Three pairs of gastric mucosal biopsy specimens were collected from each of 28 dyspeptic patients undergoing endoscopy. Nineteen patients were not pretreated with antibiotics, while nine had received eradication therapy earlier. One pair of biopsy specimens was used for histopathologic examination, the second for urease test and the third was simultaneously cultured on nonselective and selective solid media. Isolate was identified as H. pylori on the basis of colony morphology, morphological properties and biochemical tests. Results In 14 out of 28 patients, H. pylori infection was confirmed on the basis of results of all diagnostic procedures. The concordance of these three methods was very good, because the results of histopathology, urease test and culture corresponded in 26 from 28 patients. Conclusion The conclusion of our study is that culture, as the method with high degree of concordance with other two procedures and the only that can give information on drug susceptibility of Helicobacter, is recommended for diagnosis of Helicobacter pylori infection along with histopathology and urease test.

  9. Histopathologic criteria to confirm white-nose syndrome in bats

    Science.gov (United States)

    Meteyer, C.U.; Buckles, E.L.; Blehert, D.S.; Hicks, A.C.; Green, D.E.; Shearn-Bochsler, V.; Thomas, N.J.; Gargas, A.; Behr, M.J.

    2009-01-01

    White-nose syndrome (WNS) is a cutaneous fungal disease of hibernating bats associated with a novel Geomyces sp. fungus. Currently, confirmation of WNS requires histopathologic examination. Invasion of living tissue distinguishes this fungal infection from those caused by conventional transmissible dermatophytes. Although fungal hyphae penetrate the connective tissue of glabrous skin and muzzle, there is typically no cellular inflammatory response in hibernating bats. Preferred tissue samples to diagnose this fungal infection are rostral muzzle with nose and wing membrane fixed in 10% neutral buffered formalin. To optimize detection, the muzzle is trimmed longitudinally, the wing membrane is rolled, and multiple cross-sections are embedded to increase the surface area examined. Periodic acid-Schiff stain is essential to discriminate the nonpigmented fungal hyphae and conidia. Fungal hyphae form cup-like epidermal erosions and ulcers in the wing membrane and pinna with involvement of underlying connective tissue. In addition, fungal hyphae are present in hair follicles and in sebaceous and apocrine glands of the muzzle with invasion of tissue surrounding adnexa. Fungal hyphae in tissues are branching and septate, but the diameter and shape of the hyphae may vary from parallel walls measuring 2 ??m in diameter to irregular walls measuring 3-5 ??m in diameter. When present on short aerial hyphae, curved conidia are approximately 2.5 ??m wide and 7.5 ??m in curved length. Conidia have a more deeply basophilic center, and one or both ends are usually blunt. Although WNS is a disease of hibernating bats, severe wing damage due to fungal hyphae may be seen in bats that have recently emerged from hibernation. These recently emerged bats also have a robust suppurative inflammatory response.

  10. Characteristics of histologically confirmed endometriosis in cynomolgus monkeys

    Science.gov (United States)

    Nishimoto-Kakiuchi, A.; Netsu, S.; Matsuo, S.; Hayashi, S.; Ito, T.; Okabayashi, S.; Yasmin, L.; Yuzawa, K.; Kondoh, O.; Kato, A.; Suzuki, M.; Konno, R.; Sankai, T.

    2016-01-01

    STUDY QUESTION What are the characteristics of spontaneous endometriosis in cynomolgus monkeys? SUMMARY ANSWER Spontaneous endometriosis in cynomolgus monkeys exhibited similar characteristics to the human disease. WHAT IS KNOWN ALREADY One previous report described the prevalence and the basic histopathology of spontaneous endometriosis in cynomolgus monkeys. STUDY DESIGN, SIZE, DURATION Endometriotic lesions that had been histologically confirmed in 8 female cynomolgus monkeys between 5 and 21 years old were subjected to study. PARTICIPANTS/MATERIALS, SETTING, METHODS The monkeys died of, or were sacrificed because of, sickness consequent on endometriosis. Specimens were evaluated histopathologically with haematoxylin and eosin staining, iron staining and immunohistochemistry (CD10, CD31, α-SMA and PGP9.5), and by observing them under a microscope. MAIN RESULTS AND THE ROLE OF CHANCE Endometriotic and stromal cells (CD10-positive) with haemorrhage and inflammation were observed. Smooth muscle metaplasia and nerve fibres were also noted in the endometriotic lesions. Endometriotic lesions in lymph nodes were incidentally found. LIMITATIONS AND REASONS FOR CAUTION Since laparoscopic analysis for monitoring the disease state was not set as a parameter of the current study, time course changes (progression) of the disease were not assessed. WIDER IMPLICATIONS OF THE FINDINGS Further investigation of spontaneous endometriosis in cynomolgus monkeys may contribute to better understanding of the disease pathobiology. STUDY FUNDING/COMPETING INTEREST(S) No external funds were used for this study. A.N.K., S.M., S.H., T.I., O.K., A.K. and M.S. are full-time employees of Chugai Pharmaceutical Co., Ltd. R.K. received lecture fees from Chugai Pharmaceutical Co., Ltd., unrelated to the submitted work. S.N., S. O., L.Y., K.Y. and T.S. have nothing to declare. TRIAL REGISTRATION NUMBER N/A. PMID:27591226

  11. Confirmation of elevated arsenic levels in groundwater of Myanmar

    Science.gov (United States)

    van Geen, Alexander; Win, Kyi Htut; Zaw, Than; Naing, Win; Mey, Jacob L.; Mailloux, Brian

    2014-01-01

    Millions of villagers across South and Southeast Asia are exposed to toxic levels of arsenic (As) by drinking well water. In order to confirm field-kit results that Myanmar is also affected, a total of 55 wells were tested in the field in January 2013 and sampled for laboratory analysis across seven villages spanning a range of As contamination in the lower Ayeyarwady basin. Elevated concentrations of As (50–630 μg/L) were measured in wells up to 60 m deep and associated with high levels of Fe (up to 21 mg/L) and low concentrations of SO4 (<0.05 mg/L). Concentrations of As <10 μg/L were measured in some shallow (<30 m) grey sands and in both shallow and deep orange sands. These results indicate that the main mechanism of As release to groundwater in Myanmar is the reductive dissolution of Fe oxyhydroxides, as in the neighboring Bengal, Mekong, and Red River basins. Concentrations of As in groundwater of Myanmar are therefore unlikely to change rapidly over time and switching to existing low-As wells is a viable way of reducing exposure in the short term. However, only 17 of the 55 well owners interviewed correctly recalled the status of their well despite extensive testing in the region. A renewed effort is thus needed to test existing wells and new wells that continue to be installed and to communicate the health risks of exposure to As for infants, children, and adults. PMID:24530581

  12. 酵母双杂交系统筛选HBV PreS1相互作用蛋白%Screening the hepatitis B virus PreS1 associated proteins in yeast two-hybrid system

    Institute of Scientific and Technical Information of China (English)

    叶峰; 张曦; 邸莹; 王小清; 刘小静; 孔颖; 赵英仁; 陈天艳; 刘敏

    2012-01-01

    Objective To screen the interacted protein hepatitis B virus (HBV) PreSl with human hepatocytes from normal human liver cDNA library by sos-recruitment system (SRS) and explore the mechanism of HBV endocylosis. Methods PCR was performed to amplify the gene of HBV PreSl from the plasmid PCP10/ HBV ayw subtype containing the whole fragment of HBV;the PCR product was cloned into yeast expression plasmid pSos. and reconstituted plasmid was tested by auto-sequencing assay and named pSos- PreSl. The pSos-PreSl fusion protein expressed in the yeast cells was confirmed by Western blot after pSos- PreSl was transfected into the yeast cell cdc25.Self-activation of the bait protein was determined by cotransformation of pSos- PreSl and pMyr-Lamin C, and the cytoplasmic localization of the bait protein was verified by cotransformation of pSos- PreSl and pMyr SB. Yeast cells co-transfected with pSos- PreSl and the normal human liver cDNA library grew in selective nutrition and temperature. The true positive clones were submitted for sequencing. The results were submitted to the BLAST notebook of NCBI to seek homologous sequence. Results The yeast expression vector of HBV PreSl gene was constructed successfully and its expression in yeast was verified. The recombinant bait plasmid did not have self-activation and toxicity to yeast cdc25H cells. Furthermore, the cytoplasmic localization of the bait protein was verified correctly. After yeast cells were co-transfected with pSos-PreSl and the normal human liver cDNA library, 5 clones were positive and showed high homology with KCMF1, cyt C, vitamin D binding protein, Homo sapiens albumin (ALB) and Homo sapiens asialoglycoprotein receptor (ASGPR). Conclusion We obtained 5 proteins which may interact with HBV PreSl protein by SRS. This is helpful for exploring the mechanism of HBV endocytosis.%目的 利用Sos招募系统(SRS),构建含HBV PreS1基因的酵母双杂交诱饵载体,筛选人肝细胞与HBV PreS1蛋白相互作用的

  13. Cytogenetic status of healthy children assessed with the alkaline comet assay and the cytokinesis-block micronucleus cytome assay.

    Science.gov (United States)

    Gajski, Goran; Gerić, Marko; Oreščanin, Višnja; Garaj-Vrhovac, Vera

    2013-01-20

    In the present study the alkaline comet assay and the cytokinesis-block micronucleus cytome (CBMN Cyt) assay were used to evaluate the baseline frequency of cytogenetic damage in peripheral blood lymphocytes (PBLs) of 50 healthy children from the general population in Croatia (age, 11.62±1.81 years). Mean values of tail length, tail intensity and tail moment, as comet assay parameters, were 12.92±0.10, 0.73±0.06 and 0.08±0.01, respectively. The mean frequency of micronuclei (MN) for all subjects was 2.32±0.28 per 1000 bi-nucleated cells, while the mean frequency of nucleoplasmic bridges (NPBs) was 1.72±0.24 and of nuclear buds (NBUDs) 1.44±0.19. The mean nuclear division index (NDI) was 1.70±0.05. When comet-assay parameters were considered, higher mean values for all three were found for the female population. According to the Mann-Whitney U test applied on the results of the comet assay, the only statistically significant difference between the male and female populations was found for tail length. Similar to the results obtained by the comet assay, girls showed higher mean values of all three measured parameters of the CBMN Cyt assay. This difference was statistically significant for total number of NPBs only. In the case of the NDI, a higher mean value was also obtained in girls, but this difference was not statistically significant. The results obtained present background data that could be considered as normal values for healthy children living in urban areas, and can later on serve as baseline values for further toxicological monitoring. Additionally, the usefulness of both techniques in measuring cytogenetic damage during bio-monitoring of children is confirmed.

  14. Dose estimation using dicentric chromosome assay and cytokinesis block micronucleus assay: comparison between manual and automated scoring in triage mode.

    Science.gov (United States)

    De Amicis, Andrea; De Sanctis, Stefania; Di Cristofaro, Sara; Franchini, Valeria; Regalbuto, Elisa; Mammana, Giacomo; Lista, Florigio

    2014-06-01

    In cases of an accidental overexposure to ionizing radiation, it is essential to estimate the individual absorbed dose of a potentially radiation-exposed person. For this purpose, biological dosimetry can be performed to confirm, complement or even replace physical dosimetry when this proves to be unavailable. The most validated biodosimetry techniques for dose estimation are the dicentric chromosome assay, the "gold standard" for individual dose assessment, and cytokinesis-block micronucleus assay. However, both assays are time consuming and require skilled scorers. In case of large-scale accidents, different strategies have been developed to increase the throughput of cytogenetic service laboratories. These are the decrease of cell numbers to be scored for triage dosimetry; the automation of procedures including the scoring of, for example, aberrant chromosomes and micronuclei; and the establishment of laboratory networks in order to enable mutual assistance if necessary. In this study, the authors compared the accuracy of triage mode biodosimetry by dicentric chromosome analysis and the cytokinesis block micronucleus assay performing both the manual and the automated scoring mode. For dose estimation using dicentric chromosome assay of 10 blind samples irradiated up to 6.4 Gy of x-rays, a number of metaphase spreads were analyzed ranging from 20 up to 50 cells for the manual and from 20 up to 500 cells for the automatic scoring mode. For dose estimation based on the cytokinesis block micronucleus assay, the micronucleus frequency in both 100 and 200 binucleated cells was determined by manual and automatic scoring. The results of both assays and scoring modes were compared and analyzed considering the sensitivity, specificity, and accuracy of dose estimation with regard to the discrimination power of clinically relevant binary categories of exposure doses.

  15. Correlation between the genotoxicity endpoints measured by two different genotoxicity assays: comet assay and CBMN assay

    OpenAIRE

    Carina Ladeira; Susana Viegas; Manuel C. Gomes

    2015-01-01

    The cytokinesis-block micronucleus cytome (CBMN) assay is a comprehensive system for measuring DNA damage; cytostasis and cytotoxicity-DNA damage events are scored specifically in once-divided binucleated cells. The endpoints possible to be measured are micronuclei (MN), a biomarker of chromosome breakage and/or whole chromosome loss, nucleoplasmic bridges (NPB), a biomarker of DNA misrepair and/or telomere end-fusions, and nuclear buds (NBUD), a biomarker of elimination of amplified DNA and/...

  16. Novel assay to quantify recombination in a calicivirus.

    Science.gov (United States)

    Symes, Sally J; Job, Natalie; Ficorilli, Nino; Hartley, Carol A; Browning, Glenn F; Gilkerson, James R

    2015-05-15

    Recombination is an important contributor to genomic evolution in many viral families, including the Caliciviridae. While it is known that genomic recombination in caliciviruses contributes to their rapid evolution, the precise molecular mechanisms are poorly understood. The majority of reported recombination events in feline calicivirus (FCV) occur at a "hot spot" between the non-structural protein coding region (open reading frame 1) and structural protein coding region (open reading frame 2). To gain a better understanding of the rate of recombination at this point, we developed a quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay to quantify the rate of recombination between two divergent strains of FCV during co-infection in cell culture. The assay utilised virus-specific primers upstream and downstream of the recombinational "hot spot" that hybridise with only one of the strains in the co-infection. Recombinant progeny that shared ORF1 sequence identity with one parental virus and ORF2 sequence identity with the other parental virus, and the site of recombination, was confirmed by sequencing the amplicon generated by the assay. Recombinants were detected in co-infected cells using this assay, but not in cells infected with single strains that were mixed together following infection, thus confirming its specificity. Recombination between two FCVs in co-infected cell cultures was estimated to occur at a rate of at least 6.8×10(-6) single direction recombinant genomes per parental virus genome. Further application of this assay will enable factors influencing recombination in caliciviruses to be explored in greater detail, both in vitro and in vivo. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Detection of aerosolized biological agents by immunoassay followed by autonomous PCR confirmation

    Energy Technology Data Exchange (ETDEWEB)

    Dzenitis, J M; Hindson, B J; McBride, M T; Makarewicz, A J; Henderer, B D; Sathyam, U S; Smith, S M; Gutierrez, D M; Metz, T R; Venkateswaran, K S; Colston, B W; Farrow, S W

    2003-12-15

    An Autonomous Pathogen Detection System (APDS) unit is an automated, podium-sized system that monitors the air for all three biological threat agents (bacteria, viruses, and toxins). The system has been developed under the auspices of the U. S. Department of Energy and Department of Homeland Security by the University of California, Lawrence Livermore National Laboratory (LLNL) to protect people in critical or high-traffic facilities and at special events. The system performs continuous aerosol collection, sample preparation, and multiplexed biological tests using advanced immunoassays as the primary screen. Over ten agents are assayed at once, and results are reported hourly. R&D work this year focused on incorporating polymerase chain-reaction (PCR) techniques for detecting DNA as confirmation of immunoassay positives. The primary objective of the Dugway testing was to demonstrate the APDS with immunoassay identification and PCR confirmation of bacteria. A secondary objective was to demonstrate immunoassay identification of a protein toxoid (denatured toxin) aerosol release. A total of 12 agent trials were conducted over 14 days of testing, for a total of four work weeks at Dugway. Both testing objectives were achieved with multiple releases and clear identifications. The APDS was shown to be effective for identifying aerosolized Bacillus anthracis, Yersinia pestis, Bacillus globigii, and botulinum toxoid. The two areas for improvement were operational as opposed to hardware-related. The first was slowing the PCR thermal cycling to achieve stronger signals, which was demonstrated during the later phases of testing. The second area is to improve the parameters for autonomous PCR triggering; this is one of the focuses of the upcoming year's work.

  18. Feature Detection, Characterization and Confirmation Methodology: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Karasaki, Kenzi; Apps, John; Doughty, Christine; Gwatney, Hope; Onishi, Celia Tiemi; Trautz, Robert; Tsang, Chin-Fu

    2007-03-01

    This is the final report of the NUMO-LBNL collaborative project: Feature Detection, Characterization and Confirmation Methodology under NUMO-DOE/LBNL collaboration agreement, the task description of which can be found in the Appendix. We examine site characterization projects from several sites in the world. The list includes Yucca Mountain in the USA, Tono and Horonobe in Japan, AECL in Canada, sites in Sweden, and Olkiluoto in Finland. We identify important geologic features and parameters common to most (or all) sites to provide useful information for future repository siting activity. At first glance, one could question whether there was any commonality among the sites, which are in different rock types at different locations. For example, the planned Yucca Mountain site is a dry repository in unsaturated tuff, whereas the Swedish sites are situated in saturated granite. However, the study concludes that indeed there are a number of important common features and parameters among all the sites--namely, (1) fault properties, (2) fracture-matrix interaction (3) groundwater flux, (4) boundary conditions, and (5) the permeability and porosity of the materials. We list the lessons learned from the Yucca Mountain Project and other site characterization programs. Most programs have by and large been quite successful. Nonetheless, there are definitely 'should-haves' and 'could-haves', or lessons to be learned, in all these programs. Although each site characterization program has some unique aspects, we believe that these crosscutting lessons can be very useful for future site investigations to be conducted in Japan. One of the most common lessons learned is that a repository program should allow for flexibility, in both schedule and approach. We examine field investigation technologies used to collect site characterization data in the field. An extensive list of existing field technologies is presented, with some discussion on usage and limitations

  19. Feature Detection, Characterization and Confirmation Methodology: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Karasaki, Kenzi; Apps, John; Doughty, Christine; Gwatney, Hope; Onishi, Celia Tiemi; Trautz, Robert; Tsang, Chin-Fu

    2007-03-01

    This is the final report of the NUMO-LBNL collaborative project: Feature Detection, Characterization and Confirmation Methodology under NUMO-DOE/LBNL collaboration agreement, the task description of which can be found in the Appendix. We examine site characterization projects from several sites in the world. The list includes Yucca Mountain in the USA, Tono and Horonobe in Japan, AECL in Canada, sites in Sweden, and Olkiluoto in Finland. We identify important geologic features and parameters common to most (or all) sites to provide useful information for future repository siting activity. At first glance, one could question whether there was any commonality among the sites, which are in different rock types at different locations. For example, the planned Yucca Mountain site is a dry repository in unsaturated tuff, whereas the Swedish sites are situated in saturated granite. However, the study concludes that indeed there are a number of important common features and parameters among all the sites--namely, (1) fault properties, (2) fracture-matrix interaction (3) groundwater flux, (4) boundary conditions, and (5) the permeability and porosity of the materials. We list the lessons learned from the Yucca Mountain Project and other site characterization programs. Most programs have by and large been quite successful. Nonetheless, there are definitely 'should-haves' and 'could-haves', or lessons to be learned, in all these programs. Although each site characterization program has some unique aspects, we believe that these crosscutting lessons can be very useful for future site investigations to be conducted in Japan. One of the most common lessons learned is that a repository program should allow for flexibility, in both schedule and approach. We examine field investigation technologies used to collect site characterization data in the field. An extensive list of existing field technologies is presented, with some discussion on usage and limitations

  20. Cosmic Forensics Confirms Gamma-Ray Burst And Supernova Connection

    Science.gov (United States)

    2003-03-01

    Scientists announced today that they have used NASA's Chandra X-ray Observatory to confirm that a gamma-ray burst was connected to the death of a massive star. This result is an important step in understanding the origin of gamma-ray bursts, the most violent events in the present-day universe. "If a gamma-ray burst were a crime, then we now have strong circumstantial evidence that a supernova explosion was at the scene," said Nathaniel Butler of Massachusetts Institute of Technology in Cambridge, lead author of a paper presented today at the meeting of the High Energy Division of the American Astronomical Society. Chandra was able to obtain an unusually long observation (approximately 21 hours) of the afterglow of GRB 020813 (so named because the High-Energy Transient Explorer, HETE, discovered it on August 13, 2002.) A grating spectrometer aboard Chandra revealed an overabundance of elements characteristically dispersed in a supernova explosion. Narrow lines, or bumps, due to silicon and sulfur ions (atoms stripped of most of their electrons) were clearly identified in the X-ray spectrum of GRB 020813. "Our observation of GRB 020813 supports two of the most important features of the popular supra-nova model for gamma-ray bursts," said Butler. "An extremely massive star likely exploded less than two months prior to the gamma-ray burst, and the radiation from the gamma-ray burst was beamed into a narrow cone." An analysis of the data showed that the ions were moving away from the site of the gamma-ray burst at a tenth the speed of light, probably as part of a shell of matter ejected in the supernova explosion. The line features were observed to be sharply peaked, indicating that they were coming from a narrow region of the expanding shell. This implies that only a small fraction of the shell was illuminated by the gamma-ray burst, as would be expected if the burst was beamed into a narrow cone. The observed duration of the afterglow suggests a delay of about 60 days

  1. The Role of 16S rRNA Gene Sequencing in Confirmation of Suspected Neonatal Sepsis.

    Science.gov (United States)

    El Gawhary, Somaia; El-Anany, Mervat; Hassan, Reem; Ali, Doaa; El Gameel, El Qassem

    2016-02-01

    Different molecular assays for the detection of bacterial DNA in the peripheral blood represented a diagnostic tool for neonatal sepsis. We targeted to evaluate the role of 16S rRNA gene sequencing to screen for bacteremia to confirm suspected neonatal sepsis (NS) and compare with risk factors and septic screen testing. Sixty-two neonates with suspected NS were enrolled. White blood cells count, I/T ratio, C-reactive protein, blood culture and 16S rRNA sequencing were performed. Blood culture was positive in 26% of cases, and PCR was positive in 26% of cases. Evaluation of PCR for the diagnosis of NS showed sensitivity 62.5%, specificity 86.9%, PPV 62.5%, NPV 86.9% and accuracy of 79.7%. 16S rRNA PCR increased the sensitivity of detecting bacterial DNA in newborns with signs of sepsis from 26 to 35.4%, and its use can be limited to cases with the most significant risk factors and positive septic screen. © The Author [2015]. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. The comet assay in testing the potential genotoxicity of nanomaterials

    Directory of Open Access Journals (Sweden)

    Amaya Azqueta

    2015-06-01

    validation. The comet assay has not been yet proposed as an appropriate test to check the genotoxic potential of NMs, though at a research level it is the most used in vitro assay and the second most used in vivo assay. Moreover, the combination of the comet assay with enzymes that convert altered bases to breaks allows the identification of DNA damage induced by secondary mechanisms (e.g. oxidative stress induced by inflammation, which is very relevant in the case of NMs. Possible problems with the use of the comet assay have been suggested: NMs have been detected in close association with comets, and might interact with the DNA; or NMs might inhibit the action of enzymes. However, control experiments have not confirmed that these interactions are significant.

  3. Cytotoxicity and genotoxicity assessment of Euphorbia hirta in MCF-7 cell line model using comet assay

    Institute of Scientific and Technical Information of China (English)

    Kwan Yuet Ping; Ibrahim Darah; Yeng Chen; Sreenivasan Sasidharan

    2013-01-01

    Objective:To evaluate the cytotoxicity and genotoxicity activity of Euphorbia hirta (E. hirta) in MCF-7 cell line model using comet assay. Methods: The cytotoxicity of E. hirta extract was investigated by employing brine shrimp lethality assay and the genotoxicity of E. hirta was assessed by using Comet assay. Results: Both toxicity tests exhibited significant toxicity result. In the comet assay, the E. hirta extract exhibited genotoxicity effects against MCF-7 DNA in a time-dependent manner by increasing mean percentage of DNA damage. The extract of E. hirta showed significant toxicity against brine shrimp with an LC50 value of 620.382 μg/mL (24 h). Comparison with positive control potassium dichromate signifies that cytotoxicity exhibited by the methanol extract might have moderate activity. Conclusion:The present work confirmed the cytotoxicity and genotoxicity of E. hirta. However, the observed toxicity of E. hirta extracts needs to be confirmed in additional studies.

  4. 21 CFR 864.7525 - Heparin assay.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Heparin assay. 864.7525 Section 864.7525 Food and... HEMATOLOGY AND PATHOLOGY DEVICES Hematology Kits and Packages § 864.7525 Heparin assay. (a) Identification. A heparin assay is a device used to determine the level of the anticoagulant heparin in the...

  5. A colorimetric assay for cytokinin oxidase.

    Science.gov (United States)

    Libreros-Minotta, C A; Tipton, P A

    1995-11-01

    A simple and rapid colorimetric assay for cytokinin oxidase is described. The assay is based on the formation of a Schiff base between the enzymatic reaction product 3-methyl-2-butenal and p-aminophenol. The assay is effective in the submicromolar concentration range and can be used in crude plant extracts as well as in more highly purified preparations.

  6. Multicentre comparison of a diagnostic assay

    DEFF Research Database (Denmark)

    Waters, Patrick; Reindl, Markus; Saiz, Albert;

    2016-01-01

    ) assays in neuromyelitis optica spectrum disorders (NMOSD). METHODS: Coded samples from patients with neuromyelitis optica (NMO) or NMOSD (101) and controls (92) were tested at 15 European diagnostic centres using 21 assays including live (n=3) or fixed cell-based assays (n=10), flow cytometry (n=4...

  7. 21 CFR 866.3210 - Endotoxin assay.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Endotoxin assay. 866.3210 Section 866.3210 Food... DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3210 Endotoxin assay. (a) Identification. An endotoxin assay is a device that uses serological techniques in whole blood. The device...

  8. Capillary Electrophoresis Analysis of Conventional Splicing Assays

    DEFF Research Database (Denmark)

    de Garibay, Gorka Ruiz; Acedo, Alberto; García-Casado, Zaida;

    2014-01-01

    of these assays is often challenging. Here, we explore this issue by conducting splicing assays in 31 BRCA2 genetic variants. All variants were assessed by RT-PCR followed by capillary electrophoresis and direct sequencing. If assays did not produce clear-cut outputs (Class-2 or Class-5 according to analytical...

  9. Screening of proteins binding to mouse cytomegalovirus M122 protein from mouse brain cDNA library by yeast two-hybrid system%酵母双杂交技术筛选小鼠脑cDNA文库中鼠巨细胞病毒即刻早期蛋白M122相互作用蛋白的研究

    Institute of Scientific and Technical Information of China (English)

    王慧; 周玉峰; 舒赛男; 罗丹; 田佳; 张慧娟; 杜小弋; 方峰

    2010-01-01

    histone acetyltransferase(monocytic leukemia)4,Myst4]、透明质酸和蛋白多糖连接蛋白1(hyaluronan and proteoglycan link protein 1,Hapln1)、自噬相关蛋白3(autophagy-related 3,Atg3)、精氨酸/色氨酸富集的剪切因子5(splicing factor,arginine/serine-rich 5,Sfrs5)、C3HC型锌指蛋白(zinc finger,C3HC-type containing 1,Zc3hc1)、硫氧还蛋白相关的跨膜蛋白1(thioredoxin-related transmembrane protein 1,Txndc1)、接头蛋白复合物AP-1亚单位(adaptor protein complex AP-1,gamma 1 subunit,Aplg1)和Cul1蛋白(cullin 1,Cul1).回返验证实验进一步证实这些蛋白与M122蛋白能够在酵母细胞AH109发生相互作用,但Aplg1和Cul1被证实具有自激活作用.结论 筛选到的其中19种已知基因编码的蛋白可能与巨细胞病毒的致病机制相关,但仍需进一步的验证.%Objective To investigate the biological function of M122 in pathogenesis of MCMV in developmental brain disorders and brain damage, screening for mouse brain cDNA library interacting with M122 was performed by a yeast two-hybrid system. Methods The reconstructed bait plasmid pGBKT7-M122 was transformed into yeast cells AH109 and screened on the nutrient deficiency medium SD/-Trp. After express of the bait protein in AH109 yeast strains was detected by Western blot analysis, yeast-two hybrid screening was performed by mating AH109 with Y187 containing mouse brain cDNA library plasmid. The diploid yeast cells were plated on the nutrient deficiency medium SD/-Trp/-Leu/-His/-Ade. The second screening was performed with SD/-Trp/-Leu/-His/-Ade containing X-α-gal. The plasmids in positive colonies were extracted and transformed into E. coli JM109 cells. After plasmid DNA in JM109 cells were extracted form positive colonies and sequenced, the results were analyzed by bioinformatic methods. The interactions between M122 protein and the protein obtained from positive colonies were further confirmed by repeating yeast-two hybrid. Then, autoactivations of

  10. Steroid assays in paediatric endocrinology.

    Science.gov (United States)

    Honour, John W

    2010-01-01

    Most steroid disorders of the adrenal cortex come to clinical attention in childhood and in order to investigate these problems, there are many challenges to the laboratory which need to be appreciated to a certain extent by clinicians. The analysis of sex steroids in biological fluids from neonates, over adrenarche and puberty present challenges of specificities and concentrations often in small sample sizes. Different reference ranges are also needed for interpretations. For around 40 years, quantitative assays for the steroids and their regulatory peptide hormones have been possible using immunoassay techniques. Problems are recognised and this review aims to summarise the benefits and failings of immunoassays and introduce where tandem mass spectrometry is anticipated to meet the clinical needs for steroid analysis in paediatric endocrine investigations. It is important to keep a dialogue between clinicians and the laboratory, especially when any laboratory result does not make sense in the clinical investigation.

  11. O-5S quantitative real-time PCR: a new diagnostic tool for laboratory confirmation of human onchocerciasis.

    Science.gov (United States)

    Mekonnen, Solomon A; Beissner, Marcus; Saar, Malkin; Ali, Solomon; Zeynudin, Ahmed; Tesfaye, Kassahun; Adbaru, Mulatu G; Battke, Florian; Poppert, Sven; Hoelscher, Michael; Löscher, Thomas; Bretzel, Gisela; Herbinger, Karl-Heinz

    2017-10-02

    Onchocerciasis is a parasitic disease caused by the filarial nematode Onchocerca volvulus. In endemic areas, the diagnosis is commonly confirmed by microscopic examination of skin snip samples, though this technique is considered to have low sensitivity. The available melting-curve based quantitative real-time PCR (qPCR) using degenerated primers targeting the O-150 repeat of O. volvulus was considered insufficient for confirming the individual diagnosis, especially in elimination studies. This study aimed to improve detection of O. volvulus DNA in clinical samples through the development of a highly sensitive qPCR assay. A novel hydrolysis probe based qPCR assay was designed targeting the specific sequence of the O. volvulus O-5S rRNA gene. A total of 200 clinically suspected onchocerciasis cases were included from Goma district in South-west Ethiopia, from October 2012 through May 2013. Skin snip samples were collected and subjected to microscopy, O-150 qPCR, and the novel O-5S qPCR. Among the 200 individuals, 133 patients tested positive (positivity rate of 66.5%) and 67 negative by O-5S qPCR, 74 tested positive by microscopy (37.0%) and 78 tested positive by O-150 qPCR (39.0%). Among the 133 O-5S qPCR positive individuals, microscopy and O-150 qPCR detected 55.6 and 59.4% patients, respectively, implying a higher sensitivity of O-5S qPCR than microscopy and O-150 qPCR. None of the 67 individuals who tested negative by O-5S qPCR tested positive by microscopy or O-150 qPCR, implying 100% specificity of the newly designed O-5S qPCR assay. The novel O-5S qPCR assay is more sensitive than both microscopic examination and the existing O-150 qPCR for the detection of O. volvulus from skin snip samples. The newly designed assay is an important step towards appropriate individual diagnosis and control of onchocerciasis.

  12. Predictive Assay For Cancer Targets

    Energy Technology Data Exchange (ETDEWEB)

    Suess, A; Nguyen, C; Sorensen, K; Montgomery, J; Souza, B; Kulp, K; Dugan, L; Christian, A

    2005-09-19

    Early detection of cancer is a key element in successful treatment of the disease. Understanding the particular type of cancer involved, its origins and probable course, is also important. PhIP (2-amino-1-methyl-6 phenylimidazo [4,5-b]pyridine), a heterocyclic amine produced during the cooking of meat at elevated temperatures, has been shown to induce mammary cancer in female, Sprague-Dawley rats. Tumors induced by PhIP have been shown to contain discreet cytogenetic signature patterns of gains and losses using comparative genomic hybridization (CGH). To determine if a protein signature exists for these tumors, we are analyzing expression levels of the protein products of the above-mentioned tumors in combination with a new bulk protein subtractive assay. This assay produces a panel of antibodies against proteins that are either on or off in the tumor. Hybridization of the antibody panel onto a 2-D gel of tumor or control protein will allow for identification of a distinct protein signature in the tumor. Analysis of several gene databases has identified a number of rat homologs of human cancer genes located in these regions of gain and loss. These genes include the oncogenes c-MYK, ERBB2/NEU, THRA and tumor suppressor genes EGR1 and HDAC3. The listed genes have been shown to be estrogen-responsive, suggesting a possible link between delivery of bio-activated PhIP to the cell nucleus via estrogen receptors and gene-specific PhIP-induced DNA damage, leading to cell transformation. All three tumors showed similar silver staining patterns compared to each other, while they all were different than the control tissue. Subsequent screening of these genes against those from tumors know to be caused by other agents may produce a protein signature unique to PhIP, which can be used as a diagnostic to augment optical and radiation-based detection schemes.

  13. Validation of the micronucleus-centromere assay for biological dosimetry

    Directory of Open Access Journals (Sweden)

    Wojcik A.

    2000-01-01

    Full Text Available The micronucleus assay is frequently used for purposes of biological dosimetry. Due to high interindividual variability in the spontaneous frequency of micronuclei, its sensitivity in the low dose region is poor. It has been suggested that this problem can be mitigated by selectively analyzing the frequency of those micronuclei which contain only acentric fragments. Using a pan-centromeric FISH probe we have studied the dose dependence of micronuclei with centromeres in peripheral lymphocytes of human donors. In contrast to previous publications, our approach is based on determining the relative frequency of micronuclei with and without centromeric signals. Our results confirm previous observations that in the low dose range of ionizing radiation, the micronucleus-centromere assay is more sensitive than the conventional micronucleus test.

  14. MicroRNA markers for forensic body fluid identification obtained from microarray screening and quantitative RT-PCR confirmation.

    Science.gov (United States)

    Zubakov, Dmitry; Boersma, Anton W M; Choi, Ying; van Kuijk, Patricia F; Wiemer, Erik A C; Kayser, Manfred

    2010-05-01

    MicroRNAs (miRNAs) are non-protein coding molecules with important regulatory functions; many have tissue-specific expression patterns. Their very small size in principle makes them less prone to degradation processes, unlike messenger RNAs (mRNAs), which were previously proposed as molecular tools for forensic body fluid identification. To identify suitable miRNA markers for forensic body fluid identification, we first screened total RNA samples derived from saliva, semen, vaginal secretion, and venous and menstrual blood for the expression of 718 human miRNAs using a microarray platform. All body fluids could be easily distinguished from each other on the basis of complete array-based miRNA expression profiles. Results from quantitative reverse transcription PCR (RT-PCR; TaqMan) assays for microarray candidate markers confirmed strong over-expression in the targeting body fluid of several miRNAs for venous blood and several others for semen. However, no candidate markers from array experiments for other body fluids such as saliva, vaginal secretion, or menstrual blood could be confirmed by RT-PCR. Time-wise degradation of venous blood and semen stains for at least 1 year under lab conditions did not significantly affect the detection sensitivity of the identified miRNA markers. The detection limit of the TaqMan assays tested for selected venous blood and semen miRNA markers required only subpicogram amounts of total RNA per single RT-PCR test, which is considerably less than usually needed for reliable mRNA RT-PCR detection. We therefore propose the application of several stable miRNA markers for the forensic identification of blood stains and several others for semen stain identification, using commercially available TaqMan assays. Additional work remains necessary in search for suitable miRNA markers for other forensically relevant body fluids.

  15. Activity assay of membrane transport proteins

    Institute of Scientific and Technical Information of China (English)

    Hao Xie

    2008-01-01

    Membrane transport proteins are integral membrane proteins and considered as potential drug targets. Activity assay of transport proteins is essential for developing drugs to target these proteins. Major issues related to activity assessment of transport proteins include availability of transporters,transport activity of transporters, and interactions between ligands and transporters. Researchers need to consider the physiological status of proteins (bound in lipid membranes or purified), availability and specificity of substrates, and the purpose of the activity assay (screening, identifying, or comparing substrates and inhibitors) before choosing appropriate assay strategies and techniques. Transport proteins bound in vesicular membranes can be assayed for transporting substrate across membranes by means of uptake assay or entrance counterflow assay. Alternatively, transport proteins can be assayed for interactions with ligands by using techniques such as isothermal titration calorimetry, nuclear magnetic resonance spectroscopy, or surface plasmon resonance. Other methods and techniques such as fluorometry, scintillation proximity assay, electrophysiological assay, or stopped-flow assay could also be used for activity assay of transport proteins. In this paper the major strategies and techniques for activity assessment of membrane transport proteins are reviewed.

  16. Biological Assay of Toxoplasma gondii Egyptian Mutton Isolates

    Directory of Open Access Journals (Sweden)

    N.A. Hassanain

    2011-01-01

    Full Text Available Mutton signifies one of the most prevalent sources for human toxoplasmosis. However, sheep serological assays don't categorize the virulent strains initiating antibodies, so the biological bioassay of Egyptian mutton isolates with reference to their pathogenicity in both mice and kittens were done in this study for indicating to how extent their zoonotic bio-hazard. A total number of 280 of each sheep blood and tissue samples were collected during slaughtering at Cairo abattoir, Egypt. Sera assayed using Latex Agglutination Test (LAT and immunosorbant assay (ELISA and their corresponding mutton samples were microscopically examined after pepsin digestion for detection of Toxoplasma gondii infection. The sero-positive percent of the naturally infected sheep was 50.4 and 61.4 by LAT and ELISA, respectively, 47.9% of samples were confirmedly positive in both LAT and ELISA results. The microscopical examination revealed that only 28 out of 134 (20.9% of the confirmed sero-positive animals by both tests were found harboring T. gondii tissue cysts in their mutton samples, while high percentage of confirmed sero-positve animals (79.1% (106 out of 134 were biologically tissue cysts free mutton. Biological typing of the 28 T. gondii sheep isolates with reference to mice and kittens' bioassay indicated that 10.7, 50, 21.4 and 17.9% were type I, II, III and avirulent strains, respectively. The high T. gondii infection rate resulted in this study concludes that the feeding of under cooked mutton is a bad health habit as a source for human toxoplasmosis moreover; the T. gondii virulent strains obtained by mutton bioassay indicated that not all sero-positive sheep are connecting zoonotic bio-hazard through their mutton strains.

  17. Enzyme inhibition assay for pyruvate dehydrogenase complex: Clinical utility for the diagnosis of primary biliary cirrhosis

    Institute of Scientific and Technical Information of China (English)

    Katsuhisa Omagri; Hiroaki Hazama; Shigeru Kohno

    2005-01-01

    Primary biliary cirrhosis (PBC) is usually diagnosed by the presence of characteristic histopathological features of the liver and/or antimitochondrial antibodies (AMA) in the serum traditionally detected by immunofluorescence.Recently, new and more accurate serological assays for the detection of AMA, such as enzyme-linked immunosorbent assay (ELISA), immunoblotting, and enzyme inhibition assay, have been developed. Of these,the enzyme inhibition assay for the detection of antipyruvate dehydrogenase complex (PDC) antibodies offers certain advantages such as objectivity, rapidity,simplicity, and low cost. Since this assay has almost 100% specificity, it may have particular applicability in screening the at-risk segment of the population in developing countries. Moreover, this assay could be also used for monitoring the disease course in PBC. Almost all sera of PBC-suspected patients can be confirmed for PBC or non-PBC by the combination results of immunoblotting and enzyme inhibition assay without histopathological examination. For the development of a "complete" or "gold standard" diagnostic assay for PBC, similar assays of the enzyme inhibition for anti2-oxoglutarate dehydrogenase complex (OGDC) and anti-branched chain oxo-acid dehydrogenase complex (BCOADC) antibodies will be needed in future.

  18. Urolithins display both antioxidant and pro-oxidant activities depending on assay system and conditions.

    Science.gov (United States)

    Kallio, Tuija; Kallio, Johanna; Jaakkola, Mari; Mäki, Marianne; Kilpeläinen, Pekka; Virtanen, Vesa

    2013-11-13

    The biological effects of polyphenolic ellagitannins are mediated by their intestinal metabolites, urolithins. This study investigated redox properties of urolithins A and B using ORAC assay, three cell-based assays, copper-initiated pro-oxidant activity (CIPA) assay, and cyclic voltammetry. Urolithins were strong antioxidants in the ORAC assay, but mostly pro-oxidants in cell-based assays, although urolithin A was an antioxidant in cell culture medium. Parent compound ellagic acid was a strong extracellular antioxidant, but showed no response in the intracellular assay. The CIPA assay confirmed the pro-oxidant activity of ellagitannin metabolites. In the cell proliferation assay, urolithins but not ellagic acid decreased growth and metabolism of HepG2 liver cells. In cyclic voltammetry, the oxidation of urolithin A was partly reversible, but that of urolithin B was irreversible. These results illustrate how strongly measured redox properties depend on the employed assay system and conditions and emphasize the importance of studying pro-oxidant and antioxidant activities in parallel.

  19. The chemical-in-plug bacterial chemotaxis assay is prone to false positive responses

    Directory of Open Access Journals (Sweden)

    Ward Mandy J

    2010-03-01

    Full Text Available Abstract Background Chemical-in-plug assays are commonly used to study bacterial chemotaxis, sometimes in the absence of stringent controls. Results We report that non-chemotactic and non-motile mutants in two distinct bacterial species (Shewanella oneidensis and Helicobacter pylori show apparent zones of accumulation or clearing around test plugs containing potential attractants or repellents, respectively. Conclusions Our results suggest that the chemical-in-plug assay should be used with caution, that non-motile or non-chemotactic mutants should be employed as controls, and that results should be confirmed with other types of assays.

  20. The importance of serological assays in diagnosing acute pulmonary histoplasmosis

    Directory of Open Access Journals (Sweden)

    RS Freitas

    2009-01-01

    Full Text Available Histoplasmosis is a systemic mycosis caused by inhalation of Histoplasma capsulatum microconidia. The disease does not normally affect immunocompetent individuals after a single, transient inhalation exposure. However, longer exposure may cause chronic or disseminated acute pulmonary infection. Herein, we report the case of a 24-year-old immunocompetent patient, who presented fever, cough and dyspnea for one month. The chest radiography revealed interstitial infiltrate and diffuse micronodules. The patient reported having had close and prolonged contact with bats. Diagnosis was confirmed by positive double immunodifusion and immunoblotting assays. She was treated with ketoconazole (400 mg and there was complete resolution of the disease.

  1. 玉米胚芽鞘负向重力生长时期的酵母双杂交文库构建及评价%Construction and Appreciation of Yeast Two Hybrid Library of Maize Coleoptile during Negtive-gravitropic Growth

    Institute of Scientific and Technical Information of China (English)

    姜川; 陈化榜

    2012-01-01

    [目的]构建玉米胚芽鞘负向重力生长时期的酵母双杂交文库,并对其进行评价.[方法]以玉米骨干自交系B73为材料,利用Trizol试剂提取玉米胚芽鞘在负向生长时期所表达的总RNA,再利用SMART技术构建酵母双杂交文库,并转化进酵母Y187中.[结果]试验得到的原始文库库容量高达1×106个单克隆;文库中插入的片段集中在0.5~1.5 kb,平均插入长度为800 bp.[结论]试验构建得到了高质量的米胚芽鞘酵母双杂交文库,为研究胚芽鞘的负向重力反应机制奠定了基础.%[Objective] The aim was to construct and appraise the yeast two hybrid library of maize coleoptile during its negative-gravitropic growth. [ Method] Using maize inbred line B73 as materials, the total RNA which expressed during negative-gravitropic growth period of maize coleoptile was extracted by Trizol, and the yeast two hybrid library was constructed by SMART technology and transformed into yeast Y187. [ Result] The results showed that the library contained 1 × 106 monoclones and the predominant size of inserted fragments in library was 0.5-1.5 kb, average size was 800 bp. [ Conclusion ] High-quailty yeast two hybrid library of maize coleoptile was constructed and it prepared the ground for the study of negative-gravitropic reaction mechanism of coleoptile.

  2. A secondary dengue 4 infection in a traveler returning from Haiti confirmed by virus isolation, complete genome sequencing and neutralisation assay: a brief report.

    Science.gov (United States)

    Menard, Amelie; Ninove, Laetitia; Zandotti, Christine; Leparc-Goffart, Isabelle; Klitting, Raphaelle; Baronti, Cecile; Stein, Andreas; de Lamballerie, Xavier; Charrel, Rémi N

    2015-01-01

    Here we report the clinical and laboratory findings of a dengue 4 virus (DENV) secondary infection in a patient returning from Haiti to France. The diagnostic of acute DEN-4 virus infection was demonstrated by (i) the presence of DEN-4 RNA in two successive serum samples, (ii) the isolation of a DEN-4 virus in Vero cells and subsequent identification of subtype IIb through complete genome sequencing, (iii) the presence of dengue NS1 antigen, (iv) the seroconversion with detection of dengue IgM in the second serum while negative in the first serum. The diagnosis of secondary dengue episode was demonstrated by (i) the presence of dengue IgG in the early serum, and (ii) the demonstration that neutralising antibodies against DEN-3 were present at the acute stage of the disease. Next-generation sequencing has a primary role to play in phylogeographic studies including database sequences, sequences from imported cases, and sequences from autochthonous cases. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Polarisation confirmed

    CERN Multimedia

    Anaïs Schaeffer

    2014-01-01

    The polarisation of photons emitted in the decay of a bottom quark into a strange quark, as predicted by the Standard Model, has just been observed for the first time by the LHCb collaboration. More detailed research is still required to determine the value of this polarisation with precision.   In this LHCb event, K, π and γ are emitted from a B+ → K+π-π+γ decay. This was investigated by the LHCb collaboration in order to study the photon (γ) polarisation.   If we imagine that photons are like little spinning tops which spin around an axis aligned with their direction of propagation, we can identify two types of photons. Those that are “right-handed” turn in the same direction as a corkscrew, and those that are “left-handed” turn in the opposite direction. If for a large number of decays of a given type we can observe an imbalance between the production of right-han...

  4. Development of a multiplexed urine assay for prostate cancer diagnosis.

    Science.gov (United States)

    Vener, Tatiana; Derecho, Carlo; Baden, Jonathan; Wang, Haiying; Rajpurohit, Yashoda; Skelton, Joanne; Mehrotra, Jyoti; Varde, Shobha; Chowdary, Dondapati; Stallings, Walt; Leibovich, Bradley; Robin, Howard; Pelzer, Alexandre; Schäfer, Georg; Auprich, Marco; Mannweiler, Sebastian; Amersdorfer, Peter; Mazumder, Abhijit

    2008-05-01

    Several studies have demonstrated the value of DNA methylation in urine-based assays for prostate cancer diagnosis. However, a multicenter validation with a clinical prototype has not been published. We developed a multiplexed, quantitative methylation-specific polymerase chain reaction (MSP) assay consisting of 3 methylation markers, GSTP1, RARB, and APC, and an endogenous control, ACTB, in a closed-tube, homogeneous assay format. We tested this format with urine samples collected after digital rectal examination from 234 patients with prostate-specific antigen (PSA) concentrations > or =2.5 microg/L in 2 independent patient cohorts from 9 clinical sites. In the first cohort of 121 patients, we demonstrated 55% sensitivity and 80% specificity, with area under the curve (AUC) 0.69. In the second independent cohort of 113 patients, we found a comparable sensitivity of 53% and specificity of 76% (AUC 0.65). In the first cohort, as well as in a combined cohort, the MSP assay in conjunction with total PSA, digital rectal examination status, and age improved the AUC without MSP, although the difference was not statistically significant. Importantly, the GSTP1 cycle threshold value demonstrated a good correlation (R = 0.84) with the number of cores found to contain prostate cancer or premalignant lesions on biopsy. Moreover, samples that exhibited methylation for either GSTP1 or RARB typically contained higher tumor volumes at prostatectomy than those samples that did not exhibit methylation. These data confirm and extend previously reported studies and demonstrate the performance of a clinical prototype assay that should aid urologists in identifying men who should undergo biopsy.

  5. Evaluation of the automated ADVIA centaur® XP syphilis assay for serological testing.

    Science.gov (United States)

    Saw, Sharon; Zhao, Huiqin; Tan, Phyllis; Saw, Betty; Sethi, Sunil

    2017-05-01

    We evaluated the performance of the ADVIA Centaur XP Syphilis assay (Siemens Healthcare Diagnostics, Tarrytown, NY, USA) using samples previously tested on the ARCHITECT i4000SR system (Abbott Diagnostics, Lake Forest, IL, USA) and confirmed by the Treponema pallidum particle agglutination assay (TPPA) (SERODIA-TPPA, Fujirebio Diagnostics Inc., Malvern, PA, USA). Clinical patient information was included to aid resolution of discordant samples where available. Precision, interference, and cross-reactivity were also assessed. Relative to patient clinical status, the sensitivity of both the ADVIA Centaur XP and the ARCHITECT assays was 100% (95% CI, 93.9-100), and the specificity of the ADVIA Centaur XP assay was 95.5% (95% CI, 90.4-98.3), which was slightly higher than that of the ARCHITECT assay at 93.9% (95% CI, 88.4-97.3). Overall agreement relative to patient clinical status was 96.9% (95% CI, 93.3-98.8) for the ADVIA Centaur XP assay and 95.8% (95% CI, 91.9-98.2) for the ARCHITECT assay. Overall agreement between the two automated assays was 96.9% (95% CI, 93.3-98.8). ADVIA Centaur XP assay precision was <5% at all index values tested. No significant interference was observed for lipemia or hemolysis; a small effect was seen with some samples for bilirubin. The assay exhibited no significant cross-reactivity with a number of potential interfering factors. The ADVIA Centaur XP Syphilis assay can be considered a sensitive and accurate assay for identification of treponemal antibodies in screening populations as well as patients presenting with suspicion of syphilitic infection. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Molecular confirmation of ovine herpesvirus 2-induced malignant catarrhal fever lesions in cattle from Rio Grande do Norte, Brazil

    Directory of Open Access Journals (Sweden)

    Selwyn A. Headley

    2012-12-01

    Full Text Available Molecular findings that confirmed the participation of ovine herpesvirus 2 (OVH-2 in the lesions that were consistent with those observed in malignant catarrhal fever of cattle are described. Three mixed-breed cattle from Rio Grande do Norte state demonstrated clinical manifestations that included mucopurulent nasal discharge, corneal opacity and motor incoordination. Routine necropsy examination demonstrated ulcerations and hemorrhage of the oral cavity, corneal opacity, and lymph node enlargement. Significant histopathological findings included widespread necrotizing vasculitis, non-suppurative meningoencephalitis, lymphocytic interstitial nephritis and hepatitis, and thrombosis. PCR assay performed on DNA extracted from kidney and mesenteric lymph node of one animal amplified a product of 423 base pairs corresponding to a target sequence within the ovine herpesvirus 2 (OVH-2 tegument protein gene. Direct sequencing of the PCR products, from extracted DNA of the kidney and mesenteric lymph node of one cow, amplified the partial nucleotide sequences (423 base pairs of OVH-2 tegument protein gene. Blast analysis confirmed that these sequences have 98-100% identity with similar OVH-2 sequences deposited in GenBank. Phylogenetic analyses, based on the deduced amino acid sequences, demonstrated that the strain of OVH-2 circulating in ruminants from the Brazilian states of Rio Grande do Norte and Minas Gerais are similar to that identified in other geographical locations. These findings confirmed the active participation of OVH-2 in the classical manifestations of sheep associated malignant catarrhal fever.

  7. Use of conventional and real-time polymerase chain reaction for confirmation of Mycobacterium avium subsp. paratuberculosis in a broth-based culture system ESP II.

    Science.gov (United States)

    Kim, Sung G; Kim, Eun H; Lafferty, Caroline J; Miller, Loretta J; Koo, Hye J; Stehman, Susan M; Shin, Sang J

    2004-09-01

    The ESP II Culture System (ESP II), a broth-based culture system, has been modified and optimized for culturing Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) in animal feces since 2000. Conventional and real-time polymerase chain reaction (PCR) assays based on the IS900 sequence were performed as confirmatory tests for M. paratuberculosis in ESP II liquid culture medium. There were no differences between test results of conventional and real-time PCR assays. During the 5-week incubation period, if acid-fast bacilli (AFB) were detected in ESP culture-positive samples, IS900 PCR assays were performed to confirm whether those AFB were M. paratuberculosis. At the end of the 5-week incubation, AF staining was performed on all ESP II-negative cultures to screen any false-negative cultures; IS900 PCR assays were performed on AFB-positive cultures. During a period of 1 year, of a total of 18,499 ESP II cultures, 2,814 (15.2%) PCR confirmation assays were performed. Of those, 2,259 (80%) were both ESP and PCR positive; 104 (4%) were ESP positive and PCR negative; 423 (15%) were ESP negative and PCR positive; 28 (1%) were both ESP and PCR negative. The AF-staining step after the 5-week incubation produced 423 (15%) more PCR-positive cultures. Of a total of 2,814 AFB-positive cultures, 132 (5%) were not confirmed as M. paratuberculosis. Further studies are needed for speciation of non-M. paratuberculosis isolates.

  8. Development and application of assays for serotonin

    Energy Technology Data Exchange (ETDEWEB)

    Gow, I.F.

    1987-01-01

    In this thesis, two assays for serotonin were developed, validated, and used to investigate the relationship between platelet aggregation, serotonin levels and sodium status and serotonin levels and platelet function in patients with cardiovascular disease. A radioimmunoassay (RIA) using an (/sup 125/I)-labelled tracer was developed and validated for the measurement of serotonin in human platelet-rich plasma (PRP) and rat serum. Antisera were raised against N-succinamylserotonin conjugated to bovine albumin and, to improve assay sensitivity, the analyte was made chemically similar to the immunogen by conversion to N-acetylserotonin prior to assay, using the specific amino reagent N-acetoxysuccinimide. An assay for serotonin using high-pressure liquid chromatography with electrochemical detection (HPLC-ECD) was developed, and used to validate the RIA. The RIA can be used to assay up to 100 samples/day compared with 10-20/day by the HPLC-ECD assay.

  9. A Functional Henipavirus Envelope Glycoprotein Pseudotyped Lentivirus Assay System

    Directory of Open Access Journals (Sweden)

    Broder Christopher C

    2010-11-01

    Full Text Available Abstract Background Hendra virus (HeV and Nipah virus (NiV are newly emerged zoonotic paramyxoviruses discovered during outbreaks in Queensland, Australia in 1994 and peninsular Malaysia in 1998/9 respectively and classified within the new Henipavirus genus. Both viruses can infect a broad range of mammalian species causing severe and often-lethal disease in humans and animals, and repeated outbreaks continue to occur. Extensive laboratory studies on the host cell infection stage of HeV and NiV and the roles of their envelope glycoproteins have been hampered by their highly pathogenic nature and restriction to biosafety level-4 (BSL-4 containment. To circumvent this problem, we have developed a henipavirus envelope glycoprotein pseudotyped lentivirus assay system using either a luciferase gene or green fluorescent protein (GFP gene encoding human immunodeficiency virus type-1 (HIV-1 genome in conjunction with the HeV and NiV fusion (F and attachment (G glycoproteins. Results Functional retrovirus particles pseudotyped with henipavirus F and G glycoproteins displayed proper target cell tropism and entry and infection was dependent on the presence of the HeV and NiV receptors ephrinB2 or B3 on target cells. The functional specificity of the assay was confirmed by the lack of reporter-gene signals when particles bearing either only the F or only G glycoprotein were prepared and assayed. Virus entry could be specifically blocked when infection was carried out in the presence of a fusion inhibiting C-terminal heptad (HR-2 peptide, a well-characterized, cross-reactive, neutralizing human mAb specific for the henipavirus G glycoprotein, and soluble ephrinB2 and B3 receptors. In addition, the utility of the assay was also demonstrated by an examination of the influence of the cytoplasmic tail of F in its fusion activity and incorporation into pseudotyped virus particles by generating and testing a panel of truncation mutants of NiV and HeV F

  10. Direct Spectrophotometric Assay for Benzaldehyde Lyase Activity

    Directory of Open Access Journals (Sweden)

    Dessy Natalia

    2011-01-01

    Full Text Available Benzaldehyde lyase from Pseudomonas fluorescens Biovar I. (BAL, EC 4.1.2.38 is a versatile catalyst for the organic synthesis of chiral α-hydroxy ketones. To allow fast assessment of enzyme activity, a direct spectrophotometric assay is desirable. Here, a new robust and easy-to-handle assay based on UV absorption is presented. The assay developed is based on the ligation of the α-hydroxy ketone (R-2,2′-furoin from 2-furaldehyde. A robust assay with direct monitoring of the product is facilitated with a convenient concentration working range minimising experimental associated with low concentrations.

  11. Immunoassay screening of lysergic acid diethylamide (LSD) and its confirmation by HPLC and fluorescence detection following LSD ImmunElute extraction.

    Science.gov (United States)

    Grobosch, T; Lemm-Ahlers, U

    2002-04-01

    In all, 3872 urine specimens were screened for lysergic acid diethylamide (LSD) using the CEDIA DAU LSD assay. Forty-eight samples, mainly from psychiatric patients or drug abusers, were found to be LSD positive, but only 13 (27%) of these could be confirmed by high-performance liquid chromatography with fluorescence detection (HPLC-FLD) following immunoaffinity extraction (IAE). Additional analysis for LSD using the DPC Coat-a-Count RIA was performed to compare the two immunoassay screening methods. Complete agreement between the DPC RIA assay and HPLC-FLD results was observed at concentrations below a cutoff concentration of 500 pg/mL. Samples that were LSD positive in the CEDIA DAU assay but not confirmed by HPLC-FLD were also investigated for interfering compounds using REMEDI HS drug-profiling system. REMEDI HS analysis identified 15 compounds (parent drugs and metabolites) that are believed to cross-react in the CEDIA DAU LSD assay: ambroxol, prilocaine, pipamperone, diphenhydramine, metoclopramide, amitriptyline, doxepine, atracurium, bupivacaine, doxylamine, lidocaine, mepivacaine, promethazine, ranitidine, and tramadole. The IAE/HPLC-FLD combination is rapid, easy to perform and reliable. It can reduce costs when standard, rather than more advanced, HPLC equipment is used, especially for labs that perform analyses for LSD infrequently. The chromatographic analysis of LSD, nor-LSD, and iso-LSD is not influenced by any of the tested cross-reacting compounds even at a concentration of 100 ng/mL.

  12. Premature chromosome condensation (PCC) assay for dose assessment in mass casualty accidents.

    Science.gov (United States)

    Lindholm, Carita; Stricklin, Daniela; Jaworska, Alicja; Koivistoinen, Armi; Paile, Wendla; Arvidsson, Eva; Deperas-Standylo, Joanna; Wojcik, Andrzej

    2010-01-01

    The study was undertaken to establish a dose calibration curve for a practical PCC ring assay and to apply it in a simulated mass casualty accident. The PCC assay was validated against the conventional dicentric assay. A linear relationship was established for PCC rings after (60)Co gamma irradiation with doses up to 20 Gy. In the simulated accident experiment, 62 blood samples were analyzed with both the PCC ring assay and the conventional dicentric assay, applying a triage approach. Samples received various uniform and non-uniform (10-40% partial-body) irradiations up to doses of 13 Gy. The results indicated that both assays yielded good dose estimates for the whole-body exposure scenario, although in the lower-dose range (0-6 Gy) dicentric scoring resulted in more accurate whole-body estimates, whereas PCC rings were better in the high-dose range (>6 Gy). Neither assay was successful in identifying partial-body exposures, most likely due to the low numbers of cells scored in the triage mode. In conclusion, the study confirmed that the PCC ring assay is suitable for use as a biodosimeter after whole-body exposure to high doses of radiation. However, there are limitations for its use in the triage of people exposed to high, partial-body doses.

  13. Rapid and specific identification of Brucella abortus using the loop-mediated isothermal amplification (LAMP) assay.

    Science.gov (United States)

    Kang, Sung-Il; Her, Moon; Kim, Ji-Yeon; Lee, Jin Ju; Lee, Kichan; Sung, So-Ra; Jung, Suk Chan

    2015-06-01

    A rapid and accurate diagnosis of brucellosis is required to reduce and prevent the spread of disease among animals and the risk of transfer to humans. In this study, a Brucella abortus-specific (Ba) LAMP assay was developed, that had six primers designed from the BruAb2_0168 region of chromosome I. The specificity of this LAMP assay was confirmed with Brucella reference strains, B. abortus vaccine strains, B. abortus isolates and phylogenetically or serologically related strains. The detection limit of target DNA was up to 20 fg/μl within 60 min. The sensitivity of the new LAMP assay was equal to or slightly higher than other PCR based assays. Moreover, this Ba-LAMP assay could specifically amplify all B. abortus biovars compared to previous PCR assays. To our knowledge, this is the first report of specific detection of B. abortus using a LAMP assay. The Ba-LAMP assay can offer a rapid, sensitive and accurate diagnosis of bovine brucellosis in the field.

  14. A robotic BG1Luc reporter assay to detect estrogen receptor agonists.

    Science.gov (United States)

    Stoner, Matthew A; Yang, Chun Z; Bittner, George D

    2014-08-01

    Endocrine disrupting chemicals with estrogenic activity (EA) have been associated with various adverse health effects. US agencies (ICCVAM/NICEATM) tasked to assess in vitro transcription activation assays to detect estrogenic receptor (ER) agonists for EA have recently validated a BG1Luc assay in manual format, but prefer robotic formats. We have developed a robotic BG1Luc EA assay to detect EA that demonstrated 100% concordance with ICCVAM meta-analyses and ICCVAM BG1Luc results in manual format for 27 ICCVAM test substances, i.e. no false negatives or false positives. This robotic assay also consistently assessed other, more problematic ICCVAM test substances such as clomiphene citrate, L-thyroxin, and tamoxifen. Agonist responses using this robotic BG1Luc assay were consistently inhibited by the ER antagonist ICI 182,780, confirming that agonist responses were due to binding to ERs rather than to a non-specific agonist response. This robotic assay also detected EA in complex mixtures of substances such as extracts of personal care products, plastic resins or plastic consumer products. This robotic BG1Luc assay had at least as high accuracy and greater sensitivity and repeatability when compared to its manual version or to the other ICCVAM/OECD validated assays for EA (manual BG1Luc and CERI).

  15. Development of a heavy metals enzymatic-based assay using papain

    Energy Technology Data Exchange (ETDEWEB)

    Shukor, Yunus [Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Selangor (Malaysia)]. E-mail: yunus@biotech.upm.edu.my; Baharom, Nor Azlan [Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Selangor (Malaysia); Rahman, Fadhil Abd. [Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Selangor (Malaysia); Abdullah, Mohd. Puad [Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Selangor (Malaysia); Shamaan, Nor Aripin [Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Selangor (Malaysia); Syed, Mohd. Arif [Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Selangor (Malaysia)

    2006-05-04

    A heavy metals enzymatic-based assay using papain was developed. Papain was assayed using the Casein-coomassie-dye-binding assay. The assay is sensitive to several heavy metals. The IC{sub 50} (concentration of toxicant giving 50% inhibition) of Hg{sup 2+}, Ag{sup 2+}, Pb{sup 2}, Zn{sup 2+} is 0.39, 0.40, 2.16, 2.11 mg l{sup -1}, respectively. For Cu{sup 2+} and Cd{sup 2+} the LOQ (limits of quantitation) is 0.004 and 0.1 mg l{sup -1}, respectively. The IC{sub 50} and LOQ values were found to be generally comparable to several other enzymatic and bioassays tests such as: immobilized urease, 15-min Microtox{sup TM}, 48 h Daphnia magna, and 96 h Rainbow trout. The papain assay is xenobiotics tolerant, has a wide pH for optimum activity, is temperature stable, and has a relatively quick assay time. The papain assay was used to identify polluted water samples from industrial sources in Penang, Malaysia. We found one site where the assay gave a positive toxic response. The toxicity of the site was confirmed using Atomic Emission Spectrometry analysis.

  16. Quantification of Human Kallikrein-Related Peptidases in Biological Fluids by Multiplatform Targeted Mass Spectrometry Assays.

    Science.gov (United States)

    Karakosta, Theano D; Soosaipillai, Antoninus; Diamandis, Eleftherios P; Batruch, Ihor; Drabovich, Andrei P

    2016-09-01

    Human kallikrein-related peptidases (KLKs) are a group of 15 secreted serine proteases encoded by the largest contiguous cluster of protease genes in the human genome. KLKs are involved in coordination of numerous physiological functions including regulation of blood pressure, neuronal plasticity, skin desquamation, and semen liquefaction, and thus represent promising diagnostic and therapeutic targets. Until now, quantification of KLKs in biological and clinical samples was accomplished by enzyme-linked immunosorbent assays (ELISA). Here, we developed multiplex targeted mass spectrometry assays for the simultaneous quantification of all 15 KLKs. Proteotypic peptides for each KLK were carefully selected based on experimental data and multiplexed in single assays. Performance of assays was evaluated using three different mass spectrometry platforms including triple quadrupole, quadrupole-ion trap, and quadrupole-orbitrap instruments. Heavy isotope-labeled synthetic peptides with a quantifying tag were used for absolute quantification of KLKs in sweat, cervico-vaginal fluid, seminal plasma, and blood serum, with limits of detection ranging from 5 to 500 ng/ml. Analytical performance of assays was evaluated by measuring endogenous KLKs in relevant biological fluids, and results were compared with selected ELISAs. The multiplex targeted proteomic assays were demonstrated to be accurate, reproducible, sensitive, and specific alternatives to antibody-based assays. Finally, KLK4, a highly prostate-specific protein and a speculated biomarker of prostate cancer, was unambiguously detected and quantified by immunoenrichment-SRM assay in seminal plasma and blood serum samples from individuals with confirmed prostate cancer and negative biopsy. Mass spectrometry revealed exclusively the presence of a secreted isoform and thus unequivocally resolved earlier disputes about KLK4 identity in seminal plasma. Measurements of KLK4 in either 41 seminal plasma or 58 blood serum samples

  17. [Interest of the cholinesterase assay during organophosphate poisonings].

    Science.gov (United States)

    Jalady, A-M; Dorandeu, F

    2013-12-01

    Cholinesterases are the main targets of organophosphorus compounds. The two enzymes present in the blood (butyrylcholinesterase, BChE; acetylcholinesterase, AChE) are biomarkers of their systemic toxicity. Activity of the plasma BChE is very often determined as it allows a rapid diagnostic of poisoning and is a marker of the persistence of the toxicant in the blood. The activity of the red blood cell AChE gives a better picture of the synaptic inhibition in the nervous system but the assay is less commonly available in routine laboratories. Better biomarker of the exposure, it allows a diagnosis of the severity of the poisoning and helps to assess the efficacy of oxime therapy. Besides the practical aspects of blood collection and sample processing, and the interpretation of the assays, this review stresses the complementarity of both enzyme assays and recalls their crucial interest for the confirmation of poisoning with an organophosphorus in a situation of war or terrorist attack and for the monitoring of occupational exposures.

  18. Quantification and confirmation of flunixin in equine plasma by liquid chromatography-quadrupole time-of-flight tandem mass spectrometry.

    Science.gov (United States)

    Luo, Yi; Rudy, Jeffrey A; Uboh, Cornelius E; Soma, Lawrence R; Guan, Fuyu; Enright, James M; Tsang, Deborah S

    2004-03-05

    The method describes quantification and confirmation of flunixin in equine plasma by liquid chromatography-quadrupole time-of-flight mass spectrometry (LC/Q-TOF/MS/MS). Samples were screened by enzyme-linked immunosorbent assay (ELISA) and only those samples presumptively declared positive were subjected to quantification and confirmation for the presence of flunixin by this method. The method is also readily adaptable to instrumental screening for the analyte. Flunixin was recovered from plasma by liquid-liquid extraction (LLE). The sample was diluted with 2 ml saturated phosphate buffer (pH 3.10) prior to LLE. The dried extract was reconstituted in acetonitrile:water:formic acid (50:50:0.1, v/v/v) and subsequently analyzed on a Q-TOF tandem mass spectrometer (Micromass) operated under electrospray ionization positive ion mode. The concentration of flunixin was determined by the internal standard (IS) calibration method using the peak area ratio with clonixin as the IS. The limits of detection (LOD) and quantification (LOQ) for flunixin in equine plasma were 0.1 and 1 ng/ml, respectively, whereas the limit of confirmation (LOC) was 2.5 ng/ml. The qualifying ions for the identification of flunixin were m/z 297 [M+H](+), 279 (BP), 264, 259, 239 and those for clonixin (IS) were m/z 263 [M+H](+), 245 (BP) and 210. The measurement uncertainty about the result was 8.7%. The method is simple, sensitive, robust and reliably fast in the quantification and confirmation of flunixin in equine plasma. Application of this method will assist racing authorities in the enforcement of tolerance plasma concentration of flunixin in the racehorse on race day.

  19. 75 FR 59611 - Microbiology Devices; Reclassification of Herpes Simplex Virus Types 1 and 2 Serological Assays...

    Science.gov (United States)

    2010-09-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration 21 CFR Part 866 Microbiology Devices; Reclassification of Herpes Simplex Virus Types 1 and 2 Serological Assays; Confirmation of Effective Date AGENCY: Food and...

  20. Diploid Musa acuminata genetic diversity assayed with sequence-tagged microsatellite sites.

    Science.gov (United States)

    Grapin, A; Noyer, J L; Carreel, F; Dambier, D; Baurens, F C; Lanaud, C; Lagoda, P J

    1998-06-01

    The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.

  1. Genomic Assays for Identification of Chikungunya Virus in Blood Donors, Puerto Rico, 2014.

    Science.gov (United States)

    Chiu, Charles Y; Bres, Vanessa; Yu, Guixia; Krysztof, David; Naccache, Samia N; Lee, Deanna; Pfeil, Jacob; Linnen, Jeffrey M; Stramer, Susan L

    2015-08-01

    A newly developed transcription-mediated amplification assay was used to detect chikungunya virus infection in 3 of 557 asymptomatic donors (0.54%) from Puerto Rico during the 2014-2015 Caribbean epidemic. Viral detection was confirmed by using PCR, microarray, and next-generation sequencing. Molecular clock analysis dated the emergence of the Puerto Rico strains to early 2013.

  2. Assay-dependent variability of serum insulin concentrations: a comparison of eight assays.

    Science.gov (United States)

    Tohidi, Maryam; Arbab, Parvaneh; Ghasemi, Asghar

    2017-04-01

    Although insulin measurement is essential for both clinical and research purposes, there is currently no reference method for insulin assays. The aim of this study was to compare results of serum insulin determined by a number of commercially available assays. We compared eight insulin assays by analyzing 165 serum samples. Assays included two chemiluminescence (Roche and DiaSorin), four ELISA (Tosoh, Mercodia, Monobind, and Diametra), and two IRMA (Izotop and BioSource) methods. Each assay was compared with the mean of all assay methods and Bland-Altman difference plots were used to measure agreement between each assay and overall mean. Least squared perpendicular distance regression analysis (Deming's method) was used to calculate slope and intercept for bias and also for each assay vs. mean of eight assays. Findings showed that the lowest and highest median insulin concentrations varied by a factor of 1.8. Maximum and minimum correlations with mean of assays were observed for Roche (0.992) and BioSource (0.844), respectively. Significant bias was observed in six assays. In pairwise comparisons of different assays, the highest and least mean differences were 7.78 μU/mL and -0.14 μU/mL, respectively. In conclusion, serum insulin measurement with different assays showed a maximum of 1.8-fold difference, a point that should be taken into consideration in the interpretation of circulating insulin levels in both clinical and research fields.

  3. Hemizona Assay and Sperm Penetration Assay in the Prediction of IVF Outcome: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Paraskevi Vogiatzi

    2013-01-01

    Full Text Available The limited predictive value of semen analysis in achieving natural conception or in IVF outcome confirms the need for sperm function tests to determine optimal management. We reviewed HZA and SPA predictive power in IVF outcome, with statistical significance of diagnostic power of the assays. HZA was readily efficient in predicting IVF outcome, while evident inconsistency among the studies analysed framed the SPA’s role in male fertility evaluation. Considerable variation was noted in the diagnostic accuracy values of SPA with wide sensitivity (52–100%, specificity (0–100%, and PPV (18–100% and NPV (0–100% together with fluctuation and notable differentiation in methodology and cutoff values employed by each group. HZA methodology was overall consistent with minor variation in cutoff values and oocyte source, while data analysis reported strong correlation between HZA results with IVF outcome, high sensitivity (75–100%, good specificity (57–100%, and high PPV (79–100% and NPV (68–100%. HZA correlated well with IVF outcome and demonstrated better sensitivity/specificity and positive/negative predictive power. Males with normal or slightly abnormal semen profiles could benefit by this intervention and could be evaluated prior to referral to assisted reproduction. HZA should be used in a sequential fashion with semen analysis and potentially other bioassays in an IVF setting.

  4. Confirmation of the spinal motor neuron gene 2 (SMN2) copy numbers by real-time PCR.

    Science.gov (United States)

    Wieme, Maamouri-Hicheri; Monia Ben, Hammer; Yosr, Bouhlal; Sihem, Souilem; Nawel, Toumi; Ines, Manai-Azizi; Wajdi, Bennour; Najla, Khmiri; Houda, Nahdi; Faycal, Hentati; Rim, Amouri

    2012-09-01

    Spinal muscular atrophy (SMA) is an autosomal recessive disease caused by mutation or deletion of the survival motor neuron gene 1 (SMN1). SMN2, a copy gene, influences the severity of SMA and may be used in somatic gene therapy of patients with SMA in the future. The SMA carrier analysis developed at the Institute of Medical Genetics, Catholic University (Rome), on the Applied Biosystems real-time PCR instruments by Dr Danilo Tiziano and his group, provides a robust workflow to evaluate SMA carrier status. In this study, the SMN2 copy number was confirmed on 22 patients by developing our own assay on the basis of a relative real-time PCR system using the 7500 Fast Real-Time PCR System.

  5. METHODOLOGICAL ASPECTS OF QUANTITATIVE RECEPTOR ASSAYS

    NARCIS (Netherlands)

    SMISTEROVA, J; ENSING, K; DEZEEUW, RA

    1994-01-01

    Receptor assays occupy a particular position in the methods used in bioanalysis, as they do not exploit the physico-chemical properties of the analyte. These assays make use of the property of the analyte to bind to the specific binding site (receptor) and to competitively replace a labelled ligand

  6. Assessing sediment contamination using six toxicity assays

    Directory of Open Access Journals (Sweden)

    Allen G. BURTON Jr.

    2001-08-01

    Full Text Available An evaluation of sediment toxicity at Lake Orta, Italy was conducted to compare a toxicity test battery of 6 assays and to evaluate the extent of sediment contamination at various sediment depths. Lake Orta received excessive loadings of copper and ammonia during the 1900’s until a large remediation effort was conducted in 1989-90 using lime addition. Since that time, the lake has shown signs of a steady recovery of biological communities. The study results showed acute toxicity still exists in sediments at a depth of 5 cm and greater. Assays that detected the highest levels of toxicity were two whole sediment exposures (7 d using Hyalella azteca and Ceriodaphnia dubia. The MicrotoxR assay using pore water was the third most sensitive assay. The Thamnotox, Rototox, Microtox solid phase, and Seed Germination-Root Elongation (pore and solid phase assays showed occasional to no toxicity. Based on similarity of responses and assay sensitivity, the two most useful assays were the C. dubia (or H. azteca and Microtox pore water. These assays were effective at describing sediment toxicity in a weight-of-evidence approach.

  7. Radioreceptor assay: theory and applications to pharmacology

    Energy Technology Data Exchange (ETDEWEB)

    Perret, G. (U.E.R. de Medecine, Sante et Biologie Humaine, 93 - Bobigny (France)); Simon, P. (Faculte de Medecine Pitie-Salpetriere, 75 - Paris (France))

    The aim of the first part of this work is to present the theory of the radioreceptor assay and to compare it to the other techniques of radioanalysis (radioimmunoassay, competitive protein binding assays). The technology of the radioreceptor assay is then presented and its components (preparation of the receptors, radioligand, incubation medium) are described. The analytical characteristics of the radioreceptor assay (specificity, sensitivity, reproductibility, accuracy) and the pharmacological significance of the results are discussed. The second part is devoted to the description of the radioreceptor assays of some pharmacological classes (neuroleptics, tricyclic antidepressants, benzodiazepines, ..beta..-blockers, anticholinergic drugs) and to their use in therapeutic drug monitoring. In conclusion, by their nature, radioreceptor assays are highly sensitive, reliable, precise, accurate and simple to perform. Their chief disadvantage relates to specificity, since any substance having an appreciable affinity to the receptor site will displace the specifically bound radioligand. Paradoxically in some cases, this lack of specificity may be advantageous in that it allows for the detection of not only the apparent compound but of active metabolites and endogenous receptor agonists as well and in that radioreceptors assays can be devised for a whole pharmacological class and not only for one drug as it is the case for classical physico-chemical techniques. For all these reasons future of radioreceptor assay in pharmacology appears promising.

  8. A Continuous, Fluorogenic Sirtuin 2 Deacylase Assay

    DEFF Research Database (Denmark)

    Galleano, Iacopo; Schiedel, Matthias; Jung, Manfred

    2016-01-01

    and kinetic insight regarding sirtuin inhibitors, it is important to have access to efficient assays. In this work, we report readily synthesized fluorogenic substrates enabling enzyme-economical evaluation of SIRT2 inhibitors in a continuous assay format as well as evaluation of the properties of SIRT2...

  9. Acellular comet assay: a tool for assessing variables influencing the alkaline comet assay.

    Science.gov (United States)

    Kennedy, Erin K; McNamee, James P; Prud'homme Lalonde, Louise; Jones, Trevor; Wilkinson, Diana

    2012-01-01

    In this study, an acellular modification to the alkaline comet assay to further evaluate key variables within the assay that may influence the outcome of genotoxicity studies is described. This acellular comet assay can detect differences of 0.2 Gy of (60)Co gamma-ray radiation between 0 and 1 Gy and differences of 1 Gy between 0 and 8 Gy; thus, this assay is applicable for a wide range of DNA damage levels. It is also shown that DNA damage from different radiation energies was not significantly different from (60)Co gamma-ray. This assay displayed a statistical increase in DNA damage due to uncontrolled exposure to natural light; however, the slope of the dose-response curve for light-exposed samples was similar to that for samples protected from light. A comparison of the alkaline comet assay with the acellular comet assay allowed for the intrinsic repair capacity of the alkaline comet assay to be quantified.

  10. Assays for Determination of Protein Concentration.

    Science.gov (United States)

    Olson, Bradley J S C

    2016-06-01

    Biochemical analysis of proteins relies on accurate quantification of protein concentration. Detailed in this appendix are some commonly used methods for protein analysis, e.g., Lowry, Bradford, bicinchoninic acid (BCA), UV spectroscopic, and 3-(4-carboxybenzoyl)quinoline-2-carboxaldehyde (CBQCA) assays. The primary focus of this report is assay selection, emphasizing sample and buffer compatibility. The fundamentals of generating protein assay standard curves and of data processing are considered, as are high-throughput adaptations of the more commonly used protein assays. Also included is a rapid, inexpensive, and reliable BCA assay of total protein in SDS-PAGE sample buffer that is used for equal loading of SDS-PAGE gels. © 2016 by John Wiley & Sons, Inc.

  11. 77 FR 55903 - Confirmation, Portfolio Reconciliation, Portfolio Compression, and Swap Trading Relationship...

    Science.gov (United States)

    2012-09-11

    ... documentation, including master netting agreements, definitions, schedules, and confirmations, to document their... Agreement and related definitions, schedules, and confirmations specific to particular asset classes, offers... and regulators about pricing dislocations and associated credit risks and a static, rigid...

  12. Alveolar pentraxin 3 as an early marker of microbiologically confirmed pneumonia: a threshold-finding prospective observational study.

    Science.gov (United States)

    Mauri, Tommaso; Coppadoro, Andrea; Bombino, Michela; Bellani, Giacomo; Zambelli, Vanessa; Fornari, Carla; Berra, Lorenzo; Bittner, Edward A; Schmidt, Ulrich; Sironi, Marina; Bottazzi, Barbara; Brambilla, Paolo; Mantovani, Alberto; Pesenti, Antonio

    2014-10-15

    Timely diagnosis of pneumonia in intubated critically ill patients is rather challenging. Pentraxin 3 (PTX3) is an acute-phase mediator produced by various cell types in the lungs. Animal studies have shown that, during pneumonia, PTX3 participates in fine-tuning of inflammation (for example, microbial clearance and recruitment of neutrophils). We previously described an association between alveolar PTX3 and lung infection in a small group of intubated patients. The aim of the present study was to determine a threshold level of alveolar PTX3 with elevated sensitivity and specificity for microbiologically confirmed pneumonia. We recruited 82 intubated patients from two intensive care units (San Gerardo Hospital, Monza, Italy, and Massachusetts General Hospital, Boston, MA, USA) undergoing bronchoalveolar lavage (BAL) as per clinical decision. We collected BAL fluid and plasma samples, together with relevant clinical and microbiological data. We assayed PTX3 and soluble triggering receptor expressed on myeloid cells 1 (sTREM-1) in BAL fluid and PTX3, sTREM-1, C-reactive protein (CRP) and procalcitonin (PCT) in plasma. Two blinded independent physicians reviewed patient data to confirm pneumonia. We determined the PTX3 threshold in BAL fluid for pneumonia and compared it to other biomarkers. Microbiologically confirmed pneumonia of bacterial (n =12), viral (n =4) or fungal (n =8) etiology was diagnosed in 24 patients (29%). PTX3 levels in BAL fluid predicted pneumonia with an area under the receiving operator curve of 0.815 (95% CI =0.710 to 0.921, P <0.0001), whereas none of the other biomarkers were effective. In particular, PTX3 levels ≥1 ng/ml in BAL fluid predicted pneumonia in univariate analysis (β =2.784, SE =0.792, P <0.001) with elevated sensitivity (92%), specificity (60%) and negative predictive value (95%). Net reclassification index PTX3 values ≥1 ng/ml in BAL fluid for pneumonia indicated gain in sensitivity and/or specificity vs. all other

  13. Comet Assay on Daphnia magna in eco-genotoxicity testing.

    Science.gov (United States)

    Pellegri, Valerio; Gorbi, Gessica; Buschini, Annamaria

    2014-10-01

    Detection of potentially hazardous compounds in water bodies is a priority in environmental risk assessment. For the evaluation and monitoring of water quality, a series of methodologies may be applied. Among them, the worldwide used toxicity tests with organisms of the genus Daphnia is one of the most powerful. In recent years, some attempts were made to utilize Daphnia magna in genotoxicity testing as many of the new environmental contaminants are described as DNA-damaging agents in aquatic organisms. The aim of this research was to develop a highly standardized protocol of the Comet Assay adapted for D. magna, especially regarding the isolation of cells derived from the same tissue (haemolymph) from newborn organisms exposed in vivo. Several methods for haemolymph extraction and different Comet Assay parameters were compared. Electrophoretic conditions were adapted in order to obtain minimum DNA migration in cells derived from untreated organisms and, at the same time, maximum sensitivity in specimens treated with known genotoxicants (CdCl2 and H2O2). Additional tests were performed to investigate if life-history traits of the cladoceran (such as the age of adult organisms that provide newborns, the clutch size of origin, the number of generations reared in standard conditions) and the water composition as well, might influence the response of the assay. This study confirms the potential application of the Comet Assay in D. magna for assessing genotoxic loads in aqueous solution. The newly developed protocol could integrate the acute toxicity bioassay, thus expanding the possibility of using this model species in freshwater monitoring (waters, sediment and soil elutriates) and is in line with the spirit of the EU Water Framework Directive in reducing the number of bioassays that involve medium-sized species.

  14. 75 FR 10413 - New Animal Drug Applications; Confirmation of Effective Date

    Science.gov (United States)

    2010-03-08

    ... of Effective Date AGENCY: Food and Drug Administration, HHS. ACTION: Direct final rule; confirmation of effective date. SUMMARY: The Food and Drug Administration (FDA) is confirming the effective date... animal drug products. This document confirms the effective date of the direct final rule....

  15. 77 FR 53769 - Receipts-Based, Small Business Size Standard; Confirmation of Effective Date

    Science.gov (United States)

    2012-09-04

    ... and 171 RIN 3150-AJ14 Receipts-Based, Small Business Size Standard; Confirmation of Effective Date AGENCY: Nuclear Regulatory Commission. ACTION: Direct final rule; confirmation of effective date. SUMMARY: The U.S. Nuclear Regulatory Commission (NRC) is confirming the effective date of August 22, 2012,...

  16. Improved benzodiazepine radioreceptor assay using the MultiScreen (R) Assay System

    NARCIS (Netherlands)

    Janssen, MJ; Ensing, K; de Zeeuw, RA

    1999-01-01

    In this article, an improved benzodiazepine radioreceptor assay is described, which allows substantial reduction in assay time, The filtration in this method was performed by using the MultiScreen(R) Assay System. The latter consists of a 96-well plate with glass fibre filters sealed at the bottom,

  17. Confirmation of Plasmodium falciparum in vitro resistance to monodesethylamodiaquine and chloroquine in Dakar, Senegal, in 2015.

    Science.gov (United States)

    Diawara, Silman; Madamet, Marylin; Kounta, Mame Bou; Lo, Gora; Wade, Khalifa Ababacar; Nakoulima, Aminata; Bercion, Raymond; Amalvict, Rémy; Gueye, Mamadou Wague; Fall, Bécaye; Diatta, Bakary; Pradines, Bruno

    2017-03-16

    In response to increasing resistance to anti-malarial drugs, Senegal adopted artemisinin-based combination therapy (ACT) as the first-line treatment for uncomplicated malaria in 2006. However, resistance of Plasmodium falciparum parasites to artemisinin derivatives, characterized by delayed parasite clearance after treatment with ACT or artesunate monotherapy, has recently emerged and rapidly spread in Southeast Asia. After 10 years of stability with rates ranging from 5.6 to 11.8%, the prevalence of parasites with reduced susceptibility in vitro to monodesethylamodiaquine, the active metabolite of an ACT partner drug, increased to 30.6% in 2014 in Dakar. Additionally, after a decrease of the in vitro chloroquine resistance in Dakar in 2009-2011, the prevalence of parasites that showed in vitro chloroquine resistance increased again to approximately 50% in Dakar since 2013. The aim of this study was to follow the evolution of the susceptibility to ACT partners and other anti-malarial drugs in 2015 in Dakar. An in vitro test is the only method currently available to provide an early indication of resistance to ACT partners. Thirty-two P. falciparum isolates collected in 2015 in Dakar were analysed using a standard ex vivo assay based on an HRP2 ELISA. The prevalence of P. falciparum parasites with reduced susceptibility in vitro to monodesethylamodiaquine, chloroquine, mefloquine, doxycycline and quinine was 28.1, 46.9, 45.2, 31.2 and 9.7%, respectively. None of the parasites were resistant to lumefantrine, piperaquine, pyronaridine, dihydroartemisinin and artesunate. These results confirm an increase in the reduced susceptibility to monodesethylamodiaquine observed in 2014 in Dakar and the chloroquine resistance observed in 2013. The in vitro resistance seems to be established in Dakar. Additionally, the prevalence of parasites with reduced susceptibility to doxycycline has increased two-fold compared to 2014. The establishment of a reduced susceptibility to

  18. Molecular confirmation of the occurrence in Germany of Anopheles daciae (Diptera, Culicidae

    Directory of Open Access Journals (Sweden)

    Kronefeld Mandy

    2012-11-01

    Full Text Available Abstract Background Anopheles daciae, a newly described member of the Maculipennis group, was recently reported from western, southern and eastern Europe. Before its recognition, it had commonly been listed under the name of An. messeae, due to its extreme morphological and genetic similarities. As the sibling species of the Maculipennis group are known to differ in their vector competences for malaria parasites and other pathogens, the occurrence of An. daciae in a given region might have an impact on the epidemiology of mosquito-borne diseases. Mosquito collections from different localities in Germany were therefore screened for An. daciae. Methods Adult and immature Maculipennis group mosquitoes were collected between May 2011 and June 2012 at 23 different sites in eight federal states of Germany. A standard PCR assay was used to differentiate the previously known sibling species while the ITS2 rDNA of specimens preliminarily identified as An. messeae/daciae was sequenced and analysed for species-specific nucleotide differences. Results Four hundred and seventy-seven Anopheles specimens were successively identified to Maculipennis group level by morphology and to species level by DNA-based methods. Four species of the Maculipennis group were registered: An. messeae (n = 384, An. maculipennis (n = 82, An. daciae (n = 10 and An. atroparvus (n = 1. Anopheles daciae occurred at four sites in three federal states of Germany, three of the sites being located in north-eastern Germany (federal states of Brandenburg and Saxony while one collection site was situated in the northern Upper Rhine Valley in the federal state of Hesse, south-western Germany. Conclusions The detection of An. daciae represents the first recognition of this species in Germany where it was found to occur in sympatry with An. messeae and An. maculipennis. As the collection sites were in both north-eastern and south-western parts of Germany, the species is

  19. Nano-immunosafety: issues in assay validation

    Energy Technology Data Exchange (ETDEWEB)

    Boraschi, Diana; Italiani, Paola [Institute of Biomedical Technologies, National Research Council, Via G. Moruzzi 1, 56124 Pisa (Italy); Oostingh, Gertie J; Duschl, Albert [Department of Molecular Biology, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Casals, Eudald; Puntes, Victor F [Institut Catala de Nanotecnologia, Campus de la UAB - Facultat de Ciencies, Edifici CM7, 08193 Bellaterra (Spain); Nelissen, Inge, E-mail: diana.boraschi@itb.cnr.it [VITO NV, Boeretang 200, BE-2400 Mol (Belgium)

    2011-07-06

    Assessing the safety of engineered nanomaterials for human health must include a thorough evaluation of their effects on the immune system, which is responsible for defending the integrity of our body from damage and disease. An array of robust and representative assays should be set up and validated, which could be predictive of the effects of nanomaterials on immune responses. In a trans-European collaborative work, in vitro assays have been developed to this end. In vitro tests have been preferred for their suitability to standardisation and easier applicability. Adapting classical assays to testing the immunotoxicological effects of nanoparticulate materials has raised a series of issues that needed to be appropriately addressed in order to ensure reliability of results. Besides the exquisitely immunological problem of selecting representative endpoints predictive of the risk of developing disease, assay results turned out to be significantly biased by artefactual interference of the nanomaterials or contaminating agents with the assay protocol. Having addressed such problems, a series of robust and representative assays have been developed that describe the effects of engineered nanoparticles on professional and non-professional human defence cells. Two of such assays are described here, one based on primary human monocytes and the other employing human lung epithelial cells transfected with a reporter gene.

  20. Mobile non-destructive assay system

    Energy Technology Data Exchange (ETDEWEB)

    Colarusso, A.P.; Audas, J.H.; Bieri, J.M.; Herrera, G.C.; Hastings, R.D.; Horton, W.S.; Kuckertz, T.H.; Kunz, W.E.; Medvick, P.A.; Vogel, P.A.

    1987-07-01

    A mobile system for non-destructive assay (NDA), developed at the Los Alamos National Laboratory, provides accurate and sensitive measurements for transuranic (TRU) isotopes contained in 208-iota drums of miscellaneous nuclear wastes. The NDA unit consists of four major subsystems: an assay chamber, counting and digital electronics, data acquisition, and a neutron generator. It performs both active and passive neutron waste measurements. The former determines the amount of fissile isotopes at a sensitivity level of 1 mg plutonium. The latter determines spontaneous fission and ..cap alpha..,n) isotopes at a comparable level. A complete assay consists of sequential active and passive measurements. The assay measurement and other supporting data are incorporated in a commercial spreadsheet program (Lotus 1,2,3) for further analysis, which includes various matrix corrections and a determination of whether or not the drum exceeds the 100-nCi/g threshold for TRU wastes. Field tests have been performed on three separate occasions, accomplishing more than 1800 waste drum assays. These waste drum assays are discussed, especially those comparing passive and active neutron measurements with independent segmented gamma scan assays. Results obtained with a set of 15 drums containing plutonium prepared from standards and actual hot waste matrices are also reviewed.

  1. Analytical characterization of the APTIMA HPV Assay.

    Science.gov (United States)

    Dockter, Janel; Schroder, Astrid; Eaton, Barbara; Wang, Ann; Sikhamsay, Nathan; Morales, Liezel; Giachetti, Cristina

    2009-07-01

    Human papillomavirus (HPV) testing has improved the sensitivity for the detection of cervical pre-cancer and cancer as compared to Pap testing. Several HPV tests are commercially available and most target the DNA from 13 or 14 high-risk HPV types. The APTIMA HPV Assay however, detects HPV E6/E7 mRNA from 14 high-risk types of HPV: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68. To determine the analytical performance characteristics of the APTIMA HPV Assay. Analytical sensitivity, analytical specificity, reproducibility, and the effect of potentially interfering substances was determined for the APTIMA HPV Assay on both the DTS (semi-automated) and TIGRIS DTS (fully automated) systems. The 95% detection limit for both systems was between 17 and 488 copies/reaction, depending on the HPV type. The assay did not cross-react with normal flora and opportunistic organisms that may be found in cervical samples, or low-risk HPV types. Spermicides, anti-fungal and anti-itch medications, whole blood, glacial acetic acid, and most lubricants did not interfere with assay performance. Those lubricants containing polyquaternium 15 did interfere with assay performance. Inter-instrument, inter-operator, inter-lot, and inter-run signal variability were 99% of the data. Intra-run variability was HPV Assay showed excellent performance and robustness.

  2. 蛋白质相互作用的分析:利用酵母两性杂交系统探索蛋白质功能%Analysis of Protein Interactions:Probing the Function of Proteins with Yeast Two-Hybrid System

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    酵母两性杂交系统是近年来发展起来的广泛应用于蛋白质相互作用研究的分子遗传学方法.它的研究过程包括诱捕质粒的构建,融合蛋白质粒文库的筛选,假阳性的消除和真阳性的探测.这个实验方法有利于利用已知蛋白去探测和它相互作用的未知蛋白及编码未知蛋白的cDNA.越来越多的研究证明酵母两性杂交系统是探索动植物蛋白质功能的有用技术.这一技术正被广泛应用于世界上许多重要的实验室.该文综述了酵母两性杂交技术在蛋白质相互作用研究中的最新进展.%The yeast two-hybrid system is a molecular genetic approach for protein interaction and it is widely used to screen for proteins that interact with a protein of interest in recent years. This process includes, construction and testing of the bait plasmid, screening a plasmid library for interacting fusion protein, elimination of false positives and delection analysis of true positives. This procedure is designed to allow investigators to identify proteins and their encoding cDNAs that have a biologically significant interaction with a protein of interest. More and more studies have demonstrated that the two-hybrid system is a powerful and sensitive technique for the identification of genes that code for proteins that interact in a biologically significant fashion with a protein of interest in higher plants. This method has been used to identify new interaction protein in many laboratories. The recently reported yeast tri-brid system, should allow the investigation of more complex protein-protein interactions. The aim of this review is to outline the recent progress made in protein interactions by using yeast two-hybrid system.

  3. Genetic Testing Confirmed the Early Diagnosis of X-Linked Hypophosphatemic Rickets in a 7-Month-Old Infant

    Directory of Open Access Journals (Sweden)

    Kok Siong Poon BSc

    2015-08-01

    Full Text Available Loss-of-function mutations in the phosphate regulating gene with homologies to endopeptidases on the X-chromosome (PHEX have been causally associated with X-linked hypophosphatemic rickets (XLHR. The early diagnosis of XLHR in infants is challenging when it is based solely on clinical features and biochemical findings. We report a 7-month-old boy with a family history of hypophosphatemic rickets., who demonstrated early clinical evidence of rickets, although serial biochemical findings could not definitively confirm rickets. A sequencing assay targeting the PHEX gene was first performed on the mother’s DNA to screen for mutations in the 5′UTR, 22 coding exons, and the exon-intron junctions. Targeted mutation analysis and mRNA studies were subsequently performed on the boys’ DNA to investigate the pathogenicity of the identified mutation. Genetic screening of the PHEX gene revealed a novel mutation, c.1080-2A>C, at the splice acceptor site in intron 9. The detection of an aberrant mRNA transcript with skipped (loss of exon 10 establishes its pathogenicity and confirms the diagnosis of XLHR in this infant. Genetic testing of the PHEX gene resulted in early diagnosis of XLHR, thus enabling initiation of therapy and prevention of progressive rachitic changes in the infant.

  4. A large multicenter analysis of CTGF -945 promoter polymorphism does not confirm association with Systemic Sclerosis susceptibility or phenotype

    Science.gov (United States)

    Rueda, B; Simeon, C; Hesselstrand, R; Herrick, A; Worthington, J; Ortego-Centeno, N; Riemekasten, G; Fonollosa, V; Vonk, MC; van den Hoogen, FHJ; Sanchez-Román, J; Aguirre-Zamorano, MA; García-Portales, R; Pros, A; Camps, MT; Gonzalez-Gay, MA; Gonzalez-Escribano, MF; Coenen, MJ; Lambert, N; Nelson, JL; Radstake, TRDJ; Martin, J.

    2009-01-01

    Objective In this work we conducted a replication study to investigate whether the -945 CTGF genetic variant is associated with SSc susceptibility or specific SSc phenotype. Methods The study population comprised of 1180 SSc patients and 1784 healthy controls from seven independent case-control sets of European ancestry (Spanish, French, Dutch, German, British, Swedish and North American). The –945 CTGF genetic variant was genotyped using a Taqman 5′ allelic discrimination assay. Results First we conducted an independent association study that revealed in all case-control cohorts under study no association of the CTGF -945 polymorphism with SSc susceptibility. These findings were confirmed by a meta-analysis that reached a pooled OR of 1.12 (95 % CI 0.99–1.25, P=0.06). In addition, the possible contribution of the -945 CTGF genetic variant to SSc phenotype was investigated. However, stratification according to SSc subtypes (limited or diffuse), selective autoantibodies (antitopoisomerase I or anti-centromere) or pulmonary involvement reached no statistically significant skewing. Conclusion Our results do not confirm previous findings and suggest that the CTGF –945 promoter polymorphism does not play a major role in SSc susceptibility or clinical phenotype. PMID:19054816

  5. Measles outbreak in South Africa: epidemiology of laboratory-confirmed measles cases and assessment of intervention, 2009-2011.

    Directory of Open Access Journals (Sweden)

    Genevie M Ntshoe

    Full Text Available BACKGROUND: Since 1995, measles vaccination at nine and 18 months has been routine in South Africa; however, coverage seldom reached >95%. We describe the epidemiology of laboratory-confirmed measles case-patients and assess the impact of the nationwide mass vaccination campaign during the 2009 to 2011 measles outbreak in South Africa. METHODS: Serum specimens collected from patients with suspected-measles were tested for measles-specific IgM antibodies using an enzyme-linked immunosorbent assay and genotypes of a subset were determined. To estimate the impact of the nationwide mass vaccination campaign, we compared incidence in the seven months pre- (1 September 2009-11 April 2010 and seven months post-vaccination campaign (24 May 2010-31 December 2010 periods in seven provinces of South Africa. RESULTS: A total of 18,431 laboratory-confirmed measles case-patients were reported from all nine provinces of South Africa (cumulative incidence 37 per 100,000 population. The highest cumulative incidence per 100,000 population was in children aged 5 years.

  6. Real-time immuno-PCR assay for detecting PCBs in soil samples.

    Science.gov (United States)

    Chen, Han-Yu; Zhuang, Hui-Sheng

    2009-06-01

    A fast and robust assay, based on immuno-polymerase chain reaction (IPCR) techniques, was developed for the detection of polychlorinated biphenyls (PCBs) in soil samples. Real-time IPCR (rt-IPCR) is a powerful technique that combines enzyme-linked immunosorbent assay (ELISA) with the specificity and sensitivity of PCR. In our assay, indirect ELISAs based on immobilization of PCB37 hapten-ovalbumin conjugates was used for evaluation of the immune response. The effect of optimal reagent concentrations to reduce background fluorescence was also investigated. Using the optimized assay, the linear sensitivity range of the assay covered more than six orders of magnitude, and the minimum detection limits reached 5 fg ml(-1) antigen. Rt-IPCR was tested for its cross-reactivity profiles using four selected congeners and four Aroclor products. The assays were highly specific for congeners but less specific for Aroclor1242. We took four soil samples to validate the method, and the results were confirmed by gas chromatography/mass spectrometry (GC/MS). The rt-IPCR results for soil samples correlated well with the concentrations of PCBs obtained by GC/MS (r = 0.99, n = 6). These data indicate that this highly specific, sensitive, and robust assay can be modified for detecting PCB compounds in the environment.

  7. Necessity to critically review the automatic results of the Xpert Flu assay.

    Science.gov (United States)

    Engelmann, Ilka; Alidjinou, Enagnon Kazali; Lazrek, Mouna; Dewilde, Anny; Hober, Didier

    2017-02-02

    While using the Xpert Flu assay we became aware of false-negative results. The study aimed to analyze the causes of these false-negative results. One hundred fifty-nine respiratory specimens were tested in the Xpert Flu assay and in multiplex reverse transcription-polymerase chain reactions (RT-PCRs) for respiratory viruses. Discordant specimens were tested in the Influenza A/B r-gene assay. One hundred fifty-two (96%) and 151 (95%) specimens yielded concordant results for influenza A and B, respectively. Fifteen specimens tested negative in the Xpert Flu assay and positive in a multiplex RT-PCR. Positive results were confirmed for 12 of these specimens in the Influenza A/B r-gene assay. Xpert Flu assay amplification curves and endpoints suggested that the false-negative results were mainly due to erroneous automatic result interpretation. We report false-negative results of the Xpert Flu assay due to erroneous automatic result interpretation. Careful analysis of amplification curves and endpoints is needed to avoid reporting of false-negative results.

  8. Development of an opioid self-administration assay to study drug seeking in zebrafish.

    Science.gov (United States)

    Bossé, Gabriel D; Peterson, Randall T

    2017-09-29

    The zebrafish (Danio rerio) has become an excellent tool to study mental health disorders, due to its physiological and genetic similarity to humans, ease of genetic manipulation, and feasibility of small molecule screening. Zebrafish have been shown to exhibit characteristics of addiction to drugs of abuse in non-contingent assays, including conditioned place preference, but contingent assays have been limited to a single assay for alcohol consumption. Using inexpensive electronic, mechanical, and optical components, we developed an automated opioid self-administration assay for zebrafish, enabling us to measure drug seeking and gain insight into the underlying biological pathways. Zebrafish trained in the assay for five days exhibited robust self-administration, which was dependent on the function of the μ-opioid receptor. In addition, a progressive ratio protocol was used to test conditioned animals for motivation. Furthermore, conditioned fish continued to seek the drug despite an adverse consequence and showed signs of stress and anxiety upon withdrawal of the drug. Finally, we validated our assay by confirming that self-administration in zebrafish is dependent on several of the same molecular pathways as in other animal models. Given the ease and throughput of this assay, it will enable identification of important biological pathways regulating drug seeking and could lead to the development of new therapeutic molecules to treat addiction. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Quantification of Atlantic salmon type-I interferon using an Mx1 promoter reporter gene assay.

    Science.gov (United States)

    Johansen, Audny; Collet, Bertrand; Sandaker, Elin; Secombes, Christopher J; Jørgensen, Jorunn B

    2004-02-01

    We here describe an assay for the detection of interferon-like activity in Atlantic salmon based on the transient transfection of chinook salmon embryo cells (CHSE-214 cells) with a rainbow trout Mx1 promoter linked to a luciferase reporter. A beta-galactosidase gene under the control of a constitutively expressed beta-actin promoter was used as a transfection standard, and luciferase and beta gal expression were measured by a commercially available kit. Interferon containing supernatants from poly I:C- or CpG-stimulated leucocytes added to transfected CHSE-cells induced high luciferase expression (>60-fold induction compared to supernatants from non-stimulated cells). There was no response to supernatants from LPS- and ConA/PMA-stimulated leucocytes, demonstrating the specificity for type I interferon-like activity. Duplicate samples analysed using a cell protection assay for detection of antiviral activity correlated well with levels obtained by the Mx1 promoter reporter gene assay (R2=0.97), confirming the reporter assay as a reliable substitute for the standard antiviral assay. The Mx reporter gene assay also has advantages in terms of sensitivity, high dynamic range and reliability over the conventional cell protection assay.

  10. Determination of cell survival after irradiation via clonogenic assay versus multiple MTT Assay - A comparative study

    Directory of Open Access Journals (Sweden)

    Buch Karl

    2012-01-01

    Full Text Available Abstract For studying proliferation and determination of survival of cancer cells after irradiation, the multiple MTT assay, based on the reduction of a yellow water soluble tetrazolium salt to a purple water insoluble formazan dye by living cells was modified from a single-point towards a proliferation assay. This assay can be performed with a large number of samples in short time using multi-well-plates, assays can be performed semi-automatically with a microplate reader. Survival, the calculated parameter in this assay, is determined mathematically. Exponential growth in both control and irradiated groups was proven as the underlying basis of the applicability of the multiple MTT assay. The equivalence to a clonogenic survival assay with its disadvantages such as time consumption was proven in two setups including plating of cells before and after irradiation. Three cell lines (A 549, LN 229 and F 98 were included in the experiment to study its principal and general applicability.

  11. Confirm the HCV NS5A protein interaction with aconitase 1%HCV NS5A结合蛋白顺乌头酸酶1的验证研究

    Institute of Scientific and Technical Information of China (English)

    王晓杰; 相久全; 韩乐强; 张锦前; 成军

    2011-01-01

    Objective To screen proteins of human liver cDNA library interacting with HCV NS5A and confirm the interaction between HCV N55A protein and aconitate 1 protein.Methods Yeast two hybrid was performed by mating AH109 ( HCV NS5A) with Y187 ( liver cDNA lihrary of human) .The interacted proteins with HCV NS5A were screened from the library.The aconitate 1 gene was amplified at first.The expression vectors of aconitate 1 were constructed.Then the interaction between HCV N55A protein and Homo sapiens aconitate 1 protein was confirmed using co-imruunoprecipitation and mammalian two hybrid experiment.Results The eukaryotic expression vectors of aconitate 1 were constructed.These results showed that Homo sapiens aconitate 1 protein interacted with HCV NS5A protein by co-immunoprecipitation and mammalian two hybrids experiment Conclusion HCV NS5A and Homo sapiens aconitate 1 protein can interact in HepCJ2 cells.%目的 筛选人肝脏cDNA文库中与HCV NS5A的结合蛋白基因,验证其中顺乌头酸酶1与HCV NS5A的相互作用.方法 应用酵母双杂交系统3筛选人肝脏cDNA文库中的HCV NS5A结合蛋白基因,应用哺乳动物双杂交及免疫共沉淀技术验证其中顺乌头酸酶1蛋白与HCV NS5A之间的相瓦作用.结果 成功筛选出人肝脏cD-NA文库中与HCV NS5A存在相瓦作用的蛋白基因,哺乳动物双杂交及免疫共沉淀实验结果 证实HCV NS5A与顺乌头酸酶1蛋白在HepG2细胞内存在相互作用.结论 本实验成功筛选人肝脏cDNA文库中的HCV NS5A结合蛋白基因,并且在体外水平即细胞内证实HCV NS5A与其中的顺乌头酸酶1蛋白之间的相互作用,为进一步细胞内及体内的糖、脂类代谢等功能研究奠定基础.

  12. A molecular-beacon-based asymmetric PCR assay for easy visualization of amplicons in the diagnosis of trichomoniasis.

    Science.gov (United States)

    Sonkar, Subash C; Sachdev, Divya; Mishra, Prashant K; Kumar, Anita; Mittal, Pratima; Saluja, Daman

    2016-12-15

    The currently available nucleic acid amplification tests (NAATs) for trichomoniasis are accurate, quick and confirmative with superior sensitivity than traditional culture-based microbiology assays. However, these assays are associated with problems of carry over contamination, false positive results, requirement of technical expertise for performance and detection of end product. Hence, a diagnostic assay with easy visualization of the amplified product will be profitable. An in-house, rapid, sensitive, specific molecular-beacon-based PCR assay, using primers against pfoB gene of Trichomonas vaginalis, was developed and evaluated using dry ectocervical swabs (n=392) from symptomatic females with vaginal discharge. Total DNA was isolated and used as template for the PCR assays. The performance and reproducibility of PCR assay was evaluated by composite reference standard (CRS). For easy visualization of the amplified product, molecular-beacon was designed and amplicons were visualized directly using fluorescent handheld dark reader or by Micro-Plate Reader. Molecular-beacons are single-stranded hairpin shaped nucleic acid probes composed of a stem, with fluorophore/quencher pair and a loop region complementary to the desired DNA. The beacon-based PCR assay designed in the present study is highly specific as confirmed by competition experiments and extremely sensitive with detection limit of 20fg of genomic DNA (3-4 pathogens). The minimum infrastructure requirement and ease to perform the assay makes this method highly useful for resource poor countries for better disease management. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Confirming the presence of HTLV-1 infection and the absence of HTLV-2 in blood donors from Arequipa, Peru.

    Science.gov (United States)

    Quispe, Nadia Carmela Santos; Feria, Edwin Bengoa; Santos-Fortuna, Elizabeth de los; Caterino-de-Araujo, Adele

    2009-01-01

    Epidemiological studies conducted in Peru disclosed HTLV-1 to be prevalent in different ethnic groups, and found HTLV-2 in some Amazonian Indians and in men who have sex with men. No data concerning HTLV-1/2 infection in blood donors from Arequipa, a highlands region in southern Peru, is available. We searched for the presence of HTLV-1 and HTLV-2 antibodies in 2,732 serum samples obtained from blood donors from this geographic area. HTLV-1/2-specific antibodies were detected using an enzyme-linked immunosorbent assay (ELISA) and were confirmed by Western blot (WB). Reactive sera had their blood bags discarded from donation, and the demographic characteristics of the donors were analyzed. Thirty-five sera (1.2%) were HTLV seroreactive by ELISA, and 25 were confirmed HTLV-1-positive by WB. One serum disclosed HTLV-positivity, and the remaining nine serum samples showed indeterminate results by WB; three of which had an HTLV-1 indeterminate Gag profile. The median age of HTLV-positive individuals was 34.6 years; 27 were male and eight were female. All individuals were from southern Peru: 27 from Arequipa, five from Puno, and three from Cuzco. HTLV co-positivity with hepatitis B (five sera) and syphilis (one serum) were detected. Previous transfusion and tattooing were observed in two and one individuals, respectively. No serum was positive for HTLV/HIV co-infection. This study confirmed, for the first time, HTLV-1 infection and the absence of HTLV-2 infection in blood donors from Arequipa, Peru and suggests vertical transmission as the major route of HTLV-1 transmission and acquisition in this geographic region.

  14. Isolation, production, purification, assay and characterization of ...

    African Journals Online (AJOL)

    Isolation, production, purification, assay and characterization of fibrinolytic ... are isolated from Bacillus subtilis, β-haemolytic Streptococci and urine sample. ... recombinant E.coli containing short fragment genomic DNA of Pseudomonas sp.

  15. 21 CFR 864.7250 - Erythropoietin assay.

    Science.gov (United States)

    2010-04-01

    ... erythropoietin (an enzyme that regulates the production of red blood cells) in serum or urine. This assay provides diagnostic information for the evaluation of erythrocytosis (increased total red cell mass)...

  16. 极细链格孢菌蛋白激发子PeaT1在酵母双杂交系统中转录激活活性的检测%Detection for Transcriptional Activity of Alternaria Tenuissim Protein Elicitor in Yeast Two-hybrid System

    Institute of Scientific and Technical Information of China (English)

    刘延锋; 邱德文; 曾洪梅; 杨秀芬

    2008-01-01

    The peaT1 gene fragment was amplified from pGEM-6p-1-peaT1 by PCR,and recovered target gene was cloned into pLexA vector.After digestion and sequencing,the bait vector pLexA-peaT1 was transformed into yeast strain EGY48[p8op-lacZ]by PEG/LiAC,and the transcriptional activity of bait vector was detected.The results showed that recombinant bait plasmid pLexA-PEMG1 was constructed,for the two bands of recombinant bait plasmid in agarase gel electrophoresis were expected after digesting by restriction endonuclease EcoR I and Xho I.Therefore,the recombinant bait plasmid could be used in yeast two-hybrid system to screen a cDNA library.

  17. The comet assay: a heavenly method!

    Science.gov (United States)

    Collins, Andrew R

    2015-01-01

    The contributions to this special issue of Mutagenesis have been selected to cover the main research areas served by the comet assay, namely genotoxicology, environmental toxicology, human biomonitoring and fundamental investigations into mechanisms of DNA damage and repair. Innovative methods are described, technical issues are explored, and guidelines are given for venturing into relatively new or unexploited areas of research. The popularity of the comet assay in a historical context is illustrated by a bibliometric survey.

  18. Electrochemical Assay of Gold-Plating Solutions

    Science.gov (United States)

    Chiodo, R.

    1982-01-01

    Gold content of plating solution is assayed by simple method that required only ordinary electrochemical laboratory equipment and materials. Technique involves electrodeposition of gold from solution onto electrode, the weight gain of which is measured. Suitable fast assay methods are economically and practically necessary in electronics and decorative-plating industries. If gold content in plating bath is too low, poor plating may result, with consequent economic loss to user.

  19. Variables Affecting Two Electron Transport System Assays

    OpenAIRE

    Burton, G. Allen; Lanza, Guy R.

    1986-01-01

    Several methodological variables were critical in two commonly used electron transport activity assays. The dehydrogenase assay based on triphenyl formazan production exhibited a nonlinear relationship between formazan production (dehydrogenase activity) and sediment dilution, and linear formazan production occurred for 1 h in sediment slurries. Activity decreased with increased time of sediment storage at 4°C. Extraction efficiencies of formazan from sediment varied with alcohol type; methan...

  20. Evaluation of red blood cell Pig-a assay and PIGRET assay in rats using chlorambucil.

    Science.gov (United States)

    Maeda, Akihisa; Takahashi, Kei; Tsuchiyama, Hiromi; Oshida, Keiyu

    2016-11-15

    The Pig-a assay is a novel method to assess the in vivo mutagenicity of compounds, and it is expected to be useful for the detection of genotoxicity. In this study, to assess the performance of the Pig-a assay targeting red blood cells (RBCs; RBC Pig-a assay) and reticulocytes (RETs; PIGRET assay), chlorambucil, which is a genotoxicant, was orally administered to male rats once at 10, 20 and 40mg/kg on Day 1, and the mutant frequencies (MFs) of RBCs and RETs were examined periodically. In the RBC Pig-a assay, significant increases in MFs were observed at 40mg/kg on Day 15 and at 20mg/kg or higher on Day 29. In the PIGRET assay, MFs increased significantly at all dose levels on Day 8 and only at 20mg/kg on Day 15, but there was no increase in MFs in the treatment groups on Day 29. In conclusion, the RBC Pig-a assay and PIGRET assay in rats have sufficient sensitivity to detect the mutagenicity of chlorambucil, and the PIGRET assay could detect its mutagenicity earlier and at a lower dose than the RBC Pig-a assay. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Assessing HTS performance using BioAssay Ontology: screening and analysis of a bacterial phospho-N-acetylmuramoyl-pentapeptide translocase campaign.

    Science.gov (United States)

    Moberg, Andreas; Zander Balderud, Linda; Hansson, Eva; Boyd, Helen

    2014-01-01

    With the public availability of biochemical assays and screening data constantly increasing, new applications for data mining and method analysis are evolving in parallel. One example is BioAssay Ontology (BAO) for systematic classification of assays based on screening setup and metadata annotations. In this article we report a high-throughput screening (HTS) against phospho-N-acetylmuramoyl-pentapeptide translocase (MraY), an attractive antibacterial drug target involved in peptidoglycan synthesis. The screen resulted in novel chemistry identification using a fluorescence resonance energy transfer assay. To address a subset of the false positive hits, a frequent hitter analysis was performed using an approach in which MraY hits were compared with hits from similar assays, previously used for HTS. The MraY assay was annotated according to BAO and three internal reference assays, using a similar assay design and detection technology, were identified. Analyzing the assays retrospectively, it was clear that both MraY and the three reference assays all showed a high false positive rate in the primary HTS assays. In the case of MraY, false positives were efficiently identified by applying a method to correct for compound interference at the hit-confirmation stage. Frequent hitter analysis based on the three reference assays with similar assay method identified additional false actives in the primary MraY assay as frequent hitters. This article demonstrates how assays annotated using BAO terms can be used to identify closely related reference assays, and that analysis based on these assays clearly can provide useful data to influence assay design, technology, and screening strategy.

  2. Study on Construction of Database for Confirmation of Rural Homestead Right

    Institute of Scientific and Technical Information of China (English)

    Yuan WANG; Dingtong LI

    2015-01-01

    Confirmation of homestead right is helpful for planning of rural construction land and comprehensive development of new socialist countryside construction. At present,China is carrying out confirmation of rural homestead right on a large scale. Theoretical analysis on construction of database for confirmation of rural homestead right is of great significance for promoting confirmation of rural homestead right. Using the Mapgis urban cadastral management system database,this paper studied the process of creating database for conformation of rural homestead right,and came up with recommendations for update and maintenance of the database.

  3. HBV表面抗原大蛋白与人胰腺突触角蛋白6之间的相互作用%Confirmation of the interaction between hepatitis B virus large surface protein and homo sapiens pancreatic syntaxin 6 protein

    Institute of Scientific and Technical Information of China (English)

    张海栋; 成军; 张锦前; 赵龙凤; 贾因棠; 王琦; 刘顺爱; 温少芳; 孙荣华; 李卓

    2012-01-01

    Objective To confirm the intra-cellular interaction between HBV large surface protein ( LHBs ) and homo sapiens syntaxin 6 protein ( STX6 ), which brought some new clues for studying on the molecular biology mechanism of glucose and lipid. Methods Eukaryotic expression vector pACT-STX6 and confirmed the interaction between LHBs and homo sapiens syntaxin protein through mammalian two-hybrid experiment. Results The research constructed eukaryotic expression vector pACT-STX6. Mammalian two-hybrid experiment showed that there were significant differences in the relative luciferase activity value between experimental group and each negative control group were( P < 0. 05 ). Conclusions LHBs might be interacted with homo sapiens syntaxin 6 protein in cells.%目的 验证HBV表面抗原大蛋白(LHBs)与人胰腺突触角蛋白6 (STX6)在细胞内是否存在相互作用,为进一步研究HBV影响糖、脂代谢机制奠定研究基础.方法 构建真核表达质粒pACT-STX6,采用哺乳动物双杂交技术验证LHBs与STX6之间的相互作用.结果 实验组和各阴性对照组相对荧光素酶活性值均存在差异,且均具有显著统计学意义(P< 0.01).结论 LHBs与人胰腺STX6在胰腺细胞内存在相互作用.

  4. Development of Rapid Isothermal Amplification Assays for Detection of Phytophthora spp. in Plant Tissue.

    Science.gov (United States)

    Miles, Timothy D; Martin, Frank N; Coffey, Michael D

    2015-02-01

    Several isothermal amplification techniques recently have been developed that are tolerant of inhibitors present in many plant extracts, which can reduce the need for obtaining purified DNA for running diagnostic assays. One such commercially available technique that has similarities with real-time polymerase chain reaction (PCR) for designing primers and a labeled probe is recombinase polymerase amplification (RPA). This technology was used to develop two simple and rapid approaches for detection of Phytophthora spp.: one genus-specific assay multiplexed with a plant internal control and the other species-specific assays for Phytophthora ramorum and P. kernoviae. All assays were tested for sensitivity (ranging from 3 ng to 1 fg of DNA) and specificity using DNA extracted from more than 136 Phytophthora taxa, 21 Pythium spp., 1 Phytopythium sp., and a wide range of plant species. The lower limit of linear detection using purified DNA was 200 to 300 fg of DNA in all pathogen RPA assays. Six different extraction buffers were tested for use during plant tissue maceration and the assays were validated in the field by collecting 222 symptomatic plant samples from over 50 different hosts. Only 56 samples were culture positive for Phytophthora spp. whereas 91 were positive using the Phytophthora genus-specific RPA test and a TaqMan real-time PCR assay. A technique for the generation of sequencing templates from positive RPA amplifications to confirm species identification was also developed. These RPA assays have added benefits over traditional technologies because they are rapid (results can be obtained in as little as 15 min), do not require DNA extraction or extensive training to complete, use less expensive portable equipment than PCR-based assays, and are significantly more specific than current immunologically based methods. This should provide a rapid, field-deployable capability for pathogen detection that will facilitate point-of-sample collection processing

  5. International network for comparison of HIV neutralization assays: the NeutNet report II.

    Directory of Open Access Journals (Sweden)

    Leo Heyndrickx

    Full Text Available BACKGROUND: Neutralizing antibodies provide markers for vaccine-induced protective immunity in many viral infections. By analogy, HIV-1 neutralizing antibodies induced by immunization may well predict vaccine effectiveness. Assessment of neutralizing antibodies is therefore of primary importance, but is hampered by the fact that we do not know which assay(s can provide measures of protective immunity. An international collaboration (NeutNet involving 18 different laboratories previously compared different assays using monoclonal antibodies (mAbs and soluble CD4 (Phase I study. METHODS: In the present study (Phase II, polyclonal reagents were evaluated by 13 laboratories. Each laboratory evaluated nine plasmas against an 8 virus panel representing different genetic subtypes and phenotypes. TriMab, a mixture of three mAbs, was used as a positive control allowing comparison of the results with Phase I in a total of nine different assays. The assays used either uncloned virus produced in peripheral blood mononuclear cells (PBMCs (Virus Infectivity Assays, VIA, or Env (gp160-pseudotyped viruses (pseudoviruses, PSV produced in HEK293T cells from molecular clones or from uncloned virus. Target cells included PBMC and genetically engineered cell lines in either single- or multiple-cycle infection format. Infection was quantified by using a range of assay read-outs including extra- or intra-cellular p24 antigen detection, luciferase, beta-galactosidase or green fluorescent protein (GFP reporter gene expression. FINDINGS: Using TriMab, results of Phase I and Phase II were generally in agreement for six of the eight viruses tested and confirmed that the PSV assay is more sensitive than PBMC (p = 0.014. Comparisons with the polyclonal reagents showed that sensitivities were dependent on both virus and plasma. CONCLUSIONS: Here we further demonstrate clear differences in assay sensitivities that were dependent on both the neutralizing reagent and the virus

  6. International Network for Comparison of HIV Neutralization Assays: The NeutNet Report II

    Science.gov (United States)

    Heyndrickx, Leo; Heath, Alan; Sheik-Khalil, Enas; Alcami, Jose; Bongertz, Vera; Jansson, Marianne; Malnati, Mauro; Montefiori, David; Moog, Christiane; Morris, Lynn; Osmanov, Saladin; Polonis, Victoria; Ramaswamy, Meghna; Sattentau, Quentin; Tolazzi, Monica; Schuitemaker, Hanneke; Willems, Betty; Wrin, Terri; Fenyö, Eva Maria; Scarlatti, Gabriella

    2012-01-01

    Background Neutralizing antibodies provide markers for vaccine-induced protective immunity in many viral infections. By analogy, HIV-1 neutralizing antibodies induced by immunization may well predict vaccine effectiveness. Assessment of neutralizing antibodies is therefore of primary importance, but is hampered by the fact that we do not know which assay(s) can provide measures of protective immunity. An international collaboration (NeutNet) involving 18 different laboratories previously compared different assays using monoclonal antibodies (mAbs) and soluble CD4 (Phase I study). Methods In the present study (Phase II), polyclonal reagents were evaluated by 13 laboratories. Each laboratory evaluated nine plasmas against an 8 virus panel representing different genetic subtypes and phenotypes. TriMab, a mixture of three mAbs, was used as a positive control allowing comparison of the results with Phase I in a total of nine different assays. The assays used either uncloned virus produced in peripheral blood mononuclear cells (PBMCs) (Virus Infectivity Assays, VIA), or Env (gp160)-pseudotyped viruses (pseudoviruses, PSV) produced in HEK293T cells from molecular clones or from uncloned virus. Target cells included PBMC and genetically engineered cell lines in either single- or multiple-cycle infection format. Infection was quantified by using a range of assay read-outs including extra- or intra-cellular p24 antigen detection, luciferase, beta-galactosidase or green fluorescent protein (GFP) reporter gene expression. Findings Using TriMab, results of Phase I and Phase II were generally in agreement for six of the eight viruses tested and confirmed that the PSV assay is more sensitive than PBMC (p = 0.014). Comparisons with the polyclonal reagents showed that sensitivities were dependent on both virus and plasma. Conclusions Here we further demonstrate clear differences in assay sensitivities that were dependent on both the neutralizing reagent and the virus

  7. Genotoxicity of Euphorbia hirta: an Allium cepa assay.

    Science.gov (United States)

    Yuet Ping, Kwan; Darah, Ibrahim; Yusuf, Umi Kalsom; Yeng, Chen; Sasidharan, Sreenivasan

    2012-06-26

    The potential genotoxic effects of methanolic extracts of Euphorbia hirta which is commonly used in traditional medicine to treat a variety of diseased conditions including asthma, coughs, diarrhea and dysentery was investigated using Allium cepa assay. The extracts of 125, 250, 500 and 1,000 µg/mL were tested on root meristems of A. cepa. Ethylmethanesulfonate was used as positive control and distilled water was used as negative control. The result showed that mitotic index decreased as the concentrations of E. hirta extract increased. A dose-dependent increase of chromosome aberrations was also observed. Abnormalities scored were stickiness, c-mitosis, bridges and vagrant chromosomes. Micronucleated cells were also observed at interphase. Result of this study confirmed that the methanol extracts of E. hirta exerted significant genotoxic and mitodepressive effects at 1,000 µg/mL.

  8. Thermostability of IFN-γ and IP-10 release assays for latent infection with Mycobacterium tuberculosis

    DEFF Research Database (Denmark)

    Blauenfeldt, Thomas; Wagner, Dirk; Aabye, Martine Grosos;

    2016-01-01

    INTRODUCTION: Interferon-γ (IFN-γ) inducible protein 10kD (IP-10) and IFN-γ release assays (IGRAs) are immunodiagnostic tests aiming to identify the presence of specific cellular immune responses, interpreted as markers for latent infection with Mycobacterium tuberculosis. Incubation at higher...... accuracy of IP-10 release assay and IGRAs. RESULTS: We included 65 patients with confirmed pulmonary tuberculosis and 160 healthy controls from 6 European centres collaborating in the TBnet. In patients, IP-10 responses increased 1.07 (IQR 0.90-1.36) fold and IFN-γ responses decreased 0.88 (IQR 0...

  9. Application of a coupled enzyme assay to characterize nicotinamide riboside kinases.

    Science.gov (United States)

    Dölle, Christian; Ziegler, Mathias

    2009-02-15

    The recently identified nicotinamide riboside kinases (Nrks) constitute a distinct pathway of nicotinamide adenine dinucleotide (NAD) biosynthesis. Here we present the combination of an established optical adenosine triphosphatase (ATPase) test, the pyruvate kinase/lactate dehydrogenase system, with the Nrk-catalyzed reaction to determine kinetic properties of these enzymes, in particular affinities for ATP. The assay allows variation of both nucleoside and phosphate donor substrates, thereby providing major advantages for the characterization of these enzymes. We confirm previously established kinetic parameters and identify differences in substrate selectivity between the two human Nrk isoforms. The proposed assay is inexpensive and may be applied for high-throughput screening.

  10. Screening of Putative Proteins That are Interacted with NBS-LRR Protein Pik-h by the Yeast Two-Hybrid System%水稻NBS-LRR类抗稻瘟病蛋白Pik-h的互作蛋白筛选

    Institute of Scientific and Technical Information of China (English)

    王加峰; 刘浩; 王慧; 陈志强

    2016-01-01

    信号蛋白、4个参与光合作用的叶绿体蛋白、1个含有U-BOX结构域的蛋白及4个未知功能蛋白。【结论】成功构建了适宜于研究抗病基因(R基因)介导反应途径的酵母双杂交cDNA文库,筛选出Pik-h的互作蛋白,为进一步研究Pik-h或其他抗稻瘟病基因介导的抗病机制打下了基础。%[Objective] To further investigate the signaling pathways activated directly by the resistance proteins Pikh-1 and Pikh-2 from the resistance gene Pik-h, yeast two-hybrid assay was performed to screen a rice leaf cDNA library using Pikh-1 and Pikh-2 as bait, respectively.[Method] All rice leaves of IRBL8 (Pik-hNIL) from the time points (12 and 24 h after inoculation with GD0193) were harvested for total RNA preparation. The rice leaf cDNA library was further constructed with the Make Your Own Mate&Plate Library System kit (Clontech). Bait plasmids pGBKT7-Pikh1 and pGBKT7-Pikh2 were constructed using the rapid homologous recombination method. The expression of the two proteins in the Y2H Gold strain was further detected with Western blot and the self-activation and cytotoxicity were also tested. Proteins interacting with the baits Pikh1 and Pikh2 were screened on SD/-Ade/-His/-Leu/-Trp/X-α-Gal plates from the rice leaf cDNA library with the mating strategy. Then the plasmids were prepared from the blue interacting clones and retransformed back into Y2H Gold strain with the corresponding bait. The plasmids that passed the reconfirmation were sequenced and the DNA sequences were further used to blast rice genome annotation project database. The functions of the interaction proteins were further analyzed with gene ontology (GO) annotation.[Result] The rice leaf cDNA library contained 2.2×106 independent clones. The sizes of most inserts were above 400 bp in the cDNA library. Bait plasmids (pGBKT7-Pikh1 and pGBKT7-Pikh2) expressed the corresponding proteins (BD-Pikh-1 and BD-Pikh-2) well and showed no self-activation and cytotoxicity

  11. Controlling variation in the comet assay

    Directory of Open Access Journals (Sweden)

    Andrew Richard Collins

    2014-10-01

    Full Text Available Variability of the comet assay is a serious issue, whether it occurs from experiment to experiment in the same laboratory, or between different laboratories analysing identical samples. Do we have to live with high variability, just because the comet assay is a biological assay rather than analytical chemistry? Numerous attempts have been made to limit variability by standardising the assay protocol, and the critical steps in the assay have been identified; agarose concentration, duration of alkaline incubation, and electrophoresis conditions (time, temperature and voltage gradient are particularly important. Even when these are controlled, variation seems to be inevitable. It is helpful to include in experiments reference standards, i.e. cells with a known amount of specific damage to the DNA. They can be aliquots frozen from a single large batch of cells, either untreated (negative controls or treated with, for example, H2O2 or X-rays to induce strand breaks (positive control for the basic assay, or photosensitiser plus light to oxidise guanine (positive control for Fpg- or OGG1-sensitive sites. Reference standards are especially valuable when performing a series of experiments over a long period - for example, analysing samples of white blood cells from a large human biomonitoring trial - to check that the assay is performing consistently, and to identify anomalous results necessitating a repeat experiment. The reference values of tail intensity can also be used to iron out small variations occurring from day to day. We present examples of the use of reference standards in human trials, both within one laboratory and between different laboratories, and describe procedures that can be used to control variation.

  12. Cell Culture Assay for Human Noroviruses [response

    Energy Technology Data Exchange (ETDEWEB)

    Straub, Tim M.; Honer Zu Bentrup, Kerstin; Orosz Coghlan, Patricia; Dohnalkova, Alice; Mayer, Brooke K.; Bartholomew, Rachel A.; Valdez, Catherine O.; Bruckner-Lea, Cindy J.; Gerba, Charles P.; Abbaszadegan, Morteza A.; Nickerson, Cheryl A.

    2007-07-01

    We appreciate the comments provided by Leung et al., in response to our recently published article “In Vitro Cell Culture Infectivity Assay for Human Noroviruses” by Straub et al. (1). The specific aim of our project was to develop an in vitro cell culture infectivity assay for human noroviruses (hNoV) to enhance risk assessments when they are detected in water supplies. Reverse transcription (RT) qualitative or quantitative PCR are the primary assays for waterborne NoV monitoring. However, these assays cannot distinguish between infectious vs. non-infectious virions. When hNoV is detected in water supplies, information provided by our infectivity assay will significantly improve risk assessment models and protect human health, regardless of whether we are propagating NoV. Indeed, in vitro cell culture infectivity assays for the waterborne pathogen Cryptosporidium parvum that supplement approved fluorescent microscopy assays, do not result in amplification of the environmentally resistant hard-walled oocysts (2). However, identification of life cycle stages in cell culture provides evidence of infectious oocysts in a water supply. Nonetheless, Leung et al.’s assertion regarding the suitability of our method for the in vitro propagation of high titers of NoV is valid for the medical research community. In this case, well-characterized challenge pools of virus would be useful for developing and testing diagnostics, therapeutics, and vaccines. As further validation of our published findings, we have now optimized RT quantitative PCR to assess the level of viral production in cell culture, where we are indeed finding significant increases in viral titer. The magnitude and time course of these increases is dependent on both virus strain and multiplicity of infection. We are currently preparing a manuscript that will discuss these findings in greater detail, and the implications this may have for creating viral challenge pools

  13. Comparison of a combined nontreponemal (VDRL) and treponemal immunoblot to traditional nontreponemal and treponemal assays.

    Science.gov (United States)

    Franken, Alicia A; Oliver, Joyce H; Litwin, Christine M

    2015-01-01

    Serology is the mainstay for the diagnosis and management of patients with syphilis. Newer technologies such as immunoblotting are now available for the diagnosis of syphilis. A commercial IgM/IgG immunoblot assay that detects both nontreponemal (VDRL-Venereal Disease Research Laboratory) and treponemal antibodies was compared with standard nontreponemal and treponemal assays. The immunoblot and T. pallidum particle agglutination assay (TP-PA) were performed on 198 samples. Ninety-seven samples were Rapid plasma reagin (RPR)-positive and one hundred one were RPR-negative. Positive RPR samples were titered by VDRL. The agreement, sensitivity, and specificity of the IgM/IgG VDRL results of the immunoblot compared to RPR were 74.2% (95% CI: 67.2-80.2), 77.3% (95% CI: 70.2-83.4), and 71.3% (95% CI: 64.4-77.1), respectively. The agreement, sensitivity, and specificity of the IgM/IgG treponemal immunoblot compared to TP-PA were 100% for all parameters, if the ten equivocal results were not used in the calculation. The treponemal portion of the ViraBlot IgM/IgG immunoblot compared well with the treponemal confirmation assay and could be a useful supplemental method to fluorescent treponemal antibody or TP-PA for the confirmation of syphilis. The addition of the detection of nontreponemal antibodies to the immunoblot assay, however, may not be of added benefit to the overall assay, due to decreased sensitivity and specificity compared to standard assays. © 2014 Wiley Periodicals, Inc.

  14. The Comet Assay: Tails of the (Unexpected. Use of the comet assay in pharmaceutical development.

    Directory of Open Access Journals (Sweden)

    Bas-jan Van Der Leede

    2015-08-01

    Full Text Available In genotoxicity testing of pharmaceuticals the rodent alkaline comet assay is being increasingly used as a second in vivo assay in addition to the in vivo micronucleus assay to mitigate in vitro positive results as recommended by regulatory guidance. In this presentation we want to give insight into the circumstances in vivo comet assay is deployed in a Genetic Toxicology Department of a pharmaceutical company. As the in vivo comet assay is a salvage assay, it means that some events have occurred in an in vitro assay and that the compound (or metabolite responsible for this signal is potentially deselected for further development. More than often the decision to perform an in vivo comet assay is at a very early stage in development and the first time that the compound will be tested in vivo at high/toxic dose levels. As almost no toxicokinetic data and tissue distribution data are available a careful design with maximizes the chances for successful mitigation is necessary. Decisions on acute or repeated dosing need to be made and arrangements for combining the in vivo comet assay with the in vivo micronucleus assay are to be considered. Often synthesis methods need to be scaled up fast to provide the required amount of compound and information on suitable formulations needs to be in place. As exposure data is crucial for interpretation of results, analytical methods need to be brought in place rapidly. An experienced multi skilled and communicative team needs to be available to deploy successfully this kind of assays at an early stage of development. We will present a few scenarios on study conduct and demonstrate how this assay can make a difference for the further development of a new drug.

  15. Field evaluation of rapid HIV serologic tests for screening and confirming HIV-1 infection in Honduras.

    Science.gov (United States)

    Stetler, H C; Granade, T C; Nunez, C A; Meza, R; Terrell, S; Amador, L; George, J R

    1997-03-01

    To determine the ability of simple, rapid tests to identify HIV-1 antibody-positive specimens in field settings using the World Health Organization's (WHO) alternative testing strategies. Three-phase evaluation of simple, rapid assays using banked specimens and prospectively collected serum specimens at regional hospitals and rural clinics. Seven test (Retrocell, Genie, HIVCHEK, SUDS HIV-1, Testpack, Serodia HIV-1, and HIV-1/2 RTD) were evaluated and results compared with standard enzyme immunoassay (EIA) and Western blot results (phase 1). Further evaluation consisted of prospective testing of routine specimens at regional (phase 2; n = 900) and rural, peripheral laboratories (phase 3; n = 1266) throughout Honduras with selected assays. Sensitivity and specificity were calculated for each assay and combination of assays for each phase to evaluate the effectiveness of the WHO alternative testing strategies. All tests in all phases were > 99% sensitive after correcting for technical errors, with two exceptions (SUDS, phase 1; HIVCHEK, phase 3). In phase 3, where the testing algorithm was diagnostic, several combinations of assays were 100% sensitive and specific using WHO strategy II or III. For the Honduras Ministry of Health, the combination of Retrocell and Genie was found to be equally sensitive, more specific (no indeterminate results), and less expensive than EIA/Western blot. Combinations of rapid, simple HIV antibody assays provide sensitivity and specificity performance comparable to EIA/Western blot. Application of these combinations in the WHO alternative testing strategies provides an inexpensive and effective method of determining HIV status. Assay combinations using these strategies can be easily performed in small, rural laboratories and have been implemented in routine HIV screening in Honduras.

  16. Evaluation of Five Chromogenic Agar Media and the Rosco Rapid Carb Screen Kit for Detection and Confirmation of Carbapenemase Production in Gram-Negative Bacilli

    Science.gov (United States)

    Gilmour, Matthew W.; DeGagne, Pat; Nichol, Kim; Karlowsky, James A.

    2014-01-01

    An efficient workflow to screen for and confirm the presence of carbapenemase-producing Gram-negative bacilli was developed by evaluating five chromogenic screening agar media and two confirmatory assays, the Rapid Carb screen test (Rosco Diagnostica A/S, Taastrup, Denmark) and the modified Hodge test. A panel of 150 isolates was used, including 49 carbapenemase-producing isolates representing a variety of β-lactamase enzyme classes. An evaluation of analytical performance, assay cost, and turnaround time indicated that the preferred workflow (screening test followed by confirmatory testing) was the chromID Carba agar medium (bioMérieux, Marcy l'Étoile, France), followed by the Rapid Carb screen test, yielding a combined sensitivity of 89.8% and a specificity of 100%. As an optional component of the workflow, a determination of carbapenemase gene class via molecular means could be performed subsequent to confirmatory testing. PMID:25355764

  17. Evaluation of five chromogenic agar media and the Rosco Rapid Carb screen kit for detection and confirmation of carbapenemase production in Gram-negative bacilli.

    Science.gov (United States)

    Simner, Patricia J; Gilmour, Matthew W; DeGagne, Pat; Nichol, Kim; Karlowsky, James A

    2015-01-01

    An efficient workflow to screen for and confirm the presence of carbapenemase-producing Gram-negative bacilli was developed by evaluating five chromogenic screening agar media and two confirmatory assays, the Rapid Carb screen test (Rosco Diagnostica A/S, Taastrup, Denmark) and the modified Hodge test. A panel of 150 isolates was used, including 49 carbapenemase-producing isolates representing a variety of β-lactamase enzyme classes. An evaluation of analytical performance, assay cost, and turnaround time indicated that the preferred workflow (screening test followed by confirmatory testing) was the chromID Carba agar medium (bioMérieux, Marcy l'Étoile, France), followed by the Rapid Carb screen test, yielding a combined sensitivity of 89.8% and a specificity of 100%. As an optional component of the workflow, a determination of carbapenemase gene class via molecular means could be performed subsequent to confirmatory testing. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  18. [Clinical evaluation of a novel HBsAg quantitative assay].

    Science.gov (United States)

    Takagi, Kazumi; Tanaka, Yasuhito; Naganuma, Hatsue; Hiramatsu, Kumiko; Iida, Takayasu; Takasaka, Yoshimitsu; Mizokami, Masashi

    2007-07-01

    The clinical implication of the hepatitis B surface antigen (HBsAg) concentrations in HBV-infected individuals remains unclear. The aim of this study was to evaluate a novel fully automated Chemiluminescence Enzyme Immunoassay (Sysmex HBsAg quantitative assay) by comparative measurements of the reference serum samples versus two independent commercial assays (Lumipulse f or Architect HBsAg QT). Furthermore, clinical usefulness was assessed for monitoring of the serum HBsAg levels during antiviral therapy. A dilution test using 5 reference-serum samples showed linear correlation curve in range from 0.03 to 2,360 IU/ml. The HBsAg was measured in total of 400 serum samples and 99.8% had consistent results between Sysmex and Lumipulse f. Additionally, a positive linear correlation was observed between Sysmex and Architect. To compare the Architect and Sysmex, both methods were applied to quantify the HBsAg in serum samples with different HBV genotypes/subgenotypes, as well as in serum contained HBV vaccine escape mutants (126S, 145R). Correlation between the methods was observed in results for escape mutants and common genotypes (A, B, C) in Japan. Observed during lamivudine therapy, an increase in HBsAg and HBV DNA concentrations preceded the aminotransferase (ALT) elevation associated with drug-resistant HBV variant emergence (breakthrough hepatitis). In conclusion, reliability of the Sysmex HBsAg quantitative assay was confirmed for all HBV genetic variants common in Japan. Monitoring of serum HBsAg concentrations in addition to HBV DNA quantification, is helpful in evaluation of the response to lamivudine treatment and diagnosis of the breakthrough hepatitis.

  19. Surface modification of poly(dimethylsiloxane) for microfluidic assay applications

    Energy Technology Data Exchange (ETDEWEB)

    Seguin, Christine; McLachlan, Jessica M.; Norton, Peter R. [Department of Chemistry, University of Western Ontario, 1151 Richmond St., London, ON, N6A 5B7 (Canada); Lagugne-Labarthet, Francois, E-mail: flagugne@uwo.ca [Department of Chemistry, University of Western Ontario, 1151 Richmond St., London, ON, N6A 5B7 (Canada)

    2010-02-01

    The surface of a poly(dimethylsiloxane) (PDMS) film was imparted with patterned functionalities at the micron-scale level. Arrays of circles with diameters of 180 and 230 {mu}m were functionalized using plasma oxidation coupled with aluminum deposition, followed by silanization with solutions of 3-aminopropyltrimethoxy silane (3-APTMS) and 3-mercaptopropyltrimethoxy silane (3-MPTMS), to obtain patterned amine and thiol functionalities, respectively. The modification of the samples was confirmed using X-ray photoelectron spectroscopy (XPS), gold nanoparticle adhesion coupled with optical microscopy, as well as by derivatization with fluorescent dyes. To further exploit the novel surface chemistry of the modified PDMS, samples with surface amine functionalities were used to develop a protein assay as well as an array capable of cellular capture and patterning. The modified substrate was shown to successfully selectively immobilize fluorescently labeled immunoglobulin G (IgG) by tethering Protein A to the surface, and, for the cellular arrays, C2C12 rat endothelial cells were captured. Finally, this novel method of patterning chemical functionalities onto PDMS has been incorporated into microfluidic channels. Finally, we demonstrate the in situ chemical modification of the protected PDMS oxidized surface within a microfluidic device. This emphasizes the potential of our method for applications involving micron-scale assays since the aluminum protective layer permits to functionalize the oxidized PDMS surface several weeks after plasma treatment simply after etching away the metallic thin film.

  20. Random assay in radioimmunoassay: Feasibility and application compared with batch assay

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jung Min; Lee, Hwan Hee; Park, Sohyun; Kim, Tae Sung; Kim, Seok Ki [Dept. of Nuclear MedicineNational Cancer Center, Goyang (Korea, Republic of)

    2016-12-15

    The batch assay has been conventionally used for radioimmunoassay (RIA) because of its technical robustness and practical convenience. However, it has limitations in terms of the relative lag of report time due to the necessity of multiple assays in a small number of samples compared with the random assay technique. In this study, we aimed to verify whether the random assay technique can be applied in RIA and is feasible in daily practice. The coefficients of variation (CVs) of eight standard curves within a single kit were calculated in a CA-125 immunoradiometric assay (IRMA) for the reference of the practically ideal CV of the CA-125 kit. Ten standard curves of 10 kits from 2 prospectively collected lots (pLot) and 85 standard curves of 85 kits from 3 retrospectively collected lots (Lot) were obtained. Additionally, the raw measurement data of both 170 control references and 1123 patients' sera were collected retrospectively between December 2015 and January 2016. A standard curve of the first kit of each lot was used as a master standard curve for a random assay. The CVs of inter-kits were analyzed in each lot, respectively. All raw measurements were normalized by decay and radioactivity. The CA-125 values from control samples and patients' sera were compared using the original batch assay and random assay. In standard curve analysis, the CVs of inter-kits in pLots and Lots were comparable to those within a single kit. The CVs from the random assay with normalization were similar to those from the batch assay in the control samples (CVs % of low/high concentration; Lot1 2.71/1.91, Lot2 2.35/1.83, Lot3 2.83/2.08 vs. Lot1 2.05/1.21, Lot2 1.66/1.48, Lot3 2.41/2.14). The ICCs between the batch assay and random assay using patients' sera were satisfactory (Lot1 1.00, Lot2 0.999, Lot3 1.00). The random assay technique could be successfully applied to the conventional CA-125 IRMA kits. The random assay showed strong agreement with the batch assay. The

  1. Using the CPTAC Assay Portal to identify and implement highly characterized targeted proteomics assays

    Science.gov (United States)

    Whiteaker, Jeffrey R; Halusa, Goran N; Hoofnagle, Andrew N; Sharma, Vagisha; MacLean, Brendan; Yan, Ping; Wrobel, John A; Kennedy, Jacob; Mani, DR; Zimmerman, Lisa J; Meyer, Matthew R.; Mesri, Mehdi; Abbatiello, Susan E; Boja, Emily; Carr, Steven A.; Chan, Daniel W.; Chen, Xian; Chen, Jing; Davies, Sherri R; Ellis, Matthew J. C.; Fenyö, David; Hiltke, Tara; Ketchum, Karen A.; Kinsinger, Chris; Kuhn, Eric; Liebler, Daniel C.; Lin, De; Liu, Tao; Loss, Michael; MacCoss, Michael J; Qian, Wei-Jun; Rivers, Robert; Rodland, Karin D.; Ruggles, Kelly V; Scott, Mitchell G; Smith, Richard D.; Thomas, Stefani; Townsend, R. Reid; Whiteley, Gordon; Wu, Chaochao; Zhang, Hui; Zhang, Zhen; Rodriguez, Henry; Paulovich, Amanda G

    2016-01-01

    Summary The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as an open-source repository of well-characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and post-translational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories. PMID:26867747

  2. Using the CPTAC Assay Portal to identify and implement highly characterized targeted proteomics assays

    Energy Technology Data Exchange (ETDEWEB)

    Whiteaker, Jeffrey R.; Halusa, Goran; Hoofnagle, Andrew N.; Sharma, Vagisha; MacLean, Brendan; Yan, Ping; Wrobel, John; Kennedy, Jacob; Mani, DR; Zimmerman, Lisa J.; Meyer, Matthew R.; Mesri, Mehdi; Boja, Emily; Carr, Steven A.; Chan, Daniel W.; Chen, Xian; Chen, Jing; Davies, Sherri; Ellis, Matthew; Fenyo, David; Hiltket, Tara; Ketchum, Karen; Kinsinger, Christopher; Kuhn, Eric; Liebler, Daniel; Liu, Tao; Loss, Michael; MacCoss, Michael; Qian, Weijun; Rivers, Robert; Rodland, Karin D.; Ruggles, Kelly; Scott, Mitchell; Smith, Richard D.; Thomas, Stefani N.; Townsend, Reid; Whiteley, Gordon; Wu, Chaochao; Zhang, Hui; Zhang, Zhen; Rodriguez, Henry; Paulovich, Amanda G.

    2016-02-12

    The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as an open-source repository of well-characterized targeted proteomic assays. The portal is designed to curate and disseminate highly characterized, targeted mass spectrometry (MS)-based assays by providing detailed assay performance characterization data, standard operating procedures, and access to reagents. Assay content is accessed via the portal through queries to find assays targeting proteins associated with specific cellular pathways, protein complexes, or specific chromosomal regions. The position of the peptide analytes for which there are available assays are mapped relative to other features of interest in the protein, such as sequence domains, isoforms, single nucleotide polymorphisms, and post-translational modifications. The overarching goals are to enable robust quantification of all human proteins and to standardize the quantification of targeted MS-based assays to ultimately enable harmonization of results over time and across laboratories.

  3. Comet assay on mice testicular cells

    Directory of Open Access Journals (Sweden)

    Anoop Kumar Sharma

    2015-05-01

    Full Text Available Heritable mutations may result in a variety of adverse outcomes including genetic disease in the offspring. In recent years the focus on germ cell mutagenicity has increased and the “Globally Harmonized System of Classification and Labelling of Chemicals (GHS” has published classification criteria for germ cell mutagens (Speit et al., 2009. The in vivo Comet assay is considered a useful tool for investigating germ cell genotoxicity. In the present study DNA strand breaks in testicular cells of mice were investigated. Different classes of chemicals were tested in order to evaluate the sensitivity of the comet assay in testicular cells. The chemicals included environmentally relevant substances such as Bisphenol A, PFOS and Tetrabrombisphenol A. Statistical power calculations will be presented to aid in the design of future Comet assay studies on testicular cells. Power curves were provided with different fold changes in % tail DNA, different number of cells scored and different number of gels (Hansen et al., 2014. An example is shown in Figure 1. A high throughput version of the Comet assay was used. Samples were scored with a fully automatic comet assay scoring system that provided faster scoring of randomly selected cells.

  4. Research highlights: digital assays on chip.

    Science.gov (United States)

    Kim, Donghyuk; Wei, Qingshan; Kong, Janay Elise; Ozcan, Aydogan; Di Carlo, Dino

    2015-01-07

    The ability to break up a volume of fluid into smaller pieces that are confined or separated to prevent molecular communication/transport is a key capability intrinsic to microfluidic systems. This capability has been used to develop or implement digital versions of traditional molecular analysis assays, including digital PCR and digital immunoassays/ELISA. In these digital versions, the concentration of the target analyte is in a range such that, when sampled into smaller fluid volumes, either a single molecule or no molecule may be present. Subsequent amplification is sensitive enough to obtain a digital readout of the presence of these target molecules. Advantages of such approaches that are claimed include quantification without calibration and robustness to variations in reaction conditions or times because the digital readout is less sensitive to absolute signal intensity levels. Weaknesses of digital approaches include a lower dynamic range of concentrations over which the assay is sensitive, which depends on the total volume that can be analyzed. We highlight recent efforts to expand the dynamic range of digital assays based on exploiting reaction/diffusion phenomena. A side-by-side study that evaluates the strengths of digital assays reveals that the majority of these claims are supported, with specific caveats. Finally, we highlight approaches to apply digital assays to analyze new types of reactions, including the active transport of protons across membranes by ATPases at the single protein level - perhaps opening up new biophysical understanding and screening opportunities, similar to widely deployed single-molecule ion channel analysis.

  5. Isolation of Ehrlichia chaffeensis from wild white-tailed deer (Odocoileus virginianus) confirms their role as natural reservoir hosts.

    Science.gov (United States)

    Lockhart, J M; Davidson, W R; Stallknecht, D E; Dawson, J E; Howerth, E W

    1997-07-01

    Field and experimental studies have implicated white-tailed deer (Odocoileus virginianus) as probable reservoir hosts for Ehrlichia chaffeensis, the causative agent of human monocytic ehrlichiosis, but natural infection in deer has not been confirmed through isolation of E. chaffeensis. Thirty-five white-tailed deer collected from three Amblyomma americanum-infested populations in Georgia were examined for evidence of E. chaffeensis infection by serologic, molecular, cell culture, and xenodiagnostic methods. Twenty-seven deer (77%) had E. chaffeensis-reactive indirect fluorescent-antibody assay titers of > or = 1:64; and the blood, spleens, or lymph nodes of seven (20%) deer were positive in a nested PCR assay with E. chaffeensis-specific primers. E. chaffeensis was isolated in DH82 cell cultures from the blood of five (14%) deer, including two deer that were PCR negative. Combination of culture and PCR results indicated that six (17%) deer were probably rickettsemic and that nine (26%) were probably infected. Restriction digestion of PCR products amplified from deer tissues and cell culture isolates resulted in a banding pattern consistent with the E. chaffeensis 16S rRNA gene sequence. The sequences of all PCR products from deer tissues or cell culture isolates were identical to the sequence of the Arkansas type strain of E. chaffeensis. Xenodiagnosis with C3H mice inoculated intraperitoneally with deer blood, spleen, or lymph node suspensions was unsuccessful. When viewed in the context of previous studies, these findings provide strong evidence that E. chaffeensis is maintained in nature primarily by a tick vector-vertebrate reservoir system consisting of lone star ticks and white-tailed deer.

  6. 34 CFR 668.136 - Institutional determinations of eligibility based on INS responses to secondary confirmation...

    Science.gov (United States)

    2010-07-01

    ... INS responses to secondary confirmation requests. 668.136 Section 668.136 Education Regulations of the... determinations of eligibility based on INS responses to secondary confirmation requests. (a) Except as provided...) by relying on the INS response to the Form G-845. (b) An institution shall make its...

  7. 75 FR 81519 - Confirmation, Portfolio Reconciliation, and Portfolio Compression Requirements for Swap Dealers...

    Science.gov (United States)

    2010-12-28

    ... portfolio compression. Federal Reserve Bank of New York Staff Report No. 424: ``Policy Perspectives on OTC... COMMISSION 17 CFR Part 23 RIN 3038-AC96 Confirmation, Portfolio Reconciliation, and Portfolio Compression... requirements for swap confirmation, portfolio reconciliation, and portfolio compression for swap dealers...

  8. Chromatography as Method for Analytical Confirmation of Paracetamol in Postmortem Material Together with Psychoactive Substances

    Science.gov (United States)

    Biscevic-Tokic, Jasmina; Tokic, Nedim; Ibrahimpasic, Elma

    2015-01-01

    for determining the drug, and the drug substance. Used GC-MS instrument was an Agilent 7890A with helium as the carrier gas. Results: The analysis of blood samples, urine, bile and stomach contents, obtained after the autopsy of deceased persons, by using gas chromatography with mass spectrometry, in analytical manner confirmed the fact that paracetamol is a very common component of psychoactive substances poisoning. In our assay of samples we detected psychoactive substances (heroin, codeine, morphine, sertraline, diazepam), and almost all were found in the combination with paracetamol, indicating the poor quality of illicit drugs sold on the market. Discussion: Paracetamol (Acetaminophen) is a very common component in mixtures of street drugs. Such mixtures almost anyone can afford, but the very quality of these drugs has become extremely low, because it does not sell the pure substance, but is mixed with various medications. According to research Pantazia et al. the heroin mixture proportion of the heroin is very small so a lot of that mixture has only 3% of heroin, a large number of cases can be only 1% of pure heroin. Most of the time it replaces caffeine and paracetamol. According to the Risser et al. reason why acetaminophen component is present in these mixtures is because it can be purchased without a prescription, it is cheap, well tolerated by most people and shows no side effects. Conclusion: When we talk about illegal drugs, we must emphasize the fact that there is no quality control, or the composition of the drug. The composition of the drug purchased on the black market is still unknown to potential user. While reaching the final drug users it pass through many hands, and at each step something is added to increase earnings. Most often present additives or impurities in narcotic drugs that are added are caffeine, ephedrine, acetaminophen, acetylsalicylic acid (aspirin) and additives such as powders, cement and chalk. PMID:26635443

  9. Validation of an immunodiagnostic assay for detection of 13 Streptococcus pneumoniae serotype-specific polysaccharides in human urine.

    Science.gov (United States)

    Pride, Michael W; Huijts, Susanne M; Wu, Kangjian; Souza, Victor; Passador, Sherry; Tinder, Chunyan; Song, Esther; Elfassy, Arik; McNeil, Lisa; Menton, Ronald; French, Roger; Callahan, Janice; Webber, Chris; Gruber, William C; Bonten, Marc J M; Jansen, Kathrin U

    2012-08-01

    To improve the clinical diagnosis of pneumococcal infection in bacteremic and nonbacteremic community-acquired pneumonia (CAP), a Luminex technology-based multiplex urinary antigen detection (UAD) diagnostic assay was developed and validated. The UAD assay can simultaneously detect 13 different serotypes of Streptococcus pneumoniae by capturing serotype-specific S. pneumoniae polysaccharides (PnPSs) secreted in human urine. Assay specificity is achieved by capturing the polysaccharides with serotype-specific monoclonal antibodies (MAbs) on spectrally unique microspheres. Positivity for each serotype was based on positivity cutoff values calculated from a standard curve run on each assay plate together with positive- and negative-control urine samples. The assay is highly specific, since significant signals are detected only when each PnPS was paired with its homologous MAb-coated microspheres. Validation experiments demonstrated excellent accuracy and precision. The UAD assay and corresponding positivity cutoff values were clinically validated by assessing 776 urine specimens obtained from patients with X-ray-confirmed CAP. The UAD assay demonstrated 97% sensitivity and 100% specificity using samples obtained from patients with bacteremic, blood culture-positive CAP. Importantly, the UAD assay identified Streptococcus pneumoniae (13 serotypes) in a proportion of individuals with nonbacteremic CAP, a patient population for which the pneumococcal etiology of CAP was previously difficult to assess. Therefore, the UAD assay provides a specific, noninvasive, sensitive, and reproducible tool to support vaccine efficacy as well as epidemiological evaluation of pneumococcal disease, including CAP, in adults.

  10. Evaluation of the Procleix Ultrio Plus ID NAT assay for detection of HIV 1, HBV and HCV in blood donors

    Directory of Open Access Journals (Sweden)

    Raj Nath Makroo

    2015-01-01

    Full Text Available Introduction: The Procleix Ultrio Plusassay is a new-generation qualitative in vitro nucleic acid amplification test used to screen for human immunodeficiency virus type 1 (HIV-1 RNA, hepatitis C virus (HCV RNA and hepatitis B virus (HBV DNA in blood donors. This study was performed to compare the Procleix Ultrio assay with the new-generation Procleix Ultrio Plus Nucleic Acid Test (NAT assays. Materials and Methods: Ten thousand three hundred and two donor samples were run in parallel for ID NAT using the Procleix Ultrio and the Procleix Ultrio Plus assay. Simultaneously, enzyme-linked immunosorbent assay testing was performed on an EVOLIS Walk away System for HIV, HCV, HBsAg and anti-HBc. Reactive samples were confirmed using polymerase chain reaction. Results: In the 10,302 samples tested during the study period, we identified 15 NAT yields, and all these revealed HBV DNA in the discriminatory assays. Eight of these were exclusive yields from the Ultrio Plus assay and the remaining seven cases were determined as HBV NAT yield, both by the Procleix Ultrio as well as the Ultrio Plus assays, i.e. "Combined" yields. No HCV or HIV 1 yields were detected during the study period by either of two assays. Conclusion: With an overall yield rate of 1 in 687 and an exclusive yield rate of 1 in 1287, the Procleix Ultrio Plus assay proved to be highly sensitive in detecting occult HBV infections.

  11. Evaluation of a novel PCR-based diagnostic assay for detection of Mycobacterium tuberculosis in sputum samples.

    Science.gov (United States)

    Maher, M; Glennon, M; Martinazzo, G; Turchetti, E; Marcolini, S; Smith, T; Dawson, M T

    1996-01-01

    We report on a PCR-based assay we have developed for the detection of Mycobacterium tuberculosis in sputum samples. One hundred sputum specimens, which included 34 culture-positive and 66 culture-negative specimens, were evaluated with this system. Of the 34 culture-positive specimens, 31 were PCR positive, and 60 of the culture-negative specimens were PCR negative. An internal standard has been included in the assay system to monitor PCR inhibition and to confirm the reliability of the PCR assay. PMID:8862607

  12. Diagnosis and classification of von Willebrand disease: a review of the differential utility of various functional von Willebrand factor assays.

    Science.gov (United States)

    Favaloro, Emmanuel J

    2011-10-01

    von Willebrand disease (VWD) is considered to be the most common inherited bleeding disorder. VWD is diagnosed following a clinical and physical review, with personal and familial evidence of (primarily mucocutaneous) bleeding, and confirmed by laboratory testing. The latter typically entails initial plasma testing of factor VIII coagulant, von Willebrand factor (VWF) protein ('antigen') and VWF function which has classically been assessed using the ristocetin cofactor (VWF:RCo) assay. More recent attention has focussed on other functional VWF assays, such as collagen binding and so-called 'VWF activity' assays, as possible replacements to the VWF:RCo, or as supplementary tests of VWF 'function'. Additional laboratory testing can comprise a battery of confirmatory and VWD-type assisting assays, including VWF:multimer and von Willebrand factor VIII binding. This review aims to update knowledge of current VWD diagnostics with a particular emphasis on 'functional' VWF assays.

  13. Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers.

    Science.gov (United States)

    Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J; Iqbal, Nayyer

    2015-01-01

    Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program.

  14. Increase of vitamin D assays prescriptions and associated factors: a population-based cohort study.

    Science.gov (United States)

    Caillet, Pascal; Goyer-Joos, Anne; Viprey, Marie; Schott, Anne-Marie

    2017-09-04

    A worldwide increase in the frequency of testing for serum 25-hydroxyvitamin D (25OHD) levels has been observed over the last years. Our aim was to measure the evolution in the number of vitamin D assays performed in France from 2008 to 2013 and to investigate some of the drivers that may explain this increase. Patients within the representative 1/97th sample of the French health insurance system reimbursement database (EGBS database) who had at least one 25OHD or 1-25(OH)2D assay between 2008 and 2013 were included. Trends over time in number of vitamin D assays were analysed globally and per year in a multivariable Poisson regression model with GEE. Among the 639,163 patients of the EGBS database, 118,509 (18.5%) had at least one vitamin D assay over the 6-year study period. Among the individuals tested, 52.1% had only one test. The number of vitamin D assays (25OHD or 1-25(OH)2D) increased 7.5-fold from 9,620 in 2008 to 81,641 in 2013. This study confirms the rapid and dramatic increase in vitamin D assays prescriptions and shows that this is mostly due to a global increase of the proportion of patients tested rather than an increase in repetition of tests in some individual patients.

  15. Development of an Immunochromatography Assay (QuickNavi-Ebola) to Detect Multiple Species of Ebolaviruses.

    Science.gov (United States)

    Yoshida, Reiko; Muramatsu, Shino; Akita, Hiroshi; Saito, Yuji; Kuwahara, Miwa; Kato, Daisuke; Changula, Katendi; Miyamoto, Hiroko; Kajihara, Masahiro; Manzoor, Rashid; Furuyama, Wakako; Marzi, Andrea; Feldmann, Heinz; Mweene, Aaron; Masumu, Justin; Kapeteshi, Jimmy; Muyembe-Tamfum, Jean-Jacques; Takada, Ayato

    2016-10-15

    The latest outbreak of Ebola virus disease (EVD) in West Africa has highlighted the urgent need for the development of rapid and reliable diagnostic assays. We used monoclonal antibodies specific to the ebolavirus nucleoprotein to develop an immunochromatography (IC) assay (QuickNavi-Ebola) for rapid diagnosis of EVD. The IC assay was first evaluated with tissue culture supernatants of infected Vero E6 cells and found to be capable of detecting 10(3)-10(4) focus-forming units/mL of ebolaviruses. Using serum samples from experimentally infected nonhuman primates, we confirmed that the assay could detect the viral antigen shortly after disease onset. It was also noted that multiple species of ebolaviruses could be detected by the IC assay. Owing to the simplicity of the assay procedure and absence of requirements for special equipment and training, QuickNavi-Ebola is expected to be a useful tool for rapid diagnosis of EVD. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  16. EDTA interference in electrochemiluminescence ACTH assay.

    Science.gov (United States)

    Toprak, Burak; Yalcin, Hulya; Arı, Elif; Colak, Ayfer

    2016-11-01

    Background As plasma is the recommended sample type for Roche adrenocorticotropic hormone (ACTH) assay, we evaluated the effect of EDTA concentration on Cobas ACTH assay. Methods Samples containing twofold and fourfold higher concentrations of EDTA were prepared by adding plasma to empty K2EDTA tubes and by making under-filled EDTA tubes. All measurements were performed with four replicates. Results Increased EDTA concentration resulted in a significant decrease in ACTH concentration. Fifty-per cent-filled EDTA tube showed 19% decrease in ACTH concentration and 25% filled EDTA tube showed 50% decrease in ACTH concentration. Conclusion We recommend that inadequately filled EDTA specimens should be rejected when using Cobas ACTH assay.

  17. Comet assay on tetraploid yeast cells

    DEFF Research Database (Denmark)

    Rank, Jette; Syberg, Kristian; Jensen, Klara

    2009-01-01

    Tetraploid yeast cells (Saccharomyces cerevisiae) were used in the comet assay with the intention of developing a new, fast and easy assay for detecting environmental genotoxic agents without using higher organisms. Two DNA-damaging chemicals, H2O2 and acrylamide, together with wastewater from...... three municipal treatment plants were tested for their effect on the yeast-cell DNA. The main problem with using yeast in the comet assay is the necessity to degrade the cell wall. This was achieved by using Zymolase 100 T twice during the procedure, since Zymolase 20 T did not open the cell wall....... Analytical problems that arose due to the small amount of DNA in the yeast nuclei in haploid and diploid cells, which contain 13 Mbp and 26 Mbp DNA per cell, respectively, were solved by using tetraploid yeast cells (52 Mbp) instead. DNA damage was shown after exposure to H2O2 and acrylamide. The lowest dose...

  18. Fungicide resistance assays for fungal plant pathogens.

    Science.gov (United States)

    Secor, Gary A; Rivera, Viviana V

    2012-01-01

    Fungicide resistance assays are useful to determine if a fungal pathogen has developed resistance to a fungicide used to manage the disease it causes. Laboratory assays are used to determine loss of sensitivity, or resistance, to a fungicide and can explain fungicide failures and for developing successful fungicide recommendations in the field. Laboratory assays for fungicide resistance are conducted by measuring reductions in growth or spore germination of fungi in the presence of fungicide, or by molecular procedures. This chapter describes two techniques for measuring fungicide resistance, using the sugarbeet leaf spot fungus Cercospora beticola as a model for the protocol. Two procedures are described for fungicides from two different classes; growth reduction for triazole (sterol demethylation inhibitor; DMI) fungicides, and inhibition of spore germination for quinone outside inhibitor (QoI) fungicides.

  19. N. Sarkozy confirms the continued operation of the Fessenheim plant; N. Sarkozy confirme la poursuite de l'exploitation de la centrale de Fessenheim

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    2012-01-15

    In january 2012, the French authority for nuclear safety (ASN) assured that all the reactors operating in France are safe, including the oldest plant: Fessenheim. President Sarkozy has confirmed the decision not to decommission the Fessenheim plant. The socialist candidate F. Hollande has promised to stop Fessenheim plant and to decrease the contribution of nuclear energy in the production of electricity from 75% to 50% by 2025 if he is elected. (A.C.)

  20. Detection of Eperythrozoon wenyoni by PCR assay

    Institute of Scientific and Technical Information of China (English)

    Jian WANG; Yutao ZHU; Jianhua QIN; Fumei ZHANG; Yuelan ZHAO

    2009-01-01

    The objective of this research was to develop a detection method for Eperythrozoon wenyoni infection using polymerase chain reaction (PCR) assay technique. A pair of primers was designed and synthesized according to the conservative sequence 16S rRNA. The PCR assay was performed with the primers. A 985-bp fragment was amplified by using PCR. The amplified fragments with the expected size were identified by EcoR I restriction digestion. The crossing-reaction, specific-reaction and duplicate-reaction indicated that the PCR method is a specific, sensitive, fast and effective method for diagnosing E. Wenyoni infection at group level.

  1. Instructions for Uploading Data to the Assay Portal - Instructions for Uploading Data to the Assay Portal

    Science.gov (United States)

    This document provides instructions for configuring and uploading data files to the CPTAC Assay Portal. It is divided into sections, with an overview checklist provided at the end. If help is needed at any stage of the process, please use the support page: https://assays.cancer.gov/support/

  2. A focus reduction neutralization assay for hepatitis C virus neutralizing antibodies

    Directory of Open Access Journals (Sweden)

    Wychowski Czeslaw

    2007-03-01

    Full Text Available Abstract Background/Aim The role of humoral immunity in hepatitis C virus (HCV infection is poorly understood. Nevertheless, there is increasing interest in characterizing the neutralizing antibodies in the serum of HCV-infected patients. Focus reduction assays have been widely used to evaluate neutralizing antibody responses against a range of non-cytopathic viruses. Based on the recent development of a HCV cell culture system using the genotype 2 JFH-1-strain, we developed a focus reduction assay for HCV-neutralizing antibodies. Methods The focus reduction assay was based on a standard microneutralization assay in which immunostained foci on tissue culture plates are counted. The neutralizing anti-HCV antibodies titers of purified serum immunoglobulin samples from seventy-seven individuals were determined using a 50% focus reduction neutralization assay. Each titer was determined as the log value of the reciprocal antibody dilution that reduced the number of viral foci by 50%. IgG antibodies were first purified from each serum in order to avoid the facilitating effect of HDL on HCV entry. Results The assay's cut-off using an ELISA and RNA HCV-negative samples was found to be 1.25 log, corresponding to a dilution of 1:18. The assay was compared with a commercial HCV ELISA and exhibited specificity and sensitivity values of 100% and 96.5%, respectively, and good reproducibility (with intra-assay and inter-assay coefficients of variation of 6.7% and 12.6%, respectively. The assay did not show any cross-reactivity with anti-HIV, anti-HBs or heterophile antibody-positive samples. The neutralizing antibodies titers were 2.13 log (1:134 for homologous samples from HCV genotype 2 infected patients harboring the same genotype as JFH-1 and 1.93 log (1:85 for heterologous samples from patients infected by genotypes other than type 2. These results confirm the presence of broadly cross-neutralizing antibodies already reported using the HCV pseudoparticles

  3. Added value of PCR-testing for confirmation of invasive meningococcal disease in England.

    Science.gov (United States)

    Heinsbroek, Ellen; Ladhani, Shamez; Gray, Steve; Guiver, Malcolm; Kaczmarski, Ed; Borrow, Ray; Ramsay, Mary

    2013-11-01

    In England, national guidance recommends that all patients with suspected invasive meningococcal disease (IMD) should be investigated by blood culture and polymerase chain reaction (PCR) testing. The Meningococcal Reference Unit (MRU) provides a national service for meningococcal species confirmation and PCR-testing of clinical samples. We performed a population-level assessment of the added value of PCR-testing for IMD to augment traditional culture confirmation. We analysed all PCR-samples and invasive meningococcal isolates received by MRU in 2009 and 2010. We assumed that all patients with PCR-samples submitted to MRU also had blood cultures performed and that positive blood cultures were referred to MRU. We confirmed this assertion by case ascertainment. In total, 25,379 specimens from 22,039 patients were submitted for PCR-testing and 1492 (6.8%) tested PCR-positive. MRU received 825 invasive meningococcal isolates; 393 confirmed by PCR and culture, 405 without a PCR-specimen submitted and 27 with a PCR-negative result. Thus, of 1924 reported IMD cases, 1099 (57.1%) were confirmed by PCR only, 432 (22.5%) by culture only and 393 (20.4%) by both tests. More than half of all confirmed IMD cases were confirmed by PCR only, indicating this service ensures high case ascertainment for national surveillance. Copyright © 2013 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  4. [Improvement of sensitivity in the second generation HCV core antigen assay by a novel concentration method using polyethylene glycol (PEG)].

    Science.gov (United States)

    Higashimoto, Makiko; Takahashi, Masahiko; Jokyu, Ritsuko; Syundou, Hiromi; Saito, Hidetsugu

    2007-11-01

    A HCV core antigen (Ag) detection assay system, Lumipulse Ortho HCV Ag has been developed and is commercially available in Japan with a lower detection level limit of 50 fmol/l, which is equivalent to 20 KIU/ml in PCR quantitative assay. HCV core Ag assay has an advantage of broader dynamic range compared with PCR assay, however the sensitivity is lower than PCR. We developed a novel HCV core Ag concentration method using polyethylene glycol (PEG), which can improve the sensitivity five times better than the original assay. The reproducibility was examined by consecutive five-time measurement of HCV patients serum, in which the results of HCV core Ag original and concentrated method were 56.8 +/- 8.1 fmol/l (mean +/- SD), CV 14.2% and 322.9 +/- 45.5 fmol/l CV 14.0%, respectively. The assay results of HCV negative samples in original HCV core Ag were all 0.1 fmol/l and the results were same even in the concentration method. The results of concentration method were 5.7 times higher than original assay, which was almost equal to theoretical rate as expected. The assay results of serially diluted samples were also as same as expected data in both original and concentration assay. We confirmed that the sensitivity of HCV core Ag concentration method had almost as same sensitivity as PCR high range assay in the competitive assay study using the serially monitored samples of five HCV patients during interferon therapy. A novel concentration method using PEG in HCV core Ag assay system seems to be useful for assessing and monitoring interferon treatment for HCV.

  5. Fluorescent Receptor Binding Assay for Detecting Ciguatoxins in Fish

    Science.gov (United States)

    Hardison, D. Ransom; Holland, William C.; McCall, Jennifer R.; Bourdelais, Andrea J.; Baden, Daniel G.; Darius, H. Taiana; Chinain, Mireille; Tester, Patricia A.; Shea, Damian; Flores Quintana, Harold A.; Morris, James A.; Litaker, R. Wayne

    2016-01-01

    Ciguatera fish poisoning is an illness suffered by > 50,000 people yearly after consumption of fish containing ciguatoxins (CTXs). One of the current methodologies to detect ciguatoxins in fish is a radiolabeled receptor binding assay (RBA(R)). However, the license requirements and regulations pertaining to radioisotope utilization can limit the applicability of the RBA(R) in certain labs. A fluorescence based receptor binding assay (RBA(F)) was developed to provide an alternative method of screening fish samples for CTXs in facilities not certified to use radioisotopes. The new assay is based on competition binding between CTXs and fluorescently labeled brevetoxin-2 (BODIPY®- PbTx-2) for voltage-gated sodium channel receptors at site 5 instead of a radiolabeled brevetoxin. Responses were linear in fish tissues spiked from 0.1 to 1.0 ppb with Pacific ciguatoxin-3C (P-CTX-3C) with a detection limit of 0.075 ppb. Carribean ciguatoxins were confirmed in Caribbean fish by LC-MS/MS analysis of the regional biomarker (C-CTX-1). Fish (N = 61) of six different species were screened using the RBA(F). Results for corresponding samples analyzed using the neuroblastoma cell-based assay (CBA-N2a) correlated well (R2 = 0.71) with those of the RBA(F), given the low levels of CTX present in positive fish. Data analyses also showed the resulting toxicity levels of P-CTX-3C equivalents determined by CBA-N2a were consistently lower than the RBA(F) affinities expressed as % binding equivalents, indicating that a given amount of toxin bound to the site 5 receptors translates into corresponding lower cytotoxicity. Consequently, the RBA(F), which takes approximately two hours to perform, provides a generous estimate relative to the widely used CBA-N2a which requires 2.5 days to complete. Other RBA(F) advantages include the long-term (> 5 years) stability of the BODIPY®- PbTx-2 and having similar results as the commonly used RBA(R). The RBA(F) is cost-effective, allows high sample

  6. Fluorescent Receptor Binding Assay for Detecting Ciguatoxins in Fish.

    Science.gov (United States)

    Hardison, D Ransom; Holland, William C; McCall, Jennifer R; Bourdelais, Andrea J; Baden, Daniel G; Darius, H Taiana; Chinain, Mireille; Tester, Patricia A; Shea, Damian; Quintana, Harold A Flores; Morris, James A; Litaker, R Wayne

    2016-01-01

    Ciguatera fish poisoning is an illness suffered by > 50,000 people yearly after consumption of fish containing ciguatoxins (CTXs). One of the current methodologies to detect ciguatoxins in fish is a radiolabeled receptor binding assay (RBA(R)). However, the license requirements and regulations pertaining to radioisotope utilization can limit the applicability of the RBA(R) in certain labs. A fluorescence based receptor binding assay (RBA(F)) was developed to provide an alternative method of screening fish samples for CTXs in facilities not certified to use radioisotopes. The new assay is based on competition binding between CTXs and fluorescently labeled brevetoxin-2 (BODIPY®-PbTx-2) for voltage-gated sodium channel receptors at site 5 instead of a radiolabeled brevetoxin. Responses were linear in fish tissues spiked from 0.1 to 1.0 ppb with Pacific ciguatoxin-3C (P-CTX-3C) with a detection limit of 0.075 ppb. Carribean ciguatoxins were confirmed in Caribbean fish by LC-MS/MS analysis of the regional biomarker (C-CTX-1). Fish (N = 61) of six different species were screened using the RBA(F). Results for corresponding samples analyzed using the neuroblastoma cell-based assay (CBA-N2a) correlated well (R2 = 0.71) with those of the RBA(F), given the low levels of CTX present in positive fish. Data analyses also showed the resulting toxicity levels of P-CTX-3C equivalents determined by CBA-N2a were consistently lower than the RBA(F) affinities expressed as % binding equivalents, indicating that a given amount of toxin bound to the site 5 receptors translates into corresponding lower cytotoxicity. Consequently, the RBA(F), which takes approximately two hours to perform, provides a generous estimate relative to the widely used CBA-N2a which requires 2.5 days to complete. Other RBA(F) advantages include the long-term (> 5 years) stability of the BODIPY®-PbTx-2 and having similar results as the commonly used RBA(R). The RBA(F) is cost-effective, allows high sample

  7. Enzymatic assays for the diagnosis of bradykinin-dependent angioedema.

    Directory of Open Access Journals (Sweden)

    Federica Defendi

    Full Text Available BACKGROUND: The kinins (primarily bradykinin, BK represent the mediators responsible for local increase of vascular permeability in hereditary angioedema (HAE, HAE I-II associated with alterations of the SERPING1 gene and HAE with normal C1-Inhibitor function (HAE-nC1INH. Besides C1-Inhibitor function and concentration, no biological assay of kinin metabolism is actually available to help physicians for the diagnosis of angioedema (AE. We describe enzymatic tests on the plasma for diagnosis of BK-dependent AE. METHODS: The plasma amidase assays are performed using the Pro-Phe-Arg-p-nitroanilide peptide substrate to evaluate the spontaneous amidase activity and the proenzyme activation. We analyzed data of 872 patients presenting with BK-dependent AE or BK-unrelated diseases, compared to 303 controls. Anti-high MW kininogen (HK immunoblot was achieved to confirm HK cleavage in exemplary samples. Reproducibility, repeatability, limit of blank, limit of detection, precision, linearity and receiver operating characteristics (ROC were used to calculate the diagnostic performance of the assays. RESULTS: Spontaneous amidase activity was significantly increased in all BK-dependent AE, associated with the acute phase of disease in HAE-nC1INH, but preserved in BK-unrelated disorders. The increase of the amidase activity was associated to HK proteolysis, indicating its relevance to identify kininogenase activity. The oestrogens, known for precipitating AE episodes, were found as triggers of enzymatic activity. Calculations from ROC curves gave the optimum diagnostic cut-off for women (9.3 nmol⋅min(-1⋅mL(-1, area under curve [AUC] 92.1%, sensitivity 80.0%, and specificity 90.1% and for men (6.6 nmol·min(-1⋅mL(-1, AUC 91.0%, sensitivity 87.0% and specificity 81.2%. CONCLUSION: The amidase assay represents a diagnostic tool to help physicians in the decision to distinguish between BK-related and -unrelated AE.

  8. Validation of the Filovirus Plaque Assay for Use in Preclinical Studies.

    Science.gov (United States)

    Shurtleff, Amy C; Bloomfield, Holly A; Mort, Shannon; Orr, Steven A; Audet, Brian; Whitaker, Thomas; Richards, Michelle J; Bavari, Sina

    2016-04-21

    A plaque assay for quantitating filoviruses in virus stocks, prepared viral challenge inocula and samples from research animals has recently been fully characterized and standardized for use across multiple institutions performing Biosafety Level 4 (BSL-4) studies. After standardization studies were completed, Good Laboratory Practices (GLP)-compliant plaque assay method validation studies to demonstrate suitability for reliable and reproducible measurement of the Marburg Virus Angola (MARV) variant and Ebola Virus Kikwit (EBOV) variant commenced at the United States Army Medical Research Institute of Infectious Diseases (USAMRIID). The validation parameters tested included accuracy, precision, linearity, robustness, stability of the virus stocks and system suitability. The MARV and EBOV assays were confirmed to be accurate to ±0.5 log10 PFU/mL. Repeatability precision, intermediate precision and reproducibility precision were sufficient to return viral titers with a coefficient of variation (%CV) of ≤30%, deemed acceptable variation for a cell-based bioassay. Intraclass correlation statistical techniques for the evaluation of the assay's precision when the same plaques were quantitated by two analysts returned values passing the acceptance criteria, indicating high agreement between analysts. The assay was shown to be accurate and specific when run on Nonhuman Primates (NHP) serum and plasma samples diluted in plaque assay medium, with negligible matrix effects. Virus stocks demonstrated stability for freeze-thaw cycles typical of normal usage during assay retests. The results demonstrated that the EBOV and MARV plaque assays are accurate, precise and robust for filovirus titration in samples associated with the performance of GLP animal model studies.

  9. “The Prevalence of Confirmed Maltreatment Among American Children, 2004-2011”

    Science.gov (United States)

    Wildeman, Christopher; Emanuel, Natalia; Leventhal, John M.; Putnam-Hornstein, Emily; Waldfogel, Jane; Lee, Hedwig

    2016-01-01

    Importance Child maltreatment is a risk factor for poor health throughout the life course. Existing estimates of the proportion of the U.S. population maltreated during childhood are based on retrospective self-reports. Records of officially confirmed maltreatment have been used to produce annual rather than cumulative counts of maltreated individuals. Objective To estimate the proportion of U.S. children who are substantiated or indicated for maltreatment by Child Protective Services (referred to as confirmed maltreatment) by age 18. Design, Setting, and Participants The National Child Abuse and Neglect Data System (NCANDS) Child File includes information on all U.S. children with a confirmed report of maltreatment, totaling 5,689,900 children (2004-2011). We developed synthetic cohort life tables to estimate the cumulative prevalence of confirmed childhood maltreatment by age 18. Main Outcome Measure The cumulative prevalence of confirmed child maltreatment between birth and age 18 by race/ethnicity, sex, and year. Results At 2011 rates, 12.5% [95% CI: 12.5%, 12.6%] of U.S. children will experience a confirmed case of maltreatment by age 18. Girls have a higher cumulative prevalence than boys (13.0% [95% CI: 12.9%, 13.0%] vs. 12.0% [95% CI: 12.0%, 12.1%]). Black (20.9% [95% CI: 20.8%, 21.1%]), Native American (14.5% [95% CI: 14.2%, 14.9%]), and Hispanic (13.0% [95% CI: 12.9%, 13.1%]) children have higher prevalences than White (10.7% [95% CI: 10.6%, 10.8%]) or Asian/Pacific Islander (3.8% [95% CI: 3.7%, 3.8%]) children. The risk of maltreatment is highest in the first few years of life; 2.1% [95% CI: 2,1%, 2.1%] of children have confirmed maltreatment by age 1, and 5.8% [95% CI: 5.8%, 5.9%] have confirmed maltreatment by age 5. Estimates from 2011 were consistent with those from 2004-2010. Conclusions and Relevance Annual rates of confirmed child maltreatment dramatically understate the cumulative number of children confirmed as maltreated during childhood. Our

  10. Evaluation of Geno Type MTBDRplus Line Probe Assay for Early Detection of Drug Resistance in Tuberculous Meningitis Patients in India

    Directory of Open Access Journals (Sweden)

    Renu Gupta

    2015-01-01

    Full Text Available Background: Molecular methods which allow for rapid and reliable detection of drug resistance have yet not been sufficiently evaluated for timely management of patients with tuberculous meningitis. Aims: We aimed to evaluate Geno Type MTBDRplus line probe assay for early detection of drug resistance in Mycobacterium tuberculosis isolates and CSF samples of confirmed tuberculous meningitis patients. Settings and Design: This was a multicentric prospective study carried out from July 2011 to December 2013 in tertiary care hospitals of Delhi. Materials and Methods: The assay was performed on 89 M. tuberculosis isolates and 31 direct CSF samples from microbiologically confirmed tuberculous meningitis patients. The sensitivity and specificity of this assay was calculated in comparison to drug susceptibility testing by BACTEC MGIT 960 system. Results: The sensitivity, specificity for detection of resistance to Isoniazid was 93%, 97% and to Rifampicin was 80%, 98.8%, respectively by this assay in comparison with the phenotypic drug susceptibility testing. The line probe assay could detect M. tuberculosis in 55% of CSF samples from patients with microbiologically confirmed tuberculous meningitis. Only 5/89 isolates (5.6% were resistant to both Isoniazid and Rifampicin while 9/89 (10% isolates were additionally resistant to Isoniazid. Resistance to any of the drugs, namely Isoniazid, Rifampicin, Streptomycin or Ethambutol, was seen in 24.7% of strains. Conclusion: The line probe assay has a good sensitivity and specificity for detection of drug resistance to Isoniazid and Rifampicin in M. tuberculosis culture isolates. However, this assay has limited role in detection of M. tuberculosis and drug resistance from direct samples with confirmed diagnosis of tuberculous meningitis.

  11. Screening of Host Cell Proteins that Interact with Toxoplasma gondii ROP18 via Yeast Two-hybrid System%酵母双杂交筛选与弓形虫毒力因子ROP18相互作用的宿主蛋白

    Institute of Scientific and Technical Information of China (English)

    都建; 安然; 程里; 陈滢; 沈继龙

    2013-01-01

    目的 利用酵母双杂交方法,筛选与弓形虫毒力因子ROP18相互作用的宿主蛋白. 方法 RT-PCR扩增弓形虫RH株速殖子ROP18基因片段,扩增产物经双酶切后插入酵母双杂交诱饵载体pGBKT7中,将重组质粒导入酵母AH109菌株中,检测诱饵载体有无毒性和自激活作用,利用酵母双杂交系统从人胚胎脑cDNA文库中筛选与ROP18相互作用的宿主蛋白. 结果 构建了诱饵载体pGBKT7-ROP18,ROP18具有自激活功能.用ROP1825-251aa为诱饵,筛选获得一系列与ROP18相互作用的宿主蛋白:DNA损伤特异性结合蛋白1(DDB1)、torsin A相互作用蛋白1(TOR1AIP1)、整联蛋白β31 (integrinβ1)、溶质运载蛋白3(SLC3A2)、酪氨酸硫化转移酶2(TPST2)、Derl样域家族成员2 (DERL2)和OCIA结构域蛋白1(OCIAD1). 结论 通过酵母双杂交技术筛选出与弓形虫毒力因子ROP18相互作用的多种宿主蛋白.%Objective To screen the host cell proteins that can interact with Toxoplasma gondii ROP18 by using yeast two-hybrid system. Methods The ROP18 gene fragments were amplified by RT-PCR from mRNA of T. gondii RH strain. The product of RT-PCR was digested with double restriction enzyme and was subcloned into the bait vector pGBKT7. The recombinant plasmid was transferred into yeast AH109 strain. Its toxicity and the autonomous activating activity were tested. The human fetal brain cDNA library was screened with pGBKT7-ROP1825-25laa as the bait plasmid by yeast two-hybrid system. Results The bait was constructed and AH109/PGBKT7-ROP18 showed an autonomous activity. The yeast strain AH109/pGBKT7-ROP1825-251aa line was then mated with the Mate & PlateTM Human Fetal Brain cDNA library. Using the selection procedures, eight novel host cell proteins were obtained: damage-specific DNA binding protein 1 (DDB1), torsin A interacting protein 1 (TOR1AIP1), integrin beta 1, solute carrier family 3 (SLC3A2), tyrosylprotein sulfotransferase (TPST2), OCIA domain containing 1 (OCIAD1

  12. 酵母双杂交筛选胎肾上腺cDNA文库中HNP-1结合蛋白%SCREENING THE GENE SEQUENCES OF THE INTERACTION PROTEINS OF HNP-1 FROM HUMAN FETAL ADRENAL CDNA LIBRARY BY YEAST TWO HYBRID SYSTEM

    Institute of Scientific and Technical Information of China (English)

    杜润滋; 邓璐霞; 黄宁; 罗朝志

    2011-01-01

    [Objective] To screen proteins binding with α-defensin (HNP-1) mature peptide from placenta cDNA libraty by yeast two hybrid technique. [Methods] The cDNA fragment encoding HNP-1 mature peptide was amplified by polymera-sechain reaction (PCR) and constructed into pGBK-T7 vector as the bait plasmid in yeast two hybrid system 3. Subsequently , the RNA from fetal adrenal gland was obtained and then transformed into cDNA library using SMART technology. The fetal adrenal cDNA library was screened with pGBKT7-HNP-1 as bait plasmid by yeast-two hybrid system Matchmaker Lexa. Finally, the positive clone was obtained by PCR and then identified by sequence. Then the interaction between them was determined by GST pull down in vitro and coimmunoprecipitates experiments in vivo. [Results] Bait and cDNA library have been constructed successfully and transformed into yeast. Then the interaction protein was found-melanocortin 2 receptor (ACTHR), CCAAT-enhancer-binding proteins (C/EBP), Tramembrane trafficking protein (TMP21), low density lipoprotein receptor-related protein 6 (LRP6). Therefore, melanocortin 2 receptor (ACTH-R) was determined into the major subjects. And bands which can demonstrate the relationship between HNP-1 and ACTH-R was obtained in GST pull down and coimmunoprecipitates experiments. [Conclusion] ACTH-R can bind to HNP-1 we obtained from fetal adrenal cDNA library and it may play important roles in the function of HNP-1 mature peptide.%[目的]筛选胎肾上腺cDNA文库中与α防御素HNP-1成熟肽具有相互作用的蛋白分子.[方法]通过聚合酶链反应(PCR)成功获得HNP-1成熟肽基因插入酵母表达载体pGBK-T7中构建诱饵质粒,同时提取胎肾上腺RNA,SMART技术制备人胎肾上腺cDNA文库,并采用Matchmaker LexA酵母双杂交系统从胎肾上腺cDNA文库中筛选与HNP-1成熟肽相互作用的蛋白.最后通过PCR筛选获得阳性克隆并测序,而后经回转实验,GST pull down以及免疫共沉淀再次验证

  13. Differential detection of Human Papillomavirus genotypes and cervical intraepithelial neoplasia by four commercial assays

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Bonde, Jesper; Preisler, Sarah;

    2016-01-01

    Laboratories can nowadays choose from >100 Human Papillomavirus (HPV) assays for cervical screening. Our previous analysis based on the data from the Danish Horizon study, however, showed that four widely used assays, Hybrid Capture 2 (HC2), cobas, CLART and APTIMA, frequently do not detect...... the same HPV infections. Here, we determined the characteristics of the concordant (all four assays returning a positive HPV test result) and discordant samples (all other HPV-positive samples) in primary cervical screening at 30-65 years (n=2859) and in a concurrent referral population from the same...... catchment area (n=885). HPV testing followed the manufacturers' protocols. Women with abnormal cytology were managed according to the routine recommendations. Cytology-normal/HPV-positive women were invited for repeated testing in 18 months. Screening history and histologically confirmed cervical...

  14. Assay of tyrosol and hydroxytyrosol in olive oil by tandem mass spectrometry and isotope dilution method.

    Science.gov (United States)

    Mazzotti, Fabio; Benabdelkamel, Hicham; Di Donna, Leonardo; Maiuolo, Loredana; Napoli, Anna; Sindona, Giovanni

    2012-12-01

    Hydroxytyrosol and tyrosol, the strong antioxidant present in large amount in virgin olive oil have been assayed by LC-MS/MS under MRM condition and isotope dilution method, using d(2)-labelled internal standards obtained by simple synthetic procedures. The assay has been performed under MRM condition monitoring two transitions for each analyte to improve the specificity. This paper deals with a modern approach for assaying the content of this polyphenols in virgin olive oil down to a limit of a few hundreds of parts per billion. Tyrosol and hydroxytyrosol ranged from 10 to 47ppm and from 5 to 25ppm in commercial olive oil, respectively. The accuracy (98-107%) and analytical parameters values confirm the reliability of the proposed approach. The method can be extended to any natural matrices, including mill wastes, after a simple step of sample preparation.

  15. Drugs and brain death: drug assay perspectives.

    Science.gov (United States)

    Morris, R G

    1996-08-01

    The ability to make any meaningful interpretation of a drug assay result is very dependent upon a knowledge of the limitations of the method(s) used (sensitivity, specificity etc.), and the concentration that may be measured in plasma and its relationship to CNS effects. We need more information about 'critical' concentrations for each drug and sedation in the setting of the brain-injured patient before meaningful interpretation can be applied to such data. While the above discussion is critical of screen-type assays, the alternative specific assays are not easily provided for, as obviously the resourcing of laboratories to be able to deliver such specialized services for a range of therapeutic drugs, in addition to 'social' drugs or other toxins (e.g. glues, pesticides, solvents, environmental substances etc), becomes an increasingly complex issue in the current economic climate. Hence, the analytical laboratory can offer valuable support to the clinical team however, the interpretation of such results must be assessed in the light of many limitations of such assay methods and not seen as the 'gold standard' for assessment of brain function.

  16. Functionalized Nanofiber Meshes Enhance Immunosorbent Assays.

    Science.gov (United States)

    Hersey, Joseph S; Meller, Amit; Grinstaff, Mark W

    2015-12-01

    Three-dimensional substrates with high surface-to-volume ratios and subsequently large protein binding capacities are of interest for advanced immunosorbent assays utilizing integrated microfluidics and nanosensing elements. A library of bioactive and antifouling electrospun nanofiber substrates, which are composed of high-molecular-weight poly(oxanorbornene) derivatives, is described. Specifically, a set of copolymers are synthesized from three 7-oxanorbornene monomers to create a set of water insoluble copolymers with both biotin (bioactive) and triethylene glycol (TEG) (antifouling) functionality. Porous three-dimensional nanofiber meshes are electrospun from these copolymers with the ability to specifically bind streptavidin while minimizing the nonspecific binding of other proteins. Fluorescently labeled streptavidin is used to quantify the streptavidin binding capacity of each mesh type through confocal microscopy. A simplified enzyme-linked immunosorbent assay (ELISA) is presented to assess the protein binding capabilities and detection limits of these nanofiber meshes under both static conditions (26 h) and flow conditions (1 h) for a model target protein (i.e., mouse IgG) using a horseradish peroxidase (HRP) colorimetric assay. Bioactive and antifouling nanofiber meshes outperform traditional streptavidin-coated polystyrene plates under flow, validating their use in future advanced immunosorbent assays and their compatibility with microfluidic-based biosensors.

  17. Endoproteolytic activity assay in malting barley

    Directory of Open Access Journals (Sweden)

    Blanca Gómez Guerrero

    2013-12-01

    Full Text Available Hydrolysis of barley proteins into peptides and amino acids is one of the most important processes during barley germination.The degradation of the endosperm stored proteins facilitates water and enzyme movements, enhances modification, liberates starch granules and increases soluble amino nitrogen. Protease activity is the result of the activities of a mixture of exo- and endo-proteases. The barley proteins are initially solubilized by endo-proteases and the further by exo-proteases. Four classes of endo-proteases have been described: serine-proteases, cysteine-proteases, aspartic-proteases and metallo-proteases. The objective of this work was to develop a rapid and colorimetric enzymatic assay to determine the endo-proteolytic activity of the four endo-protease classes using two different substrates: azo-gelatin and azo-casein. Optimum conditions for the assays such as: pH,reaction time and temperature and absorbance scale were determined. Azo-gelatin presented several difficulties in standardizing an “in solution” assay. On the other hand, azo-casein allowed standardization of the assay for the four enzyme classes to produce consistent results. The endo-proteoteolytic method developed was applied to determine the endo-protease activity in barley, malt and wort.

  18. Comet assay on mice testicular cells

    DEFF Research Database (Denmark)

    Sharma, Anoop Kumar

    2015-01-01

    for germ cell mutagens (Speit et al., 2009). The in vivo Comet assay is considered a useful tool for investigating germ cell genotoxicity. In the present study DNA strand breaks in testicular cells of mice were investigated. Different classes of chemicals were tested in order to evaluate the sensitivity...

  19. In vitro solubility assays in drug discovery.

    Science.gov (United States)

    Kerns, Edward H; Di, Li; Carter, Guy T

    2008-11-01

    The solubility of a compound depends on its structure and solution conditions. Structure determines the lipophilicity, hydrogen bonding, molecular volume, crystal energy and ionizability, which determine solubility. Solution conditions are affected by pH, co-solvents, additives, ionic strength, time and temperature. Many drug discovery experiments are conducted under "kinetic" solubility conditions. In drug discovery, solubility has a major impact on bioassays, formulation for in vivo dosing, and intestinal absorption. A good goal for the solubility of drug discovery compounds is >60 ug/mL. Equilibrium solubility assays can be conducted in moderate throughput, by incubating excess solid with buffer and agitating for several days, prior to filtration and HPLC quantitation. Kinetic solubility assays are performed in high throughput with shorter incubation times and high throughput analyses using plate readers. The most frequently used of these are the nephelometric assay and direct UV assay, which begin by adding a small volume of DMSO stock solution of each test compound to buffer. In nephelometry, this solution is serially diluted across a microtitre plate and undissolved particles are detected via light scattering. In direct UV, undissolved particles are separated by filtration, after which the dissolved material is quantitated using UV absorption. Equilibrium solubility is useful for preformulation. Kinetic solubility is useful for rapid compound assessment, guiding optimization via structure modification, and diagnosing bioassays. It is often useful to customize solubility experiments using conditions that answer specific research questions of drug discovery teams, such as compound selection and vehicle development for pharmacology and PK studies.

  20. Benzodiazepine Synthesis and Rapid Toxicity Assay

    Science.gov (United States)

    Fletcher, James T.; Boriraj, Grit

    2010-01-01

    A second-year organic chemistry laboratory experiment to introduce students to general concepts of medicinal chemistry is described. Within a single three-hour time window, students experience the synthesis of a biologically active small molecule and the assaying of its biological toxicity. Benzodiazepine rings are commonly found in antidepressant…

  1. CONFIRMATION OF THE PRESENCE OF RIPARIA RIPARIA IN ITE WETLANDS, SOUTHWEST OF PERU

    Directory of Open Access Journals (Sweden)

    Vizcarra, Jhonson

    2011-01-01

    Full Text Available The presence of Riparia riparia (Linnaeus, 1758 in Ite Wetlands is confirmed. Two individuals were observed in January 2011. This record occurs 13 years after the first mention of its presence in these wetlands.

  2. Editorial Commentary: Radiographic Inclusion and Exclusion Diagnostic Criteria for Femoroacetabular Impingement Require Confirmation.

    Science.gov (United States)

    Lubowitz, James H

    2015-07-01

    Femoroacetabular impingement radiographic diagnosis is a hot topic because sensitivity and specificity, and intraobserver and interobserver observational consistency, require confirmation. As a result, hip arthroscopic surgeons must rely on expert clinical examination.

  3. Confirmed record of Monodactylus argenteus (Linnaeus, 1758 (Family Monodactylidae from Jubail, Saudi Arabia, Arabian Gulf

    Directory of Open Access Journals (Sweden)

    Jawad, L. A.

    2014-02-01

    Full Text Available The first record of M. argenteus from the Arabian Gulf coasts of Saudi Arabia is confirmed, based on a sample measuring 158 mm in SL. Morphometric and meristic data are provided for this specimen.

  4. A collective opinion formation model under Bayesian updating and confirmation bias

    CERN Document Server

    Nishi, Ryosuke

    2013-01-01

    We propose a collective opinion formation model with a so-called confirmation bias. The confirmation bias is a psychological effect with which, in the context of opinion formation, an individual in favor of an opinion is prone to misperceive new incoming information as supporting the current belief of the individual. Our model modifies a Bayesian decision-making model for single individuals (Rabin and Schrag, Q. J. Econ. 114, 37 (1999)) to the case of a well-mixed population of interacting individuals in the absence of the external input. We numerically simulate the model to show that all the agents eventually agree on one of the two opinions only when the confirmation bias is weak. Otherwise, the stochastic population dynamics ends up creating a disagreement configuration (also called polarization), particularly for large system sizes. A strong confirmation bias allows various final disagreement configurations with different fractions of the individuals in favor of the opposite opinions.

  5. Confirmation of endovenous placement of central catheter using the ultrasonographic "bubble test"

    Directory of Open Access Journals (Sweden)

    Ajit S Baviskar

    2015-01-01

    Full Text Available Insertion of central venous catheter (CVC is the most common procedure to be performed in Intensive Care Units. Addition of ultrasonographic guidance to this procedure, which was initially performed blindly, has improved safety of this procedure. Confirmation of endovenous placement of CVC though, is tricky, as methods for confirmation are either operator dependent, time-consuming or not available at bedside. Prospective observational study was carried out to study feasibility of use of sonobubble test to confirm the presence of CVC within central vein. After insertion of CVC in the internal jugular, subclavian or axillary vein, a 10 ml bolus of shaken saline microbubble is injected through port of CVC, and opacification of right atrium is observed in xiphoid view on ultrasonography. The Sonobubble test was helpful for dynamic confirmation of endovenous placement of CVC and prevented complications such as arterial puncture and cannulation. We recommend its use following CVC insertion.

  6. 78 FR 68713 - Listing of Color Additives Exempt From Certification; Spirulina Extract; Confirmation of...

    Science.gov (United States)

    2013-11-15

    ... final rule published August 13, 2013 (78 FR 49117), is confirmed as September 13, 2013. FOR FURTHER... the Federal Register of August 13, 2013 (78 FR 49117), we amended the color additive regulations...

  7. Miscarriage after sonographic confirmation of an ongoing pregnancy in women with moderate and severe obesity.

    LENUS (Irish Health Repository)

    O'Dwyer, Vicky

    2012-01-01

    To compare the incidence of spontaneous miscarriage in women with moderate to severe obesity to that in women with a normal BMI after sonographic confirmation of the foetal heart rate in the first trimester.

  8. Predictors of HIV/AIDS confirmation and differences by guardian status in HIV+ adolescents in Jamaica

    National Research Council Canada - National Science Library

    Pilgrim, N; Kershaw, T; Pierre, R B; Moore, J; Palmer, P; Davis, D; Christie, C D C

    2008-01-01

    ...) from September 1, 2002 to August 31, 2006 (2). To identify predictors of HIV/AIDS confirmation as well as factors associated or uniquely present in these adolescents by their guardian status. Seventy-two HIV...

  9. Towards Confirming Neural Circuit Inference from Population Calcium Imaging. NIPS Workshop on Connectivity Inference in Neuroimaging

    OpenAIRE

    NeuroData; Mishchenko, Y.; AM, Packer; TA, Machado; Yuste, R.; Paninski, L

    2015-01-01

    Vogelstein JT, Mishchenko Y, Packer AM, Machado TA, Yuste R, Paninski L. Towards Confirming Neural Circuit Inference from Population Calcium Imaging. NIPS Workshop on Connectivity Inference in Neuroimaging, 2009

  10. Multi-class determination and confirmation of antibiotic residues in honey using LC-MS/MS

    Science.gov (United States)

    A multi-class method was developed for the determination and confirmation in honey of tetracyclines (chlortetracycline, doxycycline, oxytetracycline, and tetracycline), fluoroquinolones (ciprofloxacin, danofloxacin, difloxacin, enrofloxacin, and sarafloxacin), macrolides (tylosin), lincosamides (lin...

  11. Dexamethasone and diclofenac confirmation by LC-MS-MS as herbal product adulterants

    Directory of Open Access Journals (Sweden)

    Lourdes Garza-Ocañas

    2013-09-01

    Full Text Available Objective. To confirm the presence of dexamethasone and diclofenac as adulterants of an herbal product. Materials and methods. For identificaction and confirmation of drugs a method of instrumental analysis by liquid chromatography coupled with high pressure tandem mass spectrometry was used. Results. The presence of dexamethasone and diclofenac was confirmed in samples of 11 bottles of Reumofan Plus obtained from patients and/or physicians. The methodology used, allowed separation of stereoisomers dexamethasone and betamethasone, the relative abundances of product ions 237.2 and 279.2 m / z spectrally differentiate the compounds. Conclusions. The presence of dexamethasone and diclofenac was confirmed in samples of a product marketed as “100% natural” obtained from patients and / or physicians in a period from January to December, 2011.

  12. Production and assay of forskolin antibodies

    Energy Technology Data Exchange (ETDEWEB)

    Ho, L.T.; Ho, R.J.

    1986-05-01

    Forskolin (Fo), a cardiovascular active diterpene of plant origin, has been widely used as a research tool in regulation of the catalytic activity of adenylate cyclase (AC). A linear relationship of Fo binding to plasma membrane with activation of AC has been reported. The present abstract describes the production and assay of Fo antibodies (AB). 7-0-Hemisuccinyl-7-deacetyl Fo, coupled to either human serum albumin or goat IgG, was injected into goats to elicit AB to Fo haptan. AB to Fo in antiserum or an isolated IgG fraction was tested by two assay methods, a radioimmunoassay using /sup 3/H-Fo as a tracer and a colorimetric enzyme-linked immunosorbent assay (ELISA) using horse radish peroxidase-rabbit anti goat IgG as indicator. The titers for Fo antiserum were 4000-10,000. In the defined assay condition, approximately 20-25% of the added /sup 3/H-Fo was found to bind to AB. The bound radioactivity was displaced by Fo-HSA or Fo-goat IgG or free unlabelled Fo ranging from 0.5-50 pmol/tube, or 5-500 nM. The IC/sub 50/ was approximately 8-10 pmol/tube or 80-100 nM. The binding of HRP-rabbit anti goat IgG in the ELISA was inhibited by proper Fo conjugate. The development of methods for production and assay for Fo AB may be useful in the study of mechanism of activation of AC by Fo and Fo-like compound.

  13. Development of a novel in vitro assay for the evaluation of integron DNA integrase activity

    Directory of Open Access Journals (Sweden)

    Fatemeh Tohidi

    2016-05-01

    Full Text Available Integrons play an important role in multidrug resistance. The integron platform codes for integrase (intI that is required for gene cassette integration through site-specific recombination. The recombination crossover occurs between the G and TT nucleotides in non-palindromic attI and palindromic attC sites. The aim of this study was to establish an efficient in vitro assay for integrase purification and activity detection. To this end, the intI gene was cloned into the pET-22b plasmid. Then, the resulting recombinant plasmid was transformed into Escherichia coli Origami™ strain. The recombinant protein expression was confirmed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE and western blot assays. The recombinant intI protein was purified by nickel–nitrilotriacetic acid (Ni–NTA affinity chromatography, and its activity was measured by a newly introduced assay. Briefly, specific primers for each side of attI and attC were used, thereby, a polymerase chain reaction would be performed, if a fused plasmid containing both attI and attC sites was created upon recombination. SDS-PAGE and western blotting confirmed the presence of a 38-kDa recombinant protein. Optimum conditions were established for the measurement of the integrase activity and a new model assay was conducted to analyse the recombination activity in vitro. Although the electrophoretic mobility shift assay is an efficient and reliable method, the newly introduced assay provided new or enhanced capability to determine the integrase activity, suggesting that there is no need for expensive and advanced equipment.

  14. Confirmation of a predicted lack of IgE binding to Cry3Bb1 from genetically modified (GM) crops.

    Science.gov (United States)

    Nakajima, Osamu; Koyano, Satoru; Akiyama, Hiroshi; Sawada, Jun-Ichi; Teshima, Reiko

    2010-04-01

    Some GM crops including MON863 corn and stack varieties contain Cry3Bb1 protein. Cry3Bb1 is very important from the standpoint of assessing the safety of GM crops. In this study Cry3Bb1 was assessed from the standpoint of possible binding to IgE from allergy patients. First, an ELISA that was improved in our laboratory was used to test serum samples from 13 corn allergy patients in the United States with recombinant Cry3Bb1 expressed in Escherichia coli, and serum samples from 55 patients in Japan with various food allergies were also assayed. Two samples from the Japanese allergy patients were suspected of being positive, but Western blotting analysis with purified Cry3Bb1 indicated that the binding between IgE and Cry3Bb1 was nonspecific. Ultimately, no specific binding between IgE and recombinant Cry3Bb1 was detected. Next, all proteins extracted from MON863 corn and non-GM corn were probed with IgE antibodies in serum samples from the corn allergy patients by Western blotting, but the staining patterns of MON863 and non-GM corn were similar, meaning that unintended allergic reactions to MON863 are unlikely to occur. Our study provides additional information that confirms the predicted lack of IgE binding to Cry3Bb1 in people with existing food allergies. Copyright 2009 Elsevier Inc. All rights reserved.

  15. Replication intermediate analysis confirms that chromosomal replication origin initiates from an unusual intergenic region in Caulobacter crescentus.

    Science.gov (United States)

    Brassinga, A K; Marczynski, G T

    2001-11-01

    The alpha-proteobacterium Caulobacter crescentus possesses a developmental cell cycle that restricts chromosome replication to a stalked cell type. The proposed C.crescentus chromosome replication origin (Cori) lies between hemE and RP001, an unusual intergenic region not previously associated with bacterial replication origins, although a similar genomic arrangement is also present at the putative replication origin in the related bacterium Rickettsia prowazekii. The cloned Cori supports autonomous plasmid replication selectively in the stalked cell type implying that replication of the entire chromosome also initiates between hemE and RP001. To confirm this location, we applied the 2-D (N/N) agarose gel electrophoresis technique to resolve and identify chromosome replication intermediates throughout a 30 kb region spanning Cori. Replication initiation in Cori was uniquely characterized by an 'origin bubble and Y-arc' pattern and this observation was supported by simple replication fork 'Y-arc' patterns that characterized the regions flanking Cori. These replication forks originated bi-directionally from within Cori as determined by the fork direction assay. Therefore, chromosomal replication initiates from the unusual hemE/RP001 intergenic region that we propose represents a new class of replication origins.

  16. KCNA5 gene is not confirmed as a systemic sclerosis-related pulmonary arterial hypertension genetic susceptibility factor

    Science.gov (United States)

    2012-01-01

    Introduction Potassium voltage-gated channel shaker-related subfamily member 5 (KCNA5) is implicated in vascular tone regulation, and its inhibition during hypoxia produces pulmonary vasoconstriction. Recently, a protective association of the KCNA5 locus with systemic sclerosis (SSc) patients with pulmonary arterial hypertension (PAH) was reported. Hence, the aim of this study was to replicate these findings in an independent multicenter Caucasian SSc cohort. Methods The 2,343 SSc cases (179 PAH positive, confirmed by right-heart catheterization) and 2,690 matched healthy controls from five European countries were included in this study. Rs10744676 single-nucleotide polymorphism (SNP) was genotyped by using a TaqMan SNP genotyping assay. Results Individual population analyses of the selected KCNA5 genetic variant did not show significant association with SSc or any of the defined subsets (for example, limited cutaneous SSc, diffuse cutaneous SSc, anti-centromere autoantibody positive and anti-topoisomerase autoantibody positive). Furthermore, pooled analyses revealed no significant evidence of association with the disease or any of the subsets, not even the PAH-positive group. The comparison of PAH-positive patients with PAH-negative patients showed no significant differences among patients. Conclusions Our data do not support an important role of KCNA5 as an SSc-susceptibility factor or as a PAH-development genetic marker for SSc patients. PMID:23270786

  17. Confirmed low prevalence of Listeria mastitis in she-camel milk delivers a safe, alternative milk for human consumption.

    Science.gov (United States)

    Osman, Kamelia M; Samir, Ahmed; Orabi, Ahmed; Zolnikov, Tara Rava

    2014-02-01

    She-camel milk is an alternative solution for people allergic to milk; unfortunately, potential harmful bacteria have not been tested in she-camel milk. Listeria monocytogenes is one harmful bacterium that causes adverse health effects if chronically or acutely ingested by humans. The purpose of this study was to estimate the prevalence, characterize the phenotypic, genetic characterization, virulence factors, and antibiopotential harmful bacteria resistance profile of Listeria isolated from the milk of she-camel. Udder milk samples were collected from 100 she-camels and screened for mastitis using the California mastitis test (46 healthy female camels, 24 subclinical mastitic animals and 30 clinical mastitic animals). Samples were then examined for the presence of pathogenic Listeria spp; if located, the isolation of Listeria was completed using the International Organization for Standards technique to test for pathogenicity. The isolates were subjected to PCR assay for virulence-associated genes. Listeria spp. were isolated from 4% of samples and only 1.0% was confirmed as L. monocytogenes. The results of this study provide evidence for the low prevalence of intramammary Listeria infection; additionally, this study concludes she-camel milk in healthy camels milked and harvested in proper hygienic conditions may be used as alternative milk for human consumption.

  18. Using the MMPB technique to confirm microcystin concentrations in water measured by ELISA and HPLC (UV, MS, MS/MS).

    Science.gov (United States)

    Foss, Amanda J; Aubel, Mark T

    2015-09-15

    Microcystins have been detected in raw and finished drinking water using a variety of techniques, including assays (immunoassay, phosphatase inhibition) and HPLC (UV, MS/(MS)). The principal challenge to microcystin analysis is accounting for the over 150 variants that have been described. A confirmatory individual variant HPLC analysis is prone to under-reporting total microcystins due to method specificity. One method that allows for total microcystin quantitation is the MMPB technique. In this study, water samples with native microcystins were oxidized to cleave the Adda moiety, common to all microcystin variants. LC-MS/MS analysis was conducted on the subsequent MMPB (3-methoxy-2-methyl-4-phenylbutyric acid) molecule and calibrated using a certified reference standard (microcystin-LR) and 4-phenylbutyric acid. Total microcystin concentrations from MMPB were compared to Adda ELISA and individual variant analyses (LC-UV, LC-MS/(MS)). Variants of microcystin, including [DAsp(3)]MC-RR, [Dha(7)]MC-RR, MC-RR, MC-YR, MC-LR, [DAsp(3)]MC-LR, [Dha(7)]MC-LR, MC-WR, MC-LA, and MC-LY were detected and quantified in samples. The individual variant analyses did not account for total microcystins present in samples, as indicated by ELISA and MMPB data. Results demonstrated the MMPB technique is a simple and valuable approach to confirm ELISA data when analyzing microcystins, with method detection limits of 0.05 μg L(-1) for total microcystins.

  19. Native Valve Endocarditis due to Corynebacterium striatum confirmed by 16S Ribosomal RNA Sequencing: A Case Report and Literature Review

    Science.gov (United States)

    2016-01-01

    Corynebacterium species are non-fermentous Gram-positive bacilli that are normal flora of human skin and mucous membranes and are commonly isolated in clinical specimens. Non-diphtheriae Corynebacterium are regarded as contaminants when found in blood culture. Currently, Corynebacterium striatum is considered one of the emerging nosocomial agents implicated in endocarditis and serious infections. We report a case of native-valve infective endocarditis caused by C. striatum, which was misidentified by automated identification system but identified accurately by 16S ribosomal RNA sequencing, in a 55-year-old male patient. The patient had two mobile vegetations on his mitral valve, both of which had high embolic risk. Through surgical valve replacement and an antibiotic regimen, the patient recovered completely. In unusual clinical scenarios, C. striatum should not be simply dismissed as a contaminant when isolated from clinical specimens. The possibility of C. striatum infection should be considered even in an immunocompetent patient, and we suggest a genotypic assay, such as 16S rRNA sequencing, to confirm species identity. PMID:27659439

  20. Impedimetric toxicity assay in microfluidics using free and liposome-encapsulated anticancer drugs.

    Science.gov (United States)

    Caviglia, Claudia; Zór, Kinga; Montini, Lucia; Tilli, Valeria; Canepa, Silvia; Melander, Fredrik; Muhammad, Haseena B; Carminati, Marco; Ferrari, Giorgio; Raiteri, Roberto; Heiskanen, Arto; Andresen, Thomas L; Emnéus, Jenny

    2015-02-17

    In this work, we have developed a microfluidic cytotoxicity assay for a cell culture and detection platform, which enables both fluid handling and electrochemical/optical detection. The cytotoxic effect of anticancer drugs doxorubicin (DOX), oxaliplatin (OX) as well as OX-loaded liposomes, developed for targeted drug delivery, was evaluated using real-time impedance monitoring. The time-dependent effect of DOX on HeLa cells was monitored and found to have a delayed onset of cytotoxicity in microfluidics compared with static culture conditions based on data obtained in our previous study. The result of a fluorescent microscopic annexin V/propidium iodide assay, performed in microfluidics, confirmed the outcome of the real-time impedance assay. In addition, the response of HeLa cells to OX-induced cytotoxicity proved to be slower than toxicity induced by DOX. A difference in the time-dependent cytotoxic response of fibrosarcoma cells (HT1080) to free OX and OX-loaded liposomes was observed and attributed to incomplete degradation of the liposomes, which results in lower drug availability. The matrix metalloproteinase (MMP)-dependent release of OX from OX-loaded liposomes was also confirmed using laryngopharynx carcinoma cells (FaDu). The comparison and the observed differences between the cytotoxic effects under microfluidic and static conditions highlight the importance of comparative studies as basis for implementation of microfluidic cytotoxic assays.

  1. Laryngo-tracheal ultrasonography to confirm correct endotracheal tube and laryngeal mask airway placement

    OpenAIRE

    Wojtczak, Jacek A.; Davide Cattano

    2014-01-01

    Waveform capnography was recommended as the most reliable method to confirm correct endotracheal tube or laryngeal mask airway placements. However, capnography may be unreliable during cardiopulmonary resuscitation and during low flow states. It may lead to an unnecessary removal of a well-placed endotracheal tube, re-intubation and interruption of chest compressions. Real-time upper airway (laryngo-tracheal) ultrasonography to confirm correct endotracheal tube placement was sh...

  2. Epidemiology of laboratory confirmed measles virus cases in the southern nations of Ethiopia, 2007–2014

    OpenAIRE

    Getahun, Mekonen; Beyene, Berhane; Ademe, Ayesheshem; Teshome, Birke; Tefera, Mesfin; Afework, Aklog; HaileMariam, Yoseph; Assefa, Esete; Hailegiorgis, Yonas; Asha, Anjelo

    2017-01-01

    Background In Ethiopia, measles case-based surveillance was introduced in 2004 as one strategy for measles control by laboratory confirmation of suspected cases. In this article, epidemiological distribution of laboratory-confirmed measles cases were reported from the Southern Nation Nationalities and Peoples Region (SNNPR) of Ethiopia between 2007 and 2014, as the region is one of the highly measles affected areas in Ethiopia. Method A serum sample was collected from all measles suspected ca...

  3. Rapid confirmation of enzyme multiplied immunoassay technique (EMIT) cocaine positive urine samples by capillary gas-liquid chromatography/nitrogen phosphorus detection (GLC/NPD).

    Science.gov (United States)

    Verebey, K; DePace, A

    1989-01-01

    A rapid gas-liquid chromatographic (GLC) method was developed for the confirmation of benzoylecgonine (BE) positive urine samples screened by the enzyme multiplied immunoassay technique (EMIT) assay. The procedure is performed by solvent extraction of BE from 0.1 or 0.2 mL of urine, followed by an aqueous wash of the solvent and evaporation. The dried residue was derivatized with 50 microL of pentafluoropropionic anhydride and 25 microL of pentafluoropropropanol at 90 degrees C for 15 min. The derivatizing reagents were evaporated to dryness, and the derivatized BE, and cocaine if present, were reconstituted and injected into the gas chromatograph. The column was a 15-m by 0.2-mm fused silica capillary column, coated with 0.25 micron of DB-1, terminating in a nitrogen phosphorus detector (NPD). Cocaine and the pentafluoro BE derivatives retention times were 3.2 and 2.6 min, respectively. Nalorphine was used as reference or internal standard with a retention time of 4.78 min. The complete procedure can be performed in approximately 1.5 h. The EMIT cutoff between positive and negative urine samples is 300 ng/mL of BE. The lower limit of sensitivity of this method is 25 ng of BE extracted from urine. Validation studies resulted in confirmation of 101 out of 121 EMIT cocaine positive urine samples that could not be confirmed by thin-layer chromatography (TLC). This represents 84% confirmation efficiency.

  4. Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation

    Directory of Open Access Journals (Sweden)

    Alex M. Clark

    2014-08-01

    Full Text Available Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO project, using a hybrid of machine learning based on natural language processing, and a simplified user interface designed to help scientists curate their data with minimum effort. We have carried out this work based on the premise that pure machine learning is insufficiently accurate, and that expecting scientists to find the time to annotate their protocols manually is unrealistic. By combining these approaches, we have created an effective prototype for which annotation of bioassay text within the domain of the training set can be accomplished very quickly. Well-trained annotations require single-click user approval, while annotations from outside the training set domain can be identified using the search feature of a well-designed user interface, and subsequently used to improve the underlying models. By drastically reducing the time required for scientists to annotate their assays, we can realistically advocate for semantic annotation to become a standard part of the publication process. Once even a small proportion of the public body of bioassay data is marked up, bioinformatics researchers can begin to construct sophisticated and useful searching and analysis algorithms that will provide a diverse and powerful set of tools for drug discovery researchers.

  5. Livers provide a reliable matrix for real-time PCR confirmation of avian botulism.

    Science.gov (United States)

    Le Maréchal, Caroline; Ballan, Valentine; Rouxel, Sandra; Bayon-Auboyer, Marie-Hélène; Baudouard, Marie-Agnès; Morvan, Hervé; Houard, Emmanuelle; Poëzevara, Typhaine; Souillard, Rozenn; Woudstra, Cédric; Le Bouquin, Sophie; Fach, Patrick; Chemaly, Marianne

    2016-04-01

    Diagnosis of avian botulism is based on clinical symptoms, which are indicative but not specific. Laboratory investigations are therefore required to confirm clinical suspicions and establish a definitive diagnosis. Real-time PCR methods have recently been developed for the detection of Clostridium botulinum group III producing type C, D, C/D or D/C toxins. However, no study has been conducted to determine which types of matrices should be analyzed for laboratory confirmation using this approach. This study reports on the comparison of different matrices (pooled intestinal contents, livers, spleens and cloacal swabs) for PCR detection of C. botulinum. Between 2013 and 2015, 63 avian botulism suspicions were tested and 37 were confirmed as botulism. Analysis of livers using real-time PCR after enrichment led to the confirmation of 97% of the botulism outbreaks. Using the same method, spleens led to the confirmation of 90% of botulism outbreaks, cloacal swabs of 93% and pooled intestinal contents of 46%. Liver appears to be the most reliable type of matrix for laboratory confirmation using real-time PCR analysis.

  6. Genetic toxicity assessment: employing the best science for human safety evaluation. Part II: Performances of the in vitro micronucleus test compared to the mouse lymphoma assay and the in vitro chromosome aberration assay.

    Science.gov (United States)

    Lorge, Elisabeth; Lambert, Carine; Gervais, Véronique; Becourt-Lhote, Nathalie; Delongeas, Jean-Luc; Claude, Nancy

    2007-04-01

    The in vitro micronucleus test is commonly used in the early stages of pharmaceutical development as a predictive tool for the regulatory mouse lymphoma assay or in vitro chromosome aberration test. The accumulated data from this assay leads to the suggestion that it could be used as an alternative to the chromosome aberration test or the mouse lymphoma assay in the regulatory genotoxicity battery. In this paper, we present the results of the in vitro micronucleus test on L5178Y mouse lymphoma cells with 25 compounds from Servier research and have compared these results to those obtained in the genotoxicity regulatory battery. All the negative compounds were also negative in the in vitro micronucleus assay. Among the 14 positive compounds, two of them, positive in the mouse lymphoma assay, were found negative in the in vitro micronucleus test. However, this apparent discordance was likely to be due to cytotoxicity- or high concentration-related false positive responses in the mouse lymphoma assay. In addition, we confirmed that the in vitro micronucleus assay is useful for detecting aneugens, especially, when cells in metaphasis and multinucleated cells are also scored and when cells are allowed to recover after the long treatment. On this series of compounds, the in vitro micronucleus assay showed high sensitivity and possibly a better specificity than the mouse lymphoma assay. Thus, the in vitro micronucleus assay was shown to be at least as adequate as the mouse lymphoma assay or the in vitro chromosome aberration test to be used in the standard genotoxicity battery.

  7. Development of an Easy and High-Throughput Cell Assay System with a Culture Chip and an Assay Chip

    Science.gov (United States)

    Sugiura, Kanako; Kaji, Noritada; Okamoto, Yukihiro; Tokeshi, Manabu; Baba, Yoshinobu

    High throughput cell assay is significantly important in drug screening, assessment of toxicity etc. Cell assay with a microchip is one of the candidates for high throughput cell assay. However, reported cell assay system with the microchip requires expensive apparatus for refluxing medium and investigation of optimum experimental condition for steady data. For an inexpensive, easy and high throughput cell assay, we introduce a new cell assay system combined with a culture chip and an assay chip made of poly(dimethyl siloxane). Cell culture chips enabled cell to proliferate along the microchannel without refluxing medium and permitted to prepare cell patterning easily. Also, assay chips formed concentration gradient inside the chip and allowed the cell assay with different concentrations of drug at the same time. Thus, our developed cell assay system can overcome the problems of the present cell assay and would promote the drug discovery, assessment of toxicity etc.

  8. Laboratory confirmation of Buruli ulcer disease in Togo, 2007-2010.

    Directory of Open Access Journals (Sweden)

    Gisela Bretzel

    2011-07-01

    Full Text Available BACKGROUND: Since the early 1990s more than 1,800 patients with lesions suspicious for Buruli ulcer disease (BUD have been reported from Togo. However, less than five percent of these were laboratory confirmed. Since 2007, the Togolese National Buruli Ulcer Control Program has been supported by the German Leprosy and Tuberculosis Relief Association (DAHW. Collaboration with the Department for Infectious Diseases and Tropical Medicine (DITM, University Hospital, Munich, Germany, allowed IS2404 PCR analysis of diagnostic samples from patients with suspected BUD during a study period of three years. METHODOLOGY/PRINCIPAL FINDINGS: The DAHW integrated active BUD case finding in the existing network of TB/Leprosy Controllers and organized regular training and outreach activities to identify BUD cases at community level. Clinically suspected cases were referred to health facilities for diagnosis and treatment. Microscopy was carried out locally, external quality assurance (EQA at DITM. Diagnostic samples from 202 patients with suspected BUD were shipped to DITM, 109 BUD patients (54% were confirmed by PCR, 43 (29.9% by microscopy. All patients originated from Maritime Region. EQA for microscopy resulted in 62% concordant results. CONCLUSIONS/SIGNIFICANCE: This study presents a retrospective analysis of the first cohort of clinically suspected BUD cases from Togo subjected to systematic laboratory analysis over a period of three years and confirms the prevalence of BUD in Maritime Region. Intensified training in the field of case finding and sample collection increased the PCR case confirmation rate from initially less than 50% to 70%. With a PCR case confirmation rate of 54% for the entire study period the WHO standards (case confirmation rate ≥50% have been met. EQA for microscopy suggests the need for intensified supervision and training. In January 2011 the National Hygiene Institute, Lomé, has assumed the role of a National Reference Laboratory

  9. [Use of procalcitonine in intensive care units: comparison of semi quantitative PCT-Q Brahms assay with automated PCT-Kryptor assay].

    Science.gov (United States)

    Schuch, Géraldine; Duc-Marchand, Catherine; Venet, Cyrille; Mann, Hubert; Tixier, Anne; Bionda, Clara

    2011-01-01

    Procalcitonine (PCT) is recognized as a major and specific biomarker in diagnosis of bacterial infection. Used early in sepsis, it allows immediate administration of antibiotics and monitoring its effectiveness. Confronted on systemic inflammation response syndrom (SIRS), physicians must react quickly and effectively to evaluate bacterial infection and sepsis. The objective of this study was to compare analytical and clinical performances of semi-quantitative PCT-Q assay (Brahms) with quantitative and automated assay such on Kryptor (Brahms). Fifty blood samples of intensive care patients were compared. The analytical performance observed with PCT-Q assay is accurate: linear ratio kappa of 0.912 (95% CI 0.61, 0.97) and a good correlation between these techniques (p < 0.0001) (MedCalc software) were observed. Three discordances were observed and confirm the difficulties of reading for values close to 0.5 ng/mL. For these patients, PCT result showed its interest to discriminate local infection of a sepsis, to stop antibiotherapy with broad spectrum and to consolidate a therapeutic effectiveness in multi-visceral failure context. The semi-quantitative assay seems adapted for a fast and reliable evaluation of PCT in a general-purpose laboratory, not requiring neither dedicated analyzer, nor complex technicality but a control of the visual evaluation of results. It could be used for diagnosis of sepsis without monitoring precisely therapeutic follow-up.

  10. Development and validation of a multiplex add-on assay of biomarkers related to sepsis using xMAP technology

    DEFF Research Database (Denmark)

    Kofoed, Kristian; Vest Schneider, Uffe; Scheel, Troels

    2006-01-01

    %, respectively. Recoveries of suPAR, sTREM-1, and MIF calibrators were 108%, 88%, and 51%, respectively. In plasma collected from 10 patients with bacterial sepsis confirmed by blood culture, the assay detected significantly increased concentrations of all 8 analytes compared with healthy controls. CONCLUSIONS...

  11. A sensitive in vitro assay for the detection of residual viable rabies virus in inactivated rabies vaccines.

    Science.gov (United States)

    Takayama-Ito, Mutsuyo; Nakamichi, Kazuo; Kinoshita, Hitomi; Kakiuchi, Satsuki; Kurane, Ichiro; Saijo, Masayuki; Lim, Chang-Kweng

    2014-01-01

    Rabies is a viral disease transmitted through bites from rabid animals and can be prevented by vaccines. Clinically used rabies vaccines are prepared from inactivated rabies viruses grown in cell cultures or embryonated eggs. In Japan and across the world, tests that confirm complete inactivation, such as the in vivo suckling mouse assay, in which suckling mice are intracerebrally inoculated with vaccine products, are required for quality control. In this study, we developed a novel cell-based immunofluorescence assay that does not require mice for testing rabies vaccine inactivation for human use. The sensitivity of this cell-based in vitro assay was 5.7 times that of the in vivo suckling mouse assay, with a detection limit of one focus forming units per ml of test sample. This newly developed in vitro assay may replace the established in vivo suckling mouse assay for confirming viral vaccine inactivation. Copyright © 2013 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  12. Lump corrections for radioactive waste assay.

    Science.gov (United States)

    Miller, T J

    2009-09-01

    Previous studies have shown that automated radioactive waste assay techniques, such as segmented gamma scanner (SGS) and automated qualitative and quantitative (AQ2), have severely underestimated fissile material due to either the malfunction or absence of appropriate lump correction routines. This paper examines the application of manual techniques, such as Monte Carlo N particle (MCNP) and spectral non-destructive assay platform (SNAP) software, to lump corrections in plutonium (Pu), enriched uranium (EU) and depleted uranium (DU) waste streams. Excellent results have been obtained when comparing MCNP with SNAP and applying the SNAP lump correction routine to a range of simulated and typical wastes containing various Pu and EU lump sizes. It has been concluded that the need for lump corrections was relatively rare and usually apparent from abnormal gamma ray peak area ratios, since most AWE waste streams are only lightly shielded.

  13. Transient expression assays in tobacco protoplasts.

    Science.gov (United States)

    Vanden Bossche, Robin; Demedts, Brecht; Vanderhaeghen, Rudy; Goossens, Alain

    2013-01-01

    The sequence information generated through genome and transcriptome analysis from plant tissues has reached unprecedented sizes. Sequence homology-based annotations may provide hints for the possible function and roles of particular plant genes, but the functional annotation remains nonexistent or incomplete for many of them. To discover gene functions, transient expression assays are a valuable tool because they can be done more rapidly and at a higher scale than generating stably transformed tissues. Here, we describe a transient expression assay in protoplasts derived from suspension cells of tobacco (Nicotiana tabacum) for the study of the transactivation capacities of transcription factors. To enhance throughput and reproducibility, this method can be automated, allowing medium-throughput screening of interactions between large compendia of potential transcription factors and gene promoters.

  14. Identification of irradiated pepper with comet assay

    Energy Technology Data Exchange (ETDEWEB)

    Prieto Miranda, Enrique Fco.; Moreno Alvarez, Damaris L.; Carro Palacio, Sandra [Centro de Aplicaciones Tecnologicas y Desarrollo Nuclear. (CEADEN), Ciudad de La Habana (Cuba)]. E-mail: efprieto@ceaden.edu.cu; damaris@ceaden.edu.cu; Iglesia Enriquez, Isora [Instituto de Investigacion para la Industria Alimenticia (IIIA), Ciudad de La Habana (Cuba)

    2007-07-01

    The treatment of foods with ionizing radiations is a technological process utilized in order to increase the hygienic quality and the storage time of the foods. Several methods of detection of irradiated foods have been recommended. The comet assay of DNA is one fast and economical technique for the qualitative identification of irradiated foods. The objective of the present paper was to identify with the comet assay technique the modifications of the DNA molecule of irradiated pepper storage at environment and refrigeration temperatures and different post-irradiation times for different absorbed dose values, (0.1, 0.3 and 0.5 kGy). It was demonstrated that for the high absorbed dose values was observed a greater break into fragments of the DNA molecule, which shows the application of this technique for the identification of irradiated foods. (author)

  15. Posttranslational Modification Assays on Functional Protein Microarrays.

    Science.gov (United States)

    Neiswinger, Johnathan; Uzoma, Ijeoma; Cox, Eric; Rho, HeeSool; Jeong, Jun Seop; Zhu, Heng

    2016-10-03

    Protein microarray technology provides a straightforward yet powerful strategy for identifying substrates of posttranslational modifications (PTMs) and studying the specificity of the enzymes that catalyze these reactions. Protein microarray assays can be designed for individual enzymes or a mixture to establish connections between enzymes and substrates. Assays for four well-known PTMs-phosphorylation, acetylation, ubiquitylation, and SUMOylation-have been developed and are described here for use on functional protein microarrays. Phosphorylation and acetylation require a single enzyme and are easily adapted for use on an array. The ubiquitylation and SUMOylation cascades are very similar, and the combination of the E1, E2, and E3 enzymes plus ubiquitin or SUMO protein and ATP is sufficient for in vitro modification of many substrates.

  16. Comparative assay of Vipera ammodytes antivenom potency.

    Science.gov (United States)

    Capitanescu, Cristian; Macovei Oprescu, Anca Monica; Supeanu, Alexandru; Coculescu, Bogdan Ioan; Strambu, Victor; Macovei, Radu Alexandru; Manole, Gheorghe

    2016-12-01

    The finding of the most appropriate way to assess precisely the antivenom efficacy represents one of the major issues for antivenom standardization and success increasing of antivenom therapy. The efficacy of experimental Vipera ammodytes antivenom raised in sheep was determined using in vivo mouse lethality test, respectively, L-aminoacid oxidase, total proteinase and phospholipase A2 antienzymatic effectiveness. The values gained for the antivenom potency depend on the method of measure. So, some of the most toxic venom proteins own phospholipase A2 activity and provide the highest antivenom potency (lowest effective dose) values by antienzymatic assay method. This value is similar with total antiproteolytic antivenom potency value, but almost three times higher than value obtained by L-aminoacid oxidase (low toxic viper venom protein) antienzymatic assay method.

  17. An accurate assay for HCV based on real-time fluorescence detection of isothermal RNA amplification.

    Science.gov (United States)

    Wu, Xuping; Wang, Jianfang; Song, Jinyun; Li, Jiayan; Yang, Yongfeng

    2016-09-01

    Hepatitis C virus (HCV) is one of the common reasons of liver fibrosis and hepatocellular carcinoma (HCC). Early, rapid and accurate HCV RNA detection is important to prevent and control liver disease. A simultaneous amplification and testing (SAT) assay, which is based on isothermal amplification of RNA and real-time fluorescence detection, was designed to optimize routine HCV RNA detection. In this study, HCV RNA and an internal control (IC) were amplified and analyzed simultaneously by SAT assay and detection of fluorescence using routine real-time PCR equipment. The assay detected as few as 10 copies of HCV RNA transcripts. We tested 705 serum samples with SAT, among which 96.4% (680/705) showed consistent results compared with routine real-time PCR. About 92% (23/25) discordant samples were confirmed to be same results as SAT-HCV by using a second real-time PCR. The sensitivity and specificity of SAT-HCV assay were 99.6% (461/463) and 100% (242/242), respectively. In conclusion, the SAT assay is an accurate test with a high specificity and sensitivity which may increase the detection rate of HCV. It is therefore a promising tool to diagnose HCV infection.

  18. An improved Bathocuproine assay for accurate valence identification and quantification of copper bound by biomolecules.

    Science.gov (United States)

    Chen, Dinglong; Darabedian, Narek; Li, Zhiqiang; Kai, Tianhan; Jiang, Dianlu; Zhou, Feimeng

    2016-03-15

    Copper is an essential metal in all organisms. Reliably quantifying and identifying the copper content and oxidation state is crucial, since the information is essential to understanding protein structure and function. Chromophoric ligands, such as Bathocuproine (BC) and its water-soluble analog, Bathocuproinedisulfonic acid (BCS), preferentially bind Cu(I) over Cu(II), and therefore have been widely used as optical probes to determine the oxidation state of copper bound by biomolecules. However, the BCS assay is commonly misused, leading to erroneous conclusions regarding the role of copper in biological processes. By measuring the redox potential of Cu(II)-BCS2 and conducting UV-vis absorption measurements in the presence of oxidizable amino acids, the thermodynamic origin of the potential artifacts becomes evident. The BCS assay was improved by introducing a strong Cu(II) chelator EDTA prior to the addition of BCS to prevent interference that might arise from Cu(II) present in the sample. The strong Cu(II) chelator rids of all the potential errors inherent in the conventional BCS assay. Applications of the improved assay to peptides and protein containing oxidizable amino acid residues confirm that free Cu(II) no longer leads to artifacts, thereby resolving issues related to this persistently misused colorimetric assay of Cu(I) in biological systems.

  19. Evaluation of an improved bioluminescence assay for the detection of bacteria in soy milk.

    Science.gov (United States)

    Shinozaki, Yohei; Sato, Jun; Igarashi, Toshinori; Suzuki, Shigeya; Nishimoto, Kazunori; Harada, Yasuhiro

    2013-01-01

    Because soy milk is nutrient rich and nearly neutral in pH, it favors the growth of microbial contaminants. To ensure that soy milk meets food-safety standards, it must be pasteurized and have its sterility confirmed. ATP bioluminescence assay has become a widely accepted means of detecting food microorganisms. However, the high background bioluminescence intensity of soy milk has rendered it unsuitable for ATP analysis. Here, we tested the efficacy of an improved pre-treated bioluminescence assay on soy milk. By comparing background bioluminescence intensities obtained by the conventional and improved methods, we demonstrated that our method significantly reduces soy milk background bioluminescence. The dose-response curve of the assay was tested with serial dilutions of Bacillus sp. culture. An extremely strong log-linear relation between the bioluminescence intensity relative light units and colony formation units CFU/ml emerged for the tested strain. The detection limit of the assay was estimated as 5.2×10(3) CFU/ml from the dose-response curve and an imposed signal limit was three times the background level. The results showed that contaminated samples could be easily detected within 24 h using our improved bioluminescence assay.

  20. Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays.

    Science.gov (United States)

    Sipes, Nisha S; Martin, Matthew T; Kothiya, Parth; Reif, David M; Judson, Richard S; Richard, Ann M; Houck, Keith A; Dix, David J; Kavlock, Robert J; Knudsen, Thomas B

    2013-06-17

    Understanding potential health risks is a significant challenge due to the large numbers of diverse chemicals with poorly characterized exposures and mechanisms of toxicities. The present study analyzes 976 chemicals (including failed pharmaceuticals, alternative plasticizers, food additives, and pesticides) in Phases I and II of the U.S. EPA's ToxCast project across 331 cell-free enzymatic and ligand-binding high-throughput screening (HTS) assays. Half-maximal activity concentrations (AC50) were identified for 729 chemicals in 256 assays (7,135 chemical-assay pairs). Some of the most commonly affected assays were CYPs (CYP2C9 and CYP2C19), transporters (mitochondrial TSPO, norepinephrine, and dopaminergic), and GPCRs (aminergic). Heavy metals, surfactants, and dithiocarbamate fungicides showed promiscuous but distinctly different patterns of activity, whereas many of the pharmaceutical compounds showed promiscuous activity across GPCRs. Literature analysis confirmed >50% of the activities for the most potent chemical-assay pairs (54) but also revealed 10 missed interactions. Twenty-two chemicals with known estrogenic activity were correctly identified for the majority (77%), missing only the weaker interactions. In many cases, novel findings for previously unreported chemical-target combinations clustered with known chemical-target interactions. Results from this large inventory of chemical-biological interactions can inform read-across methods as well as link potential targets to molecular initiating events in adverse outcome pathways for diverse toxicities.