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Sample records for acid hybridization assays

  1. Nonenzymatic catalytic signal amplification for nucleic acid hybridization assays

    NASA Technical Reports Server (NTRS)

    Fan, Wenhong (Inventor); Cassell, Alan M. (Inventor); Han, Jie (Inventor)

    2006-01-01

    Devices, methods, and kits for amplifying the signal from hybridization reactions between nucleic acid probes and their cognate targets are presented. The devices provide partially-duplexed, immobilized probe complexes, spatially separate from and separately addressable from immobilized docking strands. Cognate target acts catalytically to transfer probe from the site of probe complex immobilization to the site of immobilized docking strand, generating a detectable signal. The methods and kits of the present invention may be used to identify the presence of cognate target in a fluid sample.

  2. Final Report Nucleic Acid System - Hybrid PCR and Multiplex Assay Project Phase 2

    SciTech Connect

    Koopman, R P; Langlois, R G; Nasarabadi, S; Benett, W J; Colston, B W; Johnson, D C; Brown, S B; Stratton, P L; Milanovich, F P

    2002-04-17

    This report covers phase 2 (year 2) of the Nucleic Acid System--Hybrid PCR and Multiplex Assay project. The objective of the project is to reduce to practice the detection and identification of biological warfare pathogens by the nucleic acid recognition technique of PCR (polymerase chain reaction) in a multiplex mode using flow cytometry. The Hybrid instrument consists of a flow-through PCR module capable of handling a multiplexed PCR assay, a hybridizing module capable of hybridizing multiplexed PCR amplicons and beads, and a flow cytometer module for bead-based identification, all controlled by a single computer. Multiplex immunoassay using bead-based Luminex flow cytometry is available, allowing rapid screening for many agents. PCR is highly specific and complements and verifies immunoassay. It can also be multiplexed and detection provided using the bead-based Luminex flow cytometer. This approach allows full access to the speed and 100-fold multiplex capability of flow cytometry for rapid screening as well as the accuracy and specificity of PCR. This project has two principal activities: (1) Design, build and test a prototype hybrid PCR/flow cytometer with the basic capabilities for rapid, broad spectrum detection and identification, and (2) Develop and evaluate multiplex flow analysis assay protocols and reagents for the simultaneous detection of PCR products. This project requires not only building operationally functional instrumentation but also developing the chemical assays for detection of priority pathogens. This involves development and evaluation of multiplex flow analysis assay protocols and reagents for the simultaneous detection of PCR products.

  3. Fabrication of Uniform DNA-Conjugated Hydrogel Microparticles via Replica Molding for Facile Nucleic Acid Hybridization Assays

    PubMed Central

    Lewis, Christina L.; Choi, Chang-Hyung; Lin, Yan; Lee, Chang-Soo; Yi, Hyunmin

    2010-01-01

    We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust nucleic acid hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of probe and target DNA, femtomole sensitivity, and sequence specificity. Combined these findings demonstrate a significant step toward simple, robust, and scalable procedures to manufacture highly uniform and high capacity hybridization assay particles in a well-controlled manner by exploiting many advantages that the batch processing-based RM technique offers. We envision that the results presented here may be readily applied to rapid and high throughput hybridization assays for a wide variety of applications in bioprocess monitoring, food safety, and biological threat detection. PMID:20527819

  4. Fabrication of uniform DNA-conjugated hydrogel microparticles via replica molding for facile nucleic acid hybridization assays.

    PubMed

    Lewis, Christina L; Choi, Chang-Hyung; Lin, Yan; Lee, Chang-Soo; Yi, Hyunmin

    2010-07-01

    We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust nucleic acid hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of the probe and target DNA, femtomole sensitivity, and sequence specificity. Combined, these findings demonstrate a significant step toward simple, robust, and scalable procedures to manufacture highly uniform and high-capacity hybridization assay particles in a well-controlled manner by exploiting many advantages that the batch processing-based RM technique offers. We envision that the results presented here may be readily applied to rapid and high-throughput hybridization assays for a wide variety of applications in bioprocess monitoring, food safety, and biological threat detection. PMID:20527819

  5. Nucleic Acid Sandwich Hybridization Assay with Quantum Dot-Induced Fluorescence Resonance Energy Transfer for Pathogen Detection

    PubMed Central

    Chou, Cheng-Chung; Huang, Yi-Han

    2012-01-01

    This paper reports a nucleic acid sandwich hybridization assay with a quantum dot (QD)-induced fluorescence resonance energy transfer (FRET) reporter system. Two label-free hemagglutinin H5 sequences (60-mer DNA and 630-nt cDNA fragment) of avian influenza viruses were used as the targets in this work. Two oligonucleotides (16 mers and 18 mers) that specifically recognize two separate but neighboring regions of the H5 sequences were served as the capturing and reporter probes, respectively. The capturing probe was conjugated to QD655 (donor) in a molar ratio of 10:1 (probe-to-QD), and the reporter probe was labeled with Alexa Fluor 660 dye (acceptor) during synthesis. The sandwich hybridization assay was done in a 20 μL transparent, adhesive frame-confined microchamber on a disposable, temperature-adjustable indium tin oxide (ITO) glass slide. The FRET signal in response to the sandwich hybridization was monitored by a homemade optical sensor comprising a single 400 nm UV light-emitting diode (LED), optical fibers, and a miniature 16-bit spectrophotometer. The target with a concentration ranging from 0.5 nM to 1 μM was successfully correlated with both QD emission decrease at 653 nm and dye emission increase at 690 nm. To sum up, this work is beneficial for developing a portable QD-based nucleic acid sensor for on-site pathogen detection. PMID:23211753

  6. Polydimethylsiloxane-Paper Hybrid Lateral Flow Assay for Highly Sensitive Point-of-Care Nucleic Acid Testing.

    PubMed

    Choi, Jane Ru; Liu, Zhi; Hu, Jie; Tang, Ruihua; Gong, Yan; Feng, Shangsheng; Ren, Hui; Wen, Ting; Yang, Hui; Qu, Zhiguo; Pingguan-Murphy, Belinda; Xu, Feng

    2016-06-21

    In nucleic acid testing (NAT), gold nanoparticle (AuNP)-based lateral flow assays (LFAs) have received significant attention due to their cost-effectiveness, rapidity, and the ability to produce a simple colorimetric readout. However, the poor sensitivity of AuNP-based LFAs limits its widespread applications. Even though various efforts have been made to improve the assay sensitivity, most methods are inappropriate for integration into LFA for sample-to-answer NAT at the point-of-care (POC), usually due to the complicated fabrication processes or incompatible chemicals used. To address this, we propose a novel strategy of integrating a simple fluidic control strategy into LFA. The strategy involves incorporating a piece of paper-based shunt and a polydimethylsiloxane (PDMS) barrier to the strip to achieve optimum fluidic delays for LFA signal enhancement, resulting in 10-fold signal enhancement over unmodified LFA. The phenomena of fluidic delay were also evaluated by mathematical simulation, through which we found the movement of fluid throughout the shunt and the tortuosity effects in the presence of PDMS barrier, which significantly affect the detection sensitivity. To demonstrate the potential of integrating this strategy into a LFA with sample-in-answer-out capability, we further applied this strategy into our prototype sample-to-answer LFA to sensitively detect the Hepatitis B virus (HBV) in clinical blood samples. The proposed strategy offers great potential for highly sensitive detection of various targets for wide application in the near future. PMID:27012657

  7. Nucleic acid detection assays

    DOEpatents

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann; Dahlberg, James E.

    2005-04-05

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  8. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes

    PubMed Central

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. PMID:26305575

  9. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes.

    PubMed

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. PMID:26305575

  10. DETECTION OF ANEUPLOIDY BY A MONOCHROMOSOMAL HYBRID CELL ASSAY

    EPA Science Inventory

    A short-term assay utilizing human/mouse monochromosomal hybrid cells to detect chemically-induced aneuploidy in mammalian cells is described. A single human chromosome transferred into mouse cells was used as a cytogenetic marker to quantitate abnormal chromosome segregation fol...

  11. Hybridization assay based on evanescent fluorescence excitation and collection

    NASA Astrophysics Data System (ADS)

    Sumner, James J.; Mmerole, Robert U.; Stratis-Cullum, Dimitra N.; Yi, Hyunmin; Bentley, William E.; Gillespie, James B.

    2003-08-01

    There is a great need for high throughput and sensitive sensors for genetic analysis. These sensors can be used for varied purposes from monitoring gene expression in organims to speciation of possible pathogens. Consequently, an instrument capable of these tasks would be a great benefit for food and water safety, medical diagnostics and defense of military and civilian populations from biological threats. This work examines the development of a hybridization-based biosensor using a novel tapered fiber optic rpobe. The immobilization of single-stranded, synthetic ologinucleotides utilizing aminoproplytriethoxysilane and glutaraldehyde was implemented on the fiber optic sensor. Hybridization takes place with a complementary analyte sequence followed by a fluorescent, labeled signaling probe to form a sandwich assay. Following hybridization, the fiber is interrogated with a diode laser source and the resulting fluorescence signal is detected using a miniature spectrometer.

  12. Hybridization behavior of mixed DNA/alkylthiol monolayers on gold: characterization by surface plasmon resonance and 32P radiometric assay.

    PubMed

    Gong, Ping; Lee, Chi-Ying; Gamble, Lara J; Castner, David G; Grainger, David W

    2006-05-15

    Nucleic acid assay from a complex biological milieu is attractive but currently difficult and far from routine. In this study, DNA hybridization from serum dilutions into mixed DNA/mercaptoundecanol (MCU) adlayers on gold was monitored by surface plasmon resonance (SPR). Immobilized DNA probe and hybridized target densities on these surfaces were quantified using 32P-radiometric assays as a function of MCU diluent exposure. SPR surface capture results correlated with radiometric analysis for hybridization performance, demonstrating a maximum DNA hybridization on DNA/MCU mixed adlayers. The maximum target surface capture produced by MCU addition to the DNA probe layer correlates with structural and conformational data on identical mixed DNA/MCU adlayers on gold derived from XPS, NEXAFS, and fluorescence intensity measurements reported in a related study (Lee, C.-Y.; Gong, P.; Harbers, G. M.; Grainger, D. W.; Castner, D. G.; Gamble, L. J. Anal. Chem. 2006, 78, 3316-3325.). MCU addition into the DNA adlayer on gold also improved surface resistance to both nonspecific DNA and serum protein adsorption. Target DNA hybridization from serum dilutions was monitored with SPR on the optimally mixed DNA/MCU adlayers. Both hybridization kinetics and efficiency were strongly affected by nonspecific protein adsorption from a complex milieu even at a minimal serum concentration (e.g., 1%). No target hybridization was detected in SPR assays from serum concentrations above 30%, indicating nonspecific protein adsorption interference of DNA capture and hybridization from complex milieu. Removal of nonsignal proteins from nucleic acid targets prior to assay represents a significant issue for direct sample-to-assay nucleic acid diagnostics from food, blood, tissue, PCR mixtures, and many other biologically complex sample formats. PMID:16689533

  13. Base-acid hybrid water electrolysis.

    PubMed

    Chen, Long; Dong, Xiaoli; Wang, Fei; Wang, Yonggang; Xia, Yongyao

    2016-02-21

    A base-acid hybrid electrolytic system with a low onset voltage of 0.78 V for water electrolysis was developed by using a ceramic Li-ion exchange membrane to separate the oxygen-evolving reaction (OER) in a basic electrolyte solution containing the Li-ion and hydrogen-evolving reaction (HER) in an acidic electrolyte solution. PMID:26804323

  14. Bicinchoninic acid (BCA) assay in low volume.

    PubMed

    Bainor, Anthony; Chang, Lyra; McQuade, Thomas J; Webb, Brian; Gestwicki, Jason E

    2011-03-15

    The BCA assay is a colorimetric method for estimating protein concentration. In 96-well plates, the relationship between protein content and absorbance is nearly linear over a wide range; however, performance is reduced in lower volume. To overcome this limitation, we performed the BCA assays in opaque, white 384-well plates. These plates emit fluorescence between 450-600 nm when excited at 430 nm; thus, their fluorescence is quenched by the BCA chromophore (λ(max) 562 nm). This arrangement allowed accurate determination of protein content using only 2 μL of sample. Moreover, soluble flourescein could replace the white plates, creating a homogenous format. PMID:21078286

  15. Multicenter evaluation of the Verigene Clostridium difficile nucleic acid assay.

    PubMed

    Carroll, Karen C; Buchan, Blake W; Tan, Sokha; Stamper, Paul D; Riebe, Katherine M; Pancholi, Preeti; Kelly, Cheryl; Rao, Arundhati; Fader, Robert; Cavagnolo, Robert; Watson, Wendy; Goering, Richard V; Trevino, Ernest A; Weissfeld, Alice S; Ledeboer, Nathan A

    2013-12-01

    The Verigene Clostridium difficile Nucleic Acid test (Verigene CDF test) (Nanosphere, Northbrook, IL) is a multiplex qualitative PCR assay that utilizes a nanoparticle-based array hybridization method to detect C. difficile tcdA and tcdB in fecal specimens. In addition, the assay detects binary toxin gene sequences and the single base pair deletion at nucleotide 117 (Δ 117) in tcdC to provide a presumptive identification of the epidemic strain 027/NAP1/BI (referred to here as ribotype 027). This study compared the Verigene CDF test with anaerobic direct and enriched toxigenic culture on stool specimens from symptomatic patients among five geographically diverse laboratories within the United States. The Verigene CDF test was performed according to the manufacturer's instructions, and the reference methods performed by a central laboratory included direct culture onto cycloserine cefoxitin fructose agar (CCFA) and enriched culture using cycloserine cefoxitin mannitol broth with taurocholate and lysozyme. Recovered isolates were identified as C. difficile using gas liquid chromatography and were tested for toxin using a cell culture cytotoxicity neutralization assay. Strains belonging to ribotype 027 were determined by PCR ribotyping and bidirectional sequencing for Δ 117 in tcdC. A total of 1,875 specimens were evaluable. Of these, 275 specimens (14.7%) were culture positive by either direct or enriched culture methods. Compared to direct culture alone, the overall sensitivity, specificity, positive predictive value, and negative predictive value for the Verigene CDF test were 98.7%, 87.5%, 42%, and 99.9%, respectively. Compared to combined direct and enriched culture results, the sensitivity, specificity, positive predictive value, and negative predictive values of the Verigene CDF test were 90.9%, 92.5%, 67.6%, and 98.3%, respectively. Of the 250 concordantly culture-positive specimens, 59 (23.6%) were flagged as "hypervirulent"; 53 were confirmed as ribotype

  16. Multicenter Evaluation of the Verigene Clostridium difficile Nucleic Acid Assay

    PubMed Central

    Buchan, Blake W.; Tan, Sokha; Stamper, Paul D.; Riebe, Katherine M.; Pancholi, Preeti; Kelly, Cheryl; Rao, Arundhati; Fader, Robert; Cavagnolo, Robert; Watson, Wendy; Goering, Richard V.; Trevino, Ernest A.; Weissfeld, Alice S.; Ledeboer, Nathan A.

    2013-01-01

    The Verigene Clostridium difficile Nucleic Acid test (Verigene CDF test) (Nanosphere, Northbrook, IL) is a multiplex qualitative PCR assay that utilizes a nanoparticle-based array hybridization method to detect C. difficile tcdA and tcdB in fecal specimens. In addition, the assay detects binary toxin gene sequences and the single base pair deletion at nucleotide 117 (Δ 117) in tcdC to provide a presumptive identification of the epidemic strain 027/NAP1/BI (referred to here as ribotype 027). This study compared the Verigene CDF test with anaerobic direct and enriched toxigenic culture on stool specimens from symptomatic patients among five geographically diverse laboratories within the United States. The Verigene CDF test was performed according to the manufacturer's instructions, and the reference methods performed by a central laboratory included direct culture onto cycloserine cefoxitin fructose agar (CCFA) and enriched culture using cycloserine cefoxitin mannitol broth with taurocholate and lysozyme. Recovered isolates were identified as C. difficile using gas liquid chromatography and were tested for toxin using a cell culture cytotoxicity neutralization assay. Strains belonging to ribotype 027 were determined by PCR ribotyping and bidirectional sequencing for Δ 117 in tcdC. A total of 1,875 specimens were evaluable. Of these, 275 specimens (14.7%) were culture positive by either direct or enriched culture methods. Compared to direct culture alone, the overall sensitivity, specificity, positive predictive value, and negative predictive value for the Verigene CDF test were 98.7%, 87.5%, 42%, and 99.9%, respectively. Compared to combined direct and enriched culture results, the sensitivity, specificity, positive predictive value, and negative predictive values of the Verigene CDF test were 90.9%, 92.5%, 67.6%, and 98.3%, respectively. Of the 250 concordantly culture-positive specimens, 59 (23.6%) were flagged as “hypervirulent”; 53 were confirmed as

  17. Kit for detecting nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2001-01-01

    A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the

  18. Simple Bulk Readout of Digital Nucleic Acid Quantification Assays.

    PubMed

    Morinishi, Leanna S; Blainey, Paul

    2015-01-01

    Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are still not routinely applied, due to the cost and specific equipment associated with commercially available methods. Here we present a simplified method for readout of digital droplet assays using a conventional real-time PCR instrument to measure bulk fluorescence of droplet-based digital assays. We characterize the performance of the bulk readout assay using synthetic droplet mixtures and a droplet digital multiple displacement amplification (MDA) assay. Quantitative MDA particularly benefits from a digital reaction format, but our new method applies to any digital assay. For established digital assay protocols such as digital PCR, this method serves to speed up and simplify assay readout. Our bulk readout methodology brings the advantages of partitioned assays without the need for specialized readout instrumentation. The principal limitations of the bulk readout methodology are reduced dynamic range compared with droplet-counting platforms and the need for a standard sample, although the requirements for this standard are less demanding than for a conventional real-time experiment. Quantitative whole genome amplification (WGA) is used to test for contaminants in WGA reactions and is the most sensitive way to detect the presence of DNA fragments with unknown sequences, giving the method great promise in diverse application areas including pharmaceutical quality control and astrobiology. PMID:26436576

  19. MONOCHROMOSOMAL HYBRID CELL ASSAY FOR EVALUATING THE GENOTOXICITY OF ENVIRONMENTAL CHEMICALS

    EPA Science Inventory

    The development and utilization of a monochromosomal hybrid cell assay for detecting aneuploidy and chromosomal aberrations are described. The monochromosomal hybrid cell lines were produced by a two-step process involving transfer of a marker bacterial gene to a human chromosome...

  20. 21 CFR 866.3225 - Enterovirus nucleic acid assay.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Enterovirus nucleic acid assay. 866.3225 Section 866.3225 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3225...

  1. 21 CFR 866.3225 - Enterovirus nucleic acid assay.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Enterovirus nucleic acid assay. 866.3225 Section 866.3225 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3225...

  2. 21 CFR 866.3225 - Enterovirus nucleic acid assay.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Enterovirus nucleic acid assay. 866.3225 Section 866.3225 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3225...

  3. 21 CFR 866.3225 - Enterovirus nucleic acid assay.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Enterovirus nucleic acid assay. 866.3225 Section 866.3225 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3225...

  4. 21 CFR 866.3225 - Enterovirus nucleic acid assay.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Enterovirus nucleic acid assay. 866.3225 Section 866.3225 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3225...

  5. Hybridization and sequencing of nucleic acids using base pair mismatches

    DOEpatents

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  6. DNA-DNA hybridization assay for detection of Salmonella spp. in foods.

    PubMed Central

    Fitts, R; Diamond, M; Hamilton, C; Neri, M

    1983-01-01

    We have developed a DNA-DNA hybridization test for the presence of Salmonella spp. in foods. This test requires an initial pre-enrichment of food samples in nutrient broth but does not require selective enrichment. Samples of food cultures are collected on membrane filters and assayed by molecular hybridization to labeled probes. The probes consist of DNA sequences which are unique to the genus Salmonella and are widely distributed in the genus. A diverse panel of foods was assayed successfully by this methodology. Images PMID:6360046

  7. Interference of N-hydroxysuccinimide with bicinchoninic acid protein assay.

    PubMed

    Vashist, Sandeep Kumar; Dixit, Chandra Kumar

    2011-07-29

    We report here substantial interference from N-hydroxysuccinimide (NHS) in the bicinchoninic acid (BCA) protein assay. NHS is one of the most commonly used crosslinking agents in bioanalytical sciences, which can lead to serious potential errors in the BCA protein assay based protein estimation if it is present in the protein analyte solution. It was identified to be a reducing substance, which interferes with the BCA protein assay by reducing Cu(2+) in the BCA working reagent. The absorbance peak and absorbance signal of NHS were very similar to those of bovine serum albumin (BSA), thereby indicating a similar BCA reaction mechanism for NHS and protein. However, the combined absorbance of NHS and BSA was not additive. The time-response measurements of the BCA protein assay showed consistent single-phase kinetics for NHS and gradually decreasing kinetics for BSA. The error in protein estimation due to the presence of NHS was counteracted effectively by plotting additional BCA standard curve for BSA with a fixed concentration of NHS. The difference between the absorbance values of BSA and BSA with a fixed NHS concentration provided the absorbance contributed by NHS, which was then subtracted from the total absorbance of analyte sample to determine the actual absorbance of protein in the analyte sample. PMID:21762678

  8. Development of a stable isotope dilution assay for tenuazonic acid.

    PubMed

    Asam, Stefan; Liu, Yang; Konitzer, Katharina; Rychlik, Michael

    2011-04-13

    A stable isotope dilution assay (SIDA) for the Alternaria mycotoxin tenuazonic acid was developed. Therefore, [(13)C(6),(15)N]-tenuazonic acid was synthesized from [(13)C(6),(15)N]-isoleucine by Dieckmann intramolecular cyclization after acetoacetylation with diketene. The synthesized [(13)C(6),(15)N]-tenuazonic acid was used as the internal standard for determination of tenuazonic acid in tomato products by liquid chromatography tandem mass spectrometry after derivatization with 2,4-dinitrophenylhydrazine. Method validation revealed a limit of detection of 0.1 μg/kg and a limit of quantitation of 0.3 μg/kg. Recovery was close to 100% in the range of 3-300 μg/kg. Determination of tenuazonic acid in two samples of different tomato ketchups (naturally contaminated) was achieved with a coefficient of variation of 2.3% and 4.7%. Different tomato products (n = 16) were analyzed for their content of tenuazonic acid using the developed SIDA. Values were between 15 and 195 μg/kg (tomato ketchup, n = 9), 363 and 909 μg/kg (tomato paste, n = 2), and 8 and 247 μg/kg (pureed tomatoes and comparable products, n = 5). PMID:21370870

  9. Nucleic acid in-situ hybridization detection of infectious agents

    NASA Astrophysics Data System (ADS)

    Thompson, Curtis T.

    2000-04-01

    Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

  10. A competitive enzyme hybridization assay for plasma determination of phosphodiester and phosphorothioate antisense oligonucleotides.

    PubMed Central

    Deverre, J R; Boutet, V; Boquet, D; Ezan, E; Grassi, J; Grognet, J M

    1997-01-01

    An enzyme competitive hybridization assay was developed and validated for determination of mouse plasma concentrations of a 15mer antisense phosphodiester oligodeoxyribonucleotide and of two phosphorothioate analogs. Assays were performed in 96-well microtiter plates. The phosphodiester sense sequence was covalently bound to the microwells. The 5'-biotinylated antisense sequence was used as tracer. The principle of the assay involves competitive hybridization of tracer and antisense nucleotide to the solid phase-immobilized sense oligonucleotide. Solid phase- bound tracer oligonucleotide was assayed after reaction with a streptavidin-acetylcholinesterase conjugate, using the colorimetric method of Ellman. As in competitive enzyme immunoassays, coloration was inversely related to the amount of analyte initially present in the sample. The limit of quantification was 900 pM for phosphodiester antisense oligonucleotide using a 100 microl volume of plasma without extraction. Cross-reactivity was negligible after a four base deletion in either the 3'or 5'position. The assay was simple and sensitive, suitable for in vitro screening of oligonucleotide hybridization potency in biological fluids and for measuring the plasma pharmacokinetics of phosphorothioate and phosphodiester sequences. PMID:9278477

  11. GENETIC ASSAY FOR ANEUPLOIDY: QUANTITATION OF CHROMOSOME LOSS USING A MOUSE/HUMAN MONOCHROMOSOMAL HYBRID CELL LINE (JOURNAL VERSION)

    EPA Science Inventory

    A genetic assay is described in which a mouse/human hybrid cell line R3-5 containing a single human chromosome (a monochromosomal hybrid) is used to detect chemically induced aneuploidy. The hybrid cells are deficient in hypoxanthine guanine phosphoribosyltransferase (HGPRT) and ...

  12. Comparison of amino acid digestibility of feedstuffs determined with the precision-fed cecectomized rooster assay and the standardized ileal amino acid digestibility assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate and compare amino acid digestibility of several feedstuffs using 2 commonly accepted methods: the precision-fed cecectomized rooster assay (PFR) and the standardized ileal amino acid assay (SIAAD). Six corn, 6 corn distillers dried grains with or without s...

  13. Bioluminescence regenerative cycle (BRC) system for nucleic acid quantification assays

    NASA Astrophysics Data System (ADS)

    Hassibi, Arjang; Lee, Thomas H.; Davis, Ronald W.; Pourmand, Nader

    2003-07-01

    A new label-free methodology for nucleic acid quantification has been developed where the number of pyrophosphate molecules (PPi) released during polymerization of the target nucleic acid is counted and correlated to DNA copy number. The technique uses the enzymatic complex of ATP-sulfurylase and firefly luciferase to generate photons from PPi. An enzymatic unity gain positive feedback is also implemented to regenerate the photon generation process and compensate any decay in light intensity by self regulation. Due to this positive feedback, the total number of photons generated by the bioluminescence regenerative cycle (BRC) can potentially be orders of magnitude higher than typical chemiluminescent processes. A system level kinetic model that incorporates the effects of contaminations and detector noise was used to show that the photon generation process is in fact steady and also proportional to the nucleic acid quantity. Here we show that BRC is capable of detecting quantities of DNA as low as 1 amol (10-18 mole) in 40μlit aqueous solutions, and this enzymatic assay has a controllable dynamic range of 5 orders of magnitude. The sensitivity of this technology, due to the excess number of photons generated by the regenerative cycle, is not constrained by detector performance, but rather by possible PPi or ATP (adenosine triphosphate) contamination, or background bioluminescence of the enzymatic complex.

  14. Competitive Assays of Label-Free DNA Hybridization with Single-Molecule Fluorescence Imaging Detection.

    PubMed

    Peterson, Eric M; Manhart, Michael W; Harris, Joel M

    2016-06-21

    Single-molecule imaging of fluorescently labeled biomolecules is a powerful technique for measuring association interactions; however, care must be taken to ensure that the fluorescent labels do not influence the system being probed. Label-free techniques are needed to understand biomolecule interactions free from the influence of an attached label, but these techniques often lack sensitivity and specificity. To solve these challenges, we have developed a competitive assay that uses single-molecule detection to track the population of unlabeled target single-stranded DNA (ssDNA) hybridized with probe DNA immobilized at a glass interface by detecting individual duplexes with a fluorescently labeled "tracer" ssDNA. By labeling a small fraction (<0.2%) of target molecules, the "tracer" DNA tracks the available probe DNA sites without significant competition with the unlabeled target population. Single-molecule fluorescence imaging is a good read-out scheme for competitive assays, as it is sufficiently sensitive to detect tracer DNA on substrates with relatively low densities of probe DNA, ∼10(-3) of a monolayer, so that steric interactions do not hinder DNA hybridization. Competitive assays are used to measure the association constant of complementary strand DNA hybridization of 9- and 10-base pair targets, where the tracer assay predicts the same association constant as a traditional displacement competitive assay. This methodology was used to compare the Ka of hybridization for identical DNA strands differing only by the presence of a fluorescent label tethered to the 5' end of the solution-phase target. The addition of the fluorescent label significantly stabilizes the DNA duplex by 3.6 kJmol(-1), adding more stability than an additional adenine-thymine base-pairing interaction, 2.7 kJmol(-1). This competitive tracer assay could be used to screen a number of labeled and unlabeled target DNA strands to measure the impact of fluorescent labeling on duplex stability

  15. Automatic on-chip RNA-DNA hybridization assay with integrated phase change microvalves

    NASA Astrophysics Data System (ADS)

    Weng, Xuan; Jiang, Hai; Wang, Junsheng; Chen, Shu; Cao, Honghe; Li, Dongqing

    2012-07-01

    An RNA-DNA hybridization assay microfluidic chip integrated with electrothermally actuated phase change microvalves for detecting pathogenic bacteria is presented in this paper. In order to realize the sequential loading and washing processes required in such an assay, gravity-based pressure-driven flow and phase-change microvalves were used in the microfluidic chip. Paraffin wax was used as the phase change material in the valves and thin film heaters were used to electrothermally actuate microvalves. Light absorption measured by a photodetector to determine the concentrations of the samples. The automatic control of the complete assay was implemented by a self-coded LabVIEW program. To examine the performance of this chip, Salmonella was used as a sample pathogen. Significantly, reduction in reagent/sample consumption (up to 20 folds) was achieved by this on-chip assay, compared with using the commercial test kit following the same protocol in conventional labs. The experimental results show that the quantitative detection can be obtained in approximately 26 min, and the detection limit is as low as 103 CFU ml-1. This RNA-DNA hybridization assay microfluidic chip shows an excellent potential in the development of a portable device for point-of-testing applications.

  16. Chemically modified nucleic acids as immunodetectable probes in hybridization experiments.

    PubMed Central

    Tchen, P; Fuchs, R P; Sage, E; Leng, M

    1984-01-01

    Guanine residues in nucleic acids can be modified by treatment with N-acetoxy-N-2-acetylaminofluorene and its 7-iodo derivative in an in vitro nonenzymatic reaction. The modified nucleic acids (ribo or deoxyribo, single or double stranded) are recognized by specific antibodies. They can be immunoprecipitated or used as probes in hybridization experiments and detected by immunochemical techniques. Images PMID:6374657

  17. Hybride magnetic nanostructure based on amino acids functionalized polypyrrole

    SciTech Connect

    Nan, Alexandrina Bunge, Alexander; Turcu, Rodica

    2015-12-23

    Conducting polypyrrole is especially promising for many commercial applications because of its unique optical, electric, thermal and mechanical properties. We report the synthesis and characterization of novel pyrrole functionalized monomers and core-shell hybrid nanostructures, consisting of a conjugated polymer layer (amino acids functionalized pyrrole copolymers) and a magnetic nanoparticle core. For functionalization of the pyrrole monomer we used several amino acids: tryptophan, leucine, phenylalanine, serine and tyrosine. These amino acids were linked via different types of hydrophobic linkers to the nitrogen atom of the pyrrole monomer. The magnetic core-shell hybrid nanostructures are characterized by various methods such as FTIR spectroscopy, transmission electron microscopy (TEM) and magnetic measurements.

  18. Hybride magnetic nanostructure based on amino acids functionalized polypyrrole

    NASA Astrophysics Data System (ADS)

    Nan, Alexandrina; Bunge, Alexander; Turcu, Rodica

    2015-12-01

    Conducting polypyrrole is especially promising for many commercial applications because of its unique optical, electric, thermal and mechanical properties. We report the synthesis and characterization of novel pyrrole functionalized monomers and core-shell hybrid nanostructures, consisting of a conjugated polymer layer (amino acids functionalized pyrrole copolymers) and a magnetic nanoparticle core. For functionalization of the pyrrole monomer we used several amino acids: tryptophan, leucine, phenylalanine, serine and tyrosine. These amino acids were linked via different types of hydrophobic linkers to the nitrogen atom of the pyrrole monomer. The magnetic core-shell hybrid nanostructures are characterized by various methods such as FTIR spectroscopy, transmission electron microscopy (TEM) and magnetic measurements.

  19. Chromogenic nitrophenolate-based substrates for light-driven hybrid P450 BM3 enzyme assay.

    PubMed

    Lam, Quan; Cortez, Alejandro; Nguyen, Thanh Truc; Kato, Mallory; Cheruzel, Lionel

    2016-05-01

    The incorporation of a p-nitrophenoxy moiety in substrates has enabled the development of colorimetric assays to rapidly screen for O-demethylation activity of P450 enzymes. For the light-driven hybrid P450 BM3 enzymes, where a Ru(II) photosensitizer powers the enzyme upon visible light irradiation, we have investigated a family of p-nitrophenoxy derivatives as useful chromogenic substrates compatible with the light-driven approach. The validation of this assay and its adaptability to a 96-well plate format will enable the screening of the next generation of hybrid P450 BM3 enzymes towards C-H bond functionalization of non-natural substrates. PMID:26712653

  20. Target-driven self-assembly of stacking deoxyribonucleic acids for highly sensitive assay of proteins.

    PubMed

    Cao, Ya; Chen, Weiwei; Han, Peng; Wang, Zhuxin; Li, Genxi

    2015-08-26

    In this paper, we report a new signal amplification strategy for highly sensitive and enzyme-free method to assay proteins based on the target-driven self-assembly of stacking deoxyribonucleic acids (DNA) on an electrode surface. In the sensing procedure, binding of target protein with the aptamer probe is used as a starting point for a scheduled cycle of DNA hairpin assembly, which consists of hybridization, displacement and target regeneration. Following numbers of the assembly repeats, a great deal of DNA duplexes can accordingly be formed on the electrode surface, and then switch on a succeeding propagation of self-assembled DNA concatemers that provide further signal enhancement. In this way, each target binding event can bring out two cascaded DNA self-assembly processes, namely, stacking DNA self-assembly, and therefore can be converted into remarkably intensified electrochemical signals by associating with silver nanoparticle-based readout. Consequently, highly sensitive detection of target proteins can be achieved. Using interferon-gamma as a model, the assay method displays a linear range from 1 to 500 pM with a detection limit of 0.57 pM, which is comparable or even superior to other reported amplified assays. Moreover, the proposed method eliminates the involvement of any enzymes, thereby enhancing the feasibility in clinical diagnosis. PMID:26347164

  1. Development of a model ribosomal RNA hybridization assay for the detection of Sarcocystis and other coccidia.

    PubMed Central

    Gajadhar, A A; Marquardt, W C; Blair, C D

    1992-01-01

    Two regions of the primary structure of the small subunit rRNA of Sarcocystis muris bradyzoites were compared with nucleotide sequences of S. gigantea, Toxoplasma gondii, Plasmodium berghei and Mus musculus and used to design genus- and species-specific probes for the detection and identification of coccidia. Total cellular RNA of purified S. muris, S. cruzi, T. gondii and Eimeria nieschulzi and coccidia-infected tissues of mouse, ox, sheep and pig, were assayed using twenty-base oligomers labelled with 32P. Hybridization occurred at temperatures ranging from 21 degrees C to 41 degrees C or 51 degrees C. One probe detected only S. muris and another successfully hybridized to several members of coccidia, including S. muris, S. cruzi, T. gondii and E. nieschulzi. One ng of total cellular RNA was sufficient to yield detectable hybrids in slot blot assays. The excellent sensitivity suggests that rRNA-based probes are capable of detecting individual parasites, and can assay low levels of coccidial infections not detectable by other methods. The results of this study show that it is possible to customize the specificity of rRNA-based probes for diagnostic, epidemiological or taxonomic purposes. Images Fig. 2. Fig. 3. PMID:1423056

  2. Paper-based fluorescence resonance energy transfer assay for directly detecting nucleic acids and proteins.

    PubMed

    Li, Hua; Fang, Xueen; Cao, Hongmei; Kong, Jilie

    2016-06-15

    Paper-based fluorescence resonance energy transfer assay (FRET) is gaining great interest in detecting macro-biological molecule. It is difficult to achieve conveniently and fast detection for macro-biological molecule. Herein, a graphene oxide (GO)-based paper chip (glass fiber) integrated with fluorescence labeled single-stranded DNA (ssDNA) for fast, inexpensive and direct detection of biological macromolecules (proteins and nucleic acids) has been developed. In this paper, we employed the Cy3/FAM-labeled ssDNA as the reporter and the GO as quencher and the original glass fiber paper as data acquisition substrates. The chip which was designed and fabricated by a cutting machine is a miniature biosensor that monitors fluorescence recovery from resonance energy transfer. The hybridization assays and fluorescence detection were all simplified, and the surface of the chip did not require immobilization or washing. A Nikon Eclipse was employed as excited resource and a commercial digital camera was employed for capturing digital images. This paper-based microfluidics chip has been applied in the detection of proteins and nucleic acids. The biosensing capability meets many potential requirements for disease diagnosis and biological analysis. PMID:26807518

  3. A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target

    PubMed Central

    Gillet, Benjamin; Montagnac, Gilles; Daniel, Isabelle; Hänni, Catherine

    2011-01-01

    In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics. PMID:21655320

  4. Detection and Identification of Entamoeba Species in Stool Samples by a Reverse Line Hybridization Assay

    PubMed Central

    Verweij, Jaco J.; Laeijendecker, Daphne; Brienen, Eric A. T.; van Lieshout, Lisette; Polderman, Anton M.

    2003-01-01

    Classically, detection of Entamoeba histolytica is performed by microscopic examination for characteristic cysts and/or trophozoites in fecal preparations. Differentiation of E. histolytica cysts and those of nonpathogenic amoebic species is made on the basis of the appearance and the size of the cysts. However, by classical means objective tools for confirmation and quality control do not exist. Therefore, a reverse line blot hybridization assay was developed to detect a variety of Entamoeba species and genetic variants known to infect humans. The assay was performed after amplification with general Entamoeba-specific primers. The assay could identify four genetic variants of Entamoeba polecki-like cysts as well as E. histolytica, Entamoeba dispar, Entamoeba hartmanni, Entamoeba moshkovskii and Entamoeba coli and even mixed infections in a range of controls and fecal samples. This technique can be used as an additional standard for diagnosis, epidemiology, and quality control for amoebic infections. PMID:14605136

  5. Detection and identification of entamoeba species in stool samples by a reverse line hybridization assay.

    PubMed

    Verweij, Jaco J; Laeijendecker, Daphne; Brienen, Eric A T; van Lieshout, Lisette; Polderman, Anton M

    2003-11-01

    Classically, detection of Entamoeba histolytica is performed by microscopic examination for characteristic cysts and/or trophozoites in fecal preparations. Differentiation of E. histolytica cysts and those of nonpathogenic amoebic species is made on the basis of the appearance and the size of the cysts. However, by classical means objective tools for confirmation and quality control do not exist. Therefore, a reverse line blot hybridization assay was developed to detect a variety of Entamoeba species and genetic variants known to infect humans. The assay was performed after amplification with general Entamoeba-specific primers. The assay could identify four genetic variants of Entamoeba polecki-like cysts as well as E. histolytica, Entamoeba dispar, Entamoeba hartmanni, Entamoeba moshkovskii and Entamoeba coli and even mixed infections in a range of controls and fecal samples. This technique can be used as an additional standard for diagnosis, epidemiology, and quality control for amoebic infections. PMID:14605136

  6. The theory of the deoxyribonucleic acid - ribonucleic acid hybridization reaction.

    PubMed Central

    Thomou, H; Katsanos, N A

    1976-01-01

    A general equation is derived describing data of DNA-RNA hybridization in the presence of a competing self-annealing reaction of RNA. The well known double-reciprocal relation and the Scatchard equation are shown to be limiting cases of this general equation. Some new hybridization data at various temperatures are presented and analysed by using the new equation. The results can only be explained if we assume that the behavior of DNA towards single RNA molecules is the same as that towards the annealed form, (RNA12. The variation of the equilibrium constant of the hybridization reaction with temperature is small, indicating a small heat of reaction. The maximum amount of hybridized RNA at equilibrium appears to be independent of temperature. PMID:1275887

  7. Multiplex PCR and Reverse Line Blot Hybridization Assay (mPCR/RLB)

    PubMed Central

    O'Sullivan, Matthew V. N.; Zhou, Fei; Sintchenko, Vitali; Kong, Fanrong; Gilbert, Gwendolyn L.

    2011-01-01

    Multiplex PCR/Reverse Line Blot Hybridization assay allows the detection of up to 43 molecular targets in 43 samples using one multiplex PCR reaction followed by probe hybridization on a nylon membrane, which is re-usable. Probes are 5' amine modified to allow fixation to the membrane. Primers are 5' biotin modified which allows detection of hybridized PCR products using streptavidin-peroxidase and a chemiluminescent substrate via photosensitive film. With low setup and consumable costs, this technique is inexpensive (approximately US$2 per sample), high throughput (multiple membranes can be processed simultaneously) and has a short turnaround time (approximately 10 hours). The technique can be utilized in a number of ways. Multiple probes can be designed to detect sequence variation within a single amplified product, or multiple products can be amplified simultaneously, with one (or more) probes used for subsequent detection. A combination of both approaches can also be used within a single assay. The ability to include multiple probes for a single target sequence makes the assay highly specific. Published applications of mPCR/RLB include detection of antibiotic resistance genes1,2, typing of methicillin-resistant Staphylococcus aureus3-5 and Salmonella sp6, molecular serotyping of Streptococcus pneumoniae7,8, Streptococcus agalactiae9 and enteroviruses10,11, identification of Mycobacterium sp12, detection of genital13-15 and respiratory tract16 and other17 pathogens and detection and identification of mollicutes18. However, the versatility of the technique means the applications are virtually limitless and not restricted to molecular analysis of micro-organisms. The five steps in mPCR/RLB are a) Primer and Probe design, b) DNA extraction and PCR amplification c) Preparation of the membrane, d) Hybridization and detection, and e) Regeneration of the Membrane. PMID:21847083

  8. Fluorescence In Situ Hybridization (FISH) Assays for Diagnosing Malaria in Endemic Areas

    PubMed Central

    Shah, Jyotsna; Mark, Olivia; Weltman, Helena; Barcelo, Nicolas; Lo, Wai; Wronska, Danuta; Kakkilaya, Srinivas; Rao, Aravinda; Bhat, Shalia T.; Sinha, Ruchi; Omar, Sabah; Moro, Manuel; Gilman, Robert H.; Harris, Nick

    2015-01-01

    Malaria is a responsible for approximately 600 thousand deaths worldwide every year. Appropriate and timely treatment of malaria can prevent deaths but is dependent on accurate and rapid diagnosis of the infection. Currently, microscopic examination of the Giemsa stained blood smears is the method of choice for diagnosing malaria. Although it has limited sensitivity and specificity in field conditions, it still remains the gold standard for the diagnosis of malaria. Here, we report the development of a fluorescence in situ hybridization (FISH) based method for detecting malaria infection in blood smears and describe the use of an LED light source that makes the method suitable for use in resource-limited malaria endemic countries. The Plasmodium Genus (P-Genus) FISH assay has a Plasmodium genus specific probe that detects all five species of Plasmodium known to cause the disease in humans. The P. falciparum (PF) FISH assay and P. vivax (PV) FISH assay detect and differentiate between P. falciparum and P. vivax respectively from other Plasmodium species. The FISH assays are more sensitive than Giemsa. The sensitivities of P-Genus, PF and PV FISH assays were found to be 98.2%, 94.5% and 98.3%, respectively compared to 89.9%, 83.3% and 87.9% for the detection of Plasmodium, P. falciparum and P. vivax by Giemsa staining respectively. PMID:26333092

  9. Fluorescence in situ hybridization in combination with the comet assay and micronucleus test in genetic toxicology

    PubMed Central

    2010-01-01

    Comet assay and micronucleus (MN) test are widely applied in genotoxicity testing and biomonitoring. While comet assay permits to measure direct DNA-strand breaking capacity of a tested agent MN test allows estimating the induced amount of chromosome and/or genome mutations. The potential of these two methods can be enhanced by the combination with fluorescence in situ hybridization (FISH) techniques. FISH plus comet assay allows the recognition of targets of DNA damage and repairing directly. FISH combined with MN test is able to characterize the occurrence of different chromosomes in MN and to identify potential chromosomal targets of mutagenic substances. Thus, combination of FISH with the comet assay or MN test proved to be promising techniques for evaluation of the distribution of DNA and chromosome damage in the entire genome of individual cells. FISH technique also permits to study comet and MN formation, necessary for correct application of these methods. This paper reviews the relevant literature on advantages and limitations of Comet-FISH and MN-FISH assays application in genetic toxicology. PMID:20840797

  10. Upconverting phosphors in a dual-parameter LRET-based hybridization assay.

    PubMed

    Rantanen, Terhi; Järvenpää, Marja-Leena; Vuojola, Johanna; Arppe, Riikka; Kuningas, Katri; Soukka, Tero

    2009-08-01

    Upconverting phosphors (UCPs) are lanthanide-doped sub-micrometer-sized particles, which produce multiple narrow and well-separated anti-Stokes emission bands at visible wavelengths under infrared excitation (980 nm). The advantageous features of UCPs were utilized to construct a dual-parameter, homogeneous sandwich hybridization assay based on a UCP donor and lanthanide resonance energy transfer (LRET). UCPs with two emission bands (540 nm and 653 nm) were exploited together with two appropriate fluorophores as acceptors. The energy transfer excited emissions of the acceptors were measured at 600 nm and 740 nm without any significant interference from each other. The autofluorescence limitation associated with conventional fluorescence was totally avoided as the measurements were carried out at shorter wavelength relative to the excitation. In the sandwich hybridization assay two different single-stranded target-oligonucleotide sequences were detected simultaneously and quantitatively with a dynamic range from 0.03 to 0.4 pmol (corresponding 0.35-5.4 nM). The UCPs enable multiplexed homogeneous LRET-based assay requiring only a single excitation wavelength, which simplifies the detection and extends the applicability of upconversion in bioanalytical measurements. PMID:20448942

  11. Standard in vitro assays for protein-nucleic acid interactions--gel shift assays for RNA and DNA binding.

    PubMed

    Mitchell, Sarah F; Lorsch, Jon R

    2014-01-01

    The characterization of protein-nucleic acid interactions is necessary for the study of a wide variety of biological processes. One straightforward and widely used approach to this problem is the electrophoretic mobility shift assay (EMSA), in which the binding of a nucleic acid to one or more proteins changes its mobility through a nondenaturing gel matrix. Usually, the mobility of the nucleic acid is reduced, but examples of increased mobility do exist. This type of assay can be used to investigate the affinity of the interaction between the protein and nucleic acid, the specificity of the interaction, the minimal binding site, and the kinetics of the interaction. One particular advantage of EMSA is the ability to analyze multiple proteins, or protein complexes, binding to nucleic acids. This assay is relatively quick and easy and utilizes equipment available in most laboratories; however, there are many variables that can only be determined empirically; therefore, optimization is necessary and can be highly dependent upon the system. The protocol described here is for the poly(A)-binding protein (PABP) binding to an unstructured RNA probe of 43 bases. While this may be a useful protocol for some additional assays, it is recommended that both reaction conditions and gel running conditions be tailored to the individual interaction to be probed. PMID:24674072

  12. Direct RNA detection without nucleic acid purification and PCR: Combining sandwich hybridization with signal amplification based on branched hybridization chain reaction.

    PubMed

    Xu, Yao; Zheng, Zhi

    2016-05-15

    We have developed a convenient, robust and low-cost RNA detection system suitable for high-throughput applications. This system uses a highly specific sandwich hybridization to capture target RNA directly onto solid support, followed by on-site signal amplification via 2-dimensional, branched hybridizing chain polymerization through toehold-mediated strand displacement reaction. The assay uses SYBR Green to detect targets at concentrations as low as 1pM, without involving nucleic acid purification or any enzymatic reaction, using ordinary oligonucleotides without modification or labeling. The system was demonstrated in the detection of malaria RNA in blood and GAPDH gene expression in cell lysate. PMID:26761615

  13. Photoinitiator Nucleotide for Quantifying Nucleic Acid Hybridization

    PubMed Central

    Johnson, Leah M.; Hansen, Ryan R.; Urban, Milan; Kuchta, Robert D.; Bowman, Christopher N.

    2010-01-01

    This first report of a photoinitiator-nucleotide conjugate demonstrates a novel approach for sensitive, rapid and visual detection of DNA hybridization events. This approach holds potential for various DNA labeling schemes and for applications benefiting from selective DNA-based polymerization initiators. Here, we demonstrate covalent, enzymatic incorporation of an eosin-photoinitiator 2′-deoxyuridine-5′-triphosphate (EITC-dUTP) conjugate into surface-immobilized DNA hybrids. Subsequent radical chain photoinitiation from these sites using an acrylamide/bis-acrylamide formulation yields a dynamic detection range between 500pM and 50nM of DNA target. Increasing EITC-nucleotide surface densities leads to an increase in surface-based polymer film heights until achieving a film height plateau of 280nm ±20nm at 610 ±70 EITC-nucleotides/μm2. Film heights of 10–20 nm were obtained from eosin surface densities of approximately 20 EITC-nucleotides/μm2 while below the detection limit of ~10 EITC-nucleotides/μm2, no detectable films were formed. This unique threshold behavior is utilized for instrument-free, visual quantification of target DNA concentration ranges. PMID:20337438

  14. DNA hybridization assay for detection of gypsy moth nuclear polyhedrosis virus in infected gypsy moth (Lymantria dispar L. ) larvae

    SciTech Connect

    Keating, S.T.; Burand, J.P.; Elkinton, J.S. )

    1989-11-01

    Radiolabeled Lymantria dispar nuclear polyhedrosis virus DNA probes were used in a DNA hybridization assay to detect the presence of viral DNA in extracts from infected larvae. Total DNA was extracted from larvae, bound to nitrocellulose filters, and assayed for the presence of viral DNA by two methods: slot-blot vacuum filtration and whole-larval squashes. The hybridization results were closely correlated with mortality observed in reared larvae. Hybridization of squashes of larvae frozen 4 days after receiving the above virus treatments also produced accurate measures of the incidence of virus infection.

  15. New drug susceptibility test for Mycobacterium tuberculosis using the hybridization protection assay.

    PubMed Central

    Miyamoto, J; Koga, H; Kohno, S; Tashiro, T; Hara, K

    1996-01-01

    We developed a novel method for early detection of drug-resistant strains of Mycobacterium tuberculosis by using the hybridization protection assay (HPA). The number of viable bacteria during the incubation period correlated well with the number of relative light units measured by the HPA. In addition, the relative light unit values of susceptible strains on the first, third and fifth days of incubation were significantly different from those of resistant strains for both isoniazid and rifampin. Our results suggest that after isolation of the organism from clinical specimens, drug-resistant strains of M. tuberculosis are accurately detected by the HPA even after 1 day of incubation with the drug. PMID:8727932

  16. Hybrid Enrichment Assay Methods for a UF6 Cylinder Verification Station: FY10 Progress Report

    SciTech Connect

    Smith, Leon E.; Jordan, David V.; Orton, Christopher R.; Misner, Alex C.; Mace, Emily K.

    2010-08-01

    Pacific Northwest National Laboratory (PNNL) is developing the concept of an automated UF6 cylinder verification station that would be located at key measurement points to positively identify each cylinder, measure its mass and enrichment, store the collected data in a secure database, and maintain continuity of knowledge on measured cylinders until the arrival of International Atomic Energy Agency (IAEA) inspectors. At the center of this unattended system is a hybrid enrichment assay technique that combines the traditional enrichment-meter method (based on the 186 keV peak from 235U) with non-traditional neutron-induced high-energy gamma-ray signatures (spawned primarily by 234U alpha emissions and 19F(alpha, neutron) reactions). Previous work by PNNL provided proof-of-principle for the non-traditional signatures to support accurate, full-volume interrogation of the cylinder enrichment, thereby reducing the systematic uncertainties in enrichment assay due to UF6 heterogeneity and providing greater sensitivity to material substitution scenarios. The work described here builds on that preliminary evaluation of the non-traditional signatures, but focuses on a prototype field system utilizing NaI(Tl) and LaBr3(Ce) spectrometers, and enrichment analysis algorithms that integrate the traditional and non-traditional signatures. Results for the assay of Type-30B cylinders ranging from 0.2 to 4.95 wt% 235U, at an AREVA fuel fabrication plant in Richland, WA, are described for the following enrichment analysis methods: 1) traditional enrichment meter signature (186 keV peak) as calculated using a square-wave convolute (SWC) algorithm; 2) non-traditional high-energy gamma-ray signature that provides neutron detection without neutron detectors and 3) hybrid algorithm that merges the traditional and non-traditional signatures. Uncertainties for each method, relative to the declared enrichment for each cylinder, are calculated and compared to the uncertainties from an attended

  17. 21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... Test Systems § 866.5910 Quality control material for cystic fibrosis nucleic acid assays. (a... cystic fibrosis nucleic acid assays is a device intended to help monitor reliability of a test system by... testing. This type of device includes recombinant, synthetic, and cell line-based DNA controls....

  18. 21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Test Systems § 866.5910 Quality control material for cystic fibrosis nucleic acid assays. (a... cystic fibrosis nucleic acid assays is a device intended to help monitor reliability of a test system by... testing. This type of device includes recombinant, synthetic, and cell line-based DNA controls....

  19. 21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... Test Systems § 866.5910 Quality control material for cystic fibrosis nucleic acid assays. (a... cystic fibrosis nucleic acid assays is a device intended to help monitor reliability of a test system by... testing. This type of device includes recombinant, synthetic, and cell line-based DNA controls....

  20. 21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Test Systems § 866.5910 Quality control material for cystic fibrosis nucleic acid assays. (a... cystic fibrosis nucleic acid assays is a device intended to help monitor reliability of a test system by... testing. This type of device includes recombinant, synthetic, and cell line-based DNA controls....

  1. 21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... Test Systems § 866.5910 Quality control material for cystic fibrosis nucleic acid assays. (a... cystic fibrosis nucleic acid assays is a device intended to help monitor reliability of a test system by... testing. This type of device includes recombinant, synthetic, and cell line-based DNA controls....

  2. A Fluorescent Assay for Plant Caffeic Acid O-methyltransferases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed a facile, sensitive and continuous assay to measure the activities of plant COMTs using s-adenosyl homocysteine hydrolase as a coupling enzyme and and adeonsine a thiol-specific fluor, Thioglo1, as the detecting reagent. This assay was validated using recombinant sorghum COMT (BMR-...

  3. Electric field directed nucleic acid hybridization on microchips.

    PubMed Central

    Edman, C F; Raymond, D E; Wu, D J; Tu, E; Sosnowski, R G; Butler, W F; Nerenberg, M; Heller, M J

    1997-01-01

    Selection and adjustment of proper physical parameters enables rapid DNA transport, site selective concentration, and accelerated hybridization reactions to be carried out on active microelectronic arrays. These physical parameters include DC current, voltage, solution conductivity and buffer species. Generally, at any given current and voltage level, the transport or mobility of DNA is inversely proportional to electrolyte or buffer conductivity. However, only a subset of buffer species produce both rapid transport, site specific concentration and accelerated hybridization. These buffers include zwitterionic and low conductivity species such as: d- and l-histidine; 1- and 3-methylhistidines; carnosine; imidazole; pyridine; and collidine. In contrast, buffers such as glycine, beta-alanine and gamma-amino-butyric acid (GABA) produce rapid transport and site selective concentration but do not facilitate hybridization. Our results suggest that the ability of these buffers (histidine, etc.) to facilitate hybridization appears linked to their ability to provide electric field concentration of DNA; to buffer acidic conditions present at the anode; and in this process acquire a net positive charge which then shields or diminishes repulsion between the DNA strands, thus promoting hybridization. PMID:9396795

  4. Synthesis and Characterization of Hybrid Hyaluronic Acid-Gelatin Hydrogels

    PubMed Central

    Camci-Unal, Gulden; Cuttica, Davide; Annabi, Nasim; Demarchi, Danilo; Khademhosseini, Ali

    2013-01-01

    Biomimetic hybrid hydrogels have generated broad interest in tissue engineering and regenerative medicine. Hyaluronic acid (HA) and gelatin (hydrolyzed collagen) are naturally derived polymers and biodegradable under physiological conditions. Moreover, collagen and HA are major components of the extracellular matrix (ECM) in most of the tissues (e.g. cardiovascular, cartilage, neural). When used as a hybrid material, HA-gelatin hydrogels may enable mimicking the ECM of native tissues. Although HA-gelatin hybrid hydrogels are promising biomimetic substrates, their material properties have not been thoroughly characterized in the literature. Herein, we generated hybrid hydrogels with tunable physical and biological properties by using different concentrations of HA and gelatin. The physical properties of the fabricated hydrogels including swelling ratio, degradation, and mechanical properties were investigated. In addition, in vitro cellular responses in both two and three dimensional (2D and 3D) culture conditions were assessed. It was found that the addition of gelatin methacrylate (GelMA) into HA methacrylate (HAMA) promoted cell spreading in the hybrid hydogels. Moreover, the hybrid hydrogels showed significantly improved mechanical properties compared to their single component analogs. The HAMA-GelMA hydrogels exhibited remarkable tunability behavior and may be useful for cardiovascular tissue engineering applications. PMID:23419055

  5. Synthesis and characterization of hybrid hyaluronic acid-gelatin hydrogels.

    PubMed

    Camci-Unal, Gulden; Cuttica, Davide; Annabi, Nasim; Demarchi, Danilo; Khademhosseini, Ali

    2013-04-01

    Biomimetic hybrid hydrogels have generated broad interest in tissue engineering and regenerative medicine. Hyaluronic acid (HA) and gelatin (hydrolyzed collagen) are naturally derived polymers and biodegradable under physiological conditions. Moreover, collagen and HA are major components of the extracellular matrix (ECM) in most of the tissues (e.g., cardiovascular, cartilage, neural). When used as a hybrid material, HA-gelatin hydrogels may enable mimicking the ECM of native tissues. Although HA-gelatin hybrid hydrogels are promising biomimetic substrates, their material properties have not been thoroughly characterized in the literature. Herein, we generated hybrid hydrogels with tunable physical and biological properties by using different concentrations of HA and gelatin. The physical properties of the fabricated hydrogels including swelling ratio, degradation, and mechanical properties were investigated. In addition, in vitro cellular responses in both two and three-dimensional culture conditions were assessed. It was found that the addition of gelatin methacrylate (GelMA) into HA methacrylate (HAMA) promoted cell spreading in the hybrid hydogels. Moreover, the hybrid hydrogels showed significantly improved mechanical properties compared to their single component analogs. The HAMA-GelMA hydrogels exhibited remarkable tunability behavior and may be useful for cardiovascular tissue engineering applications. PMID:23419055

  6. Natural cinnamic acids, synthetic derivatives and hybrids with antimicrobial activity.

    PubMed

    Guzman, Juan David

    2014-01-01

    Antimicrobial natural preparations involving cinnamon, storax and propolis have been long used topically for treating infections. Cinnamic acids and related molecules are partly responsible for the therapeutic effects observed in these preparations. Most of the cinnamic acids, their esters, amides, aldehydes and alcohols, show significant growth inhibition against one or several bacterial and fungal species. Of particular interest is the potent antitubercular activity observed for some of these cinnamic derivatives, which may be amenable as future drugs for treating tuberculosis. This review intends to summarize the literature data on the antimicrobial activity of the natural cinnamic acids and related derivatives. In addition, selected hybrids between cinnamic acids and biologically active scaffolds with antimicrobial activity were also included. A comprehensive literature search was performed collating the minimum inhibitory concentration (MIC) of each cinnamic acid or derivative against the reported microorganisms. The MIC data allows the relative comparison between series of molecules and the derivation of structure-activity relationships. PMID:25429559

  7. Lactobacillus casei microbiological assay of folic acid derivatives in 96-well microtiter plates.

    PubMed

    Horne, D W; Patterson, D

    1988-11-01

    Microbiological assay is still widely used for estimating folic acid derivatives in serum and other biological samples. We describe here a modification of this procedure involving use of 96-well microtiter plates. This procedure, used with modern, computer-interfaced microtiter-plate readers and data-reduction software, greatly shortens the time and minimizes reagent costs for this assay. Under the conditions of our assay procedures, all folic acid derivatives tested gave equal growth response for Lactobacillus casei. Results for assays of rat liver extracts showed excellent agreement between the standard bioassay and the 96-well procedure. PMID:3141087

  8. DNA hybridization assay for detection of nucleopolyhedrovirus in whitemarked tussock moth (Orgyia leucostigma) larvae.

    PubMed

    Ebling, P M; Smith, P A; van Frankenhuyzen, K

    2001-01-01

    DNA dot-blot hybridization assays utilizing a horseradish peroxidase-labelled whole genomic DNA probe and enhanced chemiluminescence were conducted to quantify detection thresholds of nucleopolyhedrovirus (NPV) in whitemarked tussock moth (Orgyia leucostigma) larvae. The minimum detection thresholds for an aqueous suspension of occlusion bodies (OBs), OBs added to macerates of non-infected larvae and OBs in macerates of diseased larvae were 7.8 x 10(3), 7.8 x 10(3), and 1.5 x 10(3) OBs, respectively. Purified viral DNA was detected at a concentration of 1.6 x 10(-1) ng in a 20 microliters volume. The presence of pre-occluded viral nucleocapsids and DNA, inherent to infected larvae, improved the detection threshold five-fold compared with OBs alone. Larval tissues did not block the detection system utilized, nor did they bind non-specifically to the probe. Detection thresholds, upon sequential hybridization of the same membrane, on average deteriorated two-fold between the first and second hybridization and an additional six-fold between the second and third hybridization. NPV infection was detected two days post-inoculation (pi) in about one-third of the larvae examined and in almost all larvae three days pi. Microscopic analysis of stained larval smears missed NPV infection in almost all larvae two days pi and about two-thirds of the larvae three days pi. Results from the two methods of analysis were not comparable until four days pi. The detection system utilized is a reliable, efficient and simple method for the early detection of NPV infection in large numbers of larvae and may be used for further studies quantifying the role of this baculovirus in the ecology of whitemarked tussock moth populations. PMID:11455634

  9. Development of an assay to simultaneously measure orotic acid, amino acids, and acylcarnitines in dried blood spots

    PubMed Central

    Held, Patrice K.; Haynes, Christopher A.; De Jesús, Víctor R.; Baker, Mei W.

    2016-01-01

    Background Orotic aciduria in the presence of hyperammonemia is a key indicator for a defect in the urea cycle, specifically ornithine transcarbamylase (OTC) deficiency. Current newborn screening (NBS) protocols can detect several defects of the urea cycle, but screening for OTC deficiency remains a challenge due to the lack of a suitable assay. The purpose of this study was to develop a high-throughput assay to measure orotic acid in dried blood spot (DBS) specimens as an indicator for urea cycle dysfunction, which can be readily incorporated into routine NBS. Methods Orotic acid was extracted from DBS punches and analyzed using flow-injection analysis tandem mass spectrometry (FIA–MS/MS) with negative-mode ionization, requiring <2 min/sample run time. This method was then multiplexed into a conventional newborn screening assay for analysis of amino acids, acylcarnitines, and orotic acid. Results We describe 2 assays which can quantify orotic acid in DBS: a stand-alone method and a combined method for analysis of orotic acid, amino acids, and acylcarnitines. Both methods demonstrated orotic acid recovery of 75–85% at multiple levels of enrichment. Precision was also comparable to traditional FIA–MS/MS methods. Analysis of residual presumptively normal NBS specimens demonstrated a 5:1 signal to noise ratio and the average concentration of orotic acid was approximately 1.2 μmol/l. The concentration of amino acids and acylcarnitines as measured by the combined method showed no significant differences when compared to the conventional newborn screening assay. In addition, retrospective analysis of confirmed patients and presumptively normal newborn screening specimens suggests potential for the methods to identify patients with OTC deficiency, as well as other urea cycle defects. Conclusion The assays described here quantify orotic acid in DBS using a simple extraction and FIA–MS/MS analysis procedures that can be implemented into current NBS protocols. PMID

  10. Electrophoretic Mobility Shift Assay (EMSA) for Detecting Protein-Nucleic Acid Interactions

    PubMed Central

    Hellman, Lance M.; Fried, Michael G.

    2009-01-01

    The gel electrophoresis mobility shift assay (EMSA) is used to detect protein complexes with nucleic acids. It is the core technology underlying a wide range of qualitative and quantitative analyses for the characterization of interacting systems. In the classical assay, solutions of protein and nucleic acid are combined and the resulting mixtures are subjected to electrophoresis under native conditions through polyacrylamide or agarose gel. After electrophoresis, the distribution of species containing nucleic acid is determined, usually by autoradiography of 32P-labeled nucleic acid. In general, protein-nucleic acid complexes migrate more slowly than the corresponding free nucleic acid. In this article, we identify the most important factors that determine the stabilities and electrophoretic mobilities of complexes under assay conditions. A representative protocol is provided and commonly used variants are discussed. Expected outcomes are briefly described. References to extensions of the method and a troubleshooting guide are provided. PMID:17703195

  11. In situ hybridization assay-based small molecule screening in zebrafish

    PubMed Central

    Jing, Lili; Durand, Ellen M.; Ezzio, Catherine; Pagliuca, Stephanie M.; Zon, Leonard I.

    2012-01-01

    In vitro biochemical and cell-based small molecule screens have been widely used to identify compounds that target specific signaling pathways. But the identified compounds frequently fail at the animal testing stage, largely due to the in vivo absorption, metabolism and toxicity of chemicals. Zebrafish has recently emerged as a vertebrate whole organism model for small molecule screening. The in vivo bioactivity and specificity of compounds are examined from the very beginning of zebrafish screens. In addition, zebrafish is suitable for chemical screens at a large scale similar to cellular assays. This protocol describes an approach for in situ hybridization (ISH)-based chemical screening in zebrafish, which, in principle, can be used to screen any gene product. The described protocol has been used to identify small molecules affecting specific molecular pathways and biological processes. It can also be adapted to zebrafish screens with different readouts. PMID:23001521

  12. Ferulic acid-carbazole hybrid compounds: Combination of cholinesterase inhibition, antioxidant and neuroprotection as multifunctional anti-Alzheimer agents.

    PubMed

    Fang, Lei; Chen, Mohao; Liu, Zhikun; Fang, Xubin; Gou, Shaohua; Chen, Li

    2016-02-15

    In order to search for novel multifunctional anti-Alzheimer agents, a series of ferulic acid-carbazole hybrid compounds were designed and synthesized. Ellman's assay revealed that the hybrid compounds showed moderate to potent inhibitory activity against the cholinesterases. Particularly, the AChE inhibition potency of compound 5k (IC50 1.9μM) was even 5-fold higher than that of galantamine. In addition, the target compounds showed pronounced antioxidant ability and neuroprotective property, especially against the ROS-induced toxicity. Notably, the neuroprotective effect of 5k was obviously superior to that of the mixture of ferulic acid and carbazole, indicating the therapeutic effect of the hybrid compound is better than the combination administration of the corresponding mixture. PMID:26795115

  13. Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification.

    PubMed

    Guan, Weihua; Chen, Liben; Rane, Tushar D; Wang, Tza-Huei

    2015-01-01

    We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples. PMID:26333806

  14. Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

    NASA Astrophysics Data System (ADS)

    Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

    2015-09-01

    We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

  15. Quantum Dot-Bead-DNA Probe-Based Hybridization Fluorescence Assays on Microfluidic Chips.

    PubMed

    Ankireddy, Seshadri Reddy; Kim, Jongsung

    2015-10-01

    The development of chip-based, quantum dot (QD)-bead-DNA conjugate probes for hybridization detection is a prime research focus in the field of microfluidics. QD-Bead-DNA probe-based hybridization detection methods are often called "bead-based assays," and their success is substantially influenced by the dispensing and manipulation capabilities of microfluidic technology. Met was identified as a prognostic marker in different cancers including lung, renal, liver, head and neck, stomach, and breast. In this report, the cancer causing Met gene was detected with QDs attached to polystyrene microbeads. We constructed a microfluidic platform using a flexible PDMS polymer. The chip consists of two channels, with two inlets and two outlets. The two channels were integrated with QD-bead-DNA probes for simultaneous detection of wild type target DNA and mutant DNA, containing three nucleotide changes compared to the wild type sequence. The fluorescence quenching ability of QDs within the channels of microfluidic chips were compared for both DNAs. PMID:26726440

  16. Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

    PubMed Central

    Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

    2015-01-01

    We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples. PMID:26333806

  17. Detection of North American eastern and western equine encephalitis viruses by nucleic acid amplification assays.

    PubMed

    Lambert, Amy J; Martin, Denise A; Lanciotti, Robert S

    2003-01-01

    We have developed nucleic acid sequence-based amplification (NASBA), standard reverse transcription PCR (RT-PCR), and TaqMan nucleic acid amplification assays for the rapid detection of North American eastern equine encephalitis (EEE) and western equine encephalitis (WEE) viral RNAs from samples collected in the field and clinical samples. The sensitivities of these assays have been compared to that of virus isolation. While all three types of nucleic acid amplification assays provide rapid detection of viral RNAs comparable to the isolation of viruses in Vero cells, the TaqMan assays for North American EEE and WEE viral RNAs are the most sensitive. We have shown these assays to be specific for North American EEE and WEE viral RNAs by testing geographically and temporally distinct strains of EEE and WEE viruses along with a battery of related and unrelated arthropodborne viruses. In addition, all three types of nucleic acid amplification assays have been used to detect North American EEE and WEE viral RNAs from mosquito and vertebrate tissue samples. The sensitivity, specificity, and rapidity of nucleic acid amplification demonstrate the usefulness of NASBA, standard RT-PCR, and TaqMan assays, in both research and diagnostic settings, to detect North American EEE and WEE viral RNAs. PMID:12517876

  18. Performance of PCR-reverse blot hybridization assay for detection of rifampicin-resistant Mycobacterium leprae.

    PubMed

    Wang, Hye-young; Kim, Hyunjung; Kim, Yeun; Bang, Hyeeun; Kim, Jong-Pill; Hwang, Joo Hwan; Cho, Sang-Nae; Kim, Tae Ue; Lee, Hyeyoung

    2015-10-01

    Drug resistance in Mycobacterium leprae is a significant problem in countries where leprosy is endemic. A sensitive, specific, and high-throughput reverse blot hybridization assay (REBA) for the detection of genotypic resistance to rifampicin (RIF) was designed and evaluated. It has been shown that resistance to RIF in M. leprae involves mutations in the rpoB gene encoding the -subunit of the RNA polymerase. The PCR-REBA simultaneously detects both 6 wild-type regions and 5 different mutations (507 AGC, 513 GTG, 516 TAT, 531 ATG, and 531 TTC) including the most prevalent mutations at positions 507 and 531. Thirty-one clinical isolates provided by Korea Institute of Hansen-s Disease were analyzed by PCR-REBA with RIF resistance of rpoB gene. As a result, missense mutations at codons 507 AGC and 531 ATG with 2-nucleotide substitutions were found in one sample, and a missense mutation at codon 516 TAT and ΔWT6 (deletion of 530-534) was found in another sample. These cases were confirmed by DNA sequence analysis. This rapid, simple, and highly sensitive assay provides a practical alternative to sequencing for genotypic evaluation of RIF resistance in M. leprae. PMID:26428919

  19. Helicase Assays

    PubMed Central

    Wang, Xin; Li, Jing; Diaz, Jason; You, Jianxin

    2016-01-01

    Helicases are a class of enzymes which are motor proteins using energy derived from ATP hydrolysis to move directionally along a nucliec acid phosphodiester backbone (such as DNA, RNA and DNA-RNA hybrids) and separate two annealed nucleic acid strands. Many cellular processes, such as transcription, DNA replication, recombination and DNA repair involve helicase activity. Here, we provide a protocol to analyze helicase activities in vitro. In this protocol, the DNA helicase protein Merkel cell polyomavirus large T-antigen was expressed in the mammalian cell line HEK293 and immoblized on an IgG resin. The helicase assay is performing while the protein is immoblized on IgG resin.

  20. Highly accurate boronimeter assay of concentrated boric acid solutions

    SciTech Connect

    Ball, R.M. )

    1992-01-01

    The Random-Walk Boronimeter has successfully been used as an on-line indicator of boric acid concentration in an operating commercial pressurized water reactor. The principle has been adapted for measurement of discrete samples to high accuracy and to concentrations up to 6000 ppm natural boron in light water. Boric acid concentration in an aqueous solution is a necessary measurement in many nuclear power plants, particularly those that use boric acid dissolved in the reactor coolant as a reactivity control system. Other nuclear plants use a high-concentration boric acid solution as a backup shutdown system. Such a shutdown system depends on rapid injection of the solution and frequent surveillance of the fluid to ensure the presence of the neutron absorber. The two methods typically used to measure boric acid are the chemical and the physical methods. The chemical method uses titration to determine the ionic concentration of the BO[sub 3] ions and infers the boron concentration. The physical method uses the attenuation of neutrons by the solution and infers the boron concentration from the neutron absorption properties. This paper describes the Random-Walk Boronimeter configured to measure discrete samples to high accuracy and high concentration.

  1. Bipolar lead-acid battery for hybrid vehicles

    NASA Astrophysics Data System (ADS)

    Saakes, M.; Woortmeijer, R.; Schmal, D.

    Within the framework of the European project bipolar lead-acid power source (BILAPS), a new production route is being developed for the bipolar lead-acid battery. The performance targets are 500 W kg -1, 30 Wh kg -1 and 100 000 power-assist life cycles (PALCs). The operation voltage of the battery can be, according to the requirements, 12, 36 V or any other voltage. Tests with recently developed 4 and 12 V prototypes, each of 30 Ah capacity have demonstrated that the PALC can be operated using 10 C discharge and 9 C charge peaks. The tests show no overvoltage or undervoltage problems during three successive test periods of 16 h with 8 h rest in between. The temperature stabilizes during these tests at 40-45 °C using a thermal-management system. The bipolar lead acid battery is operated at an initial 50% state-of-charge. During the tests, the individual cell voltages display only very small differences. Tests are now in progress to improve further the battery-management system, which has been developed at the cell level, during the period no PALCs are run in order to improve the hybrid behaviour of the battery. The successful tests show the feasibility of operating the bipolar lead-acid battery in a hybrid mode. The costs of the system are estimated to be much lower than those for nickel-metal-hydride or Li-ion based high-power systems. An additional advantage of the lead-acid system is that recycling of lead-acid batteries is well established.

  2. MAMMALIAN CELL CULTURE ASSAY TO QUANTITATE CHEMICALLY INDUCED ANEUPLOIDY: USE OF A MONOCHROMOSOMAL HUMAN/MOUSE CELL HYBRID

    EPA Science Inventory

    A short-term assay utilizing a human/mouse monochromosomal hybrid cell line R3-5, to detect chemically induced aneuploidy in mammalian cells is described. A single human chromosome transferred into mouse cells was used as a cytogenetic marker to quantitate abnormal chromosome seg...

  3. Automated UF6 Cylinder Enrichment Assay: Status of the Hybrid Enrichment Verification Array (HEVA) Project: POTAS Phase II

    SciTech Connect

    Jordan, David V.; Orton, Christopher R.; Mace, Emily K.; McDonald, Benjamin S.; Kulisek, Jonathan A.; Smith, Leon E.

    2012-06-01

    Pacific Northwest National Laboratory (PNNL) intends to automate the UF6 cylinder nondestructive assay (NDA) verification currently performed by the International Atomic Energy Agency (IAEA) at enrichment plants. PNNL is proposing the installation of a portal monitor at a key measurement point to positively identify each cylinder, measure its mass and enrichment, store the data along with operator inputs in a secure database, and maintain continuity of knowledge on measured cylinders until inspector arrival. This report summarizes the status of the research and development of an enrichment assay methodology supporting the cylinder verification concept. The enrichment assay approach exploits a hybrid of two passively-detected ionizing-radiation signatures: the traditional enrichment meter signature (186-keV photon peak area) and a non-traditional signature, manifested in the high-energy (3 to 8 MeV) gamma-ray continuum, generated by neutron emission from UF6. PNNL has designed, fabricated, and field-tested several prototype assay sensor packages in an effort to demonstrate proof-of-principle for the hybrid assay approach, quantify the expected assay precision for various categories of cylinder contents, and assess the potential for unsupervised deployment of the technology in a portal-monitor form factor. We refer to recent sensor-package prototypes as the Hybrid Enrichment Verification Array (HEVA). The report provides an overview of the assay signatures and summarizes the results of several HEVA field measurement campaigns on populations of Type 30B UF6 cylinders containing low-enriched uranium (LEU), natural uranium (NU), and depleted uranium (DU). Approaches to performance optimization of the assay technique via radiation transport modeling are briefly described, as are spectroscopic and data-analysis algorithms.

  4. The highly abundant urinary metabolite urobilin interferes with the bicinchoninic acid assay.

    PubMed

    Sampson, D L; Chng, Y L; Upton, Z; Hurst, C P; Parker, A W; Parker, T J

    2013-11-01

    Estimation of total protein concentration is an essential step in any protein- or peptide-centric analysis pipeline. This study demonstrates that urobilin, a breakdown product of heme and a major constituent of urine, interferes considerably with the bicinchoninic acid (BCA) assay. This interference is probably due to the propensity of urobilin to reduce cupric ions (Cu(2+)) to cuprous ions (Cu(1+)), thus mimicking the reduction of copper by proteins, which the assay was designed to do. In addition, it is demonstrated that the Bradford assay is more resistant to the influence of urobilin and other small molecules. As such, urobilin has a strong confounding effect on the estimate of total protein concentrations obtained by BCA assay and thus this assay should not be used for urinary protein quantification. It is recommended that the Bradford assay be used instead. PMID:23911526

  5. Time-Resolved Nucleic Acid Hybridization Beacons Utilizing Unimolecular and Toehold-Mediated Strand Displacement Designs.

    PubMed

    Massey, Melissa; Ancona, Mario G; Medintz, Igor L; Algar, W Russ

    2015-12-01

    Nucleic acid hybridization probes are sought after for numerous assay and imaging applications. These probes are often limited by the properties of fluorescent dyes, prompting the development of new probes where dyes are paired with novel or nontraditional luminescent materials. Luminescent terbium complexes are an example of such a material, and these complexes offer several unique spectroscopic advantages. Here, we demonstrate two nonstem-loop designs for light-up nucleic acid hybridization beacons that utilize time-resolved Förster resonance energy transfer (TR-FRET) between a luminescent Lumi4-Tb cryptate (Tb) donor and a fluorescent reporter dye, where time-resolved emission from the dye provides an analytical signal. Both designs are based on probe oligonucleotides that are labeled at their opposite termini with Tb and a fluorescent reporter dye. In one design, a probe is partially blocked with a quencher dye-labeled oligonucleotide, and target hybridization is signaled through toehold-mediated strand displacement and loss of a competitive FRET pathway. In the other design, the intrinsic folding properties of an unblocked probe are utilized in combination with a temporal mechanism for signaling target hybridization. This temporal mechanism is based on a recently elucidated "sweet spot" for TR-FRET measurements and exploits distance control over FRET efficiencies to shift the Tb lifetime within or outside the time-gated detection window for measurements. Both the blocked and unblocked beacons offer nanomolar (femtomole) detection limits, response times on the order of minutes, multiplexing through the use of different reporter dyes, and detection in complex matrices such as serum and blood. The blocked beacons offer better mismatch selectivity, whereas the unblocked beacons are simpler in design. The temporal mechanism of signaling utilized with the unblocked beacons also plays a significant role with the blocked beacons and represents a new and effective

  6. Melamine and Cyanuric Acid do not interfere with Bradford and Ninhydrin assays for protein determination

    PubMed Central

    Field, Anjalie; Field, Jeffrey

    2010-01-01

    In the fall of 2007 pet food contaminated with melamine and cyanuric acid caused kidney stones in thousands of animals. In the summer of 2008, a more serious outbreak of adulterated dairy food caused the deaths of six infants and sickened about 290,000 children in China. In all cases, melamine was likely added to inflate the apparent protein content of the foods. To determine if we could measure protein without interference from melamine and cyanuric acid we tested these compounds in the Bradford and Ninhydrin assays, two common dye-based assays for protein, as well as by ammonia release, the most common assay used in the food industry. Neither compound was detected in the Ninhydrin and Bradford assays at concentrations of >100 μg/ml. The ammonia assay detected melamine but was inconclusive with respect to cyanuric acid. To develop an accurate test for food that would not detect either chemical as a protein, assays were run on cat food and reconstituted milk powder. The Bradford assay readily measured the protein content of each food, and importantly, the addition of melamine or cyanuric acid to reconstituted milk did not affect the readings. The protein concentrations obtained for reconstituted milk powder were as expected, but those for the cat food were 10 to 30-fold lower, due to its low solubility. We conclude that dye-binding assays can be employed to detect protein in food without interference from melamine and cyanuric acid, thus reducing the incentive to use them as additives. PMID:20228949

  7. A hybrid neural network structure for application to nondestructive TRU waste assay

    SciTech Connect

    Becker, G.

    1995-12-31

    The determination of transuranic (TRU) and associated radioactive material quantities entrained in waste forms is a necessary component. of waste characterization. Measurement performance requirements are specified in the National TRU Waste Characterization Program quality assurance plan for which compliance must be demonstrated prior to the transportation and disposition of wastes. With respect to this criterion, the existing TRU nondestructive waste assay (NDA) capability is inadequate for a significant fraction of the US Department of Energy (DOE) complex waste inventory. This is a result of the general application of safeguard-type measurement and calibration schemes to waste form configurations. Incompatibilities between such measurement methods and actual waste form configurations complicate regulation compliance demonstration processes and illustrate the need for an alternate measurement interpretation paradigm. Hence, it appears necessary to supplement or perhaps restructure the perceived solution and approach to the waste NDA problem. The first step is to understand the magnitude of the waste matrix/source attribute space associated with those waste form configurations in inventory and how this creates complexities and unknowns with respect to existing NDA methods. Once defined and/or bounded, a conceptual method must be developed that specifies the necessary tools and the framework in which the tools are used. A promising framework is a hybridized neural network structure. Discussed are some typical complications associated with conventional waste NDA techniques and how improvements can be obtained through the application of neural networks.

  8. Rapid assay to identify the two genetic forms of Culex (Culex) pipiens L. (Diptera: Culicidae) and hybrid populations.

    PubMed

    Bahnck, Carolyn M; Fonseca, Dina M

    2006-08-01

    A previously developed method to identify members of the Culex pipiens complex exploiting polymorphisms in a nuclear intron (acetylcholinesterase [ACE] based-assay) cannot differentiate the two forms of Cx. pipiens: form pipiens and form molestus. Notably, the two forms seem to differ extensively in behavior and physiology and likely have very different epidemiologic importance. Because they are morphologically indistinguishable, molecular methods are critical for the evaluation of their relative importance. Although the two forms of Cx. pipiens have been distinguished using a panel of microsatellite loci, such a protocol is laborious and expensive. We developed a rapid assay based on polymorphisms in the flanking region of a microsatellite locus. Used in conjunction with the ACE-assay, this new assay allows the identification of pure and hybrid populations of the two Cx. pipiens forms as well as those including Cx. quinquefasciatus. We discuss the usefulness of the method as well as limitations to its application. PMID:16896127

  9. Identification of new quinic acid derivatives as histone deacetylase inhibitors by fluorescence-based cellular assay.

    PubMed

    Son, Dohyun; Kim, Chung Sub; Lee, Kang Ro; Park, Hyun-Ju

    2016-05-01

    A fluorescence-based cellular assay system was established to identify potential epigenetic modulator ligands. This assay method is to detect the de-repression of an EGFP reporter in cancer cells by the treatment of HDAC (histone deacetylase) or DNMT (DNA methyltransferase) inhibitor. Using this system, we conducted a preliminary screening of in-house natural product library containing extracts and pure compounds, and identified several active compounds. Among them, novel quinic acid derivatives were recognized as excellent HDAC inhibitors by both enzymatic and cell-based HDAC assays. PMID:26996372

  10. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1997-01-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

  11. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  12. "Inosaminoacids": novel inositol-amino acid hybrid structures accessed by microbial arene oxidation.

    PubMed

    Pilgrim, Sarah; Kociok-Köhn, Gabriele; Lloyd, Matthew D; Lewis, Simon E

    2011-04-28

    Microbial 1,2-dihydroxylation of sodium benzoate permits the rapid construction of novel inositol-amino acid hybrid structures. Both β- and γ-amino acids are accessible by means of an acylnitroso Diels-Alder cycloaddition. PMID:21409268

  13. Fully Automated RNAscope In Situ Hybridization Assays for Formalin-Fixed Paraffin-Embedded Cells and Tissues.

    PubMed

    Anderson, Courtney M; Zhang, Bingqing; Miller, Melanie; Butko, Emerald; Wu, Xingyong; Laver, Thomas; Kernag, Casey; Kim, Jeffrey; Luo, Yuling; Lamparski, Henry; Park, Emily; Su, Nan; Ma, Xiao-Jun

    2016-10-01

    Biomarkers such as DNA, RNA, and protein are powerful tools in clinical diagnostics and therapeutic development for many diseases. Identifying RNA expression at the single cell level within the morphological context by RNA in situ hybridization provides a great deal of information on gene expression changes over conventional techniques that analyze bulk tissue, yet widespread use of this technique in the clinical setting has been hampered by the dearth of automated RNA ISH assays. Here we present an automated version of the RNA ISH technology RNAscope that is adaptable to multiple automation platforms. The automated RNAscope assay yields a high signal-to-noise ratio with little to no background staining and results comparable to the manual assay. In addition, the automated duplex RNAscope assay was able to detect two biomarkers simultaneously. Lastly, assay consistency and reproducibility were confirmed by quantification of TATA-box binding protein (TBP) mRNA signals across multiple lots and multiple experiments. Taken together, the data presented in this study demonstrate that the automated RNAscope technology is a high performance RNA ISH assay with broad applicability in biomarker research and diagnostic assay development. J. Cell. Biochem. 117: 2201-2208, 2016. © 2016 Wiley Periodicals, Inc. PMID:27191821

  14. Creatinyl amino acids: new hybrid compounds with neuroprotective activity.

    PubMed

    Burov, Sergey; Leko, Maria; Dorosh, Marina; Dobrodumov, Anatoliy; Veselkina, Olga

    2011-09-01

    Prolonged oral creatine administration resulted in remarkable neuroprotection in experimental models of brain stroke. However, because of its polar nature creatine has poor ability to penetrate the blood-brain barrier (BBB) without specific creatine transporter (CRT). Thus, synthesis of hydrophobic derivatives capable of crossing the BBB by alternative pathway is of great importance for the treatment of acute and chronic neurological diseases including stroke, traumatic brain injury and hereditary CRT deficiency. Here we describe synthesis of new hybrid compounds-creatinyl amino acids, their neuroprotective activity in vivo and stability to degradation in different media. The title compounds were synthesized by guanidinylation of corresponding sarcosyl peptides or direct creatine attachment using isobutyl chloroformate method. Addition of lipophilic counterion (p-toluenesulfonate) ensures efficient creatine dissolution in DMF with simultaneous protection of guanidino group towards intramolecular cyclization. It excludes the application of expensive guanidinylating reagents, permits to simplify synthetic procedure and adapt it to large-scale production. The biological activity of creatinyl amino acids was tested in vivo on ischemic stroke and NaNO(2) -induced hypoxia models. One of the most effective compounds-creatinyl-glycine ethyl ester increases life span of experimental animals more than two times in hypoxia model and has neuroprotective action in brain stroke model when applied both before and after ischemia. These data evidenced that creatinyl amino acids can represent promising candidates for the development of new drugs useful in stroke treatment. PMID:21644247

  15. Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    2000-01-01

    A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

  16. Development of fluorescent nanoparticle-labeled lateral flow assay for the detection of nucleic acids.

    PubMed

    Wang, Yuhong; Nugen, Sam R

    2013-10-01

    The rapid, specific and sensitive detection of nucleic acids is of utmost importance for the identification of infectious agents, diagnosis and treatment of genetic diseases, and the detection of pathogens related to human health and safety. Here we report the development of a simple and sensitive nucleic acid sequence-based and Ru(bpy)3 (2+)-doped silica nanoparticle-labeled lateral flow assay which achieves low limit of detection by using fluorescencent nanoparticles. The detection of the synthetic nucleic acid sequences representative of Trypanosoma mRNA, the causative agent for African sleeping sickness, was utilized to demonstrate this assay. The 30 nm spherical Ru(bpy)3 (2+)-doped silica nanoparticles were prepared in aqueous medium by a novel method recently reported. The nanoparticles were modified by 3-glycidoxypropyl trimethoxysilane in order to conjugate to amine-capped oligonucleotide reporter probes. The fluorescent intensities of the fluorescent assays were quantified on a mictrotiter plate reader using a custom holder. The experimental results showed that the lateral flow fluorescent assay developed was more sensitive compared with the traditional colloidal gold test strips. The limit of detection for the fluorescent lateral flow assay developed is approximately 0.066 fmols as compared to approximately 15 fmols for the colloidal gold. The limit of detection can further be reduced about one order of magnitude when "dipstick" format was used. PMID:23525961

  17. Improved sensitivity of an acid sphingomyelinase activity assay using a C6:0 sphingomyelin substrate.

    PubMed

    Chuang, Wei-Lien; Pacheco, Joshua; Cooper, Samantha; Kingsbury, Jonathan S; Hinds, John; Wolf, Pavlina; Oliva, Petra; Keutzer, Joan; Cox, Gerald F; Zhang, Kate

    2015-06-01

    Short-chain C6-sphingomyelin is an artificial substrate that was used in an acid sphingomyelinase activity assay for a pilot screening study of patients with Niemann-Pick disease types A and B. Using previously published multiplex and single assay conditions, normal acid sphingomyelinase activity levels (i.e. false negative results) were observed in two sisters with Niemann-Pick B who were compound heterozygotes for two missense mutations, p.C92W and p.P184L, in the SMPD1 gene. Increasing the sodium taurocholate detergent concentration in the assay buffer lowered the activity levels of these two patients into the range observed with other patients with clear separation from normal controls. PMID:26937397

  18. Improved sensitivity of an acid sphingomyelinase activity assay using a C6:0 sphingomyelin substrate

    PubMed Central

    Chuang, Wei-Lien; Pacheco, Joshua; Cooper, Samantha; Kingsbury, Jonathan S.; Hinds, John; Wolf, Pavlina; Oliva, Petra; Keutzer, Joan; Cox, Gerald F.; Zhang, Kate

    2015-01-01

    Short-chain C6-sphingomyelin is an artificial substrate that was used in an acid sphingomyelinase activity assay for a pilot screening study of patients with Niemann–Pick disease types A and B. Using previously published multiplex and single assay conditions, normal acid sphingomyelinase activity levels (i.e. false negative results) were observed in two sisters with Niemann–Pick B who were compound heterozygotes for two missense mutations, p.C92W and p.P184L, in the SMPD1 gene. Increasing the sodium taurocholate detergent concentration in the assay buffer lowered the activity levels of these two patients into the range observed with other patients with clear separation from normal controls. PMID:26937397

  19. Development and Evaluation of a Calibrator Material for Nucleic Acid-Based Assays for Diagnosing Aspergillosis

    PubMed Central

    Abdul-Ali, Deborah; Loeffler, Juergen; White, P. Lewis; Wickes, Brian; Herrera, Monica L.; Alexander, Barbara D.; Baden, Lindsey R.; Clancy, Cornelius; Denning, David; Nguyen, M. Hong; Sugrue, Michele; Wheat, L. Joseph; Wingard, John R.; Donnelly, J. Peter; Barnes, Rosemary; Patterson, Thomas F.; Caliendo, Angela M.

    2013-01-01

    Twelve laboratories evaluated candidate material for an Aspergillus DNA calibrator. The DNA material was quantified using limiting-dilution analysis; the mean concentration was determined to be 1.73 × 1010 units/ml. The calibrator can be used to standardize aspergillosis diagnostic assays which detect and/or quantify nucleic acid. PMID:23616459

  20. Analysis of Citric Acid in Beverages: Use of an Indicator Displacement Assay

    ERIC Educational Resources Information Center

    Umali, Alona P.; Anslyn, Eric V.; Wright, Aaron T.; Blieden, Clifford R.; Smith, Carolyne K.; Tian, Tian; Truong, Jennifer A.; Crumm, Caitlin E.; Garcia, Jorge E.; Lee, Soal; Mosier, Meredith; Nguyen, Chester P.

    2010-01-01

    The use of an indicator displacement assay permits the visualization of binding events between host and guest molecules. An undergraduate laboratory experiment is described to demonstrate the technique in the determination of citric acid content in commercially available beverages such as soda pop and fruit juices. Through the technique, students…

  1. Biological Monitoring of 3-Phenoxybenzoic Acid in Urine by an Enzyme -Linked Immunosorbent Assay

    EPA Science Inventory

    An enzyme-linked immunosorbent assay (ELISA) method was employed for determination of the pyrethroid biomarker, 3-phenoxybenzoic acid (3-PBA) in human urine samples. The optimized coating antigen concentration was 0.5 ng/mL with a dilution of 1:4000 for the 3-PBA antibody and 1:6...

  2. Response to oxalic acid as a resistance assay for Sclerotinia minor in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Response to oxalic acid was evaluated as a potential assay for screening peanut breeding lines for resistance to Sclerotinia blight caused by Sclerotinia minor. Detached stems of seven Spanish- and six runner-type peanut cultivars and advanced breeding lines, varying in resistance to Sclerotinia bl...

  3. 21 CFR 866.3980 - Respiratory viral panel multiplex nucleic acid assay.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... detection and identification of a combination of the following viruses: (1) Influenza A and Influenza B; (2) Influenza A subtype H1 and Influenza A subtype H3; (3) Respiratory Syncytial Virus subtype A and Respiratory... Metapneumovirus (hMPV) Using Nucleic Acid Assays;” and (3) For a device that detects and differentiates...

  4. 21 CFR 866.3980 - Respiratory viral panel multiplex nucleic acid assay.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... detection and identification of a combination of the following viruses: (1) Influenza A and Influenza B; (2) Influenza A subtype H1 and Influenza A subtype H3; (3) Respiratory Syncytial Virus subtype A and Respiratory... Metapneumovirus (hMPV) Using Nucleic Acid Assays;” and (3) For a device that detects and differentiates...

  5. 21 CFR 866.3980 - Respiratory viral panel multiplex nucleic acid assay.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... detection and identification of a combination of the following viruses: (1) Influenza A and Influenza B; (2) Influenza A subtype H1 and Influenza A subtype H3; (3) Respiratory Syncytial Virus subtype A and Respiratory... Metapneumovirus (hMPV) Using Nucleic Acid Assays;” and (3) For a device that detects and differentiates...

  6. 21 CFR 866.3980 - Respiratory viral panel multiplex nucleic acid assay.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... detection and identification of a combination of the following viruses: (1) Influenza A and Influenza B; (2) Influenza A subtype H1 and Influenza A subtype H3; (3) Respiratory Syncytial Virus subtype A and Respiratory... Metapneumovirus (hMPV) Using Nucleic Acid Assays;” and (3) For a device that detects and differentiates...

  7. 21 CFR 866.3980 - Respiratory viral panel multiplex nucleic acid assay.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... detection and identification of a combination of the following viruses: (1) Influenza A and Influenza B; (2) Influenza A subtype H1 and Influenza A subtype H3; (3) Respiratory Syncytial Virus subtype A and Respiratory... Metapneumovirus (hMPV) Using Nucleic Acid Assays;” and (3) For a device that detects and differentiates...

  8. Protecting Quantum Dot Fluorescence from Quenching to Achieve a Reliable Automated Multiplex Fluorescence In Situ Hybridization Assay.

    PubMed

    Zhang, Wenjun; Hubbard, Antony; Pang, Lizhen; Parkinson, Leslie Baca; Brunhoeber, Patrick; Wang, Yixin; Tang, Lei

    2015-09-01

    Quantum dots (QD) are novel inorganic fluorochromes that are ultra-bright, photo-stable, and available in multiple, highly-resolvable colors. QDs represent an ideal detection material for in situ hybridization (ISH) because they may provide unprecedented resolution and strong signal intensities that are not attainable with traditional fluorophores. Unfortunately, lack of reliability has been an impediment to widespread adoption of QD-based fluorescence in situ hybridization (QD FISH) technology. By optimizing QD-to-target accessibility, we have developed a QD FISH staining procedure that dramatically improves the reliability of an automated ERG/PTEN QD FISH assay (91% 1st pass rate). Here, we report improvements to the assay that protects QD fluorescence from quenching due to trace amounts of heavy metals and minimizes QD background signals. When using this method, highly-consistent staining was observed with the ERG/PTEN QD FISH assay in prostate tissue. Successful staining of several other clinically-relevant genetic markers was also possible. We further demonstrated improved reliability for determining HER2 gene status in breast cancer, identifying anaplastic lymphoma kinase (ALK) gene break-apart in non-small cell lung cancer, and detecting human papillomavirus 16 (HPV16) in cervical intraepithelial neoplasia. The enhanced QD FISH assay allows for examining complicated genetic aberrances without use of enzymatic amplification. Our optimized methods now demonstrate reliability sufficient for QD FISH technology to be a diagnostic tool in a clinical setting. PMID:26485928

  9. Method for nucleic acid hybridization using single-stranded DNA binding protein

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1996-01-01

    Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.

  10. Adenovirus Type 2-Simian Virus 40 Hybrid Population: Evidence for a Hybrid Deoxyribonucleic Acid Molecule and the Absence of Adenovirus-Encapsidated Circular Simian Virus 40 Deoxyribonucleic Acid

    PubMed Central

    Crumpacker, Clyde S.; Levin, Myron J.; Wiese, William H.; Lewis, Andrew M.; Rowe, Wallace P.

    1970-01-01

    The deoxyribonucleic acid (DNA) from the adenovirus-encapsidated particles of the adenovirus type 2 (Ad2)-simian virus 40 (SV40) hybrid population plaque variant (Ad2++ HEY), known to yield SV40 virus with high efficiency, was studied by equilibrium density centrifugation followed by ribonucleic acid-DNA hybridization employing virus-specific complementary ribonucleic acids synthesized in vitro. These techniques establish linkage between the Ad2 and SV40 components in the adenovirus-encapsidated particles of this population. The linkage is alkali-resistant and presumably covalent; thus, the Ad2 DNA and SV40 DNA are present in a hybrid molecule. Velocity centrifugation studies in alkaline sucrose gradients eliminated the possibility that supercoiled circular SV40 DNA is present in the adenovirus capsids. The DNA obtained from the adenovirus-encapsidated particles of the Ad2++ HEY population appears to consist of nonhybrid Ad2 DNA and Ad2-SV40 hybrid DNA molecules. PMID:4322081

  11. Nucleic Acid-Peptide Complex Phase Controlled by DNA Hybridization

    NASA Astrophysics Data System (ADS)

    Vieregg, Jeffrey; Lueckheide, Michael; Leon, Lorraine; Marciel, Amanda; Tirrell, Matthew

    When polyanions and polycations are mixed, counterion release drives formation of polymer-rich complexes that can either be solid (precipitates) or liquid (coacervates) depending on the properties of the polyelectrolytes. These complexes are important in many fields, from encapsulation of industrial polymers to membrane-free segregation of biomolecules such as nucleic acids and proteins. Condensation of long double-stranded DNA has been studied for several decades, but comparatively little attention has been paid to the polyelectrolyte behavior of oligonucleotides. We report here studies of DNA oligonucleotides (10 - 88 nt) complexed with polylysine (10 - 100 aa). Unexpectedly, we find that the phase of the resulting complexes is controlled by the hybridization state of the nucleic acid, with double-stranded DNA forming precipitates and single-stranded DNA forming coacervates. Stability increases with polyelectrolyte length and decreases with solution salt concentration, with complexes of the longer double-stranded polymers undergoing precipitate/coacervate/soluble transitions as ionic strength is increased. Mixing coacervates formed by complementary single-stranded oligonucleotides results in precipitate formation, raising the possibility of stimulus-responsive material design.

  12. Real-time quantification of fatty acid uptake using a novel fluorescence assay.

    PubMed

    Liao, Jinfang; Sportsman, Richard; Harris, Jeff; Stahl, Andreas

    2005-03-01

    Uptake of nonesterified long-chain fatty acids (LCFAs) into many cell types and organs such as liver, heart, intestine, and skeletal muscle occurs primarily through a saturable, protein-mediated mechanism. Membrane proteins that increase the uptake of LCFAs, such as FAT/CD36 and fatty acid transport proteins, represent significant therapeutic targets for the treatment of metabolic disorders, including type 2 diabetes. However, currently available methods for the quantification of LCFA uptake neither allow for real-time measurements of uptake kinetics nor are ideally suited for the development of LCFA uptake inhibitors in high-throughput screens. To address both problems, we developed a LCFA uptake assay using a fluorescently labeled fatty acid and a nontoxic cell-impermeable quenching agent that allows fatty acid transport to be measured in real time using fluorescence plate readers or standard fluorescence microscopy. With this assay, we faithfully reproduced known differentiation- and hormone-induced changes in LCFA uptake by 3T3-L1 cells and determined LCFA uptake kinetics with previously unobtainable temporal resolution. Applications of this novel assay should facilitate new insights into the biology of fatty acid uptake and provide new means for obesity-related drug discovery. PMID:15547301

  13. A simple and highly sensitive radioenzymatic assay for lysophosphatidic acid quantification

    PubMed Central

    Saulnier-Blache, Jean Sébastien; Girard, Alexia; Simon, Marie-Françoise; Lafontan, Max; Valet, Philippe

    2000-01-01

    The objective of the present work was to develop a simple and sensitive radioenzymatic assay to quantify lysophosphatidic acid (LPA). For that, a recombinant rat lysophosphatidic acid acyl transferase (LPAAT) produced in Escherichia coli was used. In the presence of [14C]oleoyl CoA, LPAAT selectively catalyzes the transformation of LPA and alkyl-LPA into [14C]phosphatidic acid. Acylation of LPA was complete and linear from 0 to 200 pmoles with a minimal detection of 0.2 pmoles. This method was used to quantify LPA in butanol- extracted lipids from bovine sera, as well as from human and mouse plasma. This radioenzymatic assay represents a new, simple, and highly sensitive method to quantify LPA in various biological fluids. PMID:11108727

  14. The uronic acids assay: a method for the determination of chemical activity on biofilm EPS.

    PubMed

    Mojica, Kristina D A; Cooney, Michael J

    2010-01-01

    In this work, the uronic acids assay was evaluated for its potential to function as a bioassay to screen for antagonistic activity against the production of microbial biofilm exopolysaccharide (EPS). The assay was first applied to biofilms produced in the presence of two universal disinfectants (sodium hypochlorite and sodium dodecyl sulfate) known to inhibit microbial growth and biofilm formation. The performance of the assay was then characterized through statistical assessment of threshold concentrations for disinfection efficiency and consistency relative to values reported in the literature. The assay was then evaluated for its utility in screening for enzymatic or chemical inhibitors of biofilm formation (eg glycosidases, halogenated furanones, and semi-crude fractions extracted from minimally fouled marine plants) and its ability to distinguish between true anti-biofilm activity and simple disinfection. Activity was characterized as (i) no effect, (ii) a true positive effect (ie increased biofilm EPS), (iii) anti-bacterial activity (ie decreased biofilm EPS and analogous decrease in planktonic growth), and (iv) anti-biofilm EPS activity (ie decreased biofilm EPS, without analogous decrease in planktonic growth). Results demonstrate that the uronic acids assay can augment existing biofilm characterization methods by providing a quantitative measure of biofilm EPS. PMID:20087802

  15. Comparison of Onclarity Human Papillomavirus (HPV) Assay with Hybrid Capture II HPV DNA Assay for Detection of Cervical Intraepithelial Neoplasia Grade 2 and 3 Lesions

    PubMed Central

    Sideri, M.; Gulmini, C.; Igidbashian, S.; Tricca, A.; Casadio, C.; Carinelli, S.; Boveri, S.; Ejegod, D.; Bonde, J.; Sandri, M. T.

    2015-01-01

    Analytical and clinical performance validation is essential before introduction of a new human papillomavirus (HPV) assay into clinical practice. This study compares the new BD Onclarity HPV assay, which detects E6/E7 DNA from 14 high-risk HPV types, to the Hybrid Capture II (HC2) HPV DNA test, to concurrent cytology and histology results, in order to evaluate its performance in detecting high-grade cervical lesions. A population of 567 women, including 325 with ≥ASCUS (where ASCUS stands for atypical cells of undetermined significance) and any HC2 result and 242 with both negative cytology and negative HC2 results, were prospectively enrolled for the study. The overall agreement between Onclarity and HC2 was 94.6% (95% confidence intervals [CI], 92.3% to 96.2%). In this population with a high prevalence of disease, the relative sensitivities (versus adjudicated cervical intraepithelial neoplasia grades 2 and 3 [CIN2+] histology endpoints) of the Onclarity and HC2 tests were 95.2% (95% CI, 90.7% to 97.5%) and 96.9% (95% CI, 92.9% to 98.7%), respectively, and the relative specificities were 50.3% (95% CI, 43.2% to 57.4%) for BD and 40.8% (95% CI, 33.9%, 48.1%) for HC2. These results indicate that the BD Onclarity HPV assay has sensitivity comparable to that of the HC2 assay, with a trend to an increased specificity. Moreover, as Onclarity gives the chance to discriminate between the different genotypes, we calculated the genotype prevalence and the absolute risk of CIN2+: HPV 16 was the most prevalent genotype (19.8%) with an absolute risk of CIN2+ of 77.1%. PMID:25903574

  16. Comparison of Onclarity Human Papillomavirus (HPV) Assay with Hybrid Capture II HPV DNA Assay for Detection of Cervical Intraepithelial Neoplasia Grade 2 and 3 Lesions.

    PubMed

    Bottari, F; Sideri, M; Gulmini, C; Igidbashian, S; Tricca, A; Casadio, C; Carinelli, S; Boveri, S; Ejegod, D; Bonde, J; Sandri, M T

    2015-07-01

    Analytical and clinical performance validation is essential before introduction of a new human papillomavirus (HPV) assay into clinical practice. This study compares the new BD Onclarity HPV assay, which detects E6/E7 DNA from 14 high-risk HPV types, to the Hybrid Capture II (HC2) HPV DNA test, to concurrent cytology and histology results, in order to evaluate its performance in detecting high-grade cervical lesions. A population of 567 women, including 325 with ≥ASCUS (where ASCUS stands for atypical cells of undetermined significance) and any HC2 result and 242 with both negative cytology and negative HC2 results, were prospectively enrolled for the study. The overall agreement between Onclarity and HC2 was 94.6% (95% confidence intervals [CI], 92.3% to 96.2%). In this population with a high prevalence of disease, the relative sensitivities (versus adjudicated cervical intraepithelial neoplasia grades 2 and 3 [CIN2+] histology endpoints) of the Onclarity and HC2 tests were 95.2% (95% CI, 90.7% to 97.5%) and 96.9% (95% CI, 92.9% to 98.7%), respectively, and the relative specificities were 50.3% (95% CI, 43.2% to 57.4%) for BD and 40.8% (95% CI, 33.9%, 48.1%) for HC2. These results indicate that the BD Onclarity HPV assay has sensitivity comparable to that of the HC2 assay, with a trend to an increased specificity. Moreover, as Onclarity gives the chance to discriminate between the different genotypes, we calculated the genotype prevalence and the absolute risk of CIN2+: HPV 16 was the most prevalent genotype (19.8%) with an absolute risk of CIN2+ of 77.1%. PMID:25903574

  17. A facile assay to monitor secretory phospholipase A₂ using 8-anilino-1-naphthalenesulfonic acid.

    PubMed

    Vivek, Hamse K; Swamy, Supritha G; Priya, Babu S; Sethi, Gautam; Rangappa, Kanchugarakoppal S; Swamy, S Nanjunda

    2014-09-15

    Secretory phospholipases A2 (sPLA2s) are present in snake venoms, serum, and biological fluids of patients with various inflammatory, autoimmune and allergic disorders. Lipid mediators in the inflammatory processes have potential value for controlling phospholipid metabolism through sPLA2 inhibition. Thus, it demands the need for screening of potential leads for sPLA2 inhibition. To date, sPLA2 activity has been assayed using expensive radioactive or chromogenic substrates, thereby limiting a large number of assays. In this study, a simple and sensitive NanoDrop assay was developed using non-fluorogenic and non-chromogenic phospholipid substrate 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 8-anilino-1-naphthalenesulfonic acid (ANS) as interfacial hydrophobic probe. The modified assay required a 10ng concentration of sPLA2. ANS, as a strong anion, binds predominantly to cationic group of choline head of DMPC through ion pair formation, imparting hydrophobicity and lipophilicity and resulting in an increase in fluorescence. Triton X-100 imparts correct geometrical space during sPLA2 catalyzing DMPC, releasing lysophospholipid and acidic myristoyl acid, which in turn alters the hydrophobic environment prevailing around ANS-DMPC, which leads to weakening of the electrostatic ion pair interaction between DMPC and ANS ensuing decrease in fluorescence. These characteristic fluorescence changes between DMPC and ANS in response to sPLA2 catalysis are well documented and validated in this study. PMID:24915638

  18. Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids.

    PubMed

    Yang, Li; Li, Bosheng; Zheng, Xiao-yu; Li, Jigang; Yang, Mei; Dong, Xinnian; He, Guangming; An, Chengcai; Deng, Xing Wang

    2015-01-01

    Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits in Arabidopsis thaliana, but its effect on defence remains largely unexplored. Here, we show that hybrids between some A. thaliana accessions show increased resistance to the biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. Comparisons of transcriptomes between these hybrids and their parents after inoculation reveal that several key salicylic acid (SA) biosynthesis genes are significantly upregulated in hybrids. Moreover, SA levels are higher in hybrids than in either parent. Increased resistance to Pst DC3000 is significantly compromised in hybrids of pad4 mutants in which the SA biosynthesis pathway is blocked. Finally, increased histone H3 acetylation of key SA biosynthesis genes correlates with their upregulation in infected hybrids. Our data demonstrate that enhanced activation of SA biosynthesis in A. thaliana hybrids may contribute to their increased resistance to a biotrophic bacterial pathogen. PMID:26065719

  19. Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids

    PubMed Central

    Yang, Li; Li, Bosheng; Zheng, Xiao-yu; Li, Jigang; Yang, Mei; Dong, Xinnian; He, Guangming; An, Chengcai; Deng, Xing Wang

    2015-01-01

    Heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits in Arabidopsis thaliana, but its effect on defence remains largely unexplored. Here, we show that hybrids between some A. thaliana accessions show increased resistance to the biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. Comparisons of transcriptomes between these hybrids and their parents after inoculation reveal that several key salicylic acid (SA) biosynthesis genes are significantly upregulated in hybrids. Moreover, SA levels are higher in hybrids than in either parent. Increased resistance to Pst DC3000 is significantly compromised in hybrids of pad4 mutants in which the SA biosynthesis pathway is blocked. Finally, increased histone H3 acetylation of key SA biosynthesis genes correlates with their upregulation in infected hybrids. Our data demonstrate that enhanced activation of SA biosynthesis in A. thaliana hybrids may contribute to their increased resistance to a biotrophic bacterial pathogen. PMID:26065719

  20. Integrated sample-to-detection chip for nucleic acid test assays.

    PubMed

    Prakash, R; Pabbaraju, K; Wong, S; Tellier, R; Kaler, K V I S

    2016-06-01

    Nucleic acid based diagnostic techniques are routinely used for the detection of infectious agents. Most of these assays rely on nucleic acid extraction platforms for the extraction and purification of nucleic acids and a separate real-time PCR platform for quantitative nucleic acid amplification tests (NATs). Several microfluidic lab on chip (LOC) technologies have been developed, where mechanical and chemical methods are used for the extraction and purification of nucleic acids. Microfluidic technologies have also been effectively utilized for chip based real-time PCR assays. However, there are few examples of microfluidic systems which have successfully integrated these two key processes. In this study, we have implemented an electro-actuation based LOC micro-device that leverages multi-frequency actuation of samples and reagents droplets for chip based nucleic acid extraction and real-time, reverse transcription (RT) PCR (qRT-PCR) amplification from clinical samples. Our prototype micro-device combines chemical lysis with electric field assisted isolation of nucleic acid in a four channel parallel processing scheme. Furthermore, a four channel parallel qRT-PCR amplification and detection assay is integrated to deliver the sample-to-detection NAT chip. The NAT chip combines dielectrophoresis and electrostatic/electrowetting actuation methods with resistive micro-heaters and temperature sensors to perform chip based integrated NATs. The two chip modules have been validated using different panels of clinical samples and their performance compared with standard platforms. This study has established that our integrated NAT chip system has a sensitivity and specificity comparable to that of the standard platforms while providing up to 10 fold reduction in sample/reagent volumes. PMID:27165104

  1. Development of a Quantitative BRET Affinity Assay for Nucleic Acid-Protein Interactions

    PubMed Central

    Vickers, Timothy A.; Crooke, Stanley T.

    2016-01-01

    Protein-nucleic acid interactions play a crucial role in the regulation of diverse biological processes. Elucidating the roles that protein-nucleic acid complexes play in the regulation of transcription, translation, DNA replication, repair and recombination, and RNA processing continues to be a crucial aspect of understanding of cell biology and the mechanisms of disease. In addition, proteins have been demonstrated to interact with antisense oligonucleotide therapeutics in a sequence and chemistry dependent manner, influencing ASO potency and distribution in cells and in vivo. While many assays have been developed to measure protein-nucleic acid interactions, many suffer from lack of throughput and sensitivity, or challenges with protein purification and scalability. In this report we present a new BRET assay for the analysis of DNA-protein interactions which makes use of an extremely bright luciferase as a tag for the binding protein, along with a long-wavelength fluorophore conjugated to the nucleic acid. The resulting assay is high throughput, sensitive, does not require protein purification, and even allows for quantitative characterization of these interactions within the biologically relevant context of whole cells. PMID:27571227

  2. Development of a Quantitative BRET Affinity Assay for Nucleic Acid-Protein Interactions.

    PubMed

    Vickers, Timothy A; Crooke, Stanley T

    2016-01-01

    Protein-nucleic acid interactions play a crucial role in the regulation of diverse biological processes. Elucidating the roles that protein-nucleic acid complexes play in the regulation of transcription, translation, DNA replication, repair and recombination, and RNA processing continues to be a crucial aspect of understanding of cell biology and the mechanisms of disease. In addition, proteins have been demonstrated to interact with antisense oligonucleotide therapeutics in a sequence and chemistry dependent manner, influencing ASO potency and distribution in cells and in vivo. While many assays have been developed to measure protein-nucleic acid interactions, many suffer from lack of throughput and sensitivity, or challenges with protein purification and scalability. In this report we present a new BRET assay for the analysis of DNA-protein interactions which makes use of an extremely bright luciferase as a tag for the binding protein, along with a long-wavelength fluorophore conjugated to the nucleic acid. The resulting assay is high throughput, sensitive, does not require protein purification, and even allows for quantitative characterization of these interactions within the biologically relevant context of whole cells. PMID:27571227

  3. Duplex PCR assay and in situ hybridization for detection of Francisella spp. and Francisella noatunensis subsp. orientalis in red tilapia.

    PubMed

    Dong, Ha T; Gangnonngiw, Warachin; Phiwsaiya, Kornsunee; Charoensapsri, Walaiporn; Nguyen, Vuong V; Nilsen, Pål; Pradeep, Padmaja J; Withyachumnarnkul, Boonsirm; Senapin, Saengchan; Rodkhum, Channarong

    2016-06-15

    Conventional isolation and identification based on phenotypic characteristics is challenging with the highly fastidious, intracellular bacterium Francisella noatunensis subsp. orientalis (Fno). Here, we developed a duplex PCR method for simultaneous detection of the Francisella genus and Fno in one PCR reaction and an in situ hybridization method for paraffin section based diagnosis of Fno. The PCR results showed genus- and species-specific bands (1140 and 203 bp) from Fno but only one genus-specific band (1140 bp) from F. noatunensis subsp. noatunensis. Sensitivity of the duplex PCR assay revealed a detection limit of 20 to 200 fg genomic DNA (~10 to 100 genome equivalents) depending on DNA template extraction methods. The newly developed duplex PCR assay could be used to detect Fno from clinically sick fish exhibiting signs of visceral granulomas and would also be able to detect Fno infection in naturally diseased fish without symptoms of francisellosis, indicating potential application for diagnosis of field samples. The in situ hybridization assay using Fno species-specific probe revealed positive signals in multiple organs including the spleen, liver, kidney, gills and intestine of infected fish. PMID:27304869

  4. Gibberellic Acid-induced Phase Change in Hedera helix as Studied by Deoxyribonucleic Acid-Ribonucleic Acid Hybridization 1

    PubMed Central

    Rogler, Charles E.; Dahmus, Michael E.

    1974-01-01

    Applications of gibberellic acid to the mature form of Hedera helix induce morphological reversions to the juvenile form of growth. The juvenile forms produced are stable with time and differ dramatically from the mature in phenotype. DNA-RNA hybridization techniques have been used to study the RNA populations of juvenile, mature and gibberellic acid-treated mature apices. Hybridization competition experiments using RNA extracted by a hot phenol technique and uniformly labeled in vitro with 3H dimethylsulfate show no qualitative differences between the species of RNA present in juvenile and mature apices. However, differences are observed in the frequency distribution of RNA species using both uniformly labeled or pulse-labeled RNA as a reference. RNA extracted from gibberellic acid-treated mature buds was a less effective competitor than control mature RNA and the difference observed was comparable to that observed between mature and juvenile RNA. These results indicate that at least part of the molecular basis of phase change and gibberellic acid action may involve an alteration in the rate of transcription of certain genes in the apices of the mature form. RNA extracted using the hot phenol procedure contained a fraction of rapidly labeled RNA which was not extractable with cold phenol. When RNA extracted only with cold phenol was used in competition experiments sequences unique to the juvenile were detected and sequences unique to the mature were not detected. Implications of these results in relation to possible post-transcriptional control mechanisms are discussed. PMID:16658844

  5. Novel Conjugates of 1,3-Diacylglycerol and Lipoic Acid: Synthesis, DPPH Assay, and RP-LC-MS-APCI Analysis

    PubMed Central

    Madawala, Samanthi R. P.; Andersson, Rolf E.; Jastrebova, Jelena A.; Almeida, Maria; Dutta, Paresh C.

    2011-01-01

    1,3-Diacylglycerol is known to reduce body weight and fat deposits in humans. α-Lipoic acid is a potent antioxidant and effective against many pathological conditions, including obesity and related metabolic syndromes. The present work is based on the hypothesis that the hybrid molecules of 1,3-diacylglycerol and lipoic acid possess synergistic and/or additive effects compared with the parent compounds against obesity, overweight, and related metabolic syndromes. Laboratory scale synthesis of 1,3-dioleoyl-2-lipoyl-sn-glycerol (yield 80%) and 1,3-dioleoyl-2-dihydrolipoyl-sn-glycerol (yield 70%) was performed for the first time and supported by NMR and MS data. Free radical scavenging capacity of the conjugates was assayed using DPPH test. A remarkably high in vitro free radical scavenging capacity was demonstrated for the 1,3-dioleoyl-2-dihydrolipoyl-sn-glycerol (EC50 value 0.21). RP-HPLC-MS-APCI analysis showed satisfactory separation between the conjugates (R~1). Protonated molecular ion of the conjugates at m/z 809 and m/z at 811, respectively, and their characteristic fragment ions were abundant. PMID:21966595

  6. Mfold web server for nucleic acid folding and hybridization prediction

    PubMed Central

    Zuker, Michael

    2003-01-01

    The abbreviated name, ‘mfold web server’, describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as ‘MFOLDROOT’. PMID:12824337

  7. Rapid Sensitive Assay for Interferons Based on the Inhibition of MM Virus Nucleic Acid Synthesis

    PubMed Central

    Allen, Patton T.; Giron, David J.

    1970-01-01

    A method for assaying mouse interferon based on the inhibition of viral ribonucleic acid (RNA) synthesis was devised. The amount of MM virus and RNA synthesized in interferon-treated L-cell cultures was determined by measuring the amount of 3H-uridine converted into a trichloroacetic acid-insoluble form after treatment of the infected cultures with 2.5 μg of actinomycin D per ml. The amount of RNA synthesized was inversely related to the concentration of interferon used for treatment. A linear dose-response regression curve was obtained by plotting the log of the amount of RNA made, expressed as a percentage of the control, versus the log of the reciprocal of the interferon dilution. A unit of interferon was defined as that concentration which inhibited nucleic acid synthesis by 50% (INAS50). The concentration of mouse interferon could be determined within 24 hr. This assay method, on the average, was approximately half as sensitive as the method which measured the 50% reduction of MM virus plaque number (PDD50-MM method), but was, on the average, almost 1.7 times as sensitive as the PDD50-VSV method. It averaged approximately 20 times the sensitivity of the methods which used as end points the 70% reduction in yield of MM virus or the complete inhibition of cytopathic effect by MM virus. The reproducibility of the INAS50 technique was tested in two ways. (i) Four independent assays of an interferon specimen were performed with replicate cultures. The standard deviation was 11.2% of the mean titer. (ii) On different dates, one interferon specimen was assayed seven times and another was assayed four times. The standard deviations were 21.5 and 26.6% of the respective mean titers. PMID:4320919

  8. Final Report Nucleic Acid System - PCR, Multiplex Assays and Sample Preparation Project

    SciTech Connect

    Koopman, R.P.; Langlois, R.G.; Nasarabadi, S.; Benett, W.J.; Richards, J.B.; Hadley, D.R.; Miles, R.R.; Brown, S.B.; Stratton, P.L.; Milanovich, F.P.

    2001-04-20

    The objective of this project was to reduce to practice the detection and identification of biological warfare pathogens by the nucleic acid recognition technique of PCR (polymerase chain reaction). This entailed not only building operationally functional instrumentation but also developing the chemical assays for detection of priority pathogens. This project had two principal deliverables: (1) design, construct, test and deliver a 24 chamber, multiplex capable suitcase sized PCR instrument, and (2) develop and reduce to practice a multiplex assay for the detection of PCR product by flow cytometry. In addition, significant resources were allocated to test and evaluation of the Hand-held Advanced Nucleic Acid Analyzer (HANAA). This project helps provide the signature and intelligence gathering community the ability to perform, on-site or remote, rapid analysis of environmental or like samples for the presence of a suite of biological warfare pathogens.

  9. Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm

    PubMed Central

    Öhrmalm, Christina; Jobs, Magnus; Eriksson, Ronnie; Golbob, Sultan; Elfaitouri, Amal; Benachenhou, Farid; Strømme, Maria; Blomberg, Jonas

    2010-01-01

    One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes. PMID:20864443

  10. A helicase assay based on the displacement of fluorescent, nucleic acid-binding ligands.

    PubMed Central

    Eggleston, A K; Rahim, N A; Kowalczykowski, S C

    1996-01-01

    We have developed a new helicase assay that overcomes many limitations of other assays used to measure this activity. This continuous, kinetic assay is based on the displacement of fluorescent dyes from dsDNA upon DNA unwinding. These ligands exhibit significant fluorescence enhancement when bound to duplex nucleic acids and serve as the reporter molecules of DNA unwinding. We evaluated the potential of several dyes [acridine orange, ethidium bromide, ethidium homodimer, bis-benzimide (DAPI), Hoechst 33258 and thiazole orange] to function as suitable reporter molecules and demonstrate that the latter three dyes can be used to monitor the helicase activity of Escherichia coli RecBCD enzyme. Both the binding stoichiometry of RecBCD enzyme for the ends of duplex DNA and the apparent rate of unwinding are not significantly perturbed by two of these dyes. The effects of temperature and salt concentration on the rate of unwinding were also examined. We propose that this dye displacement assay can be readily adapted for use with other DNA helicases, with RNA helicases, and with other enzymes that act on nucleic acids. PMID:8614617

  11. Bioprocess monitoring: minimizing sample matrix effects for total protein quantification with bicinchoninic acid assay.

    PubMed

    Reichelt, Wieland N; Waldschitz, Daniel; Herwig, Christoph; Neutsch, Lukas

    2016-09-01

    Determining total protein content is a routine operation in many laboratories. Despite substantial work on assay optimization interferences, the widely used bicinchoninic acid (BCA) assay remains widely recognized for its robustness. Especially in the field of bioprocess engineering the inaccuracy caused by interfering substances remains hardly predictable and not well understood. Since the introduction of the assay, sample pre-treatment by trichloroacetic acid (TCA) precipitation has been indicated as necessary and sufficient to minimize interferences. However, the sample matrix in cultivation media is not only highly complex but also dynamically changing over process time in terms of qualitative and quantitative composition. A significant misestimation of the total protein concentration of bioprocess samples is often observed when following standard work-up schemes such as TCA precipitation, indicating that this step alone is not an adequate means to avoid measurement bias. Here, we propose a modification of the BCA assay, which is less influenced by sample complexity. The dynamically changing sample matrix composition of bioprocessing samples impairs the conventional approach of compensating for interfering substances via a static offset. Hence, we evaluated the use of a correction factor based on an internal spike measurement for the respective samples. Using protein spikes, the accuracy of the BCA protein quantification could be improved fivefold, taking the BCA protein quantification to a level of accuracy comparable to other, more expensive methods. This will allow reducing expensive iterations in bioprocess development to due inaccurate total protein analytics. PMID:27314233

  12. In situ screening assay for cell viability using a dimeric cyanine nucleic acid stain.

    PubMed

    Becker, B; Clapper, J; Harkins, K R; Olson, J A

    1994-08-15

    A rapid and sensitive assay is described for the determination of cell viability of adherent and nonadherent cells that can be performed in situ in 96-well microtiter plates using fluorescence plate scanners. The assay, based on dye exclusion, utilizes a plasma membrane-impermeable, dimeric cyanine dye (YOYO-1). YOYO-1 fluoresces brightly only when bound to nucleic acids. Cells are incubated with YOYO-1, and fluorescence is measured before and after the addition of detergent, which allows the dye to enter the cells. The fluorescence before detergent treatment originates from nonviable cells that have membrane damage and take up YOYO-1. The fluorescence after detergent treatment originates from all cells in the sample. The ratio of the two fluorescence values is used as an indicator of cell viability. The cell viability results of this microplate assay closely resemble those of dye exclusion studies by flow cytometry and are similar but not identical to those of the thiazolyl blue assay, which uses a metabolic indicator of cell death. Because the assay can be performed in situ, without removing the medium, disintegrated cells, cell aggregates, and cells that stick to culture vessel walls are all included in the measurement. PMID:7527190

  13. Fluorometric assay for quantitation of biotin covalently attached to proteins and nucleic acids.

    PubMed

    Batchelor, Robert H; Sarkez, Adam; Cox, W Gregory; Johnson, Iain

    2007-10-01

    As a component of the (strept)avidin affinity system, biotin is often covalently linked to proteins or nucleic acids. We describe here a microplate-based high-throughput fluorometric assay for biotin linked to either proteins or nucleic acids based on fluorescence resonance energy transfer (FRET). This assay utilizes a complex of Alexa Fluoro 488 dye-labeled avidin with a quencher dye, 2-(4'-hydroxyazobenzene) benzoic acid (HABA), occupying the biotin binding sites of the avidin. In the absence of biotin, HABA quenches the fluorescence emission of the Alexa Fluor 488 dyes via FRET HABA is displaced when biotin binds to the Alexa Fluor 488 dye-labeled avidin, resulting in decreased FRET efficiency. This mechanism results in an increase in fluorescence intensity directly related to the amount of biotin present in the sample. The assay is able to detect as little as 4 pmol biotin in a 0.1 mL volume within 15 min of adding sample to the reagent, with a Z-factor > 0.9. PMID:18019342

  14. Determination of boron in produced water using the carminic acid assay.

    PubMed

    Floquet, Cedric F A; Sieben, Vincent J; MacKay, Bruce A; Mostowfi, Farshid

    2016-04-01

    Using the carminic acid assay, we determined the concentration of boron in oilfield waters. We investigated the effect of high concentrations of salts and dissolved metals on the assay performance. The influence of temperature, development time, reagent concentration, and water volume was studied. Ten produced and flowback water samples of different origins were measured, and the method was successfully validated against ICP-MS measurements. In water-stressed regions, produced water is a potential source of fresh water for irrigation, industrial applications, or consumption. Therefore, boron concentration must be determined and controlled to match the envisaged waste water reuse. Fast, precise, and onsite measurements are needed to minimize errors introduced by sample transportation to laboratories. We found that the optimum conditions for our application were a 5:1 mixing volume ratio (reagent to sample), a 1 g L(-1) carminic acid concentration in 99.99% sulfuric acid, and a 30 min reaction time at ambient temperature (20 °C to 23 °C). Absorption values were best measured at 610 nm and 630 nm and baseline corrected at 865 nm. Under these conditions, the sensitivity of the assay to boron was maximized while its cross-sensitivity to dissolved titanium, iron, barium and zirconium was minimized, alleviating the need for masking agents and extraction methods. PMID:26838405

  15. Synthesis and Monolayer Behaviors of Novel Hybrid Corynomycolic Acids Containing Semifluoroalkyl Groups.

    PubMed

    Kawase, Tokuzo; Tamaki, Kazuki; Oida, Tatsuo

    2016-01-01

    In this work, novel hybrid-type corynomycolic acids [hybrid-OH and hybrid-COOH, with semifluoroalkyl groups (Rf-(CH2)n-: Rf = C4F9, n = 6 and Rf = C6F13, n = 3) located on the carbon atoms attached to the hydroxyl and carboxylic acid groups (C-OH and C-COOH), respectively] were successfully synthesized. The behaviors and formation of hybrid corynomycolic acid monolayers at the air-water interface were investigated by surface tension and surface pressure-area (π-A) measurements to clarify the effects of the Rf chain length, position of the semifluoroalkyl group, and surfactant molecule stereochemistry. Compared to dialkyl corynomycolic acid, both the critical micelle concentration (CMC) and the surface tension at the CMC (γCMC) of hybrid corynomycolic acids were reduced by the presence of the Rf group. With respect to the surface tension versus log concentration (γ vs. log C) isotherms, all syn-isomers of the hybrid-OH and hybrid-COOH acids showed two break points, while the anti-isomers showed only one break point. These different isotherms can be explained in terms of the steric repulsion between the two hydrophilic groups (OH and COO(-)), which depend on the stereochemistry of the surfactant. No effect of the location of the semifluoroalkyl group was observed. With respect to the formation of a monolayer film, four parameters-the lift-off area (AL), zero-pressure molecular area (A0), maximum of the Gibbs elastic modulus [EG (max)], and monolayer collapse pressure (πc)-were measured. Both AL and A0 of all hybrid corynomycolic acids were larger than the corresponding dialkyl acids due to the bulky and rigid Rf groups. Interestingly, syn- and anti-hybrids had almost identical isotherms on compression, although the values of πc of anti-hybrids were higher than those of syn-isomers. In addition, the values of EG (max) of hybrid-COOHs were slightly larger than those of the corresponding hybrid-OHs. Using the nascent soap method (agent-in-oil method), we found that

  16. DEVELOPMENT OF ENZYME-LINKED IMMUNOSORBENT ASSAYS FOR ISOCUPRESSIC ACID AND SERUM METABOLITES OF ISOCUPRESSIC ACID

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The consumption of ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), common juniper (Juniperus communis) and Monterey cypress (Cupressus macrocarpa) causes abortions in pregnant cattle. Recent studies have identified isocupressic acid as the primary abortifacient compound in these ...

  17. Photodegradation and inhibition of drug-resistant influenza virus neuraminidase using anthraquinone-sialic acid hybrids.

    PubMed

    Aoki, Yusuke; Tanimoto, Shuho; Takahashi, Daisuke; Toshima, Kazunobu

    2013-02-11

    The anthraquinone-sialic acid hybrids designed effectively degraded not only non-drug-resistant neuraminidase but also drug-resistant neuraminidase, which is an important target of anti-influenza therapy. Degradation was achieved using long-wavelength UV radiation in the absence of any additives and under neutral conditions. Moreover, the hybrids efficiently inhibited neuraminidase activities upon photo-irradiation. PMID:23282898

  18. A hybrid microfluidic platform for cell-based assays via diffusive and convective trans-membrane perfusion

    PubMed Central

    Vereshchagina, Elizaveta; Mc Glade, Declan; Glynn, Macdara; Ducrée, Jens

    2013-01-01

    We present a novel 3D hybrid assembly of a polymer microfluidic chip with polycarbonate track-etched membrane (PCTEM) enabling membrane-supported cell culture. Two chip designs have been developed to establish either diffusive or convective reagent delivery using the integrated PCTEM. While it is well suited to a range of cell-based assays, we specifically employ this platform for the screening of a common antitumor chemotoxic agent (mitomycin C – MMC) on the HL60 myeloid leukemia cell line. The toxic activity of MMC is based on the generation of severe DNA damage in the cells. Using either mode of operation, the HL60 cells were cultured on-chip before, during, and after exposure to MMC at concentrations ranging from 0 to 50 μM. Cell viability was analysed off-chip by the trypan blue dye exclusion assay. The results of the on-chip viability assay were found to be consistent with those obtained off-chip and indicated ca. 40% cell survival at MMC concentration of 50 μM. The catalogue of capabilities of the here described cell assay platform comprises of (i) the culturing of cells either under shear-free conditions or under induced through-membrane flows, (ii) the tight time control of the reagent exposure, (iii) the straightforward assembly of devices, (iv) the flexibility on the choice of the membrane, and, prospectively, (v) the amenability for large-scale parallelization. PMID:24404021

  19. Catalytic performance of hybrid nanocatalyst for levulinic acid production from glucose

    NASA Astrophysics Data System (ADS)

    Ya'aini, Nazlina; Amin, Nor Aishah Saidina

    2012-11-01

    Levulinic acid is one of the potential and versatile biomass-derived chemicals. Product analysis via HPLC revealed that the heterogeneous dehydration of glucose over hybrid nanocatalyst exhibited better performance compared to single catalyst. Hybrid nanocatalyst containing H-Y zeolite and CrCl3 could substitute homogenous acid catalyst for attaining high levulinic acid yield. Different CrC3 and H-Y zeolite weight ratios of 1:1, 1:2 and 2:1 were prepared according to the wetness impregnation method. The hybrid catalyst with a 1:1 weight ratio performed better compared to others with the highest levulinic acid yield reported (93.5%) at 140 °C, 180 min reaction time, 0.1 g catalyst loading and 0.1 g glucose feed. Characterization results revealed that properties such as surface area, mesoporosity and acidic strength of the catalyst have significant effects on glucose dehydration for levulinic acid production.

  20. Regulation of ASIC activity by ASIC4--new insights into ASIC channel function revealed by a yeast two-hybrid assay.

    PubMed

    Donier, Emmanuelle; Rugiero, François; Jacob, Céline; Wood, John N

    2008-07-01

    ASIC4 is a member of the acid-sensing ion channel family that is broadly expressed in the mammalian nervous system, but has no known function. We demonstrate here that transfected ASIC4 is targeted to the plasma membrane in CHO-K1 cells, where it associates with ASIC1a and downregulates exogenous ASIC1a expression. This effect could also be observed on endogenous H+-gated currents in TSA-201 cells and ASIC3 currents in CHO-K1 cells, suggesting a physiological role for ASIC4 in regulating ASIC currents involved in pain mechanisms. Using a yeast two-hybrid assay we found that ASICs interact with proteins involved in diverse functions, including cytoskeletal proteins, enzymes, regulators of endocytosis and G-protein-coupled pathways. ASIC4 is the sole member of this ion channel class to interact strongly with polyubiquitin. The distinct functionally related sets of interacting proteins that bind individual ASICs identified in the yeast two-hybrid screen suggest potential roles for ASICs in a variety of cellular functions. PMID:18662336

  1. A fluorometric assay platform for caffeic acid detection based on the G-quadruplex/hemin DNAzyme.

    PubMed

    Cai, Nan; Li, Yan; Chen, Shufan; Su, Xingguang

    2016-07-21

    In this paper, a fluorometric assay platform for fluorescence detection of caffeic acid was designed based on the peroxidase-mimicking activities of G-quadruplex/hemin DNAzyme. Under the catalysis of the formed G-quadruplex/hemin complex, H2O2 could be decomposed into hydroxyl radicals with strong oxidation properties. Then caffeic acid would be oxidized by the released hydroxyl radicals, resulting in the product caffeic acid-quinone. Normally, caffeic acid has no influence on the fluorescence of graphene quantum dots. But when mixed with the G-quadruplex/hemin complex and H2O2, the fluorescence of graphene quantum dots was obviously quenched by the oxidized caffeic acid. Under the optimized experimental conditions, the quenched fluorescence intensity was linearly correlated with the concentration of caffeic acid, ranging from 2 μM to 350 μM with a detection limit of 200 nM. The proposed method was applied to the determination of caffeic acid in human serum samples with satisfactory results. PMID:27220084

  2. Identification and analysis of hepatitis C virus NS3 helicase inhibitors using nucleic acid binding assays

    PubMed Central

    Mukherjee, Sourav; Hanson, Alicia M.; Shadrick, William R.; Ndjomou, Jean; Sweeney, Noreena L.; Hernandez, John J.; Bartczak, Diana; Li, Kelin; Frankowski, Kevin J.; Heck, Julie A.; Arnold, Leggy A.; Schoenen, Frank J.; Frick, David N.

    2012-01-01

    Typical assays used to discover and analyze small molecules that inhibit the hepatitis C virus (HCV) NS3 helicase yield few hits and are often confounded by compound interference. Oligonucleotide binding assays are examined here as an alternative. After comparing fluorescence polarization (FP), homogeneous time-resolved fluorescence (HTRF®; Cisbio) and AlphaScreen® (Perkin Elmer) assays, an FP-based assay was chosen to screen Sigma’s Library of Pharmacologically Active Compounds (LOPAC) for compounds that inhibit NS3-DNA complex formation. Four LOPAC compounds inhibited the FP-based assay: aurintricarboxylic acid (ATA) (IC50 = 1.4 μM), suramin sodium salt (IC50 = 3.6 μM), NF 023 hydrate (IC50 = 6.2 μM) and tyrphostin AG 538 (IC50 = 3.6 μM). All but AG 538 inhibited helicase-catalyzed strand separation, and all but NF 023 inhibited replication of subgenomic HCV replicons. A counterscreen using Escherichia coli single-stranded DNA binding protein (SSB) revealed that none of the new HCV helicase inhibitors were specific for NS3h. However, when the SSB-based assay was used to analyze derivatives of another non-specific helicase inhibitor, the main component of the dye primuline, it revealed that some primuline derivatives (e.g. PubChem CID50930730) are up to 30-fold more specific for HCV NS3h than similarly potent HCV helicase inhibitors. PMID:22740655

  3. Rapid turbidimetric assay for quantification of fusidic acid in a dermatological cream.

    PubMed

    Curbete, Mariane Machado; Salgado, Hérida Regina Nunes

    2016-06-01

    Fusidic acid is an antibiotic steroid widely used for the treatment of serious infections caused by methicillin-resistant Staphylococcus aureus (MRSA) strains. Microbiological methods are indispensable to determine the mean percentage of antimicrobial in medicaments during manufacturing and quality control processes. The aim of this study was to develop and validate a microbiological method for the quantification of fusidic acid in dermatological cream by turbidimetry, using Staphylococcus epidermidis (ATCC 12228) and casoy broth as the culture medium. The validation parameters were in accordance with ICH specifications and demonstrated accuracy, precision, selectivity, and robustness, with linear ranges from 0.25 to 2.25μgmL(-1). This method is an alternative to the diffusion agar assay currently employed to quantify fusidic acid in dermatological cream, since it is sensitive, fast, and more economical. PMID:27130089

  4. Degradation of caffeic acid in subcritical water and online HPLC-DPPH assay of degradation products.

    PubMed

    Khuwijitjaru, Pramote; Suaylam, Boonyanuch; Adachi, Shuji

    2014-02-26

    Caffeic acid was subjected to degradation under subcritical water conditions within 160-240 °C and at a constant pressure of 5 MPa in a continuous tubular reactor. Caffeic acid degraded quickly at these temperatures; the main products identified by liquid chromatography-diode array detection/mass spectrometry were hydroxytyrosol, protocatechuic aldehyde, and 4-vinylcatechol. The reaction rates for the degradation of caffeic acid and the formation of products were evaluated. Online high-performance liquid chromatography/2,2-diphenyl-1-picryhydrazyl assay was used to determine the antioxidant activity of each product in the solution. It was found that the overall antioxidant activity of the treated solution did not change during the degradation process. This study showed a potential of formation of antioxidants from natural phenolic compounds under these subcritical water conditions, and this may lead to a discovering of novel antioxidants compounds during the extraction by this technique. PMID:24483598

  5. Phagocytosis of hybrid molecular nanosomal compositions containing oxidized dextrans conjugated with isonicotinic acid hydrazide by macrophages.

    PubMed

    Shkurupy, V A; Arkhipov, S A; Troitsky, A V; Luzgina, N G; Zaikovskaja, M V; Ufimceva, E G; Iljine, D A; Akhramenko, E S; Gulyaeva, E P; Bistrova, T N

    2009-12-01

    We studied phagocytic activity of macrophages towards hybrid molecular nanosomal compositions consisting of 150-800-nm nanoliposomes containing oxidized dextrans with a molecular weight of 35 and 60 kDa obtained by chemical ("permanganate") and radiochemical oxidation of dextran conjugated with isonicotinic acid hydrazide (dextrazides, intracellular prolonged antituberculous drugs). Phagocytic activity of macrophages towards hybrid molecular nanosomal compositions containing dextrazides obtained by chemical oxidation of dextrans is higher than activity towards hybrid molecular nanosomal compositions containing dextrazides prepared by radiochemical oxidation and depends on the size of hybrid molecular nanosomal compositions and molecular weight of oxidized dextrans. PMID:21116494

  6. Nonradioactive colony hybridization assay for detection and enumeration of enterotoxigenic Clostridium perfringens in raw beef.

    PubMed Central

    Baez, L A; Juneja, V K

    1995-01-01

    A DNA probe endolabeled with digoxigenin by PCR was developed to detect and enumerate enterotoxigenic Clostridium perfringens in raw beef. After 2 h of hybridization, membranes were developed by using an anti-digoxigenin-alkaline phosphatase conjugated antibody. The resulting chromogenic reaction allowed us to detect and enumerate < or = 10 CFU of C. perfringens per g. PMID:7574619

  7. Enzyme-linked immunosorbent assay (ELISA) for the anthropogenic marker isolithocholic acid in water.

    PubMed

    Baldofski, Stefanie; Hoffmann, Holger; Lehmann, Andreas; Breitfeld, Stefan; Garbe, Leif-Alexander; Schneider, Rudolf J

    2016-11-01

    Bile acids are promising chemical markers to assess the pollution of water samples with fecal material. This study describes the optimization and validation of a direct competitive enzyme-linked immunosorbent assay for the bile acid isolithocholic acid (ILA). The quantification range of the optimized assay was between 0.09 and 15 μg/L. The assay was applied to environmental water samples. Most studies until now were focused on bile acid fractions in the particulate phase of water samples. In order to avoid tedious sample preparation, we undertook to evaluate the dynamics and significance of ILA levels in the aqueous phase. Very low concentrations in tap and surface water samples made a pre-concentration step necessary for this matrix as well as for wastewater treatment plant (WWTP) effluent. Mean recoveries for spiked water samples were between 97% and 109% for tap water and WWTP influent samples and between 102% and 136% for WWTP effluent samples. 90th percentiles of intra-plate and inter-plate coefficients of variation were below 10% for influents and below 20% for effluents and surface water. ILA concentrations were quantified in the range of 33-72 μg/L in influent, 21-49 ng/L in effluent and 18-48 ng/L in surface water samples. During wastewater treatment the ILA levels were reduced by more than 99%. ILA concentrations of influents determined by ELISA and LC-MS/MS were in good agreement. However, findings in LC-ELISA experiments suggest that the true ILA levels in concentrated samples are lower due to interfering effects of matrix compounds and/or cross-reactants. Yet, the ELISA will be a valuable tool for the performance check and comparison of WWTPs and the localization of fecal matter input into surface waters. PMID:27544648

  8. An electrochemical clamp assay for direct, rapid analysis of circulating nucleic acids in serum

    NASA Astrophysics Data System (ADS)

    Das, Jagotamoy; Ivanov, Ivaylo; Montermini, Laura; Rak, Janusz; Sargent, Edward H.; Kelley, Shana O.

    2015-07-01

    The analysis of cell-free nucleic acids (cfNAs), which are present at significant levels in the blood of cancer patients, can reveal the mutational spectrum of a tumour without the need for invasive sampling of the tissue. However, this requires differentiation between the nucleic acids that originate from healthy cells and the mutated sequences shed by tumour cells. Here we report an electrochemical clamp assay that directly detects mutated sequences in patient serum. This is the first successful detection of cfNAs without the need for enzymatic amplification, a step that normally requires extensive sample processing and is prone to interference. The new chip-based assay reads out the presence of mutations within 15 minutes using a collection of oligonucleotides that sequester closely related sequences in solution, and thus allow only the mutated sequence to bind to a chip-based sensor. We demonstrate excellent levels of sensitivity and specificity and show that the clamp assay accurately detects mutated sequences in a collection of samples taken from lung cancer and melanoma patients.

  9. Real-time PCR Detection of Brucella Abortus: A Comparative Study of SYBR Green I, 5'-exonuclease, and Hybridization Probe Assays

    SciTech Connect

    Newby, Deborah Trishelle; Hadfield, Ted; Roberto, Francisco Figueroa

    2003-08-01

    Real-time PCR provides a means of detecting and quantifying DNA targets by monitoring PCR product accumulation during cycling as indicated by increased fluorescence. A number of different approaches can be used to generate the fluorescence signal. Three approaches—SYBR Green I (a double-stranded DNA intercalating dye), 5'-exonuclease (enzymatically released fluors), and hybridization probes (fluorescence resonance energy transfer)—were evaluated for use in a real-time PCR assay to detect Brucella abortus. The three assays utilized the same amplification primers to produce an identical amplicon. This amplicon spans a region of the B. abortus genome that includes portions of the alkB gene and the IS711 insertion element. All three assays were of comparable sensitivity, providing a linear assay over 7 orders of magnitude (from 7.5 ng down to 7.5 fg). However, the greatest specificity was achieved with the hybridization probe assay.

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

    PubMed

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

    1993-12-01

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

  11. Lead-acid batteries in micro-hybrid vehicles

    NASA Astrophysics Data System (ADS)

    Albers, Joern; Meissner, Eberhard; Shirazi, Sepehr

    More and more vehicles hit the European automotive market, which comprise some type of micro-hybrid functionality to improve fuel efficiency and reduce emissions. Most carmakers already offer at least one of their vehicles with an optional engine start/stop system, while some other models are sold with micro-hybrid functions implemented by default. But these car concepts show a wide variety in detail-the term "micro-hybrid" may mean a completely different functionality in one vehicle model compared to another. Accordingly, also the battery technologies are not the same. There is a wide variety of batteries from standard flooded and enhanced flooded to AGM which all are claimed to be "best choice" for micro-hybrid applications. A technical comparison of micro-hybrid cars available on the European market has been performed. Different classes of cars with different characteristics have been identified. Depending on the scope and characteristics of micro-hybrid functions, as well as on operational strategies implemented by the vehicle makers, the battery operating duties differ significantly between these classes of vehicles. Additional laboratory investigations have been carried out to develop an understanding of effects observed in batteries operated in micro-hybrid vehicles pursuing different strategies, to identify limitations for applications of different battery technologies.

  12. Optimization of levulinic acid from lignocellulosic biomass using a new hybrid catalyst.

    PubMed

    Ya'aini, Nazlina; Amin, Nor Aishah Saidina; Asmadi, Mohd

    2012-07-01

    Conversion of glucose, empty fruit bunch (efb) and kenaf to levulinic acid over a new hybrid catalyst has been investigated in this study. The characterization and catalytic performance results revealed that the physico-chemical properties of the new hybrid catalyst comprised of chromium chloride and HY zeolite increased the levulinic acid production from glucose compared to the parent catalysts. Optimization of the glucose conversion process using two level full factorial designs (2(3)) with two center points reported 55.2% of levulinic acid yield at 145.2 °C, 146.7 min and 12.0% of reaction temperature, reaction time and catalyst loading, respectively. Subsequently, the potential of efb and kenaf for producing levulinic acid at the optimum conditions was established after 53.2% and 66.1% of efficiencies were reported. The observation suggests that the hybrid catalyst has a potential to be used in biomass conversion to levulinic acid. PMID:22609656

  13. Evaluation for Resistance to Powdery Mildew in Cornus Species and Hybrids Using a Leafy Disk Assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using a leaf disk assay, eight cultivars or/and breeding lines in Cornus florida L., C. kousa (Buerger ex Miq.) Hance, five cultivars in C. kousa × C. florida, one cultivar in C. kousa × C. nuttallii Aud. and one cultivar in (C. kousa × C. nuttallii) × C. kousa were evaluated for resistance to powde...

  14. Chemical synthesis and characterization of branched oligodeoxyribonucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays.

    PubMed Central

    Horn, T; Chang, C A; Urdea, M S

    1997-01-01

    The divergent synthesis of bDNA structures is described. This new type of branched DNA contains one unique oligonucleotide, the primary sequence, covalently attached through a comb-like branching network to many identical copies of a different oligonucleotide, the secondary sequence. The bDNA comb molecules were assembled on a solid support using parameters optimized for bDNA synthesis. The chemistry was used to synthesize bDNA comb molecules containing 15 secondary sequences. The bDNA comb molecules were elaborated by enzymatic ligation into branched amplification multimers, large bDNA molecules (a total of 1068 nt) containing an average of 36 repeated DNA oligomer sequences, each capable of hybridizing specifically to an alkaline phosphatase-labeled oligonucleotide. The bDNA comb molecules were characterized by electrophoretic methods and by controlled cleavage at periodate-cleavable moieties incorporated during synthesis. The branched amplification multimers have been used as signal amplifiers in nucleic acid quantification assays for detection of viral infection. It is possible to detect as few as 50 molecules with bDNA technology. PMID:9365266

  15. Antioxidant assay-guided purification and LC determination of ellagic acid in pomegranate peel.

    PubMed

    Panichayupakarananta, Pharkphoom; Issuriya, Atcharaporn; Sirikatitham, Anusak; Wang, Wei

    2010-07-01

    On the basis of 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging assay-guided purification, ellagic acid was isolated from the methanol extract of pomegranate fruit peel by liquid-liquid extraction and chromatographic techniques. A reversed-phase high-performance liquid chromatography was described for determination of ellagic acid in pomegranate fruit peel extract. The method involved the use of a TSK-gel ODS-80Tm column with a mixture of 2% aqueous acetic acid and methanol (gradient elution mode: 0-15 min, 40-60% v/v methanol and 15-20 min, 60% v/v methanol) as the mobile phase and detection at 254 nm. The parameters of linearity, repeatability, reproducibility, accuracy, and specificity of the method were evaluated. The recovery of the method was 98.5% and linearity (r(2) > 0.9995) was obtained for ellagic acid. A high degree of specificity as well as repeatability and reproducibility (relative standard deviation values less than 5%) were also achieved. The limits of detection and quantification were 1.00 and 2.50 microg/mL, respectively. The solvent for extraction of ellagic acid from pomegranate fruit peel was examined in order to maximize the ellagic acid content of the extract. A solution of 10% v/v water in methanol was capable of increasing the ellagic acid content in the extract up to 7.66% w/w. The ellagic acid content and antioxidant activity of the ethyl acetate fraction separated from the crude extract using water and ethyl acetate partition was higher than that of the crude extract. PMID:20822660

  16. QUANTIFICATION OF GLIAL FIBRILLARY ACIDIC PROTEIN: COMPARISON OF SLOT-IMMUNOBINDING ASSAYS WITH A NOVEL SANDWICH ELISA

    EPA Science Inventory

    Detailed protocols are presented for assaying glial fibrillary acidic protein (GFAP), an astrocyte localized protein rich serves as a quantitative marker of toxicant- induced injury to the central nervous system. wo different solid-phase assay procedures are described: 1) a nitro...

  17. Selection of direct transesterification as the preferred method for assay of fatty acid content of microalgae.

    PubMed

    Griffiths, M J; van Hille, R P; Harrison, S T L

    2010-11-01

    Assays for total lipid content in microalgae are usually based on the Folch or the Bligh and Dyer methods of solvent extraction followed by quantification either gravimetrically or by chromatography. Direct transesterification (DT) is a method of converting saponifiable lipids in situ directly to fatty acid methyl esters which can be quantified by gas chromatography (GC). This eliminates the extraction step and results in a rapid, one-step procedure applicable to small samples. This study compared the effectiveness of DT in quantifying the total fatty acid content in three species of microalgae to extraction using the Folch, the Bligh and Dyer and the Smedes and Askland methods, followed by transesterification and GC. The use of two catalysts in sequence, as well as the effect of reaction water content on the efficiency of DT were investigated. The Folch method was the most effective of the extraction methods tested, but comparison with DT illustrated that all extraction methods were incomplete. Higher levels of fatty acid in the cells were obtained with DT in comparison with the extraction-transesterification methods. A combination of acidic and basic transesterification catalysts was more effective than each individually when the sample contained water. The two-catalyst reaction was insensitive to water up to 10% of total reaction volume. DT proved a convenient and more accurate method than the extraction techniques for quantifying total fatty acid content in microalgae. PMID:20820931

  18. Enzymatic Amplification of DNA/RNA Hybrid Molecular Beacon Signaling in Nucleic Acid Detection

    PubMed Central

    Jacroux, Thomas; Rieck, Daniel C.; Cui, Rong; Ouyang, Yexin; Dong, Wen-Ji

    2012-01-01

    A rapid assay operable under isothermal or non-isothermal conditions is described wherein the sensitivity of a typical molecular beacon (MB) system is improved by utilizing thermostable RNase H to enzymatically cleave an MB comprised of a DNA stem and RNA loop (R/D-MB). Upon hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7x above background) due to an opening of the probe and concomitant reduction in the Förster resonance energy transfer efficiency. Addition of thermostable RNase H resulted in the cleavage of the RNA loop which eliminated energy transfer. The cleavage step also released bound target DNA, enabling it to bind to another R/D-MB probe and rendering the approach a cyclic amplification scheme. Full processing of R/D-MBs maximized the fluorescence signal to the fullest extent possible (12.9x above background), resulting in a ~2–2.8 fold increase in the signal-to-noise ratio observed isothermally at 50 °C following the addition of RNase H. The probe was also used to monitor real-time PCR reactions by measuring enhancement of donor fluorescence upon R/D-MB binding to amplified pUC19 template dilutions. Hence, the R/D-MB-RNase H scheme can be applied to a broad range of nucleic acid amplification methods. PMID:23000602

  19. Enzymatic amplification of DNA/RNA hybrid molecular beacon signaling in nucleic acid detection.

    PubMed

    Jacroux, Thomas; Rieck, Daniel C; Cui, Rong; Ouyang, Yexin; Dong, Wen-Ji

    2013-01-15

    A rapid assay operable under isothermal or nonisothermal conditions is described, where the sensitivity of a typical molecular beacon (MB) system is improved by using thermostable RNase H to enzymatically cleave an MB composed of a DNA stem and an RNA loop (R/D-MB). On hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7× above background) due to an opening of the probe and a concomitant reduction in the Förster resonance energy transfer efficiency. The addition of thermostable RNase H resulted in the cleavage of the RNA loop, which eliminated energy transfer. The cleavage step also released bound target DNA, enabling it to bind to another R/D-MB probe and rendering the approach a cyclic amplification scheme. Full processing of R/D-MBs maximized the fluorescence signal to the fullest extent possible (12.9× above background), resulting in an approximately 2- to 2.8-fold increase in the signal-to-noise ratio observed isothermally at 50 °C following the addition of RNase H. The probe was also used to monitor real-time polymerase chain reactions by measuring enhancement of donor fluorescence on R/D-MB binding to amplified pUC19 template dilutions. Hence, the R/D-MB-RNase H scheme can be applied to a broad range of nucleic acid amplification methods. PMID:23000602

  20. Nucleic acid sequence-based amplification assays for rapid detection of West Nile and St. Louis encephalitis viruses.

    PubMed

    Lanciotti, R S; Kerst, A J

    2001-12-01

    The development and application of nucleic acid sequence-based amplification (NASBA) assays for the detection of West Nile (WN) and St. Louis encephalitis (SLE) viruses are reported. Two unique detection formats were developed for the NASBA assays: a postamplification detection step with a virus-specific internal capture probe and electrochemiluminescence (NASBA-ECL assay) and a real-time assay with 6-carboxyfluorescein-labeled virus-specific molecular beacon probes (NASBA-beacon assay). The sensitivities and specificities of these NASBA assays were compared to those of a newly described standard reverse transcription (RT)-PCR and TaqMan assays for SLE virus and to a previously published TaqMan assay for WN virus. The NASBA assays demonstrated exceptional sensitivities and specificities compared to those of virus isolation, the TaqMan assays, and standard RT-PCR, with the NASBA-beacon assay yielding results in less than 1 h. These assays should be of utility in the diagnostic laboratory to complement existing diagnostic testing methodologies and as a tool in conducting flavivirus surveillance in the United States. PMID:11724870

  1. Improved rapid molecular diagnosis of multidrug-resistant tuberculosis using a new reverse hybridization assay, REBA MTB-MDR

    PubMed Central

    Bang, Hyeeun; Park, Sangjung; Hwang, Joohwan; Jin, Hyunwoo; Cho, Eunjin; Kim, Dae Yoon; Song, Taeksun; Shamputa, Isdore Chola; Via, Laura E.; Barry, Clifton E.; Cho, Sang-Nae

    2011-01-01

    Rapid diagnosis of multidrug-resistant tuberculosis (MDR-TB) is essential for the prompt initiation of effective second-line therapy to improve treatment outcome and limit transmission of this obstinate disease. A variety of molecular methods that enable the rapid detection of mutations implicated in MDR-TB have been developed. The sensitivity of the methods is dependent, in principle, on the repertoire of mutations being detected, which is typically limited to mutations in the genes rpoB, katG and the promoter region of inhA. In this study, a new reverse hybridization assay, REBA MTB-MDR (M&D), that probes mutations in the oxyR–ahpC intergenic region, in addition to those in rpoB, katG and the inhA promoter region, was evaluated. A set of 240 Mycobacterium tuberculosis clinical isolates from patients receiving retreatment regimens was subjected to conventional phenotypic drug-susceptibility testing (DST) and the REBA MTB-MDR assay. The nucleotide sequences of the loci known to be involved in drug resistance were determined for comparison. In brief, the results showed that the REBA MTB-MDR assay efficiently recognized nucleotide changes in the oxyR–ahpC intergenic region as well as those in rpoB, katG and the inhA promoter region with higher sensitivity, resulting in an 81.0 % detection rate for isoniazid resistance. Inclusion of the oxyR–ahpC intergenic region in the REBA MTB-MDR assay improved the overall sensitivity of molecular DST for MDR-TB from 73.1 to 79.9 %. PMID:21596910

  2. Assay of deoxyribonucleic acid homology using a single-strand-specific nuclease at 75 C.

    PubMed Central

    Barth, P T; Grinter, N J

    1975-01-01

    We investigated the conditions under which a crude preparation of endonuclease S1 gives maximal hydrolysis of denatured deoxyribonucleic acid (DNA) while giving minimal hydrolysis of native DNA. The hydrolysis was measured by filtering and determining the acid-insoluble reaction product using 3H-labeled substrates. We also investigated various parameters in making this measurement. Under appropriate conditions (in 1 mM ZnSO-4, 0.168 M NaCl at pH 4.8) denatured DNA is hydrolyzed within 3% of completion whereas native DNA is essentially unaffected. The reaction was applied to assay plasmid DNA homoand heteroduplexes for which the method proves to be simple, fast, and reproducible. PMID:234416

  3. Producing a trimethylpentanoic acid using hybrid polyketide synthases

    SciTech Connect

    Katz, Leonard; Fortman, Jeffrey L; Keasling, Jay D

    2014-10-07

    The present invention provides for a polyketide synthase (PKS) capable of synthesizing trimethylpentanoic acid. The present invention also provides for a host cell comprising the PKS and when cultured produces the trimethylpentanoic acid. The present invention also provides for a method of producing the trimethylpentanoic acid, comprising: providing a host cell of the present invention, and culturing said host cell in a suitable culture medium such that the trimethylpentanoic acid is produced, optionally isolating the trimethylpentanoic acid, and optionally, reducing the isolated trimethylpentanoic acid into a trimethylpentanol or an iso-octane.

  4. Microwell hybridization assay for detection of PCR products from Mycobacterium tuberculosis complex and the recombinant Mycobacterium smegmatis strain 1008 used as an internal control.

    PubMed Central

    Kox, L F; Noordhoek, G T; Kunakorn, M; Mulder, S; Sterrenburg, M; Kolk, A H

    1996-01-01

    A microwell hybridization assay was developed for the detection of the PCR products from both Mycobacterium tuberculosis complex bacteria and the recombinant Mycobacterium smegmatis strain 1008 that is used as an internal control to monitor inhibition in the PCR based on the M. tuberculosis complex-specific insertion sequence IS6110. The test is based on specific detection with digoxigenin-labeled oligonucleotide probes of biotinylated PCR products which are captured in a microtiter plate coated with streptavidin. The captured PCR products are hybridized separately with two probes, one specific for the PCR product from IS6110 from M. tuberculosis complex and the other specific for the PCR fragment from the modified IS6110 fragment from the recombinant M. smegmatis 1008. The microwell hybridization assay discriminates perfectly between the two types of amplicon. The amount of PCR product that can be detected by this assay is 10 times less than that which can be detected by agarose gel electrophoresis. The test can be performed in 2 h. It is much faster and less laborious than Southern blot hybridization. Furthermore, the interpretation of results is objective. The assay was used with 172 clinical samples in a routine microbiology laboratory, and the results were in complete agreement with those of agarose gel electrophoresis and Southern blot hybridization. PMID:8862568

  5. Validation of a UV Spectrometric Method for the Assay of Tolfenamic Acid in Organic Solvents

    PubMed Central

    Ahmed, Sofia; Mustaan, Nafeesa; Sheraz, Muhammad Ali; Nabi, Syeda Ayesha Ahmed un; Ahmad, Iqbal

    2015-01-01

    The present study has been carried out to validate a UV spectrometric method for the assay of tolfenamic acid (TA) in organic solvents. TA is insoluble in water; therefore, a total of thirteen commonly used organic solvents have been selected in which the drug is soluble. Fresh stock solutions of TA in each solvent in a concentration of 1 × 10−4 M (2.62 mg%) were prepared for the assay. The method has been validated according to the guideline of International Conference on Harmonization and parameters like linearity, range, accuracy, precision, sensitivity, and robustness have been studied. Although the method was found to be efficient for the determination of TA in all solvents on the basis of statistical data 1-octanol, followed by ethanol and methanol, was found to be comparatively better than the other studied solvents. No change in the stock solution stability of TA has been observed in each solvent for 24 hours stored either at room (25 ± 1°C) or at refrigerated temperature (2–8°C). A shift in the absorption maxima has been observed for TA in various solvents indicating drug-solvent interactions. The studied method is simple, rapid, economical, accurate, and precise for the assay of TA in different organic solvents. PMID:26783497

  6. Total protein quantitation using the bicinchoninic acid assay and gradient elution moving boundary electrophoresis.

    PubMed

    Kralj, Jason G; Munson, Matthew S; Ross, David

    2014-07-01

    We investigated the ability of gradient elution moving boundary electrophoresis (GEMBE) with capacitively coupled contactless conductivity detection (C(4) D) to assay total protein concentration using the bicinchoninic acid (BCA) reaction. We chose this format because GEMBE-C(4) D behaves as a concentration dependent detection system, unlike optical methods that also rely on pathlength (due to Beer's law). This system tolerates proteins well compared with other capillary electrophoretic methods, allowing the capillary to be reused without coatings or additional hydroxide wash steps. The typical reaction protocol was modified by reducing the pH slightly from 11.25 to 9.4, which enabled elimination of tartrate from the reagents. We estimated that copper (I) could be detected at approximately 3.0 μmol/L, which agrees with similar GEMBE and CZE systems utilizing C(4) D. Under conditions similar to the BCA "micro method" assay, we determined the LOD for three common proteins (insulin, BSA, and bovine gamma globulin) and found that they agree well with the existing spectroscopic detection methods. Further, we investigated how long reaction times impact the LOD and found that the conversion was proportional to log(time). This indicated that little sensitivity is gained by extending the reaction past 1 h. Hence, GEMBE provides an alternative platform for total protein assays while maintaining the excellent sensitivity of the optical-based methods. PMID:24648165

  7. Nucleic acid hybridization with RNA immobilized on filter paper.

    NASA Technical Reports Server (NTRS)

    Saxinger, W. C.; Ponnamperuma, C.; Gillespie, D.

    1972-01-01

    RNA has been immobilized in a manner suitable for use in molecular hybridization experiments with dissolved RNA or DNA by a nonaqueous solid-phase reaction with carbonyldiimidazole and RNA 'dry coated' on cellulose or, preferably, on previously activated phosphocellulose filters. Immobilization of RNA does not appear to alter its chemical character or cause it to acquire affinity for unspecific RNA or DNA. The versatility and efficiency of this method make it potentially attractive for use in routine analytical or preparative hybridization experiments, among other applications.

  8. A rapid assay for affinity and kinetics of molecular interactions with nucleic acids.

    PubMed

    Donaldson, Gregory P; Roelofs, Kevin G; Luo, Yiling; Sintim, Herman O; Lee, Vincent T

    2012-04-01

    The Differential Radial Capillary Action of Ligand Assay (DRaCALA) allows detection of protein interactions with low-molecular weight ligands based on separation of the protein-ligand complex by differential capillary action. Here, we present an application of DRaCALA to the study of nucleic acid-protein interactions using the Escherichia coli cyclic AMP receptor protein (CRP). CRP bound in DRaCALA specifically to (32)P-labeled oligonucleotides containing the consensus CRP binding site, but not to oligonucleotides with point mutations known to abrogate binding. Affinity and kinetic studies using DRaCALA yielded a dissociation constant and dissociation rate similar to previously reported values. Because DRaCALA is not subject to ligand size restrictions, whole plasmids with a single CRP-binding site were used as probes, yielding similar results. DNA can also function as an easily labeled carrier molecule for a conjugated ligand. Sequestration of biotinylated nucleic acids by streptavidin allowed nucleic acids to take the place of the protein as the immobile binding partner. Therefore, any molecular interactions involving nucleic acids can be tested. We demonstrate this principle utilizing a bacterial riboswitch that binds cyclic-di-guanosine monophosphate. DRaCALA is a flexible and complementary approach to other biochemical methods for rapid and accurate measurements of affinity and kinetics at near-equilibrium conditions. PMID:22210888

  9. Properties of kojic acid and curcumin: Assay on cell B16-F1

    NASA Astrophysics Data System (ADS)

    Sugiharto, Ariff, Arbakariya; Ahmad, Syahida; Hamid, Muhajir

    2016-03-01

    Ultra violet (UV) exposure and oxidative stress are casually linked to skin disorders. They can increase melanin synthesis, proliferation of melanocytes, and hyperpigmentation. It is possible that antioxidants or inhibitors may have a beneficial effect on skin health to reduce hyperpigmentation. In the last few years, a huge number of natural herbal extracts have been tested to reduce hyperpigmentation. The objective of this study was to determine and to compare of kojic acid and curcumin properties to viability cell B16-F1. In this study, our data showed that the viability of cell B16-F1 was 63.91% for kojic acid and 64.12% for curcumin at concentration 100 µg/ml. Further investigation assay of antioxidant activities, indicated that IC50 for kojic acid is 63.8 µg/ml and curcumin is 16.05 µg/ml. Based on the data, kojic acid and curcumin have potential antioxidant properties to reduce hyperpigmentation with low toxicity effect in cell B16-F1.

  10. An enzymic assay for uric acid in serum and urine compared with HPLC.

    PubMed

    Dubois, H; Delvoux, B; Ehrhardt, V; Greiling, H

    1989-03-01

    We evaluated a colorimetric method for the assay of uric acid in serum or urine, which utilises a Trinder chromogenic system modified by the inclusion of 2,4,6-tribromo-3-hydroxybenzoic acid for oxidative coupling to p-aminophenazone. Colour development (Amax: 512 nm) is complete within five minutes. Measurement of a sample blank is not needed. The procedure involves pre-incubation with ascorbic acid oxidase and detergent to eliminate interference by ascorbic acid and to abolish turbidity due to lipaemia; this pretreatment was effective up to 1.14 mmol/l ascorbate and up to at least 25 mmol/l triacylglycerol. Interference by icteric sera was insignificant up to about 170 mumol/l bilirubin. The method is linear up to at least 1428 mumol/l. In human serum and urine the procedure correlates well with HPLC and the uricase p-aminophenazone method on the SMAC analyser. Within-run and between-run imprecisions of the enzymic test were higher than for HPLC, but did not exceed 1.2% (CV) and 2.5% (CV), respectively. PMID:2708944

  11. Continuous colorimetric screening assays for the detection of specific L- or D-α-amino acid transaminases in enzyme libraries.

    PubMed

    Heuson, Egon; Petit, Jean-Louis; Debard, Adrien; Job, Aurélie; Charmantray, Franck; de Berardinis, Véronique; Gefflaut, Thierry

    2016-01-01

    In the course of a project devoted to the stereoselective synthesis of non-proteinogenic α-amino acids using α-transaminases (α-TA), we report the design and optimization of generic high-throughput continuous assays for the screening of α-TA libraries. These assays are based on the use of L- or D-cysteine sulfinic acid (CSA) as irreversible amino donor and subsequent sulfite titration by colorimetry. The assays' quality was assessed under screening conditions. Hit selection thresholds were accurately determined for every couple of substrates and a library of 232 putative transaminases expressed in Escherichia coli host cells was screened. The reported high throughput screening assays proved very sensitive allowing the detection with high confidence of activities as low as 10 μU (i.e., 0.01 nmol substrate converted per min). The assays were also evidenced to be stereochemically discriminant since L-CSA and D-CSA allowed the exclusive detection of L-TA and D-TA, respectively. These generic assays thus allow testing the stereoselective conversion of a wide range of α-keto acids into α-amino acids of interest. As a proof of principle, the use of 2-oxo-4-phenylbutyric acid as acceptor substrate led to the identification of 54 new α-TA offering an access to valuable L- or D-homophenylalanine. PMID:26452497

  12. Fabrication and structure analysis of poly(lactide-co-glycolic acid)/silk fibroin hybrid scaffold for wound dressing applications.

    PubMed

    Shahverdi, Sheida; Hajimiri, Mirhamed; Esfandiari, Mohammad Amin; Larijani, Bagher; Atyabi, Fatemeh; Rajabiani, Afsaneh; Dehpour, Ahmad Reza; Gharehaghaji, Ali Akbar; Dinarvand, Rassoul

    2014-10-01

    Silk fibroin (SF) and poly(lactide-co-glycolic acid) (PLGA) have been proved to be invaluable polymers in the field wound healing. This study aims at optimizing the electrospinning process of those polymers to make a hybrid membrane as a chronic wounds dressing. After characterizing the scaffolds, PLGA/SF (2:1), and PLGA scaffolds were selected for further study according to their superior tensile mechanical properties. The attachment and proliferation of mouse fibroblasts (L929) on scaffolds were measured using colorimetric assay and scanning electron microscopy. Furthermore, to evaluate the wound healing effect of the scaffolds in comparison with gauze and Comfeel(®) dressings, an excision wound model was conducted on diabetic rats. On the postoperative days of 3, 6, 9, 12, and 15, residual wound area was calculated using macroscopic data. In vitro results showed that the attachment and proliferation of L929 were significantly increased on PLGA/SF (2:1) hybrid scaffold. Animal study and histopathological evaluation outcomes confirmed the in vitro results as well. On day 15, the residual wound area in PLGA/SF (2:1) hybrid membrane group was significantly smaller than PLGA and control groups. This promising scaffold has the potential to be used for the upcoming development of wound dressings with or without biological drugs. PMID:25051110

  13. Uric acid photo-oxidation assay: in vitro comparison of sunscreening agents.

    PubMed

    Dunlap, W C; Yamamoto, Y; Inoue, M; Kashiba-Iwatsuki, M; Yamaguchi, M; Tomita, K

    1998-02-01

    We present a new method to evaluate the photo-oxidative activity of sunscreening agents based on the photodynamic oxidation of uric acid. Uric acid was selected as the oxidant probe for its high reactivity to singlet oxygen and oxygen radicals, high sensitivity of detection using electrochemical (EC) techniques, low light absorptivity and high photochemical stability in the UVA/B region of interest, and stability to autoxidation. The method is demonstrated by the photodynamic oxidation of uric acid on co-irradiation with Rose Bengal, a highly efficient photosensitizing dye for the production of singlet oxygen (1O2). Using this assay we found that the relative photodynamic oxidation rates of UVB-absorbing sunscreens in 80% methanol on irradiation with >290 nm light decreased in the order 2-ethylhexyl 4-dimethylaminobenzoate (DMABA-2EH) > 2-ethylhexyl 4-methoxycinnamate (MCA-2EH) and the experimental sunscreens, 1-(1,1-dimethylethyl)-3-octanoyl-4,4-dimethyl- 1,4,5,6,-tetrahydropyridine (ICI-319) and 1-(2-methylpropyl)-3-propionyl-4,4-dimethyl-1,4,5,6-tetrahydropyridine (ICI-855). The relative photodynamic oxidation rates of UVA-absorbing sunscreens decreased in the order 4-tert-butyl-4'-methoxydibenzoylmethane (BMDBM) and 4-(2-propyl)benzophenone (PB) > 2-hydroxy-4'-methoxy-benzophenone (HMB) and 2,2'-dihydroxy-4-methoxybenzophenone (DHMB). We have confirmed the photodynamic activity of DMABA-2EH for the production of singlet oxygen (1O2) using electron paramagnetic resonance (EPR) spectroscopy and the reagent 2,2,6,6-tetramethyl-4-piperidone (4-oxo-TEMP). We failed to detect the photodynamic production of the oxyradicals, superoxide (O2.-) and hydroxyl radical (HO.) using N-tert-butyl-a-phenylnitrone (PBN) and 5,5-dimethyl-1-pyrrolidine-1-oxide (DMPO) as a result of photochemical interference caused by these spin-trapping reagents. The uric acid photo-oxidation assay was also used to compare the photodynamic reactivity of light-reflective, microfine oxides TiO2, Zn

  14. Design and Synthesis of Novel Isoxazole Tethered Quinone-Amino Acid Hybrids

    PubMed Central

    Ravi Kumar, P.; Sambaiah, M.; Kandula, Venu; Payili, Nagaraju; Jaya Shree, A.; Yennam, Satyanarayana

    2014-01-01

    A new series of isoxazole tethered quinone-amino acid hybrids has been designed and synthesized involving 1,3-dipolar cycloaddition reaction followed by an oxidation reaction using cerium ammonium nitrate (CAN). Using this method, for the first time various isoxazole tethered quinone-phenyl alanine and quinone-alanine hybrids were synthesized from simple commercially available 4-bromobenzyl bromide, propargyl bromide, and 2,5-dimethoxybenzaldehyde in good yield. PMID:25709839

  15. Pantothenic acid quantification by a stable isotope dilution assay based on liquid chromatography-tandem mass spectrometry.

    PubMed

    Rychlik, Michael

    2003-07-01

    A stable isotope dilution assay for the quantification of free and total pantothenic acid has been developed by using [13C3,15N]-pantothenic acid as the internal standard. The three-dimensional specificity of liquid chromatography-tandem mass spectrometry enabled unequivocal determination of the vitamin. Due to the very simple extraction and clean-up procedure, free pantothenic acid could be analysed within 2 h, which is much faster than by microbiological or gas chromatographic assays. For quantification of total pantothenic acid, the vitamin was liberated from its conjugates by an overnight incubation with pigeon liver pantetheinase and alkaline phosphatase. In analyses of corn flour, the intra-assay coefficient of variation was 8.5% (n = 5) and 15.3% (n = 4) for free and total pantothenic acid, respectively. When pantothenic acid was added to corn starch at a level of 6 mg kg(-1), a recovery of 97.5% was found. Application of the stable isotope dilution assay to whole egg powder, hazel nuts and corn revealed similar data compared to those listed in nutrition data bases, whereas the content in mushrooms and porcine liver determined by the newly developed assay appeared to be lower and that of cocoa higher than reported in the literature. PMID:12894818

  16. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism.

    PubMed

    Zhang, Qingzhu; Li, Yanqiang; Xu, Tao; Srivastava, Ashish Kumar; Wang, Dong; Zeng, Liang; Yang, Lan; He, Li; Zhang, Heng; Zheng, Zhimin; Yang, Dong-Lei; Zhao, Cheng; Dong, Juan; Gong, Zhizhong; Liu, Renyi; Zhu, Jian-Kang

    2016-01-01

    In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms; however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits. PMID:27551435

  17. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism

    PubMed Central

    Zhang, Qingzhu; Li, Yanqiang; Xu, Tao; Srivastava, Ashish Kumar; Wang, Dong; Zeng, Liang; Yang, Lan; He, Li; Zhang, Heng; Zheng, Zhimin; Yang, Dong-Lei; Zhao, Cheng; Dong, Juan; Gong, Zhizhong; Liu, Renyi; Zhu, Jian-Kang

    2016-01-01

    In plants, hybrid vigor is influenced by genetic and epigenetic mechanisms; however, the molecular pathways are poorly understood. We investigated the potential contributions of epigenetic regulators to heterosis in Arabidposis and found that the chromatin remodeler DECREASED DNA METHYLATION 1 (DDM1) affects early seedling growth heterosis in Col/C24 hybrids. ddm1 mutants showed impaired heterosis and increased expression of non-additively expressed genes related to salicylic acid metabolism. Interestingly, our data suggest that salicylic acid is a hormetic regulator of seedling growth heterosis, and that hybrid vigor arises from crosses that produce optimal salicylic acid levels. Although DNA methylation failed to correlate with differential non-additively expressed gene expression, we uncovered DDM1 as an epigenetic link between salicylic acid metabolism and heterosis, and propose that the endogenous salicylic acid levels of parental plants can be used to predict the heterotic outcome. Salicylic acid protects plants from pathogens and abiotic stress. Thus, our findings suggest that stress-induced hormesis, which has been associated with increased longevity in other organisms, may underlie specific hybrid vigor traits. PMID:27551435

  18. An integrated closed-tube 2-plex PCR amplification and hybridization assay with switchable lanthanide luminescence based spatial detection.

    PubMed

    Lahdenperä, Susanne; Spangar, Anni; Lempainen, Anna-Maija; Joki, Laura; Soukka, Tero

    2015-06-21

    Switchable lanthanide luminescence is a binary probe technology that inherently enables a high signal modulation in separation-free detection of DNA targets. A luminescent lanthanide complex is formed only when the two probes hybridize adjacently to their target DNA. We have now further adapted this technology for the first time in the integration of a 2-plex polymerase chain reaction (PCR) amplification and hybridization-based solid-phase detection of the amplification products of the Staphylococcus aureus gyrB gene and an internal amplification control (IAC). The assay was performed in a sealed polypropylene PCR chip containing a flat-bottom reaction chamber with two immobilized capture probe spots. The surface of the reaction chamber was functionalized with NHS-PEG-azide and alkyne-modified capture probes for each amplicon, labeled with a light harvesting antenna ligand, and covalently attached as spots to the azide-modified reaction chamber using a copper(i)-catalyzed azide-alkyne cycloaddition. Asymmetric duplex-PCR was then performed with no template, one template or both templates present and with a europium ion carrier chelate labeled probe for each amplicon in the reaction. After amplification europium fluorescence was measured by scanning the reaction chamber as a 10 × 10 raster with 0.6 mm resolution in time-resolved mode. With this assay we were able to co-amplify and detect the amplification products of the gyrB target from 100, 1000 and 10,000 copies of isolated S. aureus DNA together with the amplification products from the initial 5000 copies of the synthetic IAC template in the same sealed reaction chamber. The addition of 10,000 copies of isolated non-target Escherichia coli DNA in the same reaction with 5000 copies of the synthetic IAC template did not interfere with the amplification or detection of the IAC. The dynamic range of the assay for the synthetic S. aureus gyrB target was three orders of magnitude and the limit of detection of 8 p

  19. Nanofiltration, bipolar electrodialysis and reactive extraction hybrid system for separation of fumaric acid from fermentation broth.

    PubMed

    Prochaska, Krystyna; Staszak, Katarzyna; Woźniak-Budych, Marta Joanna; Regel-Rosocka, Magdalena; Adamczak, Michalina; Wiśniewski, Maciej; Staniewski, Jacek

    2014-09-01

    A novel approach based on a hybrid system allowing nanofiltration, bipolar electrodialysis and reactive extraction, was proposed to remove fumaric acid from fermentation broth left after bioconversion of glycerol. The fumaric salts can be concentrated in the nanofiltration process to a high yield (80-95% depending on pressure), fumaric acid can be selectively separated from other fermentation components, as well as sodium fumarate can be conversed into the acid form in bipolar electrodialysis process (stack consists of bipolar and anion-exchange membranes). Reactive extraction with quaternary ammonium chloride (Aliquat 336) or alkylphosphine oxides (Cyanex 923) solutions (yield between 60% and 98%) was applied as the final step for fumaric acid recovery from aqueous streams after the membrane techniques. The hybrid system permitting nanofiltration, bipolar electrodialysis and reactive extraction was found effective for recovery of fumaric acid from the fermentation broth. PMID:24983693

  20. Development of in situ hybridization and RT-PCR assay for the detection of a nodavirus (PvNV) that causes muscle necrosis in Penaeus vannamei.

    PubMed

    Tang, Kathy F J; Pantoja, Carlos R; Redman, Rita M; Lightner, Donald V

    2007-05-01

    A nodavirus (tentatively named PvNV, Penaeus vannamei nodavirus) that causes muscle necrosis in P. vannamei was found in Belize in 2004. From 2004 to 2006, shrimp samples collected from Belize exhibited clinical signs, white, opaque lesions in the tails and histopathology similar to those of shrimps infected by infectious myonecrosis virus (IMNV). Histological examination revealed multifocal necrosis and hemocytic fibrosis in the skeletal muscle. In addition, basophilic, cytoplasmic inclusions were found in striated muscle, lymphoid organ and connective tissues. However, IMNV was not detected in these shrimps by either RT-PCR or in situ hybridization, suggesting that these lesions may be caused by another RNA virus. Thus, a cDNA library was constructed from total RNA extracted from hemolymph collected from infected shrimp. One clone (designated PvNV-4) with a 928 bp insert was sequenced and found to be similar (69% similarity when comparing the translated amino acid sequences) to the capsid protein gene of MrNV (Macrobrachium rosenbergii nodavirus). The insert of PvNV-4 was labeled with digoxigenin-11-deoxyuridine triphosphate (dUTP) and hybridized to tissue sections of P. vannamei with muscle necrosis collected in Belize and from laboratory bioassays. The samples were positive for PvNV infection. Positively reacting tissues included skeletal muscle, connective tissues, the lymphoid organ, and hemocytes in the heart and gills. In addition, we experimentally infected both P. vannamei and P. monodon with PvNV prepared from Belize samples. A nested RT-PCR assay developed from the PvNV-4 cloned sequence showed that both species are susceptible to PvNV infection. PMID:17629112

  1. Sequence-specific purification of nucleic acids by PNA-controlled hybrid selection.

    PubMed

    Orum, H; Nielsen, P E; Jørgensen, M; Larsson, C; Stanley, C; Koch, T

    1995-09-01

    Using an oligohistidine peptide nucleic acids (oligohistidine-PNA) chimera, we have developed a rapid hybrid selection method that allows efficient, sequence-specific purification of a target nucleic acid. The method exploits two fundamental features of PNA. First, that PNA binds with high affinity and specificity to its complementary nucleic acid. Second, that amino acids are easily attached to the PNA oligomer during synthesis. We show that a (His)6-PNA chimera exhibits strong binding to chelated Ni2+ ions without compromising its native PNA hybridization properties. We further show that these characteristics allow the (His)6-PNA/DNA complex to be purified by the well-established method of metal ion affinity chromatography using a Ni(2+)-NTA (nitrilotriactic acid) resin. Specificity and efficiency are the touchstones of any nucleic acid purification scheme. We show that the specificity of the (His)6-PNA selection approach is such that oligonucleotides differing by only a single nucleotide can be selectively purified. We also show that large RNAs (2224 nucleotides) can be captured with high efficiency by using multiple (His)6-PNA probes. PNA can hybridize to nucleic acids in low-salt concentrations that destabilize native nucleic acid structures. We demonstrate that this property of PNA can be utilized to purify an oligonucleotide in which the target sequence forms part of an intramolecular stem/loop structure. PMID:7495562

  2. Genotoxic effects of boric acid and borax in zebrafish, Danio rerio using alkaline comet assay.

    PubMed

    Gülsoy, Nagihan; Yavas, Cüneyd; Mutlu, Özal

    2015-01-01

    The present study is conducted to determine the potential mechanisms of Boron compounds, boric acid (BA) and borax (BX), on genotoxicity of zebrafish Danio rerio for 24, 48, 72 and 96-hours acute exposure (level:1, 4, 16, 64 mg/l BA and BX) in semi-static bioassay experiment. For that purpose, peripheral erythrocytes were drawn from caudal vein and Comet assay was applied to assess genotoxicity. Acute (96 hours) exposure and high concentrations of boric acid and borax increases % tail DNA and Olive tail moment. Genotoxicity was found for BA as concentration-dependent and BX as concentration and time dependent manner. In general, significant effects (P < 0,05) on both concentrations and exposure times were observed in experimental groups. DNA damage was highest at 96 h and 24 h for all BX and BA concentrations, respectively in peripheral blood of D. rerio. For the first time, our study demonstrates the effect of waterborne BA and BX exposure on genotoxicity at the molecular level, which may contribute to understanding the mechanism of boric acid and borax-induced genotoxicity in fish. PMID:26862320

  3. Urinary Excretion of Phenolic Acids by Infants and Children: A Randomised Double-Blind Clinical Assay

    PubMed Central

    Uberos, J.; Fernández-Puentes, V.; Molina-Oya, M.; Rodríguez-Belmonte, R.; Ruíz-López, A.; Tortosa-Pinto, P.; Molina-Carballo, A.; Muñoz-Hoyos, A.

    2012-01-01

    Objectives: The present study, which is part of the ISRCTN16968287 clinical assay, is aimed at determining the effects of cranberry syrup or trimethoprim treatment for UTI. Methods: This Phase III randomised clinical trial was conducted at the San Cecilio Clinical Hospital (Granada, Spain) with a study population of 192 patients, aged between 1 month and 13 years. Criteria for inclusion were a background of recurrent UTI, associated or otherwise with vesico-ureteral reflux of any degree, or renal pelvic dilatation associated with urinary infection. Each child was randomly given 0.2 mL/Kg/day of either cranberry syrup or trimethoprim (8 mg/mL). The primary and secondary objectives, respectively, were to determine the risk of UTI and the levels of phenolic acids in urine associated with each intervention. Results: With respect to UTI, the cranberry treatment was non-inferior to trimethoprim. Increased urinary excretion of ferulic acid was associated with a greater risk of UTI developing in infants aged under 1 year (RR 1.06; CI 95% 1.024–1.1; P = 0.001). Conclusions: The results obtained show the excretion of ferulic acid is higher in infants aged under 1 year, giving rise to an increased risk of UTI, for both treatment options. PMID:23641168

  4. Genotoxic effects of boric acid and borax in zebrafish, Danio rerio using alkaline comet assay

    PubMed Central

    Gülsoy, Nagihan; Yavas, Cüneyd; Mutlu, Özal

    2015-01-01

    The present study is conducted to determine the potential mechanisms of Boron compounds, boric acid (BA) and borax (BX), on genotoxicity of zebrafish Danio rerio for 24, 48, 72 and 96-hours acute exposure (level:1, 4, 16, 64 mg/l BA and BX) in semi-static bioassay experiment. For that purpose, peripheral erythrocytes were drawn from caudal vein and Comet assay was applied to assess genotoxicity. Acute (96 hours) exposure and high concentrations of boric acid and borax increases % tail DNA and Olive tail moment. Genotoxicity was found for BA as concentration-dependent and BX as concentration and time dependent manner. In general, significant effects (P < 0,05) on both concentrations and exposure times were observed in experimental groups. DNA damage was highest at 96 h and 24 h for all BX and BA concentrations, respectively in peripheral blood of D. rerio. For the first time, our study demonstrates the effect of waterborne BA and BX exposure on genotoxicity at the molecular level, which may contribute to understanding the mechanism of boric acid and borax-induced genotoxicity in fish. PMID:26862320

  5. Immunochemical Assays and Nucleic-Acid Detection Techniques for Clinical Diagnosis of Prostate Cancer

    PubMed Central

    Kanyong, Prosper; Rawlinson, Sean; Davis, James

    2016-01-01

    Prostate cancer (PCa) is a significant cause of morbidity and mortality and the most common cancer in men in Europe, North America, and some parts of Africa. The established methods for detecting PCa are normally based on tests using Prostate Specific Antigen (PSA) in blood, Prostate cancer antigen 3 (PCA3) in urine and tissue Alpha-methylacyl-CoA racemase (AMACR) as tumour markers in patient samples. Prior to the introduction of PSA in clinics, prostatic acid phosphatase (PAP) was the most widely used biomarker. An early diagnosis of PCa through the detection of these biomarkers requires the availability of simple, reliable, cost-effective and robust techniques. Immunoassays and nucleic acid detection techniques have experienced unprecedented growth in recent years and seem to be the most promising analytical tools. This growth has been driven in part by the surge in demand for near-patient-testing systems in clinical diagnosis. This article reviews immunochemical assays, and nucleic-acid detection techniques that have been used to clinically diagnose PCa. PMID:26958088

  6. Studies towards the development of chemically synthesized non-radioactive biotinylated nucleic acid hybridization probes.

    PubMed Central

    Al-Hakim, A H; Hull, R

    1986-01-01

    Non-radioactive nucleic acid hybridization probes have been constructed in which the reporter group is long chain biotin chemically linked to a basic macromolecule (histone H1, cytochrome C or polyethyleneimine). The modified basic macromolecule which carries many biotin residues can, in turn, be covalently linked to nucleic acids (DNA) via the bifunctional cross-linking reagents, glutaraldehyde, 1,2,7,8-diepoxyoctane, bis (succinimidyl) suberate or bis (sulfonosuccinimidyl) suberate. This provides a very sensitive probe by which as little as between 10-50fg of target DNA can be visualized using dot-blot hybridization procedures in conjunction with avidin or streptavidin enzyme conjugates. PMID:3027670

  7. Discrimination of clostridium species using a magnetic bead based hybridization assay

    NASA Astrophysics Data System (ADS)

    Pahlow, Susanne; Seise, Barbara; Pollok, Sibyll; Seyboldt, Christian; Weber, Karina; Popp, Jürgen

    2014-05-01

    Clostridium chauvoei is the causative agent of blackleg, which is an endogenous bacterial infection. Mainly cattle and other ruminants are affected. The symptoms of blackleg are very similar to those of malignant edema, an infection caused by Clostridium septicum. [1, 2] Therefore a reliable differentiation of Clostridium chauvoei from other Clostridium species is required. Traditional microbiological detection methods are time consuming and laborious. Additionally, the unique identification is hindered by the overgrowing tendency of swarming Clostridium septicum colonies when both species are present. [1, 3, 4] Thus, there is a crucial need to improve and simplify the specific detection of Clostridium chauvoei and Clostridium septicum. Here we present an easy and fast Clostridium species discrimination method combining magnetic beads and fluorescence spectroscopy. Functionalized magnetic particles exhibit plentiful advantages, like their simple manipulation in combination with a large binding capacity of biomolecules. A specific region of the pathogenic DNA is amplified and labelled with biotin by polymerase chain reaction (PCR). These PCR products were then immobilized on magnetic beads exploiting the strong biotin-streptavidin interaction. The specific detection of different Clostridium species is achieved by using fluorescence dye labeled probe DNA for the hybridization with the immobilized PCR products. Finally, the samples were investigated by fluorescence spectroscopy. [5

  8. Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy.

    PubMed

    Zhang, Linqun; Liu, Yuanjian; Li, Ying; Zhao, Yuewu; Wei, Wei; Liu, Songqin

    2016-08-24

    A mimic-hybridization chain reaction (mimic-HCR) amplified strategy was proposed for sensitive electrochemically detection of DNA methylation and methyltransferase (MTase) activity In the presence of methylated DNA, DNA-gold nanoparticles (DNA-AuNPs) were captured on the electrode by sandwich-type assembly. It then triggered mimic-HCR of two hairpin probes to produce many long double-helix chains for numerous hexaammineruthenium (III) chloride ([Ru(NH3)6](3+), RuHex) inserting. As a result, the signal for electrochemically detection of DNA MTase activity could be amplified. If DNA was non-methylated, however, the sandwich-type assembly would not form because the short double-stranded DNAs (dsDNA) on the Au electrode could be cleaved and digested by restriction endonuclease HpaII (HapII) and exonuclease III (Exo III), resulting in the signal decrement. Based on this, an electrochemical approach for detection of M.SssI MTase activity with high sensitivity was developed. The linear range for M.SssI MTase activity was from 0.05 U mL(-1) to 10 U mL(-1), with a detection limit down to 0.03 U mL(-1). Moreover, this detecting strategy held great promise as an easy-to-use and highly sensitive method for other MTase activity and inhibition detection by exchanging the corresponding DNA sequence. PMID:27496999

  9. Determination of Chitin Based on the Colorimetric Assay of Glucosamine in Acidic Hydrolysate.

    PubMed

    Katano, Hajime; Takakuwa, Masahiro; Hayakawa, Hajime; Kimoto, Hisashi

    2016-01-01

    A colorimetric method for the glucosamine (GlcN) assay was applied for the determination of chitin, which can be hydrolyzed to produce GlcN. A 10-mg sample was mixed with 10 mL of a 5 mol/L HCl aqueous solution, and the mixture was kept at 100°C for 12 h. Under these conditions, chitin was completely depolymerized and deacetylated to produce GlcN, even when the sample was a crab shell. A 20-μL aliquot of the hydrolysate was mixed with 20 μL of a 5 mol/L NaOH aqueous solution and 200 μL of a 50 mmol/L Na2SiO3, 600 mmol/L Na2MoO4, 1.5 mol/L CH3COOH and 30% (v/v) dimethyl sulfoxide solution. The mixture was kept at 70°C for 30 min. In the mixture, GlcN reduced the Mo(VI) species to form a blue molybdosilicate anion, which gave an absorbance maximum at around 750 nm. Since N-acetylglucosamine and chitin oligosaccharides could not render the reaction mixture blue, GlcN in the hydrolysate could be assayed colorimetrically with high selectivity. When a standard chitin sample was examined, the GlcN concentration in the hydrolysate was determined to be 0.97 ± 0.02 g/L (as hydrochloride salt), indicating that the sample contained 10.0 ± 0.2 mg chitin (as an N-acetylglucosamine homopolymer). Calcium cation, amino acids, and proteins did not interfere with the GlcN assay. Thus, the proposed method was successfully applied to determine chitin in a crab shell sample. PMID:27302593

  10. Promising Nucleic Acid Lateral Flow Assay Plus PCR for Shiga Toxin-Producing Escherichia coli.

    PubMed

    Terao, Yoshitaka; Takeshita, Kana; Nishiyama, Yasutaka; Morishita, Naoki; Matsumoto, Takashi; Morimatsu, Fumiki

    2015-08-01

    Shiga toxin (Stx)-producing Escherichia coli (STEC) is a frequent cause of foodborne infections, and methods for rapid and reliable detection of STEC are needed. A nucleic acid lateral flow assay (NALFA) plus PCR was evaluated for detecting STEC after enrichment. When cell suspensions of 45 STEC strains, 14 non-STEC strains, and 13 non-E. coli strains were tested with the NALFA plus PCR, all of the STEC strains yielded positive results, and all of the non-STEC and non-E. coli strains yielded negative results. The lower detection limit for the STEC strains ranged from 0.1 to 1 pg of genomic DNA (about 20 to 200 CFU) per test, and the NALFA plus PCR was able to detect Stx1- and Stx2-producing E. coli strains with similar sensitivities. The ability of the NALFA plus PCR to detect STEC in enrichment cultures of radish sprouts, tomato, raw ground beef, and beef liver inoculated with 10-fold serially diluted STEC cultures was comparable to that of a real-time PCR assay (at a level of 100 to 100,000 CFU/ml in enrichment culture). The bacterial inoculation test in raw ground beef revealed that the lower detection limit of the NALFA plus PCR was also comparable to that obtained with a real-time PCR assay that followed the U.S. Department of Agriculture guidelines. Although further evaluation is required, these results suggest that the NALFA plus PCR is a specific and sensitive method for detecting STEC in a food manufacturing plant. PMID:26219371

  11. A versatile solid support system for oligodeoxynucleotide probe-based hybridization assays.

    PubMed Central

    Van Ness, J; Kalbfleisch, S; Petrie, C R; Reed, M W; Tabone, J C; Vermeulen, N M

    1991-01-01

    A procedure for immobilization of well-defined quantities of oligodeoxyribonucleotides (ODNs) to a versatile nylon support is described. The solid support, a nylon-6/6 bead, is covalently coated with poly(ethyleneimine) to provide a reactive spacer-arm for attachment of ODNs. 5'-Aminohexyl-tailed ODNs are selectively activated using 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and then covalently attached to the bead via the triazine moiety. The modified nylon support has a low level of binding of nonspecific nucleic acid and efficiently captures both RNA and DNA targets. PMID:2062652

  12. Light and heavy dansyl reporter groups in food chemistry: amino acid assay in beverages.

    PubMed

    Mazzotti, Fabio; Benabdelkamel, Hicham; Di Donna, Leonardo; Athanassopoulos, Constantinos M; Napoli, Anna; Sindona, Giovanni

    2012-07-01

    5-Dimethylamino-1-sulfonyl naphthalene (DNS, commonly referred as dansyl) is a functionality, bearing well-established properties in directing the fragmentation, by mass spectrometry (MS), of the corresponding ionized sulfonylated derivatives. This property is shared also by its labeled analogs. The use of d(0)/d(6) DNS derivatives is now exploited in the application of the well-established isotope dilution mass spectrometric approach in the assay of complex mixtures. A new method for the quantitation of amino acids (AAs) in beverages is therefore presented, which relies on liquid chromatographic separation of their N-dansylated derivatives followed by comparative electrospray tandem MS/MS of the d(0)/d(6) isobaric mixtures. Labeled and unlabeled DNS derivatives of the selected AAs are readily available by microwave-assisted synthetic protocols. The novelty of the method is represented by the use of heavy and light DNS-isotopologue providing suitable reporter groups. Multiple-reaction monitoring has been applied in the assay of AAs in wine, pineapple juice and bergamot juice with good-to-excellent results as proved by both relative standard deviation, lower than 15%, and by the accuracy values in the range 90-110%. PMID:22791261

  13. Local sustained delivery of acetylsalicylic acid via hybrid stent with biodegradable nanofibers reduces adhesion of blood cells and promotes reendothelialization of the denuded artery

    PubMed Central

    Lee, Cheng-Hung; Lin, Yu-Huang; Chang, Shang-Hung; Tai, Chun-Der; Liu, Shih-Jung; Chu, Yen; Wang, Chao-Jan; Hsu, Ming-Yi; Chang, Hung; Chang, Gwo-Jyh; Hung, Kuo-Chun; Hsieh, Ming-Jer; Lin, Fen-Chiung; Hsieh, I-Chang; Wen, Ming-Shien; Huang, Yenlin

    2014-01-01

    Incomplete endothelialization, blood cell adhesion to vascular stents, and inflammation of arteries can result in acute stent thromboses. The systemic administration of acetylsalicylic acid decreases endothelial dysfunction, potentially reducing thrombus, enhancing vasodilatation, and inhibiting the progression of atherosclerosis; but, this is weakened by upper gastrointestinal bleeding. This study proposes a hybrid stent with biodegradable nanofibers, for the local, sustained delivery of acetylsalicylic acid to injured artery walls. Biodegradable nanofibers are prepared by first dissolving poly(D,L)-lactide-co-glycolide and acetylsalicylic acid in 1,1,1,3,3,3-hexafluoro-2-propanol. The solution is then electrospun into nanofibrous tubes, which are then mounted onto commercially available bare-metal stents. In vitro release rates of pharmaceuticals from nanofibers are characterized using an elution method, and a highperformance liquid chromatography assay. The experimental results suggest that biodegradable nanofibers release high concentrations of acetylsalicylic acid for three weeks. The in vivo efficacy of local delivery of acetylsalicylic acid in reducing platelet and monocyte adhesion, and the minimum tissue inflammatory reaction caused by the hybrid stents in treating denuded rabbit arteries, are documented. The proposed hybrid stent, with biodegradable acetylsalicylic acid-loaded nanofibers, substantially contributed to local, sustained delivery of drugs to promote re-endothelialization and reduce thrombogenicity in the injured artery. The stents may have potential applications in the local delivery of cardiovascular drugs. Furthermore, the use of hybrid stents with acetylsalicylic acid-loaded nanofibers that have high drug loadings may provide insight into the treatment of patients with high risk of acute stent thromboses. PMID:24421640

  14. On-chip mitochondrial assay microfluidic devices and protein nanopore/nanotube hybrid transistor

    NASA Astrophysics Data System (ADS)

    Lim, Taesun

    Tremendous efforts to understand the cause, mechanism of development and the way to treat various diseases as well as an early diagnosis have been made so far and people are still working hardly on these researches. Even now, countless people are suffering from diseases such as Alzhemer's disease, Parkinson's disease, diabetes and cancer without knowing clues to cure their diseases completely. Generally speaking, we still have a long way to go through to comprehensively figure out these our long-lasting homeworks. One of possible solutions is to merge current advanced technology and science together to find a powerful synergetic effect for a specific purpose that can be tailored depending on user's need. Here this research tried to put nanotechnology and biological science together to find a way to resolve current challenges by developing a new generation of the analytical sensing device. Mitochondrial functions and biological roles in regulating life and death control will be discussed indicating mitochondrion is a crucial organism to monitor to obtain important information regarding degenerative diseases and aging process. On-chip mitochondrial functional assay microsensor that could facilitate the mitochondrial evaluation will be extensively demonstrated and discussed in both technical and biological perspectives. The novel fusion technological approach will be demonstrated by combining artificial cell membrane with carbon nanotube electronics to interrogate interactions between biomolecules and electronic circuitries. In addition, molecular dynamics at the cell membrane could be investigated closely which can help understand the cell-cell communication and the regulation of ion transport.

  15. Unsaturated fatty acids show clear elicitation responses in a modified local lymph node assay with an elicitation phase, and test positive in the direct peptide reactivity assay.

    PubMed

    Yamashita, Kunihiko; Shinoda, Shinsuke; Hagiwara, Saori; Miyazaki, Hiroshi; Itagaki, Hiroshi

    2015-12-01

    The Organisation for Economic Co-operation and Development (OECD) Test Guidelines (TG) adopted the murine local lymph node assay (LLNA) and guinea pig maximization test (GPMT) as stand-alone skin sensitization test methods. However, unsaturated carbon-carbon double-bond and/or lipid acids afforded false-positive results more frequently in the LLNA compared to those in the GPMT and/or in human subjects. In the current study, oleic, linoleic, linolenic, undecylenic, fumaric, maleic, and succinic acid and squalene were tested in a modified LLNA with an elicitation phase (LLNA:DAE), and in a direct peptide reactivity assay (DPRA) to evaluate their skin-sensitizing potential. Oleic, linoleic, linolenic, undecylenic and maleic acid were positive in the LLNA:DAE, of which three, linoleic, linolenic, and maleic acid were positive in the DPRA. Furthermore, the results of the cross-sensitizing tests using four LLNA:DAE-positive chemicals were negative, indicating a chemical-specific elicitation response. In a previous report, the estimated concentration needed to produce a stimulation index of 3 (EC3) of linolenic acid, squalene, and maleic acid in the LLNA was < 10%. Therefore, these chemicals were classified as moderate skin sensitizers in the LLNA. However, the skin-sensitizing potential of all LLNA:DAE-positive chemicals was estimated as weak. These results suggested that oleic, linoleic, linolenic, undecylenic, and maleic acid had skin-sensitizing potential, and that the LLNA overestimated the skin-sensitizing potential compared to that estimated by the LLNA:DAE. PMID:26558466

  16. Evaluation of the hybrid capture 2 assay for detecting anal high-grade dysplasia.

    PubMed

    Goldstone, Stephen E; Lowe, Brian; Rothmann, Thomas; Nazarenko, Irina

    2012-10-01

    Hybrid Capture 2 (HC2) Human Papillomavirus (HPV) DNA Test® is FDA approved and is a proven aid in detecting HPV infections of the cervix and as an aid in diagnosing, with cytology, cervical disease. A prospective feasibility study was conducted to determine if HC2 testing has utility when screening for high-grade anal dysplasia (AIN2+). We enrolled 298 patients (45% HIV+) who had AIN2+ screening with cytology, histology and HC2 testing for two specimens: a swab into liquid-based cytology medium and either a swab or a brush collection in specimen transport medium (STM). High-resolution anoscopy was performed on all patients with biopsy of AIN2+ suspicious lesions. Cytology was benign (42%), atypical squamous cells of undetermined significance (30%), low-grade squamous intraepithelial lesion (18%), high-grade squamous intraepithelial lesion (1%), ASCUS possibly high-grade dysplasia (1.7%) and nondiagnostic (7%) and 36% had AIN2+ histology. Sensitivity and specificity for predicting AIN2+ histology for any abnormal cytology were 77 and 52%, whereas HC2 sensitivity and specificity were 91 and 40% (p = 0.005 for sensitivity), respectively. There was no significant difference in HC2 sensitivity or specificity between brush and swab or STM and residual cells from cytology. AIN2+ was found in 20% of patients with benign cytology. Only nine AIN2+ specimens were HC2-. This prospective study indicates that HC2 may be useful when screening for anal dysplasia; however, a larger study is recommended. PMID:22234750

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

    SciTech Connect

    Bloch, Donald B. 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.

  18. Bioactivity in silica/poly(γ-glutamic acid) sol-gel hybrids through calcium chelation.

    PubMed

    Valliant, Esther M; Romer, Frederik; Wang, Daming; McPhail, David S; Smith, Mark E; Hanna, John V; Jones, Julian R

    2013-08-01

    Bioactive glasses and inorganic/organic hybrids have great potential as biomedical implant materials. Sol-gel hybrids with interpenetrating networks of silica and biodegradable polymers can combine the bioactive properties of a glass with the toughness of a polymer. However, traditional calcium sources such as calcium nitrate and calcium chloride are unsuitable for hybrids. In this study calcium was incorporated by chelation to the polymer component. The calcium salt form of poly(γ-glutamic acid) (γCaPGA) was synthesized for use as both a calcium source and as the biodegradable toughening component of the hybrids. Hybrids of 40wt.% γCaPGA were successfully formed and had fine scale integration of Ca and Si ions, according to secondary ion mass spectrometry imaging, indicating a homogeneous distribution of organic and inorganic components. (29)Si magic angle spinning nuclear magnetic resonance data demonstrated that the network connectivity was unaltered with changing polymer molecular weight, as there was no perturbation to the overall Si speciation and silica network formation. Upon immersion in simulated body fluid a hydroxycarbonate apatite surface layer formed on the hybrids within 1week. The polymer molecular weight (Mw 30-120kDa) affected the mechanical properties of the resulting hybrids, but all hybrids had large strains to failure, >26%, and compressive strengths, in excess of 300MPa. The large strain to failure values showed that γCaPGA hybrids exhibited non-brittle behaviour whilst also incorporating calcium. Thus calcium incorporation by chelation to the polymer component is justified as a novel approach in hybrids for biomedical materials. PMID:23632373

  19. Ligand-dependent interactions of the Ah receptor with coactivators in a mammalian two-hybrid assay

    SciTech Connect

    Zhang Shu; Rowlands, Craig; Safe, Stephen

    2008-03-01

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a high affinity ligand for the aryl hydrocarbon receptor (AhR). In this study, we investigated structure-dependent differences in activation of the AhR by a series of halogenated aromatic hydrocarbons. TCDD, 1,2,3,7,8-pentachlorodibenzo-p-dioxin (PeCDD), 2,3,7,8-tetrachlorodibenzofuran (TCDF), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF), and 3,3',4,4',5-pentachlorobiphenyl (PCB126) induced CYP1A1-dependent activities in HEK293 human embryonic kidney, Panc1 pancreatic cancer, and Hepa1c1c7 mouse hepatoma cell lines. There was a structure-dependent difference in the efficacy of TCDF and PCB126 in HEK293 and Panc1 cells since induced CYP1A1 mRNA levels were lower than observed for the other congeners. A mammalian two-hybrid assay in cells transfected with GAL4-coactivator and AhR-VP16 chimeras was used to investigate structure-dependent interactions of these chimeras in Panc1, HEK293, and Hepa1c1c7 cells. The reporter construct pGAL4-luc contains five tandem GAL4 response elements linked to the luciferase gene and the GAL4-coactivator chimeras express several coactivators including steroid receptor coactivator 1 (SRC-1), SRC-2 and SRC-3, the mediator coactivator TRAP220, coactivator associated arginine methyl transferase 1 (CARM-1), and peroxisome proliferator-activated receptor {gamma} coactivator 1 (PGC-1). Results of the mammalian two-hybrid studies clearly demonstrate that activation of pGAL4-luc in cells transfected with VP-AhR and GAL4-coactivator chimeras is dependent on the structure of the HAH congener, cell context, and coactivator, suggesting that the prototypical HAH congeners used in this study exhibit selective AhR modulator activity.

  20. Direct Assay of δ-Aminolevulinic Acid Dehydratase in Heme Biosynthesis for the Detection of Porphyrias by Tandem Mass Spectrometry

    PubMed Central

    Choiniere, John R.; Scott, C. Ronald; Gelb, Michael H.; Tureček, František

    2010-01-01

    We report a new assay of human δ-aminolevulinic acid dehydratase (ALAD), an enzyme converting δ-aminolevulinic acid (ALA) into porphobilinogen. The assay is developed for use in the clinical diagnosis of δ-aminolevulinic acid dehydratase-deficient porphyria, a rare enzymatic deficiency of the heme biosynthetic pathway. The assay involves the incubation of erythrocyte lysate with the natural substrate, ALA, followed by quantitative in situ conversion of porphobilinogen to its butyramide, and liquid-liquid extraction into a mass spectrometer-friendly solvent. Quantitation of the butyrylated porphobilinogen is done by electrospray ionization tandem mass spectrometry, using a deuterium labeled internal standard. The assay stays well within the range wherein ALAD activity is linear with time. The Km of ALAD for ALA was measured as 333 μM, and the Vmax was 19.3 μM/hr. Average enzyme activity among a random sample of 36 anonymous individuals was 277 μmol/L erythrocyte lysate/hour with a standard deviation of 90 μmol/L erythrocyte lysate/hour. The tandem mass spectrometric assay should easily detect the enzyme deficiency, which causes a reduction of activity by 95–99%. The assay shows good reproducibility, low background, requires a simple workup, and uses a commercially available substrate. PMID:20583792

  1. [Development of direct competitive enzyme-linked immunosorbent assay for the determination of domoic acid].

    PubMed

    Wang, Qian; Cheng, Jin-Ping; Gao, Li-Li; Dong, Yu; Xi, Lei

    2012-02-01

    To develop a direct competitive enzyme-linked immunosorbent assay (ELISA) for rapid detection of domoic acid concentrations, HRP (horse radish peroxidase) was successfully linked to DA using EDC. The concentration of DA was quantitatively analyzed on the basic of the specific immune responses between the DA- HRP and the monoclonal antibodies made in advance. Calibration curve were established after the optimization of reaction conditions such as the type of blocking solution, the blocking time and the incubation temperature. The results show that, the best reaction condition of the direct competitive ELISA is 1% gelatin, blocking 1 h at 37 degrees C, incubating 1 h at 37 degrees C after the monoclonal antibodies added. The detect limit is 3.58 ng x mL(-1), the coefficient of variation between the holes is below 15%, and the recovery is 80% - 120%. The whole analysis process could be completed within 1.5 h. It meets the requirements of rapid and batch detection of domoic acid. The method will have broad development prospects. PMID:22509610

  2. Photoluminescence and quantum yields of organic/inorganic hybrids prepared through formic acid solvolysis

    NASA Astrophysics Data System (ADS)

    Fu, Lianshe; Sá Ferreira, R. A.; Fernandes, M.; Nunes, S. C.; de Zea Bermudez, V.; Hungerford, Graham; Rocha, J.; Carlos, L. D.

    2008-03-01

    Three undoped di-urea cross-linked poly(oxyethylene) (POE)/siloxane hybrid matrices, classed as di-ureasils, incorporating POE segments with different lengths were prepared through the carboxylic acid solvolysis sol-gel method using formic acid. The resulting hybrids were characterized by X-ray diffraction, Fourier transform mid-infrared spectroscopy, 29Si and cross-polarization 13C magic-angle spinning nuclear magnetic resonance and photoluminescence spectroscopy. The hybrids' structure is essentially independent of the polymer chain length and the materials are room temperature white-light emitters with emission quantum yields of ˜10 ± 1% and lifetime average values between 2 and 4 ns. For the di-ureasil host with short polymer chains the solvolysis method favours the increase of the PL quantum yields relatively to conventional sol-gel route.

  3. Medical devices; immunology and microbiology devices; classification of quality control material for cystic fibrosis nucleic acid assays. Final rule.

    PubMed

    2007-01-10

    The Food and Drug Administration (FDA) is classifying quality control material for cystic fibrosis nucleic acid assays into class II (special controls). The special control that will apply to the device is the guidance document entitled "Class II Special Controls Guidance Document: Quality Control Material for Cystic Fibrosis Nucleic Acid Assays." The agency is classifying the device into class II (special controls) in order to provide a reasonable assurance of safety and effectiveness of the device. Elsewhere in this issue of the Federal Register, FDA is announcing the availability of the guidance document that will serve as the special control for this device. PMID:17294552

  4. Optimization of pH values to formulate the bireagent kit for serum uric acid assay.

    PubMed

    Huang, Ya; Chen, Yuanxiang; Yang, Xiaolan; Zhao, Hua; Hu, Xiaolei; Pu, Jun; Liao, Juan; Long, Gaobo; Liao, Fei

    2015-01-01

    A new formulation of the bireagent kit for serum uric acid assay was developed based on the effects of pH on enzyme stability. At 4 °C, half-lives of uricases from Bacillus fastidious and Arthrobacter globiforms were longer than 15 months at pH 9.2, but became shorter at pH below 8.0; half-lives of ascorbate oxidase and peroxidase were comparable at pH 6.5 and 7.0, but became much shorter at pH higher than 7.4. In the new formulation of the bireagent kit, Reagent A contained peroxidase, 4-aminoantipyrine, and ascorbate oxidase in 50 mM phosphate buffer at pH 6.5; Reagent B contained B. fastidious or A. globiforms uricase in 50 mM sodium borate buffer at pH 9.2; Reagents A and B were mixed at 4:1 to produce a final pH from 7.2 to 7.6 for developing a stable color. The new bireagent kit consumed smaller quantities of three enzymes for the same shelf life. With the new bireagent kit, there were linear responses of absorbance at 546 nm to uric acid up to 34 mM in reaction mixtures and a good correlation of uric acid levels in clinical sera with those by a commercial kit, but stronger resistance to ascorbate. Therefore, the new formulation was advantageous. PMID:24673428

  5. Comparative study of colony hybridization with synthetic oligonucleotide probes and enzyme-linked immunosorbent assay for identification of enterotoxigenic Escherichia coli.

    PubMed Central

    Sommerfelt, H; Svennerholm, A M; Kalland, K H; Haukanes, B I; Bjorvatn, B

    1988-01-01

    On the basis of the published nucleotide sequences of the genes that code for the heat-labile toxin LTh and the heat-stable toxins STaI and STaII of human enterotoxigenic Escherichia coli, a 34-mer and two 33-mer oligonucleotide probes were synthesized. To compare their relative efficacies in the detection and differentiation of enterotoxigenic E. coli, a colony hybridization technique using these probes and a GM1 ganglioside enzyme-linked immunosorbent assay using monoclonal anti-LT and anti-ST antibodies were used with 76 strains of E. coli with known enterotoxin profiles. For further evaluation of probe specificity, the enterotoxigenic bacteria Vibrio cholerae O1 and non-O1 and Yersinia enterocolitica were examined with the colony hybridization technique. The sensitivity of colony hybridization compared favorably with that of GM1 ganglioside enzyme-linked immunosorbent assay, and the two assays showed a high level of concordance in specific detection and differentiation of E. coli with various enterotoxin profiles (kappa = 0.906, P less than 0.00001). The probes did not hybridize with DNAs from strains of V. cholerae O1 or non-O1 or Y. enterocolitica. PMID:3281978

  6. Isotope-dilution assay for urinary methylmalonic acid in the diagnosis of vitamin B12 deficiency. A prospective clinical evaluation

    SciTech Connect

    Matchar, D.B.; Feussner, J.R.; Millington, D.S.; Wilkinson, R.H. Jr.; Watson, D.J.; Gale, D.

    1987-05-01

    Vitamin B12 deficiency is a frequently considered diagnosis for which there is no single, commonly available and accurate test. A urinary methylmalonic acid assay using gas chromatography-mass spectrometry has been proposed as the preferred test. We reviewed vitamin B12 assays on 1599 consecutive patients and prospectively studied all patients with low serum B12 levels (n = 75) and a random sample of patients with normal levels (n = 68). Of 96 evaluable patients, 7 had clinical deficiency. All 7 deficient patients had urinary methylmalonic acid levels greater than 5 micrograms/mg creatine (sensitivity, 100%; confidence interval, 65% to 100%). Of the 89 patients who were not clinically deficient, 88 had urinary methylmalonic acid levels less than or equal to 5 micrograms/mg creatinine (specificity, 99%). The overall test accuracy in this population was 99%. If the high sensitivity and specificity of the gas chromatography-mass spectrometry assay for urinary methylmalonic acid is supported by other clinical studies, the methylmalonic acid assay may become the reference standard for the diagnosis of vitamin B12 deficiency.

  7. Nucleic Acid Hybridization Studies within the Genus Cucurbita

    PubMed Central

    Goldberg, Robert B.; Bemis, William P.; Siegel, Albert

    1972-01-01

    The DNAs of Cucurbita species were examined by several methods. All Cucurbita DNAs have a similar CsCl isopycnic banding pattern consisting of a major band at 1.695 g/cc and a well separated satellite band at 1.707 g/cc. Compared to other plant and animal genera, Cucurbita species have a large genomic proportion of rDNA; this value ranging from 1.4% to 3.1%. The genomic proportion of rDNA was found not to be useful as a characteristic indicating degree of relatedness of the various Cucurbita species. However, Cucurbita DNAs can be distinguished by the extent to which their repetitive sequences cross-hybridize to each other and an assessment of species relationships can be made on this basis. PMID:17248582

  8. Use of submitochondrial particle (SMP) assays for assessing wetlands constructed for sequestering acid mine runoff

    SciTech Connect

    Bettermann, A.D.; Haahr, J.E.; Lazorchak, J.M.

    1995-12-31

    Use of constructed wetlands to sequester metals from acid mine drainage is part of a USEPA SITE demonstration at Burleigh Tunnel near Silverplume, Colorado. Samples are collected on a seasonal basis for toxicity evaluation of two different pilot treatment systems. Water samples were obtained from the outflow of two experimental wetland cells utilizing either upflow and downflow treatment, as well as upstream and downstream of the discharge of Burleigh Tunnel to Clear Creek. Submitochondrial Particle (SMP), Ceriodaphnia dubia and Pimephales promelas acute bioassays were used to evaluate the water quality. The SMP bioassay is based on the electron transfer complex derived from mitochondria. Toxic responses result from subcellular perturbations of various subsets of enzyme systems contained in the complex. In prior work, a 0.79 r{sup 2} was reported between the SMP bioassay and P. promelas for 11 inorganics on the EPA Priority Pollutant list. The SMP bioassay provided data consistent with the whole organism results. The two most toxic samples: the Burleigh outflow, and the Clear Creek Upstream sample, gave C. dubia LC50s of 1.01% and 8.41%, respectively. The Burleigh outflow P. promelas LC50 was 1.55%. SMP EC50s for the Burleigh outflow and the Clear Creek Upstream sample were 0.63% and 1.63%, respectively. As the SMP bioassay requires 1 hour to run and costs approximately 1/10th of whole organism assays, it was feasible to determine EC50 values for 7 samples vs. the two sample LC50s determined using whole organism assays. The SMP bioassays can provide sufficient sampling density, at low cost, allowing effective delineation of wetland performance over time.

  9. Should South Africa Be Performing Nucleic Acid Testing on HIV Enzyme-Linked Immunosorbent Assay-Negative Samples?▿

    PubMed Central

    Gous, Natasha; Scott, Lesley; Perovic, Olga; Venter, Francios; Stevens, Wendy

    2010-01-01

    The frequency of acute HIV infection (AHI) among HIV-1 enzyme-linked immunosorbent assay (ELISA)-negative samples received from general hospital patient admissions was assessed. Of 3,005 samples pooled for nucleic acid testing, a prevalence of 0.13% was found. Pooled nucleic acid testing may be feasible for low-cost identification of AHI in high-prevalence settings. PMID:20610671

  10. Synthesis, Aqueous Reactivity, and Biological Evaluation of Carboxylic Acid Ester-Functionalized Platinum–Acridine Hybrid Anticancer Agents

    PubMed Central

    Graham, Leigh A.; Suryadi, Jimmy; West, Tiffany K.; Kucera, Gregory L.; Bierbach, Ulrich

    2012-01-01

    The synthesis of platinum–acridine hybrid agents containing carboxylic acid ester groups is described. The most active derivatives and the unmodified parent compounds showed up to 6-fold higher activity in ovarian cancer (OVCAR-3) and breast cancer (MCF-7, MDA-MB-23) cell lines than cisplatin. Inhibition of cell proliferation at nanomolar concentrations was observed in pancreatic (PANC-1) and non-small cell lung cancer cells (NSCLC, NCI-H460) of 80- and 150-fold, respectively. Introduction of the ester groups did not affect the cytotoxic properties of the hybrids, which form the same monofunctional–intercalative DNA adducts as the parent compounds, as demonstrated in a plasmid unwinding assay. In-line high-performance liquid chromatography and electrospray mass spectrometry (LC-ESMS) shows that the ester moieties undergo platinum-mediated hydrolysis in a chloride concentration-dependent manner to form carboxylate chelates. Potential applications of the chloride-sensitive ester hydrolysis as a self-immolative release mechanism for tumor-selective delivery of platinum–acridines are discussed. PMID:22871158

  11. Hydroxyapatite-phosphonoformic acid hybrid compounds prepared by hydrothermal method

    NASA Astrophysics Data System (ADS)

    Turki, Thouraya; Othmani, Masseoud; Bantignies, Jean-Louis; Bouzouita, Khaled

    2014-01-01

    Hydroxyapatites were prepared in the presence of different amounts of phosphonoformic acid (PFA) via the hydrothermal method. The obtained powders were characterized through chemical analysis, XRD, IR, 31P MAS-NMR, TEM, and TG-TDA. The XRD showed that the PFA did not affect the apatite composition. Indeed, only a reduction of the crystallite size was noted. After grafting of PFA, the IR spectroscopy revealed the appearance of new bands belonging to HPO42- and carboxylate groups of the apatite and organic moiety, respectively. Moreover, the 31P MAS-NMR spectra exhibited a peak with a low intensity assigned to the terminal phosphonate group of the organic moiety in addition to that of the apatite. Based on these results, a reaction mechanism involving the surface hydroxyl groups (tbnd Casbnd OH) of the apatite and the carboxyl group of the acid was proposed.

  12. Advanced bipolar lead-acid battery for hybrid electric vehicles

    NASA Astrophysics Data System (ADS)

    Saakes, Michel; Kleijnen, Christian; Schmal, Dick; ten Have, Peter

    A large size 80 V bipolar lead acid battery was constructed and tested successfully with a drive cycle especially developed for a HEV. The bipolar battery was made using the bipolar plate developed at TNO and an optimised paste developed by Centurion. An empirical model was derived for calculating the Ragone plot from the results from a small size 12 V bipolar lead-acid battery. This resulted in a specific power of 340 W/kg for the 80 V module. The Ragone plot was calculated at t=5 and t=10 s after the discharge started for current densities varying from 0.02 to 1.2 A/cm 2. A further development of the bipolar lead-acid battery will result in a specific power of 500 W/kg or more. From the economic analysis we estimate that the price of this high power battery will be in the order of 500 US$/kWh. This price is substantially lower than for comparable high power battery systems. This makes it an acceptable candidate future for HEV.

  13. Microfluidic platform for isolating nucleic acid targets using sequence specific hybridization

    PubMed Central

    Wang, Jingjing; Morabito, Kenneth; Tang, Jay X.; Tripathi, Anubhav

    2013-01-01

    The separation of target nucleic acid sequences from biological samples has emerged as a significant process in today's diagnostics and detection strategies. In addition to the possible clinical applications, the fundamental understanding of target and sequence specific hybridization on surface modified magnetic beads is of high value. In this paper, we describe a novel microfluidic platform that utilizes a mobile magnetic field in static microfluidic channels, where single stranded DNA (ssDNA) molecules are isolated via nucleic acid hybridization. We first established efficient isolation of biotinylated capture probe (BP) using streptavidin-coated magnetic beads. Subsequently, we investigated the hybridization of target ssDNA with BP bound to beads and explained these hybridization kinetics using a dual-species kinetic model. The number of hybridized target ssDNA molecules was determined to be about 6.5 times less than that of BP on the bead surface, due to steric hindrance effects. The hybridization of target ssDNA with non-complementary BP bound to bead was also examined, and non-specific hybridization was found to be insignificant. Finally, we demonstrated highly efficient capture and isolation of target ssDNA in the presence of non-target ssDNA, where as low as 1% target ssDNA can be detected from mixture. The microfluidic method described in this paper is significantly relevant and is broadly applicable, especially towards point-of-care biological diagnostic platforms that require binding and separation of known target biomolecules, such as RNA, ssDNA, or protein. PMID:24404041

  14. Efficacy of reducing sugar and phenol-sulfuric acid assays for analysis of soluble carbohydrates in feedstuffs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reducing sugar (RSA) and phenol–sulfuric acid (PSA) assays are commonly used to analyze water-soluble carbohydrates. However, questions have arisen as to their accuracy for measurement of feedstuffs with diverse carbohydrate profiles. This study evaluated the efficacy of RSA and PSA as they would co...

  15. SENSITIVE ASSAY, BASED ON HYDROXY FATTY ACIDS FROM LIPOPOLYSACCHARIDE LIPID A, FOR GRAM-NEGATIVE BACTERIA IN SEDIMENTS

    EPA Science Inventory

    Biochemical measures have provided insight into the biomass and community structure of sedimentary microbiota without the requirement of selection by growth or quantitative removal from the sediment grains. This study used the assay of the hydroxy fatty acids released from the li...

  16. Molecular Assay for Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae Isolates from Cultures and Clinical Nucleic Acid Amplification Test Specimens

    PubMed Central

    Peterson, S. W.; Martin, I.; Demczuk, W.; Bharat, A.; Hoang, L.; Wylie, J.; Allen, V.; Lefebvre, B.; Tyrrell, G.; Horsman, G.; Haldane, D.; Garceau, R.; Wong, T.

    2015-01-01

    We developed a real-time PCR assay to detect single nucleotide polymorphisms associated with ciprofloxacin resistance in specimens submitted for nucleic acid amplification testing (NAAT). All three single nucleotide polymorphism (SNP) targets produced high sensitivity and specificity values. The presence of ≥2 SNPs was sufficient to predict ciprofloxacin resistance in an organism. PMID:26292300

  17. Development of a precision-fed ileal amino acid digestibility assay using 3-week-old broiler chicks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of these studies was to develop a precision-fed ileal digestibility assay, primarily for amino acids (AA), using 3-wk-old broiler chicks. For all experiments, day-old Ross × Ross 708 broiler chicks were fed a standard corn-soybean meal starter diet until 21 d of age. In experiment 1, f...

  18. Whole-cell microtiter plate screening assay for terminal hydroxylation of fatty acids by P450s.

    PubMed

    Weissenborn, Martin J; Notonier, Sandra; Lang, Sarah-Luise; Otte, Konrad B; Herter, Susanne; Turner, Nicholas J; Flitsch, Sabine L; Hauer, Bernhard

    2016-05-01

    A readily available galactose oxidase (GOase) variant was used to develop a whole cell screening assay. This endpoint detection system was applied in a proof-of-concept approach by screening a focussed mutant library. This led to the discovery of the thus far most active P450 Marinobacter aquaeolei mutant catalysing the terminal hydroxylation of fatty acids. PMID:27074906

  19. A Sensitive Peptide Nucleic Acid Probe Assay for Detection of BRAF V600 Mutations in Melanoma.

    PubMed

    Chen, Tai-Long; Chang, John Wen-Cheng; Hsieh, Jia-Juan; Cheng, Hsin-Yi; Chiou, Chiuan-Chian

    Mutated v-Raf murine sarcoma viral oncogene homolog B (BRAF) is an important biomarker for the prediction of therapeutic efficacy of several anticancer drugs. The detection of BRAF mutation faces two challenges: Firstly, there are multiple types of mutations, and secondly, tumor samples usually contain various amounts of wild-type, normal tissues. Here, we describe a newly established method for sensitive detection of multiple types of BRAF V600 mutations in excess wild-type background. The method introduced a fluorophore-tagged peptide nucleic acid (PNA) to serve as both polymerase chain reaction (PCR) clamp and sensor probe, which inhibited the amplification of wild-type templates during PCR and revealed multiple types of mutant signals during melting analysis. We demonstrated the design and optimization process of the method, and applied it in the detection of BRAF mutations in 49 melanoma samples. This PNA probe assay method detected three types of mutations in 17 samples, and was much more sensitive than conventional PCR plus Sanger sequencing. PMID:27566656

  20. Heteropoly Acid/Nitrogen Functionalized Onion-like Carbon Hybrid Catalyst for Ester Hydrolysis Reactions.

    PubMed

    Liu, Wei; Qi, Wei; Guo, Xiaoling; Su, Dangsheng

    2016-02-18

    A novel heteropoly acid (HPA)/nitrogen functionalized onion-like carbon (NOLC) hybrid catalyst was synthesized through supramolecular (electrostatic and hydrogen bond) interactions between the two components. The chemical structure and acid strength of the HPA/NOLC hybrid have been fully characterized by thermogravimetric analysis, IR spectroscopy, X-ray photoelectron spectroscopy, NH3 temperature-programmed desorption and acid-base titration measurements. The proposed method for the fabrication of the HPA/NOLC hybrid catalyst is a universal strategy for different types of HPAs to meet various requirements of acidic or redox catalysis. The hydrophobic environment of NOLC effectively prevents the deactivation of HPA in an aqueous system, and the combination of uniformly dispersed HPA clusters and the synergistic effect between NOLC and HPA significantly promotes its activity in ester hydrolysis reactions, which is higher than that of bare PWA as homogeneous catalyst. The kinetics of the hydrolysis reactions indicate that the aggregation status of the catalyst particles has great influence on the apparent activity. PMID:26606266

  1. A novel biocompatible hyaluronic acid-chitosan hybrid hydrogel for osteoarthrosis therapy.

    PubMed

    Kaderli, S; Boulocher, C; Pillet, E; Watrelot-Virieux, D; Rougemont, A L; Roger, T; Viguier, E; Gurny, R; Scapozza, L; Jordan, O

    2015-04-10

    A conventional therapy for the treatment of osteoarthrosis is intra-articular injection of hyaluronic acid, which requires repeated, frequent injections. To extend the viscosupplementation effect of hyaluronic acid, we propose to associate it with another biopolymer in the form of a hybrid hydrogel. Chitosan was chosen because of its structural similarity to synovial glycosaminoglycans, its anti-inflammatory effects and its ability to promote cartilage growth. To avoid polyelectrolyte aggregation and obtain transparent, homogeneous gels, chitosan was reacetylated to a 50% degree, and different salts and formulation buffers were investigated. The biocompatibility of the hybrid gels was tested in vitro on human arthrosic synoviocytes, and in vivo assessments were made 1 week after subcutaneous injection in rats and 1 month after intra-articular injection in rabbits. Hyaluronic acid-chitosan polyelectrolyte complexes were prevented by cationic complexation of the negative charges of hyaluronic acid. The different salts tested were found to alter the viscosity and thermal degradation of the gels. Good biocompatibility was observed in rats, although the calcium-containing formulation induced calcium deposits after 1 week. The sodium chloride formulation was further tested in rabbits and did not show acute clinical signs of pain or inflammation. Hybrid HA-Cs hydrogels may be a valuable alternative viscosupplementation agent. PMID:25666331

  2. Reverse Cross Blot Hybridization Assay for Rapid Detection of PCR-Amplified DNA from Candida Species, Cryptococcus neoformans, and Saccharomyces cerevisiae in Clinical Samples

    PubMed Central

    Posteraro, Brunella; Sanguinetti, Maurizio; Masucci, Luca; Romano, Lucio; Morace, Giulia; Fadda, Giovanni

    2000-01-01

    A PCR-based assay was developed to detect and identify medically important yeasts in clinical samples. Using a previously described set of primers (G. Morace et al., J. Clin. Microbiol. 35:667–672, 1997), we amplified a fragment of the ERG11 gene for cytochrome P-450 lanosterol 14α-demethylase, a crucial enzyme in the biosynthesis of ergosterol. The PCR product was analyzed in a reverse cross blot hybridization assay with species-specific probes directed to a target region of the ERG11 gene of Candida albicans (pCal), C. guilliermondii (pGui), C. (Torulopsis) glabrata (pGla), C. kefyr (pKef), C. krusei (pKru), C. parapsilosis (pPar), C. tropicalis (pTro), the newly described species C. dubliniensis (pDub), Saccharomyces cerevisiae (pSce), and Cryptococcus neoformans (pCry). The PCR-reverse cross blot hybridization assay correctly identified multiple isolates of each species tested. No cross-hybridization was detected with any other fungal, bacteria, or human DNAs tested. The method was tested against conventional identification on 140 different clinical samples, including blood and cerebrospinal fluid, from patients with suspected fungal infections. The results agreed with those of culture and phenotyping for all but six specimens (two of which grew yeasts not included in the PCR panel of probes and four in which PCR positivity-culture negativity was justified by clinical findings). Species identification time was reduced from a mean of 4 days with conventional identification to 7 h with the molecular method. The PCR-reverse cross blot hybridization assay is a rapid method for the direct detection and identification of yeasts in clinical samples. PMID:10747151

  3. DNA-based hybridization chain reaction amplification for assaying the effect of environmental phenolic hormone on DNA methyltransferase activity.

    PubMed

    Xu, Zhenning; Yin, Huanshun; Han, Yunxiang; Zhou, Yunlei; Ai, Shiyun

    2014-06-01

    In this work, a novel electrochemical protocol with signal amplification for determination of DNA methylation and methyltransferase activity using DNA-based hybridization chain reaction (HCR) was proposed. After the gold electrode was modified with dsDNA, it was treated with M.SssI MTase, HpaII endonuclease, respectively. And then the HCR was initiated by the target DNA and two hairpin helper DNAs, which lead to the formation of extended dsDNA polymers on the electrode surface. The signal was amplified by the labeled biotin on the hairpin probes. As a result, the streptavidin-alkaline phosphatase (S-ALP) conjugated on the electrode surface through the specific interaction between biotin and S-ALP. ALP could convert 1-naphthyl phosphate into 1-naphthol and the latter could be electrochemically oxidized, which was used to monitor the methylation event and MTase activity. The HCR assay presents good electrochemical responses for the determination of M.SssI MTase at a concentration as low as 0.0067 uni tmL(-1). Moreover, the effects of anti-cancer drug and environmental phenolic hormone on M.SssI MTase activity were also investigated. The results indicated that 5-fluorouracil and daunorubicin hydrochloride could inhibit the activity, and the opposite results were obtained with bisphenol A and nonylphenol. Therefore, this method can not only provide a platform to screen the inhibitors of DNA MTase and develop new anticancer drugs, but also offer a novel technique to investigate the possible carcinogenesis mechanism. PMID:24856396

  4. Camera-based ratiometric fluorescence transduction of nucleic acid hybridization with reagentless signal amplification on a paper-based platform using immobilized quantum dots as donors.

    PubMed

    Noor, M Omair; Krull, Ulrich J

    2014-10-21

    Paper-based diagnostic assays are gaining increasing popularity for their potential application in resource-limited settings and for point-of-care screening. Achievement of high sensitivity with precision and accuracy can be challenging when using paper substrates. Herein, we implement the red-green-blue color palette of a digital camera for quantitative ratiometric transduction of nucleic acid hybridization on a paper-based platform using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). A nonenzymatic and reagentless means of signal enhancement for QD-FRET assays on paper substrates is based on the use of dry paper substrates for data acquisition. This approach offered at least a 10-fold higher assay sensitivity and at least a 10-fold lower limit of detection (LOD) as compared to hydrated paper substrates. The surface of paper was modified with imidazole groups to assemble a transduction interface that consisted of immobilized QD-probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as an acceptor. A hybridization event that brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs was responsible for a FRET-sensitized emission from the acceptor dye, which served as an analytical signal. A hand-held UV lamp was used as an excitation source and ratiometric analysis using an iPad camera was possible by a relative intensity analysis of the red (Cy3 photoluminescence (PL)) and green (gQD PL) color channels of the digital camera. For digital imaging using an iPad camera, the LOD of the assay in a sandwich format was 450 fmol with a dynamic range spanning 2 orders of magnitude, while an epifluorescence microscope detection platform offered a LOD of 30 fmol and a dynamic range spanning 3 orders of magnitude. The selectivity of the hybridization assay was demonstrated by detection of a single nucleotide polymorphism at a contrast ratio of 60:1. This work provides an

  5. Systematic Evaluation of Different Nucleic Acid Amplification Assays for Cytomegalovirus Detection: Feasibility of Blood Donor Screening.

    PubMed

    Vollmer, T; Knabbe, C; Dreier, J

    2015-10-01

    Acute primary cytomegalovirus (CMV) infections, which commonly occur asymptomatically among blood donors, represent a significant risk for serious morbidity in immunocompromised patients (a major group of transfusion recipients). We implemented a routine CMV pool screening procedure for plasma for the identification of CMV DNA-positive donors, and we evaluated the sensitivities and performance of different CMV DNA amplification systems. Minipools (MPs) of samples from 18,405 individual donors (54,451 donations) were screened for CMV DNA using the RealStar CMV PCR assay (Altona Diagnostic Technologies), with a minimum detection limit of 11.14 IU/ml. DNA was extracted with a high-volume protocol (4.8 ml, Chemagic Viral 5K kit; PerkinElmer) for blood donor pool screening (MP-nucleic acid testing [NAT]) and with the Nuclisens easyMAG system (0.5 ml; bioMérieux) for individual donation (ID)-NAT. In total, six CMV DNA-positive donors (0.03%) were identified by routine CMV screening, with DNA concentrations ranging from 4.35 × 10(2) to 4.30 × 10(3) IU/ml. Five donors already showed seroconversion and detectable IgA, IgM, and/or IgG antibody titers (IgA(+)/IgM(+)/IgG(-) or IgA(+)/IgM(+)/IgG(+)), and one donor showed no CMV-specific antibodies. Comparison of three commercial assays, i.e., the RealStar CMV PCR kit, the Sentosa SA CMV quantitative PCR kit (Vela Diagnostics), and the CMV R-gene PCR kit (bioMérieux), for MP-NAT and ID-NAT showed comparably good analytical sensitivities, ranging from 10.23 to 11.14 IU/ml (MP-NAT) or from 37.66 to 57.94 IU/ml (ID-NAT). The clinical relevance of transfusion-associated CMV infections requires further investigation, and the evaluated methods present powerful basic tools providing sensitive possibilities for viral testing. The application of CMV MP-NAT facilitated the identification of one donor with a window-phase donation during acute primary CMV infection. PMID:26202109

  6. Comparison of the Simplexa™ Flu A/B & RSV kit (nucleic acid extraction-dependent assay) and the Prodessa ProFlu+™ assay for detecting influenza and respiratory syncytial viruses.

    PubMed

    Selvaraju, Suresh B; Bambach, Adrienne V; Leber, Amy L; Patru, Maria-Magdalena; Patel, Anami; Menegus, Marilyn A

    2014-09-01

    The relative performance of 2 widely used reverse transcription polymerase chain reaction (RT-PCR) assays, the Focus diagnostics Simplexa™ Flu A/B & RSV kit (nucleic acid extraction-dependent assay) and the Prodessa Proflu+™ assay, was evaluated using 735 prospectively and retrospectively collected nasopharyngeal swab specimens. Overall, the assays showed positive and negative agreements of 100% and 99.7% for influenza A, 98.1% and 99.9% for influenza B, and 99.3% and 99.5% for respiratory syncytial virus. The relative analytical sensitivity of the 2 assays was also similar. PMID:25209363

  7. New high-performance liquid chromatography assay for glycosyltransferases based on derivatization with anthranilic acid and fluorescence detection.

    PubMed

    Anumula, Kalyan Rao

    2012-07-01

    Assays were developed using the unique labeling chemistry of 2-aminobenzoic acid (2AA; anthranilic acid, AA) for measuring activities of both β1-4 galactosyltransferase (GalT-1) and α2-6 sialyltransferase (ST-6) by high-performance liquid chromatography (HPLC) with fluorescence detection (Anumula KR. 2006. Advances in fluorescence derivatization methods for high-performance liquid chromatographic analysis of glycoprotein carbohydrates. Anal Biochem. 350:1-23). N-Acetylglucosamine (GlcNAc) and N-acetyllactosamine were used as acceptors and uridine diphosphate (UDP)-galactose and cytidine monophosphate (CMP)-N-acetylneuraminic acid (NANA) as donors for GalT-1 and ST-6, respectively. Enzymatic products were labeled in situ with AA and were separated from the substrates on TSKgel Amide 80 column using normal-phase conditions. Enzyme units were determined from the peak areas by comparison with the concomitantly derivatized standards Gal-β1-4GlcNAc and NANA-α2-6 Gal-β1-4GlcNAc. Linearity (time and enzyme concentration), precision (intra- and interassay) and reproducibility for the assays were established. The assays were found to be useful in monitoring the enzyme activities during isolation and purification. The assays were highly sensitive and performed equal to or better than the traditional radioactive sugar-based measurements. The assay format can also be used for measuring the activity of other transferases, provided that the carbohydrate acceptors contain a reducing end for labeling. An assay for glycoprotein acceptors was developed using IgG. A short HPLC profiling method was developed for the separation of IgG glycans (biantennary G0, G1, G2, mono- and disialylated), which facilitated the determination of GalT-1 and ST-6 activities in a rapid manner. Furthermore, this profiling method should prove useful for monitoring the changes in IgG glycans in clinical settings. PMID:22459802

  8. Ileal amino acid digestibility assay for the growing meat chicken--comparison of ileal and excreta amino acid digestibility in the chicken.

    PubMed

    Kadim, I T; Moughan, P J; Ravindran, V

    2002-09-01

    1. The apparent and true amino acid digestibilities in sorghum, wheat, soyabean meal, meat-and-bone meal, fish meal and blood meal for growing meat chickens were determined using an assay based on the collection of digesta from the terminal ileum and comparison was made with digestibility values determined using an excreta-based assay. 2. Five-week-old meat chickens were given maize-soyabean meal basal diet or mixtures of the basal diet and test diets containing the 6 ingredients as the sole source of dietary protein (50:50 on weight basis). Apparent amino acid digestibility values of assay diets at ileal and excreta levels were calculated using chromic oxide as the indigestible marker. True digestibility values were calculated using endogenous outputs determined by feeding a protein-free diet. Amino acid digestibilities of the ingredients were calculated by difference. 3. The site of measurement had no influence on endogenous amino acid output, the exceptions being aspartic acid and glutamic acid. The output of these two amino acids was higher in the excreta. 4. Significant differences were found between ileal and excreta-based digestibility of certain amino acids in some ingredients, with excreta values being usually higher than the ileal values, indicating a net catabolism of amino acids in the large intestine. The degree of net amino acid disappearance was found to be variable among amino acids and ingredients. In general, threonine had the lowest digestibility at the ileal level and, compared with other amino acids, the highest degredation during passage through the hindgut. 5. The results showed that digestibility determination based on excreta collection will overestimate the uptake for some amino acids in some feeds. The degree of overestimation was often considerable, ranging from 8.9% (apparent digestibility of threonine in soyabean meal) to 56% (apparent digestibility of aspartic acid in wheat). It is concluded that digestibility values measured at the

  9. Effects of novel hybrids of caffeic acid phenethyl ester and NSAIDs on experimental ocular inflammation.

    PubMed

    Pittalà, Valeria; Salerno, Loredana; Romeo, Giuseppe; Siracusa, Maria Angela; Modica, Maria Nunziata; Romano, Giovanni Luca; Salomone, Salvatore; Drago, Filippo; Bucolo, Claudio

    2015-04-01

    In this study, we report the design and synthesis of novel hybrids of caffeic acid phenetyl ester (CAPE) and non-steroidal anti-inflammatory drugs (NSAIDs). We assessed their effects on an experimental ocular inflammation in New Zealand rabbits. The formulations of CAPE-aspirin and CAPE-indomethacin hybrids were topical instilled in the rabbit׳s eye. Afterwards, the anti-inflammatory activity was evaluated by grading the clinical signs and by assessing the inflammatory cell count, protein, PGE2 and TNFα levels in the aqueous humor. Furthermore, ocular tolerability of hybrids formulations was evaluated in a separate set of animals by using a modified Draize test. The ocular inflammation in the control group was significantly higher than in both the hybrid-treated groups, as indicated by clinical grading and biomarkers assessment. However, only the CAPE-aspirin hybrid reduced, in a significant dose-dependent manner, the ocular inflammation elicited by paracentesis. CAPE-indomethacin hybrid was able to significantly attenuate the clinical grading and the PGE2 aqueous levels only at the highest dose (0.1%). CAPE-aspirin significantly reduced PGE2 and TNFα levels in the aqueous humor as well as proteins and PMNs. Finally, all formulations showed no ocular irritation compared with vehicle-treated group. In conclusion, CAPE-aspirin shows full anti-inflammatory efficacy in experimental model of ocular inflammation demonstrating an optimal pharmacological and safety profile. Taken together these data indicate that CAPE-aspirin hybrid represents a valid and safe new chemical entity potentially useful for the treatment of ocular inflammation. PMID:25704612

  10. Amino acids interference on the quantification of reducing sugars by the 3,5-dinitrosalicylic acid assay mislead carbohydrase activity measurements.

    PubMed

    Teixeira, Ricardo Sposina Sobral; da Silva, Ayla Sant'Ana; Ferreira-Leitão, Viridiana Santana; da Silva Bon, Elba Pinto

    2012-12-01

    This study evaluated the interference of the amino acids tryptophan, cysteine, histidine, tyrosine, hydroxyproline, leucine, proline, serine, glycine, valine, glutamic acid, phenylalanine, and methionine on the measurement of reducing sugars using a phenol-free 3,5-dinitrosalicylic acid (DNS) reagent. It was found that in reaction mixtures containing 20mM of either tryptophan, cysteine, histidine, tyrosine, or hydroxyproline the measurement of 3.7 mM glucose was overestimated by 76%, 50%, 35%, 18%, and 10%, respectively. The amino acids valine, glutamic acid, and phenylalanine did not affect the DNS reaction, while methionine decreased the color development by 5%. The measurement of glucose, xylose, arabinose, and cellobiose at the 3.7-12.4 mM range in the presence of 20 mM cysteine resulted in an overestimated concentration of 34.8-50%. Enzymatic assays for measuring xylanolytic and filter paper activity (FPAse) were conducted in the presence of 20-60 mM cysteine, and compared to cysteine-free assays. In the presence of cysteine, the measured xylanase activity increased threefold and the FPAse activity increased twofold due to the overestimation of the reducing sugar concentrations in the assays. The interference from cysteine was reduced to a maximum of 8.6% when a DNS reagent containing phenol was used. PMID:23103512

  11. Growth characteristics of Ti-based fumaric acid hybrid thin films by molecular layer deposition.

    PubMed

    Cao, Yan-Qiang; Zhu, Lin; Li, Xin; Cao, Zheng-Yi; Wu, Di; Li, Ai-Dong

    2015-09-01

    Ti-based fumaric acid hybrid thin films were successfully prepared using inorganic TiCl4 and organic fumaric acid as precursors by molecular layer deposition (MLD). The effect of deposition temperature from 180 °C to 350 °C on the growth rate, composition, chemical state, and topology of hybrid films has been investigated systematically by means of a series of analytical tools such as spectroscopic ellipsometry, atomic force microscopy (AFM), high resolution X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR). The MLD process of the Ti-fumaric acid shows self-limiting surface reaction with a reasonable growth rate of ∼0.93 Å per cycle and small surface roughness of ∼0.59 nm in root-mean-square value at 200 °C. A temperature-dependent growth characteristic has been observed in the hybrid films. On increasing the temperature from 180 °C to 300 °C, the growth rate decreases from 1.10 to 0.49 Å per cycle and the XPS composition of the film's C : O : Ti ratio changes from 8.35 : 7.49 : 1.00 to 4.66 : 4.80 : 1.00. FTIR spectra indicate that the hybrid films show bridging bonding mode at a low deposition temperature of 200 °C and bridging/bidentate mixed bonding mode at elevated deposition temperatures of 250 and 300 °C. The higher C and O amounts deviating from the ideal composition may be ascribed to increased organic incorporation into the hybrid films at lower deposition temperature and temperature-dependent density of reactive sites (-OH). The composition of hybrid films grown at 350 °C shows a dramatic decrease in C and O elemental composition (C : O : Ti = 1.97 : 2.76 : 1.00) due to the thermal decomposition of the fumaric acid precursor. The produced by-product H2O changes the structure of the hybrid films, resulting in the formation of more Ti-O bonds at high temperatures. The stability of the hybrid films against chemical and thermal treatment, and long-term storage by

  12. Development of betulinic acid as an agonist of TGR5 receptor using a new in vitro assay

    PubMed Central

    Lo, Shih-Hsiang; Cheng, Kai-Chung; Li, Ying-Xiao; Chang, Chin-Hong; Cheng, Juei-Tang; Lee, Kung-Shing

    2016-01-01

    Background G-protein-coupled bile acid receptor 1, also known as TGR5 is known to be involved in glucose homeostasis. In animal models, treatment with a TGR5 agonist induces incretin secretion to reduce hyperglycemia. Betulinic acid, a triterpenoid present in the leaves of white birch, has been introduced as a selective TGR5 agonist. However, direct activation of TGR5 by betulinic acid has not yet been reported. Methods Transfection of TGR5 into cultured Chinese hamster ovary (CHO-K1) cells was performed to establish the presence of TGR5. Additionally, TGR5-specific small interfering RNA was employed to silence TGR5 in cells (NCI-H716 cells) that secreted incretins. Uptake of glucose by CHO-K1 cells was evaluated using a fluorescent indicator. Amounts of cyclic adenosine monophosphate and glucagon-like peptide were quantified using enzyme-linked immunosorbent assay kits. Results Betulinic acid dose-dependently increases glucose uptake by CHO-K1 cells transfected with TGR5 only, which can be considered an alternative method instead of radioligand binding assay. Additionally, signals coupled to TGR5 activation are also increased by betulinic acid in cells transfected with TGR5. In NCI-H716 cells, which endogenously express TGR5, betulinic acid induces glucagon-like peptide secretion via increasing calcium levels. However, the actions of betulinic acid were markedly reduced in NCI-H716 cells that received TGR5-silencing treatment. Therefore, the present study demonstrates the activation of TGR5 by betulinic acid for the first time. Conclusion Similar to the positive control lithocholic acid, which is the established agonist of TGR5, betulinic acid has been characterized as a useful agonist of TGR5 and can be used to activate TGR5 in the future. PMID:27578964

  13. Optimization of time-resolved fluorescence assay for detection of europium-tetraazacyclododecyltetraacetic acid-labeled ligand-receptor interactions.

    PubMed

    De Silva, Channa R; Vagner, Josef; Lynch, Ronald; Gillies, Robert J; Hruby, Victor J

    2010-03-01

    Lanthanide-based luminescent ligand binding assays are superior to traditional radiolabel assays due to improving sensitivity and affordability in high-throughput screening while eliminating the use of radioactivity. Despite significant progress using lanthanide(III)-coordinated chelators such as diethylenetriaminepentaacetic acid (DTPA) derivatives, dissociation-enhanced lanthanide fluoroimmunoassays (DELFIAs) have not yet been successfully used with more stable chelators (e.g., tetraazacyclododecyltetraacetic acid [DOTA] derivatives) due to the incomplete release of lanthanide(III) ions from the complex. Here a modified and optimized DELFIA procedure incorporating an acid treatment protocol is introduced for use with Eu(III)-DOTA-labeled peptides. Complete release of Eu(III) ions from DOTA-labeled ligands was observed using hydrochloric acid (2.0M) prior to the luminescent enhancement step. [Nle(4),d-Phe(7)]-alpha-melanocyte-stimulating hormone (NDP-alpha-MSH) labeled with Eu(III)-DOTA was synthesized, and the binding affinity to cells overexpressing the human melanocortin-4 (hMC4) receptor was evaluated using the modified protocol. Binding data indicate that the Eu(III)-DOTA-linked peptide bound to these cells with an affinity similar to its DTPA analogue. The modified DELFIA procedure was further used to monitor the binding of an Eu(III)-DOTA-labeled heterobivalent peptide to the cells expressing both hMC4 and cholecystokinin-2 (CCK-2) receptors. The modified assay provides superior results and is appropriate for high-throughput screening of ligand libraries. PMID:19852924

  14. Automated assay of methylmalonic acid in serum and urine by derivatization with 1-pyrenyldiazomethane, liquid chromatography, and fluorescence detection.

    PubMed

    Schneede, J; Ueland, P M

    1993-03-01

    Determination of methylmalonic acid (MMA) in serum has been established as an accurate test for the diagnosis of cobalamin deficiency. We describe here the development and performance of a liquid-chromatographic assay of MMA in blood and urine. The assay is based on our recent finding that one of the carboxylic acid moieties of some short-chain dicarboxylic acids reacts with the fluorogenic reagent 1-pyrenyldiazomethane in an aqueous medium, whereas the other remains underivatized (Anal Chem 1992; 63:315-9). The pH-dependent ionization of the free carboxylic acid group of 1-pyrenylmethyl monoesters permits retention on anion-exchange columns, which are used for solid-phase extraction. The analysis is done with a cyanopropyl column coupled in series with an octadecyldimethylsilyl column. Solid-phase extraction and sample injection are carried out automatically by a Gilson ASPEC sample processor. The assay response varies linearly with MMA concentration in the range 0.1-1000 mumol/L in serum. The within-day and between-day CVs are 2.8-10.9%, and the detection limit of 5 fmol injected (approximately 20 nmol/L in serum) is sufficiently low to determine MMA in serum (mean 0.187 mumol/L, SD 0.084, range 0.044-0.431, n = 44) and urine from healthy subjects. PMID:8448848

  15. Transposon-5 mutagenesis transforms Corynebacterium matruchotii to synthesize novel hybrid fatty acids that functionally replace corynomycolic acid.

    PubMed Central

    Takayama, Kuni; Hayes, Barry; Vestling, Matha M; Massey, Randall J

    2003-01-01

    Enzymes within the biosynthetic pathway of mycolic acid (C(60)-C(90) a-alkyl,b-hydroxyl fatty acid) in Mycobacterium tuberculosis are attractive targets for developing new anti-tuberculosis drugs. We have turned to the simple model system of Corynebacterium matruchotii to study the terminal steps in the anabolic pathway of a C32 mycolic acid called corynomycolic acid. By transposon-5 mutagenesis, we transformed C. matruchotii into a mutant that is unable to synthesize corynomycolic acid. Instead, it synthesized two related series of novel fatty acids that were released by saponification from the cell wall fraction and from two chloroform/methanol-extractable glycolipids presumed to be analogues of trehalose mono- and di-corynomycolate. By chemical analyses and MS, we determined the general structure of the two series to be 2,4,6,8,10-penta-alkyl decanoic acid for the larger series (C(70)-C(77)) and 2,4,6,8-tetra-alkyl octanoic acid for the smaller series (C(52)-C(64)), both containing multiple keto groups, hydroxy groups and double bonds. The mutant was temperature-sensitive, aggregated extensively, grew very slowly relative to the wild type, and was resistant to the presence of lysozyme. We suggest that a regulatory protein that normally prevents the transfer of the condensation product back to b-ketoacyl synthase in the corynomycolate synthase system of the wild type was inactivated in the mutant. This will result in multiple Claisen-type condensation and the formation of two similar series of these complex hybrid fatty acids. A similar protein in M. tuberculosis would be an attractive target for new drug discovery. PMID:12879902

  16. Naturally occurring hybrids derived from γ-amino acids and sugars with potential tail to tail ether-bonds

    PubMed Central

    Feng, Zi-ming; Zhan, Zhi-lai; Yang, Ya-nan; Jiang, Jian-shuang; Zhang, Pei-cheng

    2016-01-01

    The basic substances of life include various amino acids and sugars. To search such molecules is the precondition to understand the essential nature. Here we reported four unprecedented hybrids of γ-amino acids and sugars from the roots of Ranunculus ternatus, which possess potential tail to tail ether-connected (6,6-ether-connected) modes in the sugar moiety. The structures of these hybrids were elucidated by extensive analyses of spectra and calculated electronic circular dichroism (ECD) method. PMID:27166276

  17. Naturally occurring hybrids derived from γ-amino acids and sugars with potential tail to tail ether-bonds.

    PubMed

    Feng, Zi-Ming; Zhan, Zhi-Lai; Yang, Ya-Nan; Jiang, Jian-Shuang; Zhang, Pei-Cheng

    2016-01-01

    The basic substances of life include various amino acids and sugars. To search such molecules is the precondition to understand the essential nature. Here we reported four unprecedented hybrids of γ-amino acids and sugars from the roots of Ranunculus ternatus, which possess potential tail to tail ether-connected (6,6-ether-connected) modes in the sugar moiety. The structures of these hybrids were elucidated by extensive analyses of spectra and calculated electronic circular dichroism (ECD) method. PMID:27166276

  18. Naturally occurring hybrids derived from γ-amino acids and sugars with potential tail to tail ether-bonds

    NASA Astrophysics Data System (ADS)

    Feng, Zi-Ming; Zhan, Zhi-Lai; Yang, Ya-Nan; Jiang, Jian-Shuang; Zhang, Pei-Cheng

    2016-05-01

    The basic substances of life include various amino acids and sugars. To search such molecules is the precondition to understand the essential nature. Here we reported four unprecedented hybrids of γ-amino acids and sugars from the roots of Ranunculus ternatus, which possess potential tail to tail ether-connected (6,6-ether-connected) modes in the sugar moiety. The structures of these hybrids were elucidated by extensive analyses of spectra and calculated electronic circular dichroism (ECD) method.

  19. Retinoic acid-mediated repression of human papillomavirus 18 transcription and different ligand regulation of the retinoic acid receptor beta gene in non-tumorigenic and tumorigenic HeLa hybrid cells.

    PubMed Central

    Bartsch, D; Boye, B; Baust, C; zur Hausen, H; Schwarz, E

    1992-01-01

    Human papillomavirus type 18 (HPV18) belongs to the group of genital papillomaviruses involved in the development of cervical carcinomas. Since retinoic acid (RA) is a key regulator of epithelial cell differentiation and a growth inhibitor in vitro of HPV18-positive HeLa cervical carcinoma cells, we have used HeLa and HeLa hybrid cells in order to analyse the effects of RA on expression of the HPV18 E6 and E7 oncogenes and of the cellular RA receptor genes RAR-beta and -gamma. We show here that RA down-regulates HPV18 mRNA levels apparently due to transcriptional repression. Transient cotransfection assays indicated that RARs negatively regulate the HPV18 upstream regulatory region and that the central enhancer can confer RA-dependent repression on a heterologous promoter. RA treatment resulted in induction of RAR-beta mRNA levels in non-tumorigenic HeLa hybrid cells, but not in tumorigenic hybrid segregants nor in HeLa cells. No alterations of the RAR-beta gene or of the HeLa RAR-beta promoter could be revealed by Southern and DNA sequence analysis, respectively. As determined by transient transfection assays, however, the RAR-beta control region was activated by RA more strongly in non-tumorigenic hybrid cells than in HeLa cells, thus indicating differences in trans-acting regulatory factors. Our data suggest that the RARs are potential negative regulators of HPV18 E6 and E7 gene expression, and that dysregulation of the RAR-beta gene either causatively contributes to or is an indicator of tumorigenicity in HeLa and HeLa hybrid cells. Images PMID:1318198

  20. Point-of-care multiplexed assays of nucleic acids using microcapillary-based loop-mediated isothermal amplification.

    PubMed

    Zhang, Yi; Zhang, Lu; Sun, Jiashu; Liu, Yulei; Ma, Xingjie; Cui, Shangjin; Ma, Liying; Xi, Jianzhong Jeff; Jiang, Xingyu

    2014-07-15

    This report demonstrates a straightforward, robust, multiplexed and point-of-care microcapillary-based loop-mediated isothermal amplification (cLAMP) for assaying nucleic acids. This assay integrates capillaries (glass or plastic) to introduce and house sample/reagents, segments of water droplets to prevent contamination, pocket warmers to provide heat, and a hand-held flashlight for a visual readout of the fluorescent signal. The cLAMP system allows the simultaneous detection of two RNA targets of human immunodeficiency virus (HIV) from multiple plasma samples, and achieves a high sensitivity of two copies of standard plasmid. As few nucleic acid detection methods can be wholly independent of external power supply and equipment, our cLAMP holds great promise for point-of-care applications in resource-poor settings. PMID:24937125

  1. Colorimetric Detection of Ehrlichia Canis via Nucleic Acid Hybridization in Gold Nano-Colloids

    PubMed Central

    Muangchuen, Ajima; Chaumpluk, Piyasak; Suriyasomboon, Annop; Ekgasit, Sanong

    2014-01-01

    Canine monocytic ehrlichiosis (CME) is a major thick-bone disease of dog caused by Ehrlichia canis. Detection of this causal agent outside the laboratory using conventional methods is not effective enough. Thus an assay for E. canis detection based on the p30 outer membrane protein gene was developed. It was based on the p30 gene amplification using loop-mediated isothermal DNA amplification (LAMP). The primer set specific to six areas within the target gene were designed and tested for their sensitivity and specificity. Detection of DNA signals was based on modulation of gold nanoparticles' surface properties and performing DNA/DNA hybridization using an oligonucleotide probe. Presence of target DNA affected the gold colloid nanoparticles in terms of particle aggregation with a plasmonic color change of the gold colloids from ruby red to purple, visible by the naked eye. All the assay steps were completed within 90 min including DNA extraction without relying on standard laboratory facilities. This method was very specific to target bacteria. Its sensitivity with probe hybridization was sufficient to detect 50 copies of target DNA. This method should provide an alternative choice for point of care control and management of the disease. PMID:25111239

  2. Screening and identification of proteins interacting with IL-24 by the yeast two-hybrid screen, Co-IP, and FRET assays.

    PubMed

    Hu, Hui; Wang, Tao; Chen, Jiaojiao; Yu, Fang; Liu, Huilin; Zuo, Zhenyu; Yang, Zhonghua; Fan, Handong

    2016-04-01

    Interleukin-24 (IL-24) is an ideal tumor-suppressor gene, but the mechanisms underlying its antitumor specificity remain to be elucidated. The best way to investigate these problems is to begin from the initiation of corresponding signaling cascades activated by IL-24 with screening and identifying those proteins that interacted with IL-24. With the aim of identifying these initial interactions, a yeast two-hybrid screening was performed by transforming AH109 cells containing PGBKT7-IL-24 with a liver cDNA plasmid library. These cells were then plated on synthetic nutrient medium (SD/-Trp/-Leu/-His) for the first screening and on quadruple dropout medium containing X-α-gal for the second screening. Positive colonies were further verified by repeating the MATE experiments, co-immunoprecipitation (Co-IP) analysis, and fluorescence resonance energy transfer (FRET) assays in vitro. Following the yeast two-hybrid screening, 15 genes were selected for sequencing, with two genes, HLA-C and NDUFA13, further verified using Co-IP assays and FRET assays. Both HLA-C and NDUFA13 were found to interact with IL-24. We found that HLA-C and NDUFA13 could interact with IL-24 and it may be involved in the signal induced by IL-24. Overall, this study contributes further insight into the cancer-specific apoptosis-inducing abilities of IL-24 to potentially enhance its therapeutic potential, and it also provides outlets for other biological functions of IL-24. PMID:26930462

  3. Hybrid Compounds Strategy in the Synthesis of Oleanolic Acid Skeleton-NSAID Derivatives.

    PubMed

    Pawełczyk, Anna; Olender, Dorota; Sowa-Kasprzak, Katarzyna; Zaprutko, Lucjusz

    2016-01-01

    The current study focuses on the synthesis of several hybrid individuals combining a natural oleanolic acid skeleton and synthetic nonsteroidal anti-inflammatory drug moieties (NSAIDs). It studied structural modifications of the oleanolic acid structure by use of the direct reactivity of hydroxyl or hydroxyimino groups at position C-3 of the triterpenoid skeleton with the carboxylic function of anti-inflammatory drugs leading to new perspective compounds with high potential pharmacological activities. Novel ester- and iminoester-type derivatives of oleanolic unit with the different NSAIDs, such as ibuprofen, aspirin, naproxen, and ketoprofen, were obtained and characterized. Moreover, preliminary research of compounds obtaining structure stability under acidic conditions was examined and the PASS method of prediction of activity spectra for substances was used to estimate the potential biological activity of these compounds. PMID:27077841

  4. Porous Zirconium-Phytic Acid Hybrid: a Highly Efficient Catalyst for Meerwein-Ponndorf-Verley Reductions.

    PubMed

    Song, Jinliang; Zhou, Baowen; Zhou, Huacong; Wu, Lingqiao; Meng, Qinglei; Liu, Zhimin; Han, Buxing

    2015-08-01

    The utilization of compounds from natural sources to prepare functional materials is of great importance. Herein, we describe for the first time the preparation of organic-inorganic hybrid catalysts by using natural phytic acid as building block. Zirconium phosphonate (Zr-PhyA) was synthesized by reaction of phytic acid and ZrCl4 and was obtained as a mesoporous material with pore sizes centered around 8.5 nm. Zr-PhyA was used to catalyze the mild and selective Meerwein-Ponndorf-Verley (MPV) reduction of various carbonyl compounds, e.g., of levulinic acid and its esters into γ-valerolactone. Further studies indicated that both Zr and phosphate groups contribute significantly to the excellent performance of Zr-PhyA. PMID:26177726

  5. Effect of acidic solutions on the surface degradation of a micro-hybrid composite resin.

    PubMed

    Münchow, Eliseu A; Ferreira, Ana Cláudia A; Machado, Raissa M M; Ramos, Tatiana S; Rodrigues-Junior, Sinval A; Zanchi, Cesar H

    2014-01-01

    Composite resins may undergo wear by the action of chemical substances (e.g., saliva, alcohol, bacterial acids) of the oral environment, which may affect the material's structure and surface properties. This study evaluated the effect of acidic substances on the surface properties of a micro-hybrid composite resin (Filtek Z-250). Eighty specimens were prepared, and baseline hardness and surface roughness (KMN0 and Ra0, respectively) were measured. The specimens were subjected to sorption (SO) and solubility (SL) tests according to ISO 4049:2009, but using different storage solutions: deionized water; 75/25 vol% ethanol/water solution; lactic acid; propionic acid; and acetic acid. The acids were used in two concentrations: PA and 0.02 N. pH was measured for all solutions and final hardness (KMN1) and surface roughness (Ra1) were measured. Data were analyzed with paired t-tests and one-way ANOVA and Tukey's test (a=5%). All solutions decreased hardness and increased the Ra values, except for the specimens stored in water and 0.02 N lactic acid, which maintained the hardness. All solutions produced similar SO and SL phenomena, except for the 0.02 N lactic acid, which caused lower solubility than the other solutions. Ethanol showed the highest pH (6.6) and the 0.02 N lactic acid the lowest one (2.5). The solutions affected negatively the surface properties of the composite resin; in addition, an acidic pH did not seem to be a significant factor that intensifies the surface degradation phenomena. PMID:25250496

  6. Deoxyribonucleic acid-based hybrid thin films for potential application as high energy density capacitors

    NASA Astrophysics Data System (ADS)

    Joyce, Donna M.; Venkat, Narayanan; Ouchen, Fahima; Singh, Kristi M.; Smith, Steven R.; Grabowski, Christopher A.; Terry Murray, P.; Grote, James G.

    2014-03-01

    Deoxyribonucleic acid (DNA) based hybrid films incorporating sol-gel-derived ceramics have shown strong promise as insulating dielectrics for high voltage capacitor applications. Our studies of DNA-CTMA (cetyltrimethylammonium) complex/sol-gel ceramic hybrid thin film devices have demonstrated reproducibility and stability in temperature- and frequency-dependent dielectric properties with dielectric constant k ˜ 5.0 (1 kHz), as well as reliability in DC voltage breakdown measurements, attaining values consistently in the range of 300-350 V/μm. The electrical/dielectric characteristics of DNA-CTMA films with sol-gel-derived ceramics were examined to determine the critical energy storage parameters such as voltage breakdown and dielectric constant.

  7. Testing and evaluation of EV-1300 lead-acid modules for the hybrid vehicle application

    SciTech Connect

    Gay, E.C.; Webster, C.E.; Hornstra, F.; Yao, N.P.

    1984-01-01

    This paper presents the results of testing and evaluation of GE/Globe EV-1300 lead-acid modules developed by Globe Battery Division of Johnson Controls, Inc. for the hybrid vehicle, HTV-I, developed by General Electric (GE) for the Department of Energy. The design of this battery was derived from that of the Globe Improved State of the Art (ISOA) battery under development for the ETV-1 all-electric vehicle. Key differences in the battery performance requirements for the HTV-1 hybrid vehicle, as opposed to the ETV-1, are higher specific power (137 W/kg versus 104 W/kg sustained for 15 seconds at 50% depth of discharge (DOD)) and less specific energy (36.1 Wh/kg versus 37.5 Wh/kg at a 3h discharge rate).

  8. Porous polylactic acid-silica hybrids: preparation, characterization, and study of mesenchymal stem cell osteogenic differentiation.

    PubMed

    Pandis, Christos; Trujillo, Sara; Matos, Joana; Madeira, Sara; Ródenas-Rochina, Joaquín; Kripotou, Sotiria; Kyritsis, Apostolos; Mano, João F; Gómez Ribelles, José Luis

    2015-02-01

    A novel approach to reinforce polymer porous membranes is presented. In the prepared hybrid materials, the inorganic phase of silica is synthesized in-situ and inside the pores of aminolyzed polylactic acid (PLA) membranes by sol-gel reactions using tetraethylorthosilicate (TEOS) and glycidoxypropyltrimethoxysilane (GPTMS) as precursors. The hybrid materials present a porous structure with a silica layer covering the walls of the pores while GPTMS serves also as coupling agent between the organic and inorganic phase. The adjustment of silica precursors ratio allows the modulation of the thermomechanical properties. Culture of mesenchymal stem cells on these supports in osteogenic medium shows the expression of characteristic osteoblastic markers and the mineralization of the extracellular matrix. PMID:25303745

  9. Heavy metal removal from acid mine drainage by calcined eggshell and microalgae hybrid system.

    PubMed

    Choi, Hee-Jeong; Lee, Seung-Mok

    2015-09-01

    This study investigates the use of calcined eggshells and microalgae for the removal of heavy metals from acid mine drainage (AMD) and the simultaneous enhancement of biomass productivity. The experiment was conducted over a period of 6 days in a hybrid system containing calcined eggshells and the microalgae Chlorella vulgaris. The results show that the biomass productivity increased to ~8.04 times its initial concentration of 0.367 g/L as measured by an optical panel photobioreactor (OPPBR) and had a light transmittance of 95 % at a depth of 305 mm. On the other hand, the simultaneous percent removal of Fe, Cu, Zn, Mn, As, and Cd from the AMD effluent was found to be 99.47 to 100 %. These results indicate that the hybrid system with calcined eggshells and microalgae was highly effective for heavy metal removal in the AMD. PMID:25940497

  10. Structure and DNA Hybridization Properties of Mixed Nucleic Acid/Maleimide-Ethylene Glycol Monolayers

    SciTech Connect

    Lee,C.; Nguyen, P.; Grainger, D.; Gamble, L.; Castner, D.

    2007-01-01

    The surface structure and DNA hybridization performance of thiolated single-strand DNA (HS-ssDNA) covalently attached to a maleimide-ethylene glycol disulfide (MEG) monolayer on gold have been investigated. Monolayer immobilization chemistry and surface coverage of reactive ssDNA probes were studied by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry. Orientation of the ssDNA probes was determined by near-edge X-ray absorption fine structure (NEXAFS). Target DNA hybridization on the DNA-MEG probe surfaces was measured by surface plasmon resonance (SPR) to demonstrate the utility of these probe surfaces for detection of DNA targets from both purified target DNA samples and complex biological mixtures such as blood serum. Data from complementary techniques showed that immobilized ssDNA density is strongly dependent on the spotted bulk DNA concentration and buffer ionic strength. Variation of the immobilized ssDNA density had a profound influence on the DNA probe orientation at the surface and subsequent target hybridization efficiency. With increasing surface probe density, NEXAFS polarization dependence results (followed by monitoring the N 1s {yields} {pi}* transition) indicate that the immobilized ssDNA molecules reorient toward a more upright position on the MEG monolayer. SPR assays of DNA targets from buffer and serum showed that DNA hybridization efficiency increased with decreasing surface probe density. However, target detection in serum was better on the 'high-density' probe surface than on the 'high-efficiency' probe surface. The amounts of target detected for both ssDNA surfaces were several orders of magnitude poorer in serum than in purified DNA samples due to nonspecific serum protein adsorption onto the sensing surface.

  11. Multicenter evaluation of the Quidel Lyra Direct C. difficile nucleic acid amplification assay.

    PubMed

    Beck, Eric T; Buchan, Blake W; Riebe, Katherine M; Alkins, Brenda R; Pancholi, Preeti; Granato, Paul A; Ledeboer, Nathan A

    2014-06-01

    Clostridium difficile is a Gram-positive bacterium commonly found in health care and long-term-care facilities and is the most common cause of antibiotic-associated diarrhea. Rapid detection of this bacterium can assist physicians in implementing contact precautions and appropriate antibiotic therapy in a timely manner. The purpose of this study was to compare the clinical performance of the Quidel Lyra Direct C. difficile assay (Lyra assay) (Quidel, San Diego, CA) to that of a direct cell culture cytotoxicity neutralization assay (CCNA) and enhanced toxigenic culture. This study was performed at three geographically diverse laboratories within the United States using residual stool specimens submitted for routine C. difficile testing. Residual samples were tested using the Lyra assay on three real-time PCR platforms, and results were compared to those for direct CCNA and enhanced toxigenic culture. The test results for all platforms were consistent across all three test sites. The sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500 Fast DX, and ABI QuantStudio DX instruments compared to CCNA were 90.0% and 93.3%, 95.0% and 94.2%, and 93.8% and 95.0%, respectively. Compared to enhanced toxigenic culture, the sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500, and QuantStudio instruments were 82.1% and 96.9%, 89.3% and 98.8%, and 85.7% and 99.0%, respectively. Overall, the Lyra assay is easy to use and versatile and compares well to C. difficile culture methods. PMID:24671790

  12. Multicenter Evaluation of the Quidel Lyra Direct C. difficile Nucleic Acid Amplification Assay

    PubMed Central

    Beck, Eric T.; Buchan, Blake W.; Riebe, Katherine M.; Alkins, Brenda R.; Pancholi, Preeti; Granato, Paul A.

    2014-01-01

    Clostridium difficile is a Gram-positive bacterium commonly found in health care and long-term-care facilities and is the most common cause of antibiotic-associated diarrhea. Rapid detection of this bacterium can assist physicians in implementing contact precautions and appropriate antibiotic therapy in a timely manner. The purpose of this study was to compare the clinical performance of the Quidel Lyra Direct C. difficile assay (Lyra assay) (Quidel, San Diego, CA) to that of a direct cell culture cytotoxicity neutralization assay (CCNA) and enhanced toxigenic culture. This study was performed at three geographically diverse laboratories within the United States using residual stool specimens submitted for routine C. difficile testing. Residual samples were tested using the Lyra assay on three real-time PCR platforms, and results were compared to those for direct CCNA and enhanced toxigenic culture. The test results for all platforms were consistent across all three test sites. The sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500 Fast DX, and ABI QuantStudio DX instruments compared to CCNA were 90.0% and 93.3%, 95.0% and 94.2%, and 93.8% and 95.0%, respectively. Compared to enhanced toxigenic culture, the sensitivity and specificity of the Lyra assay on the SmartCycler II, ABI 7500, and QuantStudio instruments were 82.1% and 96.9%, 89.3% and 98.8%, and 85.7% and 99.0%, respectively. Overall, the Lyra assay is easy to use and versatile and compares well to C. difficile culture methods. PMID:24671790

  13. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1998-01-01

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  14. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1998-03-24

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

  15. A sandwich-hybridization assay for simultaneous determination of HIV and tuberculosis DNA targets based on signal amplification by quantum dots-PowerVision™ polymer coding nanotracers.

    PubMed

    Yan, Zhongdan; Gan, Ning; Zhang, Huairong; Wang, De; Qiao, Li; Cao, Yuting; Li, Tianhua; Hu, Futao

    2015-09-15

    A novel sandwich-hybridization assay for simultaneous electrochemical detection of multiple DNA targets related to human immune deficiency virus (HIV) and tuberculosis (TB) was developed based on the different quantum dots-PowerVision(TM) polymer nanotracers. The polymer nanotracers were respectively fabricated by immobilizing SH-labeled oligonucleotides (s-HIV or s-TB), which can partially hybrid with virus DNA (HIV or TB), on gold nanoparticles (Au NPs) and then modified with PowerVision(TM) (PV) polymer-encapsulated quantum dots (CdS or PbS) as signal tags. PV is a dendrimer enzyme linked polymer, which can immobilize abundant QDs to amplify the stripping voltammetry signals from the metal ions (Pb or Cd). The capture probes were prepared through the immobilization of SH-labeled oligonucleotides, which can complementary with HIV and TB DNA, on the magnetic Fe3O4@Au (GMPs) beads. After sandwich-hybridization, the polymer nanotracers together with HIV and TB DNA targets were simultaneously introduced onto the surface of GMPs. Then the two encoding metal ions (Cd(2+) and Pb(2+)) were used to differentiate two viruses DNA due to the different subsequent anodic stripping voltammetric peaks at -0.84 V (Cd) and -0.61 V (Pb). Because of the excellent signal amplification of the polymer nanotracers and the great specificity of DNA targets, this assay could detect targets DNA as low as 0.2 femtomolar and exhibited excellent selectivity with the dynamitic range from 0.5 fM to 500 pM. Those results demonstrated that this electrochemical coding assay has great potential in applications for screening more viruses DNA while changing the probes. PMID:25911447

  16. Application of locked nucleic acid-based probes in fluorescence in situ hybridization.

    PubMed

    Fontenete, Sílvia; Carvalho, Daniel; Guimarães, Nuno; Madureira, Pedro; Figueiredo, Céu; Wengel, Jesper; Azevedo, Nuno Filipe

    2016-07-01

    Fluorescence in situ hybridization (FISH) employing nucleic acid mimics as probes is becoming an emerging molecular tool in the microbiology area for the detection and visualization of microorganisms. However, the impact that locked nucleic acid (LNA) and 2'-O-methyl (2'-OMe) RNA modifications have on the probe that is targeting microorganisms is unknown. In this study, the melting and hybridization efficiency properties of 18 different probes in regards to their use in FISH for the detection of the 16S rRNA of Helicobacter pylori were compared. For the same sequence and target, probe length and the type of nucleic acid mimics used as mixmers in LNA-based probes strongly influence the efficiency of detection. LNA probes with 10 to 15 mers showed the highest efficiency. Additionally, the combination of 2'-OMe RNA with LNA allowed an increase on the fluorescence intensities of the probes. Overall, these results have significant implications for the design and applications of LNA probes for the detection of microorganisms. PMID:26969040

  17. Use of agar diffusion assay to measure bactericidal activity of alkaline salts of fatty acids against bacteria associated with poultry processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The agar diffusion assay was used to examine antibacterial activity of alkaline salts of caproic, caprylic, capric, lauric, and myristic acids. A 0.5M concentration of each fatty acid was dissolved in 1.0 M potassium hydroxide (KOH), and pH of the mixtures was adjusted to 10.5 with citric acid. Solu...

  18. The dietary branched chain amino acid requirements of hybrid striped bass(Morone chrysops x M. saxatilis)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The requirements for branched chain amino acids (BCAAs) are unknown in hybrid striped bass and necessary for formulating efficient and nutritious diets. Moreover, the dietary balance among these three amino acids can substantially influence the performance of meat animals fed those diets. The diet...

  19. Quantitation of 5-Methyltetrahydrofolic Acid in Dried Blood Spots and Dried Plasma Spots by Stable Isotope Dilution Assays

    PubMed Central

    Kopp, Markus; Rychlik, Michael

    2015-01-01

    Because of minimal data available on folate analysis in dried matrix spots (DMSs), we combined the advantages of stable isotope dilution assays followed by LC-MS/MS analysis with DMS sampling to develop a reliable method for the quantitation of plasma 5-methyltetrahydrofolic acid in dried blood spots (DBSs) and dried plasma spots (DPSs) as well as for the quantitation of whole blood 5-methyltetrahydrofolic acid in DBSs. We focused on two diagnostically conclusive parameters exhibited by the plasma and whole blood 5-methyltetrahydrofolic acid levels that reflect both temporary and long-term folate status. The method is performed using the [2H4]-labeled isotopologue of the vitamin as the internal standard, and three steps are required for the extraction procedure. Elution of the punched out matrix spots was performed using stabilization buffer including Triton X-100 in a standardized ultrasonication treatment followed by enzymatic digestion (whole blood only) and solid-phase extraction with SAX cartridges. This method is sensitive enough to quantify 27 nmol/L whole blood 5-methyltetrahydrofolic acid in DBSs and 6.3 and 4.4 nmol/L plasma 5-methyltetrahydrofolic acid in DBSs and DPSs, respectively. The unprecedented accurate quantification of plasma 5-methyltetrahydrofolic acid in DBSs was achieved by thermal treatment prior to ultrasonication, inhibiting plasma conjugase activity. Mass screenings are more feasible and easier to facilitate for this method in terms of sample collection and storage compared with conventional clinical sampling for the assessment of folate status. PMID:26605791

  20. Sensitive assay, based on hydroxy fatty acids from lipopolysaccharide lipid A, for Gram-negative bacteria in sediments.

    PubMed Central

    Parker, J H; Smith, G A; Fredrickson, H L; Vestal, J R; White, D C

    1982-01-01

    Biochemical measures have provided insight into the biomass and community structure of sedimentary microbiota without the requirement of selection by growth or quantitative removal from the sediment grains. This study used the assay of the hydroxy fatty acids released from the lipid A of the lipopolysaccharide in sediments to provide an estimate of the gram-negative bacteria. The method was sensitive to picomolar amounts of hydroxy fatty acids. The recovery of lipopolysaccharide hydroxy fatty acids from organisms added to sediments was quantitative. The lipids were extracted from the sediments with single-phase chloroform-methanol extraction. The lipid-extraction residue was hydrolyzed in 1 N HCl, and the hydroxy fatty acids of the lipopolysaccharide were recovered in chloroform for analysis by gas-liquid chromatography. This method proved to be about fivefold more sensitive than the classical phenol-water or trichloroacetic acid methods when applied to marine sediments. By examination of the patterns of hydroxy fatty acids, it was also possible to help define the community structure of the sedimentary gram-negative bacteria. PMID:6817712

  1. Validation and application of a liquid-chromatographic/enzymatic assay for individual bile acids in the serum of rats.

    PubMed

    Thompson, M B; Blair, P C; Morris, R W; Neptun, D A; Deyo, D F; Popp, J A

    1987-10-01

    A liquid-chromatographic technique with a post-column enzymatic reaction and fluorescence detection was validated for analysis of individual bile acids in the serum of rats. Extraction recoveries averaged 91.1% (SD 6.9%) for all bile acids. The assay was sensitive (minimum detection of 16.8 pmol per 100-microL injection), linear (r greater than 0.999 for concentrations ranging between 45 and 112,500 pmol per 100-microL injection), and reproducible (mean CVs for three different concentrations of standards and a serum pool ranged from 4.4% to 12.2%). In rats treated for three days with either neomycin, carbon tetrachloride, alpha-naphthylisothiocyanate, or total bile-duct ligation (five animals per group), total concentrations of bile acids were significantly increased (P less than 0.004). Concentrations of 16 of 17 individual bile acids differed significantly between groups (P less than 0.04). Examination of the relative concentrations (percent of total) of individual bile acids by canonical discriminant analysis placed each animal into the appropriate treatment or control group. Use of this technique in toxicological studies can help detect and identify specific types of disruptions in the enterohepatic circulation of bile acids. PMID:3665040

  2. Internalization of Locked Nucleic Acids/DNA Hybrid Oligomers into Escherichia coli.

    PubMed

    Traglia, German M; Sala, Carol Davies; Fuxman Bass, Juan I; Soler-Bistué, Alfonso J C; Zorreguieta, Angeles; Ramírez, María Soledad; Tolmasky, Marcelo E

    2012-10-01

    Delivery inside the cells is essential for practical application of antisense technologies. The hybrid locked nucleic acid (LNA)/DNA CAAGTACTGTTCCACCA (LNA residues are underlined) was labeled by conjugation to Alexa Fluor 488 (fLNA/DNA) and tested to determine its ability to penetrate Escherichia coli cells and reach the cytoplasm. Flow cytometry analysis showed that the fLNA/DNA was associated with 14% of cells from a stationary phase culture, while association with a labeled isosequential oligodeoxynucleotide was negligible. Laser scanning confocal microscopy confirmed that the fLNA/DNA was located inside the cytoplasm. PMID:23515318

  3. A novel chaotic based image encryption using a hybrid model of deoxyribonucleic acid and cellular automata

    NASA Astrophysics Data System (ADS)

    Enayatifar, Rasul; Sadaei, Hossein Javedani; Abdullah, Abdul Hanan; Lee, Malrey; Isnin, Ismail Fauzi

    2015-08-01

    Currently, there are many studies have conducted on developing security of the digital image in order to protect such data while they are sending on the internet. This work aims to propose a new approach based on a hybrid model of the Tinkerbell chaotic map, deoxyribonucleic acid (DNA) and cellular automata (CA). DNA rules, DNA sequence XOR operator and CA rules are used simultaneously to encrypt the plain-image pixels. To determine rule number in DNA sequence and also CA, a 2-dimension Tinkerbell chaotic map is employed. Experimental results and computer simulations, both confirm that the proposed scheme not only demonstrates outstanding encryption, but also resists various typical attacks.

  4. A simple and rapid detection assay for peptides based on the specific recognition of aptamer and signal amplification of hybridization chain reaction.

    PubMed

    Ma, Chao; Liu, Haiyun; Tian, Tian; Song, Xianrang; Yu, Jinghua; Yan, Mei

    2016-09-15

    A simple and rapid assay for the detection of peptides is designed based on the specific recognition of aptamer, the quenching effect of graphene oxide (GO) and the efficient signal amplification of hybrid chain reaction (HCR). In this assay, the hairpin structure of aptamer is opened after binding with targets, and the initiation sequence could be exposed to hairpin probe 1 (H1) to open its hairpin structure. Then the opened H1 will open the hairpin structure of hairpin probe 2 (H2), and in turn, the opened initiation sequence of H2 continues to open H1. As a result, the specific recognition of target and fluorescent signals are accumulated through the process in short 1h. Attentively, the aptamer can not only identify target peptides, but also initiate the HCR between H1 and H2. More importantly, the HCR is initiated only after the target recognition of aptamer. After HCR, the excess hairpin probes will be anchored on the GO surface, and the background is greatly reduced due to the quenching effect of GO. By using Mucin-1(MUC1) as a model peptide, the assay has a wide linear range as two orders of magnitude and the detection range is from 0.01 to 5nM with low detection limit of 3.33pM. Therefore, the simple and rapid detection of the target can be realized, and the novel assay has great potential in detecting various peptides and even cancer cells. PMID:27093485

  5. Simultaneous Detection of CDC Category “A” DNA and RNA Bioterrorism Agents by Use of Multiplex PCR & RT-PCR Enzyme Hybridization Assays

    PubMed Central

    He, Jie; Kraft, Andrea J.; Fan, Jiang; Van Dyke, Meredith; Wang, Lihua; Bose, Michael E.; Khanna, Marilyn; Metallo, Jacob A.; Henrickson, Kelly J.

    2009-01-01

    Assays to simultaneously detect multiple potential agents of bioterrorism are limited. Two multiplex PCR and RT-PCR enzyme hybridization assays (mPCR-EHA, mRT-PCR-EHA) were developed to simultaneously detect many of the CDC category “A” bioterrorism agents. The “Bio T” DNA assay was developed to detect: Variola major (VM), Bacillus anthracis (BA), Yersinia pestis (YP), Francisella tularensis (FT) and Varicella zoster virus (VZV). The “Bio T” RNA assay (mRT-PCR-EHA) was developed to detect: Ebola virus (Ebola), Lassa fever virus (Lassa), Rift Valley fever (RVF), Hantavirus Sin Nombre species (HSN) and dengue virus (serotypes 1–4). Sensitivity and specificity of the 2 assays were tested by using genomic DNA, recombinant plasmid positive controls, RNA transcripts controls, surrogate (spiked) clinical samples and common respiratory pathogens. The analytical sensitivity (limit of detection (LOD)) of the DNA asssay for genomic DNA was 1×100∼1×102 copies/mL for BA, FT and YP. The LOD for VZV whole organism was 1×10−2 TCID50/mL. The LOD for recombinant controls ranged from 1×102∼1×103copies/mL for BA, FT, YP and VM. The RNA assay demonstrated LOD for RNA transcript controls of 1×104∼1×106 copies/mL without extraction and 1×105∼1×106 copies/mL with extraction for Ebola, RVF, Lassa and HSN. The LOD for dengue whole organisms was ∼1×10−4 dilution for dengue 1 and 2, 1×104 LD50/mL and 1×102 LD50/mL for dengue 3 and 4. The LOD without extraction for recombinant plasmid DNA controls was ∼1×103 copies/mL (1.5 input copies/reaction) for Ebola, RVF, Lassa and HSN. No cross-reactivity of primers and probes used in both assays was detected with common respiratory pathogens or between targeted analytes. Clinical sensitivity was estimated using 264 surrogate clinical samples tested with the BioT DNA assay and 549 samples tested with the BioT RNA assay. The clinical specificity is 99.6% and 99.8% for BioT DNA assay and BioT RNA assay

  6. Electrochemical sensor for dopamine based on imprinted silica matrix-poly(aniline boronic acid) hybrid as recognition element.

    PubMed

    Li, Jian; Zhang, Ning; Sun, Qingqing; Bai, Zhanming; Zheng, Jianbin

    2016-10-01

    A novel imprinted silica matrix-poly(aniline boronic acid) hybrid for electrochemical detection of dopamine (DA) was developed. Boronic acid functionalized conducting polymer was electrochemically prepared on Au electrode. The number of covalent binding sites toward DA templates was controlled by potential cycles. A precursory sol solution of ammonium fluorosilicate (as cross-linking monomer) containing DA was spin-coated on the polymer modified electrode. Under NH3 atmosphere, the hydroxyl ions were generated in the solution and catalyzed the hydrolysis of fluorosilicate to form silica matrix. After this aqueous sol-gel process, an inorganic framework around the DA template was formed and the imprinted hybrid for DA was also produced. As revealed by scanning electron microscopy, UV-vis spectroscopy and cyclic voltammetry characterization, DA was embedded in the imprinted hybrid successfully. The affinity and selectivity of the imprinted hybrid were also characterized by cyclic voltammetry. The imprinted hybrid showed higher affinity for DA than that for epinephrine, and little or no affinity for ascorbic acid and uric acid due to the combined effects of covalent interaction, cavities matching and electrostatic repulsion. The imprinted hybrid sensor exhibited a quick response (within 5min) to DA in the concentration range from 0.05 to 500μmolL(-1) with a detection limit of 0.018μmolL(-1). The prepared sensor was also applied to detect DA in real samples with a satisfactory result. PMID:27474321

  7. Screening metagenomic data for viruses using the E-Probe Diagnostic Nucleic Acid Assay (EDNA)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are many plant pathogen-specific diagnostic assays, based on PCR and immune-detection. However, the ability to test for large numbers of pathogens simultaneously is lacking. Next generation sequencing (NGS) allows one to detect all organisms within a given sample, but has computational limitat...

  8. Tartaric Acid-Assisted Self-Assembly of Hybrid Block Copolymer Composites

    NASA Astrophysics Data System (ADS)

    Yao, Li; Lin, Ying; Watkins, James

    2014-03-01

    Enantiopure tartaric acid was used as an additive to increase the segregation strength of poly(ethylene oxide-block-tert-butyl acrylate) (PEO-b-PtBA) copolymers through strong, selective interactions with one of the polymer chain segments. Addition of tartaric acid to PEO-b-PtBA exhibiting cylindrical morphologies resulted in the formation of helical superstructures as observed by transmission electron microscopy. It was also found that this small acid additive can also enable phase-selective ultra-high loading of nanoparticles (NPs) into target domains of the block copolymer composites. The loading of tartaric acid can increase enthalpically favorable interactions between the nanoparticle ligands and the host domain and mitigate entropic penalties associated with NP incorporation into the target domain. A metal content of over 40 weight percent by mass of the resulting well ordered composites was achieved as measured by thermal gravimetric analysis in PEO-b-PtBA/tartaric acid/4-hydroxythiophenol functionalized Au NP hybrid system. Funding from Center for Hierarchical Manufacturing (CHM); Facility support from Materials Research Science and Engineering Center at UMass Amherst.

  9. High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean is a primary source of vegetable oil, accounting for 53% of the total vegetable oil consumption in the USA in 2013. Soybean oil with high oleic acid and low linolenic acid content is desired, because it not only improves the oxidative stability of the oil, but also reduces the amount of unde...

  10. Nucleic acid hybridization for detection of cell culture-amplified adenovirus.

    PubMed Central

    Huang, C; Deibel, R

    1988-01-01

    A number of recombinant plasmids containing genomic segments of adenovirus were constructed. Seven cloned probes, as well as total adenovirus type 2 (Ad2) and Ad16 genomic DNA, were tested by a nucleic acid hybridization technique for sensitivity and specificity in detecting adenoviruses in infected cells. Adenovirus DNA was spotted onto a nitrocellulose filter and hybridized with 32P-labeled DNA probes. The probes, total Ad2 genomic DNA, and plasmid pAd2-H (containing the hexon gene from Ad2 DNA) all detected 10 reference serotypes of five genomic subgroups (A through E) with similar sensitivities. However, plasmid pAd2-H required less preparation time than did total Ad2 DNA. Probes pAd2-F (containing the fiber gene from Ad2) and pAd16-BD (containing the BamHI D fragment from Ad16) hybridized only with reference serotypes from the homologous subgroups (C and B, respectively). Of 101 patient isolates amplified in cells, pAd2-H detected 100% of all isolates from both the homologous and the heterologous subgroups. The detection rates for pAd2-F were 100% (subgroup C) and 3.6% (subgroups A, B, and D), and those for pAd16-BD were 100% (subgroup B) and 9.4% (subgroups A, C, and D). A commercial biotinylated product (Pathogene II) was also included in this study for comparison. Images PMID:3230138

  11. Hybrid polymeric hydrogels via peptide nucleic acid (PNA)/DNA complexation.

    PubMed

    Chu, Te-Wei; Feng, Jiayue; Yang, Jiyuan; Kopeček, Jindřich

    2015-12-28

    This work presents a new concept in hybrid hydrogel design. Synthetic water-soluble N-(2-hydroxypropyl)methacrylamide (HPMA) polymers grafted with multiple peptide nucleic acids (PNAs) are crosslinked upon addition of the linker DNA. The self-assembly is mediated by the PNA-DNA complexation, which results in the formation of hydrophilic polymer networks. We show that the hydrogels can be produced through two different types of complexations. Type I hydrogel is formed via the PNA/DNA double-helix hybridization. Type II hydrogel utilizes a unique "P-form" oligonucleotide triple-helix that comprises two PNA sequences and one DNA. Microrheology studies confirm the respective gelation processes and disclose a higher critical gelation concentration for the type I gel when compared to the type II design. Scanning electron microscopy reveals the interconnected microporous structure of both types of hydrogels. Type I double-helix hydrogel exhibits larger pore sizes than type II triple-helix gel. The latter apparently contains denser structure and displays greater elasticity as well. The designed hybrid hydrogels have potential as novel biomaterials for pharmaceutical and biomedical applications. PMID:26394062

  12. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS-PKS hybrid enzyme.

    PubMed

    Yun, Choong-Soo; Motoyama, Takayuki; Osada, Hiroyuki

    2015-01-01

    Tenuazonic acid (TeA) is a well-known mycotoxin produced by various plant pathogenic fungi. However, its biosynthetic gene has been unknown to date. Here we identify the TeA biosynthetic gene from Magnaporthe oryzae by finding two TeA-inducing conditions of a low-producing strain. We demonstrate that TeA is synthesized from isoleucine and acetoacetyl-coenzyme A by TeA synthetase 1 (TAS1). TAS1 is a unique non-ribosomal peptide synthetase and polyketide synthase (NRPS-PKS) hybrid enzyme that begins with an NRPS module. In contrast to other NRPS/PKS hybrid enzymes, the PKS portion of TAS1 has only a ketosynthase (KS) domain and this domain is indispensable for TAS1 activity. Phylogenetic analysis classifies this KS domain as an independent clade close to type I PKS KS domain. We demonstrate that the TAS1 KS domain conducts the final cyclization step for TeA release. These results indicate that TAS1 is a unique type of NRPS-PKS hybrid enzyme. PMID:26503170

  13. Biosynthesis of the mycotoxin tenuazonic acid by a fungal NRPS–PKS hybrid enzyme

    PubMed Central

    Yun, Choong-Soo; Motoyama, Takayuki; Osada, Hiroyuki

    2015-01-01

    Tenuazonic acid (TeA) is a well-known mycotoxin produced by various plant pathogenic fungi. However, its biosynthetic gene has been unknown to date. Here we identify the TeA biosynthetic gene from Magnaporthe oryzae by finding two TeA-inducing conditions of a low-producing strain. We demonstrate that TeA is synthesized from isoleucine and acetoacetyl-coenzyme A by TeA synthetase 1 (TAS1). TAS1 is a unique non-ribosomal peptide synthetase and polyketide synthase (NRPS–PKS) hybrid enzyme that begins with an NRPS module. In contrast to other NRPS/PKS hybrid enzymes, the PKS portion of TAS1 has only a ketosynthase (KS) domain and this domain is indispensable for TAS1 activity. Phylogenetic analysis classifies this KS domain as an independent clade close to type I PKS KS domain. We demonstrate that the TAS1 KS domain conducts the final cyclization step for TeA release. These results indicate that TAS1 is a unique type of NRPS–PKS hybrid enzyme. PMID:26503170

  14. Fibrillar networks of glycyrrhizic acid for hybrid nanomaterials with catalytic features.

    PubMed

    Saha, Abhijit; Adamcik, Jozef; Bolisetty, Sreenath; Handschin, Stephan; Mezzenga, Raffaele

    2015-04-27

    Self-assembly of the naturally occurring sweetening agent, glycyrrhizic acid (GA) in water is studied by small-angle X-ray scattering and microscopic techniques. Statistical analysis on atomic force microscopy images reveals the formation of ultralong GA fibrils with uniform thickness of 2.5 nm and right-handed twist with a pitch of 9 nm, independently of GA concentration. Transparent nematic GA hydrogels are exploited to create functional hybrid materials. Two-fold and three-fold hybrids are developed by introducing graphene oxide (GO) and in situ-synthesized gold nanoparticles (Au NPs) in the hydrogel matrix for catalysis applications. In the presence of GO, the catalytic efficiency of Au NPs in the reduction of p-nitrophenol to p-aminophenol is enhanced by 2.5 times. Gold microplate single crystals are further synthesized in the GA hydrogel, expanding the scope of these hybrids and demonstrating their versatility in materials design. PMID:25759108

  15. p-Aminophenylacetic acid-mediated synthesis of monodispersed titanium oxide hybrid microspheres in ethanol solution.

    PubMed

    Zhang, Hongye; Xie, Yun; Liu, Zhimin; Tao, Ranting; Sun, Zhenyu; Ding, Kunlun; An, Guimin

    2009-10-15

    Monodispersed TiO2 hybrid microspheres were prepared via the hydrolysis of titanium isopropoxide (TTIP) in ethanol solution containing p-aminophenylacetic acid (APA). The effects of the APA:TTIP molar ratio, water content, reaction time and reaction temperature on the morphology of the resultant spheres were investigated. The products were characterized by scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, thermogravimetric analysis, and X-ray diffraction. It was demonstrated that the diameters of the resultant TiO2 spheres could be tuned in the range of 380-800 nm by changing the APA:TTIP molar ratio (1:3 to 3:1) and water content (1-3 v/v%) in the reaction medium, and that increasing the APA:TTIP molar ratio led to larger TiO2 hybrid spheres while increasing the water content decreased their size. The loading content of APA in the hybrid spheres could reach 20 wt.% as they were prepared with the APA:TTIP ratio of 3:1. The possible formation mechanism of the hybrid spheres was also investigated. It was found that APA slowed down the hydrolysis rate of the titanium precursor so that resulted in the formation of the TiO2 spheres. In addition, the APA present in TiO2 spheres acted as a reducing agent to in situ convert HAuCl4 into metallic Au on the surface of the TiO2 spheres. The catalytic activity of the resultant Au/APA-TiO2 composite was examined using transfer hydrogenation of phenylacetone with 2-propanol, and it was indicated that the catalyst displayed high efficiency for this reaction. PMID:19616218

  16. Hybrid Processes Combining Photocatalysis and Ceramic Membrane Filtration for Degradation of Humic Acids in Saline Water

    PubMed Central

    Song, Lili; Zhu, Bo; Gray, Stephen; Duke, Mikel; Muthukumaran, Shobha

    2016-01-01

    This study explored the combined effects of photocatalysis with ceramic membrane filtration for the removal of humic acid in the presence of salt; to simulate saline wastewater conditions. The effects of operating parameters, such as salinity and TiO2 concentration on permeate fluxes, total organic carbon (TOC), and UV absorbance removal, were investigated. The interaction between the humic acids and TiO2 photocatalyst played an important role in the observed flux change during ceramic membrane filtration. The results for this hybrid system showed that the TOC removal was more than 70% for both without NaCl and with the 500 ppm NaCl concentration, and 62% and 66% for 1000 and 2000 ppm NaCl concentrations. The reduction in UV absorbance was more complete in the absence of NaCl compared to the presence of NaCl. The operation of the integrated photoreactor-ceramic membrane filter over five repeat cycles is described. It can be concluded that the overall removal performance of the hybrid system was influenced by the presence of salts, as salt leads to agglomeration of TiO2 particles by suppressing the stabilising effects of electrostatic repulsion and thereby reduces the effective surface contact between the pollutant and the photocatalyst. PMID:26938568

  17. Fatty acid membrane assembly on coacervate microdroplets as a step towards a hybrid protocell model

    NASA Astrophysics Data System (ADS)

    Dora Tang, T.-Y.; Rohaida Che Hak, C.; Thompson, Alexander J.; Kuimova, Marina K.; Williams, D. S.; Perriman, Adam W.; Mann, Stephen

    2014-06-01

    Mechanisms of prebiotic compartmentalization are central to providing insights into how protocellular systems emerged on the early Earth. Protocell models are based predominantly on the membrane self-assembly of fatty-acid vesicles, although membrane-free scenarios that involve liquid-liquid microphase separation (coacervation) have also been considered. Here we integrate these alternative models of prebiotic compartmentalization and develop a hybrid protocell model based on the spontaneous self-assembly of a continuous fatty-acid membrane at the surface of preformed coacervate microdroplets prepared from cationic peptides/polyelectrolytes and adenosine triphosphate or oligo/polyribonucleotides. We show that the coacervate-supported membrane is multilamellar, and mediates the selective uptake or exclusion of small and large molecules. The coacervate interior can be disassembled without loss of membrane integrity, and fusion and growth of the hybrid protocells can be induced under conditions of high ionic strength. Our results highlight how notions of membrane-mediated compartmentalization, chemical enrichment and internalized structuration can be integrated in protocell models via simple chemical and physical processes.

  18. Fatty acid membrane assembly on coacervate microdroplets as a step towards a hybrid protocell model.

    PubMed

    Dora Tang, T-Y; Rohaida Che Hak, C; Thompson, Alexander J; Kuimova, Marina K; Williams, D S; Perriman, Adam W; Mann, Stephen

    2014-06-01

    Mechanisms of prebiotic compartmentalization are central to providing insights into how protocellular systems emerged on the early Earth. Protocell models are based predominantly on the membrane self-assembly of fatty-acid vesicles, although membrane-free scenarios that involve liquid-liquid microphase separation (coacervation) have also been considered. Here we integrate these alternative models of prebiotic compartmentalization and develop a hybrid protocell model based on the spontaneous self-assembly of a continuous fatty-acid membrane at the surface of preformed coacervate microdroplets prepared from cationic peptides/polyelectrolytes and adenosine triphosphate or oligo/polyribonucleotides. We show that the coacervate-supported membrane is multilamellar, and mediates the selective uptake or exclusion of small and large molecules. The coacervate interior can be disassembled without loss of membrane integrity, and fusion and growth of the hybrid protocells can be induced under conditions of high ionic strength. Our results highlight how notions of membrane-mediated compartmentalization, chemical enrichment and internalized structuration can be integrated in protocell models via simple chemical and physical processes. PMID:24848239

  19. Staphylococcus aureus DNA ligase: characterization of its kinetics of catalysis and development of a high-throughput screening compatible chemiluminescent hybridization protection assay

    PubMed Central

    2004-01-01

    DNA ligases are key enzymes involved in the repair and replication of DNA. Prokaryotic DNA ligases uniquely use NAD+ as the adenylate donor during catalysis, whereas eukaryotic enzymes use ATP. This difference in substrate specificity makes the bacterial enzymes potential targets for therapeutic intervention. We have developed a homogeneous chemiluminescence-based hybridization protection assay for Staphylococcus aureus DNA ligase that uses novel acridinium ester technology and demonstrate that it is an alternative to the commonly used radiometric assays for ligases. The assay has been used to determine a number of kinetic constants for S. aureus DNA ligase catalysis. These included the Km values for NAD+ (2.75±0.1 μM) and the acridinium-ester-labelled DNA substrate (2.5±0.2 nM). A study of the pH-dependencies of kcat, Km and kcat/Km has revealed values of kinetically influential ionizations within the enzyme–substrate complexes (kcat) and free enzyme (kcat/Km). In each case, the curves were shown to be composed of one kinetically influential ionization, for kcat, pKa=6.6±0.1 and kcat/Km, pKa=7.1±0.1. Inhibition characteristics of the enzyme against two Escherichia coli DNA ligase inhibitors have also been determined with IC50 values for these being 3.30±0.86 μM for doxorubicin and 1.40±0.07 μM for chloroquine diphosphate. The assay has also been successfully miniaturized to a sufficiently low volume to allow it to be utilized in a high-throughput screen (384-well format; 20 μl reaction volume), enabling the assay to be used in screening campaigns against libraries of compounds to discover leads for further drug development. PMID:15283677

  20. Effect of Backbone Design on Hybridization Thermodynamics of Oligo-nucleic Acids: A Coarse-Grained Molecular Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Ghobadi, Ahmadreza F.; Jayaraman, Arthi

    DNA hybridization is the basis of various bio-nano technologies, such as DNA origami and assembly of DNA-functionalized nanoparticles. A hybridized double stranded (ds) DNA is formed when complementary nucleobases on hybridizing strands exhibit specific and directional hydrogen bonds through canonical Watson-Crick base-pairing interactions. In recent years, the need for cheaper alternatives and significant synthetic advances have driven design of DNA mimics with new backbone chemistries. However, a fundamental understanding of how these backbone modifications in the oligo-nucleic acids impact the hybridization and melting behavior of the duplex is still lacking. In this talk, we present our recent findings on impact of varying backbone chemistry on hybridization of oligo-nucleic acid duplexes. We use coarse-grained molecular dynamics simulations to isolate the effect of strand flexibility, electrostatic interactions and nucleobase spacing on the melting curves for duplexes with various strand sequences and concentrations. Since conjugation of oligo-nucleic acids with polymers serve as building blocks for thermo-responsive polymer networks and gels, we also present the effect of such conjugation on hybridization thermodynamics and polymer conformation.

  1. Salinomycin Hydroxamic Acids: Synthesis, Structure, and Biological Activity of Polyether Ionophore Hybrids.

    PubMed

    Borgström, Björn; Huang, Xiaoli; Chygorin, Eduard; Oredsson, Stina; Strand, Daniel

    2016-06-01

    The polyether ionophore salinomycin has recently gained attention due to its exceptional ability to selectively reduce the proportion of cancer stem cells within a number of cancer cell lines. Efficient single step strategies for the preparation of hydroxamic acid hybrids of this compound varying in N- and O-alkylation are presented. The parent hydroxamic acid, salinomycin-NHOH, forms both inclusion complexes and well-defined electroneutral complexes with potassium and sodium cations via 1,3-coordination by the hydroxamic acid moiety to the metal ion. A crystal structure of an cationic sodium complex with a noncoordinating anion corroborates this finding and, moreover, reveals a novel type of hydrogen bond network that stabilizes the head-to-tail conformation that encapsulates the cation analogously to the native structure. The hydroxamic acid derivatives display down to single digit micromolar activity against cancer cells but unlike salinomycin selective reduction of ALDH(+) cells, a phenotype associated with cancer stem cells was not observed. Mechanistic implications are discussed. PMID:27326340

  2. Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

    PubMed

    Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

    2016-01-01

    Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding. PMID:27001403

  3. Detection of inhibition of 5-aminoimidazole-4-carboxamide ribotide transformylase by thioinosinic acid and azathioprine by a new colorimetric assay.

    PubMed Central

    Ha, T; Morgan, S L; Vaughn, W H; Eto, I; Baggott, J E

    1990-01-01

    The colorimetric assay for 5-aminoimidazole-4-carboxamide ribotide (AICAR) transformylase (phosphoribosylamino-imidazolecarboxamide formyltransferase; EC 2.1.2.3) has been extensively modified. The modified assay is based upon the short-term permanganate oxidation of the folate product, tetrahydrofolate (H4folate) to p-aminobenzoyl glutamate (pABG). The modified assay was used to detect the transformylase activity in crude extracts of peripheral-blood mononuclear cells (PBMCs). Azathioprine and its metabolite, thioinosinic acid (tIMP), are competitive inhibitors (with respect to AICAR) of the chicken liver transformylase and the transformylase from PBMCs of the MRL/lpr mouse, an animal model of systemic autoimmune disease. The Ki values of tIMP and azathioprine for the chicken liver enzyme are 39 +/- 4 microM and 120 +/- 10 microM, whereas the Ki values for the enzyme from PBMCs of the MRL/lpr mouse are 110 +/- 20 microM and 90 +/- 14 microM respectively. The anti-inflammatory drugs ibuprofen and naproxen are also inhibitors of the transformylase. PMID:2268263

  4. Evaluation of Surfactants-Assisted Folic Acid-Loaded Pectin Submicrospheres: Characterization and Hemocompatibility Assay.

    PubMed

    Varuna Kumara, J B; Ravikumara, N R; Madhusudhan, Basavaraj

    2016-10-01

    Folic acid is used for preventing and treating multiple diseases and disorders, administered in the form of oral supplements. The present research work was aimed to study the influence of two non-ionic surfactants Poloxamer and Tween 80 (Polysorbate 80) on pectin submicrospheres formulations. Typical natural polymer pectin was used to encapsulate folic acid by cross linking method. The resultant submicrospheres contributed to improve the aqueous solubility to enhance the bioavailability of folic acid. During investigation, it was observed that pectin polymers influenced kinetics of the rate of reaction more intensively than the surfactants. The physical phenomenon caused the change in their size, shape and chemistry of pectin polymers transforming into submicrospheres in aqueous condition. The characteristic differences of submicrospheres were assessed by scanning electron microscopy, differential scanning calorimetry and Fourier-transform infrared spectroscopy. The average diameters of the submicrospheres ranged between 250 and 500 nm. The encapsulation efficiency of submicrospheres ranged between 80 and 96 %. The characteristic swelling behavior of lyophilized submicrospheres was influenced by the ratio of pectin polymers and folic acid used in the formulations. The submicrospheres systems exhibited controlled release of folic acid due to the pH-dependent solubility of pectin polymers in aqueous medium. The submicrospheres showed good haemocompatibility suggesting them to be promising candidates for oral delivery. PMID:27605736

  5. One-pot transformation of cellobiose to formic acid and levulinic acid over ionic-liquid-based polyoxometalate hybrids.

    PubMed

    Li, Kaixin; Bai, Linlu; Amaniampong, Prince Nana; Jia, Xinli; Lee, Jong-Min; Yang, Yanhui

    2014-09-01

    Currently, levulinic acid (LA) and formic acid (FA) are considered as important carbohydrates for the production of value-added chemicals. Their direct production from biomass will open up a new opportunity for the transformation of biomass resource to valuable chemicals. In this study, one-pot transformation of cellobiose into LA and FA was demonstrated, using a series of multiple-functional ionic liquid-based polyoxometalate (IL-POM) hybrids as catalytic materials. These IL-POMs not only markedly promoted the production of valuable chemicals including LA, FA and monosaccharides with high selectivities, but also provided great convenience of the recovery and the reuse of the catalytic materials in an environmentally friendly manner. Cellobiose conversion of 100%, LA selectivity of 46.3%, and FA selectivity of 26.1% were obtained at 423 K and 3 MPa for 3 h in presence of oxygen. A detailed catalytic mechanism for the one-pot transformation of cellobiose was also presented. PMID:25110998

  6. Comparison of the f-HPV typing™ and Hybrid Capture II® assays for detection of high-risk HPV genotypes in cervical samples.

    PubMed

    Cañadas, María-Paz; Cirigliano, Vincenzo; Darwich, Laila; Sirera, Guillermo; Coll, Josep; Clotet, Bonaventura; Videla, Sebastian

    2012-07-01

    Human papillomavirus genotyping is being considered in cervical screening programs and for monitoring the effectiveness of HPV vaccination. Both approaches require access to fast, easy and high-throughput technology. The aim of this study was to compare a new commercial assay (f-HPV typing™) with the Hybrid Capture II® (HC2) to detect HPV infection. The F-HPV typing is a multiplex fluorescent PCR method recognizing E6 and E7 regions of 13 high-risk (HR) HPV types, the same set of HR-types targeted HC2 test. A subset of 157 cervical samples was tested with both assays. The percentage of positive HR-HPV DNA samples was 24% (37/155) by HC2 and 33% (49/155) by f-HPV typing. Concordant results were found in 133/155 (overall agreement, 85.8%; Cohen's kappa=0.65). The analytical sensitivity and specificity of f-HPV were 97.6 and 93, respectively. In conclusion, this study shows that the f-HPV assay provides a good alternative to HC2 to detect HPV infection, allowing simple and rapid HPV genotyping and detecting multiple infections. PMID:22449759

  7. Polyacrylic acid-coated cerium oxide nanoparticles: An oxidase mimic applied for colorimetric assay to organophosphorus pesticides.

    PubMed

    Zhang, Shi-Xiang; Xue, Shi-Fan; Deng, Jingjing; Zhang, Min; Shi, Guoyue; Zhou, Tianshu

    2016-11-15

    It is important and urgent to develop reliable and highly sensitive methods that can provide on-site and rapid detection of extensively used organophosphorus pesticides (OPs) for their neurotoxicity. In this study, we developed a novel colorimetric assay for the detection of OPs based on polyacrylic acid-coated cerium oxide nanoparticles (PAA-CeO2) as an oxidase mimic and OPs as inhibitors to suppress the activity of acetylcholinesterase (AChE). Firstly, highly dispersed PAA-CeO2 was prepared in aqueous solution, which could catalyze the oxidation of TMB to produce a color reaction from colorless to blue. And the enzyme of AChE was used to catalyze the substrate of acetylthiocholine (ATCh) to produce thiocholine (TCh). As a thiol-containing compound with reducibility, TCh can decrease the oxidation of TMB catalyzed by PAA-CeO2. Upon incubated with OPs, the enzymatic activity of AChE was inhibited to produce less TCh, resulting in more TMB catalytically oxidized by PAA-CeO2 to show an increasing blue color. The two representative OPs, dichlorvos and methyl-paraoxon, were tested using our proposed assay. The novel assay showed notable color change in a concentration-dependent manner, and as low as 8.62 ppb dichlorvos and 26.73 ppb methyl-paraoxon can be readily detected. Therefore, taking advantage of such oxidase-like activity of PAA-CeO2, our proposed colorimetric assay can potentially be a screening tool for the precise and rapid evaluation of the neurotoxicity of a wealth of OPs. PMID:27208478

  8. A Continuous, Quantitative Fluorescent Assay for Plant Caffeic acid O-Methyltransferases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant caffeic acid O-methyltransferases (COMTs) use s-adenosylmethionine (ado-met), as a methyl donor to transmethylate their preferred (phenolic) substrates in-vivo, and will generally utilize a range of phenolic compounds in-vitro. Collazo et al. (2005; Analytical Biochemistry 342: 86-92) have pu...

  9. A SIMPLE ASSAY FOR 2,4-DICHLOROPHENOXYACETIC ACID USING COATED TEST-STRIPS

    EPA Science Inventory

    Immunoassay test strips utilizing ascending chromatography has been devised for the detection of 2.4-dichlorophenoxyacetic acid (2,4-D). This test requires no instrumentation, inexpensive reagents and relies on the application of antibodies to 2,4-D adsorbed onto colloidal gol...

  10. Amplified electrochemical detection of nucleic acid hybridization via selective preconcentration of unmodified gold nanoparticles.

    PubMed

    Li, Yuan; Tian, Rui; Zheng, Xingwang; Huang, Rongfu

    2016-08-31

    The common drawback of optical methods for rapid detection of nucleic acid by exploiting the differential affinity of single-/double-stranded nucleic acids for unmodified gold nanoparticles (AuNPs) is its relatively low sensitivity. In this article, on the basis of selective preconcentration of AuNPs unprotected by single-stranded DNA (ssDNA) binding, a novel electrochemical strategy for nucleic acid sequence identification assay has been developed. Through detecting the redox signal mediated by AuNPs on 1, 6-hexanedithiol blocked gold electrode, the proposed method is able to ensure substantial signal amplification and a low background current. This strategy is demonstrated for quantitative analysis of the target microRNA (let-7a) in human breast adenocarcinoma cells, and a detection limit of 16 fM is readily achieved with desirable specificity and sensitivity. These results indicate that the selective preconcentration of AuNPs for electrochemical signal readout can offer a promising platform for the detection of specific nucleic acid sequence. PMID:27506344

  11. An ultra-high performance liquid chromatography-tandem mass spectrometric assay for quantifying 3-ketocholanoic acid: Application to the human liver microsomal CYP3A-dependent lithocholic acid 3-oxidation assay.

    PubMed

    Bansal, Sumit; Chai, Swee Fen; Lau, Aik Jiang

    2016-06-15

    Lithocholic acid (LCA), a hepatotoxic and carcinogenic bile acid, is metabolized to 3-ketocholanoic acid (3-KCA) by cytochrome P450 3A (CYP3A). In the present study, the objectives were to develop and validate an ultra-high performance liquid chromatography-tandem mass spectrometric (UPLC-MS/MS) method to quantify 3-KCA and apply it to the human liver microsomal CYP3A-dependent LCA 3-oxidation assay. Chromatographic separation was achieved on a Waters ACQUITY™ UPLC C18 column (50×2.1mm, 1.7μm) with a gradient system consisting of 0.1% v/v formic acid in water (solvent A) and 0.1% v/v formic acid in acetonitrile (solvent B). The retention time was 3.73min for 3-KCA and 2.73min for cortisol (internal standard). Positive electrospray ionization with multiple reaction monitoring (MRM) mode was used to quantify 3-KCA (m/z 375.4→135.2) and cortisol (m/z 363.5→121.0). The limit of detection of 3-KCA was 10μM, the lower limit of quantification was 33.3μM, and the calibration curve was linear from 0.05-10μM with r(2)>0.99. Intra-day and inter-day accuracy and precision were <13.7%. The quality control samples were stable when assessed after 4h at room temperature, 24h at 4°C, 14days at -20°C, and three freeze-thaw cycles. The liver microsomal matrix did not affect 3-KCA quantification. The amount of KCA formed in the human liver microsomal LCA 3-oxidation assay was linear with respect to the amount of microsomal protein (up to 40μg) and incubation time (5-30min). Enzyme kinetics experiment indicated that LCA 3-oxidation followed the Michaelis-Menten model with an apparent Km of 26±7μM and Vmax of 303±50pmol/min/mg protein. This novel UPLC-MS/MS method for quantifying 3-KCA offers a specific, sensitive, and fast approach to determine liver microsomal LCA 3-oxidation. PMID:27153105

  12. /sup 57/Co-soap assay for plasma total non-esterified fatty acids compared with a gas-liquid chromatographic method

    SciTech Connect

    Turnell, D.C.; Price, C.P.; France, M.M.

    1980-12-01

    A relatively rapid radiochemical assay for determining plasma non-esterified fatty acids is described. Results correlated well with those by gas-liquid chromatography. The between-batch CV for 1.12 mmol of non-esterified fatty acids per liter was 7%.

  13. A hybrid Li-air battery with buckypaper air cathode and sulfuric acid electrolyte

    SciTech Connect

    Li, YF; Huang, K; Xing, YC

    2012-10-30

    We demonstrate a type of carbon nanotube based buckypaper cathode in a hybrid electrolyte Li-air battery (HyLAB) that showed outstanding discharging performances. The HyLAB has sulfuric acid as the catholyte and a large active electrode area (10 cm(2)). The active cathode layer was made from a buckypaper with 5 wt.% Pt supported on carbon nanotubes (Pt/CNTs) for oxygen reduction and evolution. A similar cathode was constructed with a catalyst of 5 wt.% Pt supported on carbon black (Pt/CB). It is demonstrated that sulfuric acid can achieve high discharging current densities while maintaining relatively high cell potentials. The cell with Pt/CNTs showed a much better performance than with Pt/CB at high current densities. The HyLAB with Pt/CNTs achieved a discharging capacity of 306 mAh/g and a cell voltage of 3.15 V at 0.2 mA/cm(2). The corresponding specific energy is 1067 Wh/kg based on the total weight of the sulfuric acid. Slow decrease in performance was observed, but it can be recovered by refilling the cell with new electrolyte after continuous discharging of more than 75 h. A charge-discharge experiment at 0.2 mA/cm(2) showed that the cell was rechargeable with a capacity of more than 300 mAh/g. (c) 2012 Elsevier Ltd. All rights reserved.

  14. Development and operation of a hybrid acid-alkaline advanced water electrolysis cell

    NASA Astrophysics Data System (ADS)

    Teschke, O.; Zwanziger, M.

    A hybrid acid-alkaline water electrolysis cell has been developed for hydrogen production. The cell is based on the use of an acidic solution at the cathode and a basic solution at the anode to reduce the minimum theoretical voltage for water decomposition from the thermoneutral potential of 1.47 V to close to 1.4 V at 25 C and 1 atm. The pH differential is maintained by the removal of OH ions from the cathode section and water removal from the anode section, which can be driven by heat energy. A practical cell has been built using a solid polymer electrolyte in which, however, the cathodic compartment is not acidic but neutral. Tests with a platinum black cathode catalyst and a platinum-iridium anode catalyst have resulted in steady-state water hydrolysis at an applied voltage of 0.9 V, and a V-I diagram with a considerably lower slope than that of a conventional cell has been obtained at 90 C.

  15. A simple and highly sensitive assay of perfluorooctanoic acid based on resonance light scattering technique.

    PubMed

    Zhang, Fang; Zheng, Yonghong; Liang, Jiaman; Long, Sha; Chen, Xianping; Tan, Kejun

    2016-04-15

    A simple, highly sensitive resonance light scattering (RLS) method for the detection of perfluorooctanoic acid (PFOA) has been developed based on the interaction with crystal violet (CV). It was found that PFOA can form complexes with CV in acid medium resulting in remarkable enhancement of the RLS intensity of the system. And the enhanced RLS intensities are in proportion to the concentration of PFOA in the range of 0.1-25.0μmol/L (R(2)=0.9998), with a detection limit of 11.0nmol/L (S/N=3). In this work, the optimum reaction conditions and the interferences of foreign substances were investigated. The reaction mechanism between CV and PFOA was also studied by the absorption spectrum and scanning electron microscope (SEM). This method is successfully applied to the determination of PFOA in tap water and Jialing river water samples with RSD≤4.04%. PMID:26824483

  16. A simple and highly sensitive assay of perfluorooctanoic acid based on resonance light scattering technique

    NASA Astrophysics Data System (ADS)

    Zhang, Fang; Zheng, Yonghong; Liang, Jiaman; Long, Sha; Chen, Xianping; Tan, Kejun

    2016-04-01

    A simple, highly sensitive resonance light scattering (RLS) method for the detection of perfluorooctanoic acid (PFOA) has been developed based on the interaction with crystal violet (CV). It was found that PFOA can form complexes with CV in acid medium resulting in remarkable enhancement of the RLS intensity of the system. And the enhanced RLS intensities are in proportion to the concentration of PFOA in the range of 0.1-25.0 μmol/L (R2 = 0.9998), with a detection limit of 11.0 nmol/L (S/N = 3). In this work, the optimum reaction conditions and the interferences of foreign substances were investigated. The reaction mechanism between CV and PFOA was also studied by the absorption spectrum and scanning electron microscope (SEM). This method is successfully applied to the determination of PFOA in tap water and Jialing river water samples with RSD ≤ 4.04%.

  17. Differential gene expression in the murine thymus assayed by quantitative hybridization of arrayed cDNA clones

    SciTech Connect

    Nguyen, C.; Rocha, D.; Granjeaud, S.

    1995-09-01

    High-throughput measurement of hybridization signatures obtained using complex probes prepared from poly(A){sup +} RNA and high-density cDNA colony filters is described. The performance of the system, elimination of artifacts, and verification of the validity of the data are discussed. cDNAs corresponding to sequences present at levels of approximately 0.01% in the complex probe can be detected. Good correlation is observed between expression profiles determined by this method and by Northern blotting. The method is applied to a preliminary investigation of differential expression in three cell types present in the murine thymus. 41 refs., 3 figs., 1 tab.

  18. Lead-acid batteries in micro-hybrid applications. Part II. Test proposal

    NASA Astrophysics Data System (ADS)

    Schaeck, S.; Stoermer, A. O.; Albers, J.; Weirather-Koestner, D.; Kabza, H.

    In the first part of this work [1] selected key parameters for applying lead-acid (LA) batteries in micro-hybrid power systems (MHPS) were investigated. Main results are integrated in an accelerated, comprehensive test proposal presented here. The test proposal aims at a realistic representation of the pSoC operation regime, which is described in Refs. [1,6]. The test is designed to be sensitive with respect to dynamic charge acceptance (DCA) at partially discharged state (critical for regenerative braking) and the internal resistance at high-rate discharge (critical for idling stop applications). First results are presented for up-to-date valve-regulated LA batteries with absorbent glass mat (AGM) separators. The batteries are close to the limits of the first proposal of pass/fail-criteria. Also flooded batteries were tested; the first out of ten units failed already.

  19. Advanced design of valve-regulated lead-acid battery for hybrid electric vehicles

    NASA Astrophysics Data System (ADS)

    Lam, L. T.; Newnham, R. H.; Ozgun, H.; Fleming, F. A.

    A novel design of lead-acid battery has been developed for use in hybrid electric vehicles (HEVs). The battery has current take-offs at both ends of each of the positive and negative plates. This feature markedly reduces battery operating temperatures, improves battery capacity, and extends cycle-life under HEV duty. The battery also performs well under partial-state-of-charge (PSoC)/fast-charge, electric-vehicle operation. The improvements in performance are attributed to more uniform utilization of the plate active-materials. The battery, combined with an internal-combustion engine and a new type of supercapacitor, will be used to power an HEV, which is being designed and constructed by an Australian industry-government consortium.

  20. Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp.

    PubMed Central

    2013-01-01

    Background Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. Results Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI), from 87.8 to 99.9%) and 100% (95% CI, from 88.0 to 100.0%), for Lactobacillus spp.; and 100% (95% CI, from 92.8 to 100%) and 100% (95% CI, from 81.5 to 100.0%) for G. vaginalis. Moreover, the probes were evaluated in mixed samples mimicking women with BV or normal vaginal microflora, demonstrating efficiency and applicability of our PNA FISH. Conclusions This quick method accurately detects Lactobacillus spp. and G. vaginalis species in mixed samples, thus enabling efficient evaluation of the two bacterial groups, most frequently encountered in the vagina. PMID:23586331

  1. Lead-acid batteries in micro-hybrid applications. Part I. Selected key parameters

    NASA Astrophysics Data System (ADS)

    Schaeck, S.; Stoermer, A. O.; Kaiser, F.; Koehler, L.; Albers, J.; Kabza, H.

    Micro-hybrid electric vehicles were launched by BMW in March 2007. These are equipped with brake energy regeneration (BER) and the automatic start and stop function (ASSF) of the internal combustion engine. These functions are based on common 14 V series components and lead-acid (LA) batteries. The novelty is given by the intelligent onboard energy management, which upgrades the conventional electric system to the micro-hybrid power system (MHPS). In part I of this publication the key factors for the operation of LA batteries in the MHPS are discussed. Especially for BER one is high dynamic charge acceptance (DCA) for effective boost charging. Vehicle rest time is identified as a particular negative parameter for DCA. It can be refreshed by regular fully charging at elevated charge voltage. Thus, the batteries have to be outstandingly robust against overcharge and water loss. This can be accomplished for valve-regulated lead-acid (VRLA) batteries at least if they are mounted in the trunk. ASSF goes along with frequent high-rate loads for warm cranking. The internal resistance determines the drop of the power net voltage during cranking and is preferably low for reasons of power net stability even after years of operation. Investigations have to be done with aged 90 Ah VRLA-absorbent glass mat (AGM) batteries. Battery operation at partial state-of-charge gives a higher risk of deep discharging (overdischarging). Subsequent re-charging then is likely to lead to the formation of micro-short circuits in the absorbent glass mat separator.

  2. Gene protein detection platform--a comparison of a new human epidermal growth factor receptor 2 assay with conventional immunohistochemistry and fluorescence in situ hybridization platforms.

    PubMed

    Stålhammar, Gustav; Farrajota, Pedro; Olsson, Ann; Silva, Cristina; Hartman, Johan; Elmberger, Göran

    2015-08-01

    Human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are widely used semiquantitative assays for selecting breast cancer patients for HER2 antibody therapy. However, both techniques have been shown to have disadvantages. Our aim was to test a recent automated technique of combined IHC and brightfield dual in situ hybridization-gene protein detection platform (GPDP)-in breast cancer HER2 protein, gene, and chromosome 17 centromere status evaluations, comparing the results in accordance to the American Society of Clinical Oncology/College of American Pathologists recommendations for HER2 testing in breast cancer from both 2007 and 2013. The GPDP technique performance was evaluated on 52 consecutive whole slide invasive breast cancer cases with HER2 IHC 2/3+ scoring results. Applying in turns the American Society of Clinical Oncology/College of American Pathologists recommendations for HER2 testing in breast cancer from 2007 and 2013 to both FISH and GPDP DISH assays, the HER2 gene amplification results showed 100% concordance among amplified/nonamplified cases, but there was a shift in 4 cases toward positive from equivocal results and toward equivocal from negative results. This might be related to the emphasis on the average HER2 copy number in the 2013 criteria. HER2 expression by IVD market IHC kit (Pathway®) has a strong correlation with GPDP HER2 protein, including a full concordance for all cases scored as 3+ and a reduction from 2+ to 1+ in 7 cases corresponding to nonamplified cases. Gene protein detection platform HER2 protein "solo" could have spared the need for 7 FISH studies. In addition, the platform offered advantages on interpretation reassurance including selecting areas for counting gene signals paralleled with protein IHC expression, on heterogeneity detection, interpretation time, technical time, and tissue expense. PMID:25921313

  3. Development of automated brightfield double In Situ hybridization (BDISH) application for HER2 gene and chromosome 17 centromere (CEN 17) for breast carcinomas and an assay performance comparison to manual dual color HER2 fluorescence In Situ hybridization (FISH)

    PubMed Central

    Nitta, Hiroaki; Hauss-Wegrzyniak, Beatrice; Lehrkamp, Megan; Murillo, Adrian E; Gaire, Fabien; Farrell, Michael; Walk, Eric; Penault-Llorca, Frederique; Kurosumi, Masafumi; Dietel, Manfred; Wang, Lin; Loftus, Margaret; Pettay, James; Tubbs, Raymond R; Grogan, Thomas M

    2008-01-01

    Background Human epidermal growth factor receptor 2 (HER2) fluorescence in situ hybridization (FISH) is a quantitative assay for selecting breast cancer patients for trastuzumab therapy. However, current HER2 FISH procedures are labor intensive, manual methods that require skilled technologists and specialized fluorescence microscopy. Furthermore, FISH slides cannot be archived for long term storage and review. Our objective was to develop an automated brightfield double in situ hybridization (BDISH) application for HER2 gene and chromosome 17 centromere (CEN 17) and test the assay performance with dual color HER2 FISH evaluated breast carcinomas. Methods The BDISH assay was developed with the nick translated dinitrophenyl (DNP)-labeled HER2 DNA probe and DNP-labeled CEN 17 oligoprobe on the Ventana BenchMark® XT slide processing system. Detection of HER2 and CEN 17 signals was accomplished with the silver acetate, hydroquinone, and H2O2 reaction with horseradish peroxidase (HRP) and the fast red and naphthol phosphate reaction with alkaline phosphatise (AP), respectively. The BDISH specificity was optimized with formalin-fixed, paraffin-embedded xenograft tumors, MCF7 (non-amplified HER2 gene) and BT-474 (amplified HER2 gene). Then, the BDISH performance was evaluated with 94 routinely processed breast cancer tissues. Interpretation of HER2 and CEN 17 BDISH slides was conducted by 4 observers using a conventional brightfield microscope without oil immersion objectives. Results Sequential hybridization and signal detection for HER2 and CEN 17 ISH demonstrated both DNA targets in the same cells. HER2 signals were visualized as discrete black metallic silver dots while CEN 17 signals were detected as slightly larger red dots. Our study demonstrated a high consensus concordance between HER2 FISH and BDISH results of clinical breast carcinoma cases based on the historical scoring method (98.9%, Simple Kappa = 0.9736, 95% CI = 0.9222 – 1.0000) and the ASCO

  4. Nanoparticle Formation from Hybrid, Multiblock Copolymers of Poly(Acrylic Acid) and VPGVG Peptide

    PubMed Central

    Grieshaber, Sarah E.; Paik, Bradford A.; Bai, Shi; Kiick, Kristi L.; Jia, Xinqiao

    2012-01-01

    Elastin-mimetic hybrid copolymers with an alternating molecular architecture were synthesized via the step growth polymerization of azide-functionalized, telechelic poly(tert-butyl acrylate) (PtBA) and an alkyne-terminated, valine and glycine-rich peptide with a sequence of (VPGVG)2 (VG2). The resultant hybrid copolymer, [PtBA-VG2]n, contains up to six constituent building blocks and has a polydispersity index (PDI) of ~1.9. Trifluoroacetic acid (TFA) treatment of [PtBA-VG2]n gave rise to an alternating copolymer of poly(acrylic acid) (PAA) and VG2 ([PAA-VG2]n). The modular design permits facile adjustment of the copolymer composition by varying the molecular weight of PAA (22 and 63 repeat units). Characterization by dynamic light scattering indicated that the multiblock copolymers formed discrete nanoparticles at room temperature in aqueous solution at pH 3.8, with an average diameter of 250-270 nm and a particle size distribution of 0.34 for multiblock copolymers containing PAA22 and 0.17 for those containing PAA63. Upon increasing the pH to 7.4, both types of particles were able to swell without being disintegrated, reaching an average diameter of 285-300 nm for [PAA22-VG2]n and 330-350 nm for [PAA63-VG2]n, respectively. The nanoparticles were not dissociated upon the addition of urea, further confirming their unusual stability. The nanoparticles were capable of sequestering a hydrophobic fluorescent dye (pyrene), and the critical aggregation concentration (CAC) was determined to be 1.09 × 10-2 or 1.05 × 10-2 mg/mL for [PAA22-VG2]n and [PAA63-VG2]n, respectively. We suggest that the multiblock copolymers form through collective H-bonding and hydrophobic interactions between the PAA and VG2 peptide units, and that the unusual stability of the multiblock nanoparticles is conferred by the multiblock architecture. These hybrid multiblock copolymers are potentially useful as pH-responsive drug delivery vehicles, with the possibility of drug loading through

  5. Evaluation of experimental teat dip containing sodium chlorite and lactic acid by excised teat assay.

    PubMed

    Schmidt, A L; Oliver, S P; Fydenkevez, M E

    1984-12-01

    An experimental teat dip containing sodium chlorite and lactic acid, diluted in water, was evaluated by excised teat protocol. The teat dip was tested against 21 microorganisms. Included were: Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Numerous strains were tested for strain differences. Environmental bacteria were included because of their increasing importance as a cause of bovine mastitis. All excised teats were dipped in a bacterial suspension containing about 1 X 10(8) cfu/ml. Negative control teats were not dipped in a germicidal compound. Positive controls were dipped in 1% iodophor. Effectiveness of the experimental teat dip was expressed as the percent reduction in mean log of bacteria recovered from dipped teats as compared to numbers recovered from control teats. The sodium chlorite - lactic acid dip caused a greater percent log reduction than iodophor for 14 of 21 strains tested. However, differences were generally slight. The experimental teat dip appeared effective against Gram-negative bacteria. Some differences in percent log reduction were observed between strains of the same species. Lowest effectiveness and greatest strain variation were observed with Staphylococcus aureus for both dips tested. PMID:6530497

  6. Identification of iopanoic acid as substrate of type 1 deiodinase by a novel nonradioactive iodide-release assay.

    PubMed

    Renko, Kostja; Hoefig, Carolin S; Hiller, Franziska; Schomburg, Lutz; Köhrle, Josef

    2012-05-01

    Enzymatic 5'- and 5-deiodination are key reactions for local and systemic activation and inactivation of iodothyronines and thyronamines. Expression of the three deiodinase (DIO) isoenzymes is regulated by a number of parameters, including thyroid status, genotype, micronutrient availability, and disease-related signaling. In addition, DIO are potential targets of pharmacological as well as environmentally derived substances, which might affect their enzymatic activity (endocrine disruptors). With the classical DIO activity assay, testing depends on the availability of radioactively labeled substrates (e.g. (125)I-rT(3)) to monitor the release of radioactive iodide. Recently, liquid chromatography-tandem mass spectrometry was described as an alternative method apparently resolving this limitation. However, it has a high demand in technical equipment and analytical routine and is limited in sample number by considerable measuring time. We therefore combined the classical deiodination assay with an easily accessible photometric method taking advantage of the Sandell-Kolthoff reaction for measuring iodide release. In brief, iodine works as a catalyst within this redox reaction between Ce(4+) and As(3+) leading to an acceleration of destaining. Furthermore, the protocol was adapted to minimize handling effort and time consumption. Because this method is not dependent on radioactivity, it expands the substrate spectrum of the classical method. Suitability of this assay was tested with tissue samples from animal experiments (hepatic Dio1 activity in hypo- and hyperthyroid mice) and established DIO inhibitors. As a new but not unexpected finding, the alleged inhibitor iopanoic acid turned out to be a DIO substrate. This finding was confirmed by liquid chromatography-tandem mass spectrometry, and its potential clinical impact requires further studies. PMID:22434082

  7. Development of Lentivirus-Based Reference Materials for Ebola Virus Nucleic Acid Amplification Technology-Based Assays

    PubMed Central

    Mattiuzzo, Giada; Ashall, James; Doris, Kathryn S.; MacLellan-Gibson, Kirsty; Nicolson, Carolyn; Wilkinson, Dianna E.; Harvey, Ruth; Almond, Neil; Anderson, Robert; Efstathiou, Stacey; Minor, Philip D.; Page, Mark

    2015-01-01

    The 2013-present Ebola virus outbreak in Western Africa has prompted the production of many diagnostic assays, mostly based on nucleic acid amplification technologies (NAT). The calibration and performance assessment of established assays and those under evaluation requires reference materials that can be used in parallel with the clinical sample to standardise or control for every step of the procedure, from extraction to the final qualitative/quantitative result. We have developed safe and stable Ebola virus RNA reference materials by encapsidating anti sense viral RNA into HIV-1-like particles. The lentiviral particles are replication-deficient and non-infectious due to the lack of HIV-1 genes and Envelope protein. Ebola virus genes were subcloned for encapsidation into two lentiviral preparations, one containing NP-VP35-GP and the other VP40 and L RNA. Each reference material was formulated as a high-titre standard for use as a calibrator for secondary or internal standards, and a 10,000-fold lower titre preparation to serve as an in-run control. The preparations have been freeze-dried to maximise stability. These HIV-Ebola virus RNA reference materials were suitable for use with in-house and commercial quantitative RT-PCR assays and with digital RT-PCR. The HIV-Ebola virus RNA reference materials are stable at up to 37°C for two weeks, allowing the shipment of the material worldwide at ambient temperature. These results support further evaluation of the HIV-Ebola virus RNA reference materials as part of an International collaborative study for the establishment of the 1st International Standard for Ebola virus RNA. PMID:26562415

  8. Single Laboratory Validation of A Ready-to-Use Phosphatase Inhibition Assay for Detection of Okadaic Acid Toxins

    PubMed Central

    Smienk, Henry G. F.; Calvo, Dolores; Razquin, Pedro; Domínguez, Elena; Mata, Luis

    2012-01-01

    A phosphatase inhibition assay for detection of okadaic acid (OA) toxins in shellfish, OkaTest, was single laboratory validated according to international recognized guidelines (AOAC, EURACHEM). Special emphasis was placed on the ruggedness of the method and stability of the components. All reagents were stable for more than 6 months and the method was highly robust under normal laboratory conditions. The limit of detection and quantification were 44 and 56 µg/kg, respectively; both below the European legal limit of 160 µg/kg. The repeatability was evaluated with 2 naturally contaminated samples. The relative standard deviation (RSD) calculated was 1.4% at a level of 276 µg/kg and 3.9% at 124 µg/kg. Intermediate precision was estimated by testing 10 different samples (mussel and scallop) on three different days and ranged between 2.4 and 9.5%. The IC50 values of the phosphatase used in this assay were determined for OA (1.2 nM), DTX-1 (1.6 nM) and DTX-2 (1.2 nM). The accuracy of the method was estimated by recovery testing for OA (mussel, 78–101%; king scallop, 98–114%), DTX-1 (king scallop, 79–102%) and DTX-2 (king scallop, 93%). Finally, the method was qualitatively compared to the mouse bioassay and LC-MS/MS. PMID:22778904

  9. An enzyme-linked immunosorbent assay for detecting 3-phenoxybenzoic acid in plasma and its application in farmers and consumers

    PubMed Central

    Thiphom, Sarunya; Prapamontol, Tippawan; Chantara, Somporn; Mangklabruks, Ampica; Suphavilai, Chaisuree; Ahn, Ki Chang; Gee, Shirley J.; Hammock, Bruce D.

    2013-01-01

    The aim of this study was to identify a plasma biomarker of exposure to pyrethroid insecticides. A major metabolite, 3-phenoxybenzoic acid (3-PBA), can be detected in urine but urinary 3-PBA cannot be used to assess the active dose. The 3-PBA-adduct represents a much more persistent class of biomarkers than metabolites excreted into urine, having half lives up to several weeks or months. We developed an enzyme-linked immunosorbent assay (ELISA) for total 3-PBA including adduct formed after alkaline hydrolysis, liquid-liquid extraction (LLE) and solid phase extraction (SPE) of the sample. The developed ELISA had an IC50 value of 26.7 ng/mL. The intra- and inter-assay coefficients of variation (%CV) were lower than 5% and were within the optimum condition variance (OCV) range. The LLE cleanup technique satisfactorily eliminated the matrix effect from plasma samples before SPE and ELISA analysis yielding good recoveries (85.9–99.4%) with a limit of quantitation (LOQ, 5 ng/mL) that was 30- to 47-fold more sensitive than previous studies. Moreover, the developed method could separate more than 80% of 3-PBA from adduct form. The method was successfully applied to the detection of the target in real samples obtained from consumers (n=50) and farmers (n=50). To our knowledge, this is the first ELISA method for detecting 3-PBA in human plasma and applied to a field study. PMID:23667388

  10. Fibrinolytic Activity and Dose-Dependent Effect of Incubating Human Blood Clots in Caffeic Acid Phenethyl Ester: In Vitro Assays

    PubMed Central

    Elnager, Abuzar; Hassan, Rosline; Idris, Zamzuri; Mustafa, Zulkifli; Wan-Arfah, Nadiah; Sulaiman, S. A.; Gan, Siew Hua; Abdullah, Wan Zaidah

    2015-01-01

    Background. Caffeic acid phenethyl ester (CAPE) has been reported to possess time-dependent fibrinolytic activity by in vitro assay. This study is aimed at investigating fibrinolytic dose-dependent activity of CAPE using in vitro assays. Methods. Standardized human whole blood (WB) clots were incubated in either blank controls or different concentrations of CAPE (3.75, 7.50, 15.00, 22.50, and 30.00 mM). After 3 hours, D-dimer (DD) levels and WB clot weights were measured for each concentration. Thromboelastography (TEG) parameters were recorded following CAPE incubation, and fibrin morphology was examined under a confocal microscope. Results. Overall, mean DD (μg/mL) levels were significantly different across samples incubated with different CAPE concentrations, and the median pre- and postincubation WB clot weights (grams) were significantly decreased for each CAPE concentration. Fibrin removal was observed microscopically and indicated dose-dependent effects. Based on the TEG test, the Ly30 fibrinolytic parameter was significantly different between samples incubated with two different CAPE concentrations (15.0 and 22.50 mM). The 50% effective dose (ED50) of CAPE (based on DD) was 1.99 mg/mL. Conclusions. This study suggests that CAPE possesses fibrinolytic activity following in vitro incubation and that it has dose-dependent activities. Therefore, further investigation into CAPE as a potential alternative thrombolytic agent should be conducted. PMID:25664321

  11. Delineation of the interaction domains of Agrobacterium tumefaciens VirB7 and VirB9 by use of the yeast two-hybrid assay.

    PubMed Central

    Das, A; Anderson, L B; Xie, Y H

    1997-01-01

    The Agrobacterium tumefaciens VirB proteins are postulated to form a transport pore for the transfer of T-DNA. Formation of the transport pore will involve interactions among the VirB proteins. A powerful genetic method to study protein-protein interaction is the yeast two-hybrid assay. To test whether this method can be used to study interactions among the VirB membrane proteins, we studied the interaction of VirB7 and VirB9 in yeast. We recently demonstrated that VirB7 and VirB9 form a protein complex linked by a disulfide bond between cysteine 24 of VirB7 and cysteine 262 of VirB9 (L. Anderson, A. Hertzel, and A. Das, Proc. Natl. Acad. Sci. USA 93:8889-8894, 1996). We now demonstrate that VirB7 and VirB9 interact in yeast, and this interaction does not require the cysteine residues essential for the disulfide linkage. By using defined segments in fusion constructions, we mapped the VirB7 interaction domain of VirB9 to residues 173 to 275. In tumor formation assays, both virB7C24S and virB9C262S expressed from a multicopy plasmid complemented the respective deletion mutation, indicating that the cysteine residues may not be essential for DNA transfer. PMID:9171381

  12. Development of a lead-acid battery for a hybrid electric vehicle

    NASA Astrophysics Data System (ADS)

    Cooper, A.

    In September 2000, a project reliable, highly optimized lead-acid battery (RHOLAB) started under the UK Foresight Vehicle Programme with the objective of developing an optimized lead-acid battery solution for hybrid electric vehicles. The work is based on a novel, individual, spirally-wound valve-regulated lead-acid 2 V cell optimized for HEV use and low variability. This cell is being used as a building block for the development of a complete battery pack that is managed at the cell level. Following bench testing, this battery pack is to be thoroughly evaluated by substituting it for the Ni-MH pack in a Honda Insight. The RHOLAB cell is based on the 8 Ah Hawker Cyclon cell which has been modified to have current take-off at both ends—the dual-tab design. In addition, a variant has been produced with modified cell chemistry to help deal with problems that can occur when these valve-regulated lead-acid battery (VRLA) cells operate in a partial-state-of-charge condition. The cells have been cycled to a specially formulated test cycle based on real vehicle data derived from testing the Honda Insight on the various test tracks at the Millbrook Proving Grounds in the UK. These cycling tests have shown that the lead-acid pack can be successfully cycled when subjected to the high current demands from the vehicle, which have been measured at up to 15 C on discharge and 8 C during regenerative recharging, and cycle life is looking very promising under this arduous test regime. Concurrent with this work, battery development has been taking place. It was decided early on to develop the 144 V battery as four 36 V modules. Data collection and control has been built-in and special steps taken to minimize the problems of interconnect in this complex system. Development of the battery modules is now at an advanced stage. The project plan then allows for extensive testing of the vehicle with its lead-acid battery at Millbrook so it can be compared with the benchmark tests which

  13. Preparation and Electrochemical Performance of Hybrid Materials Containing Heteropoly Acid with Dawson Structure and Polymers

    NASA Astrophysics Data System (ADS)

    Tong, Xia; Wu, Wen; Zhou, Shengming; Wu, Qingyin; Cao, Fahe; Yaroslavtsev, A. B.

    2012-11-01

    Highly proton-conducting hybrid materials (P2W17V/PEG and P2W17V/PEG/SiO2) were prepared by heptadecatungstovanadodiphosphoric heteropoly acid with Dawson structure (P2W17V, 90 wt.%), polyethylene glycol (PEG, 10 wt.% and 5 wt.%) and silica gel (SiO2, 0 wt.% and 5 wt.%). The products were characterized by the infrared (IR) spectrum, X-ray powder diffraction (XRD) analysis and electrochemical impedance spectrum (EIS). The result reveals that their conductivity values are 1.02 × 10-2 and 2.58 × 10-2S ṡ cm-1 at room temperature (26°C) and 75% relative humidity (RH), respectively. Their conductivities increase with higher temperature and these activation energies of proton conduction are 9.51 and 14.95 kJṡmol-1, which are lower than that of pure heteropoly acid (32.23 kJṡmol-1). These mechanisms of proton conduction for these two materials are Grotthuss mechanism.

  14. Development of Five Dual-Color, Double-Fusion Fluorescence in Situ Hybridization Assays for the Detection of Common MLL Translocation Partners

    PubMed Central

    Keefe, Jeannette G.; Sukov, William R.; Knudson, Ryan A.; Nguyen, Lai P.; Williamson, Cynthia; Sinnwell, Jason P.; Ketterling, Rhett P.

    2010-01-01

    Chromosomal rearrangements involving the mixed lineage leukemia (MLL) gene at 11q23 are frequent in adult and childhood acute leukemia and have been associated with an unfavorable prognosis. Recent evidence suggests that MLL gene partners may influence prognosis. Five translocations account for ∼80% of MLL rearrangements: t(4;11)(q21;q23), AFF1/MLL; t(6;11)(q27;q23), MLLT4/MLL; t(9;11)(p22;q23), MLLT3/MLL; t(11;19)(q23;p13.1), MLL/ELL; and t(11;19)(q23;p13.3), MLL/MLLT1. We have designed dual-color, double-fusion fluorescence in situ hybridization (D-FISH) probe sets to identify these translocations. A blinded study was performed for each probe set using 25 normal bone marrow samples, 25 t(4;11), 20 t(6;11), 20 t(9;11), 18 t(11;19p13.1), and 20 t(11;19p13.3) leukemia specimens as defined by chromosome analysis. The findings demonstrated abnormal D-FISH results for 24 of 25 AFF1/MLL, 19 of 20 MLLT4/MLL, all 20 MLLT3/MLL, all 18 MLL/ELL, and all 20 MLL/MLLT1 samples, confirming the efficacy of these D-FISH assays in detecting these common MLL/partner translocations. Our D-FISH assays were more accurate than chromosome analysis at distinguishing disruption of 19p13.1/ELL from that of 19p13.3/MLLT1. We also demonstrated a statistically significant increase in complex/unbalanced MLL/partner translocations occurring in pediatric patients versus adult patients (P = 0.02). A normal cutoff of 0.6% was established, suggesting an application for these assays in minimal residual disease detection and disease monitoring. PMID:20539022

  15. Mapping the Distribution of Cysts from the Toxic Dinoflagellate Cochlodinium polykrikoides in Bloom-Prone Estuaries by a Novel Fluorescence In Situ Hybridization Assay

    PubMed Central

    Hattenrath-Lehmann, Theresa K.; Zhen, Yu; Wallace, Ryan B.

    2015-01-01

    Cochlodinium polykrikoides is a cosmopolitan dinoflagellate that is notorious for causing fish-killing harmful algal blooms (HABs) across North America and Asia. While recent laboratory and ecosystem studies have definitively demonstrated that Cochlodinium forms resting cysts that may play a key role in the dynamics of its HABs, uncertainties regarding cyst morphology and detection have prohibited even a rudimentary understanding of the distribution of C. polykrikoides cysts in coastal ecosystems. Here, we report on the development of a fluorescence in situ hybridization (FISH) assay using oligonucleotide probes specific for the large subunit (LSU) ribosomal DNA (rDNA) of C. polykrikoides. The LSU rDNA-targeted FISH assay was used with epifluorescence microscopy and was iteratively refined to maximize the fluorescent reaction with C. polykrikoides and minimize cross-reactivity. The final LSU rDNA-targeted FISH assay was found to quantitatively recover cysts made by North American isolates of C. polykrikoides but not cysts formed by other common cyst-forming dinoflagellates. The method was then applied to identify and map C. polykrikoides cysts across bloom-prone estuaries. Annual cyst and vegetative cell surveys revealed that elevated densities of C. polykrikoides cysts (>100 cm−3) during the spring of a given year were spatially consistent with regions of dense blooms the prior summer. The identity of cysts in sediments was confirmed via independent amplification of C. polykrikoides rDNA. This study mapped C. polykrikoides cysts in a natural marine setting and indicates that the excystment of cysts formed by this harmful alga may play a key role in the development of HABs of this species. PMID:26637596

  16. Mapping the Distribution of Cysts from the Toxic Dinoflagellate Cochlodinium polykrikoides in Bloom-Prone Estuaries by a Novel Fluorescence In Situ Hybridization Assay.

    PubMed

    Hattenrath-Lehmann, Theresa K; Zhen, Yu; Wallace, Ryan B; Tang, Ying-Zhong; Gobler, Christopher J

    2015-01-01

    Cochlodinium polykrikoides is a cosmopolitan dinoflagellate that is notorious for causing fish-killing harmful algal blooms (HABs) across North America and Asia. While recent laboratory and ecosystem studies have definitively demonstrated that Cochlodinium forms resting cysts that may play a key role in the dynamics of its HABs, uncertainties regarding cyst morphology and detection have prohibited even a rudimentary understanding of the distribution of C. polykrikoides cysts in coastal ecosystems. Here, we report on the development of a fluorescence in situ hybridization (FISH) assay using oligonucleotide probes specific for the large subunit (LSU) ribosomal DNA (rDNA) of C. polykrikoides. The LSU rDNA-targeted FISH assay was used with epifluorescence microscopy and was iteratively refined to maximize the fluorescent reaction with C. polykrikoides and minimize cross-reactivity. The final LSU rDNA-targeted FISH assay was found to quantitatively recover cysts made by North American isolates of C. polykrikoides but not cysts formed by other common cyst-forming dinoflagellates. The method was then applied to identify and map C. polykrikoides cysts across bloom-prone estuaries. Annual cyst and vegetative cell surveys revealed that elevated densities of C. polykrikoides cysts (>100 cm(-3)) during the spring of a given year were spatially consistent with regions of dense blooms the prior summer. The identity of cysts in sediments was confirmed via independent amplification of C. polykrikoides rDNA. This study mapped C. polykrikoides cysts in a natural marine setting and indicates that the excystment of cysts formed by this harmful alga may play a key role in the development of HABs of this species. PMID:26637596

  17. Exploring the Hybridization Thermodynamics of Spherical Nucleic Acids to Tailor Probes for Diagnostic and Therapeutic Applications

    NASA Astrophysics Data System (ADS)

    Randeria, Pratik Shailesh

    Spherical nucleic acids (SNAs), three-dimensional nanoparticle conjugates composed of densely packed and highly oriented oligonucleotides around organic or inorganic nanoparticles, are an emergent class of nanostructures that show promise as single-entity agents for intracellular messenger RNA (mRNA) detection and gene regulation. SNAs exhibit superior biocompatibility and biological properties compared to linear oligonucleotides, enabling them to overcome many of the limitations of linear oligonucleotides for use in biomedical applications. However, the origins of these biologically attractive properties are not well understood. In this dissertation, the chemistry underlying one such property is studied in detail, and the findings are applied towards the rational design of more effective SNAs for diagnostic and therapeutic applications. Chapter 1 introduces the synthesis of SNAs, the unique properties that make them superior to linear nucleic acids for biomedicine, and previously studied applications of these structures. Chapter 2 focuses on quantitatively studying the impact of the chemical structure of the SNA on its ability to hybridize multiple complementary nucleic acids. This chapter lays the groundwork for understanding the factors that govern SNA hybridization thermodynamics and how to tailor SNAs to increase their binding affinity to target mRNA strands. Chapters 3 and 4 capitalize on this knowledge to engineer probes for intracellular mRNA detection and gene regulation applications. Chapter 3 reports the development of an SNA-based probe that can simultaneously report the expression level of two different mRNA transcripts in live cells and differentiate diseased cells from non-diseased cells. Chapter 4 investigates the use of topically-applied SNAs to down-regulate a critical mediator of impaired wound healing in diabetic mice to accelerate wound closure. This study represents the first topical therapeutic application of SNA nanotechnology to treat open

  18. THE EFFECT OF ANOLYTE PRODUCT ACID CONCENTRATION ON HYBRID SULFUR CYCLE PERFORMANCE

    SciTech Connect

    Gorensek, M.; Summers, W.

    2010-03-24

    The Hybrid Sulfur (HyS) cycle (Fig. 1) is one of the simplest, all-fluids thermochemical cycles that has been devised for splitting water with a high-temperature nuclear or solar heat source. It was originally patented by Brecher and Wu in 1975 and extensively developed by Westinghouse in the late 1970s and early 1980s. As its name suggests, the only element used besides hydrogen and oxygen is sulfur, which is cycled between the +4 and +6 oxidation states. HyS comprises two steps. One is the thermochemical (>800 C) decomposition of sulfuric acid (H{sub 2}SO{sub 4}) to sulfur dioxide (SO{sub 2}), oxygen (O{sub 2}), and water. H{sub 2}SO{sub 4} = SO{sub 2} + 1/2 O{sub 2} + H{sub 2}O. The other is the SO{sub 2}-depolarized electrolysis of water to H{sub 2}SO{sub 4} and hydrogen (H{sub 2}), SO{sub 2} + 2 H{sub 2}O = H{sub 2}SO{sub 4} + H{sub 2}, E{sup o} = -0.156 V, explaining the 'hybrid' designation. These two steps taken together split water into H{sub 2} and O{sub 2} using heat and electricity. Researchers at the Savannah River National Laboratory (SRNL) and at the University of South Carolina (USC) have successfully demonstrated the use of proton exchange membrane (PEM) electrolyzers (Fig. 2) for the SO{sub 2}-depolarized electrolysis (sulfur oxidation) step, while Sandia National Laboratories (SNL) successfully demonstrated the high-temperature sulfuric acid decomposition (sulfur reduction) step using a bayonet-type reactor (Fig. 3). This latter work was performed as part of the Sulfur-Iodine (SI) cycle Integrated Laboratory Scale demonstration at General Atomics (GA). The combination of these two operations results in a simple process that will be more efficient and cost-effective for the massive production of hydrogen than alkaline electrolysis. Recent developments suggest that the use of PEMs other than Nafion will allow sulfuric acid to be produced at higher concentrations (>60 wt%), offering the possibility of net thermal efficiencies around 50% (HHV basis

  19. Synthesis and utilization of chitin humic acid hybrid as sorbent for Cr(III)

    NASA Astrophysics Data System (ADS)

    Santosa, Sri Juari; Siswanta, Dwi; Sudiono, Sri; Sehol, Muhamad

    2007-11-01

    New types of hybrid material have been synthesized by using four different methods of immobilization of humic acid (HA) on chitin. The most stable hybrid material toward the change of medium acidity was then utilized as sorbent for Cr(III). The HA was extracted from peat soil of Gambut District, South Kalimantan, Indonesia, using the recommended procedure of International Humic Substances Society (IHSS), while the chitin was isolated from crab shell waste through deproteination using 3.5% (w/v) NaOH and followed by removal of inorganic impurities using 1 M HCl. The four methods of immobilization of HA on chitin were (i) Method A: chitin powder (4 g) was gently poured into the stirred solution of 0.4 g HA in 40 mL of 0.01 M NaOH. After overnight stirring, the solid was separated, washed with water, and dried in oven at 70 °C. (ii) Method B: gelatinous chitin (40 g) in 250 mL of 0.5 M HCl was reacted with HA (4 g) in 500 mL of 0.5 M NaOH and aged for 24 h. The product was washed with water and dried. (iii) Method C: HA powder (0.5 g) was mixed with the stirred gel of chitin (2.5 g) in 60 mL of CaCl 2 saturated methanol and the mixture was then washed with the mixed solution of 25 mL of 2 M sodium citrate and ethylene glycol 1:1. The solid was separated, washed with water, and dried. (iv) Method D: the solution of HA (0.056 g) in 10 mL of 0.01 M NaOH was reacted with the gel of chitin (0.2 g) in 10 mL of CaCl 2 saturated methanol. After 24 h stirring, the solid was separated from the reaction medium, washed with the mixed solution of 2 M sodium citrate and ethylene glycol 1:1, and followed by washing with water and drying. Parameters investigated in this study consisted of the stability test of the immobilized HA, as well as the rate constant ( k1), capacity ( b), and energy ( E) of sorption as well as the rate constant of desorption ( k-1). The k1 and k-1 were determined according to a kinetic model of first order sorption reaching equilibrium, while the b and E

  20. Organic-inorganic hybrid proton exchange membranes based on silicon-containing polyacrylate nanoparticles with phosphotungstic acid

    NASA Astrophysics Data System (ADS)

    Cui, Xuejun; Zhong, Shuangling; Wang, Hongyan

    A series of silicon-containing polyacrylate nanoparticles (SiPANPs) were successfully synthesized by simple emulsifier-free emulsion polymerization technique. The resulting latex particles were characterized by Fourier transform infrared (FTIR) spectrometry, dynamic light scattering (DLS) analysis, thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The SiPANP membranes and SiPANP/phosphotungstic acid (SiPANP/PWA) hybrid membranes were also prepared and characterized to evaluate their potential as proton exchange membranes in proton exchange membrane fuel cell (PEMFC). Compared with the pure SiPANP membrane, the hybrid membranes displayed lower thermal stability. However, the degradation temperatures were still above 190 °C, satisfying the requirement of thermal stability for PEMFC operation. In addition, the hybrid membranes showed lower water uptake but higher proton conductivity than the SiPANP precursor. The proton conductivity of the hybrid membranes was in the range of 10 -3 to 10 -2 S cm -1 and increased gradually with PWA content and temperature. The excellent hydrolytic stability was also observed in the hybrid membranes because of the existence of crosslinked silica network. The good thermal stability, reasonable water uptake, excellent hydrolytic stability, suitable proton conductivity and cost effectiveness make these hybrids quite attractive as proton exchange membranes for PEMFC applications.

  1. Cationic liposome-hyaluronic acid hybrid nanoparticles for intranasal vaccination with subunit antigens

    PubMed Central

    Ochyl, Lukasz J.; Akerberg, Jonathan; Moon, James J.

    2015-01-01

    Here we report the development of a new cationic liposome-hyaluronic acid (HA) hybrid nanoparticle (NP) system and present our characterization of these NPs as an intranasal vaccine platform using a model antigen and F1-V, a candidate recombinant antigen for Yersinia pestis, the causative agent of plague. Incubation of cationic liposomes composed of DOTAP and DOPE with anionic HA biopolymer led to efficient ionic complexation and formation of homogenous liposome-polymer hybrid NPs, as evidenced by fluorescence resonance energy transfer, dynamic light scattering, and nanoparticle tracking analyses. Incorporation of cationic liposomes with thiolated HA allowed for facile surface decoration of NPs with thiol-PEG, resulting in the formation of DOTAP/HA core-PEG shell nanostructures. These NPs, termed DOTAP-HA NPs, exhibited improved colloidal stability and prolonged antigen release. In addition, cytotoxicity associated with DOTAP liposomes (LC50 ~0.2 mg/ml) was significantly reduced by at least 20-fold with DOTAP-HA NPs (LC50 > 4 mg/ml), as measured with bone marrow dendritic cells (BMDCs). Furthermore, NPs co-loaded with ovalbumin (OVA) and a molecular adjuvant, monophosphoryl lipid A (MPLA) promoted BMDC maturation and upregulation of co-stimulatory markers, including CD40, CD86, and MHC-II, and C57BL/6 mice vaccinated with NPs via intranasal route generated robust OVA-specific CD8+ T cell and antibody responses. Importantly, intranasal vaccination with NPs co-loaded with F1-V and MPLA induced potent humoral immune responses with 11-, 23-, and 15-fold increases in F1-V-specific total IgG, IgG1, and IgG2c titers in immune sera by day 77, respectively, and induced balanced Th1/Th2 humoral immune responses, compared with the lack of sero-conversion in mice immunized with the equivalent doses of soluble F1-V vaccine. Overall, these results suggest that liposome-polymer hybrid NPs may serve as a promising vaccine delivery platform for intranasal vaccination against Y

  2. Cationic liposome-hyaluronic acid hybrid nanoparticles for intranasal vaccination with subunit antigens.

    PubMed

    Fan, Yuchen; Sahdev, Preety; Ochyl, Lukasz J; J Akerberg, Jonathan; Moon, James J

    2015-06-28

    Here we report the development of a new cationic liposome-hyaluronic acid (HA) hybrid nanoparticle (NP) system and present our characterization of these NPs as an intranasal vaccine platform using a model antigen and F1-V, a candidate recombinant antigen for Yersinia pestis, the causative agent of plague. Incubation of cationic liposomes composed of DOTAP and DOPE with anionic HA biopolymer led to efficient ionic complexation and formation of homogenous liposome-polymer hybrid NPs, as evidenced by fluorescence resonance energy transfer, dynamic light scattering, and nanoparticle tracking analyses. Incorporation of cationic liposomes with thiolated HA allowed for facile surface decoration of NPs with thiol-PEG, resulting in the formation of DOTAP/HA core-PEG shell nanostructures. These NPs, termed DOTAP-HA NPs, exhibited improved colloidal stability and prolonged antigen release. In addition, cytotoxicity associated with DOTAP liposomes (LC50~0.2mg/ml) was significantly reduced by at least 20-fold with DOTAP-HA NPs (LC50>4mg/ml), as measured with bone marrow derived dendritic cells (BMDCs). Furthermore, NPs co-loaded with ovalbumin (OVA) and a molecular adjuvant, monophosphoryl lipid A (MPLA) promoted BMDC maturation and upregulation of co-stimulatory markers, including CD40, CD86, and MHC-II, and C57BL/6 mice vaccinated with NPs via intranasal route generated robust OVA-specific CD8(+) T cell and antibody responses. Importantly, intranasal vaccination with NPs co-loaded with F1-V and MPLA induced potent humoral immune responses with 11-, 23-, and 15-fold increases in F1-V-specific total IgG, IgG1, and IgG2c titers in immune sera by day 77, respectively, and induced balanced Th1/Th2 humoral immune responses, whereas mice immunized with the equivalent doses of soluble F1-V vaccine failed to achieve sero-conversion. Overall, these results suggest that liposome-polymer hybrid NPs may serve as a promising vaccine delivery platform for intranasal vaccination against Y

  3. Hybrid hyaluronic acid hydrogel/poly(ɛ-caprolactone) scaffold provides mechanically favorable platform for cartilage tissue engineering studies.

    PubMed

    Mintz, Benjamin R; Cooper, James A

    2014-09-01

    Hybrid scaffolds for cartilage tissue engineering provide the potential for high stiffness properties in tension and compression while exhibiting the viscoelastic response found in hydrogels and native cartilage tissue. We investigate the impact of a hybrid scaffold fabricated from a hyaluronic acid (HA)-based hydrogel combined with porous poly(ε-caprolactone) (PCL) material formed by a particulate leaching method to study dedifferentiated chondrocyte response. The material properties of the hybrid scaffold showed mean Young's moduli in tension which were similar to human articular cartilage but not statistically different between the hybrid and porous PCL scaffolds at 2.02 and 2.07 MPa, respectively. For both the hybrid and porous PCL control scaffolds in compression at low loading frequencies (<1 Hz) and 10% strain peak amplitude the Young's moduli are not statistically distinct. However, at frequencies in the range of normal human gait from 1 to2 Hz, hybrid scaffolds exhibit significantly (p < 0.01) increased loss moduli indicating additional contribution of the viscous phase to stiffness. Dedifferentiated chondrocytes seeded onto the scaffolds exhibited a rounded morphology in hybrid scaffolds however ECM protein expression levels of collagen type I, collagen type II, and aggrecan are not different from the PCL control scaffolds. These results provide a model platform to investigate cell response to mechanical and chemical cues in a hybrid scaffold system with mechanical properties similar to human cartilage that does not contribute to differentiation in order to identify the appropriate design and development parameters to promote formation of extracellular matrix and investigate chondrocyte scaffold interactions. PMID:24115629

  4. Development of a monoclonal antibody against domoic acid and its application in enzyme-linked immunosorbent assay and colloidal gold immunostrip.

    PubMed

    Tsao, Zih-Jay; Liao, Yi-Chun; Liu, Biing-Hui; Su, Ching-Chyuan; Yu, Feng-Yih

    2007-06-27

    A monoclonal antibody (mAb) specific to domoic acid was produced from a stable hybridoma cell line, 9F1F11, generated by the fusion of P3/NS1/1-AG4-1 myeloma cells with spleen cells isolated from a Balb/c mouse immunized with domoic acid--keyhole limpet hemocyanin. The 9F1F11 mAb belongs to the immunoglobulin G1 (kappa-chain) isotype. A competitive direct enzyme-linked immunosorbent assay (cdELISA) and a competitive indirect ELISA were established for antibody characterization. In the cdELISA, the concentration causing 50% inhibition (IC50) of binding of domoic acid-horseradish peroxidase to the antibody by domoic acid was found to be 0.58 ng/mL. A sensitive and rapid mAb-based colloidal gold immunostrip was also developed. The immunostrip assay, which has a detection limit of 5 ng/mL for domoic acid, can be completed in 10 min. Analysis of domoic acid in blue mussel samples revealed that data obtained from immunostrip were in a good agreement with those obtained from cdELISA. The mAb-based cdELISA and immunostrip assay established in this study were sensitive and accurate for rapid screening of domoic acid in shellfish samples. PMID:17542614

  5. A continuous fluorescence displacement assay for the measurement of phospholipase A2 and other lipases that release long-chain fatty acids.

    PubMed Central

    Wilton, D C

    1990-01-01

    1. A new continuous fluorescence assay for phospholipase A2 is described which involves the displacement of the highly fluorescent fatty-acid probe 11-(dansylamino)undecanoic acid from rat liver fatty-acid-binding protein by long-chain fatty acids released as a result of phospholipase A2-catalysed hydrolysis of phospholipids. The initial rate of decrease in fluorescence is linearly related to enzyme activity. 2. The assay will detect enzyme activity down to about 10 pmol/min per ml and gives a linear response up to about 10 nmol/min per ml. 3. The assay will work with all phospholipids that have been tested including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol and phosphatidylglycerol. Substrates carrying a net negative charge showed the highest rates of hydrolysis. 4. The assay will work, in principle, with an enzyme catalysing the release of long-chain fatty acids from a fatty-acylated substrate. This has been confirmed with pancreatic lipase and cholesterol esterase. PMID:2317197

  6. Hybrid of chitin and humic acid as high performance sorbent for Ni(II)

    NASA Astrophysics Data System (ADS)

    Santosa, Sri Juari; Siswanta, Dwi; Kurniawan, Agusta; Rahmanto, Wasino H.

    2007-11-01

    Hybrid of humic acid (HA) and chitin has been synthesized and the hybrid material (chitin-HA) was then applied as sorbent to adsorb Ni(II). The HA was extracted from peat soil of Gambut District, South Kalimantan, Indonesia, according to the procedure recommended by IHSS (International Humic Substances Society). The chitin was isolated from crab shell waste of sea food restaurants through deproteination using NaOH 3.5% (w/v) and followed by removal of inorganic impurities using HCl 1 M. The synthesis of chitin-HA was performed by reacting gelatinous chitin solution in HCl 0.5 M and HA solution in NaOH 0.5 M. Parameters investigated in this work consists of effect of medium acidity on the sorption, sorption rate ( ks) and desorption rate ( kd) constants, Langmuir (monolayer) and Freundlich (multilayer) sorption capacities, and energy ( E) of sorption. The ks and kd were determined according to a kinetic model of first order sorption reaching equilibrium, monolayer sorption capacity ( b) and energy ( E) were determined according to the Langmuir isotherm model, and multilayer sorption capacity ( B) was determined based on the Freundlich isotherm model. Sorption of Ni(II) on both chitin and chitin-HA was maximum at pH 8.0. The kinetic expression resulted from the proposed kinetic model has been shown to be more applicable than the commonly known Lagergren equation obtained from the pseudo-first order sorption model. The application of the proposed model revealed that the presence of HA increased the ks from 0.018 min -1 for chitin to 0.031 min -1 for chitin-HA. As for ks, the value of b was also bigger in the presence of HA, i.e. 7.42 × 10 -5 mol/g for chitin and 9.93 × 10 -5 mol/g for the chitin-HA. Unlike ks and b, the value of E slightly decreased from 23.23 to 21.51 kJ/mol for the absence and presence of HA, respectively. It can also be deduced that the presence of HA on chitin contributed more to the additional layer of Ni(II) sorbed on sorbent. Without HA, B

  7. A direct assay of carboxyl-containing small molecules by SALDI-MS on a AgNP/rGO-based nanoporous hybrid film.

    PubMed

    Hong, Min; Xu, Lidan; Wang, Fangli; Geng, Zhirong; Li, Haibo; Wang, Huaisheng; Li, Chen-Zhong

    2016-04-25

    Silver nanoparticles (AgNPs) and reduced graphene oxide (rGO) hybrid nanoporous structures fabricated by the layer-by-layer (LBL) electrostatic self-assembly have been applied as a simple platform for the rapid analysis of carboxyl-containing small molecules by surface-assisted laser desorption/ionization (D/I) mass spectrometry (SALDI-MS). By the simple one-step deposition of analytes onto the (AgNP/rGO)9 multilayer film, the MS measurements of various carboxyl-containing small molecules (including amino acids, fatty acids and organic dicarboxylic acids) can be done. In contrast to other energy transfer materials relative to AgNPs, the signal interferences of a Ag cluster (Agn(+) or Agn(-)) and a C cluster (Cn(+) or Cn(-)) have been effectively reduced or eliminated. The effects of various factors, such as the pore structure and composition of the substrates, on the efficiency of D/I have been investigated by comparing with the (AgNP)9 LBL nanoporous structure, (AgNP/rGO)9/(SiO2NP)6 LBL multilayer film and AgNP/prGO nanocomposites. PMID:26739438

  8. Silylated melamine and cyanuric acid as precursors for imprinted and hybrid silica materials with molecular recognition properties.

    PubMed

    Arrachart, Guilhem; Carcel, Carole; Trens, Philippe; Moreau, Jöel J E; Wong Chi Man, Michel

    2009-06-15

    Two monotrialkoxysilylated compounds that consist of complementary fragments of melamine (M) and cyanuric acid (CA) have been synthesised. The molecular recognition properties of the M and CA fragments through complementary hydrogen bonds (DAD and ADA; D=donor, A=acceptor) are the key factor used to direct the formation of hybrid silica materials by using a sol-gel process. These materials were synthesised following two methods: First, an organo-bridged silsesquioxane was obtained by the hydrolysis of the two complementary monotrialkoxysilylated melamine and cyanuric acid derivatives, with fluoride ions as a catalyst. The hydrogen-bonding interactions between the two organic fragments are responsible for the formation of the bridging unit. The transcription of the assembly into the hybrid material was characterised and evidenced by solid-state NMR (29Si, 13C) and FTIR spectroscopic experiments. Second, the molecular recognition was exploited to synthesise an imprinted hybrid silica. This material was prepared by co-condensation of tetraethyl orthosilicate (TEOS) with the monosilylated cyanuric acid derivative (CA) templated by nonsilylated melamine. The melamine template was completely removed by treating the solid material with hydrochloric acid. The reintroduction of the template was performed by treating the resulting material with an aqueous suspension of melamine. These steps were monitored and analysed by several techniques, such as solid-state NMR (29Si, 13C) and FTIR spectroscopic analysis and nitrogen adsorption-desorption isotherms. PMID:19440996

  9. Development of in situ hybridization and PCR assays for the detection of Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp.

    PubMed

    Tang, Kathy F J; Pantoja, Carlos R; Redman, Rita M; Han, Jee Eun; Tran, Loc H; Lightner, Donald V

    2015-09-01

    A microsporidian parasite, Enterocytozoon hepatopenaei (abbreviated as EHP), is an emerging pathogen for penaeid shrimp. EHP has been found in several shrimp farming countries in Asia including Vietnam, Thailand, Malaysia, Indonesia and China, and is reported to be associated with growth retardation in farmed shrimp. We examined the histological features from infected shrimp collected from Vietnam and Brunei, these include the presence of basophilic inclusions in the hepatopancreas tubule epithelial cells, in which EHP is found at various developmental stages, ranging from plasmodia to mature spores. By a PCR targeting the 18S rRNA gene, a 1.1kb 18S rRNA gene fragment of EHP was amplified, and this sequence showed a 100% identity to EHP found in Thailand and China. This fragment was cloned and labeled with digoxigenin-11-dUTP, and in situ hybridized to tissue sections of infected Penaeus vannamei (from Vietnam) and P. stylirostris (Brunei). The results of in situ hybridization were specific, the probe only reacted to the EHP within the cytoplasmic inclusions, not to a Pleistophora-like microsporidium that is associated with cotton shrimp disease. Subsequently, we developed a PCR assay from this 18S rRNA gene region, this PCR is shown to be specific to EHP, did not react to 2 other parasitic pathogens, an amoeba and the cotton shrimp disease microsporidium, nor to genomic DNA of various crustaceans including polychaetes, squids, crabs and krill. EHP was detected, through PCR, in hepatopancreatic tissue, feces and water sampled from infected shrimp tanks, and in some samples of Artemia biomass. PMID:26146228

  10. High-Speed Microdialysis-Capillary Electrophoresis Assays for Measuring Branched Chain Amino Acid Uptake in 3T3-L1 cells.

    PubMed

    Harstad, Rachel K; Bowser, Michael T

    2016-08-16

    We have developed a high-throughput microdialysis-capillary electrophoresis (MD-CE) assay for monitoring branched chain amino acid (BCAA) uptake/release dynamics in 3T3-L1 cells. BCAAs (i.e., isoleucine, leucine, and valine) and their downstream metabolites (i.e., alanine, glutamine, and glutamate) are important indicators of adipocyte lipogenesis. To perform an analysis, amino acids were sampled using microdialysis, fluorescently labeled in an online reaction, separated using CE, and detected using laser-induced fluorescence (LIF) in a sheath flow cuvette. Separation conditions were optimized for the resolution of the BCAAs isoleucine, leucine, and valine, as well as 13 other amino acids, including ornithine, alanine, glutamine, and glutamate. CE separations were performed in <30 s, and the temporal resolution of the online MD-CE assay was <60 s. Limits of detection (LOD) were 400, 200, and 100 nM for isoleucine, leucine, and valine, respectively. MD-CE dramatically improved throughput in comparison to traditional offline CE methods, allowing 8 replicates of 15 samples (i.e., 120 analyses) to be assayed in <120 min. The MD-CE assay was used to assess the metabolism dynamics of 3T3-L1 cells over time, confirming the utility of the assay. PMID:27398773

  11. Comparison of gene expression regulation in mouse- and human embryonic stem cell assays during neural differentiation and in response to valproic acid exposure.

    PubMed

    Schulpen, Sjors H W; Theunissen, Peter T; Pennings, Jeroen L A; Piersma, Aldert H

    2015-08-15

    Embryonic stem cell tests (EST) are considered promising alternative assays for developmental toxicity testing. Classical mouse derived assays (mEST) are being replaced by human derived assays (hEST), in view of their relevance for human hazard assessment. We have compared mouse and human neural ESTn assays for neurodevelopmental toxicity as to regulation of gene expression during cell differentiation in both assays. Commonalities were observed in a range of neurodevelopmental genes and gene ontology (GO) terms. The mESTn showed a higher specificity in neurodevelopment than the hESTn, which may in part be caused by necessary differences in test protocols. Moreover, gene expression responses to the anticonvulsant and human teratogen valproic acid were compared. Both assays detected pharmacological and neurodevelopmental gene sets regulated by valproic acid. Common significant expression changes were observed in a subset of homologous neurodevelopmental genes. We suggest that these genes and related GO terms may provide good candidates for robust biomarkers of neurodevelopmental toxicity in hESTn. PMID:26072468

  12. Development of a scintillation proximity assay for the Mycobacterium tuberculosis KasA and KasB enzymes involved in mycolic acid biosynthesis.

    PubMed

    Schaeffer, M L Merrill L; Carson, J D Jeffrey D; Kallender, Howard; Lonsdale, J T John T

    2004-01-01

    Tuberculosis remains a global health problem, and programs dedicated to discovery of novel compounds against Mycobacterium tuberculosis require robust assays for high-throughput screening of chemical and natural product libraries. Enzymes involved in the biosynthesis of mycolic acids, vital components of the mycobacterial cell wall, have received much attention as potential drug targets. KasA and KasB, examples of the beta-ketoacyl-acyl carrier protein synthase I/II (KASI/II) class of condensing enzymes of the M. tuberculosis fatty acid synthase II system have been the focus of several studies designed to biochemically characterize these enzymes. Whilst robust methods have been developed for FabH-like proteins, fast and sensitive assays for high-throughput screening of KASI/II enzymes have not been available. Here we report the development of a direct scintillation proximity assay (SPA) for the KASI/II enzymes, KasA and KasB. The SPA was more sensitive than existing assays, as shown by its ability to measure activity using less enzyme than other assay formats, and the SPA was validated using the known KAS inhibitor thiolactomycin. In addition, the KasA and KasB SPA was adapted for use with Staphylococcus aureus FabF to show the versatility of this assay format to KAS enzymes from other pathogenic organisms. PMID:15525558

  13. Evaluation of the Punch-it™ NA-Sample kit for detecting microbial DNA in blood culture bottles using PCR-reverse blot hybridization assay.

    PubMed

    Kim, Jungho; Wang, Hye-Young; Kim, Seoyong; Park, Soon Deok; Yu, Kwangmin; Kim, Hyo Youl; Uh, Young; Lee, Hyeyoung

    2016-09-01

    DNA extraction efficiency affects the success of PCR-based method applications. The Punch-it™ NA-Sample kit for extracting DNA by using paper chromatography is technically easy to use and requires just two reagents and only 10min to complete. The Punch-it™ NA-Sample kit could be offered as a rapid, accurate, and convenient method for extracting bacterial and fungal DNA from blood culture bottles. We compared the efficiencies of the commercial kit (Punch-it™ NA-Sample kit) and an in-house conventional boiling method with Chelex-100 resin for DNA extraction from blood culture bottles. The efficiency of the two DNA extraction methods was assessed by PCR-reverse blot hybridization assay (PCR-REBA, REBA Sepsis-ID) for detecting Gram positive (GP) bacteria, Gram negative (GN) bacteria, and Candida species with 196 positive and 200 negative blood culture bottles. The detection limits of the two DNA extraction methods were 10(3)CFU/mL for GP bacteria, 10(3)CFU/mL for GN bacteria, and 10(4)CFU/mL for Candida. The sensitivity and specificity of the Punch-it™ NA-Sample kit by REBA Sepsis-ID were 95.4% (187/196) and 100% (200/200), respectively. The overall agreement of the two DNA extraction methods was 98.9% (392/396). Three of four samples showing discrepant results between the two extraction methods were more accurately matched up with the Punch-it™ NA-Sample kit based on conventional culture methods. The results indicated that the Punch-it™ NA-Sample kit extracted bacterial and fungal DNA in blood culture bottles and allowed extracted DNA to be used in molecular assay. PMID:27263831

  14. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method

    PubMed Central

    Machado, António; Castro, Joana; Cereija, Tatiana; Almeida, Carina

    2015-01-01

    Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6–99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis. PMID:25737820

  15. Material balance studies with continuous SSF for ethanol production using dilute-acid pretreated hybrid popular

    SciTech Connect

    Kadam, K.L.; Hayward, T.K.; Philippidis, G.P.

    1995-10-01

    Simultaneous saccharification and fermentation (SSF) is a leading process option for converting lignocellulosic biomass to ethanol. Economic industrial production of ethanol by SSF would likely require a continuous mode of operation, and development of a database on continuous SSF using industrial substrates is essential. To this end, a single-stage continuous SSF system was designed and used for studying ethanol production by Saccharomyces cerevisiae strain D{sub 5}A with dilute-acid preheated hybrid poplar as substrate. Material balance studies were conducted using the bench-scale system; the objectives of these studies were to gain insight into how the cells allocate carbon and to account for all the substrate flowing through the system. It was possible to close the total mass and carbon balances with {+-}3% accuracy, which is within the limits of experimental error. In a typical continuous SSF run, about 57% of the consumed carbon was used to produce ethanol and less than 1% to synthesize cell mass; thus the majority of carbon flow was to ethanol. The ethanol yields based on consumed substrate and volumetric productivities were in the range of 85% and 0.2 g ethanol/l{times}h, respectively; both values are within the expectations for a nearterm biomass-to-ethanol process. In the single-stage system used, continuous inoculation was not needed even for whole-slurry fermentations; this has significant economic implications since the inoculum cost can be significant.

  16. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method.

    PubMed

    Machado, António; Castro, Joana; Cereija, Tatiana; Almeida, Carina; Cerca, Nuno

    2015-01-01

    Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6-99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis. PMID:25737820

  17. Mapping the regioisomeric distribution of fatty acids in triacylglycerols by hybrid mass spectrometry[S

    PubMed Central

    Nagy, Kornél; Sandoz, Laurence; Destaillats, Frédéric; Schafer, Olivier

    2013-01-01

    This study describes the use of hybrid mass spectrometry for the mapping, identification, and semi-quantitation of triacylglycerol regioisomers in fats and oils. The identification was performed based on the accurate mass and fragmentation pattern obtained by data-dependent fragmentation. Quantitation was based on the high-resolution ion chromatograms, and relative proportion of sn-1(3)/sn-2 regioisomers was calculated based on generalized fragmentation models and the relative intensities observed in the product ion spectra. The key performance features of the developed method are inter-batch mass accuracy < 1 ppm (n = 10); lower limit of detection (triggering threshold) 0.1 μg/ml (equivalent to 0.2 weight % in oil); lower limit of quantitation 0.2 μg/ml (equivalent to 0.4 weight % in oil); peak area precision 6.5% at 2 μg/ml concentration and 15% at 0.2 μM concentration; inter-batch precision of fragment intensities < 1% (n = 10) independent of the investigated concentration; and averaged accuracy using the generic calibration 3.8% in the 1–10 μg/ml range and varies between 1–23% depending on analytes. Inter-esterified fat, beef tallow, pork lard, and butter fat samples were used to show how well regioisomeric distribution of palmitic acid can be captured by this method. PMID:23093552

  18. Redox-active thionine-graphene oxide hybrid nanosheet: one-pot, rapid synthesis, and application as a sensing platform for uric acid.

    PubMed

    Sun, Zhoumin; Fu, Haiying; Deng, Liu; Wang, Jianxiu

    2013-01-25

    In this paper, we fabricate a sensitive and stable amperometric UA amperometric biosensor using nanobiocomposite derived from thionine modified graphene oxide in this study. A simple wet-chemical strategy for synthesis of thionine-graphene oxide hybrid nanosheets (T-GOs) through π-π stacking has been demonstrated. Various techniques, such as UV-vis absorption spectroscopy, X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), atomic force microscopy (AFM) and electrochemistry have been utilized to characterize the formation of the T-GOs. Due to the synergistic effect between thionine and graphene oxide, the nanosheets exhibited excellent performance toward H(2)O(2) reduction. The incorporation of thionine onto graphene oxide surface resulted in more than a twice increase in the amperometric response to H(2)O(2) of the thionine modified electrode. The as-formed T-GOs also served as a biocompatible matrix for enzyme assembly and a mediator to facilitate the electron transfer between the enzyme and the electrode. Using UOx as a model system, we have developed a simple and effective sensing platform for assay of uric acid at physiological levels. UA has been successfully detected at -0.1 V without any interference due to other electroactive compounds at physiological levels of glucose (5 mM), ascorbic acid (0.1 mM), noradrenalin (0.1 mM), and dopamine (0.1 mM). The response displays a good linear range from 0.02 to 4.5 mM with detection limit 7 μM. The application of this modified electrode in blood and urine UA exhibited a good performance. The robust and advanced hybrid materials might hold great promise in biosensing, energy conversion, and biomedical and electronic systems. PMID:23312318

  19. Synthesis and biological evaluation of boswellic acid-NSAID hybrid molecules as anti-inflammatory and anti-arthritic agents.

    PubMed

    Shenvi, Suvarna; Kiran, K R; Kumar, Krishna; Diwakar, Latha; Reddy, G Chandrasekara

    2015-06-15

    Methyl esters of the β-boswellic acid (BA) and 11-keto-β-boswellic acid (KBA) obtained from Boswellia serrata resin were subjected to Steglich esterification with the different non-steroidal anti-inflammatory drugs (NSAID) viz., ibuprofen, naproxen, diclophenac and indomethacin. The novel hybrids of methyl boswellate (5-8) and that of methyl 11-keto boswellate (9-12) were evaluated for anti-inflammatory activity by carrageenan-induced rat hind paw edema model and anti-arthritic activity by Complete Freund's Adjuvant (CFA) induced arthritis in Wister albino rat. Significant inhibition on carrageenan-induced paw edema has been observed with 5, 6 and 10 where as in CFA induced rats, hybrids 5, 8, 9 and 12 exhibited pronounced antiarthritic activity. Hybrid molecules 5 and 9 have been found to be more effective in inhibiting in-vivo COX-2 than ibuprofen by itself, thus showing the synergistic effect. Hybrid 5 and 9 tested for in-vitro lipoxygenase and cyclooxygenase-2 (LOX/COX-2) inhibitory activity. The studies revealed that both 5 and 9 inhibited COX-2 relatively better than LOX enzyme. PMID:26010018

  20. Maximum power output and load matching of a phosphoric acid fuel cell-thermoelectric generator hybrid system

    NASA Astrophysics Data System (ADS)

    Chen, Xiaohang; Wang, Yuan; Cai, Ling; Zhou, Yinghui

    2015-10-01

    Based on the current models of phosphoric acid fuel cells (PAFCs) and thermoelectric generators (TGs), a new hybrid system is proposed, in which the effects of multi-irreversibilities resulting from the activation, concentration, and ohmic overpotentials in the PAFC, Joule heat and heat leak in the TG, finite-rate heat transfer between the TG and the heat reservoirs, and heat leak from the PAFC to the environment are taken into account. Expressions for the power output and efficiency of the PAFC, TG, and hybrid system are analytically derived and directly used to discuss the performance characteristics of the hybrid system. The optimal relationship between the electric currents in the PAFC and TG is obtained. The maximum power output is numerically calculated. It is found that the maximum power output density of the hybrid system will increase about 150 Wm-2, compared with that of a single PAFC. The problem how to optimally match the load resistances of two subsystems is discussed. Some significant results for practical hybrid systems are obtained.

  1. AN ENZYME LINKED IMMUNOSORBENT ASSAY (ELISA) METHOD FOR THE URINARY BIOMONITORING OF 2,4-DICHLOROPHRENOCYACETIC ACID (2,4-D)

    EPA Science Inventory

    An enzyme-linked immunosorbent assay (ELISA) method was developed to quantitatively measure 2,4-dichlorophenoyacetic acid (2,4-D) in human urine. Samples were diluted (1:5) with phosphate-buffered saline, 0.05% Tween 20, with 0.02% sodium azide, and analyzed by a 96-microwekk pl...

  2. New Real-Time PCR Assay Using Locked Nucleic Acid Probes To Assess Prevalence of ParC Mutations in Fluoroquinolone-Susceptible Streptococcus pneumoniae Isolates from France

    PubMed Central

    Decousser, Jean-Winoc; Methlouthi, Imen; Pina, Patrick; Collignon, Anne; Allouch, Pierre

    2006-01-01

    A real-time PCR assay with locked nucleic acid probes was developed to screen mutations at codons 79 and 83 of the Streptococcus pneumoniae parC gene. Only silent mutations were detected among 236 French invasive fluoroquinolone-susceptible strains. This test could be useful for some high-risk patients or in national surveys. PMID:16569894

  3. Use of agar diffusion assay to evaluate bactericidal activity of formulations of alkaline salts of fatty acids against bacteria associated with poultry processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The agar diffusion assay was used to examine antibacterial activity of alkaline salts of fatty acids (FA). Wells in agar media seeded with bacteria were filled with FA-potassium hydroxide (KOH) solutions, plates were incubated, and zones of inhibition were measured. The relationship between bacteric...

  4. Visualization of the mycelia of wood-rotting fungi by fluorescence in situ hybridization using a peptide nucleic acid probe.

    PubMed

    Nakada, Yuji; Nakaba, Satoshi; Matsunaga, Hiroshi; Funada, Ryo; Yoshida, Makoto

    2013-01-01

    White rot fungus, Phanerochaete chrysosporium, and brown rot fungus, Postia placenta, grown on agar plates, were visualized by fluorescence in situ hybridization (FISH) using a peptide nucleic acid (PNA) probe. Mycelia grown on wood chips were also clearly detected by PNA-FISH following blocking treatment. To the best of our knowledge, this is the first report on the visualization of fungi in wood by FISH. PMID:23391931

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

    NASA Astrophysics Data System (ADS)

    Shen, Yongjun; Lei, Lecheng; Zhang, Xingwang; Ding, Jiandong

    2014-11-01

    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 wire-to-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, p-benzoquinone, phenol, benzoic acid, phthalic anhydride, coumarin and 2-naphthol. Proposed degradation pathways were

  6. A long-wavelength quantum dot-concentric FRET configuration: characterization and application in a multiplexed hybridization assay.

    PubMed

    Li, Jia Jun; Algar, W Russ

    2016-06-21

    Quantum dot-based concentric Förster resonance energy transfer (cFRET) is a promising modality for the development of multifunctional fluorescent probes for bioanalysis and bioimaging. To date, the scope of cFRET has been largely limited to a prototypical configuration with a particular combination of quantum dot (QD) and fluorescent dyes linked through peptides. Expansion of the scope of cFRET is critical for its further development. Here, we expand the scope of cFRET in two capacities. First, we design and characterize a new long-wavelength cFRET configuration that combines red- and deep-red fluorescent dyes, Alexa Fluor 633 and Alexa Fluor 680, with an orange-emitting QD. Sequential and competitive energy transfer pathways are characterized through a rate analysis, where the balance of these rates more strongly favours competitive energy transfer in the new long-wavelength configuration versus sequential energy transfer in the previous prototypical configuration. Although the new cFRET configuration is more susceptible to photobleaching, its superior brightness and longer-wavelength excitation and emission provide an order of magnitude higher signal-to-background ratios in biological matrices (e.g., serum, blood) than the previous prototypical configuration. Second, we demonstrate that an oligonucleotide-linked, long-wavelength cFRET configuration has energy transfer similar to an analogous peptide-linked configuration, where the oligonucleotide-linked cFRET configuration can be combined with toehold-mediated strand displacement for the multiplexed detection of unlabeled nucleic acid targets as a single vector. Overall, this work establishes the general applicability of cFRET and introduces new strategies for its bioanalytical application. PMID:27048838

  7. Evaluation of a Commercialized In Situ Hybridization Assay for Detecting Human Papillomavirus DNA in Tissue Specimens from Patients with Cervical Intraepithelial Neoplasia and Cervical Carcinoma▿

    PubMed Central

    Guo, Ming; Gong, Yun; Deavers, Michael; Silva, Elvio G.; Jan, Yee Jee; Cogdell, David E.; Luthra, Rajyalashmi; Lin, E.; Lai, Hung Cheng; Zhang, Wei; Sneige, Nour

    2008-01-01

    To evaluate a commercialized in situ hybridization (ISH) assay for detecting human papillomavirus (HPV) DNA, we compared the ability of a new ISH probe, Inform HPV III (Ventana Medical Systems, Tucson, AZ), to that of PCR assays to detect HPV DNA in cervical tissue specimens with normal cervix (20 cases), cervical intraepithelial neoplasia (CIN; CIN 1, 27 cases; CIN 2, 28 cases; and CIN 3, 33 cases), and cervical carcinoma (29 cases). General HPV DNA was detected using consensus primer-mediated PCR assays. HPV genotyping was performed by using EasyChip HPV blot (King Car Yuan Shan Institute, I-Lan, Taiwan). HPV16 integration status (E2/E6 ratio) was determined by using quantitative real-time PCR. Our findings showed that the ISH and PCR had fair to good agreements in detecting HPV DNA across all CIN categories without significant differences (Kappa coefficient, 0.34 to 0.63; P = 0.13 to 1.0). However, ISH detected significantly fewer HPV-positive cases in carcinoma than PCR did (Kappa coefficient, 0.2; P = 0.03). Eleven cases with ISH− PCR+ results had HPV types that can be detected by Inform HPV III. Five carcinoma cases with ISH− PCR+ results showed a significantly higher level of integrated HPV16 (P = 0.008) than did the ISH+ cases. As a consequence, lower copy numbers of episomal HPV16 in carcinoma might be the cause for the false-negative ISH results. Although the punctate signal pattern of HPV significantly increased with the severity of disease (P trend = 0.01), no significant difference in the HPV16 integration status was observed between the cases with a punctate signal only and the cases with mixed punctate and diffuse signals (P = 0.4). In conclusion, ISH using the Inform HPV III probe seems comparable to PCR for detecting HPV DNA in cervical tissue with CINs. False-negative ISH results appear to be associated with the lower copy numbers of the episomal HPV16 but not with the ability of the Inform HPV III probe to detect specific HPV types. In

  8. EVALUATING EFFECTS OF NEPTUNIUM ON THE SRS METHOD FOR CONTROLLED POTENTIAL COULOMETRIC ASSAY OF PLUTONIUM IN SULFURIC ACID SUPPORTING ELECTROLYTE

    SciTech Connect

    Holland, M; Sheldon Nichols, S

    2008-05-09

    A study of the impact of neptunium on the coulometric assay of plutonium in dilute sulfuric acid was performed. Weight aliquots of plutonium standard solutions were spiked with purified neptunium solution to evaluate plutonium measurement performance for aliquots with Pu:Np ratios of 50:1, 30:1, 20:1, 15:1, and 10:1. Weight aliquots of the pure plutonium standard solution were measured as controls. Routine plutonium instrument control standards were also measured. The presence of neptunium in plutonium aliquots significantly increases the random uncertainty associated with the plutonium coulometric measurement performed in accordance with ISO12183:2005.7 However, the presence of neptunium does not appear to degrade electrode performance and conditioning as aliquots of pure plutonium that were interspersed during the measurement of the mixed Pu:Np aliquots continued to achieve the historical short-term random uncertainty for the method. Lack of adequate control of the neptunium oxidation state is suspected to be the primary cause of the elevated measurement uncertainty and will be pursued in a future study.

  9. Efficient interrupting skills of amino acid metallointercalators with DNA at physiological pH: Evaluation of biological assays

    NASA Astrophysics Data System (ADS)

    Raman, Natarajan; Selvaganapathy, Muthusamy; Radhakrishnan, Srinivasan

    2014-06-01

    The 4-aminoantipyrine derivatives (sbnd NO2, sbnd OCH3) and their mixed-ligand complexes with amino acids have been synthesized and investigated for their binding with CT DNA using UV-visible spectroscopy, cyclic voltammetry, and viscosity measurements under physiological conditions of pH (stomach 4.7; blood 7.4). The results from all techniques i.e. binding constant (Kb), and free energy change (ΔG) were in good agreement and inferred spontaneous compound-DNA complexes formation via intercalation. Among all the compounds 1 and 4 showed comparatively greater binding at pH 7.4 as evident from its greater Kb values. All the complexes exhibit oxidative cleavage of supercoiled (SC) pBR322 plasmid DNA in the presence of H2O2 as an activator. It is remarkable that at 25 μM concentration 1 and 4 completely degrade SC DNA into undetectable minor fragments and thus they act as efficient chemical nucleases. Among the new complexes, complexes 1 and 4 have highest potential against all the microorganisms tested. The results of the above biological experiments also reveal that the choice of different metal ions has little influence on the DNA binding, DNA cleavage and antimicrobial assay.

  10. Rapid Point-of-Care Isothermal Amplification Assay for the Detection of Malaria without Nucleic Acid Purification

    PubMed Central

    Modak, Sayli S.; Barber, Cheryl A.; Geva, Eran; Abrams, William R.; Malamud, Daniel; Ongagna, Yhombi Serge Yvon

    2016-01-01

    Malaria remains one of the most prevalent infectious diseases and results in significant mortality. Isothermal amplification (loop-mediated isothermal amplification) is used to detect malarial DNA at levels of ~1 parasite/µL blood in ≤30 minutes without the isolation of parasite nucleic acid from subject’s blood or saliva. The technique targets the mitochondrial cytochrome oxidase subunit 1 gene and is capable of distinguishing Plasmodium falciparum from Plasmodium vivax. Malarial diagnosis by the gold standard microscopic examination of blood smears is generally carried out only after moderate-to-severe symptoms appear. Rapid diagnostic antigen tests are available but generally require infection levels in the range of 200–2,000 parasites/µL for a positive diagnosis and cannot distinguish if the disease has been cleared due to the persistence of circulating antigen. This study describes a rapid and simple molecular assay to detect malarial genes directly from whole blood or saliva without DNA isolation. PMID:26819557

  11. Comparative Study of the One-step Nucleic Acid Amplification Assay and Conventional Histological Examination for the Detection of Breast Cancer Sentinel Lymph Node Metastases.

    PubMed

    Terada, Mizuho; Niikura, Naoki; Tsuda, Banri; Masuda, Shinobu; Kumaki, Nobue; Tang, Xiaoyan; Okamura, Takuho; Saito, Yuki; Suzuki, Yasuhiro; Tokuda, Yutaka

    2014-09-01

    Intraoperative sentinel lymph node (SLN) biopsy is widely used in patients with early-stage breast cancer and is conventionally performed using hematoxylin and eosin-based histological examination. The one-step nucleic acid amplification (OSNA) assay is a molecular diagnostic tool and a semi-automated lymph node examination method. The purpose of this study was to compare the performance of the OSNA assay and conventional histological examination with frozen sections (FSs) by using 111 SLN biopsy samples from 89 patients at the Tokai University Hospital. The SLN samples were split into 3 slices: the middle slice was used for FS histological examination and the other slices were used for the OSNA assay. The McNemar test was used to compare the differences in the sensitivity and specificity between the OSNA assay and FS histological examination. The sensitivity of the OSNA assay (97.1%) was less than that of FS histological examination (100%), but this difference was not statistically significant (P = 0.125). The specificity of both the methods was identical (96.9%). Despite previously published results suggesting that the OSNA assay is as reliable as histological examinations, our results indicate that this assay often fails to detect micrometastases or isolated tumor cells in SLNs. PMID:25248427

  12. Development of a real-time PCR assay with fluorophore-labelled hybridization probes for detection of Schistosoma mekongi in infected snails and rat feces.

    PubMed

    Sanpool, O; Intapan, P M; Thanchomnang, T; Sri-Aroon, P; Lulitanond, V; Sadaow, L; Maleewong, W

    2012-09-01

    Schistosoma mekongi, a blood-dwelling fluke, is a water-borne parasite that is found in communities along the lower Mekong River basin, i.e. Cambodia and Lao People's Democratic Republic. This study developed a real-time PCR assay combined with melting-curve analysis to detect S. mekongi in laboratory setting conditions, in experimentally infected snails, and in fecal samples of infected rats. The procedure is based on melting-curve analysis of a hybrid between an amplicon from S. mekongi mitochondrion sequence, the 260 bp sequence specific to S. mekongi, and specific fluorophore-labelled probes. This method could detect as little as a single cercaria artificially introduced into a pool of 10 non-infected snails, a single cercaria in filtered paper, and 2 eggs inoculated in 100 mg of non-infected rat feces. All S. mekongi-infected snails and fecal samples from infected rats were positive. Non-infected snails, non-infected rat feces, and genomic DNA of other parasites were negative. The method gave high sensitivity and specificity, and could be applied as a fast and reliable tool for cercarial location in water environments in endemic areas and for epidemiological studies and eradication programmes for intermediate hosts. PMID:22717071

  13. Factors affecting detection of PVY in dormant tubers by reverse transcription polymerase chain reaction and nucleic acid spot hybridization.

    PubMed

    Singh, M; Singh, R P

    1996-06-01

    A reverse transcription polymerase chain reaction (RT-PCR) protocol was developed using two 20-mer primers located in nuclear inclusion genes NIa and NIb of potato virus Y (PVY). A 1017 bp PCR-product was detected in dormant potato tubers, infected with PVY(O), but not in tubers from healthy plants. The PCR product was specific to PVY, as determined by Southern blot detection by hybridization with a PVY(O)-specific probe. As little as 1 pg of purified PVY(O)-RNA can be detected after RT-PCR amplification. The presence of phenolics or polysaccharides in tuber nucleic acids inhibited PVY(O) amplification, which was eliminated by diluting nucleic acid preparations prior to cDNA synthesis, modifying the nucleic acid extraction procedure by isopropanol precipitation and using phosphate-buffered saline-Tween in the cDNA mix. Potato cultivars differed in PVY(O) concentration in tubers as much as 128-fold. Tuber parts used for nucleic acid extractions were important in potato cultivars with low virus titres and did not result in reduced detection of PVY(O) by both nucleic acid spot hybridization and RT-PCR, but RT-PCR band intensity was lower at longer storage periods. The primer pair developed in this study exhibited broad specificities with field isolates from Peru, Scotland and North America. PMID:8795005

  14. Effect of non-specific species competition from total RNA on the static mode hybridization response of nanomechanical assays of oligonucleotides.

    PubMed

    Mishra, Rohit; Hegner, Martin

    2014-06-01

    We investigate here the nanomechanical response of microcantilever sensors in real-time for detecting a range of ultra-low concentrations of oligonucleotides in a complex background of total cellular RNA extracts from cell lines without labeling or amplification. Cantilever sensor arrays were functionalized with probe single stranded DNA (ssDNA) and reference ssDNA to obtain a differential signal. They were then exposed to complementary target ssDNA strands that were spiked in a fragmented total cellular RNA background in biologically relevant concentrations so as to provide clinically significant analysis. We present a model for prediction of the sensor behavior in competitive backgrounds with parameters that are indicators of the change in nanomechanical response with variation in the target and background concentration. For nanomechanical assays to compete with current technologies it is essential to comprehend such responses with eventual impact on areas like understanding non-coding RNA pharmacokinetics, nucleic acid biomarker assays and miRNA quantification for disease monitoring and diagnosis to mention a few. Additionally, we also achieved a femtomolar sensitivity limit for online oligonucleotide detection in a non-competitive environment with these sensors. PMID:24807191

  15. Effect of non-specific species competition from total RNA on the static mode hybridization response of nanomechanical assays of oligonucleotides

    NASA Astrophysics Data System (ADS)

    Mishra, Rohit; Hegner, Martin

    2014-06-01

    We investigate here the nanomechanical response of microcantilever sensors in real-time for detecting a range of ultra-low concentrations of oligonucleotides in a complex background of total cellular RNA extracts from cell lines without labeling or amplification. Cantilever sensor arrays were functionalized with probe single stranded DNA (ssDNA) and reference ssDNA to obtain a differential signal. They were then exposed to complementary target ssDNA strands that were spiked in a fragmented total cellular RNA background in biologically relevant concentrations so as to provide clinically significant analysis. We present a model for prediction of the sensor behavior in competitive backgrounds with parameters that are indicators of the change in nanomechanical response with variation in the target and background concentration. For nanomechanical assays to compete with current technologies it is essential to comprehend such responses with eventual impact on areas like understanding non-coding RNA pharmacokinetics, nucleic acid biomarker assays and miRNA quantification for disease monitoring and diagnosis to mention a few. Additionally, we also achieved a femtomolar sensitivity limit for online oligonucleotide detection in a non-competitive environment with these sensors.

  16. Hybrid molecularly imprinted poly(methacrylic acid-TRIM)-silica chemically modified with (3-glycidyloxypropyl)trimethoxysilane for the extraction of folic acid in aqueous medium.

    PubMed

    de Oliveira, Fernanda Midori; Segatelli, Mariana Gava; Tarley, César Ricardo Teixeira

    2016-02-01

    In the present study a hybrid molecularly imprinted poly(methacrylic acid-trimethylolpropane trimethacrylate)-silica (MIP) was synthesized and modified with (3-glycidyloxypropyl)trimethoxysilane (GPTMS) with posterior opening of epoxy ring to provide hydrophilic properties of material in the extraction of folic acid from aqueous medium. The chemical and structural aggregates of hybrid material were characterized by means of Fourier Transform Infrared (FT-IR), Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Thermogravimetric analysis (TGA) and textural data. Selectivity data of MIP were compared to non-imprinted polymer (NIP) through competitive sorption studies in the presence of caffeine, paracetamol or 4-aminobenzamide yielding relative selectivity coefficients (k′) higher than one unit, thus confirming the selective character of MIP even in the presence of structurally smaller compounds than the folic acid. The lower hydrophobic sorption by bovine serum albumin (BSA) in the MIP as compared to unmodified MIP proves the hydrophilicity of polymer surface by using GPTMS with opening ring. Under acid medium(pH 1.5) the sorption of folic acid onto MIP from batch experiments was higher than the one achieved for NIP. Equilibrium sorption of folic acid was reached at 120 min for MIP, NIP and MIP without GPTMS and kinetic sorption data were well described by pseudo-second-order, Elovich and intraparticle diffusion models. Thus, these results indicate the existence of different binding energy sites in the polymers and a complex mechanism consisting of both surface sorption and intraparticle transport of folic acid within the pores of polymers. PMID:26652418

  17. Development of a lauric acid/albumin hybrid iron oxide nanoparticle system with improved biocompatibility

    PubMed Central

    Zaloga, Jan; Janko, Christina; Nowak, Johannes; Matuszak, Jasmin; Knaup, Sabine; Eberbeck, Dietmar; Tietze, Rainer; Unterweger, Harald; Friedrich, Ralf P; Duerr, Stephan; Heimke-Brinck, Ralph; Baum, Eva; Cicha, Iwona; Dörje, Frank; Odenbach, Stefan; Lyer, Stefan; Lee, Geoffrey; Alexiou, Christoph

    2014-01-01

    The promising potential of superparamagnetic iron oxide nanoparticles (SPIONs) in various nanomedical applications has been frequently reported. However, although many different synthesis methods, coatings, and functionalization techniques have been described, not many core-shell SPION drug delivery systems are available for clinicians at the moment. Here, bovine serum albumin was adsorbed onto lauric acid-stabilized SPIONs. The agglomeration behavior, zeta potential, and their dependence on the synthesis conditions were characterized with dynamic light scattering. The existence and composition of the core-shell-matrix structure was investigated by transmission electron microscopy, Fourier transform infrared spectroscopy, and zeta potential measurements. We showed that the iron oxide cores form agglomerates in the range of 80 nm. Moreover, despite their remarkably low tendency to aggregate even in a complex media like whole blood, the SPIONs still maintained their magnetic properties and were well attractable with a magnet. The magnetic properties were quantified by vibrating sample magnetometry and a superconducting quantum interference device. Using flow cytometry, we further investigated the effects of the different types of nanoparticle coating on morphology, viability, and DNA integrity of Jurkat cells. We showed that by addition of bovine serum albumin, the toxicity of nanoparticles is greatly reduced. We also investigated the effect of the particles on the growth of primary human endothelial cells to further demonstrate the biocompatibility of the particles. As proof of principle, we showed that the hybrid-coated particles are able to carry payloads of up to 800 μg/mL of the cytostatic drug mitoxantrone while still staying colloidally stable. The drug-loaded system exhibited excellent therapeutic potential in vitro, exceeding that of free mitoxantrone. In conclusion, we have synthesized a biocompatible ferrofluid that shows great potential for clinical

  18. Development of a lauric acid/albumin hybrid iron oxide nanoparticle system with improved biocompatibility.

    PubMed

    Zaloga, Jan; Janko, Christina; Nowak, Johannes; Matuszak, Jasmin; Knaup, Sabine; Eberbeck, Dietmar; Tietze, Rainer; Unterweger, Harald; Friedrich, Ralf P; Duerr, Stephan; Heimke-Brinck, Ralph; Baum, Eva; Cicha, Iwona; Dörje, Frank; Odenbach, Stefan; Lyer, Stefan; Lee, Geoffrey; Alexiou, Christoph

    2014-01-01

    The promising potential of superparamagnetic iron oxide nanoparticles (SPIONs) in various nanomedical applications has been frequently reported. However, although many different synthesis methods, coatings, and functionalization techniques have been described, not many core-shell SPION drug delivery systems are available for clinicians at the moment. Here, bovine serum albumin was adsorbed onto lauric acid-stabilized SPIONs. The agglomeration behavior, zeta potential, and their dependence on the synthesis conditions were characterized with dynamic light scattering. The existence and composition of the core-shell-matrix structure was investigated by transmission electron microscopy, Fourier transform infrared spectroscopy, and zeta potential measurements. We showed that the iron oxide cores form agglomerates in the range of 80 nm. Moreover, despite their remarkably low tendency to aggregate even in a complex media like whole blood, the SPIONs still maintained their magnetic properties and were well attractable with a magnet. The magnetic properties were quantified by vibrating sample magnetometry and a superconducting quantum interference device. Using flow cytometry, we further investigated the effects of the different types of nanoparticle coating on morphology, viability, and DNA integrity of Jurkat cells. We showed that by addition of bovine serum albumin, the toxicity of nanoparticles is greatly reduced. We also investigated the effect of the particles on the growth of primary human endothelial cells to further demonstrate the biocompatibility of the particles. As proof of principle, we showed that the hybrid-coated particles are able to carry payloads of up to 800 μg/mL of the cytostatic drug mitoxantrone while still staying colloidally stable. The drug-loaded system exhibited excellent therapeutic potential in vitro, exceeding that of free mitoxantrone. In conclusion, we have synthesized a biocompatible ferrofluid that shows great potential for clinical

  19. A Duplex PCR-Based Assay for Measuring the Amount of Bacterial Contamination in a Nucleic Acid Extract from a Culture of Free-Living Protists

    PubMed Central

    Marron, Alan O.; Akam, Michael; Walker, Giselle

    2013-01-01

    Background Cultures of heterotrophic protists often require co-culturing with bacteria to act as a source of nutrition. Such cultures will contain varying levels of intrinsic bacterial contamination that can interfere with molecular research and cause problems with the collection of sufficient material for sequencing. Measuring the levels of bacterial contamination for the purposes of molecular biology research is non-trivial, and can be complicated by the presence of a diverse bacterial flora, or by differences in the relative nucleic acid yield per bacterial or eukaryotic cell. Principal Findings Here we describe a duplex PCR-based assay that can be used to measure the levels of contamination from marine bacteria in a culture of loricate choanoflagellates. By comparison to a standard culture of known target sequence content, the assay can be used to quantify the relative proportions of bacterial and choanoflagellate material in DNA or RNA samples extracted from a culture. We apply the assay to compare methods of purifying choanoflagellate cultures prior to DNA extraction, to determine their effectiveness in reducing bacterial contamination. Together with measurements of the total nucleic acid concentration, the assay can then be used as the basis for determining the absolute amounts of choanoflagellate DNA or RNA present in a sample. Conclusions The assay protocol we describe here is a simple and relatively inexpensive method of measuring contamination levels in nucleic acid samples. This provides a new way to establish quantification and purification protocols for molecular biology and genomics in novel heterotrophic protist species. Guidelines are provided to develop a similar protocol for use with any protistan culture. This assay method is recommended where qPCR equipment is unavailable, where qPCR is not viable because of the nature of the bacterial contamination or starting material, or where prior sequence information is insufficient to develop q

  20. Comparative quantitative analysis of hepatitis C mutations at amino acids 70 and 91 in the core region by the Q-Invader assay.

    PubMed

    Tadokoro, Kenichi; Kobayashi, Mariko; Suzuki, Fumitaka; Tanaka, Chie; Yamaguchi, Toshikazu; Nagano, Makoto; Egashira, Toru; Kumada, Hiromitsu

    2013-04-01

    Hepatitis C virus (HCV) is a major worldwide public health problem, and mutations at amino acids 70 and 91 in the genotype 1b core region predict the effectiveness of combination therapy with peginterferon and ribavirin. An assay based on the Q-Invader technology was developed to determine the relative ratios of the mutant to wild-type virus with high sensitivity. The assay detected a minor type plasmid that constituted only 1% of a mixture of plasmids containing wild-type and mutant sequences. The calculated ratios agreed with those of the template DNA. A total of 123 serum samples of HCV in Japan were examined with the Q-Invader assay. The Q-Invader assay detected all of the mutations that were detected by direct sequencing and even some mutants that direct sequencing could not. PCR with mutant specific primers confirmed those mutations found by the Q-Invader assay and not by direct sequencing. The Q-Invader assay, thus, is a useful tool for detecting mutations at positions 70 and 91 in the HCV-1b core region. PMID:23124003

  1. Synthesis and antiproliferative activity of two diastereomeric lignan amides serving as dimeric caffeic acid-l-DOPA hybrids.

    PubMed

    Magoulas, George E; Rigopoulos, Andreas; Piperigkou, Zoi; Gialeli, Chrysostomi; Karamanos, Nikos K; Takis, Panteleimon G; Troganis, Anastassios N; Chrissanthopoulos, Athanassios; Maroulis, George; Papaioannou, Dionissios

    2016-06-01

    Two new diastereomeric lignan amides (4 and 5) serving as dimeric caffeic acid-l-DOPA hybrids were synthesized. The synthesis involved the FeCl3-mediated phenol oxidative coupling of methyl caffeate to afford trans-diester 1a as a mixture of enantiomers, protection of the catechol units, regioselective saponification, coupling with a suitably protected l-DOPA derivative, separation of the two diastereomers thus obtained by flash column chromatography and finally global chemoselective deprotection of the catechol units. The effect of hybrids 4 and 5 and related compounds on the proliferation of two breast cancer cell lines with different metastatic potential and estrogen receptor status (MDA-MB-231 and MCF-7) and of one epithelial lung cancer cell line, namely A-549, was evaluated for concentrations ranging from 1 to 256μM and periods of treatment of 24, 48 and 72h. Both hybrids showed interesting and almost equipotent antiproliferative activities (IC50 64-70μM) for the MDA-MB-231 cell line after 24-48h of treatment, but they were more selective and much more potent (IC50 4-16μM) for the MCF-7 cells after 48h of treatment. The highest activity for both hybrids and both breast cancer lines was observed after 72h of treatment (IC50 1-2μM), probably as the result of slow hydrolysis of their methyl ester functions. PMID:27155809

  2. A novel asymmetric-loop molecular beacon-based two-phase hybridization assay for accurate and high-throughput detection of multiple drug resistance-conferring point mutations in Mycobacterium tuberculosis

    PubMed Central

    Chen, Qinghai; Wu, Nan; Xie, Meng; Zhang, Bo; Chen, Ming; Li, Jianjun; Zhuo, Lisha; Kuang, Hong; Fu, Weiling

    2012-01-01

    Summary The accurate and high-throughput detection of drug resistance-related multiple point mutations remains a challenge. Although the combination of molecular beacons with bio-immobilization technology, such as microarray, is promising, its application is difficult due to the ineffective immobilization of molecular beacons on the chip surface. Here, we propose a novel asymmetric-loop molecular beacon in which the loop consists of 2 parts. One is complementary to a target, while the other is complementary to an oligonucleotide probe immobilized on the chip surface. With this novel probe, a two-phase hybridization assay can be used for simultaneously detecting multiple point mutations. This assay will have advantages, such as easy probe availability, multiplex detection, low background, and high-efficiency hybridization, and may provide a new avenue for the immobilization of molecular beacons and high-throughput detection of point mutations. PMID:22460100

  3. Comparison of Analytical and Clinical Performance of HPV 9G DNA Chip, PANArray HPV Genotyping Chip, and Hybrid-Capture II Assay in Cervicovaginal Swabs

    PubMed Central

    Jung, Ho Young; Han, Hye Seung; Kim, Hyo Bin; Oh, Seo Young; Lee, Sun-Joo; Kim, Wook Youn

    2016-01-01

    Background: Human papillomavirus (HPV) infection can be detected by using several molecular methods, including Hybrid-Capture II (HC2) assay and variable HPV DNA chip tests, although each method has different sensitivities and specificities. Methods: We performed HPV 9G DNA Chip (9G) and PANArray HPV Genotyping Chip (PANArray) tests on 118 cervicovaginal swabs and compared the results with HC2, cytology, histology, and direct sequencing results. Results The overall and high-risk HPV (HR-HPV) positivity rates were 62.7% and 44.9% using 9G, and 61.0% and 30.5% using PANArray, respectively. The positivity rates for HR-HPV with these two chips were significantly lower than 55.1% when HC2 was used. The sensitivity of overall HPV positivity in detecting histologically confirmed low-grade cervical squamous intraepithelial lesions or higher was 88.7% for all three tests. The specificity was 58.5% for 9G and 61.5% for PANArray, which was significantly lower than the 72.3% for HC2. With the HR-HPV+ genotype threshold, the sensitivity decreased to 75.5% for 9G and 52.8% for PANArray, which was significantly lower than the 88.7% for HC2. Comparison of the two chips showed concordant results in 55.1% of the samples, compatible results in 16.9%, and discordant results in 28.0%, exhibiting poor agreement in detecting  certain HPV genotypes. Compared with direct sequencing, 9G yielded no discordant results, whereas PANArray yielded 31 discordant results (26.7%). Conclusions Compared with HC2, the HPV genotyping tests showed lower sensitivity in histologic correlation. When the two chips were compared, the 9G was more sensitive and accurate for detecting HR-HPV than the PANArray. PMID:26763506

  4. Cellular delivery of quantum dot-bound hybridization probe for detection of intracellular pre-microRNA using chitosan/poly(γ-glutamic acid) complex as a carrier.

    PubMed

    Geng, Yao; Lin, Dajie; Shao, Lijia; Yan, Feng; Ju, Huangxian

    2013-01-01

    A quantum dot (QD)-bound hybridization probe was designed for detection of intracellular pre-miRNA using chitosan (CS)/poly(γ-glutamic acid) (γ-PGA) complex as a gene vector. The probe was prepared by assembling thiolated RNA to gold nanoparticle (Au NP) via Au-S bond and then binding 3'-end amine of the RNA to the carboxy group capped on quantum dot surface. The QD-RNA-Au NP probe was assembled on the vector by mixing with aqueous γ-PGA solution and then CS solution to construct a gene delivery system for highly effective cellular uptake and delivery. After the probe was released from CS/γ-PGA complex to the cytoplasm by electrostatic repulsion at intracellular pH, it hybridized with pre-miRNA precursor as target. The formed product was then cleaved by RNase III Dicer, leading to the separation of QDs from Au NPs and fluorescence emission of QDs, which could be detected by confocal microscopic imaging to monitor the amount of the intracellular pre-miRNA precursor. The in vitro assays revealed that the QD-RNA-Au NP was a robust, sensitive and selective probe for quantitative detection of target pre-miRNA. Using MDA-MB231 and MCF-7 breast cancer cells as models, the relative amount of pre-miRNA let-7a could be successfully compared. Since the amount of miRNA is related to the progress and prognosis of cancer, this strategy could be expected to hold promising application potential in medical research and clinical diagnostics. PMID:23762388

  5. Library screening by means of mass spectrometry (MS) binding assays-exemplarily demonstrated for a pseudostatic library addressing γ-aminobutyric acid (GABA) transporter 1 (GAT1).

    PubMed

    Sindelar, Miriam; Wanner, Klaus T

    2012-09-01

    In the present study, the application of mass spectrometry (MS) binding assays as a tool for library screening is reported. For library generation, dynamic combinatorial chemistry (DCC) was used. These libraries can be screened by means of MS binding assays when appropriate measures are taken to render the libraries pseudostatic. That way, the efficiency of MS binding assays to determine ligand binding in compound screening with the ease of library generation by DCC is combined. The feasibility of this approach is shown for γ-aminobutyric acid (GABA) transporter 1 (GAT1) as a target, representing the most important subtype of the GABA transporters. For the screening, hydrazone libraries were employed that were generated in the presence of the target by reacting various sets of aldehydes with a hydrazine derivative that is delineated from piperidine-3-carboxylic acid (nipecotic acid), a common fragment of known GAT1 inhibitors. To ensure that the library generated is pseudostatic, a large excess of the nipecotic acid derivative is employed. As the library is generated in a buffer system suitable for binding and the target is already present, the mixtures can be directly analyzed by MS binding assays-the process of library generation and screening thus becoming simple to perform. The binding affinities of the hits identified by deconvolution were confirmed in conventional competitive MS binding assays performed with single compounds obtained by separate synthesis. In this way, two nipecotic acid derivatives exhibiting a biaryl moiety, 1-{2-[2'-(1,1'-biphenyl-2-ylmethylidene)hydrazine]ethyl}piperidine-3-carboxylic acid and 1-(2-{2'-[1-(2-thiophenylphenyl)methylidene]hydrazine}ethyl)piperidine-3-carboxylic acid, were found to be potent GAT1 ligands exhibiting pK(i) values of 6.186 ± 0.028 and 6.229 ± 0.039, respectively. This method enables screening of libraries, whether generated by conventional chemistry or DCC, and is applicable to all kinds of targets including

  6. The optimisation of grid designs for valve-regulated lead/acid batteries for hybrid electric vehicle applications

    NASA Astrophysics Data System (ADS)

    May, G. J.; Maleschitz, N.; Diermaier, H.; Haeupl, T.

    The design, construction and testing of valve-regulated lead/acid cells with grid designs optimised for high-rate partial state-of-charge cycling for hybrid electric vehicles are described. Computer modelling was used to develop the grid designs. This showed that designs with opposed tabs and terminals on the top and bottom of the cell were likely to have the best performance not only in terms of grid conductivity but also for uniformity of active material utilisation. Prototype cells were built and tested. Low rate performance was in line with the designs and the high-rate performance was substantially enhanced compared with conventional constructions. The cells were then tested to a shallow cycling regime and to a simplified hybrid electric vehicle cycle. The results showed excellent life under these conditions without the benefit of carbon or graphite additives to the negative active material that have also been shown to improve cycle life under these conditions.

  7. Human papillomavirus 35 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 35 hybridization probe comprising a member selected from the group consisting of (i) HPV 35 DNA or fragments thereof labelled with a marker and (ii) HPV 35 RNA or fragments thereof labelled with a marker.

  8. Human papillomavirus 56 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorinez, A.T.

    1990-03-13

    This patent describes an HPV 56 hybridization probe. It comprises: a member selected from the group consisting of HPV 56 DNA or fragments thereof labelled with a marker and HPV 56 RNA or fragments thereof labelled with a marker.

  9. Human papillomavirus 44 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 44 hybridization probe comprising a member selected from the group consisting of (1) HPV 44 DNA or fragments thereof labelled with a marker and (ii) HPV 44 RNA or fragments thereof labelled with a marker.

  10. Human papillomavirus 43 nucleic acid hybridization probes and methods for employing the same

    SciTech Connect

    Lorincz, A.T.

    1989-07-18

    This patent describes an HPV 43 hybridization probe comprising a member selected from the group consisting of (i) HPV 43 DNA or fragments thereof labelled with a marker and (ii) HPV 43 RNA or fragments thereof labelled with a marker.

  11. Interface engineering of hybrid perovskite solar cells with poly(3-thiophene acetic acid) under ambient conditions.

    PubMed

    Shit, Arnab; Nandi, Arun K

    2016-04-21

    The properties of methyl ammonium lead iodide (MAPbI3) perovskite solar cells with poly(3-thiophene acetic acid) (P3TAA) as a hole transporting material (HTM) and a dense layer of ZnO nanoparticle film as an electron transporting material (ETM) are described using the conventional ZnO (n)/perovskite (i)/P3TAA (p) (n-i-p) architecture. The FT-IR spectra of a MAPbI3/P3TAA mixture indicate a shift of the N-H stretching and the abolition of the N-H bending peak indicating the interaction between the components. UV-Vis spectra of the mixture exhibit a large red shift of the π-π* transition peak of the conjugated chain arising from the interaction causing an increase of the conjugation length. The cross-sectional SEM image of the device shows the sequence of the individual layers of ZnO, MAPbI3, P3TAA and Ag, respectively. The current density (J)-voltage (V) curves obtained upon illumination with a light of 100 mW cm(-2) indicate the average PCE to be 7.38 ± 0.59% under ambient conditions. The IPCE values of these cells reach about 63% across a broad range of wavelength (300-800 nm). The HOMO and the LUMO of P3TAA are measured using cyclic voltammetry and the optical band gap and the relative energy level of the components explain the operation of photocurrent in the cell. For comparison purposes a device using poly(3-hexyl thiophene) (P3HT) as the HTM is fabricated under similar conditions and it exhibits a lower PCE (5.85 ± 0.51%) than that of the P3TAA based device. The longevity of the P3TAA based cell is also found to be better than that of the P3HT based cell for storing in air. The UV-Vis and impedance spectral results clearly explain the above results, signifying the influence of the interface on the performance of hybrid solar cells. PMID:27020145

  12. pH-responsive drug delivery system based on luminescent CaF(2):Ce(3+)/Tb(3+)-poly(acrylic acid) hybrid microspheres.

    PubMed

    Dai, Yunlu; Zhang, Cuimiao; Cheng, Ziyong; Ma, Ping'an; Li, Chunxia; Kang, Xiaojiao; Yang, Dongmei; Lin, Jun

    2012-03-01

    In this study, we design a controlled release system based on CaF(2):Ce(3+)/Tb(3+)-poly(acrylic acid) (PAA) composite microspheres, which were fabricated by filling the pH-responsive PAA inside CaF(2):Ce(3+)/Tb(3+) hollow spheres via photopolymerization route. The CaF(2):Ce(3+)/Tb(3+) hollow spheres prepared by hydrothermal route possess mesoporous structure and show strong green fluorescence from Tb(3+) under UV excitation. Doxorubicin hydrochloride (DOX), a widely used anti-cancer drug, was used as a model drug to evaluate the loading and controlled release behaviors of the composite microspheres due to the good biocompatibility of the samples using MTT assay. The composite carriers provide a strongly pH-dependent drug release behavior owing to the intrinsic property of PAA and its interactions with DOX. The endocytosis process of drug-loaded microspheres was observed using confocal laser scanning microscopy (CLSM) and the in vitro cytotoxic effect against SKOV3 ovarian cancer cells of the DOX-loaded carriers was investigated. In addition, the extent of drug release could be monitored by the altering of photoluminescence (PL) intensity of CaF(2):Ce(3+)/Tb(3+). Considering the good biocompatibility, high drug loading content and pH-dependent drug release of the materials, these hybrid luminescent microspheres have potential applications in drug controlled release and disease therapy. PMID:22196902

  13. A highly sensitive photoelectrochemical detection of perfluorooctanic acid with molecularly imprined polymer-functionalized nanoarchitectured hybrid of AgI-BiOI composite.

    PubMed

    Gong, Jingming; Fang, Tian; Peng, Dinghua; Li, Aimin; Zhang, Lizhi

    2015-11-15

    A rapid and ultrasensitive signal-off photoelectrochemical sensor has been developed under visible-light irradiation, for the detection of perfluorooctanoic acid (PFOA), especially low level PFOA present in environment, whereby a novel nanostructured probe made of molecularly imprinted polymer (MIP) modified AgI nanoparticles-BiOI nanoflake arrays (AgI-BiOINFs) is designed as the photoactive electrode (denoted as MIP@AgI-BiOINFs). Here, the unique nanoarchitectured hybrid of AgI-BiOINFs was first in situ synthesized via a facile successive ionic layer adsorption and reaction (SILAR) approach and then employed as a matrix to graft the recognition element of MIP. Such a newly designed PEC sensor exhibits high sensitivity and selectivity for the determination of PFOA. The PEC analysis is highly linear over the PFOA concentration ranging from 0.02 to 1000.0 ppb with a detection limit of 0.01 ppb (S/N=3). This value obtained by using the facile PEC sensor is comparable to the results obtained by using well-established liquid chromatography-tandem mass spectrometry (LC-MS/MS). Toward practical applications, this low-cost and sensitive assay was successfully applied to measure PFOA in real water samples. PMID:26092130

  14. A hybrid of ant colony optimization and minimization of metabolic adjustment to improve the production of succinic acid in Escherichia coli.

    PubMed

    Chong, Shiue Kee; Mohamad, Mohd Saberi; Mohamed Salleh, Abdul Hakim; Choon, Yee Wen; Chong, Chuii Khim; Deris, Safaai

    2014-06-01

    This paper presents a study on gene knockout strategies to identify candidate genes to be knocked out for improving the production of succinic acid in Escherichia coli. Succinic acid is widely used as a precursor for many chemicals, for example production of antibiotics, therapeutic proteins and food. However, the chemical syntheses of succinic acid using the traditional methods usually result in the production that is far below their theoretical maximums. In silico gene knockout strategies are commonly implemented to delete the gene in E. coli to overcome this problem. In this paper, a hybrid of Ant Colony Optimization (ACO) and Minimization of Metabolic Adjustment (MoMA) is proposed to identify gene knockout strategies to improve the production of succinic acid in E. coli. As a result, the hybrid algorithm generated a list of knockout genes, succinic acid production rate and growth rate for E. coli after gene knockout. The results of the hybrid algorithm were compared with the previous methods, OptKnock and MOMAKnock. It was found that the hybrid algorithm performed better than OptKnock and MOMAKnock in terms of the production rate. The information from the results produced from the hybrid algorithm can be used in wet laboratory experiments to increase the production of succinic acid in E. coli. PMID:24763079

  15. Growth, body composition, immune response and resistance to Streptococcus iniae of hybrid tilapia, Oreochromis niloticus x O. aureaus, fed diets containing various levels of linoleic and linolenic acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effects of various levels of dietary linoleic (LA) and linolenic acids (LN) on growth, body proximate and fatty acid composition, immune response and resistance to Streptococcus iniae of juvenile, sex-reversed all-male hybrid tilapia, Oreochromis niloticus x O. areaus, were evaluated. A basal pu...

  16. A comprehensive review of the published assays for the quantitation of the immunosuppressant drug mycophenolic acid and its glucuronidated metabolites in biological fluids.

    PubMed

    Syed, Muzeeb; Srinivas, Nuggehally R

    2016-05-01

    Therapeutic use of mycophenolic acid (MPA) is steadily on the rise in combination with other immunosuppressant drugs in transplantation patients. The biotransformation of MPA resulted in the formation of glucuronide metabolites, MPAG and AcMPAG. There are a plethora of assays validated for the analysis of MPA alone or with MPAG/AcMPAG in various biological specimens including plasma/serum, urine, ultrafiltrate, saliva, PBMC, dried blood spots, tissue extract, tumor biopsies and vitreous humor. Based on the need for experimental work, a proper choice of the assay and internal standard may be made using the choices in the literature. While the chemical methods involving high-performance liquid chromatography (HPLC) or LC coupled with triple quadrupole mass spectrometry (LC-MS/MS) are popular, enzymatic assays, in spite of their higher bias, have been used for the routine drug monitoring of MPA. The objectives of the present review are: (a) to provide a focused systematic compilation of the HPLC or LC-MS/MS methods for MPA, MPAG and/or AcMPAG published in the last decade (2005 to current) to enable visual comparison of the methods; (b) to compare and contrast a few enzymatic assays with those of the chemical methods; and (c) to discuss relevant issues/limitations and perspectives on select assays under various subheadings. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26766308

  17. Nonamplification Sandwich Assay Platform for Sensitive Nucleic Acid Detection Based on AuNPs Enumeration with the Dark-Field Microscope.

    PubMed

    Li, Tian; Xu, Xiao; Zhang, Guoqing; Lin, Ruoyun; Chen, Yang; Li, Chenxi; Liu, Feng; Li, Na

    2016-04-19

    A simple and efficient assay platform with high sensitivity, convenient implementation, and moderate cost in reagents and instrumentation is most appropriate for routine applications. On the basis of the gold nanoparticle (AuNP) enumeration signal readout mode established in our laboratory, we have developed a nonamplification sandwich assay for nucleic acid detection with the 3 fM limit of detection for a sequence related to Alzheimer's disease. This AuNP counting based method takes advantages of the distinctive and strong localized surface plasmon resonance light scattering with the dark-field microscope and magnetic separation. It is shown that the presence of 20 nM random DNA sequence or calf thymus DNA with a mass up to 10(6)-fold of the targets do not significantly interfere with the assay signal. The spike recoveries of Hela cell lysate sample at 109.3% for 20 pM target and 110.5% for 100 pM target indicate the potential of this proposed method in practical sample applications. This nonamplification sandwich assay platform in principle is applicable to other assays such as the immunoassay and thus would be expected to find a breadth of applications that can make the best use of the simplicity and sensitivity. PMID:27023372

  18. Emerging applications of the single cell gel electrophoresis (Comet) assay. I. Management of invasive transitional cell human bladder carcinoma. II. Fluorescent in situ hybridization Comets for the identification of damaged and repaired DNA sequences in individual cells.

    PubMed

    McKelvey-Martin, V J; Ho, E T; McKeown, S R; Johnston, S R; McCarthy, P J; Rajab, N F; Downes, C S

    1998-01-01

    ABSTRACT I: Management of invasive transitional cell human bladder carcinoma. The two main treatment options for invasive transitional cell bladder carcinoma are radiotherapy or primary cystectomy with urinary diversion or bladder substitution. Approximately 50% of patients fail to respond to radiotherapy and such patients so treated are disadvantaged by the absence of predictive information regarding their radiosensitivity, since the tumour gains additional time for metastatic spread before cystectomy is performed. The SF2 clonogenic assay, which measures the surviving fraction of tumour cells after 2 Gy X-ray irradiation, is regarded as a good measure of radiosensitivity. However, the assay is time consuming and provides results for only approximately 70% of human tumours. In this paper three bladder transitional cell carcinoma cell lines (HT1376, UMUC-3 and RT112) were exposed to X-irradiation (0-10 Gy). We have compared the responses obtained using a clonogenic assay and a more clinically feasible alkaline single cell gel electrophoresis (Comet) assay. A very good inverse correlation was obtained between cell survival (clonogenic assay) and mean tail moment (Comet assay) for the three cell lines, indicating that the Comet assay can be used to predict the radio-responsiveness of individual cell lines. The clinical usefulness of the assay for predicting response to radiotherapy in bladder cancer patients is currently being investigated. ABSTRACT II: Fluorescent in situ hybridization (FISH) Comets for the identification of damaged and repaired DNA sequences in individual cells. In mammalian cells the extent of DNA damage is partly and the rate of DNA repair very considerably dependent on DNA position and transcription. This has been established by biochemical techniques which are labour intensive and require large numbers of cells. The Comet assay for overall DNA damage and repair is relatively simple and allows individual cells to be examined. Here we present a

  19. Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15.

    PubMed

    Huzly, Daniela; Korn, Klaus; Bierbaum, Sibylle; Eberle, Björn; Falcone, Valeria; Knöll, Antje; Steininger, Philipp; Panning, Marcus

    2016-09-01

    The influenza season 2014/15 was dominated by drift variants of influenza A(H3N2), which resulted in a reduced vaccine effectiveness. It was not clear if the performance of commercial nucleic-acid-based amplification (NAT) assays for the detection of influenza was affected. The purpose of this study was to perform a real-life evaluation of two commercial NAT assays. During January-April 2015, we tested a total of 665 samples from patients with influenza-like illness using the Fast Track Diagnostics Respiratory pathogens 21, a commercial multiplex kit, (cohorts 1 and 2, n = 563 patients) and the Xpert Flu/RSV XC assay (cohort 3, n = 102 patients), a single-use cartridge system. An in-house influenza real-time RT-PCR (cohort 1) and the RealStar Influenza RT-PCR 1.0 Kit (cohort 2 and 3) served as reference tests. Compared to the reference assay, an overall agreement of 95.9 % (cohort 1), 95 % (cohort 2), and 98 % (cohort 3) was achieved. A total of 24 false-negative results were observed using the Fast Track Diagnostics Respiratory pathogens 21 kit. No false-negative results occurred using the Xpert Flu/RSV XC assay. The Fast Track Diagnostics Respiratory pathogens 21 kit and the Xpert Flu/RSV XC assay had sensitivities of 90.7 % and 100 % and specificities of 100 % and 94.1 %, respectively, compared to the RealStar 1.0 kit. Upon modification of the Fast Track Diagnostics Respiratory pathogens 21 kit, the sensitivity increased to 97.3 %. Influenza virus strains circulating during the 2014/15 season reduced the detection sensitivity of a commercial NAT assay, and continuous monitoring of test performance is therefore necessary. PMID:27316440

  20. Expression of Serum Sialic Acid, Early Antigen-IgA, and Viral Capsid Antigen-IgA in Nasopharynx Cancer Patients: The Diagnostic Implication of Combined Assays.

    PubMed

    Sun, Yuning; Sun, Caibo; Zhang, Endong

    2015-01-01

    BACKGROUND Ebstein-Barr virus (EBV) plays a critical role in nasopharynx cancer, which can be effectively monitored by serum levels of early antigen antibody (EA-IgA) and viral capsid antigen antibody (VCA-IgA). This study explored the diagnostic value of combined assays of sialic acid (SA), EA-IgA, and VCA-IgA via the expressional assay. MATERIAL AND METHODS A total of 42 nasopharynx cancer patients and 42 benign rhinitis and healthy controls were recruited in this study. Serum EA-IgA and VCA-IgA were tested by enzyme-linked immunosorbent assay (ELISA) and enzymatic assay of serum SA. Specificity and sensitivity of those 3 assays were compared. The diagnostic value of each parameter was evaluated by ROC curves. RESULTS All 3 indexes (SA, EA-IgA and VCA-IgA) showed elevated serum levels in nasopharynx cancer patients when compared to those with rhinitis, who had higher levels than healthy individuals. Concentrations of these factors were also positively correlated with the TNM staging of cancer. The sensitivity and specificity were 30.95% and 83.33% (in SA), 57.14% and 95.24% (in EA-IgA), and 76.19% and 92.86% (in VCA-IgA), respectively. VCA-IgA had the highest sensitivity among all 3 indexes. The combined assay increased the diagnostic sensitivity to 92.86% without compromising specificity. CONCLUSIONS SA, EA-IgA, and VCA-IgA levels were significantly elevated in nasopharynx patients' serum. The combined assay may have clinical value in diagnosis and monitoring. PMID:26709095

  1. Expression of Serum Sialic Acid, Early Antigen-IgA, and Viral Capsid Antigen-IgA in Nasopharynx Cancer Patients: The Diagnostic Implication of Combined Assays

    PubMed Central

    Sun, Yuning; Sun, Caibo; Zhang, Endong

    2015-01-01

    Background Ebstein-Barr virus (EBV) plays a critical role in nasopharynx cancer, which can be effectively monitored by serum levels of early antigen antibody (EA-IgA) and viral capsid antigen antibody (VCA-IgA). This study explored the diagnostic value of combined assays of sialic acid (SA), EA-IgA, and VCA-IgA via the expressional assay. Material/Methods A total of 42 nasopharynx cancer patients and 42 benign rhinitis and healthy controls were recruited in this study. Serum EA-IgA and VCA-IgA were tested by enzyme-linked immunosorbent assay (ELISA) and enzymatic assay of serum SA. Specificity and sensitivity of those 3 assays were compared. The diagnostic value of each parameter was evaluated by ROC curves. Results All 3 indexes (SA, EA-IgA and VCA-IgA) showed elevated serum levels in nasopharynx cancer patients when compared to those with rhinitis, who had higher levels than healthy individuals. Concentrations of these factors were also positively correlated with the TNM staging of cancer. The sensitivity and specificity were 30.95% and 83.33% (in SA), 57.14% and 95.24% (in EA-IgA), and 76.19% and 92.86% (in VCA-IgA), respectively. VCA-IgA had the highest sensitivity among all 3 indexes. The combined assay increased the diagnostic sensitivity to 92.86% without compromising specificity. Conclusions SA, EA-IgA, and VCA-IgA levels were significantly elevated in nasopharynx patients’ serum. The combined assay may have clinical value in diagnosis and monitoring. PMID:26709095

  2. Localization of glucocorticoid receptor messenger ribonucleic acid in hippocampus of rat brain using in situ hybridization.

    PubMed

    Yang, G; Matocha, M F; Rapoport, S I

    1988-08-01

    An in situ hybridization procedure was applied to quantify glucocorticoid receptor (GR) mRNAs in the hippocampus of rat brain. Hybridization was carried out using a radiolabeled antisense probe complementary to the rat liver GR gene. The specificity of the method was validated by showing: 1) a high cellular grain density in sections hybridized with an antisense but not a sense probe; 2) agreement between the experimental and theoretical temperature at which 50% of the hybrids melted, and 3) a high signal distribution of GR mRNA in the hippocampus, a region of brain known to preferentially concentrate steroid hormones. Within the hippocampus, however, subregional differences in hybridization densities were observed. Quantitative autoradiography indicated that the average neuronal silver grain number was highest in the pyramidal cell layers of CA2 and CA4 and lowest in those of CA1 and CA3. Also, there was a significant difference in the average grain number between all of the cell fields except for that between CA2 and CA4. These results show that contiguous but neuroanatomically distinct cell fields of the hippocampus express different levels of GR transcripts, and indicate that differential regulation of GR expression occurs in subpopulations of hippocampal neurons. PMID:3211154

  3. Localization of glucocorticoid receptor messenger ribonucleic acid in hippocampus of rat brain using in situ hybridization

    SciTech Connect

    Yang, G.; Matocha, M.F.; Rapoport, S.I.

    1988-08-01

    An in situ hybridization procedure was applied to quantify glucocorticoid receptor (GR) mRNAs in the hippocampus of rat brain. Hybridization was carried out using a radiolabeled antisense probe complementary to the rat liver GR gene. The specificity of the method was validated by showing: 1) a high cellular grain density in sections hybridized with an antisense but not a sense probe; 2) agreement between the experimental and theoretical temperature at which 50% of the hybrids melted, and 3) a high signal distribution of GR mRNA in the hippocampus, a region of brain known to preferentially concentrate steroid hormones. Within the hippocampus, however, subregional differences in hybridization densities were observed. Quantitative autoradiography indicated that the average neuronal silver grain number was highest in the pyramidal cell layers of CA2 and CA4 and lowest in those of CA1 and CA3. Also, there was a significant difference in the average grain number between all of the cell fields except for that between CA2 and CA4. These results show that contiguous but neuroanatomically distinct cell fields of the hippocampus express different levels of GR transcripts, and indicate that differential regulation of GR expression occurs in subpopulations of hippocampal neurons.

  4. Development of a real-time PCR genotyping assay to identify high oleic acid peanuts (Arachis hypogaea L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oleic acid, a monounsaturated, omega-9 fatty acid found in peanut (Arachis hypogaea L.) oil is an important seed quality trait because it provides increased shelf life, improved flavor, enhanced fatty acid composition, and has a beneficial effect on human health. Hence, a concentrated effort has be...

  5. Strong, Thermally Superinsulating Biopolymer-Silica Aerogel Hybrids by Cogelation of Silicic Acid with Pectin.

    PubMed

    Zhao, Shanyu; Malfait, Wim J; Demilecamps, Arnaud; Zhang, Yucheng; Brunner, Samuel; Huber, Lukas; Tingaut, Philippe; Rigacci, Arnaud; Budtova, Tatiana; Koebel, Matthias M

    2015-11-23

    Silica aerogels are excellent thermal insulators, but their brittle nature has prevented widespread application. To overcome these mechanical limitations, silica-biopolymer hybrids are a promising alternative. A one-pot process to monolithic, superinsulating pectin-silica hybrid aerogels is presented. Their structural and physical properties can be tuned by adjusting the gelation pH and pectin concentration. Hybrid aerogels made at pH 1.5 exhibit minimal dust release and vastly improved mechanical properties while remaining excellent thermal insulators. The change in the mechanical properties is directly linked to the observed "neck-free" nanoscale network structure with thicker struts. Such a design is superior to "neck-limited", classical inorganic aerogels. This new class of materials opens up new perspectives for novel silica-biopolymer nanocomposite aerogels. PMID:26447457

  6. Proton conductive inorganic-organic hybrid membranes functionalized with phosphonic acid for polymer electrolyte fuel cell

    NASA Astrophysics Data System (ADS)

    Umeda, Junji; Suzuki, Masashi; Kato, Masaki; Moriya, Makoto; Sakamoto, Wataru; Yogo, Toshinobu

    Proton conductive sol-gel derived hybrid membranes were synthesized from aromatic derivatives of methoxysilanes and ethyl 2-[3-(dihydroxyphosphoryl)-2-oxapropyl]acrylate (EPA). Two aromatic derivatives of methoxysilanes with different number of methoxy groups were used as the starting materials. Hybrid membranes from difunctional (methyldimethoxysilylmethyl)styrene (MDMSMS(D))/EPA revealed a higher chemical stability and mechanical properties than those from monofunctional (dimethylmethoxysilylmethyl)styrene (DMMSMS(M))/EPA. The membrane-electrode assembly (MEA) using the hybrid membranes as electrolytes worked as a fuel cell at 100 °C under saturated humidity. The DMMSMS(M)/EPA membrane-based MEA showed a larger current density than that from MDMSMS(D)/EPA. On the other hand, the MDMSMS(D)/EPA membrane-based MEA exhibited higher open circuit voltages than the DMMSMS(M)/EPA-based MEA, and was stable during fuel cell operation at 80 °C at least for 48 h.

  7. Enantiomer separation of acidic chiral compounds on a quinine-silica/zirconia hybrid monolith by capillary electrochromatography.

    PubMed

    Tran, Le Ngoc; Park, Jung Hag

    2015-05-29

    A weak anion-exchanger chiral selector, quinine-incorporated silica/zirconia hybrid monolithic (QUI-S/ZHM) capillary column was prepared by sol-gel technology. The performance of the QUI-S/ZHM column was investigated for enantioresolution of a set of acidic chiral drugs and dinitrobenzoyl (DNB)-amino acids by capillary electrochromatography in aqueous organic mobile phases composed of acetonitrile (ACN) and triethylammonium acetate (TEAA) buffer. Effects of several parameters including the ACN content, concentration and pH of the mobile phase on the chiral separation were examined. Baseline resolutions of all the compounds were obtained in the mobile phase consisting of 70:30 ACN/TEAA (10mM, pH 6) under applied voltage of -10kV at 25°C within 20min. PMID:25892638

  8. Synthesis and properties of poly(methyl methacrylate-2-acrylamido-2-methylpropane sulfonic acid)/PbS hybrid composite

    SciTech Connect

    Preda, N.; Rusen, E.; Musuc, A.; Enculescu, M.; Matei, E.; Marculescu, B.; Fruth, V.; Enculescu, I.

    2010-08-15

    The synthesis of a new hybrid composite based on PbS nanoparticles and poly(methyl methacrylate-2-acrylamido-2-methylpropane sulfonic acid) [P(MMA-AMPSA)] copolymer is reported. The chemical synthesis consists in two steps: (i) a surfactant-free emulsion copolymerization between methyl methacrylate and 2-acrylamido-2-methylpropane sulfonic acid and (ii) the generation of PbS particles in the presence of the P(MMA-AMPSA) latex, from the reaction between lead nitrate and thiourea. The composite was studied by scanning electron microscopy (SEM), X-ray diffraction, FTIR spectroscopy, thermogravimetric analysis and differential scanning calorimetry. The microstructure observed using SEM proves that the PbS nanoparticles are well dispersed in the copolymer matrix. The X-ray diffraction measurements demonstrate that the PbS nanoparticles have a cubic rock salt structure. It was also found that the inorganic semiconductor nanoparticles improve the thermal stability of the copolymer matrix.

  9. Utilization of a rapid DNA-based assay for molecular verification of channel catfish, blue catfish, F1 hybrid, and backcross offspring at serveral life stages

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The F1 hybrid offspring of channel catfish, Ictalurus punctatus, females mated with blue catfish, I. furcatus, males contain many desirable traits for commercial production such as enhanced growth and increased survivability. Although at a low efficiency, hybrids can be produced by pond spawning, b...

  10. A split-ubiquitin two-hybrid screen for proteins physically interacting with the yeast amino acid transceptor Gap1 and ammonium transceptor Mep2.

    PubMed

    Van Zeebroeck, Griet; Kimpe, Marlies; Vandormael, Patrick; Thevelein, Johan M

    2011-01-01

    Several nutrient permeases have been identified in yeast, which combine a transport and receptor function, and are called transceptors. The Gap1 general amino acid permease and the Mep2 ammonium permease mediate rapid activation by amino acids and by ammonium, respectively, of the protein kinase A (PKA) pathway in nitrogen-starved cells. Their mode of action is not well understood. Both proteins are subject to complex controls governing their intracellular trafficking. Using a split-ubiquitin yeast two-hybrid screen with Gap1 or Mep2 as bait, we identified proteins putatively interacting with Gap1 and/or Mep2. They are involved in glycosylation, the secretory pathway, sphingolipid biosynthesis, cell wall biosynthesis and other processes. For several candidate interactors, determination of transport and signaling capacity, as well as localization of Gap1 or Mep2 in the corresponding deletion strains, confirmed a functional interaction with Gap1 and/or Mep2. Also common interacting proteins were identified. Transport and signaling were differentially affected in specific deletion strains, clearly separating the two functions of the transceptors and confirming that signaling does not require transport. We identified two new proteins, Bsc6 and Yir014w, that affect trafficking or downregulation of Gap1. Deletion of EGD2, YNL024c or SPC2 inactivates Gap1 transport and signaling, while its plasma membrane level appears normal.. Vma4 is required for Mep2 expression, while Gup1 appears to be required for proper distribution of Mep2 over the plasma membrane. Some of the interactions were confirmed by GST pull-down assay, using the C-terminal tail of Gap1 or Mep2 expressed in E.coli. Our results reveal the effectiveness of split-ubiquitin two-hybrid screening for identification of proteins functionally interacting with membrane proteins. They provide several candidate proteins involved in the transport and signaling function or in the complex trafficking control of the Gap1

  11. Flow Analysis of Amino Acids by Using a Newly Developed Aminoacyl-tRNA Synthetase-Immobilized, Small Reactor Column-Based Assay.

    PubMed

    Kugimiya, Akimitsu; Konishi, Hidenori; Fukada, Rie

    2016-03-01

    Abnormal concentrations of amino acids in blood and urine can be indicative of several diseases, including cancer and diabetes. Therefore, analyses that examine amino acid concentrations are useful for the diagnosis of such diseases. In this study, we developed an enzyme-immobilized, small reactor column for flow analysis of amino acid concentrations. For the recognition of asparagine and lysine, asparaginyl-tRNA synthetase and lysyl-tRNA synthase were immobilized onto microparticles, respectively, and coupled with coloration reagents for spectrophotometric detection. This assay has some advantages in the analytical field, such as the ability to detect small amounts of analyte, allowing for the use of a small reaction volume, and ensuring a rapid and efficient reaction rate. This approach provided selective quantitation of up to 480 μM of asparagine and lysine in 200 mM Tris-HCl buffer (pH 8.0). PMID:26554858

  12. Genotoxicity evaluation of benzene, di(2-ethylhexyl) phthalate, and trisodium ethylenediamine tetraacetic acid monohydrate using a combined rat comet/micronucleus assays.

    PubMed

    Kitamoto, Sachiko; Matsuyama, Ryoko; Uematsu, Yasuaki; Ogata, Keiko; Ota, Mika; Yamada, Toru; Miyata, Kaori; Kimura, Juki; Funabashi, Hitoshi; Saito, Koichi

    2015-07-01

    As a part of the Japanese Center for the Validation of Alternative Methods (JaCVAM)-initiative international validation study of the in vivo alkaline comet assay (comet assay), we examined DNA damage in the liver, stomach, and bone marrow of rats dosed orally three times with up to 2000 mg/kg of benzene, di(2-ethylhexyl) phthalate, and trisodium ethylenediamine tetraacetic acid monohydrate. All three compounds gave negative results in the liver and stomach. In addition, a bone marrow comet and micronucleus analysis revealed that benzene, but not di(2-ethylhexyl) phthalate or trisodium ethylenediamine tetraacetic acid monohydrate induced a significant increase in the median % tail DNA and micronucleated polychromatic erythrocytes, compared with the respective concurrent vehicle control. These results were in good agreement with the previously reported genotoxicity findings for each compound. The present study has shown that combining the micronucleus test with the comet assay and carrying out these analyses simultaneously is effective in clarifying the mechanism of action of genotoxic compounds such as benzene. PMID:26212304

  13. High-sensitivity ascorbic acid sensor using graphene sheet/graphene nanoribbon hybrid material as an enhanced electrochemical sensing platform.

    PubMed

    Lavanya, J; Gomathi, N

    2015-11-01

    A novel electrode material of graphene sheet/graphene nanoribbon (GS/GNR) hybrid material was developed by incorporating graphene nanoribbons into graphene nanosheets through simultaneous chemical reduction of graphene oxide sheets and graphene oxide ribbons. The structure and properties of synthesized GS/GNR were characterized by transmission electron microscope, scanning electron microscope, X-ray diffraction, Brunauer Emmett Teller measurements and Fourier transform infrared spectroscopy. This work compares the electro catalytic performance of the GS/GNR, chemically reduced graphene oxide sheets (CRGOS) and GS/carbon nanotube (CNT) by modifying the glassy carbon electrode (GCE) using ascorbic acid (AA) as analyte. The electrochemical impedance spectroscopy revealed that the charge transfer resistance of GS/GNR modified electrode was less than that of CRGOS modified electrode and bare GCE. The cyclic voltammetric sensing of GS/GNR modified electrode towards AA was negatively shifted (0.08 V) compared to CRGOS, GS/CNT modified electrode and bare GCE (0.222, 0.150 and 0.666 V). This catalytic oxidation allows an amperometric detection of AA with a detection limit of 230 nM and sensitivity of 22 nA μM(-1) cm(-2). GS/GNR modified GCE exhibited a high selectivity for ascorbic acid in the presence of other interferents like dopamine, uric acid and citric acid. PMID:26452874

  14. The fluorescent two-hybrid assay to screen for protein-protein interaction inhibitors in live cells: targeting the interaction of p53 with Mdm2 and Mdm4.

    PubMed

    Yurlova, Larisa; Derks, Maarten; Buchfellner, Andrea; Hickson, Ian; Janssen, Marc; Morrison, Denise; Stansfield, Ian; Brown, Christopher J; Ghadessy, Farid J; Lane, David P; Rothbauer, Ulrich; Zolghadr, Kourosh; Krausz, Eberhard

    2014-04-01

    Protein-protein interactions (PPIs) are attractive but challenging targets for drug discovery. To overcome numerous limitations of the currently available cell-based PPI assays, we have recently established a fully reversible microscopy-assisted fluorescent two-hybrid (F2H) assay. The F2H assay offers a fast and straightforward readout: an interaction-dependent co-localization of two distinguishable fluorescent signals at a defined spot in the nucleus of mammalian cells. We developed two reversible F2H assays for the interactions between the tumor suppressor p53 and its negative regulators, Mdm2 and Mdm4. We then performed a pilot F2H screen with a subset of compounds, including small molecules (such as Nutlin-3) and stapled peptides. We identified five cell-penetrating compounds as potent p53-Mdm2 inhibitors. However, none exhibited intracellular activity on p53-Mdm4. Live cell data generated by the F2H assays enable the characterization of stapled peptides based on their ability to penetrate cells and disrupt p53-Mdm2 interaction as well as p53-Mdm4 interaction. Here, we show that the F2H assays enable side-by-side analysis of substances' dual Mdm2-Mdm4 activity. In addition, they are suitable for testing various types of compounds (e.g., small molecules and peptidic inhibitors) and concurrently provide initial data on cellular toxicity. Furthermore, F2H assays readily allow real-time visualization of PPI dynamics in living cells. PMID:24476585

  15. Ampholine-functionalized hybrid organic-inorganic silica material as sorbent for solid-phase extraction of acidic and basic compounds.

    PubMed

    Wang, Tingting; Chen, Yihui; Ma, Junfeng; Chen, Mingliang; Nie, Chenggang; Hu, Minjie; Li, Ying; Jia, Zhijian; Fang, Jianghua; Gao, Haoqi

    2013-09-20

    A novel sorbent for solid-phase extraction (SPE) was synthesized by chemical immobilization of ampholine on hybrid organic-inorganic silica material. The ampholine-functionalized hybrid organic-inorganic silica sorbent is consisted of aliphatic amine groups, carboxyl groups and long carbon chains, allowing for extraction of both acidic and basic compounds. The retention properties of the developed sorbent were evaluated for 1-hydroxy-2-naphthoic acid (HNA), 1-naphthoic acid (NA), 3-hydroxybenzoic acid (HBA), benzoic acid (BA), sorbic acid (SA), vanillic aldehyde (VA), butyl 4-hydroxybenzoate (BHB), propyl 4-hydroxybenzoate (PHB), ethyl 4-hydroxybenzoate (EHB), and methyl 4-hydroxybenzoate (MHB). The results show that such a sorbent has three types of interaction, i.e., electrostatic interaction, hydrophobic interaction, and hydrogen bonding, exhibiting high extraction efficiency towards the compounds tested. The adsorption capacities of the analytes ranged from 0.61 to 6.54μgmg(-1). The reproducibility of the sorbent preparation was evaluated at three spiking concentration levels, with relative standard deviations (RSDs) of 1.0-10.5%. The recoveries of ten acidic and basic compounds spiked in beverage Coca-Cola(®) sample ranged from 82.5% to 98.2% with RSDs less than 5.8%. Under optimum conditions, the ampholine-functionalized hybrid organic-inorganic silica sorbent rendered higher extraction efficiency for acidic compounds than that of the commercially available ampholine-functionalized silica particles, and was comparable to that of the commercial Oasis WAX and Oasis WCX. PMID:23953713

  16. Novel Thiosemicarbazide Hybrids with Amino Acids and Peptides Against Hepatocellular Carcinoma: A Molecular Designing Approach Towards Multikinase Inhibitor.

    PubMed

    Chacko, Shinu; Samanta, Subir

    2015-01-01

    Hepatocellular Carcinoma is the most common primary malignant tumor of the liver. Development of multidrug resistance is the main obstacle to the success of anticancer drugs. In this study, designing and docking study of thiosemicarbazide hybrids with amino acids or peptides against hepatocellular carcinoma was performed since hybrids of biologically active compounds with amino acids or peptides may show target specificity and lower toxicity. All the structures were drawn in 2D platform and converted to the 3D platform using ChemDraw 10.0. Evaluations of ADME properties were done by using QikProp 3.0 to check for the possibility of oral delivery. In silico prediction of LD50 values were performed using Pro-Tox webserver. Interestingly, it was found that conjugation with amino acids decreases toxicity and increases the therapeutic index of thiosemicarbazide. Finally, all the compounds were docked to the crystal structure of the Vascular Endothelial Growth Factor Receptor-2 and Checkpoint kinase-1 utilizing Glide 5.0, Schrödinger 8.5, to understand the interaction of ligands with the receptor. A significant number of derivatives have been found active in both the receptors and also displayed multikinase inhibitory activity similar to Sorafenib, against hepatocellular carcinoma. Further, wet lab synthesis, in vitro ADMET and biological screening studies need to be performed to prove that designed compounds are effective against hepatocellular carcinoma as predicted by molecular modeling. However, as predicted by molecular modeling, the efficacy of designed compounds against hepatocellular carcinoma, needs to be confirmed by wet lab synthesis, in vitro ADMET and biological screening studies. PMID:26526710

  17. Self-assembly of nucleic acids, silk and hybrid materials thereof

    NASA Astrophysics Data System (ADS)

    Humenik, Martin; Scheibel, Thomas

    2014-12-01

    Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here, we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.

  18. Alkyl substituent effects on gas-phase acidities - The influence of hybridization.

    NASA Technical Reports Server (NTRS)

    Brauman, J. I.; Blair, L. K.

    1971-01-01

    Exploration of the effect on acidity of alkyl groups bonded to trigonal and digonal carbon. Some results on the relative acidities of toluene and p-xylene, and acetylene and substitute acetylenes, as determined by ion cyclotron resonance (icr) spectroscopy, are described. Some limitations of the CNDO/2 calculation method are discussed.

  19. HPLC-PDA method for quinovic acid glycosides assay in Cat's claw (Uncaria tomentosa) associated with UPLC/Q-TOF-MS analysis.

    PubMed

    Pavei, Cabral; Kaiser, Samuel; Verza, Simone Gasparin; Borre, Gustavo Luis; Ortega, George Gonzalez

    2012-03-25

    Uncaria tomentosa (Willd.) is a medicinal plant largely used in folk medicine due to its wide range of biological activities, many of which are usually ascribed to the two main classes of secondary metabolites, namely, alkaloids and quinovic acid glycosides. In this work, a reversed phase HPLC-PDA method was developed and validated for the assay of quinovic acid glycosides in crude and dried extracts of Uncaria tomentosa (Cat's claw) bark. The validation comprised tests of specificity, accuracy, linearity, intermediate precision, repeatability and limits of detection and of quantification. Alpha-hederin was used as the external standard. High coefficients of determination with lower R.S.D. were achieved for both external standard and crude extract. The structural characterization of the main quinovic acid glycosides presented in the crude extract was carried out through UPLC/Q-TOF-MS. The identities of the compounds were obtained through the comparison of their fragmentation patterns with those reported in the literature. The analytical method was successfully applied for quantifying quinovic acid glycosides in two different dried extracts from U. tomentosa and in one quinovic acid glycosides purified fraction. PMID:22296654

  20. Assay of calcium borogluconate veterinary medicines for calcium gluconate, boric acid, phosphorus, and magnesium by using inductively coupled plasma emission spectrometry

    SciTech Connect

    Lyons, D.J.; Spann, K.P.

    1985-03-01

    An inductively coupled plasma spectrometric method is described for the determination of 4 elements (Ca, B, P, and Mg) in calcium borogluconate veterinary medicines. Samples are diluted, acidified, and sprayed directly into the plasma. Reproducibility relative confidence intervals for a single sample assay are +/- 1.4% (calcium), +/- 1.8% (boron), +/- 2.6% (phosphorus), and +/- 1.4% (magnesium). The total element concentrations for each of 4 elements compared favorably with concentrations determined by alternative methods. Formulation estimates of levels of calcium gluconate, boric acid, phosphorus, and magnesium salts can be made from the analytical data.

  1. Detection of Ganoderic Acid A in Ganoderma lingzhi by an Indirect Competitive Enzyme-Linked Immunosorbent Assay.

    PubMed

    Sakamoto, Seiichi; Kohno, Toshitaka; Shimizu, Kuniyoshi; Tanaka, Hiroyuki; Morimoto, Satoshi

    2016-05-01

    Ganoderma is a genus of medicinal mushroom traditionally used for treating various diseases. Ganoderic acid A is one of the major bioactive Ganoderma triterpenoids isolated from Ganoderma species. Herein, we produced a highly specific monoclonal antibody against ganoderic acid A (MAb 12 A) and developed an indirect competitive ELISA for the highly sensitive detection of ganoderic acid A in Ganoderma lingzhi, with a limit of detection of 6.10 ng/mL. Several validation analyses support the accuracy and reliability of the developed indirect competitive ELISA for use in the quality control of Ganoderma based on ganoderic acid A content. Furthermore, quantitative analysis of ganoderic acid A in G. lingzhi revealed that the pileus exhibits the highest ganoderic acid A content compared with the stipe and spore of the fruiting body; the best extraction efficiency was found when 50 % ethanol was used, which suggests the use of a strong liquor to completely harness the potential of Ganoderma triterpenoids in daily life. PMID:27093250

  2. In vitro antioxidant assay of medium chain fatty acid rich rice bran oil in comparison to native rice bran oil.

    PubMed

    Sengupta, Avery; Ghosh, Mahua; Bhattacharyya, D K

    2015-08-01

    The study aimed to evaluate the in vitro antioxidant activity of medium chain fatty acid (MCFA) rich-rice bran oils in comparison with native rice bran oil. Different in vitro methods were used to evaluate the free radical scavenging activity, metal chelation activity, reducing acitivity, ABTS radical scavenging activity, thiobarbituric acid (TBA) value and so on at different concentrations of the oils such as 10-100 μg/mL. Inhibition of lipid peroxidation was evaluated measuring thiobarbituric acid responsive substance (TBARS) and conjugated diene formation. All the oils showed potent antioxidant activity at 100 μg/mL concentration. TBARS formation and conjugated diene formation was lower with MCFA rich oils i.e. the inhibition of lipid peroxidation was more in MCFA rich oils than original rice bran oil. Caprylic acid rich rice bran oil showed maximum antioxidant activity in comparison to capric- and lauric acid rich rice bran oils. Overall the MCFA rich rice bran oils showed to be more potent antioxidant than rice bran oil due to their lower unsaturated fatty acid content. PMID:26243941

  3. Quantification of syntrophic fatty acid-{beta}-oxidizing bacteria in a mesophilic biogas reactor by oligonucleotide probe hybridization

    SciTech Connect

    Hansen, K.H.; Ahring, B.K.; Raskin, L.

    1999-11-01

    Small-subunit rRNA sequences were obtained for two saturated fatty acid-{beta}-oxidizing syntrophic bacteria, Syntrophomonas sapovorans and Syntrophomonas wolfei LYB, and sequence analysis confirmed their classification as members of the family Syntrophomonadaceae. S.wolfei LYB was closely related to S.wolfei subsp. solfei, but S. sapovorans did not cluster with the other members of the genus Syntrophomonas. Five oligonucleotide probes targeting the small-subunit rRNA of different groups within the family Syntrophomonadaceae, which contains all currently known saturated fatty acid-{beta}-oxidizing syntrophic bacteria, were developed and characterized. The probes were designed to be specific at the family, genus, and species levels and were characterized by temperature-of-dissociation and specificity studies. To demonstrate the usefulness of the probes for the detection and quantification of saturated fatty acid-{beta}-oxidizing syntrophic bacteria in methanogenic environments, the microbial community structure of a sample from a full-scale biogas plant was determined. Hybridization results with probes for syntrophic bacteria and methanogens were compared to specific methanogenic activities and microbial numbers determined with most-probable-number estimates. Most of the methanogenic rRNA was comprised of Methanomicrobiales rRNA, suggesting that members of this order served as the main hydrogen-utilizing microorganisms. Between 0.2 and 1% of the rRNA was attributed to the Syntrophomonadaceae, or which the majority was accounted for by the genus Syntrophomonas.

  4. Multidimensional separation of chiral amino acid mixtures in a multilayered three-dimensional hybrid microfluidic/nanofluidic device.

    PubMed

    Kim, Bo Young; Yang, Jing; Gong, Maojun; Flachsbart, Bruce R; Shannon, Mark A; Bohn, Paul W; Sweedler, Jonathan V

    2009-04-01

    Microscale total analysis systems (microTAS) allow high-throughput analyses by integrating multiple processes, parallelization, and automation. Here we combine unit operations of microTAS to create a device that can perform multidimensional separations using a three-dimensional hybrid microfluidic/nanofluidic device composed of alternating layers of patterned poly(methyl methacrylate) and nanocapillary array membranes constructed from nuclear track-etched polycarbonate. Two consecutive electrophoretic separations are performed, the first being an achiral separation followed by a chiral separation of a selected analyte band. Separation conditions are optimized for a racemic mixture of fluorescein-isothiocyanate-labeled amino acids, serine and aspartic acid, chosen because there are endogenous D-forms of these amino acids in animals. The chiral separation is implemented using micellar electrokinetic chromatography using beta-cyclodextrin as the chiral selector and sodium taurocholate as the micelle-forming agent. Analyte separation is monitored by dual-beam laser-induced fluorescence detection. After separation in the first electrophoretic channel, the preselected analyte is sampled by the second-stage separation using an automated collection sequence with a zero-crossing algorithm. The controlled fluidic environment inherent to the three-dimensional architecture enables a series of separations in varying fluidic environments and allows sample stacking via different background electrolyte pH conditions. The ability to interface sequential separations, selected analyte capture, and other fluidic manipulations in the third dimension significantly improves the functionality of multilayer microfluidic devices. PMID:19271741

  5. Quantification of Syntrophic Fatty Acid-β-Oxidizing Bacteria in a Mesophilic Biogas Reactor by Oligonucleotide Probe Hybridization

    PubMed Central

    Hansen, Kaare H.; Ahring, Birgitte K.; Raskin, Lutgarde

    1999-01-01

    Small-subunit rRNA sequences were obtained for two saturated fatty acid-β-oxidizing syntrophic bacteria, Syntrophomonas sapovorans and Syntrophomonas wolfei LYB, and sequence analysis confirmed their classification as members of the family Syntrophomonadaceae. S. wolfei LYB was closely related to S. wolfei subsp. wolfei, but S. sapovorans did not cluster with the other members of the genus Syntrophomonas. Five oligonucleotide probes targeting the small-subunit rRNA of different groups within the family Syntrophomonadaceae, which contains all currently known saturated fatty acid-β-oxidizing syntrophic bacteria, were developed and characterized. The probes were designed to be specific at the family, genus, and species levels and were characterized by temperature-of-dissociation and specificity studies. To demonstrate the usefulness of the probes for the detection and quantification of saturated fatty acid-β-oxidizing syntrophic bacteria in methanogenic environments, the microbial community structure of a sample from a full-scale biogas plant was determined. Hybridization results with probes for syntrophic bacteria and methanogens were compared to specific methanogenic activities and microbial numbers determined with most-probable-number estimates. Most of the methanogenic rRNA was comprised of Methanomicrobiales rRNA, suggesting that members of this order served as the main hydrogen-utilizing microorganisms. Between 0.2 and 1% of the rRNA was attributed to the Syntrophomonadaceae, of which the majority was accounted for by the genus Syntrophomonas. PMID:10543784

  6. Structure-activity relationship of hybrids of Cinchona alkaloids and bile acids with in vitro antiplasmodial and antitrypanosomal activities.

    PubMed

    Leverrier, Aurélie; Bero, Joanne; Cabrera, Julián; Frédérich, Michel; Quetin-Leclercq, Joëlle; Palermo, Jorge A

    2015-07-15

    In this work, a series of hybrid compounds were tested as antiparasitic substances. These hybrids were prepared from bile acids and a series of antiparasitic Cinchona alkaloids by the formation of a covalent C-C bond via a decarboxylative Barton-Zard reaction between the two entities. The bile acids showed only weak antiparasitic properties, but all the hybrids exhibited high in vitro activities (IC50: 0.48-5.39 μM) against Trypanosoma brucei. These hybrids were more active than their respective parent alkaloids (up to a 135 fold increase in activity), and displayed good selectivity indices. Aditionally, all these compounds inhibited the in vitro growth of a chloroquine-sensitive strain of Plasmodium falciparum (3D7: IC50: 36.1 nM to 8.72 μM), and the most active hybrids had IC50s comparable to that of artemisinin (IC50: 36 nM). Some structure-activity relationships among the group of 48 hybrids are discussed. The increase in antiparasitic activity may be explained by an improvement in bioavailability, since the more lipophilic derivatives showed the lowest IC50s. PMID:26063305

  7. Molecular beacons: Probes that fluoresce upon hybridization

    SciTech Connect

    Tyagi, S.; Kramer, F.R.

    1996-03-01

    We have developed novel nucleic acid probes that recognize and report the presence of specific nucleic acids in homogeneous solutions. These probes undergo a spontaneous fluorogenic conformational change when they hybridize to their targets. Only perfectly complementary targets elicit this response, as hybridization does not occur when the target contains a mismatched nucleotide or a deletion. The probes are particularly suited for monitoring the synthesis of specific nucleic acids in real time. When used in nucleic acid amplification assays, gene detection is homogeneous and sensitive, and can be carried out in a sealed tube. When introduced into living cells, these probes should enable the origin, movement, and fate of specific mRNAs to be traced. 23 refs., 6 figs.

  8. Modeling of the cranking and charging processes of conventional valve regulated lead acid (VRLA) batteries in micro-hybrid applications

    NASA Astrophysics Data System (ADS)

    Gou, Jun; Lee, Anson; Pyko, Jan

    2014-10-01

    The cranking and charging processes of a VRLA battery during stop-start cycling in micro-hybrid applications were simulated by one dimensional mathematical modeling, to study the formation and distribution of lead sulfate across the cell and analyze the resulting effect on battery aging. The battery focused on in this study represents a conventional VRLA battery without any carbon additives in the electrodes or carbon-based electrodes. The modeling results were validated against experimental data and used to analyze the "sulfation" of negative electrodes - the common failure mode of lead acid batteries under high-rate partial state of charge (HRPSoC) cycling. The analyses were based on two aging mechanisms proposed in previous studies and the predictions showed consistency with the previous teardown observations that the sulfate formed at the negative interface is more difficult to be converted back than anywhere else in the electrodes. The impact of cranking pulses during stop-start cycling on current density and the corresponding sulfate layer production was estimated. The effects of some critical design parameters on sulfate formation, distribution and aging over cycling were investigated, which provided guidelines for developing models and designing of VRLA batteries in micro-hybrid applications.

  9. Luminescent molecular hybrid system derived from 2-furancarboxylic acid and silylated monomer coordinated to rare earth ions

    NASA Astrophysics Data System (ADS)

    Sui, Yu-Long; Yan, Bing

    2006-04-01

    In this study, silica-based organic-inorganic hybrids were prepared by the sol-gel method. Tetraethoxysilane (abbreviated as TEOS) and a kind of monomer (abbreviated as FA-APES) derived from modified 2-furancarboxylic acid (abbreviated as FA) with (3-aminopropyl)triethoxysilane (abbreviated as APES) were used as the inorganic and organic fragments, respectively. Coordination reaction between lanthanides (europium and terbium ions) and sbnd C dbnd O group of the monomer happened simultaneously. And after days of aging process the resultant materials showed characteristic luminescence of lanthanides. The enhancement of luminescence can be seen by the comparison with simply doped lanthanide hybrid systems. And it can be explained by the coordination ability of the organic counterpart. IR, NMR, UV-vis absorption, low-temperature phosphorescence spectroscopy and fluorescence spectroscopy were applied to characterize and the above spectroscopic data revealed that the triplet state energy of organic ligand matches with the emissive energy level of lanthanides (especially of Tb 3+).

  10. Hybrids from 4-anilinoquinazoline and hydroxamic acid as dual inhibitors of vascular endothelial growth factor receptor-2 and histone deacetylase.

    PubMed

    Peng, Fan-Wei; Wu, Ting-Ting; Ren, Zi-Wei; Xue, Jia-Yu; Shi, Lei

    2015-11-15

    A series of hybrids derived from 4-anilinoquinazoline and hydroxamic acid were designed, synthesized, and evaluated as dual inhibitors of vascular endothelia growth factor receptor-2 (VEGFR-2) tyrosine kinase and histone deacetylase (HDAC). Most of these compounds exhibited potent HDAC inhibition and moderate VEGFR-2 inhibition. Among them, compound 6l exhibited the most potent inhibitory activities against VEGFR-2 (IC50=84 nM) and HDAC (IC50=2.8 nM). It also showed the most potent antiproliferative ability against MCF-7, a human breast cancer line, with IC50 of 1.2 μM. Docking simulation supported the initial pharmacophoric hypothesis and suggested a common mode of interaction of compound 6l at the active binding sites of VEGFR-2 and HDAC. PMID:26475519

  11. Hydrofluoric-nitric-sulphuric-acid surface treatment of tungsten for carbon fibre-reinforced composite hybrids in space applications

    NASA Astrophysics Data System (ADS)

    Kanerva, M.; Johansson, L.-S.; Campbell, J. M.; Revitzer, H.; Sarlin, E.; Brander, T.; Saarela, O.

    2015-02-01

    Hybrid material systems, such as combinations of tungsten foils and carbon fibre-reinforced plastic (CFRP), are replacing metal alloy concepts in spacecraft enclosures. However, a good adhesion between the tungsten oxide scale and the epoxy resin used is required. Here, the effects of a hydrofluoric-nitric-sulphuric-acid (HFNS) treatment on tungsten oxides and subsequent adhesion to CFRP are analysed using atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and fracture testing. The work shows that HFNS treatment results in decreased oxygen content, over 50% thinner tungsten trioxide (WO3) layer and increased nano-roughness on thin tungsten foils. Fracture testing established a 39% increase in the average critical strain for tungsten-CFRP specimens after HFNS treatment was carried out on tungsten. The effect of the oxide scale modification regarding the critical strain energy release rate was ΔGc≈ 8.4 J/m2.

  12. Preparation of cyclodextrin-modified monolithic hybrid columns for the fast enantioseparation of hydroxy acids in capillary liquid chromatography.

    PubMed

    Szwed, Kamila; Ou, Junjie; Huang, Guang; Lin, Hui; Liu, Zhongshan; Wang, Hongwei; Zou, Hanfa

    2016-03-01

    Cyclodextrins and their derivatives are one of the most common and successful chiral selectors. However, there have been few publications about the use of cyclodextrin-modified monoliths. In this study, organic hybrid monoliths were prepared by the immobilization of derivatized β-cyclodextrin alone or with l-2-allylglycine hydrochloride to the polyhedral oligomeric silsesquioxane methacryl substituted monolith. The main topic of this study is a combined system with dual chiral selectors (l-2-allylglycine hydrochloride and β-cyclodextrin) as monolithic chiral stationary phase. The effect of l-2-allylglycine hydrochloride concentration on enantioseparation was investigated. The enantioseparation of the four acidic compounds with resolutions up to 2.87 was achieved within 2.5 min on the prepared chiral monolithic column in capillary liquid chromatography. Moreover, the possible mechanism of enantioseparation was discussed. PMID:27027591

  13. One-step nucleic acid amplification assay for intraoperative prediction of advanced axillary lymph node metastases in breast cancer patients with sentinel lymph node metastasis

    PubMed Central

    KUBOTA, MICHIYO; KOMOIKE, YOSHIFUMI; HAMADA, MIKA; SHINZAKI, WATARU; AZUMI, TATSUYA; HASHIMOTO, YUKIHIKO; IMOTO, SHIGERU; TAKEYAMA, YOSHIFUMI; OKUNO, KIYOTAKA

    2016-01-01

    The one-step nucleic acid amplification (OSNA) assay is used to semiquantitatively measure the cytokeratin (CK)19 mRNA copy numbers of each sentinel lymph node (SLN) in breast cancer patients. The aim of the present study was to evaluate whether the diagnosis of ≥4 LN metastases is possible using the OSNA assay intraoperatively. Between May, 2010 and December, 2014, a total of 134 patients who underwent axillary lymph node dissection (ALND) of positive SLNs were analyzed. The total tumor load (TTL) was defined as the total CK19 mRNA copies of all positive SLNs. The correlation between TTL and ≥4 LN metastases was evaluated. Of the 134 patients, 31 (23.1%) had ≥4 LN metastases. TTL ≥5.4×104 copies/µl evaluated by receiver operator characteristic curve analysis was examined along with other clinicopathological variables. In the multivariate analysis, only TTL ≥5.4×104 copies/µl was correlated with ≥4 LN metastases (odds ratio = 2.95, 95% confidence interval: 1.17–7.97, P=0.022). Therefore, TTL assessed by the OSNA assay has the potential to be a predictor of ≥4 LN metastases and it may be useful for the selection of patients with positive SLNs in whom ALND may be safely omitted. PMID:26893855

  14. Molecular amplification assays for the detection of flaviviruses.

    PubMed

    Lanciotti, Robert S

    2003-01-01

    Over the past 10 years, a number of molecular amplification assays have been developed for the detection of flaviviruses. Most of these assays utilize the reverse transcriptase-polymerase chain reaction (RT-PCR) as the amplification format with detection by either agarose gel electrophoresis and ethidium bromide staining or hybridization with molecular probes. Recently, a modification of the standard RT-PCR using fluorescent-labeled oligonucleotide probes for detection (TaqMan) has been described. As a result, several assays for detecting flaviviruses have been developed using this approach. In addition, another amplification format, nucleic acid sequence based amplification (NASBA), has been developed and utilized for the detection of several flaviviruses. The various assay formats will be described and their utility discussed. PMID:14714430

  15. Injectable hybrid hydrogels of hyaluronic Acid crosslinked by well-defined synthetic polycations: preparation and characterization in vitro and in vivo.

    PubMed

    Cross, Daisy; Jiang, Xiaoze; Ji, Weihang; Han, Wenqing; Wang, Chun

    2015-05-01

    An injectable hybrid hydrogel system was developed consisting of hyaluronic acid (HA) crosslinked by well-defined block copolymers of the cationic poly(2-aminoethyl methacrylate) (PAEM) and polyethylene glycol (PEG). Robust, shear-thinning hybrid hydrogel was produced by mixing HA and 4-arm star PEG-PAEM block copolymer at 1:1 charge ratio. The encapsulation and release of highly viable human mesenchymal stem cells in physiological media was demonstrated. After subcutaneous injection of the hybrid gel in mice, mild but resolvable inflammatory response was observed. This hybrid gel could serve as a model system for studying structure-function relationship of polyelectrolyte hydrogels and as a practical injectable biomaterial for medical applications. PMID:25630277

  16. Babesia gibsoni: detection in blood smears and formalin-fixed, paraffin-embedded tissues using deoxyribonucleic acid in situ hybridization analysis.

    PubMed

    Yamasaki, Masahiro; Kobayashi, Yusuke; Nakamura, Kensuke; Sasaki, Noboru; Murakami, Masahiro; Rajapakshage, Bandula Kumara Wickramasekara; Ohta, Hiroshi; Yamato, Osamu; Maede, Yoshimitsu; Takiguchi, Mitsuyoshi

    2011-01-01

    In this study, we attempted to detect Babesia gibsoni in blood smears and formalin-fixed, paraffin-embedded tissues obtained from B. gibsoni-infected dogs using in situ hybridization. Using a digoxigenin-conjugated deoxyribonucleic acid (DNA) probe, both intraerythrocytic and exoerythrocytic parasites in the culture could be specifically stained in blood smears fixed with 4% phosphate-buffered paraformaldehyde. This indicated that genomic DNA extracted from the parasites could be detected using in situ hybridization. Moreover, the parasite could be specifically stained in paraffin-embedded spleen, lymph node, and kidney sections using in situ hybridization. Infected erythrocytes in blood vessels in the spleen and kidney, hemosiderin-laden macrophages in the spleen, and phagocytized erythrocytes, which seemed to be infected with the parasites, in lymph nodes were also specifically stained. This suggests that in situ hybridization can be utilized to investigate both the life cycle of B. gibsoni and the pathological condition of canine babesiosis. PMID:20637756

  17. Structural and optical study of spin-coated camphorsulfonic acid-doped polyaniline/titanium-di-oxide nanoparticles hybrid thin films

    NASA Astrophysics Data System (ADS)

    Geethalakshmi, D.; Muthukumarasamy, N.; Balasundaraprabhu, R.

    2015-06-01

    Polyaniline (PANI) doped with Camphorsulfonic acid (CSA) has been prepared by chemical oxidative polymerization and blend with titanium-di-oxide (TiO2) nanoparticles prepared by sol-gel method to form CSA-doped PANI/TiO2 hybrid thin films. The properties of as-deposited and heat-treated (100 °C) hybrid thin films having different PANI:TiO2 weight ratios (1:0.5, 1:1, and 1:2) have been compared. FTIR study indicated that chemical bonding between CSA-doped PANI and TiO2 has been formed. XRD studies reveal that the as-deposited hybrid thin films are of amorphous nature and heat-treatment of such films initiates crystallization. SEM study shows that as-deposited hybrid films are rough; increase in TiO2 ratio and heat-treatment increased the roughness due to coalescing and agglomeration. UV-visible absorbance of hybrid films shows its characteristic peak in the visible region along with a peak in UV range and its intensity increased with TiO2 ratio and heat-treatment due to agglomeration of TiO2 particles. Photoluminescence spectra revealed that emission occurs in visible region (495 nm) for as-deposited hybrid thin film and this emission increased with TiO2 ratio and heat-treatment of hybrid films.

  18. Intracellular location of rabbit poxvirus nucleic acid within infected cells as determined by in situ hybridization.

    PubMed Central

    Minnigan, H; Moyer, R W

    1985-01-01

    The intracellular location of rabbit poxvirus DNA within cells during the course of infection has been determined by the hybridization in situ of labeled viral DNA probes to uninfected and infected cells under various conditions. Extensive control experiments were performed to demonstrate that DNA could be detected selectively and accurately within the cell. Our results suggest that rabbit poxvirus DNA is located only within the cytoplasm during the reproductive cycle, and we found no evidence that viral DNA enters the cell nucleus. The pattern of hybridization of viral DNA at early times (1 and 2 h postinfection) and in the presence of inhibitors of viral DNA synthesis suggests that there may be an association between the input viral DNA and some structural component of the host cell. A number of observations support the hypothesis that the host cell nucleus is required for a productive poxvirus infection. Our results are discussed in terms of the possible role of the nucleus in the replication of poxviruses. Images PMID:2991586

  19. Real-time detection of noroviruses in surface water by use of a broadly reactive nucleic acid sequence-based amplification assay.

    PubMed

    Rutjes, Saskia A; van den Berg, Harold H J L; Lodder, Willemijn J; de Roda Husman, Ana Maria

    2006-08-01

    Noroviruses are the most common agents causing outbreaks of viral gastroenteritis. Outbreaks originating from contaminated drinking water and from recreational waters have been described. Due to a lack of cell culture systems, noroviruses are detected mostly by molecular methods. Molecular detection assays for viruses in water are often repressed by inhibitory factors present in the environment, like humic acids and heavy metals. To study the effect of environmental inhibitors on the performance of nucleic acid sequence-based amplification (NASBA), we developed a real-time norovirus NASBA targeting part of the RNA-dependent RNA polymerase (RdRp) gene. Specificity of the assay was studied with 33 divergent clones that contained part of the targeted RdRp gene of noroviruses from 15 different genogroups. Viral RNA originated from commercial oysters, surface waters, and sewage treatment plants in The Netherlands. Ninety-seven percent of the clones derived from human noroviruses were detected by real-time NASBA. Two clones containing animal noroviruses were not detected by NASBA. We compared the norovirus detection by real-time NASBA with that by conventional reverse transcriptase PCR (RT-PCR) with large-volume river water samples and found that inhibitory factors of RT-PCR had little or no effect on the performance of the norovirus NASBA. This consequently resulted in a higher sensitivity of the NASBA assay than of the RT-PCR. We show that by combining an efficient RNA extraction method with real-time NASBA the sensitivity of norovirus detection in water samples increased at least 100 times, which consequently has implications for the outcome of the infectious risk assessment. PMID:16885286

  20. A novel human T-leukemia virus type 1 cell-to-cell transmission assay permits definition of SU glycoprotein amino acids important for infectivity.

    PubMed Central

    Delamarre, L; Rosenberg, A R; Pique, C; Pham, D; Dokhélar, M C

    1997-01-01

    Human T-leukemia virus type 1 (HTLV-1) envelope glycoproteins play a major role in viral transmission, which in the case of this virus occurs almost exclusively via cell-to-cell contact. Until very recently, the lack of an HTLV-1 infectivity assay precluded the determination of the HTLV-1 protein domains required for infectivity. Here, we describe an assay which allows the quantitative evaluation of HTLV-1 cell-to-cell transmission in a single round of infection. Using this assay, we demonstrate that in this system, cell-to-cell transmission is at least 100 times more efficient than transmission with free viral particles. We have examined 46 surface (SU) glycoprotein mutants in order to define the amino acids of the HTLV-1 SU glycoprotein required for full infectivity. We demonstrate that these amino acids are distributed along the entire length of the SU glycoprotein, including the N-terminus and C-terminus regions, which have not been previously defined as being important for HTLV-1 glycoprotein function. For most of the mutated glycoproteins, the capacity to mediate cell-to-cell transmission is correlated with the ability to induce formation of syncytia. This result indicates that the fusion capacity is the main factor responsible for infectivity mediated by the HTLV-1 SU envelope glycoprotein, as is the case for other retroviral glycoproteins. However, other factors must also intervene, since two of the mutated glycoproteins were correctly fusogenic but could not mediate cell-to-cell transmission. Existence of this phenotype shows that capacity for fusion is not sufficient to confer infectivity, even in cell-to-cell transmission, and could suggest that postfusion events involve the SU. PMID:8985345

  1. In situ assay of fatty acid β-oxidation by metabolite profiling following permeabilization of cell membranes[S

    PubMed Central

    Ensenauer, Regina; Fingerhut, Ralph; Schriever, Sonja C.; Fink, Barbara; Becker, Marc; Sellerer, Nina C.; Pagel, Philipp; Kirschner, Andreas; Dame, Torsten; Olgemöller, Bernhard; Röschinger, Wulf; Roscher, Adelbert A.

    2012-01-01

    Quantitative analysis of mitochondrial FA β-oxidation (FAO) has drawn increasing interest for defining lipid-induced metabolic dysfunctions, such as in obesity-induced insulin resistance, and evaluating pharmacologic strategies to improve β-oxidation function. The aim was to develop a new assay to quantify β-oxidation function in intact mitochondria and with a low amount of cell material. Cell membranes of primary human fibroblasts were permeabilized with digitonin prior to a load with FFA substrate. Following 120 min of incubation, the various generated acylcarnitines were extracted from both cells and incubation medium by protein precipitation/desalting and subjected to solid-phase extraction. A panel of 30 acylcarnitines per well was quantified by MS/MS and normalized to citrate synthase activity to analyze mitochondrial metabolite flux. Pretreatment with bezafibrate and etomoxir revealed stimulating and inhibiting regulatory effects on β-oxidation function, respectively. In addition to the advantage of a much shorter assay time due to in situ permeabilization compared with whole-cell incubation systems, the method allows the detection of multiple acylcarnitines from an only limited amount of intact cells, particularly relevant to the use of primary cells. This novel approach facilitates highly sensitive, simple, and fast monitoring of pharmacological effects on FAO. PMID:22345709

  2. Harmonization of Glutamic Acid Decarboxylase and Islet Antigen-2 Autoantibody Assays for National Institute of Diabetes and Digestive and Kidney Diseases Consortia

    PubMed Central

    Bonifacio, Ezio; Yu, Liping; Williams, Alastair K.; Eisenbarth, George S.; Bingley, Polly J.; Marcovina, Santica M.; Adler, Kerstin; Ziegler, Anette G.; Mueller, Patricia W.; Schatz, Desmond A.; Krischer, Jeffrey P.; Steffes, Michael W.; Akolkar, Beena

    2010-01-01

    Background/Rationale: Autoantibodies to islet antigen-2 (IA-2A) and glutamic acid decarboxylase (GADA) are markers for diagnosis, screening, and measuring outcomes in National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) consortia studies. A harmonization program was established to increase comparability of results within and among these studies. Methods: Large volumes of six working calibrators were prepared from pooled sera with GADA 4.8–493 World Health Organization (WHO) units/ml and IA-2A 2–235 WHO units/ml. Harmonized assay protocols for IA-2A and GADA using 35S-methionine-labelled in vitro transcribed and translated antigens were developed based on methods in use in three NIDDK laboratories. Antibody thresholds were defined using sera from patients with recent onset type 1 diabetes and healthy controls. To evaluate the impact of the harmonized assay protocol on concordance of IA-2A and GADA results, two laboratories retested stored TEDDY study sera using the harmonized assays. Results: The harmonized assays gave comparable but not identical results in the three laboratories. For IA-2A, using a common threshold of 5 DK units/ml, 549 of 550 control and patient samples were concordantly scored as positive or negative, specificity was greater than 99% with sensitivity 64% in all laboratories. For GADA, using thresholds equivalent to the 97th percentile of 974 control samples in each laboratory, 1051 (97.9%) of 1074 samples were concordant. On the retested TEDDY samples, discordance decreased from 4 to 1.8% for IA-2A (n = 604 samples; P = 0.02) and from 15.4 to 2.7% for GADA (n = 515 samples; P < 0.0001). Conclusion: Harmonization of GADA and IA-2A is feasible using large volume working calibrators and common protocols and is an effective approach to ensure consistency in autoantibody measurements. PMID:20444913

  3. A Locked Nucleic Acid (LNA)-Based Real-Time PCR Assay for the Rapid Detection of Multiple Bacterial Antibiotic Resistance Genes Directly from Positive Blood Culture

    PubMed Central

    Zhu, Lingxiang; Shen, Dingxia; Zhou, Qiming; Li, Zexia; Fang, Xiangdong; Li, Quan-Zhen

    2015-01-01

    Bacterial strains resistant to various antibiotic drugs are frequently encountered in clinical infections, and the rapid identification of drug-resistant strains is highly essential for clinical treatment. We developed a locked nucleic acid (LNA)-based quantitative real-time PCR (LNA-qPCR) method for the rapid detection of 13 antibiotic resistance genes and successfully used it to distinguish drug-resistant bacterial strains from positive blood culture samples. A sequence-specific primer-probe set was designed, and the specificity of the assays was assessed using 27 ATCC bacterial strains and 77 negative blood culture samples. No cross-reaction was identified among bacterial strains and in negative samples, indicating 100% specificity. The sensitivity of the assays was determined by spiking each bacterial strain into negative blood samples, and the detection limit was 1–10 colony forming units (CFU) per reaction. The LNA-qPCR assays were first applied to 72 clinical bacterial isolates for the identification of known drug resistance genes, and the results were verified by the direct sequencing of PCR products. Finally, the LNA-qPCR assays were used for the detection in 47 positive blood culture samples, 19 of which (40.4%) were positive for antibiotic resistance genes, showing 91.5% consistency with phenotypic susceptibility results. In conclusion, LNA-qPCR is a reliable method for the rapid detection of bacterial antibiotic resistance genes and can be used as a supplement to phenotypic susceptibility testing for the early detection of antimicrobial resistance to allow the selection of appropriate antimicrobial treatment and to prevent the spread of resistant isolates. PMID:25775001

  4. High-resolution, hybrid optical trapping methods, and their application to nucleic acid processing proteins.

    PubMed

    Chemla, Yann R

    2016-10-01

    Optical tweezers have become a powerful tool to investigate nucleic-acid processing proteins at the single-molecule level. Recent advances in this technique have now enabled measurements resolving the smallest units of molecular motion, on the scale of a single base pair of DNA. In parallel, new instrumentation combining optical traps with other functionalities have been developed, incorporating mechanical manipulation along orthogonal directions or fluorescence imaging capabilities. Here, we review these technical advances, their capabilities, and limitations, focusing on benchmark studies of protein-nucleic acid interactions they have enabled. We highlight recent work that combines several of these advances together and its application to nucleic-acid processing enzymes. Finally, we discuss future prospects for these exciting developments. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 704-714, 2016. PMID:27225537

  5. Effects of acid stress on aerobic decomposition of algal and aquatic macrophyte detritus: Direct comparison in a radiocarbon assay

    SciTech Connect

    Schoenberg, S.A.; Benner, R.; Armstrong, A.; Sobecky, P.; Hodson, R.E. )

    1990-01-01

    Radiolabeled phytoplankton and macrophyte lignocelluloses were incubated at pHs 4 and 7 in water from a naturally acidic freshwater wetland (Okefenokee Swamp; ambient pH, 3.8 to 4.2), a freshwater reservoir (L-Lake; pH 6.7 to 7.2), and a marine marsh (Sapelo Island; pH {approximately}7.8). The data suggest that acidity is an important factor in explaining the lower decomposition rates of algae in Okefenokee Swamp water relative to L-Lake or Sapelo Island water. The decomposition of algal substrate was less sensitive to low pH ({approximately}5 to 35% inhibition) than was the decomposition of lignocellulose ({approximately}30 to 70% inhibition). These substrate-dependent differences were greater and more consistent in salt marsh than in L-lake incubations. In both freshwater sites, the extent to which decomposition was suppressed by acidity was greater for green algal substrate than for mixed diatom or blue-green algal (cyanobacteria) substrates. The use of different bases to adjust pH or incubation in a defined saltwater medium had no significant effect on substrate-dependent differences. Although pH differences with lignocellulose were larger in marine incubations, amendment of lake water with marine bacteria or with calcium, known to stabilize exoenzymes in soils, did not magnify the sensitivity of decomposition to acid stress.

  6. Effects Of Haloacetic Acid Mixtures in a Mouse Embryonic Stem Cell Adherent Cell Differentiation and Cytotoxicity (ACDC) Assay

    EPA Science Inventory

    The haloacetic acids (HAAs) are a class of chemicals produced as byproducts of drinking water disinfection. Source water characteristics (such as level of bromide) affects which HAAs are present in drinking water and their concentration. For example, high bromide-source water wil...

  7. Hybrid striped bass feeds based on fish oil, beef tallow, and eicosapentaenoic acid/docosahexaenoic acid supplements: Insight regarding fish oil sparing and demand for -3 long-chain polyunsaturated fatty acids.

    PubMed

    Bowzer, J; Jackson, C; Trushenski, J

    2016-03-01

    Previous research suggests that saturated (SFA) and monounsaturated fatty acid (MUFA) rich lipids, including beef tallow, can make utilization or diet-to-tissue transfer of long-chain polyunsaturated fatty acids (LC-PUFA) more efficient. We hypothesized that using beef tallow as an alternative to fish oil may effectively reduce the LC-PUFA demand of hybrid striped bass × and allow for greater fish oil sparing. Accordingly, we evaluated growth performance and tissue fatty acid profiles of juvenile fish (23.7 ± 0.3 g) fed diets containing menhaden fish oil (considered an ideal source of LC-PUFA for this taxon), beef tallow (BEEF ONLY), or beef tallow amended with purified sources of eicosapentaenoic acid (EPA) and/or docosahexaenoic acid (DHA) to achieve levels corresponding to 50 or 100% of those observed in the FISH ONLY feed. Diets were randomly assigned to quadruplicate tanks of fish ( = 4; 10 fish/tank), and fish were fed assigned diets to apparent satiation once daily for 10 wk. Survival (98-100%) was equivalent among treatments, but weight gain (117-180%), specific growth rate (1.1-1.5% BW/d), feed intake (1.4-1.8% BW/d), thermal growth coefficient (0.50-0.70), and feed conversion ratio (FCR; 1.1-1.4, DM basis) varied. Except for FCR, no differences were observed between the FISH ONLY and BEEF ONLY treatments, but performance was generally numerically superior among fish fed the diets containing beef tallow supplemented with DHA at the 100% or both EPA and DHA at the 50% or 100% level. Tissue fatty acid composition was significantly distorted in favor among fish fed the beef tallow-based feeds; however, profile distortion was most overt in peripheral tissues. Results suggest that beef tallow may be used as a primary lipid source in practical diets for hybrid striped bass, but performance may be improved by supplementation with LC-PUFA, particularly DHA. Furthermore, our results suggest that -3 LC-PUFA requirements reported for hybrid striped bass may not be

  8. Hyaluronic Acid-Modified Cationic Lipid-PLGA Hybrid Nanoparticles as a Nanovaccine Induce Robust Humoral and Cellular Immune Responses.

    PubMed

    Liu, Lanxia; Cao, Fengqiang; Liu, Xiaoxuan; Wang, Hai; Zhang, Chao; Sun, Hongfan; Wang, Chun; Leng, Xigang; Song, Cunxian; Kong, Deling; Ma, Guilei

    2016-05-18

    Here, we investigated the use of hyaluronic acid (HA)-decorated cationic lipid-poly(lactide-co-glycolide) acid (PLGA) hybrid nanoparticles (HA-DOTAP-PLGA NPs) as vaccine delivery vehicles, which were originally developed for the cytosolic delivery of genes. Our results demonstrated that after the NPs uptake by dendritic cells (DCs), some of the antigens that were encapsulated in HA-DOTAP-PLGA NPs escaped to the cytosolic compartment, and whereas some of the antigens remained in the endosomal/lysosomal compartment, where both MHC-I and MHC-II antigen presentation occurred. Moreover, HA-DOTAP-PLGA NPs led to the up-regulation of MHC, costimulatory molecules, and cytokines. In vivo experiments further revealed that more powerful immune responses were induced from mice immunized with HA-DOTAP-PLGA NPs when compared with cationic lipid-PLGA nanoparticles and free ovalbumin (OVA); the responses included antigen-specific CD4(+) and CD8(+) T-cell responses, the production of antigen-specific IgG antibodies and the generation of memory CD4(+) and CD8(+) T cells. Overall, these data demonstrate the high potential of HA-DOTAP-PLGA NPs for use as vaccine delivery vehicles to elevate cellular and humoral immune responses. PMID:27088457

  9. Preparation and characterization of humic acid-carbon hybrid materials as adsorbents for organic micro-pollutants.

    PubMed

    Radwan, Emad K; Abdel Ghafar, Hany H; Moursy, Ahmed S; Langford, Cooper H; Bedair, Ahmed H; Achari, Gopal

    2015-08-01

    The present work involves the preparation of novel adsorbent materials by the insolubilization and hybridization of humic acid (HA) with carbon. The prepared materials were characterized by N2 adsorption, elemental analysis, Fourier transform infrared spectroscopy, scanning electron microscopy, transmission electron microscopy, solid-state (13)C cross polarization magic angle spinning nuclear magnetic resonance, and low-field nuclear magnetic resonance (NMR) relaxometry on wetted samples. The water solubility of these materials and the lack of effect of oxidants were also confirmed. With this background, the adsorption capacities toward phenol, 2,4,6-tricholrophenol, and atrazine were evaluated, using these as model compounds for organic micropollutants of concern in water. Experimental results show that the prepared materials are mesoporous and have a higher surface area than humic acid and even than the porous carbon in the case of carbon coating. They retain the basic features of the starting materials with lowered functional group content. Moreover, there are interesting new features. NMR relaxometry shows that equilibration of water uptake is very fast, making use in water simple. They have higher adsorption capacities than the pure materials, and they can be applied under a wide range of environmental conditions. PMID:25874433

  10. Detection of teratogenic substances in acidic mine water samples using the frog embryo teratogenesis assay--Xenopus (FETAX).

    PubMed

    Dawson, D A; McCormick, C A; Bantle, J A

    1985-08-01

    The FETAX (Frog Embryo Teratogenesis Assay--Xenopus) whole embryo bioassay has been developed to screen for environmental substances that cause birth defects. We have used this assay to test its effectiveness in working with actual water samples from the field. Tar Creek is contaminated by discharges from abandoned lead and zinc mines. In addition to high concentrations of zinc, iron and other metals, water samples are routinely low in pH and oxygen content. The pH values of three Tar Creek sample sites were below the established tolerance limits of the embryos. Therefore, one group of samples had no pH adjustment while a second group had the pH adjusted to 7.0. Two of the four sites contained agents that reduced embryonic growth and caused high rates of mortality. A third site contained teratogenic substances. We have determined that metal content is responsible, along with the low pH, for the biologic effects. We have identified high concentrations of toxic metals in Tar Creek by water analysis and were able to demonstrate, by removing metals via Chelex 100 ion exchange chromatography, that the observed toxicity and teratogenicity were caused by metal ions. We have concluded that FETAX is an excellent test for complex mixtures. Physicochemical parameters, such as pH, oxygen and metals content, can be altered and the effect of these changes on toxicity and teratogenicity determined using FETAX. The interaction of toxic substances and low pH are important when considering embryo survival and development. PMID:4045096

  11. Boronic acid recognition based-gold nanoparticle-labeling strategy for the assay of sialic acid expression on cancer cell surface by inductively coupled plasma mass spectrometry.

    PubMed

    Zhang, Xing; Chen, Beibei; He, Man; Zhang, Yuan; Peng, Lu; Hu, Bin

    2016-02-01

    Sialic acids are special sugars widely expressed at the termini of glycan chains on the cell surface, and their expression level on the cancer cell surface is much higher than on the normal cell surface. Herein, we reported an inductively coupled plasma mass spectrometry (ICP-MS) based method with elemental tags for the analysis of sialic acids on the cancer cell surface. The method is based on the selective recognition of sialic acids by biotinylated phenylboronic acid (biotin-APBA) at physiological pH and signal enhancement of gold nanoparticles (AuNPs) in ICP-MS when AuNPs were used as elemental tags labeled on biotin-APBA. A specificity test reveals that the proposed method has high specificity towards cancer cells. Taking HepG2 and MCF-7 cells as two model cancer cells, competitive experiments were performed to estimate the expression level of sialic acids on the cancer cell surface, and it was found that the average numbers of sialic acids expressed on the single MCF-7 and HepG2 cell surface were 7.0 × 10(9) and 5.4 × 10(9), respectively. With sialic acid as the biomarker for cancer cells, the method was further used for cell detection. The limits of detection in terms of cell number for HepG2 and MCF-7 cells were 120 and 64, respectively. And the relative standard deviations for nine replicate determinations of ca. 1000 HepG2 and MCF-7 cells were 9.6% and 8.9%, respectively. The linear ranges for HepG2 cells and MCF-7 cells were 300-10 000 and 170-11 000, respectively. The proposed approach is sensitive as well as selective for the analysis of sialic acids on the cancer cell surface, and is potentially applicable for the study of tumor malignancy and metastasis, which is helpful for biological research and clinical diagnostics. PMID:26811850

  12. Development of an Interaction Assay between Single-Stranded Nucleic Acids Trapped with Silica Particles and Fluorescent Compounds

    PubMed Central

    Isoda, T.; Maeda, R.

    2012-01-01

    Biopolymers are easily denatured by heating, a change in pH or chemical substances when they are immobilized on a substrate. To prevent denaturation of biopolymers, we developed a method to trap a polynucleotide on a substrate by hydrogen bonding using silica particles with surfaces modified by aminoalkyl chains ([A-AM silane]/SiO2). [A-AM silane]/SiO2 was synthesized by silane coupling reaction of N-2-(aminoethyl)-3-aminopropyltrimethoxysilane (A-AM silane) with SiO2 particles with a diameter of 5 μm at 100 °C for 20 min. The surface chemical structure of [A-AM silane]/SiO2 was characterized by Fourier transform infrared spectroscopy and molecular orbital calculations. The surface of the silica particles was modified with A-AM silane and primary amine groups were formed. [A-AM silane]/SiO2 was trapped with single-stranded nucleic acids [(Poly-X; X = A (adenine), G (guanine) and C (cytosine)] in PBS solution at 37 °C for 1 h. The single-stranded nucleic acids were trapped on the surface of the [A-AM silane]/SiO2 by hydrogen bonding to form conjugated materials. The resulting complexes were further conjugated by derivatives of acridine orange (AO) as fluorescent labels under the same conditions to form [AO:Poly-X:A-AM silane]/SiO2 complexes. Changes in the fluorescence intensity of these complexes originating from interactions between the single-stranded nucleic acid and aromatic compounds were also evaluated. The change in intensity displayed the order [AO: Poly-G: A-AM silane]/SiO2 > [AO:Poly-A:A-AM silane]/SiO2 >> [AO:Poly-C:A-AM silane]/SiO2. This suggests that the single-stranded nucleic acids conjugated with aminoalkyl chains on the surfaces of SiO2 particles and the change in fluorescence intensity reflected the molecular interaction between AO and the nucleic-acid base in a polynucleotide. PMID:24955635

  13. Hybrid modeling of lead-acid batteries in frequency and time domain

    NASA Astrophysics Data System (ADS)

    Thele, M.; Buller, S.; Sauer, D. U.; De Doncker, R. W.; Karden, E.

    This paper presents an improved impedance-based non-linear simulation model for lead-acid batteries. The parameterization of impedance-based models is difficult for operation profiles with high Ah throughput in short times. Such conditions result in non-steady-state conditions and do not allow precise measurements of impedance parameters. Therefore, the model has been extended by an electrolyte transport model which describes the generation and the transport of sulfuric acid inside the porous electrodes. This expands the model validity as higher Ah throughputs can be simulated now. A description of the Matlab/Simulink implementation and its parameterization in the time domain is given. Furthermore, the advantages and the limits of the improved model are discussed. The model allows for precise modeling of automotive batteries, both in conventional applications and in vehicles with electrically assisted propulsion. It is therefore an important tool for the design of automotive power nets.

  14. Growth, body fatty acid composition, immune response and resistance to Streptococcus iniae of hybrid tilapia, Oreochromis niloticus X O. aureus, fed diets containing various levels of linoleic and linolenic acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effects of dietary linoleic (LA) and linolenic acids (LN) on growth and immunity of all-male hybrid tilapia, Oreochromis niloticus × O. aureus, were evaluated for 10 weeks. Fish fed 0.12% LA + 0% LN had the lowest weight gain (WG) but was not significantly different from diets containing 0.5% LA...

  15. A Highly Sensitive Oligonucleotide Hybridization Assay for Klebsiella pneumoniae Carbapenemase with the Probes on a Gold Nanoparticles Modified Glassy Carbon Electrode.

    PubMed

    Pan, Hong-zhi; Yu, Hong- Wei; Wang, Na; Zhang, Ze; Wan, Guang-Cai; Liu, Hao; Guan, Xue; Chang, Dong

    2015-01-01

    To develop a new electrochemical DNA biosensor for determination of Klebsiella pneumoniae carbapenemase, a highly sensitive and selective electrochemical biosensor for DNA detection was constructed based on a glassy carbon electrode (GCE) modified with gold nanoparticles (Au-nano). The Au-nano/GCE was characterized by scanning electromicroscopy, cyclic voltammetry, and electrochemical impedance spectroscopy. The hybridization detection was measured by differential pulse voltammetry using methylene blue as the hybridization indicator. The dynamic range of detection of the sensor for the target DNA sequences was from 1 × 10(-11) to 1 × 10(-8) M, with an LOD of 1 × 10(-12) M. The DNA biosensor had excellent specificity for distinguishing complementary DNA sequence in the presence of non-complementary and mismatched DNA sequence. The Au-nano/GCE showed significant improvement in electrochemical characteristics, and this biosensor was successfully applied for determination of K. pneumoniae. PMID:26651586

  16. Development of a Medium-Throughput Targeted LCMS Assay to Detect Endogenous Cellular Levels of Malonyl-CoA to Screen Fatty Acid Synthase Inhibitors.

    PubMed

    Hopcroft, Philip J; Fisher, David I

    2016-02-01

    The fatty acid synthase (FAS) enzyme in mammalian cells is a large multidomain protein responsible for de novo synthesis of fatty acids. The steps catalyzed by FAS involve the condensation of acetyl-CoA and malonyl-CoA moieties in the presence of NADPH until palmitate is formed. Inhibition of FAS causes an accumulation of intracellular malonyl-CoA, as this metabolite is essentially committed to fatty acid synthesis once formed. Detection of intracellular metabolites for screening can be problematic due to a lack of appropriate tools, but here we describe a targeted liquid chromatography-mass spectroscopy (LCMS) method to directly measure endogenous levels of malonyl-CoA to drive a drug development structure-activity relationship (SAR) screening cascade. Our process involves preparation of samples at 96-well scale, normalization postpermeabilization via use of a whole-well imaging platform, and the LCMS detection methodology. The assay is amenable to multiplexing cellular endpoints, has a typical Z' of >0.6, and has high reproducibility of EC50 values. PMID:26586251

  17. Preparation of hybrid molecularly imprinted polymer with double-templates for rapid simultaneous purification of theophylline and chlorogenic acid in green tea.

    PubMed

    Tang, Weiyang; Li, Guizhen; Row, Kyung Ho; Zhu, Tao

    2016-05-15

    A novel double-templates technique was adopted for solid-phase extraction packing agent, and the obtained hybrid molecularly imprinted polymers with double-templates (theophylline and chlorogenic acid) were characterized by fourier transform infrared and field emission scanning electron microscope. The molecular recognition ability and binding capability for theophylline and chlorogenic acid of polymers was evaluated by static absorption and dynamic adsorption curves. A rapid and accurate approach was established for simultaneous purification of theophylline and chlorogenic acid in green tea by coupling hybrid molecularly imprinted solid-phase extraction with high performance liquid chromatography. With optimization of SPE procedure, a reliable analytical method was developed for highly recognition towards theophylline and chlorogenic acid in green tea with satisfactory extraction recoveries (theophylline: 96.7% and chlorogenic acid: 95.8%). The limit of detection and limit of quantity of the method were 0.01μg/mL and 0.03μg/mL for theophylline, 0.05μg/mL and 0.17μg/mL for chlorogenic acid, respectively. The recoveries of proposed method at three spiked levels analysis were 98.7-100.8% and 98.3-100.2%, respectively, with the relative standard deviation less than 1.9%. Hybrid molecularly imprinted polymers with double-templates showed good performance for two kinds of targets, and the proposed approach with high affinity of hybrid molecularly imprinted polymers might offer a novel method for the purification of complex samples. PMID:26992488

  18. Gold nanoparticle-biotinylated liposome hybrids as analytical reagents for biotin determination using a competitive assay and resonance light scattering detection.

    PubMed

    Román-Pizarro, Vanessa; Fernández-Romero, Juan Manuel; Gómez-Hens, Agustina

    2012-09-15

    The preparation of hybrid nanostructures formed by gold nanoparticles (AuNPs) into biotinylated liposomes and their analytical application are presented. The surface of negatively charged AuNPs was modified with 1-dodecanethiol and the NPs were encapsulated into biotinylated liposomes using the rapid solvent evaporation method. Liposomes were resized by both mechanical shaking and ultrasound treatments and filled liposomes were separated from empty liposomes using sucrose density gradient centrifugation. The analytical usefulness of AuNP-liposome hybrids as amplification probes for biotin determination was checked using the competitive affinity reaction based on the avidin-biotin interaction and biotilynated phospholipids for the synthesis of the liposome hybrids. The method was automatized using a flow system and measuring the resonance light scattering signal. The dynamic range of the calibration graph was 0.001-20 μg mL(-1), (r(2)=0.9998, n=14), with a detection limit of 0.3 ng mL(-1). The precision, expressed as relative standard deviation (RSD%), was lower than 5% and the sampling frequency was 9 h(-1). The approach has been applied to the determination of biotin in food samples, with recovery values ranging between 88.2 and 105.2%. PMID:22967591

  19. Testing and evaluation of EV-1300 lead-acid modules for the hybrid vehicle application

    SciTech Connect

    Gay, E.C.; Corp, D.O.; Hayes, E.R.; Webster, C.E.; Hornstra, F.; Yao, N.P.

    1984-01-01

    Tests of two 6-cell, EV-1300 modules with a capacity of 105 Ah (1235 Wh) were conducted at the computer-automated National Battery Test Laboratory at Argonne National Laboratory to verify the above design requirements. In addition, the following tests were completed to more fully characterize the performance of the battery: (1) capacity measurements over a range of constant-current discharges of 35 to 400 A (Peukert Plot); (2) energy measurements over a range of constant-power discharges of 10 to 100 W/kg (Ragone Plot); (3) open-circuit stand testing (self-discharge); (4) partial DOD testing (memory effect); (5) projected range based on simulated driving profile discharges representing the EPA urban driving schedule negotiated by the HTV-1 hybrid vehicle with minimum ICE operation; (6) projected range based on simulated driving profile discharges representing the SAE J227aD urban driving schedule negotiated by an improved ETV-1 (an all-electric vehicle); and (7) peak power measurements at various depths of discharge.

  20. Microbial populations identified by fluorescence in situ hybridization in a constructed wetland treating acid coal mine drainage.

    PubMed

    Nicomrat, Duongruitai; Dick, Warren A; Tuovinen, Olli H

    2006-01-01

    Microorganisms are an integral part of the biogeochemical processes in wetlands, yet microbial communities in sediments within constructed wetlands receiving acid mine drainage (AMD) are only poorly understood. The purpose of this study was to characterize the microbial diversity and abundance in a wetland receiving AMD using fluorescence in situ hybridization (FISH) analysis. Seasonal samples of oxic surface sediments, comprised of Fe(III) precipitates, were collected from two treatment cells of the constructed wetland system. The pH of the bulk samples ranged between pH 2.1 and 3.9. Viable counts of acidophilic Fe and S oxidizers and heterotrophs were determined with a most probable number (MPN) method. The MPN counts were only a fraction of the corresponding FISH counts. The sediment samples contained microorganisms in the Bacteria (including the subgroups of acidophilic Fe- and S-oxidizing bacteria and Acidiphilium spp.) and Eukarya domains. Archaea were present in the sediment surface samples at < 0.01% of the total microbial community. The most numerous bacterial species in this wetland system was Acidithiobacillus ferrooxidans, comprising up to 37% of the bacterial population. Acidithiobacillus thiooxidans was also abundant. Heterotrophs in the Acidiphilium genus totaled 20% of the bacterial population. Leptospirillum ferrooxidans was below the level of detection in the bacterial community. The results from the FISH technique from this field study are consistent with results from other experiments involving enumeration by most probable number, dot-blot hybridization, and denaturing gradient gel electrophoresis analyses and with the geochemistry of the site. PMID:16825452

  1. High Throughput Liquid Chromatography-Tandem Mass Spectrometry Assay for Mercapturic Acids of Acrolein and Crotonaldehyde in Cigarette Smokers’ Urine

    PubMed Central

    Carmella, Steven G.; Chen, Menglan; Zarth, Adam; Hecht, Stephen S.

    2014-01-01

    3-Hydroxypropylmercapturic acid (3-HPMA) and 3-hydroxy-1-methylpropylmercapturic acid (HMPMA) are urinary metabolites of the toxicants acrolein and crotonaldehyde, respectively. Virtually all human urine samples contain these metabolites, resulting from the action of glutathione-S-transferases on acrolein and crotonaldehyde, which are lipid peroxidation products, environmental and dietary contaminants, and constituents of cigarette smoke. We have developed a high throughput liquid chromatography-tandem mass spectrometry method for quantitative analysis of 3-HPMA and HMPMA in large numbers of small urine samples, as would be required in molecular epidemiology and clinical studies relating levels of these metabolites to cancer risk. Solid-phase extraction on mixed mode reverse phase-anion exchange 96-well plates provided sufficient purification for LC-MS/MS analysis, which was performed by auto-injection using a 96-well format, and resulted in clean, readily interpretable chromatograms, with detection limits of 4.5 pmol/mL urine for 3-HPMA and 3.5 pmol/mL urine for HMPMA. Accuracy was 92% for 3-HPMA and 97% for HMPMA while inter-day precision was 9.1% (coefficient of variation) for 3-HPMA and 11.0% for HMPMA. The method was applied to more than 2600 urine samples from smokers; mean levels of 3-HPMA and HMPMA were 4800 ± 5358 (S.D.) pmol/ml and 3302 ± 3341 pmol/ml, respectively. PMID:23934173

  2. Effect of acid or alkaline catalyst and of different capping agents on the optical properties of CdS nanoparticles incorporated within a diureasil hybrid matrix

    NASA Astrophysics Data System (ADS)

    Gonçalves, Luis F. F. F.; Silva, Carlos J. R.; Kanodarwala, Fehmida K.; Stride, John A.; Pereira, Mario R.

    2015-11-01

    CdS nanoparticles (NPs) were synthesized using colloidal methods and incorporated within a diureasil hybrid matrix. The surface capping of the CdS NPs by 3-mercaptopropyltrimethoxysilane (MPTMS) and 3-aminopropyltrimethoxysilane (APTMS) organic ligands during the incorporation of the NPs within the hybrid matrix has been investigated. The matrix is based on poly(ethylene oxide)/poly(propylene oxide) chains grafted to a siliceous skeleton through urea bonds and was produced by sol-gel process. Both alkaline and acidic catalysis of the sol-gel reaction were used to evaluate the effect of each organic ligand on the optical properties of the CdS NPs. The hybrid materials were characterized by absorption, steady-state and time-resolved photoluminescence spectroscopy and High Resolution Transmission Electron Microscopy (HR-TEM). The preservation of the optical properties of the CdS NPs within the diureasil hybrids was dependent on the experimental conditions used. Both organic ligands (APTMS and MPTMS) demonstrated to be crucial in avoiding the increase of size distribution and clustering of the NPs within the hybrid matrix. The use of organic ligands was also shown to influence the level of interaction between the hybrid host and the CdS NPs. The CdS NPs showed large Stokes shifts and long average lifetimes, both in colloidal solution and in the xerogels, due to the origin of the PL emission in surface states. The CdS NPs capped with MPTMS have lower PL lifetimes compared to the other xerogel samples but still larger than the CdS NPs in the original colloidal solution. An increase in PL lifetimes of the NPs after their incorporation within the hybrid matrix is related to interaction between the NPs and the hybrid host matrix.

  3. Lead-acid batteries for micro- and mild-hybrid applications

    NASA Astrophysics Data System (ADS)

    Valenciano, J.; Fernández, M.; Trinidad, F.; Sanz, L.

    Car manufactures have announced the launch in coming months of vehicles with reduced emissions due to the introduction of new functions like stop-start and regenerative braking. Initial performance request of automotive lead-acid batteries are becoming more and more demanding and, in addition to this, cycle life with new accelerated ageing profiles are being proposed in order to determine the influence of the new functions on the expected battery life. This paper will show how different lead-acid battery technologies comply with these new demands, from an improved version of the conventional flooded SLI battery to the high performance of spiral wound valve-regulated lead-acid (VRLA) battery. Different approaches have been studied for improving conventional flooded batteries, i.e., either by the addition of new additives for reducing electrolyte stratification or by optimisation of the battery design to extend cycling life in partial state of charge conditions. With respect to VRLA technology, two different battery designs have been compared. Spiral wound design combines excellent power capability and cycle life under different depth of discharge (DoD) cycling conditions, but flat plate design outperform the latter in energy density due to better utilization of the space available in a prismatic enclosure. This latter design is more adequate for high end class vehicles with high electrical energy demand, whereas spiral wound is better suited for high power/long life demand of commercial vehicle. High temperature behaviour (75 °C) is rather poor for both designs due to water loss, and then VRLA batteries should preferably be located out of the engine compartment.

  4. The neurotoxic effect of clindamycin - induced gut bacterial imbalance and orally administered propionic acid on DNA damage assessed by the comet assay: protective potency of carnosine and carnitine

    PubMed Central

    2013-01-01

    Background Comet assay is a quick method for assessing DNA damage in individual cells. It allows the detection of single and double DNA strand breaks, which represent the direct effect of some damaging agents. This study uses standard comet quantification models to compare the neurotoxic effect of orally administered propionic acid (PA) to that produced as a metabolite of bacterial overgrowth induced by clindamycin. Additionally, the protective effect of carnosine and carnitine as natural dietary supplements is assessed. Methods Single cell gel electrophoresis (comet assays) were performed on brain cortex and medulla samples after removal from nine groups of hamsters including: a control (untreated) group; PA-intoxicated group; clindamycin treated group; clindamycin-carnosine group and; clindamycin-carnitine group. Results There were significant double strand breaks recorded as tail length, tail moment and % DNA damage in PA and clindamycin-treated groups for the cortex and medulla compared to the control group. Neuroprotective effects of carnosine and carnitine were observed. Receiver Operating Characteristics curve (ROC) analysis showed satisfactory values of sensitivity and specificity of the comet assay parameters. Conclusion Percentage DNA damage, tail length, and tail moment are adequate biomarkers of PA neurotoxicity due to oral administration or as a metabolite of induced enteric bacterial overgrowth. Establishing biomarkers of these two exposures is important for protecting children’s health by documenting the role of the imbalance in gut microbiota in the etiology of autism through the gut-brain axis. These outcomes will help efforts directed at controlling the prevalence of autism, a disorder recently related to PA neurotoxicity. PMID:23587115

  5. Scaling of Nucleic Acid Assays on Microelectrophoresis Array Devices: High-Dynamic Range Multi-gene Readout from less than 10 Transcripts

    PubMed Central

    Ueberfeld, Joern; Ehrlich, Daniel J.

    2009-01-01

    In this paper we describe progress in using the prodigious data-collecting ability of multilane microelectrophoresis instruments to bear on problems in scaled nucleic acid assays. We emphasize compound stacking and Solid-Support loading as means to concentrate <100 pg samples for direct injection. Reaction Mapping is applied to readout of quantitative polymerase chain reaction (qPCR) gene-expression and as a way to practically overcome difficulty in interpreting amplification curves of multiplexed qPCR at 20–50 gene/well complexity. We demonstrate multiplexed readout of gene expression over an abundancy range of 9Log2 units starting with reverse-transcribed samples as small as 5 molecules in each sample. PMID:19544490

  6. Development of an enzyme-linked immunosorbent assay to determine the numbers of chemolithotrophic bacteria at acid-mine-drainage sites. Technical report (Final)

    SciTech Connect

    Blake, R.C.; Revis, N.W.; Holdsworth, G.

    1990-09-01

    Thiobacillus ferrooxidans is a prominent member of a group of chemo-lithotrophic bacteria that bear principal responsibility for the formation of acid mine drainage. A prototype enzyme-linked immunosorbent assay (ELISA) for enumerating and qualifying T. ferrooxidans was assembled and characterized. The immunoassay protocol consisted of sequential incubations of the sample with (i) the primary antibody, (ii) the enzyme-labeled secondary antibody, and (iii) a chromogenic substrate specific for the enzyme lable. The necessary reagents comprised primary polyclonal rabbit antibodies directed against T. ferrooxidans ATCC 23270, alkaline phosphatase-copled goat anti-rabbit polyclonal antibodies, and phenolphrhalein monophosphate. The ELISA developed herein correctly identified whether iron-oxidizing bacteria were present in each of 4 samples supplied and analyzed by an independent laboratory. Sufficient preliminary data was obtained to warrant further research and development activities.

  7. Re-exploration of the Codon Context Effect on Amber Codon-Guided Incorporation of Noncanonical Amino Acids in Escherichia coli by the Blue-White Screening Assay.

    PubMed

    Xu, Huan; Wang, Yan; Lu, Jiaqi; Zhang, Bo; Zhang, Ziwei; Si, Longlong; Wu, Ling; Yao, Tianzhuo; Zhang, Chuanling; Xiao, Sulong; Zhang, Lihe; Xia, Qing; Zhou, Demin

    2016-07-01

    The effect of codon context on amber codon-guided incorporation of noncanonical amino acids (NAAs) has been previously examined by antibiotic selection. Here, we re-explored this effect by screening a library in which three nucleotides upstream and downstream of the amber codon were randomised, and inserted within the lacZ-α gene. Thousands of clones were obtained and distinguished by the depth of blue colour upon exposure to X-gal. Large-scale sequencing revealed remarkable preferences in nucleotides downstream of the amber codon, and moderate preferences for upstream nucleotides. Nucleotide preference was quantified by a dual-luciferase assay, which verified that the optimum context for NAA incorporation, AATTAGACT, was applicable to different proteins. Our work provides a general guide for engineering amber codons into genes of interest in bacteria. PMID:27028123

  8. Unique honey bee (Apis mellifera) hive component-based communities as detected by a hybrid of phospholipid fatty-acid and fatty-acid methyl ester analyses.

    PubMed

    Grubbs, Kirk J; Scott, Jarrod J; Budsberg, Kevin J; Read, Harry; Balser, Teri C; Currie, Cameron R

    2015-01-01

    Microbial communities (microbiomes) are associated with almost all metazoans, including the honey bee Apis mellifera. Honey bees are social insects, maintaining complex hive systems composed of a variety of integral components including bees, comb, propolis, honey, and stored pollen. Given that the different components within hives can be physically separated and are nutritionally variable, we hypothesize that unique microbial communities may occur within the different microenvironments of honey bee colonies. To explore this hypothesis and to provide further insights into the microbiome of honey bees, we use a hybrid of fatty acid methyl ester (FAME) and phospholipid-derived fatty acid (PLFA) analysis to produce broad, lipid-based microbial community profiles of stored pollen, adults, pupae, honey, empty comb, and propolis for 11 honey bee hives. Averaging component lipid profiles by hive, we show that, in decreasing order, lipid markers representing fungi, Gram-negative bacteria, and Gram-positive bacteria have the highest relative abundances within honey bee colonies. Our lipid profiles reveal the presence of viable microbial communities in each of the six hive components sampled, with overall microbial community richness varying from lowest to highest in honey, comb, pupae, pollen, adults and propolis, respectively. Finally, microbial community lipid profiles were more similar when compared by component than by hive, location, or sampling year. Specifically, we found that individual hive components typically exhibited several dominant lipids and that these dominant lipids differ between components. Principal component and two-way clustering analyses both support significant grouping of lipids by hive component. Our findings indicate that in addition to the microbial communities present in individual workers, honey bee hives have resident microbial communities associated with different colony components. PMID:25849080

  9. Unique Honey Bee (Apis mellifera) Hive Component-Based Communities as Detected by a Hybrid of Phospholipid Fatty-Acid and Fatty-Acid Methyl Ester Analyses

    PubMed Central

    2015-01-01

    Microbial communities (microbiomes) are associated with almost all metazoans, including the honey bee Apis mellifera. Honey bees are social insects, maintaining complex hive systems composed of a variety of integral components including bees, comb, propolis, honey, and stored pollen. Given that the different components within hives can be physically separated and are nutritionally variable, we hypothesize that unique microbial communities may occur within the different microenvironments of honey bee colonies. To explore this hypothesis and to provide further insights into the microbiome of honey bees, we use a hybrid of fatty acid methyl ester (FAME) and phospholipid-derived fatty acid (PLFA) analysis to produce broad, lipid-based microbial community profiles of stored pollen, adults, pupae, honey, empty comb, and propolis for 11 honey bee hives. Averaging component lipid profiles by hive, we show that, in decreasing order, lipid markers representing fungi, Gram-negative bacteria, and Gram-positive bacteria have the highest relative abundances within honey bee colonies. Our lipid profiles reveal the presence of viable microbial communities in each of the six hive components sampled, with overall microbial community richness varying from lowest to highest in honey, comb, pupae, pollen, adults and propolis, respectively. Finally, microbial community lipid profiles were more similar when compared by component than by hive, location, or sampling year. Specifically, we found that individual hive components typically exhibited several dominant lipids and that these dominant lipids differ between components. Principal component and two-way clustering analyses both support significant grouping of lipids by hive component. Our findings indicate that in addition to the microbial communities present in individual workers, honey bee hives have resident microbial communities associated with different colony components. PMID:25849080

  10. Sialic acid and sialyl-lactose glyco-conjugates: design, synthesis and binding assays to lectins and swine influenza H1N1 virus.

    PubMed

    Zevgiti, Stella; Zabala, Juliana Gonzalez; Darji, Ayub; Dietrich, Ursula; Panou-Pomonis, Eugenia; Sakarellos-Daitsiotis, Maria

    2012-01-01

    The terminal parts of the influenza hemagglutinin (HA) receptors α2,6- and α2,3-sialyllactoses were conjugated to an artificial carrier, named sequential oligopeptide carrier (SOC(4) ), to formulate human and avian receptor mimics, respectively. SOC(4) , formed by the tripeptide unit Lys-Aib-Gly, adopts a rigid helicoids-type conformation, which enables the conjugation of biomolecules to the Lys-N(ε) H(2) groups. By doing so, it preserves their initial conformations and functionalities of the epitopes. We report that SOC(4) -glyco-conjugate bearing two copies of the α2,6-sialyllactose is specifically recognized by the biotinylated Sambucus nigra (elderberry) bark lectin, which binds preferentially to sialic acid in an α2,6-linkage. SOC(4) -glyco-conjugate bearing two copies of the α2,3-sialyllactose was not recognized by the biotinylated Maackia amurensis lectin, despite its well-known α2,3-sialyl bond specificity. However, preliminary immune blot assays showed that H1N1 virus binds to both the SOC(4) -glyco-conjugates immobilized onto nitrocellulose membrane. It is concluded that Ac-SOC(4) [(Ac)(2) ,(3'SL-Aoa)(2) ]-NH(2) 5 and Ac-SOC(4) [(Ac)(2) ,(6'SL-Aoa)(2) ]-NH(2) 6 mimic the HA receptors. These findings could be useful for easy screening of binding and inhibition assays of virus-receptor interactions. PMID:22052803

  11. Assay for the simultaneous determination of guanidinoacetic acid, creatinine and creatine in plasma and urine by capillary electrophoresis UV-detection.

    PubMed

    Zinellu, Angelo; Sotgia, Salvatore; Zinellu, Elisabetta; Chessa, Roberto; Deiana, Luca; Carru, Ciriaco

    2006-03-01

    Guanidinoacetic acid (GAA) measurement has recently become of great interest for the diagnosis of creatine (Cn) metabolism disorders, and research calls for rapid and inexpensive methods for its detection in plasma and urine in order to assess a large number of patients. We propose a new assay for the measurement of GAA by a simple CZE UV-detection without previous sample derivatization. Plasma samples were filtered by Microcon-10 microconcentrators and directly injected into the capillary, while for urine specimens a simple water dilution before injection was needed. A baseline separation was obtained in less than 8 min using a 60.2 cm x 75 microm uncoated silica capillary, 75 mmol/L Tris-phosphate buffer pH 2.25 at 15 degrees C. The performance of the developed method was assessed by measuring plasma creatinine and Cn in 32 normal subjects and comparing the data obtained by the new method with those found with the previous CE assay. Our new method seems to be an inexpensive, fast and specific tool to assess a large number of patients both in clinical and in research laboratories. PMID:16605092

  12. Monoclonal antibody production and indirect competitive enzyme-linked immunosorbent assay development of 3-methyl-quinoxaline-2-carboxylic acid based on novel haptens.

    PubMed

    Li, Guopeng; Zhao, Liang; Zhou, Feng; Li, Jiaying; Xing, Yuan; Wang, Tiangang; Zhou, Xilong; Ji, Baoping; Ren, Wanpeng

    2016-10-15

    Two novel immunizing haptens of 3-methyl-quinoxaline-2-carboxylic acid (MQCA) were synthesized and conjugated with cationized bovine serum albumin. Female BALB/c mice were immunized with above conjugates, splenocytes were fused with Sp2/0 cells to produce monoclonal antibody. Compared with previous studies, antibodies raised in this work showed higher sensitivity. Meantime, a novel heterologous coating hapten was also prepared. The indirect competitive enzyme-linked immunosorbent assay (icELISA) based on the optimum condition showed an IC50 of 3.1μg/kg (ppb), and the linear range of 0.46-10.5ppb for MQCA. The limit of detect (LOD) of MQCA in swine muscle, swine liver and chicken was 0.32, 0.54, and 0.28ppb, respectively. The LOD of this assay can satisfy the minimum required performance levels (4ppb) for MQCA. These results indicated that the proposed ELISA, with high sensitivity and specificity, as well as good reproducibility and accuracy, is suitable for determination of MQCA residues in food samples. PMID:27173564

  13. Treatment of cytomegalovirus infection and disease pre- and post-quantitative nucleic acid test standardization: does use of a more sensitive assay lead to longer treatment duration?

    PubMed

    Dioverti, M Veronica; Lahr, Brian; Razonable, Raymund R

    2016-02-01

    Quantitative cytomegalovirus (CMV) nucleic acid testing (NAT) has been standardized using the World Health Organization (WHO) international calibration standard. A new FDA-approved WHO-calibrated assay (CA) was found to be more sensitive than a laboratory-developed test (LDT). We hypothesized that monitoring therapeutic response using a more sensitive assay may lead to longer antiviral therapy in solid organ and hematopoietic stem cell transplant patients with CMV infection. We reviewed transplant patients with CMV disease retrospectively, and divided them into two groups: those diagnosed and managed based on LDT and those managed using WHO-CA. Compared to patients monitored by LDT, the time to reach an undetectable viral load was significantly longer in the group monitored by the WHO-CA. However, a trend toward shorter duration of antiviral treatment was observed (median, 34 vs. 41 d; p = 0.058), with earlier discontinuation of induction antiviral therapy upon reaching undetectable viral load using WHO-CA (11 vs. 18 d; p = 002). We concluded that despite using a more sensitive CMV NAT, the total duration of antiviral treatment was not significantly prolonged in transplant patients with CMV infection and disease. Relapse rates did not differ between the two groups. PMID:26589482

  14. A rapid and sensitive assay of perfluorocarboxylic acids in aqueous matrices by headspace solid phase microextraction-gas chromatography-triple quadrupole mass spectrometry.

    PubMed

    Monteleone, Marcello; Naccarato, Attilio; Sindona, Giovanni; Tagarelli, Antonio

    2012-08-17

    The work aims at developing a rapid and sensitive method for the quantification of perfluorocarboxylic acids in aqueous matrices. The proposed analytical approach is based on the use of solid phase microextraction in headspace mode after a fast derivatization of the carboxylate function by propylchloroformate/propanol mixture. Several fibers were evaluated and the optimization of the parameters affecting the SPME process was carried out using a central composite design. The optimum working conditions in terms of response values were achieved by performing analysis with CAR/PDMS fiber at room temperature, without addition of NaCl, with a sample volume of 6 ml and an extraction time of 10 min. Assay of PFCAs was performed by using a gas chromatography-triple quadrupole mass spectrometry (GC-QqQ MS) system in negative chemical ionization mode with ammonia as reagent gas. An overall evaluation of all analytical parameters shows that the proposed method provides satisfactory results. In particular, the observed accuracies, ranging from 84.4% to 116.8%, and the RSD values in the range 0.4% and 14.5% confirm the effectiveness of the developed protocol in the assay of PFCAs content in aqueous matrices. Moreover, LOD and LOQ values ranging from 0.08 to 6.6 ng l(-1) and from 0.17 to 14.3 ng l(-1), respectively, can be considered very satisfactory. None of the compounds were detected in six samples of river collected in Calabria. PMID:22762954

  15. A seed coat bedding assay shows that RGL2-dependent release of abscisic acid by the endosperm controls embryo growth in Arabidopsis dormant seeds.

    PubMed

    Lee, Keun Pyo; Piskurewicz, Urszula; Turecková, Veronika; Strnad, Miroslav; Lopez-Molina, Luis

    2010-11-01

    Seed dormancy is an ecologically important adaptive trait in plants whereby germination is repressed even under favorable germination conditions such as imbibition with water. In Arabidopsis and most plant species, dormancy absolutely requires an unidentified seed coat germination-repressive activity and constitutively higher abscisic acid (ABA) levels upon seed imbibition. The mechanisms underlying these processes and their possible relationship are incompletely understood. We developed a "seed coat bedding" assay monitoring the growth of dissected embryos cultured on a layer of seed coats, allowing combinatorial experiments using dormant, nondormant, and various genetically modified seed coat and embryonic materials. This assay, combined with direct ABA measurements, revealed that, upon imbibition, dormant coats, unlike nondormant coats, actively produce and release ABA to repress embryo germination, whatever the embryo origin, i.e., from dormant, nondormant, or never dormant aba seeds, unable to synthesize ABA. The persistent high ABA levels in imbibed dormant seeds requires the permanent expression of the DELLA gene RGL2, where it remains insensitive to gibberellins (GA) unlike in nondormant seeds. These findings present the seed coat as an organ actively controlling germination upon seed imbibition and provide a framework to investigate how environmental factors break seed dormancy. PMID:20956298

  16. A novel approach for measuring sphingosine-1-phosphate and lysophosphatidic acid binding to carrier proteins using monoclonal antibodies and the Kinetic Exclusion Assay.

    PubMed

    Fleming, Jonathan K; Glass, Thomas R; Lackie, Steve J; Wojciak, Jonathan M

    2016-09-01

    Sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA) are bioactive signaling lysophospholipids that activate specific G protein-coupled receptors on the cell surface triggering numerous biological events. In circulation, S1P and LPA associate with specific carrier proteins or chaperones; serum albumin binds both S1P and LPA while HDL shuttles S1P via interactions with apoM. We used a series of kinetic exclusion assays in which monoclonal anti-S1P and anti-LPA antibodies competed with carrier protein for the lysophospholipid to measure the equilibrium dissociation constants (Kd) for these carrier proteins binding S1P and the major LPA species. Fatty acid-free (FAF)-BSA binds these lysophospholipids with the following Kd values: LPA(16:0), 68 nM; LPA(18:1), 130 nM; LPA(18:2), 350 nM; LPA(20:4), 2.2 μM; and S1P, 41 μM. FAF human serum albumin binds each lysophospholipid with comparable affinities. By measuring the apoM concentration and expanding the model to include endogenous ligand, we were able to resolve the Kd values for S1P binding apoM in the context of human HDL and LDL particles (21 nM and 2.4 nM, respectively). The novel competitive assay and analysis described herein enables measurement of Kd values of completely unmodified lysophospholipids binding unmodified carrier proteins in solution, and thus provide insights into S1P and LPA storage in the circulation system and may be useful in understanding chaperone-dependent receptor activation and signaling. PMID:27444045

  17. A facile, sensitive, and highly specific trinitrophenol assay based on target-induced synergetic effects of acid induction and electron transfer towards DNA-templated copper nanoclusters.

    PubMed

    Li, Haiyin; Chang, Jiafu; Hou, Ting; Ge, Lei; Li, Feng

    2016-11-01

    Reliable, selective and sensitive approaches for trinitrophenol (TNP) detection are highly desirable with respect to national security and environmental protection. Herein, a simple and novel fluorescent strategy for highly sensitive and specific TNP assay has been successfully developed, which is based on the quenching of the fluorescent poly(thymine)-templated copper nanoclusters (DNA-CuNCs), through the synergetic effects of acid induction and electron transfer. Upon the addition of TNP, donor-acceptor complexes between the electron-deficient nitro-groups in TNP and the electron-donating DNA templates are formed, resulting in the close proximity between TNP and CuNCs. Moreover, the acidity of TNP contributes to the pH decrease of the system. These factors combine to dramatically quench the fluorescence of DNA-CuNCs, providing a "signal-off" strategy for TNP sensing. The as-proposed strategy demonstrates high sensitivity for TNP assay, and a detection limit of 0.03μM is obtained, which is lower than those reported by using organic fluorescent materials. More significantly, this approach shows outstanding selectivity over a number of TNP analogues, such as 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitrophenol (DNP), 3-nitrophenol (NP), nitrobenzene (NB), phenol (BP), and toluene (BT). Compared with previous studies, this method does not need complex DNA sequence design, fluorescent dye labeling, or sophisticated organic reactions, rendering the strategy with additional advantages of simplicity and cost-effectiveness. In addition, the as-proposed strategy has been adopted for the detection of TNP in natural water samples, indicating its great potential to be applied in the fields of public safety and environmental monitoring. PMID:27591641

  18. Characterization and multicentric validation of a common standard for Toxoplasma gondii detection using nucleic acid amplification assays.

    PubMed

    Varlet-Marie, Emmanuelle; Sterkers, Yvon; Brenier-Pinchart, Marie-Pierre; Cassaing, Sophie; Dalle, Frédéric; Delhaes, Laurence; Filisetti, Denis; Pelloux, Hervé; Touafek, Fériel; Yera, Hélène; Bastien, Patrick

    2014-11-01

    The molecular diagnosis of toxoplasmosis essentially relies upon laboratory-developed methods and suffers from lack of standardization, hence the large diversity of performances between laboratories. Moreover, quantifications of parasitic loads differ among centers, a fact which prevents the possible prediction of the severity of this disease as a function of parasitic loads. The objectives of this multicentric study performed in eight proficient laboratories of the Molecular Biology Pole of the French National Reference Center for Toxoplasmosis (NRC-T) were (i) to assess the suitability of a lyophilized preparation of Toxoplasma gondii as a common standard for use in this PCR-based molecular diagnosis and (ii) to make this standard available to the community. High-quality written procedures were used for the production and qualification of this standard. Three independent batches of this standard, containing concentrations ranging from 10(4) to 0.01 T. gondii genome equivalents per PCR, were first assessed: the linear dynamic range was ≥ 6 log, the intra-assay coefficients of variation (CV) from a sample containing 10 T. gondii organisms per PCR were 0.3% to 0.42%, and the interassay CV over a 2-week period was 0.76% to 1.47%. A further assessment in eight diagnostic centers showed that the standard is stable, robust, and reliable. These lyophilized standards can easily be produced at a larger scale when needed and can be made widely available at the national level. To our knowledge, this is the first quality control assessment of a common standard which is usable both for self-evaluation in laboratories and for accurate quantification of parasitic loads in T. gondii prenatal infections. PMID:25187637

  19. Characterization and Multicentric Validation of a Common Standard for Toxoplasma gondii Detection Using Nucleic Acid Amplification Assays

    PubMed Central

    Varlet-Marie, Emmanuelle; Sterkers, Yvon; Brenier-Pinchart, Marie-Pierre; Cassaing, Sophie; Dalle, Frédéric; Delhaes, Laurence; Filisetti, Denis; Pelloux, Hervé; Touafek, Fériel; Yera, Hélène

    2014-01-01

    The molecular diagnosis of toxoplasmosis essentially relies upon laboratory-developed methods and suffers from lack of standardization, hence the large diversity of performances between laboratories. Moreover, quantifications of parasitic loads differ among centers, a fact which prevents the possible prediction of the severity of this disease as a function of parasitic loads. The objectives of this multicentric study performed in eight proficient laboratories of the Molecular Biology Pole of the French National Reference Center for Toxoplasmosis (NRC-T) were (i) to assess the suitability of a lyophilized preparation of Toxoplasma gondii as a common standard for use in this PCR-based molecular diagnosis and (ii) to make this standard available to the community. High-quality written procedures were used for the production and qualification of this standard. Three independent batches of this standard, containing concentrations ranging from 104 to 0.01 T. gondii genome equivalents per PCR, were first assessed: the linear dynamic range was ≥6 log, the intra-assay coefficients of variation (CV) from a sample containing 10 T. gondii organisms per PCR were 0.3% to 0.42%, and the interassay CV over a 2-week period was 0.76% to 1.47%. A further assessment in eight diagnostic centers showed that the standard is stable, robust, and reliable. These lyophilized standards can easily be produced at a larger scale when needed and can be made widely available at the national level. To our knowledge, this is the first quality control assessment of a common standard which is usable both for self-evaluation in laboratories and for accurate quantification of parasitic loads in T. gondii prenatal infections. PMID:25187637

  20. A rapid and sensitive assay for determination of doxycycline using thioglycolic acid-capped cadmium telluride quantum dots.

    PubMed

    Tashkhourian, Javad; Absalan, Ghodratollah; Jafari, Marzieh; Zare, Saber

    2016-01-01

    A rapid, simple and inexpensive spectrofluorimetric sensor for determination of doxycycline based on its interaction with thioglycolic acid-capped cadmium telluride quantum dots (TGA/CdTe QDs) has been developed. Under the optimum experimental conditions, the sensor exhibited a fast response time of <10s. The results revealed that doxycycline could quench the fluorescence of TGA/CdTe QDs via electron transfer from the QDs to doxycycline through a dynamic quenching mechanism. The sensor permitted determination of doxycycline in a concentration range of 1.9×10(-6)-6.1×10(-5)molL(-1) with a detection limit of 1.1×10(-7)molL(-1). The sensor was applied for determination of doxycycline in honey and human serum samples. PMID:26204505

  1. A rapid and sensitive assay for determination of doxycycline using thioglycolic acid-capped cadmium telluride quantum dots

    NASA Astrophysics Data System (ADS)

    Tashkhourian, Javad; Absalan, Ghodratollah; Jafari, Marzieh; Zare, Saber

    2016-01-01

    A rapid, simple and inexpensive spectrofluorimetric sensor for determination of doxycycline based on its interaction with thioglycolic acid-capped cadmium telluride quantum dots (TGA/CdTe QDs) has been developed. Under the optimum experimental conditions, the sensor exhibited a fast response time of <10 s. The results revealed that doxycycline could quench the fluorescence of TGA/CdTe QDs via electron transfer from the QDs to doxycycline through a dynamic quenching mechanism. The sensor permitted determination of doxycycline in a concentration range of 1.9 × 10-6-6.1 × 10-5 mol L-1 with a detection limit of 1.1 × 10-7 mol L-1. The sensor was applied for determination of doxycycline in honey and human serum samples.

  2. Superabsorbent hydrogels via graft polymerization of acrylic acid from chitosan-cellulose hybrid and their potential in controlled release of soil nutrients.

    PubMed

    Essawy, Hisham A; Ghazy, Mohamed B M; El-Hai, Farag Abd; Mohamed, Magdy F

    2016-08-01

    Superabsorbent polymers fabricated via grafting polymerization of acrylic acid from chitosan (CTS) yields materials that suffer from poor mechanical strength. Hybridization of chitosan with cellulose (Cell) via chemical bonding using thiourea formaldehyde resin increases the flexibility of the produced hybrid (CTS/Cell). The hybridization process and post graft polymerization of acrylic acid was followed using Fourier transform infrared (FTIR). Also, the obtained structures were homogeneous and exhibited uniform surface as could be shown from imaging with scanning electron microscopy (SEM). Thus, the polymers derived from the grafting of polyacrylic acid from (CTS/Cell) gave rise to much more mechanically robust structures ((CTS/Cell)-g-PAA) that bear wide range of pH response due to presence of chitosan and polyacrylic acid in one homogeneous entity. Additionally, the obtained structures possessed greater water absorbency 390, 39.5g/g in distilled water and saline (0.9wt.% NaCl solution), respectively, and enhanced retention potential even at elevated temperatures as revealed by thermogravimetric analysis (TGA). This could be explained by the high grafting efficiency (GE%), 86.4%, and grafting yield (GY%), 750%. The new superabsorbent polymers proved to be very efficient devices for controlled release of fertilizers into the soil which expands their use in agriculture and horticultural applications. PMID:27126169

  3. Synthesis, DFT and antimicrobial activity assays in vitro for novel cis/trans-but-2-enedioic acid esters

    NASA Astrophysics Data System (ADS)

    Ma, Yan-Long; Zhou, Ru-Jin; Zeng, Xing-Ye; An, Ya-Xiong; Qiu, Song-Shan; Nie, Li-Jun

    2014-04-01

    Six novel cis/trans-but-2-enedioic acid esters had been synthesized to discover the new bioactive molecules that could kill food-related bacteria and fungi. Their structures were analyzed by melting point, LC-MS, 1H NMR and 13C NMR. 4-(Methoxycarbonyl) phenyl ethyl fumarate (6b) was also characterized by single-crystal X-ray diffraction. Their antimicrobial activities were evaluated in vitro by measuring the minimal inhibitory concentration (MIC). Compared with the single monomethyl fumarate and methyl 4-hydroxybenzoate, these compounds had stronger antimicrobial activity against all the eight microorganisms. Among the antibacterial and antifungal compounds, 4-(methoxycarbonyl) phenyl methyl fumarate (6a) showed the best antimicrobial activity. The electronic properties of these compounds were calculated by the density functional theory (DFT) method with 6-31G (d, p) basis set. DFT studies indicated that molecular electrostatic potential (MEP) map, ELUMO, energy gap, electronegativity and electrophilicity index could be helpful to understand the various antimicrobial activities among these compounds. The antimicrobial activity of compound 6a was evaluated in vitro against Salmonellacholeraesuis subsp. choleraesuis, Lactococcus lactis subsp. lactis and Saccharomyces cerevisiae by time-kill, and it was found that compound 6a exhibited significant microbiocidal activity against the three microorganisms.

  4. Anti-melanogenic effects of resveratryl triglycolate, a novel hybrid compound derived by esterification of resveratrol with glycolic acid.

    PubMed

    Park, Soojin; Seok, Jin Kyung; Kwak, Jun Yup; Choi, Yun-Hyeok; Hong, Seong Su; Suh, Hwa-Jin; Park, Woncheol; Boo, Yong Chool

    2016-07-01

    Resveratrol is known to inhibit cellular melanin synthesis by multiple mechanisms. Glycolic acid (GA) is used in skin care products for its excellent skin penetration. The purpose of this study was to examine the anti-melanogenic effects of resveratryl triglycolate (RTG), a novel hybrid compound of resveratrol and GA, in comparison with resveratrol, GA, resveratryl triacetate (RTA) and arbutin. Resveratrol, RTG, and RTA inhibited the catalytic activity human tyrosinase (TYR) more potently than arbutin or GA did. Their cytotoxic and anti-melanogenic effects were examined using murine melanoma B16/F10 cells and human epidermal melanocytes (HEMs). The cytotoxicity of RTG was similar to that of resveratrol and RTA. RTG at 3-10 μM decreased melanin levels and cellular TYR activities in α-melanocyte-stimulating hormone-stimulated B16/F10 cells, and L-tyrosine-stimulated HEMs. RTG also suppressed mRNA and protein expression of TYR, tyrosinase-related protein 1, L-3,4-dihydroxyphenylalanine chrome tautomerase, and microphthalmia-associated transcription factor (MITF) in HEMs stimulated with L-tyrosine. This study suggests that, like resveratrol and RTA, RTG can attenuate cellular melanin synthesis effectively through the suppression of MITF-dependent expression of melanogenic enzymes and the inhibition of catalytic activity of TYR enzyme. RTG therefore has potential for use as a cosmeceutical ingredient for skin whitening. PMID:27059716

  5. Hybrid organic/inorganic copolymers with strongly hydrogen-bond acidic properties for acoustic wave and optical sensors

    SciTech Connect

    Grate, J.W.; Kaganove, S.N.; Patrash, S.J.

    1997-05-01

    Hybrid organic/inorganic polymers have been prepared incorporating fluoroalkyl-substituted bisphenol groups linked using oligosiloxane spacers. These hydrogen-bond acidic materials have glass-to-rubber transition temperatures below room temperature and are excellent sorbents for basic vapors. The physical properties such as viscosity and refractive index can be tuned by varying the length of the oligosiloxane spacers and the molecular weight. In addition, the materials are easily cross-linked to yield solid elastomers. The potential use of these materials for chemical sensing has been demonstrated by applying them to surface acoustic wave devices as thin films and detecting the hydrogen-bond basic vapor dimethyl methylphosphonate with high sensitivity. It has also been demonstrated that one of these materials with suitable viscosity and refractive index can be used to clad silica optical fibers; the cladding was applied to freshly drawn fiber using a fiber drawing tower. These fibers have potential as evanescent wave optical fiber sensors. 38 refs., 2 figs.

  6. Bioinspired syntheses of dimeric hydroxycinnamic acids (lignans) and hybrids, using phenol oxidative coupling as key reaction, and medicinal significance thereof.

    PubMed

    Magoulas, George E; Papaioannou, Dionissios

    2014-01-01

    Lignans are mainly dimers of 4-hydroxycinnamic acids (HCAs) and reduced analogs thereof which are produced in Nature through phenol oxidative coupling (POC) as the primary C-C or C-O bond-forming reaction under the action of the enzymes peroxidases and laccases. They present a large structural variety and particularly interesting biological activities, therefore, significant efforts has been devoted to the development of efficient methodologies for the synthesis of lignans isolated from natural sources, analogs and hybrids with other biologically interesting small molecules. We summarize in the present review those methods which mimic Nature for the assembly of the most common lignan skeleta by using either enzymes or one-electron inorganic oxidants to effect POC of HCAs and derivatives, such as esters and amides, or cross-POC of pairs of HCAs or HCAs with 4-hydrocycinnamyl alcohols. We, furthermore, provide outlines of mechanistic schemes accounting for the formation of the coupled products and, where applicable, indicate their potential application in medicine. PMID:25460307

  7. Rapid recharge capability of valve-regulated lead-acid batteries for electric vehicle and hybrid electric vehicle applications

    NASA Astrophysics Data System (ADS)

    Fleming, F. A.; Shumard, P.; Dickinson, B.

    Range limitation is a significant drawback to the successful commercialization of electric vehicles (EVs). An apt description of an EV is `a high performance vehicle with a one-gallon fuel tank'. In the absence of a `super battery', there are at least two approaches to resolving this drawback. The first approach is rapid recharge, i.e., recharging the battery as close as possible to the same time period as it takes to fill the petrol tank of an internal-combustion-engined (ICE) vehicle. Whilst not extending the vehicle range as such, this approach does enable high usage of the vehicle without experiencing unduly long recharge times. The ability of the battery to accept rapid recharge is paramount for this approach. The second approach is the development of a hybrid electric vehicle (HEV). In this case, the demand on the battery is the ability to provide, and also absorb from regenerative braking, high specific peak-power levels over a wide range of battery state-of-charge. This paper describes the ability, and indeed limitations, of the valve-regulated Genesis® lead-acid battery in meeting such requirements.

  8. Microbial populations identified by fluorescence in situ hybridization in a constructed wetland treating acid coal mine drainage

    SciTech Connect

    Nicomrat, D.; Dick, W.A.; Tuovinen, O.H.

    2006-07-15

    Microorganisms are an integral part of the biogeochemical processes in wetlands, yet microbial communities in sediments within constructed wetlands receiving acid mine drainage (AMD) are only poorly understood. The purpose of this study was to characterize the microbial diversity and abundance in a wetland receiving AMD using fluorescence in situ hybridization (FISH) analysis. Seasonal samples of oxic surface sediments, comprised of Fe(III) precipitates, were collected from two treatment cells of the constructed wetland system. The pH of the bulk samples ranged between pH 2.1 and 3.9. Viable counts of acidophilic Fe and S oxidizers and heterotrophs were determined with a most probable number (MPN) method. The MPN counts were only a fraction of the corresponding FISH counts. The sediment samples contained microorganisms in the Bacteria (including the subgroups of acidophilic Fe- and S-oxidizing bacteria and Acidiphilium spp.) and Eukarya domains. Archaea were present in the sediment surface samples at < 0.01% of the total microbial community. The most numerous bacterial species in this wetland system was Acidithiobacillus ferrooxidans, comprising up to 37% of the bacterial population. Acidithiobacillus thiooxidans was also abundant.

  9. Comparison of AMPLICOR and Hybrid Capture II assays for high risk HPV detection in normal and abnormal liquid-based cytology: use of INNO-LiPA Genotyping assay to screen the discordant results.

    PubMed

    Mo, L Z; Monnier-Benoit, S; Kantelip, B; Petitjean, A; Riethmuller, D; Prétet, J L; Mougin, C

    2008-02-01

    The study was aimed to evaluate the feasibility of detecting human papillomavirus (HPV) in women with normal or abnormal cervical smears using the Roche Amplicor MWP HPV Test. We compared by AMPLICOR Test and Hybrid Capture II (HCII) Test, the prevalence of HR-HPV in 470 cervical samples including 55 samples with WNL cytology, 208 ASC-US, 193 LGSIL and 14 HGSIL. Samples with discordant results were retested with INNO-LiPA Genotyping HPV Test v2. The HR-HPV positivity in WNL cytology samples was similar (21.8%) by AMPLICOR and HCII. In ASC-US, the HPV positivity was 42.3% by both tests. In LGSIL, HPV positivity was 66.3% and 66.8% by AMPLICOR and HCII, respectively. In HGSIL, 92.8% of samples were positive by AMPLICOR and 85.7% by HCII. The agreement of both tests was 96.2% with a Kappa value of 0.92. Eighteen cases were discordant: 9 HCII positive/AMPLICOR negative and 9 HCII negative/AMPLICOR positive. The INNO-LiPA test revealed HPV positivity in every case. Interestingly, all HCII+/AMPLICOR- samples were found to harbour HPV53. As for the HCII-/AMPLICOR+ samples, 8 demonstrated a multiple infection with HR 16- and/or 18- and/or 56-phylogenetically related HPV types. Moreover, two of these samples were co-infected with HPV6 and two other with HPV54. By using consensus HR-HPV as our reference HPV positivity, the sensitivity (96.6%) and specificity (100%) of AMPLICOR was similar to that of HCII Test. The AMPLICOR HPV Test is sensitive, specific, feasible and appropriate for routine HPV detection. PMID:18036888

  10. A functional assay to measure postsynaptic gamma-aminobutyric acidB responses in cultured spinal cord neurons: Heterologous regulation of the same K+ channel

    SciTech Connect

    Kamatchi, G.L.; Ticku, M.K. )

    1991-02-01

    The stimulation of postsynaptic gamma-aminobutyric acid (GABA)B receptors leads to slow inhibitory postsynaptic potentials due to the influx of K(+)-ions. This was studied biochemically, in vitro in mammalian cultured spinal cord neurons by using 86Rb as a substitute for K+. (-)-Baclofen, a GABAB receptor agonist, produced a concentration-dependent increase in the 86Rb-influx. This effect was stereospecific and blocked by GABAB receptor antagonists like CGP 35 348 (3-aminopropyl-diethoxymethyl-phosphonic acid) and phaclofen. Apart from the GABAB receptors, both adenosine via adenosine1 receptors and 5-hydroxytryptamine (5-HT) via 5-HT1 alpha agonists also increased the 86Rb-influx. These agonists failed to show any additivity between them when they were combined in their maximal concentration. In addition, their effect was antagonized specifically by their respective antagonists without influencing the others. These findings suggest the presence of GABAB, adenosine1 and 5-HT1 alpha receptors in the cultured spinal cord neurons, which exhibit a heterologous regulation of the same K(+)-channel. The effect of these agonists were antagonized by phorbol 12,13-didecanoate, an activator of protein kinase C, and pretreatment with pertussis toxin. This suggests that these agonists by acting on their own receptors converge on the same K(+)-channel through the Gi/Go proteins. In summary, we have developed a biochemical functional assay for studying and characterizing GABAB synaptic pharmacology in vitro, using spinal cord neurons.

  11. A fluorescence-coupled assay for gamma aminobutyric acid (GABA) reveals metabolic stress-induced modulation of GABA content in neuroendocrine cancer.

    PubMed

    Ippolito, Joseph E; Piwnica-Worms, David

    2014-01-01

    Pathways involved in the synthesis of the neurotransmitter gamma-aminobutyric acid (GABA) have been implicated in the pathogenesis of high grade neuroendocrine (NE) neoplasms as well as neoplasms from a non-NE lineage. Using The Cancer Genome Atlas, overexpression of the GABA synthetic enzyme, glutamate decarboxylase 1 (GAD1), was found to be associated with decreased disease free-survival in prostate adenocarcinoma and decreased overall survival in clear cell renal cell carcinomas. Furthermore, GAD1 was found to be expressed in castrate-resistant prostate cancer cell lines, but not androgen-responsive cell lines. Using a novel fluorescence-coupled enzymatic microplate assay for GABA mediated through reduction of resazurin in a prostate neuroendocrine carcinoma (PNEC) cell line, acid microenvironment-induced stress increased GABA levels while alkaline microenvironment-induced stress decreased GABA through modulation of GAD1 and glutamine synthetase (GLUL) activities. Moreover, glutamine but not glucose deprivation decreased GABA through modulation of GLUL. Consistent with evidence in prokaryotic and eukaryotic organisms that GABA synthesis mediated through GAD1 may play a crucial role in surviving stress, GABA may be an important mediator of stress survival in neoplasms. These findings identify GABA synthesis and metabolism as a potentially important pathway for regulating cancer cell stress response as well as a potential target for therapeutic strategies. PMID:24551133

  12. Sulfonic acid-functionalized hybrid organic-inorganic proton exchange membranes synthesized by sol-gel using 3-mercaptopropyl trimethoxysilane (MPTMS)

    NASA Astrophysics Data System (ADS)

    Mosa, J.; Durán, A.; Aparicio, M.

    2015-11-01

    Organic/inorganic hybrid membranes based on (3-glycidoxypropyl) trimethoxysilane (GPTMS) and 3-mercaptopropyl trimethoxysilane (MPTMS) have been prepared by sol-gel method and organic polymerisation, as candidate materials for proton exchange membranes in direct alcohol fuel cell (DMFC) applications. The -SH groups of MPTMS are oxidized to sulfonic acid groups, which are attributed to enhance the proton conductivity of hybrid membranes. FTIR, XPS and contact angle were used to characterize and confirm the hybrid structure and oxidation reaction progress. Membranes characterization also includes ion exchange capacity, water uptake, methanol permeability and proton conductivity to confirm their applicability in fuel cells. All the membranes were homogeneous and thermally and chemically resistant. In particular, the hybrid membranes demonstrated proton conductivities as high as 0.16 S cm-1 at high temperature, while exhibiting a low methanol permeability as compared to Nafion®. These results are associated with proton conducting paths through the silica pseudo-PEO network in which sulfonic acid groups work as proton donor.

  13. Weathering and Biodegradation Study on Graft Copolymer Compatibilized Hybrid Bionanocomposites of Poly(Lactic Acid)

    NASA Astrophysics Data System (ADS)

    Sajna, VP; Nayak, Sanjay K.; Mohanty, Smita

    2016-06-01

    This work reports on the influence of moisture absorption and accelerated weathering on the properties of graft copolymer compatibilized bionanocomposites of poly(lactic acid) (PLA). Moisture absorption tests were conducted for 30 days by immersing the samples in a distilled water bath at room temperature, and the amount of moisture absorbed in each time interval was measured. The rate of moisture uptake decreased by incorporation of C30B nanoclay and graft copolymer into fiber-reinforced PLA composites. Changes in the mechanical properties of composites in each time interval of moisture absorption were investigated using tensile and impact tests. Exposure to moisture caused significant drops in the mechanical properties. The morphological characterization of biocomposites during the aforementioned tests has been made using SEM, while bionanocomposites were analyzed by TEM. Further, this paper also reported the effect of accelerated weathering on the mechanical properties and the results are confirmed through SEM analysis. Biodegradation behaviors of PLA biocomposites and bionanocomposites have also been studied.

  14. Weathering and Biodegradation Study on Graft Copolymer Compatibilized Hybrid Bionanocomposites of Poly(Lactic Acid)

    NASA Astrophysics Data System (ADS)

    Sajna, VP; Nayak, Sanjay K.; Mohanty, Smita

    2016-07-01

    This work reports on the influence of moisture absorption and accelerated weathering on the properties of graft copolymer compatibilized bionanocomposites of poly(lactic acid) (PLA). Moisture absorption tests were conducted for 30 days by immersing the samples in a distilled water bath at room temperature, and the amount of moisture absorbed in each time interval was measured. The rate of moisture uptake decreased by incorporation of C30B nanoclay and graft copolymer into fiber-reinforced PLA composites. Changes in the mechanical properties of composites in each time interval of moisture absorption were investigated using tensile and impact tests. Exposure to moisture caused significant drops in the mechanical properties. The morphological characterization of biocomposites during the aforementioned tests has been made using SEM, while bionanocomposites were analyzed by TEM. Further, this paper also reported the effect of accelerated weathering on the mechanical properties and the results are confirmed through SEM analysis. Biodegradation behaviors of PLA biocomposites and bionanocomposites have also been studied.

  15. Preparation of hydroxyapatite/poly(lactic acid) hybrid microparticles for local drug delivery

    NASA Astrophysics Data System (ADS)

    Loca, D.; Locs, J.; Berzina-Cimdina, L.

    2013-12-01

    Calcium phosphate (CaP) bioceramic is well known as bioactive and biocompatible material in bone tissue regeneration applications. Apatitic CaP, especially nano sized hydroxyapatite (NHAp), is more similar to the natural apatite presented in the bone tissue than CaP bioceramics. In the current research NHAp was modified using biodegradable polymer - poly(lactic acid) (PLA) to develop composites providing bone regeneration and local drug delivery. NHAp/PLA microcapsules were prepared using solid-in-water-in-oil-in-water (s/w1/o/w2) encapsulation technology. The impact of primary and secondary emulsion stability on the emulsion droplet and microparticle properties was evaluated. The stability of final emulsion can be increased by varying the process parameters. Stable s/w1/o/w2 emulsion using 3ml of NHAp suspension, not less than 100ml of 4% PVA water solution and 10ml of 10% PLA solution in dichloromethane can be obtained. S/w1/o/w2 microencapuslation method can be effectively used for the preparation of multi-domain microcapsules achieving high NHAp encapsulation efficacy (93%).

  16. Bacteriological analysis of water by potentiometric measurement of lipoic acid reduction: preliminary assays for selective detection of indicator organisms.

    PubMed Central

    Charriere, G; Jouenne, T; Lemeland, J F; Selegny, E; Junter, G A

    1984-01-01

    The practical task of adapting an original potentiometric technique to the bacteriological analysis of water is discussed. Various laboratory strains of organisms belonging to the usual aquatic flora were inoculated one by one in a minimal lactose broth supplied with lipoic (thioctic) acid. The time evolution of the redox potential of the cultures was followed during incubation by combined gold versus reference electrodes. When the incubation temperature was regulated at 36 degrees C, most organisms were able to grow and to reduce the coenzyme, generating changes in the redox potential of the culture. However, very few organisms developed significant reductive activity when the temperature was increased to 41 degrees C and when the broth was provided with sodium deoxycholate. Among the fecal coliform organisms, only Escherichia coli and Klebsiella pneumoniae exhibited early but reproducible potential-time responses. Positive potentiometric responses were also recorded with Acinetobacter calcoaceticus. E. coli showed rapid potentiometric signals as compared with K. pneumoniae. The time required for 100-mV shift of potential to be detected was related to the logarithm of the initial concentration of E. coli or K. pneumoniae in the culture broth. Experiments on natural surface water samples showed the the potentiometric method, associated with the selective incubation conditions, mainly detected E. coli among the bacterial flora of the tested environmental water. The calibration curve relating the time required for a 100-mV shift of potential to be detected to the number of fecal coliforms, as determined by control fecal coliform-selective plate counts, was consistent with the composite standard curve of detection times obtained with six different laboratory strains of E. coli.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6421230

  17. Effects of molecular liposomal hybrid compositions with oxidized dextrans and isonicotinic acid hydrazide on production of granulocytic macrophage colony-stimulating factor by macrophages.

    PubMed

    Shkurupy, V A; Arkhipov, S A; Troitsky, A V; Luzgina, N G; Zaikovskaja, M V; Ufimceva, E G; Iljine, D A; Akhramenko, E S; Gulyaeva, E P; Bistrova, T N

    2009-10-01

    The effects of molecular liposomal hybrid compositions consisting of liposomes (200-450 nm) containing oxidized dextrans (dextranals; 35-60 kDa) conjugated with isonicotinic acid hydrazide (dextrazides), their components, and native dextrans on the production of granulocytic macrophage CSF by peritoneal macrophages were studied in vitro. Dextranals proved to be more potent inductors of granulocytic macrophage CSF than native dextrans. Conjugation of nicotinic acid hydrazide with dextranals did not modify their capacity to stimulate the production of granulocytic macrophage CSF. Liposomes in the molecular liposomal hybrid compositions did not attenuate the dextrazide capacity to stimulate the production of granulocytic macrophage CSF. Molecular liposomal compositions containing 60 kDa dextrazide exhibited the most potent stimulatory effect on macrophage production of granulocytic macrophage CSF. PMID:20396775

  18. Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes for Rapid Detection of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis in Potable-Water Biofilms

    PubMed Central

    Lehtola, Markku J.; Torvinen, Eila; Miettinen, Ilkka T.; Keevil, C. William

    2006-01-01

    Here, we present for the first time a high-affinity peptide nucleic acid (PNA) oligonucleotide sequence for detecting Mycobacterium avium bacteria, including the opportunistically pathogenic subspecies M. avium subsp. avium, M. avium subsp. paratuberculosis, and M. avium subsp. silvaticum, by the fluorescence in situ hybridization (FISH) method. There is evidence that M. avium subsp. avium especially is able to survive and grow in drinking-water biofilms and possibly transmit via drinking water. The designed PNA probe (MAV148) specificity was tested with several bacterial species, including other mycobacteria and mycolic acid-containing bacteria. From the range of bacterial strains tested, only M. avium subsp. avium and M. avium subsp. paratuberculosis strains were hybridized. The PNA FISH method was applied successfully to detect M. avium subsp. avium spiked in water samples and biofilm established within a Propella biofilm reactor fed with potable water from a distribution supply. PMID:16391126

  19. Topoisomerase Assays

    PubMed Central

    Nitiss, John L.; Soans, Eroica; Rogojina, Anna; Seth, Aman; Mishina, Margarita

    2012-01-01

    Topoisomerases are nuclear enzymes that play essential roles in DNA replication, transcription, chromosome segregation, and recombination. All cells have two major forms of topoisomerases: type I, which makes single-stranded cuts in DNA, and type II enzymes, which cut and pass double-stranded DNA. DNA topoisomerases are important targets of approved and experimental anti-cancer agents. The protocols described in this unit are of assays used to assess new chemical entities for their ability to inhibit both forms of DNA topoisomerase. Included are an in vitro assay for topoisomerase I activity based on relaxation of supercoiled DNA and an assay for topoisomerase II based on the decatenation of double-stranded DNA. The preparation of mammalian cell extracts for assaying topoisomerase activity is described, along with a protocol for an ICE assay for examining topoisomerase covalent complexes in vivo and an assay for measuring DNA cleavage in vitro. PMID:22684721

  20. Evaluation of different modifications of acid-fast staining techniques and stool enzyme-linked immunosorbent assay in detecting fecal Cryptosporidium in diarrheic HIV seropositive and seronegative patients

    PubMed Central

    Parghi, Ekta; Dash, Lona; Shastri, Jayanthi

    2014-01-01

    Rational: The role of Cryptosporidium as an agent of human diarrhea has been redefined over the past decade following recognition of the strong association between cases of cryptosporidiosis and immune deficient individuals (such as those with AIDS). Purpose: The purpose of this study is to determine the prevalence of enteric parasites and to compare the diagnostic utility of stool enzyme-linked immunosorbent assay (ELISA) with various modifications of acid-fast (AF) staining in detection of Cryptosporidium in stool samples of diarrheic patients. Materials and Methods: Stool samples from 186 cases comprising of 93 HIV seropositive and 93 seronegative patients were included. These were subjected to routine and microscopic examination as well as various modifications of AF staining for detection of coccidian parasites and ELISA for the detection of Cryptosporidium. Results: The prevalence of enteric parasites was 54.8% and of Cryptosporidium was 17.2% in HIV seropositive patients while it was 29.0% and 5.4%, respectively in seronegative patients. Of the 186 cases, 33 cases (17.7%) were positive for Cryptosporidium by stool ELISA as compared to 21 (11.3%) by modified AF staining (gold standard) showing sensitivity and specificity of 100% and 92.7%, respectively. The maximum cases of Cryptosporidium (21; 11.3%) were detected by AF staining using 3% acid alcohol. Conclusion: ELISA is a simple, useful, and rapid tool for detection of Cryptosporidium in stool, especially for large scale population studies. However, the role of modified AF staining in detection of Cryptosporidium and other coccidian parasites is important. Based on the results of various modifications of AF staining, the present study recommends the use of 3% acid alcohol along with 10% H2SO4. PMID:25250230

  1. Biomineralized biomimetic organic/inorganic hybrid hydrogels based on hyaluronic acid and poloxamer.

    PubMed

    Huh, Hyun Wook; Zhao, Linlin; Kim, So Yeon

    2015-08-01

    A biomineralized hydrogel system containing hyaluronic acid (HA) and poloxamer composed of a poly(ethylene oxide)/poly(propylene oxide)/poly(ethylene oxide) (PEO-PPO-PEO) block copolymer was developed as a biomimetic thermo-responsive injectable hydrogel system for bone regeneration. Using HA and poloxamer macromers with polymerizable residues, organic/inorganic HA/poloxamer hydrogels with various compositions were prepared and subjected to a biomineralization process to mimic the bone extracellular matrix. An increase in HA content within the hydrogels enhanced intermolecular chelation with calcium ions, leading to an increase in nucleation and growth of calcium phosphate in the hydrogels. After the biomineralization procedure, a crystalline formation was observed within and on the surface of the hydrogel. All of the HA/poloxamer hydrogel samples exhibited relatively high water content of greater than 90% at 25 °C, and the water content was influenced by the HA/poloxamer composition, biomineralization, and temperature. In particular, the HA/poloxamer hydrogel was injectable through a syringe without demonstrating appreciable macroscopic fracture at room temperature, whereas it was more opaque and adopted a more rigid structure as the temperature increased because of the increasing hydrophobicity of poloxamer. The enzymatic degradation behavior of the hydrogels depended on the concentration of hyaluronidase, HA/poloxamer composition, and biomineralization. The release kinetics of model drugs from HA/poloxamer hydrogels was primarily dependent on the drug loading content, water content, biomineralization of the hydrogels, and ionic properties of the drug. These results indicate that biomineralized HA/poloxamer hydrogel is a promising candidate material for a biomimetic hydrogel system that promotes bone tissue repair and regeneration via local delivery of drugs. PMID:25933531

  2. Hexagonal cobalt oxyhydroxide-carbon dots hybridized surface: high sensitive fluorescence turn-on probe for monitoring of ascorbic acid in rat brain following brain ischemia.

    PubMed

    Li, Linbo; Wang, Chao; Liu, Kangyu; Wang, Yuhan; Liu, Kun; Lin, Yuqing

    2015-03-17

    In this study, we report a novel and efficient fluorescence probe synthesized by Tris(hydroxymethyl)aminomethane-derived carbon dots (CDs)-modified hexagonal cobalt oxyhydroxide(CoOOH) nanoflakes (Tris-derived CDs-CoOOH) for monitoring of cerebral ascorbic acid (AA) in brain microdialysate. The as-prepared Tris-derived CDs with the fluorescence quantum yield of 7.3% are prepared by a one-step pyrolysis strategy of the sole precursor and used as the signal output. After being hybridized with CoOOH nanoflakes to form Tris-derived CDs-CoOOH, the luminescence of the Tris-derived CDs can be efficiently quenched by CoOOH via fluorescence resonance energy transfer (FRET). Due to the specific redox reaction between the enediol group of AA and hexagonal CoOOH nanoflakes, AA can reduce the hexagonal CoOOH nanoflakes in the Tris-derived CDs-CoOOH and lead to collapse of the hybrized structure, then the release of Tris-derived CDs, and thus finally the fluorescence recovery. Moreover, cobalt ions (II), generated by CoOOH nanoflakes oxidizing AA, almost have no obvious interference on the fluorescence probe, i.e., Tris-derived CDs, which could be ascribed to the surface of Tris-derived CDs containing a few strong chelation groups such as amino/carboxyl/thiol groups, instead of plenty of -OH groups with weak chelation with Co(2+). On the basis of this feature, the Tris-derived CDs-CoOOH fluorescent probe demonstrates a linear range from 100 nM to 20 μM with the detection limit of ∼50 nM, i.e., with an improved sensitivity toward AA detection. Compared with other turn-on fluorescent methods using convenient fluorophore-nitroxide fluorescent probes for detection of AA, the method demonstrated here possesses a facial synthesis route, lower limit of detection, and wider linear range, which validates sensing of AA in the cerebral systems during the calm/ischemia process. This study provides a fluorescence assay for the simple yet facial detection of AA in the cerebral systems and

  3. Artificial mismatch hybridization

    DOEpatents

    Guo, Zhen; Smith, Lloyd M.

    1998-01-01

    An improved nucleic acid hybridization process is provided which employs a modified oligonucleotide and improves the ability to discriminate a control nucleic acid target from a variant nucleic acid target containing a sequence variation. The modified probe contains at least one artificial mismatch relative to the control nucleic acid target in addition to any mismatch(es) arising from the sequence variation. The invention has direct and advantageous application to numerous existing hybridization methods, including, applications that employ, for example, the Polymerase Chain Reaction, allele-specific nucleic acid sequencing methods, and diagnostic hybridization methods.

  4. Corrosion resistance of siloxane-poly(methyl methacrylate) hybrid films modified with acetic acid on tin plate substrates: Influence of tetraethoxysilane addition

    NASA Astrophysics Data System (ADS)

    Kunst, S. R.; Cardoso, H. R. P.; Oliveira, C. T.; Santana, J. A.; Sarmento, V. H. V.; Muller, I. L.; Malfatti, C. F.

    2014-04-01

    The aim of this paper is to study the corrosion resistance of hybrid films. Tin plate was coated with a siloxane-poly (methyl methacrylate) (PMMA) hybrid film prepared by sol-gel route with covalent bonds between the organic (PMMA) and inorganic (siloxane) phases obtained by hydrolysis and polycondensation of 3-(trimethoxysilylpropyl) methacrylate (TMSM) and polymerization of methyl methacrylate (MMA) using benzoyl peroxide (BPO) as a thermic initiator. Hydrolysis reactions were catalyzed by acetic acid solution avoiding the use of chlorine or stronger acids in the film preparation. The effect of the addition of tetraethoxysilane (TEOS) on the protective properties of the film was evaluated. The hydrophobicity of the film was determined by contact angle measurements, and the morphology was evaluated by scanning electron microscopy (SEM) and profilometry. The local nanostructure was investigated by Fourier transform infrared spectroscopy (FT-IR). The electrochemical behavior of the films was assessed by open circuit potential monitoring, potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) measurements in a 0.05 M NaCl solution. The mechanical behavior was evaluated by tribology. The results highlighted that the siloxane-PMMA hybrid films modified with acetic acid are promising anti-corrosive coatings that acts as an efficient diffusion barrier, protecting tin plates against corrosion. However, the coating properties were affected by the TEOS addition, which contributed for the thickness increase and irregular surface coverage.

  5. Multiplexing spheroid volume, resazurin and acid phosphatase viability assays for high-throughput screening of tumour spheroids and stem cell neurospheres.

    PubMed

    Ivanov, Delyan P; Parker, Terry L; Walker, David A; Alexander, Cameron; Ashford, Marianne B; Gellert, Paul R; Garnett, Martin C

    2014-01-01

    Three-dimensional cell culture has many advantages over monolayer cultures, and spheroids have been hailed as the best current representation of small avascular tumours in vitro. However their adoption in regular screening programs has been hindered by uneven culture growth, poor reproducibility and lack of high-throughput analysis methods for 3D. The objective of this study was to develop a method for a quick and reliable anticancer drug screen in 3D for tumour and human foetal brain tissue in order to investigate drug effectiveness and selective cytotoxic effects. Commercially available ultra-low attachment 96-well round-bottom plates were employed to culture spheroids in a rapid, reproducible manner amenable to automation. A set of three mechanistically different methods for spheroid health assessment (Spheroid volume, metabolic activity and acid phosphatase enzyme activity) were validated against cell numbers in healthy and drug-treated spheroids. An automated open-source ImageJ macro was developed to enable high-throughput volume measurements. Although spheroid volume determination was superior to the other assays, multiplexing it with resazurin reduction and phosphatase activity produced a richer picture of spheroid condition. The ability to distinguish between effects on malignant and the proliferating component of normal brain was tested using etoposide on UW228-3 medulloblastoma cell line and human neural stem cells. At levels below 10 µM etoposide exhibited higher toxicity towards proliferating stem cells, whereas at concentrations above 10 µM the tumour spheroids were affected to a greater extent. The high-throughput assay procedures use ready-made plates, open-source software and are compatible with standard plate readers, therefore offering high predictive power with substantial savings in time and money. PMID:25119185

  6. Multiplexing Spheroid Volume, Resazurin and Acid Phosphatase Viability Assays for High-Throughput Screening of Tumour Spheroids and Stem Cell Neurospheres

    PubMed Central

    Ivanov, Delyan P.; Parker, Terry L.; Walker, David A.; Alexander, Cameron; Ashford, Marianne B.; Gellert, Paul R.; Garnett, Martin C.

    2014-01-01

    Three-dimensional cell culture has many advantages over monolayer cultures, and spheroids have been hailed as the best current representation of small avascular tumours in vitro. However their adoption in regular screening programs has been hindered by uneven culture growth, poor reproducibility and lack of high-throughput analysis methods for 3D. The objective of this study was to develop a method for a quick and reliable anticancer drug screen in 3D for tumour and human foetal brain tissue in order to investigate drug effectiveness and selective cytotoxic effects. Commercially available ultra-low attachment 96-well round-bottom plates were employed to culture spheroids in a rapid, reproducible manner amenable to automation. A set of three mechanistically different methods for spheroid health assessment (Spheroid volume, metabolic activity and acid phosphatase enzyme activity) were validated against cell numbers in healthy and drug-treated spheroids. An automated open-source ImageJ macro was developed to enable high-throughput volume measurements. Although spheroid volume determination was superior to the other assays, multiplexing it with resazurin reduction and phosphatase activity produced a richer picture of spheroid condition. The ability to distinguish between effects on malignant and the proliferating component of normal brain was tested using etoposide on UW228-3 medulloblastoma cell line and human neural stem cells. At levels below 10 µM etoposide exhibited higher toxicity towards proliferating stem cells, whereas at concentrations above 10 µM the tumour spheroids were affected to a greater extent. The high-throughput assay procedures use ready-made plates, open-source software and are compatible with standard plate readers, therefore offering high predictive power with substantial savings in time and money. PMID:25119185

  7. Production of monoclonal antibody for okadaic acid and its utilization in an ultrasensitive enzyme-linked immunosorbent assay and one-step immunochromatographic strip.

    PubMed

    Liu, Biing-Hui; Hung, Chun-Tse; Lu, Chuan-Chen; Chou, Hong-Non; Yu, Feng-Yih

    2014-02-12

    Okadaic acid (OA) is a common marine biotoxin that accumulates in bivalves and causes diarrhetic shellfish poisoning (DSP). This study generated a monoclonal antibody (mAb) specific to OA from a hybridoma cell line, 6B1A3, which was obtained by fusion of myeloma cells (P3/NS1/1-AG4-1) with spleen cells isolated from a BALB/c mouse immunized with OA-γ-globulin. The 6B1A3 mAb belongs to the immunoglobulin G1 (κ chain) isotype. Both competitive direct and indirect enzyme-linked immunosorbent assays (ELISAs) were established for characterization of the antibody. The concentrations causing 50% inhibition of binding of OA-horseradish peroxidase to the antibody by OA were calculated to be 0.077 ng/mL in the cdELISA. A rapid and sensitive mAb-based gold nanoparticle immunochromatographic strip was also established. This proposed strip has a detection limit of 5 ng/mL for OA and can be finished in 10 min. Extensive analyses of 20 seafood samples with ELISA revealed that 10 were slightly contaminated with OA, with a mean concentration of 0.892 ng/g. Analysis of OA in shellfish samples showed that data acquired by the immunochromatographic strip agreed well with those acquired by the ELISA. The mAb-based ELISA and immunochromatographic strip assay developed in this study have adequate sensitivity and accuracy for rapid screening of OA in shellfish samples. PMID:24446876

  8. The epidemiology of tick-borne haemoparasites as determined by the reverse line blot hybridization assay in an intensively studied cohort of calves in western Kenya

    PubMed Central

    Njiiri, Nyawira E.; Bronsvoort, B. Mark deC.; Collins, Nicola E.; Steyn, Helena C.; Troskie, Milana; Vorster, Ilse; Thumbi, S.M.; Sibeko, Kgomotso P.; Jennings, Amy; van Wyk, Ilana Conradie; Mbole-Kariuki, Mary; Kiara, Henry; Poole, E. Jane; Hanotte, Olivier; Coetzer, Koos; Oosthuizen, Marinda C.; Woolhouse, Mark; Toye, Philip

    2015-01-01

    The development of sensitive surveillance technologies using PCR-based detection of microbial DNA, such as the reverse line blot assay, can facilitate the gathering of epidemiological information on tick-borne diseases, which continue to hamper the productivity of livestock in many parts of Africa and elsewhere. We have employed a reverse line blot assay to detect the prevalence of tick-borne parasites in an intensively studied cohort of indigenous calves in western Kenya. The calves were recruited close to birth and monitored for the presence of infectious disease for up to 51 weeks. The final visit samples from 453 calves which survived for the study period were analyzed by RLB. The results indicated high prevalences of Theileria mutans (71.6%), T. velifera (62.8%), Anaplasma sp. Omatjenne (42.7%), A. bovis (39.9%), Theileria sp. (sable) (32.7%), T. parva (12.9%) and T. taurotragi (8.5%), with minor occurrences of eight other haemoparasites. The unexpectedly low prevalence of the pathogenic species Ehrlichia ruminantium was confirmed by a species-specific PCR targeting the pCS20 gene region. Coinfection analyses of the seven most prevalent haemoparasites indicated that they were present as coinfections in over 90% of the cases. The analyses revealed significant associations between several of the Theileria parasites, in particular T. velifera with Theileria sp. sable and T. mutans, and T. parva with T. taurotragi. There was very little coinfection of the two most common Anaplasma species, although they were commonly detected as coinfections with the Theileria parasites. The comparison of reverse line blot and serological results for four haemoparasites (T. parva, T. mutans, A. marginale and B. bigemina) indicated that, except for the mostly benign T. mutans, indigenous cattle seem capable of clearing infections of the three other, pathogenic parasites to below detectable levels. Although the study site was located across four agroecological zones, there was

  9. Excellent anti-corrosive pretreatment layer on iron substrate based on three-dimensional porous phytic acid/silane hybrid

    NASA Astrophysics Data System (ADS)

    Gao, Xiang; Lu, Ke; Xu, Lei; Xu, Hua; Lu, Haifeng; Gao, Feng; Hou, Shifeng; Ma, Houyi

    2016-01-01

    A novel, highly effective and environmentally friendly film-forming material, phytic acid (PA)/silane (denoted as PAS) hybrid with a three-dimensional (3D) network structure, was prepared through a condensation reaction of PA with methyltrihydroxysilane generated from the hydrolysis of methyltriethoxysilane (MTES). Two kinds of PAS-based pretreatment layers, namely NaBrO3-free and NaBrO3-doped PAS layers, were fabricated on iron substrates using the dip-coating method. SEM and AFM observations showed that the as-fabricated PAS-based layers possessed a 3D porous microstructure at the nanoscale and a rough surface morphology. X-ray photoelectron spectroscopic (XPS) and attenuated total reflection infrared (ATR-IR) spectroscopic characterization demonstrated that the above PAS layers bound to the iron surface via the -P-O- bond. Moreover, analyses of steady-state polarization curves and electrochemical impedance spectroscopic (EIS) data indicated that the corrosion rates of the iron substrates decreased considerably in the presence of the two PAS-based pretreatment layers. In particular, the NaBrO3-dosed PAS layer displayed the better corrosion resistance ability as well as maintaining the original microstructure and surface morphology. The PAS-based pretreatment layers are expected to act as substitutes for chromate and phosphate conversion layers and will find widespread application in the surface pretreatment of iron and steel materials due to the advantages of being environmentally friendly, the rapid film-forming process, and, especially, the nanoporous microstructure and rough surface morphology.A novel, highly effective and environmentally friendly film-forming material, phytic acid (PA)/silane (denoted as PAS) hybrid with a three-dimensional (3D) network structure, was prepared through a condensation reaction of PA with methyltrihydroxysilane generated from the hydrolysis of methyltriethoxysilane (MTES). Two kinds of PAS-based pretreatment layers, namely Na

  10. Interaction of αA-crystallin F71L mutant with wild type αA- and αB-crystallins by mammalian two hybrid assay.

    PubMed

    Ramkumar, Srinivasagan; Thankappan, Bency; Fujii, Noriko; Natarajaseenivasan, Kalimuthusamy; Anbarasu, Kumarasamy

    2015-05-01

    Incidence of age related cataract (ARC) increases by a variety of factors including metabolic and environmental factors. Nonetheless, genetic mutations are responsible for the altered structural stability of the proteins, especially; the F71L mutation in αA-crystallin has been shown to be responsible for the incidence of cataracts. However, structural characteristics and chaperone function of this mutant and its interaction with wild type (WT) crystallins may aid to decipher its role in cataractogenesis. The aim of the present study is to show the interaction of F71L mutant protein with the WT α-crystallins. The F71L mutant used in this study was created by site-directed mutagenesis, overexpressed and purified. Biophysical characteristics determined by size exclusion HPLC, DLS, CD spectrometry, tryptophan fluorescence and surface hydrophobicity did not show significant structural changes in the mutant protein compared to WT counterpart. Interestingly, the F71L mutant displayed a significant loss in homogenous interaction with WT αA-crystallin and F71L mutant as well as heterogeneous interaction with αB-crystallin as evaluated by mammalian two hybrid system. Our findings suggest that F71L loses the ability to form homo and hetero-oligomers seems to result in the loss in chaperone like activity (CLA) and refractive index resulting in the development of cataracts. PMID:25720831

  11. Excellent anti-corrosive pretreatment layer on iron substrate based on three-dimensional porous phytic acid/silane hybrid.

    PubMed

    Gao, Xiang; Lu, Ke; Xu, Lei; Xu, Hua; Lu, Haifeng; Gao, Feng; Hou, Shifeng; Ma, Houyi

    2016-01-21

    A novel, highly effective and environmentally friendly film-forming material, phytic acid (PA)/silane (denoted as PAS) hybrid with a three-dimensional (3D) network structure, was prepared through a condensation reaction of PA with methyltrihydroxysilane generated from the hydrolysis of methyltriethoxysilane (MTES). Two kinds of PAS-based pretreatment layers, namely NaBrO3-free and NaBrO3-doped PAS layers, were fabricated on iron substrates using the dip-coating method. SEM and AFM observations showed that the as-fabricated PAS-based layers possessed a 3D porous microstructure at the nanoscale and a rough surface morphology. X-ray photoelectron spectroscopic (XPS) and attenuated total reflection infrared (ATR-IR) spectroscopic characterization demonstrated that the above PAS layers bound to the iron surface via the -P-O- bond. Moreover, analyses of steady-state polarization curves and electrochemical impedance spectroscopic (EIS) data indicated that the corrosion rates of the iron substrates decreased considerably in the presence of the two PAS-based pretreatment layers. In particular, the NaBrO3-dosed PAS layer displayed the better corrosion resistance ability as well as maintaining the original microstructure and surface morphology. The PAS-based pretreatment layers are expected to act as substitutes for chromate and phosphate conversion layers and will find widespread application in the surface pretreatment of iron and steel materials due to the advantages of being environmentally friendly, the rapid film-forming process, and, especially, the nanoporous microstructure and rough surface morphology. PMID:26689810

  12. Identification of differentially expressed genes in SHSY5Y cells exposed to okadaic acid by suppression subtractive hybridization

    PubMed Central

    2012-01-01

    Background Okadaic acid (OA), a toxin produced by several dinoflagellate species is responsible for frequent food poisonings associated to shellfish consumption. Although several studies have documented the OA effects on different processes such as cell transformation, apoptosis, DNA repair or embryogenesis, the molecular mechanistic basis for these and other effects is not completely understood and the number of controversial data on OA is increasing in the literature. Results In this study, we used suppression subtractive hybridization in SHSY5Y cells to identify genes that are differentially expressed after OA exposure for different times (3, 24 and 48 h). A total of 247 subtracted clones which shared high homology with known genes were isolated. Among these, 5 specific genes associated with cytoskeleton and neurotransmission processes (NEFM, TUBB, SEPT7, SYT4 and NPY) were selected to confirm their expression levels by real-time PCR. Significant down-regulation of these genes was obtained at the short term (3 and 24 h OA exposure), excepting for NEFM, but their expression was similar to the controls at 48 h. Conclusions From all the obtained genes, 114 genes were up-regulated and 133 were down-regulated. Based on the NCBI GenBank and Gene Ontology databases, most of these genes are involved in relevant cell functions such as metabolism, transport, translation, signal transduction and cell cycle. After quantitative PCR analysis, the observed underexpression of the selected genes could underlie the previously reported OA-induced cytoskeleton disruption, neurotransmission alterations and in vivo neurotoxic effects. The basal expression levels obtained at 48 h suggested that surviving cells were able to recover from OA-caused gene expression alterations. PMID:22284234

  13. Allosteric indicator displacement enzyme assay for a cyanogenic glycoside.

    PubMed

    Jose, D Amilan; Elstner, Martin; Schiller, Alexander

    2013-10-18

    Indicator displacement assays (IDAs) represent an elegant approach in supramolecular analytical chemistry. Herein, we report a chemical biosensor for the selective detection of the cyanogenic glycoside amygdalin in aqueous solution. The hybrid sensor consists of the enzyme β-glucosidase and a boronic acid appended viologen together with a fluorescent reporter dye. β-Glucosidase degrades the cyanogenic glycoside amygdalin into hydrogen cyanide, glucose, and benzaldehyde. Only the released cyanide binds at the allosteric site of the receptor (boronic acid) thereby inducing changes in the affinity of a formerly bound fluorescent indicator dye at the other side of the receptor. Thus, the sensing probe performs as allosteric indicator displacement assay (AIDA) for cyanide in water. Interference studies with inorganic anions and glucose revealed that cyanide is solely responsible for the change in the fluorescent signal. DFT calculations on a model compound revealed a 1:1 binding ratio of the boronic acid and cyanide ion. The fluorescent enzyme assay for β-glucosidase uses amygdalin as natural substrate and allows measuring Michaelis-Menten kinetics in microtiter plates. The allosteric indicator displacement assay (AIDA) probe can also be used to detect cyanide traces in commercial amygdalin samples. PMID:24123550

  14. Nucleic acid detection system and method for detecting influenza

    SciTech Connect

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  15. Label-free colorimetric protein assay and logic gates design based on the self-assembly of hemin-graphene hybrid nanosheet.

    PubMed

    Lin, Bin; Sun, Qianqian; Liu, Kai; Lu, Danqin; Fu, Ying; Xu, Zhiai; Zhang, Wen

    2014-03-01

    Here we report a label-free colorimetric method for protein assay based on the intrinsic peroxidase-like catalytic activity of DNA-hemin-graphene (DNA-GH) composite. By using aptamers as protein recognition elements, protein-mediated aggregation of the DNA-GH composite leads to the decrease or increase of the colorimetric signal depending on the sandwich or competitive design strategy. Thrombin and PDGF-BB were chosen as model analytes and the detection limits (LOD) by this method were estimated to be 0.5 nM and 5 nM, respectively. Compared to traditional ELISA method for protein detection, this method possesses the advantages of high sensitivity, simplicity, and low cost. In addition, by designing different DNA-modified hemin-graphene (GH) constructs, using proteins as inputs, the "OR" and "INHIBIT" logic gates were built. This procedure does not require chemical modification on the aptamer probes or analytes and circumvents the limitation associated with the number of target binding sites. Given the attractive analytical characteristics and distinct advantages of DNA-GH composite, the universal approach can be widely applied for the detection of diverse proteins and for the design of versatile logic gates. PMID:24559089

  16. Simultaneous determination of rosuvastatin and fenofibric acid in human plasma by LC-MS/MS with electrospray ionization: assay development, validation and application to a clinical study.

    PubMed

    Trivedi, Ravi Kumar; Kallem, Raja Reddy; Mullangi, Ramesh; Srinivas, Nuggehally R

    2005-09-15

    A simple, sensitive and specific LC-MS/MS method for simultaneous determination of rosuvastatin (RST) and fenofibric acid (FFA) was developed and validated with 500 microL human plasma using carbamazepine as an internal standard (IS). The assay procedure involved a simple one-step liquid/liquid extraction of RST and FFA and IS from plasma into ethyl acetate. The organic layer was separated and evaporated under a gentle stream of nitrogen at 40 degrees C. The residue was reconstituted in the mobile phase and injected onto X-Terra MS C-18 column (4.6 mm x 50 mm, 5.0 microm). Separation of RST, FFA and IS was achieved with a mobile phase consisting of 0.05 M formic acid:acetonitrile (45:55, v/v) at a flow rate of 0.40 ml/min. The API-3000LC-MS/MS was operated under the multiple reaction-monitoring mode (MRM) using the electrospray ionization technique. Positive ion acquisition chromatographic run was used in the present method. Nominal retention times of RST, FFA and IS were 2.35, 4.70 and 2.32 min, respectively. Absolute recovery of RST, FFA and IS was 74, 61 and 69%, respectively. The lower limit of quantification (LLOQ) of RST and FFA was 1.00 ng/ml and 0.50 microg/ml, respectively. Response function was established for the range of concentrations 1.00-50.0 ng/ml and 0.50-20.0 microg/ml for RST and FFA, respectively, with a coefficient of determination (r2) of 0.999 for both the compounds. The inter- and intra-day precision in the measurement of RST quality control (QC) samples 5, 15, 400 and 800 ng/ml, were in the range 8.93-9.37% relative standard deviation (R.S.D.) and 1.74-16.1% R.S.D., respectively. Similarly, the inter- and intra-day precision in the measurement of FFA quality control (QC) samples 0.5, 1.5, 8.0 and 15.0 microg/ml, were in the range 9.78-11.6% relative standard deviation (R.S.D.) and 0.22-17.4% R.S.D., respectively. Accuracy in the measurement of QC samples for RST and FFA were in the range 88.1-108 and 87-115%, respectively, of the nominal

  17. Detection of the marijuana metabolite 11-nor-Delta9-tetrahydrocannabinol-9-carboxylic acid in oral fluid specimens and its contribution to positive results in screening assays.

    PubMed

    Moore, Christine; Ross, Wayne; Coulter, Cynthia; Adams, Laura; Rana, Sumandeep; Vincent, Michael; Soares, James

    2006-09-01

    The detection of the marijuana metabolite 11-nor-Delta(9)-tetrahydrocannabinol-9-carboxylic acid (THC-COOH) in oral fluid specimens is described, and its contribution to an immunoassay for the detection of cannabinoids is investigated. Oral fluid specimens, screened using an enzyme-linked immunosorbent immunoassay (ELISA), were carried forward to confirmation for both tetrahydrocannabinol (THC) and THC-COOH using gas chromatography-mass spectrometry (GC-MS). One hundred and fifty-three specimens were analyzed, of which 143 screened positive for cannabinoids. Ninety-five (66.4%) of these specimens were positive for both THC and THC-COOH; 14 (9.7%) were positive for THC-COOH only, and 27 (18.8%) were positive for THC only. The GC-MS assay for the detection of THC-COOH in oral fluid was linear to 160 pg/mL with a limit of quantitation of 2 pg/mL. The detection of the marijuana metabolite, THC-COOH, in 76.2% of oral fluid specimens screening positive for cannabinoids is reported. As a potential defense against passive exposure claims, proposed SAMHSA regulations may require the simultaneous collection of a urine sample when oral fluid samples are used. The detection of the metabolite, THC-COOH, is a significant alternative to this approach because its presence in oral fluid minimizes the argument for passive exposure to marijuana in drug testing cases. PMID:16959132

  18. High-throughput LC-MS/MS assay for 6-methoxy-2-naphthylaceti