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Sample records for acid amplification methods

  1. Miniaturized isothermal nucleic acid amplification, a review.

    Science.gov (United States)

    Asiello, Peter J; Baeumner, Antje J

    2011-04-21

    Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented.

  2. Evaluation of Nucleic Acid Isothermal Amplification Methods for Human Clinical Microbial Infection Detection

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    Brett E. Etchebarne

    2017-12-01

    Full Text Available Battling infection is a major healthcare objective. Untreated infections can rapidly evolve toward the condition of sepsis in which the body begins to fail and resuscitation becomes critical and tenuous. Identification of infection followed by rapid antimicrobial treatment are primary goals of medical care, but precise identification of offending organisms by current methods is slow and broad spectrum empirical therapy is employed to cover most potential pathogens. Current methods for identification of bacterial pathogens in a clinical setting typically require days of time, or a 4- to 8-h growth phase followed by DNA extraction, purification and PCR-based amplification. We demonstrate rapid (70–120 min genetic diagnostics methods utilizing loop-mediated isothermal amplification (LAMP to test for 15 common infection pathogen targets, called the Infection Diagnosis Panel (In-Dx. The method utilizes filtration to rapidly concentrate bacteria in sample matrices with lower bacterial loads and direct LAMP amplification without DNA purification from clinical blood, urine, wound, sputum and stool samples. The In-Dx panel was tested using two methods of detection: (1 real-time thermocycler fluorescent detection of LAMP amplification and (2 visual discrimination of color change in the presence of Eriochrome Black T (EBT dye following amplification. In total, 239 duplicate samples were collected (31 blood, 122 urine, 73 mucocutaneous wound/swab, 11 sputum and two stool from 229 prospectively enrolled hospital patients with suspected clinical infection and analyzed both at the hospital and by In-Dx. Sensitivity (Se of the In-Dx panel targets pathogens from urine samples by In-Dx was 91.1% and specificity (Sp was 97.3%, with a positive predictive value (PPV of 53.7% and a negative predictive value (NPV of 99.7% as compared to clinical microbial detection methods. Sensitivity of detection of the In-Dx panel from mucocutaneous swab samples was 65.5% with a

  3. Helicase-dependent amplification of nucleic acids.

    Science.gov (United States)

    Cao, Yun; Kim, Hyun-Jin; Li, Ying; Kong, Huimin; Lemieux, Bertrand

    2013-10-11

    Helicase-dependent amplification (HDA) is a novel method for the isothermal in vitro amplification of nucleic acids. The HDA reaction selectively amplifies a target sequence by extension of two oligonucleotide primers. Unlike the polymerase chain reaction (PCR), HDA uses a helicase enzyme to separate the deoxyribonucleic acid (DNA) strands, rather than heat denaturation. This allows DNA amplification without the need for thermal cycling. The helicase used in HDA is a helicase super family II protein obtained from a thermophilic organism, Thermoanaerobacter tengcongensis (TteUvrD). This thermostable helicase is capable of unwinding blunt-end nucleic acid substrates at elevated temperatures (60° to 65°C). The HDA reaction can also be coupled with reverse transcription for ribonucleic acid (RNA) amplification. The products of this reaction can be detected during the reaction using fluorescent probes when incubations are conducted in a fluorimeter. Alternatively, products can be detected after amplification using a disposable amplicon containment device that contains an embedded lateral flow strip. Copyright © 2013 John Wiley & Sons, Inc.

  4. Digital Microfluidics for Nucleic Acid Amplification

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    Beatriz Coelho

    2017-06-01

    Full Text Available Digital Microfluidics (DMF has emerged as a disruptive methodology for the control and manipulation of low volume droplets. In DMF, each droplet acts as a single reactor, which allows for extensive multiparallelization of biological and chemical reactions at a much smaller scale. DMF devices open entirely new and promising pathways for multiplex analysis and reaction occurring in a miniaturized format, thus allowing for healthcare decentralization from major laboratories to point-of-care with accurate, robust and inexpensive molecular diagnostics. Here, we shall focus on DMF platforms specifically designed for nucleic acid amplification, which is key for molecular diagnostics of several diseases and conditions, from pathogen identification to cancer mutations detection. Particular attention will be given to the device architecture, materials and nucleic acid amplification applications in validated settings.

  5. Nucleic Acid Amplification as used in the Diagnosis and ...

    African Journals Online (AJOL)

    Nucleic Acid Amplification as used in the Diagnosis and Management of Viral Diseases: A Review. ... Bayero Journal of Pure and Applied Sciences ... are highly unculturable, fastidious or hazardous to the laboratory personnel and diagnosis depends on serological methods or culture in an expensive bio-safety level.

  6. Microfluidic "Pouch" Chips for Immunoassays and Nucleic Acid Amplification Tests.

    Science.gov (United States)

    Mauk, Michael G; Liu, Changchun; Qiu, Xianbo; Chen, Dafeng; Song, Jinzhao; Bau, Haim H

    2017-01-01

    Microfluidic cassettes ("chips") for processing and analysis of clinical specimens and other sample types facilitate point-of-care (POC) immunoassays and nucleic acid based amplification tests. These single-use test chips can be self-contained and made amenable to autonomous operation-reducing or eliminating supporting instrumentation-by incorporating laminated, pliable "pouch" and membrane structures for fluid storage, pumping, mixing, and flow control. Materials and methods for integrating flexible pouch compartments and diaphragm valves into hard plastic (e.g., acrylic and polycarbonate) microfluidic "chips" for reagent storage, fluid actuation, and flow control are described. We review several versions of these pouch chips for immunoassay and nucleic acid amplification tests, and describe related fabrication techniques. These protocols thus offer a "toolbox" of methods for storage, pumping, and flow control functions in microfluidic devices.

  7. Reliability of nucleic acid amplification methods for detection of Chlamydia trachomatis in urine: results of the first international collaborative quality control study among 96 laboratories

    NARCIS (Netherlands)

    R.P.A.J. Verkooyen (Roel); G.T. Noordhoek; P.E. Klapper; J. Reid; J. Schirm; G.M. Cleator; M. Ieven; G. Hoddevik

    2003-01-01

    textabstractThe first European Quality Control Concerted Action study was organized to assess the ability of laboratories to detect Chlamydia trachomatis in a panel of urine samples by nucleic acid amplification tests (NATs). The panel consisted of lyophilized urine samples,

  8. Isothermal amplification detection of nucleic acids by a double-nicked beacon.

    Science.gov (United States)

    Shi, Chao; Zhou, Meiling; Pan, Mei; Zhong, Guilin; Ma, Cuiping

    2016-03-01

    Isothermal and rapid amplification detection of nucleic acids is an important technology in environmental monitoring, foodborne pathogen detection, and point-of-care clinical diagnostics. Here we have developed a novel method of isothermal signal amplification for single-stranded DNA (ssDNA) detection. The ssDNA target could be used as an initiator, coupled with a double-nicked molecular beacon, to originate amplification cycles, achieving cascade signal amplification. In addition, the method showed good specificity and strong anti-jamming capability. Overall, it is a one-pot and isothermal strand displacement amplification method without the requirement of a stepwise procedure, which greatly simplifies the experimental procedure and decreases the probability of contamination of samples. With its advantages, the method would be very useful to detect nucleic acids in point-of-care or field use. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Diagnostic Devices for Isothermal Nucleic Acid Amplification

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    Chia-Chen Chang

    2012-06-01

    Full Text Available Since the development of the polymerase chain reaction (PCR technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.

  10. Diagnostic devices for isothermal nucleic acid amplification.

    Science.gov (United States)

    Chang, Chia-Chen; Chen, Chien-Cheng; Wei, Shih-Chung; Lu, Hui-Hsin; Liang, Yang-Hung; Lin, Chii-Wann

    2012-01-01

    Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.

  11. Real-time electrochemical monitoring of isothermal helicase-dependent amplification of nucleic acids.

    Science.gov (United States)

    Kivlehan, Francine; Mavré, François; Talini, Luc; Limoges, Benoît; Marchal, Damien

    2011-09-21

    We described an electrochemical method to monitor in real-time the isothermal helicase-dependent amplification of nucleic acids. The principle of detection is simple and well-adapted to the development of portable, easy-to-use and inexpensive nucleic acids detection technologies. It consists of monitoring a decrease in the electrochemical current response of a reporter DNA intercalating redox probe during the isothermal DNA amplification. The method offers the possibility to quantitatively analyze target nucleic acids in less than one hour at a single constant temperature, and to perform at the end of the isothermal amplification a DNA melt curve analysis for differentiating between specific and non-specific amplifications. To illustrate the potentialities of this approach for the development of a simple, robust and low-cost instrument with high throughput capability, the method was validated with an electrochemical system capable of monitoring up to 48 real-time isothermal HDA reactions simultaneously in a disposable microplate consisting of 48-electrochemical microwells. Results obtained with this approach are comparable to that obtained with a well-established but more sophisticated and expensive fluorescence-based method. This makes for a promising alternative detection method not only for real-time isothermal helicase-dependent amplification of nucleic acid, but also for other isothermal DNA amplification strategies.

  12. Multi-chamber nucleic acid amplification and detection device

    Science.gov (United States)

    Dugan, Lawrence

    2017-10-25

    A nucleic acid amplification and detection device includes an amplification cartridge with a plurality of reaction chambers for containing an amplification reagent and a visual detection reagent, and a plurality of optically transparent view ports for viewing inside the reaction chambers. The cartridge also includes a sample receiving port which is adapted to receive a fluid sample and fluidically connected to distribute the fluid sample to the reaction chamber, and in one embodiment, a plunger is carried by the cartridge for occluding fluidic communication to the reaction chambers. The device also includes a heating apparatus having a heating element which is activated by controller to generate heat when a trigger event is detected. The heating apparatus includes a cartridge-mounting section which positioned a cartridge in thermal communication with the heating element so that visual changes to the contents of the reaction chambers are viewable through the view ports.

  13. Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application.

    Science.gov (United States)

    Zhou, Hong; Liu, Jing; Xu, Jing-Juan; Zhang, Shu-Sheng; Chen, Hong-Yuan

    2018-03-21

    Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

  14. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

    Science.gov (United States)

    Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

    2018-02-06

    A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

  15. Comparison of the Soil Dynamic Amplification Factor and Soil Amplification by Using Microtremor and MASW Methods Respectively

    Science.gov (United States)

    Tuncel, Aykut; Cevdet Özdag, Özkan; Pamuk, Eren; Akgün, Mustafa

    2017-12-01

    Single Station Microtremor method, which is widely used nowadays, is an effective and easy applicable method. In this study, dynamic amplification factor distributions of the study area were obtained using scenario earthquake parameters with single station microtremor data gathered at 112 points. In addition, a surface wave active method, which is known as MASW (Multichannel Analysis of Surface Waves), was applied at 43 profiles to calculate the soil amplification values. Dynamic amplification factor (DAF), soil amplification, the predominant soil period (PSP), geology and topography data of the study area were analysed together. Dynamic amplification factor and soil amplification values were obtained 2 or higher at about sea level parts of the study area which are generally composed of alluvial units. Additionally, in high altitude regions that are composed of volcanic rocks, relatively lower dynamic amplification factor and soil amplification values were obtained. The minimum amplification value in the study area was 1.15, while the maximum amplification value was 3.05 according to the dynamic amplification results and the soil amplification values were between 1.16 and 3.85 in harmony. It is seen that the obtained DAF values and the soil amplification values calculated from the seismic velocities are very similar to each other numerically and regionally. Because of this, it is concluded that the values of the soil amplification obtained by the MASW method and the calculated DAF values in this study are in harmony with each other. Although the depths of research in these two calculation methods are different from each other, the similarity of the results allows us to arrive at the result of how effective the ground layer is on the amplification. It has a great importance to calculate the amplification values and other dynamic parameters by in situ measurements for a planned plot because geological units can vary even at very short distances in heterogeneously

  16. Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices.

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    David A Selck

    Full Text Available Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification. However, the mechanistic investigation and optimization of digital assays has been limited by the lack of real-time kinetic information about which factors affect the digital efficiency and analytical sensitivity of a reaction. Commercially available instruments that are capable of tracking digital reactions in real-time are restricted to only a small number of device types and sample-preparation strategies. Thus, most researchers who wish to develop, study, or optimize digital assays rely on the rate of the amplification reaction when performed in a bulk experiment, which is now recognized as an unreliable predictor of digital efficiency. To expand our ability to study how digital reactions proceed in real-time and enable us to optimize both the digital efficiency and analytical sensitivity of digital assays, we built a custom large-format digital real-time amplification instrument that can accommodate a wide variety of devices, amplification chemistries and sample-handling conditions. Herein, we validate this instrument, we provide detailed schematics that will enable others to build their own custom instruments, and we include a complete custom software suite to collect and analyze the data retrieved from the instrument. We believe assay optimizations enabled by this instrument will improve the current limits of nucleic acid detection and quantification, improving our

  17. Development of Temperature Control Solutions for Non-Instrumented Nucleic Acid Amplification Tests (NINAAT

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    Tamás Pardy

    2017-06-01

    Full Text Available Non-instrumented nucleic acid amplification tests (NINAAT are a novel paradigm in portable molecular diagnostics. They offer the high detection accuracy characteristic of nucleic acid amplification tests (NAAT in a self-contained device, without the need for any external instrumentation. These Point-of-Care tests typically employ a Lab-on-a-Chip for liquid handling functionality, and perform isothermal nucleic acid amplification protocols that require low power but high accuracy temperature control in a single well-defined temperature range. We propose temperature control solutions based on commercially available heating elements capable of meeting these challenges, as well as demonstrate the process by which such elements can be fitted to a NINAAT system. Self-regulated and thermostat-controlled resistive heating elements were evaluated through experimental characterization as well as thermal analysis using the finite element method (FEM. We demonstrate that the proposed solutions can support various NAAT protocols, as well as demonstrate an optimal solution for the loop-mediated isothermal amplification (LAMP protocol. Furthermore, we present an Arduino-compatible open-source thermostat developed for NINAAT applications.

  18. Methods for microbial DNA extraction from soil for PCR amplification

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    Yeates C

    1998-01-01

    Full Text Available Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1. DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size.

  19. Exponential isothermal amplification of nucleic acids and amplified assays for proteins, cells, and enzyme activities.

    Science.gov (United States)

    Reid, Michael S; Le, X Chris; Zhang, Hongquan

    2018-04-27

    Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in-situ assay applications. These amplification techniques eliminate the need for temperature cycling required for polymerase chain reaction (PCR) while achieving comparable amplification yield. We highlight here recent advances in exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. We discuss design strategies, enzyme reactions, detection techniques, and key features. Incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from non-specific template interactions, must be addressed to further improve isothermal and exponential amplification techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

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    Michael G. Mauk

    2015-10-01

    Full Text Available Microfluidic components and systems for rapid (<60 min, low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs are described. A microfluidic point-of-care (POC diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1 nucleic acids (NAs are extracted from relatively large (~mL volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane” to capture sample NAs in a flow-through, filtration mode; (2 NAs captured on the membrane are isothermally (~65 °C amplified; (3 amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4 paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

  1. Alternative Chemical Amplification Methods for Peroxy Radical Detection

    Science.gov (United States)

    Wood, E. C. D.

    2014-12-01

    Peroxy radicals (HO2, CH3O2, etc.) are commonly detected by the chemical amplification technique, in which ambient air is mixed with high concentrations of CO and NO, initiating a chain reaction that produces 30 - 200 NO2 molecules per sampled peroxy radical. The NO2 is then measured by one of several techniques. With the exception of CIMS-based techniques, the chemical amplification method has undergone only incremental improvements since it was first introduced in 1982. The disadvantages of the technique include the need to use high concentrations of CO and the greatly reduced sensitivity of the amplification chain length in the presence of water vapor. We present a new chemical amplification scheme in which either ethane or acetaldehyde is used in place of CO, with the NO2 product detected using Cavity Attenuated Phase Shift spectroscopy (CAPS). Under dry conditions, the amplification factor of the alternative amplifiers are approximately six times lower than the CO-based amplifier. The relative humidity "penalty" is not as severe, however, such that at typical ambient relative humidity (RH) values the amplification factor is within a factor of three of the CO-based amplifier. Combined with the NO2 sensitivity of CAPS and a dual-channel design, the detection limit of the ethane amplifier is less than 2 ppt (1 minute average, signal-to-noise ratio 2). The advantages of these alternative chemical amplification schemes are improved safety, a reduced RH correction, and increased sensitivity to organic peroxy radicals relative to HO2.

  2. Development of loop-mediated isothermal amplification method for ...

    African Journals Online (AJOL)

    A novel assay method to detect the highly virulent Porcine reproductive and respiratory syndrome virus (PRRSV) termed reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), was reported by using hydroxynaphthol blue (HNB) as the LAMP product colorimetric judgment. By the set of special primers, ...

  3. Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

    2015-07-08

    We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

  4. Implementation of antimicrobial peptides for sample preparation prior to nucleic acid amplification in point-of-care settings.

    Science.gov (United States)

    Krõlov, Katrin; Uusna, Julia; Grellier, Tiia; Andresen, Liis; Jevtuševskaja, Jekaterina; Tulp, Indrek; Langel, Ülo

    2017-12-01

    A variety of sample preparation techniques are used prior to nucleic acid amplification. However, their efficiency is not always sufficient and nucleic acid purification remains the preferred method for template preparation. Purification is difficult and costly to apply in point-of-care (POC) settings and there is a strong need for more robust, rapid, and efficient biological sample preparation techniques in molecular diagnostics. Here, the authors applied antimicrobial peptides (AMPs) for urine sample preparation prior to isothermal loop-mediated amplification (LAMP). AMPs bind to many microorganisms such as bacteria, fungi, protozoa and viruses causing disruption of their membrane integrity and facilitate nucleic acid release. The authors show that incubation of E. coli with antimicrobial peptide cecropin P1 for 5 min had a significant effect on the availability of template DNA compared with untreated or even heat treated samples resulting in up to six times increase of the amplification efficiency. These results show that AMPs treatment is a very efficient sample preparation technique that is suitable for application prior to nucleic acid amplification directly within biological samples. Furthermore, the entire process of AMPs treatment was performed at room temperature for 5 min thereby making it a good candidate for use in POC applications.

  5. Method for decoupling error correction from privacy amplification

    Energy Technology Data Exchange (ETDEWEB)

    Lo, Hoi-Kwong [Department of Electrical and Computer Engineering and Department of Physics, University of Toronto, 10 King' s College Road, Toronto, Ontario, Canada, M5S 3G4 (Canada)

    2003-04-01

    In a standard quantum key distribution (QKD) scheme such as BB84, two procedures, error correction and privacy amplification, are applied to extract a final secure key from a raw key generated from quantum transmission. To simplify the study of protocols, it is commonly assumed that the two procedures can be decoupled from each other. While such a decoupling assumption may be valid for individual attacks, it is actually unproven in the context of ultimate or unconditional security, which is the Holy Grail of quantum cryptography. In particular, this means that the application of standard efficient two-way error-correction protocols like Cascade is not proven to be unconditionally secure. Here, I provide the first proof of such a decoupling principle in the context of unconditional security. The method requires Alice and Bob to share some initial secret string and use it to encrypt their communications in the error correction stage using one-time-pad encryption. Consequently, I prove the unconditional security of the interactive Cascade protocol proposed by Brassard and Salvail for error correction and modified by one-time-pad encryption of the error syndrome, followed by the random matrix protocol for privacy amplification. This is an efficient protocol in terms of both computational power and key generation rate. My proof uses the entanglement purification approach to security proofs of QKD. The proof applies to all adaptive symmetric methods for error correction, which cover all existing methods proposed for BB84. In terms of the net key generation rate, the new method is as efficient as the standard Shor-Preskill proof.

  6. Method for decoupling error correction from privacy amplification

    International Nuclear Information System (INIS)

    Lo, Hoi-Kwong

    2003-01-01

    In a standard quantum key distribution (QKD) scheme such as BB84, two procedures, error correction and privacy amplification, are applied to extract a final secure key from a raw key generated from quantum transmission. To simplify the study of protocols, it is commonly assumed that the two procedures can be decoupled from each other. While such a decoupling assumption may be valid for individual attacks, it is actually unproven in the context of ultimate or unconditional security, which is the Holy Grail of quantum cryptography. In particular, this means that the application of standard efficient two-way error-correction protocols like Cascade is not proven to be unconditionally secure. Here, I provide the first proof of such a decoupling principle in the context of unconditional security. The method requires Alice and Bob to share some initial secret string and use it to encrypt their communications in the error correction stage using one-time-pad encryption. Consequently, I prove the unconditional security of the interactive Cascade protocol proposed by Brassard and Salvail for error correction and modified by one-time-pad encryption of the error syndrome, followed by the random matrix protocol for privacy amplification. This is an efficient protocol in terms of both computational power and key generation rate. My proof uses the entanglement purification approach to security proofs of QKD. The proof applies to all adaptive symmetric methods for error correction, which cover all existing methods proposed for BB84. In terms of the net key generation rate, the new method is as efficient as the standard Shor-Preskill proof

  7. Multiple strategies to improve sensitivity, speed and robustness of isothermal nucleic acid amplification for rapid pathogen detection

    Directory of Open Access Journals (Sweden)

    Lemieux Bertrand

    2011-05-01

    Full Text Available Abstract Background In the past decades the rapid growth of molecular diagnostics (based on either traditional PCR or isothermal amplification technologies meet the demand for fast and accurate testing. Although isothermal amplification technologies have the advantages of low cost requirements for instruments, the further improvement on sensitivity, speed and robustness is a prerequisite for the applications in rapid pathogen detection, especially at point-of-care diagnostics. Here, we describe and explore several strategies to improve one of the isothermal technologies, helicase-dependent amplification (HDA. Results Multiple strategies were approached to improve the overall performance of the isothermal amplification: the restriction endonuclease-mediated DNA helicase homing, macromolecular crowding agents, and the optimization of reaction enzyme mix. The effect of combing all strategies was compared with that of the individual strategy. With all of above methods, we are able to detect 50 copies of Neisseria gonorrhoeae DNA in just 20 minutes of amplification using a nearly instrument-free detection platform (BESt™ cassette. Conclusions The strategies addressed in this proof-of-concept study are independent of expensive equipments, and are not limited to particular primers, targets or detection format. However, they make a large difference in assay performance. Some of them can be adjusted and applied to other formats of nucleic acid amplification. Furthermore, the strategies to improve the in vitro assays by maximally simulating the nature conditions may be useful in the general field of developing molecular assays. A new fast molecular assay for Neisseria gonorrhoeae has also been developed which has great potential to be used at point-of-care diagnostics.

  8. A new ultrasonic signal amplification method for detection of bacteria

    Science.gov (United States)

    Kant Shukla, Shiva; Resa López, Pablo; Sierra Sánchez, Carlos; Urréjola, José; Segura, Luis Elvira

    2012-10-01

    A new method is presented that increases the sensitivity of ultrasound-based techniques for detection of bacteria. The technique was developed for the detection of catalase-positive microorganisms. It uses a bubble trapping medium containing hydrogen peroxide that is mixed with the sample for microbiological evaluation. The enzyme catalase is present in catalase-positive bacteria, which induces a rapid hydrolysis of hydrogen peroxide, forming bubbles which remain in the medium. This reaction results in the amplification of the mechanical changes that the microorganisms produce in the medium. The effect can be detected by means of ultrasonic wave amplitude continuous measurement since the bubbles increase the ultrasonic attenuation significantly. It is shown that microorganism concentrations of the order of 105 cells ml-1 can be detected using this method. This allows an improvement of three orders of magnitude in the ultrasonic detection threshold of microorganisms in conventional culture media, and is competitive with modern rapid microbiological methods. It can also be used for the characterization of the enzymatic activity.

  9. A new ultrasonic signal amplification method for detection of bacteria

    International Nuclear Information System (INIS)

    Shukla, Shiva Kant; López, Pablo Resa; Sánchez, Carlos Sierra; Segura, Luis Elvira; Urréjola, José

    2012-01-01

    A new method is presented that increases the sensitivity of ultrasound-based techniques for detection of bacteria. The technique was developed for the detection of catalase-positive microorganisms. It uses a bubble trapping medium containing hydrogen peroxide that is mixed with the sample for microbiological evaluation. The enzyme catalase is present in catalase-positive bacteria, which induces a rapid hydrolysis of hydrogen peroxide, forming bubbles which remain in the medium. This reaction results in the amplification of the mechanical changes that the microorganisms produce in the medium. The effect can be detected by means of ultrasonic wave amplitude continuous measurement since the bubbles increase the ultrasonic attenuation significantly. It is shown that microorganism concentrations of the order of 10 5 cells ml −1 can be detected using this method. This allows an improvement of three orders of magnitude in the ultrasonic detection threshold of microorganisms in conventional culture media, and is competitive with modern rapid microbiological methods. It can also be used for the characterization of the enzymatic activity. (paper)

  10. Colorimetric Nucleic Acid Detection on Paper Microchip Using Loop Mediated Isothermal Amplification and Crystal Violet Dye.

    Science.gov (United States)

    Roy, Sharmili; Mohd-Naim, Noor Faizah; Safavieh, Mohammadali; Ahmed, Minhaz Uddin

    2017-11-22

    Nucleic acid detection is of paramount importance in monitoring of microbial pathogens in food safety and infectious disease diagnostic applications. To address these challenges, a rapid, cost-effective label-free technique for nucleic acid detection with minimal instrumentations is highly desired. Here, we present paper microchip to detect and quantify nucleic acid using colorimetric sensing modality. The extracted DNA from food samples of meat as well as microbial pathogens was amplified utilizing loop-mediated isothermal amplification (LAMP). LAMP amplicon was then detected and quantified on a paper microchip fabricated in a cellulose paper and a small wax chamber utilizing crystal violet dye. The affinity of crystal violet dye toward dsDNA and positive signal were identified by changing the color from colorless to purple. Using this method, detection of Sus scrofa (porcine) and Bacillus subtilis (bacteria) DNA was possible at concentrations as low as 1 pg/μL (3.43 × 10 -1 copies/μL) and 10 pg/μL (2.2 × 10 3 copies/μL), respectively. This strategy can be adapted for detection of other DNA samples, with potential for development of a new breed of simple and inexpensive paper microchip at the point-of-need.

  11. Improved sensitivity of nucleic acid amplification for rapid diagnosis of tuberculous meningitis

    DEFF Research Database (Denmark)

    Johansen, Isik Somuncu; Lundgren, Bettina; Tabak, Fehmi

    2004-01-01

    Early diagnosis of tuberculous meningitis (TBM) is essential for a positive outcome; but present microbiological diagnostic techniques are insensitive, slow, or laborious. We evaluated the standard BDProbeTec ET strand displacement amplification method (the standard ProbeTec method) for the detec......Early diagnosis of tuberculous meningitis (TBM) is essential for a positive outcome; but present microbiological diagnostic techniques are insensitive, slow, or laborious. We evaluated the standard BDProbeTec ET strand displacement amplification method (the standard ProbeTec method...

  12. Improved acid tolerance of Lactobacillus pentosus by error-prone whole genome amplification.

    Science.gov (United States)

    Ye, Lidan; Zhao, Hua; Li, Zhi; Wu, Jin Chuan

    2013-05-01

    Acid tolerance of Lactobacillus pentosus ATCC 8041 was improved by error-prone amplification of its genomic DNA using random primers and Taq DNA polymerase. The resulting amplification products were transferred into wild-type L. pentosus by electroporation and the transformants were screened for growth on low-pH agar plates. After only one round of mutation, one mutant (MT3) was identified that was able to completely consume 20 g/L of glucose to produce lactic acid at a yield of 95% in 1L MRS medium at pH 3.8 within 36 h, whereas no growth or lactic acid production was observed for the wild-type strain under the same conditions. The acid tolerance of mutant MT3 remained genetically stable for at least 25 subcultures. Therefore, the error-prone whole genome amplification technique is a very powerful tool for improving phenotypes of this lactic acid bacterium and may also be applicable for other microorganisms. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Amplification of deoxyribonucleic acid (DNA) fragment using two ...

    African Journals Online (AJOL)

    user

    2011-04-11

    Apr 11, 2011 ... polymerases on this method, whether different lengths of. DNA fragments could be amplified by two-step PCR and the difference of DNA product quality produced by the two methods. MATERIALS AND METHODS. PCR template and reagents. Enterobacteria phage lambda DNA (GenBank no: V00636) ...

  14. Single primer amplification reaction methods reveal exotic and ...

    Indian Academy of Sciences (India)

    Unknown

    mulberry varieties using three different PCR based single primer amplification ..... the results of a multi- variate analysis using Mahalanobis D2 statistic in case of .... Rajan M V, Chaturvedi H K and Sarkar A 1997 Multivariate analysis as an aid ...

  15. Whole genome amplification: Use of advanced isothermal method

    African Journals Online (AJOL)

    Yomi

    2010-12-29

    Dec 29, 2010 ... 1Ph.D. Student, Department of Animal Science, Science and Research Branch, Islamic Azad University(IAU), ... sequence has a large effect on both the denaturation of ..... performance of multiple displacement amplification and OmniPlex ... Dean FB, Hosono S, Fang L, Wu L, Faruqi AF, Bray-Ward P, Sun Z,.

  16. Automated nucleic acid amplification testing in blood banks: An additional layer of blood safety

    Directory of Open Access Journals (Sweden)

    Pragati Chigurupati

    2015-01-01

    Full Text Available Context: A total of 30 million blood components are transfused each year in India. Blood safety thus becomes a top priority, especially with a population of around 1.23 billion and a high prevalence rate of human immunodeficiency virus (HIV, hepatitis B virus (HBV and hepatitis C virus (HCV in general population. Nucleic acid amplification testing (NAT in blood donor screening has been implemented in many developed countries to reduce the risk of transfusion-transmitted viral infections (TTIs. NAT takes care of the dynamics of window period of viruses and offers the safest blood pack for donation. Aims: The aim of this study is to show the value of NAT in blood screening. Settings and Design: Dhanavantari Blood Bank, Rajahmundry, Andhra Pradesh, India. Subjects and Methods: Over a period of 1 year from January 2012 to December 2012, a total number of 15,000 blood donor samples were subjected to tests for HIV, HBV, and HCV by enzyme-linked immunosorbent assay (ELISA method and 8000 ELISA nonreactive samples were subjected for NAT using multiplex polymerase chain reaction technology. Results: Of the 15,000 donors tested, 525 were seroreactive. In 8000 ELISA negative blood samples subjected to NAT, 4 donor samples were reactive for HBV. The NAT yield was 1 in 2000. Conclusions: NAT could detect HIV, HBV, and HCV cases in blood donor samples those were undetected by serological tests. NAT could interdict 2500 infectious donations among our approximate 5 million annual blood donations.

  17. One-Step Nucleic Acid Amplification in Breast Cancer Sentinel Lymph Node: A Single Institutional Experience and a Short Review

    OpenAIRE

    Brambilla, Tatiana; Fiamengo, Barbara; Tinterri, Corrado; Testori, Alberto; Grassi, Massimo Maria; Sciarra, Amedeo; Abbate, Tommaso; Gatzemeier, Wolfgang; Roncalli, Massimo; Di Tommaso, Luca

    2015-01-01

    Sentinel lymph node (SLN) examination is a standard in breast cancer patients, with several methods employed along its 20 years history, the last one represented by one-step nucleic acid amplification (OSNA). The latter is a intra-operative molecular assay searching for CK19 mRNA as a surrogate of metastatic cells. Our 3 years experience with OSNA (1122 patients) showed results overlapping those recorded in the same institution with a morphological evaluation (930 patients) of SLN. In detail,...

  18. Multicenter Clinical Evaluation of the Alere i Respiratory Syncytial Virus Isothermal Nucleic Acid Amplification Assay.

    Science.gov (United States)

    Hassan, Ferdaus; Hays, Lindsay M; Bonner, Aleta; Bradford, Bradley J; Franklin, Ruffin; Hendry, Phyllis; Kaminetsky, Jed; Vaughn, Michael; Cieslak, Kristin; Moffatt, Mary E; Selvarangan, Rangaraj

    2018-03-01

    The Alere i respiratory syncytial virus (RSV) assay is an isothermal nucleic acid amplification test capable of detecting RSV directly from respiratory specimens, with results being available in ≤13 min after test initiation. The objective of this study was to evaluate the performance characteristics of the Alere i RSV assay in a point-of-care setting by using direct nasopharyngeal (NP) swab specimens (direct NP) and nasopharyngeal swab specimens eluted and transported in viral transport medium (VTM NP). The study was a prospective, multicenter, clinical trial conducted at 9 sites across the United States to evaluate the clinical performance of the Alere i RSV assay with respiratory specimens obtained from both children (age, 60 years). The performance of the Alere i RSV assay was compared with that of the reference method, the Prodesse ProFlu+ real-time reverse transcriptase PCR (RT-PCR) assay. All specimens with discrepant test results were tested further by a second FDA-cleared PCR assay (the Verigene respiratory virus plus nucleic acid test; Luminex Inc., TX). A total of 554 subjects with signs and symptoms of respiratory infections were enrolled, and respiratory samples were collected in this study. In comparison with the ProFlu+ real-time RT-PCR, the overall sensitivity and specificity of Alere i RSV assay for the detection of RSV were 98.6% (95% confidence interval [CI], 94.4 to 99.7%) and 98.0% (95% CI, 95.8 to 99.1%), respectively, for direct NP and 98.6% (95% CI, 94.4 to 99.7%) and 97.8% (95% CI, 95.5 to 98.9%), respectively, for VTM NP. The Alere i RSV is a highly sensitive and specific molecular assay ideal for rapid RSV detection in patients in the point-of-care setting due to its minimal hands-on time and rapid result availability. Copyright © 2018 American Society for Microbiology.

  19. Construction and optimization of an efficient breathing-based isothermal emulsion amplification method

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Yanting, E-mail: shenyanting798@126.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Tian, Fei, E-mail: 642807827@qq.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Tu, Jing, E-mail: jtu@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Li, Rui, E-mail: lirui901113@163.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Chen, Zhenzhu, E-mail: zzchen_seu@163.com [Research Center for Learning Science, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Bai, Yunfei, E-mail: whitecf@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Ge, Qinyu, E-mail: geqinyu@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China); Lu, Zuhong, E-mail: zhlu@seu.edu.cn [State Key Laboratory of Bioelectronics, Southeast University, Sipailou Road no. 2, Nanjing, Jiangsu Province 210096 (China)

    2017-06-22

    The reaction temperature is one of the main factors that affect the stability of emulsion PCR (emPCR). Focusing on this point, we applied the “DNA breathing” mechanism in BEAMing (Bead, Emulsion, Amplification, and Magnetic) and proposed a more stable emulsion amplification method. Compared to the conventional emPCR, this method provided excellent results. Firstly, more stable emulsion system resulted in higher percentage of single-molecular amplifications (73.17%). Secondly, an ordinary temperature-controlling device was enough. Our outcome showed that the reaction temperature of this method was not strict so that the ordinary temperature-controlling device was enough for it (the heat block sets vs. the PCR instrument: 13.140 ± 0.110 vs. 13.008 ± 0.039, P = 0.120). Thirdly, the single-biotinylated emP{sub 1} coated streptavidin beads were stable enough to be used for this method (the control temperature vs. the reaction temperature: 2967.91 ± 409.045 vs. 3026.22 ± 442.129, P = 0.334), which could replace the double-biotinylated emP{sub 1} coated beads and was benefit for saving cost. In conclusion, the method presented here with stable emulsion system, simplified temperature-controlling device, and decreased investment would be a highly streamlined and inexpensive option for future single-molecular amplification based researches. - Highlights: • A breathing-based isothermal emulsion amplification (BIEA) method was developed. • BIEA showed excellent properties compared with conventional amplification method. • Terminal breathing of DNA duplex was firstly used in emulsion amplification.

  20. An integrated portable hand-held analyser for real-time isothermal nucleic acid amplification

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Matthew C. [College of Marine Science, University of South Florida, St Petersburg, FL (United States)], E-mail: msmith@marine.usf.edu; Steimle, George; Ivanov, Stan; Holly, Mark; Fries, David P. [College of Marine Science, University of South Florida, St Petersburg, FL (United States)

    2007-08-29

    A compact hand-held heated fluorometric instrument for performing real-time isothermal nucleic acid amplification and detection is described. The optoelectronic instrument combines a Printed Circuit Board/Micro Electro Mechanical Systems (PCB/MEMS) reaction detection/chamber containing an integrated resistive heater with attached miniature LED light source and photo-detector and a disposable glass waveguide capillary to enable a mini-fluorometer. The fluorometer is fabricated and assembled in planar geometry, rolled into a tubular format and packaged with custom control electronics to form the hand-held reactor. Positive or negative results for each reaction are displayed to the user using an LED interface. Reaction data is stored in FLASH memory for retrieval via an in-built USB connection. Operating on one disposable 3 V lithium battery >12, 60 min reactions can be performed. Maximum dimensions of the system are 150 mm (h) x 48 mm (d) x 40 mm (w), the total instrument weight (with battery) is 140 g. The system produces comparable results to laboratory instrumentation when performing a real-time nucleic acid sequence-based amplification (NASBA) reaction, and also displayed comparable precision, accuracy and resolution to laboratory-based real-time nucleic acid amplification instrumentation. A good linear response (R{sup 2} = 0.948) to fluorescein gradients ranging from 0.5 to 10 {mu}M was also obtained from the instrument indicating that it may be utilized for other fluorometric assays. This instrument enables an inexpensive, compact approach to in-field genetic screening, providing results comparable to laboratory equipment with rapid user feedback as to the status of the reaction.

  1. An integrated portable hand-held analyser for real-time isothermal nucleic acid amplification

    International Nuclear Information System (INIS)

    Smith, Matthew C.; Steimle, George; Ivanov, Stan; Holly, Mark; Fries, David P.

    2007-01-01

    A compact hand-held heated fluorometric instrument for performing real-time isothermal nucleic acid amplification and detection is described. The optoelectronic instrument combines a Printed Circuit Board/Micro Electro Mechanical Systems (PCB/MEMS) reaction detection/chamber containing an integrated resistive heater with attached miniature LED light source and photo-detector and a disposable glass waveguide capillary to enable a mini-fluorometer. The fluorometer is fabricated and assembled in planar geometry, rolled into a tubular format and packaged with custom control electronics to form the hand-held reactor. Positive or negative results for each reaction are displayed to the user using an LED interface. Reaction data is stored in FLASH memory for retrieval via an in-built USB connection. Operating on one disposable 3 V lithium battery >12, 60 min reactions can be performed. Maximum dimensions of the system are 150 mm (h) x 48 mm (d) x 40 mm (w), the total instrument weight (with battery) is 140 g. The system produces comparable results to laboratory instrumentation when performing a real-time nucleic acid sequence-based amplification (NASBA) reaction, and also displayed comparable precision, accuracy and resolution to laboratory-based real-time nucleic acid amplification instrumentation. A good linear response (R 2 = 0.948) to fluorescein gradients ranging from 0.5 to 10 μM was also obtained from the instrument indicating that it may be utilized for other fluorometric assays. This instrument enables an inexpensive, compact approach to in-field genetic screening, providing results comparable to laboratory equipment with rapid user feedback as to the status of the reaction

  2. Rapid amplification/detection of nucleic acid targets utilizing a HDA/thin film biosensor.

    Science.gov (United States)

    Jenison, Robert; Jaeckel, Heidi; Klonoski, Joshua; Latorra, David; Wiens, Jacinta

    2014-08-07

    Thin film biosensors exploit a flat, optically coated silicon-based surface whereupon formation of nucleic acid hybrids are enzymatically transduced in a molecular thin film that can be detected by the unaided human eye under white light. While the limit of sensitivity for detection of nucleic acid targets is at sub-attomole levels (60 000 copies) many clinical specimens containing bacterial pathogens have much lower levels of analyte present. Herein, we describe a platform, termed HDA/thin film biosensor, which performs helicase-dependant nucleic acid amplification on a thin film biosensor surface to improve the limit of sensitivity to 10 copies of the mecA gene present in methicillin-resistant strains of Staphylococcus. As double-stranded DNA is unwound by helicase it was either bound by solution-phase DNA primers to be copied by DNA polymerase or hybridized to surface immobilized probe on the thin film biosensor surface to be detected. Herein, we show that amplification reactions on the thin film biosensor are equivalent to in standard thin wall tubes, with detection at the limit of sensitivity of the assay occurring after 30 minutes of incubation time. Further we validate the approach by detecting the presence of the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) from positive blood culture aliquots with high specificity (signal/noise ratio of 105).

  3. Prevalence of Plasmodium spp. in malaria asymptomatic African migrants assessed by nucleic acid sequence based amplification

    Directory of Open Access Journals (Sweden)

    Schallig Henk DFH

    2009-01-01

    Full Text Available Abstract Background Malaria is one of the most important infectious diseases in the world. Although most cases are found distributed in the tropical regions of Africa, Asia, Central and South Americas, there is in Europe a significant increase in the number of imported cases in non-endemic countries, in particular due to the higher mobility in today's society. Methods The prevalence of a possible asymptomatic infection with Plasmodium species was assessed using Nucleic Acid Sequence Based Amplification (NASBA assays on clinical samples collected from 195 study cases with no clinical signs related to malaria and coming from sub-Saharan African regions to Southern Italy. In addition, base-line demographic, clinical and socio-economic information was collected from study participants who also underwent a full clinical examination. Results Sixty-two study subjects (31.8% were found positive for Plasmodium using a pan Plasmodium specific NASBA which can detect all four Plasmodium species causing human disease, based on the small subunit 18S rRNA gene (18S NASBA. Twenty-four samples (38% of the 62 18S NASBA positive study cases were found positive with a Pfs25 mRNA NASBA, which is specific for the detection of gametocytes of Plasmodium falciparum. A statistically significant association was observed between 18S NASBA positivity and splenomegaly, hepatomegaly and leukopaenia and country of origin. Conclusion This study showed that a substantial proportion of people originating from malaria endemic countries harbor malaria parasites in their blood. If transmission conditions are available, they could potentially be a reservoir. Thefore, health authorities should pay special attention to the health of this potential risk group and aim to improve their health conditions.

  4. Nucleic acid amplification test for detection of west nile virus infection in pakistani blood donors

    International Nuclear Information System (INIS)

    Niazi, S.K.; Alam, M.

    2017-01-01

    Background: The study was planned to determine the presence of West Nile Virus (WNV) infection in Pakistani blood donors, using Nucleic Acid Amplification Test (NAT). Methods: The blood donors for study were selected on the basis of the standard questionnaire and routine screening results. Six donors were pooled using an automated pipettor and NAT for WNV was performed on Roche Cobas s 201 NAT system. The reactive pools were resolved in Individual Donation-NAT (ID-NAT) format and a sample from FFP bags of reactive donations was retrieved. NAT was again performed on retrieved plasma bag (RPB) sample to confirm the reactive donations. The donors were also recalled and interviewed about history of illness related to recent WNV infection. Results: After serological screening of 1929 donors during the study period, 1860 donors were selected for NAT test for WNV detection. The mean age of the donors was 28±8.77 (range: 18–57 years). 1847 (99.3%) donors were male and 13 (0.7%) were female. NAT for WNV identified six initially reactive pools (0.32%). On follow-up testing with RPB samples, 4 donors (0.21%) were found confirmed reactive for WNV RNA (NAT yield of 1 in 465 blood donors). Conclusion: WNV is a threat to safety of blood products in Pakistan. A screening strategy can be implemented after a large-scale study and financial considerations. One of the reduced cost screening strategies is seasonal screening of blood donors for WNV, with pooling of samples. (author)

  5. Nucleic acid amplification testing in Indian blood banks: A review with perspectives

    Directory of Open Access Journals (Sweden)

    Kanjaksha Ghosh

    2017-01-01

    Full Text Available Background: Nucleic acid amplification testing (NAT is restricted to a few blood banks in India since 2008. This review was directed toward understanding NAT yield in different parts of the country and prevalence in the NAT of different types of virus. Materials and Methods: English literature was searched from 1990 to 2016 in PubMed, Scopus, Ind med, and Google database using properly constructed key words. Literature was collected and finally the data were synthesized. Results: NAT results from 11 publications and one personal communication showed that till date 389387 blood units have been NAT tested from various parts of the country. NAT yield varied from 1:476 to 1:4403 in various studies. Till date, 58/2550 (2% blood banks of India are doing NAT testing but all of them have not published their results. Majority of the centers have used ID-NAT (Individual NAT protocol and 21 blood banks are using minipool format of the test. One center has used in-house NAT testing system. In> 70% of the time, the NAT positivity with due to hepatitis B (Hep B. For individual infection, NAT yield from the pooled data showed HIV in 1:66,000, Hep C virus 1:5484 and Hep B in 1:1761 seronegative donors. Discussion and Conclusion: In view of the very high NAT yield (1:1361, NAT in some from needs to be universally applied in Indian blood banks. However, the high Hep B occult infection suggests stricter donor selection and immunization of adults for Hep B may be way forward toward ensuring the viral safety of blood components in India.

  6. A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods.

    Science.gov (United States)

    Nixon, Gavin J; Svenstrup, Helle F; Donald, Carol E; Carder, Caroline; Stephenson, Judith M; Morris-Jones, Stephen; Huggett, Jim F; Foy, Carole A

    2014-12-01

    Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR). There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These 'isothermal' methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT), akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP) assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

  7. A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods

    Directory of Open Access Journals (Sweden)

    Gavin J. Nixon

    2014-12-01

    Full Text Available Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR. There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These ‘isothermal’ methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT, akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

  8. Amplification of acid formation from diphenyliodonium salt in γ-irradiated polymers

    International Nuclear Information System (INIS)

    Yamazaki, K.; Iino, K.; Koizumi, H.; Ichikawa, T.

    2006-01-01

    The G values of acid formation from diphenyliodonium salt in γ-irradiated polymers have been measured for developing chemically amplified radiation resists that have abilities of not only amplifying chemical reactions of polymers by the acid as a catalyst but also amplifying the formation of acid itself by a radiation-induced radical chain reaction. Addition of secondary alcohols as amplifiers for acid formation, to poly(alkyl methacrylates) results in the increase of the G value, though the increase is not so significant as that expected from a liquid-phase amplification reaction. The diffusion of free radicals and added molecules is difficult in the polymers due to cage effects by polymer molecules, which causes increases of the radical combination reaction and therefore decrease of the turnover number of the chain reaction. The G values of acid formation for poly(vinyl acetals) are much higher than those for poly(alkyl methacrylates) even the amplifiers are not added in the former polymers. Poly(vinyl acetals) are synthesized by acetalyzation of poly(vinyl alcohol), a polymer composed of secondary alcohol monomer unit, so that the secondary alcohol remaining in the polymer skeleton acts as an efficient amplifier for acid formation. The secondary alcohol acts as stepping-stones for the diffusion of free radical, so that the free radical can encounter a new iodonium salt molecule to continue the radical chain reaction. (authors)

  9. Pelvic inflammatory disease risk following negative results from chlamydia nucleic acid amplification tests (NAATs) versus non-NAATs in Denmark

    DEFF Research Database (Denmark)

    Turner, Katy M E; Benfield, Thomas; Frølund, Maria

    2018-01-01

    BACKGROUND: Nucleic Acid Amplification Tests (NAATs) are the recommended test type for diagnosing Chlamydia trachomatis (chlamydia). However, less sensitive diagnostic methods-including direct immunofluorescence (IF) and enzyme-linked immunoassay (ELISA)-remain in use in lower resourced settings...... with a chlamydia test, just under half (44.78%, n = 121,857) were tested using NAATs. Overall, 6.38% (n = 17,353) tested positive for chlamydia and 0.64% (n = 1,732) were diagnosed with PID within 12 months. The risk of PID following a positive chlamydia test did not differ by test type (NAAT 0.81% [95% CI 0....... We estimate the risk of pelvic inflammatory disease (PID) following undiagnosed infection in women tested with non-NAATs and estimate the health gain from using accurate diagnostic tests. METHODS AND FINDINGS: We used Denmark's national Chlamydia Study dataset to extract all chlamydia tests performed...

  10. Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

    Science.gov (United States)

    Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

    2010-05-04

    A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

  11. CdTe amplification nanoplatforms capped with thioglycolic acid for electrochemical aptasensing of ultra-traces of ATP

    Energy Technology Data Exchange (ETDEWEB)

    Shamsipur, Mojtaba, E-mail: mshamsipur@yahoo.com [Department of Chemistry, Razi University, P.O. Box 67149-67346, Kermanshah (Iran, Islamic Republic of); Farzin, Leila [Department of Analytical Chemistry, School of Chemistry, College of Science, University of Tehran, P.O. Box 14174-66191, Tehran (Iran, Islamic Republic of); Tabrizi, Mahmoud Amouzadeh [Research Center for Science and Technology in Medicine,Tehran University of Medical Sciences, P.O. Box 14197-33131, Tehran (Iran, Islamic Republic of); Shanehsaz, Maryam [Analytical Chemistry Research Laboratory, Mobin Shimi Azma Company, P.O. Box 14768-44949, Tehran (Iran, Islamic Republic of)

    2016-12-01

    A “signal off” voltammetric aptasensor was developed for the sensitive and selective detection of ultra-low levels of adenosine triphosphate (ATP). For this purpose, a new strategy based on the principle of recognition-induced switching of aptamers from DNA/DNA duplex to DNA/target complex was designed using thioglycolic acid (TGA)-capped CdTe quantum dots (QDs) as the signal amplifying nano-platforms. Owing to the small size, high surface-to-volume ratio and good conductivity, quantum dots were immobilized on the electrode surface for signal amplification. In this work, methylene blue (MB) adsorbed to DNA was used as a sensitive redox reporter. The intensity of voltammetric signal of MB was found to decrease linearly upon ATP addition over a concentration range of 0.1 nM to 1.6 μM with a correlation coefficient of 0.9924. Under optimized conditions, the aptasensor was able to selectively detect ATP with a limit of detection of 45 pM at 3σ. The results also demonstrated that the QDs-based amplification strategy could be feasible for ATP assay and presented a potential universal method for other small biomolecular aptasensors. - Highlights: • A “signal off” voltammetric aptasensor has been reported. • The DPV technique was used for the determination of ATP. • The determination of ATP up to 1.6 μM with a detection limit 45 pM, respectively.

  12. Ternary Surface Monolayers for Ultrasensitive (Zeptomole) Amperometric Detection of Nucleic-Acid Hybridization without Signal Amplification

    Science.gov (United States)

    Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A.; Wang, Joseph

    2010-01-01

    A ternary surface monolayer, consisting of co-assembled thiolated capture probe (SHCP) mercaptohexanol (MCH) and dithiothreitol (DTT), is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers (SAMs). Remarkably low detection limits down to 40 zmole (in 4 μL samples) as well as only 1 CFU E. coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3′,5,5′-tetramethylbenzidine (HRP/TMB) system. Such dramatic improvements in the detection limits (compared to common binary alkanethiol interfaces and to most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to non-specific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration ‘backfillers’ that leads to a remarkably low background noise even in the presence of complex sample matrices. A wide range of surface compositions have been investigated and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety and forensic analysis. PMID:20883023

  13. Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification.

    Science.gov (United States)

    Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A; Wang, Joseph

    2010-11-01

    A ternary surface monolayer, consisting of coassembled thiolated capture probe, mercaptohexanol and dithiothreitol, is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers. Remarkably low detection limits down to 40 zmol (in 4 μL samples) as well as only 1 CFU Escherichia coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3',5,5'-tetramethylbenzidine system. Such dramatic improvements in the detection limits (compared to those of common binary alkanethiol interfaces and to those of most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to nonspecific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration "backfillers" that leads to a remarkably low background noise even in the presence of complex sample matrixes. A wide range of surface compositions have been investigated, and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety, and forensic analysis.

  14. Nucleic acid amplification technology screening for hepatitis C virus and human immunodeficiency virus for blood donations

    International Nuclear Information System (INIS)

    Bamaga, Mohammad S.; Bokhari, Fawzi F.; Aboud, Abdulrehman M.; Al-Malki, M.; Alenzi, Faris Q.

    2006-01-01

    To investigate the performance of the commercial Roche COBAS AmpliScreen assay, and demonstrate whether the COBAS AmpliScreen human immunodeficiency virus-1 (HIV-1) test, v1.5, and COBAS AmpliScreen hepatitis C virus (HCV) v 2.0 for screening for HIV-1 and HCV RNA in the donated blood units from which plasma mini pools were collected, by nucleic acid amplification technology (NAT), could detect the positive pools and reduce the risk of transmission of infections for those routinely tested by serological assays. The study was performed on 3288 plasma samples collected from blood donors in a period of 13 months, from August 2004 to August 2005, at Al-Hada Armed Forces Hospital, Molecular Pathology Laboratory, Taif, Kingdom of Saudi Arabia. The samples were tested by the reverse transcriptase polymerase chain reaction (RT-PCR) after RNA extraction (this represents the major method in NAT assays), in parallel with the routine serological testing to detect qualitatively for HIV-1 and HCV. The NAT assays that include an automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays, and the routine serological screening assays for the detection of the HIV-1 and HCV RNA in the plasma samples from the blood donors have shown to be a reliable combination that would meet our requirements. The collected data further confirms the results from the serological assays and enables us to decrease the residual risk of transmission to a minimum with the finding of no seronegative window period donation. The results demonstrate that out of 3288 samples, the percentages of RT-PCR (NAT) negative blood donations that were also confirmed as seronegative were 99% for HCV, and 99.1% for HIV-1. The modified combined systems (automated COBAS AmpliPrep system for RNA extraction and COBAS Amplicor Analyzer using AmpliScreen kits for RT-PCR assays) for NAT screening assays has allowed the release of all blood donations supplied in the

  15. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

    Directory of Open Access Journals (Sweden)

    Annika Brinkmann

    2017-11-01

    Full Text Available We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS-based identification of viral hemorrhagic fever (VHF agents and assess the feasibility of this approach in diagnostics.An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients.The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours.Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

  16. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

    Science.gov (United States)

    Brinkmann, Annika; Ergünay, Koray; Radonić, Aleksandar; Kocak Tufan, Zeliha; Domingo, Cristina; Nitsche, Andreas

    2017-11-01

    We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

  17. Fluorometric determination of nucleic acids based on the use of polydopamine nanotubes and target-induced strand displacement amplification.

    Science.gov (United States)

    Ge, Jia; Bai, Dong-Mei; -Geng, Xin; Hu, Ya-Lei; Cai, Qi-Yong; Xing, Ke; Zhang, Lin; Li, Zhao-Hui

    2018-01-10

    The authors describe a fluorometric method for the quantitation of nucleic acids by combining (a) cycled strand displacement amplification, (b) the unique features of the DNA probe SYBR Green, and (c) polydopamine nanotubes. SYBR Green undergoes strong fluorescence enhancement upon intercalation into double-stranded DNA (dsDNA). The polydopamine nanotubes selectively adsorb single-stranded DNA (ssDNA) and molecular beacons. In the absence of target DNA, the molecular beacon, primer and SYBR Green are adsorbed on the surface of polydopamine nanotubes. This results in quenching of the fluorescence of SYBR Green, typically measured at excitation/emission wavelengths of 488/518 nm. Upon addition of analyte (target DNA) and polymerase, the stem of the molecular beacon is opened so that it can bind to the primer. This triggers target strand displacement polymerization, during which dsDNA is synthesized. The hybridized target is then displaced due to the strand displacement activity of the polymerase. The displaced target hybridizes with another molecular beacon. This triggers the next round of polymerization. Consequently, a large amount of dsDNA is formed which is detected by addition of SYBR Green. Thus, sensitive and selective fluorometric detection is realized. The fluorescent sensing strategy shows very good analytical performances towards DNA detection, such as a wide linear range from 0.05 to 25 nM with a low limit of detection of 20 pM. Graphical abstract Schematic of a fluorometric strategy for highly sensitive and selective determination of nucleic acids by combining strand displacement amplification and the unique features of SYBR Green I (SG) and polydopamine nanotubes.

  18. Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies

    Directory of Open Access Journals (Sweden)

    Mairinger FD

    2014-08-01

    Full Text Available Fabian D Mairinger,1 Robert FH Walter,2 Claudia Vollbrecht,3 Thomas Hager,1 Karl Worm,1 Saskia Ting,1 Jeremias Wohlschläger,1 Paul Zarogoulidis,4 Konstantinos Zarogoulidis,4 Kurt W Schmid1 1Institute of Pathology, 2Ruhrlandklinik, West German Lung Center, University Hospital Essen, Essen, 3Institute of Pathology, University Hospital Cologne, Cologne, Germany; 4Pulmonary Department, Oncology Unit, G Papanikolaou General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece Background and methods: Isothermal multiple displacement amplification (IMDA can be a powerful tool in molecular routine diagnostics for homogeneous and sequence-independent whole-genome amplification of notably small tumor samples, eg, microcarcinomas and biopsies containing a small amount of tumor. Currently, this method is not well established in pathology laboratories. We designed a study to confirm the feasibility and convenience of this method for routine diagnostics with formalin-fixed, paraffin-embedded samples prepared by laser-capture microdissection. Results: A total of 250 µg DNA (concentration 5 µg/µL was generated by amplification over a period of 8 hours with a material input of approximately 25 cells, approximately equivalent to 175 pg of genomic DNA. In the generated DNA, a representation of all chromosomes could be shown and the presence of elected genes relevant for diagnosis in clinical samples could be proven. Mutational analysis of clinical samples could be performed without any difficulty and showed concordance with earlier diagnostic findings. Conclusion: We established the feasibility and convenience of IMDA for routine diagnostics. We also showed that small amounts of DNA, which were not analyzable with current molecular methods, could be sufficient for a wide field of applications in molecular routine diagnostics when they are preamplified with IMDA. Keywords: isothermal multiple displacement amplification, isothermal, whole

  19. Detection and quantification of Plasmodium falciparum in blood samples using quantitative nucleic acid sequence-based amplification

    NARCIS (Netherlands)

    Schoone, G. J.; Oskam, L.; Kroon, N. C.; Schallig, H. D.; Omar, S. A.

    2000-01-01

    A quantitative nucleic acid sequence-based amplification (QT-NASBA) assay for the detection of Plasmodium parasites has been developed. Primers and probes were selected on the basis of the sequence of the small-subunit rRNA gene. Quantification was achieved by coamplification of the RNA in the

  20. Accurate and precise DNA quantification in the presence of different amplification efficiencies using an improved Cy0 method.

    Science.gov (United States)

    Guescini, Michele; Sisti, Davide; Rocchi, Marco B L; Panebianco, Renato; Tibollo, Pasquale; Stocchi, Vilberto

    2013-01-01

    Quantitative real-time PCR represents a highly sensitive and powerful technology for the quantification of DNA. Although real-time PCR is well accepted as the gold standard in nucleic acid quantification, there is a largely unexplored area of experimental conditions that limit the application of the Ct method. As an alternative, our research team has recently proposed the Cy0 method, which can compensate for small amplification variations among the samples being compared. However, when there is a marked decrease in amplification efficiency, the Cy0 is impaired, hence determining reaction efficiency is essential to achieve a reliable quantification. The proposed improvement in Cy0 is based on the use of the kinetic parameters calculated in the curve inflection point to compensate for efficiency variations. Three experimental models were used: inhibition of primer extension, non-optimal primer annealing and a very small biological sample. In all these models, the improved Cy0 method increased quantification accuracy up to about 500% without affecting precision. Furthermore, the stability of this procedure was enhanced integrating it with the SOD method. In short, the improved Cy0 method represents a simple yet powerful approach for reliable DNA quantification even in the presence of marked efficiency variations.

  1. Nucleic acid amplification tests (NAATs for gonorrhoea diagnosis in women: Experience of a tertiary care hospital in north India

    Directory of Open Access Journals (Sweden)

    Seema Sood

    2014-01-01

    Full Text Available Background & objectives: Gonorrhoea is among the most frequent of the estimated bacterial sexually transmitted infections (STIs and has significant health implications in women. The use of nucleic acid amplification tests (NAATs has been shown to provide enhanced diagnosis of gonorrhoea in female patients. However, it is recommended that an on-going assessment of the test assays should be performed to check for any probable sequence variation occurring in the targeted region. In this study, an in-house PCR targeting opa-gene of Neisseria gonorrhoeae was used in conjunction with 16S ribosomal PCR to determine the presence of gonorrhoea in female patients attending the tertiary care hospitals. Methods: Endocervical samples collected from 250 female patients with complaints of vaginal or cervical discharge or pain in lower abdomen were tested using opa and 16S ribosomal assay. The samples were also processed by conventional methods. Results: Of the 250 female patients included in the study, only one was positive by conventional methods (microscopy and culture whereas 17 patients were found to be positive based on PCR results. Interpretation & conclusions: The clinical sensitivity of conventional methods for the detection of N. gonorrhoeae in female patients was low. The gonococcal detection rates increased when molecular method was used giving 16 additional positives. Studies should be done to find out other gene targets that may be used in the screening assays to detect the presence of gonorrhoea.

  2. The Effect of Storage and Extraction Methods on Amplification of Plasmodium falciparum DNA from Dried Blood Spots

    NARCIS (Netherlands)

    Schwartz, A.; Baidjoe, A.Y.; Rosenthal, P.J.; Dorsey, G.; Bousema, T.; Greenhouse, B.

    2015-01-01

    Extraction and amplification of DNA from dried blood spots (DBS) collected in field studies is commonly used for detection of Plasmodium falciparum. However, there have been few systematic efforts to determine the effects of storage and extraction methods on the sensitivity of DNA amplification. We

  3. DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification.

    Science.gov (United States)

    Liu, Meng; Yin, Qingxin; McConnell, Erin M; Chang, Yangyang; Brennan, John D; Li, Yingfu

    2018-03-26

    Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template. DFA begins with a stimulus-dependent RCA reaction, producing tandemly linked RCDs in long-chain DNA products. These RCDs cleave an RNA-containing DNA sequence to form additional primers that hybridize to the circular DNA molecule, giving rise to DNA assemblies that act as the new inputs for RCA. The RCA reaction and the cleavage event keep on feeding each other autonomously, resulting in exponential growth of repetitive DNA sequences that can be easily detected. This method can be used for the detection of both nucleic acid based targets and non-nucleic acid analytes. In this article, we discuss the conceptual framework of the feedback amplification approach, the essential features of this method as well as remaining challenges and possible solutions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. A quantitative comparison of single-cell whole genome amplification methods.

    Directory of Open Access Journals (Sweden)

    Charles F A de Bourcy

    Full Text Available Single-cell sequencing is emerging as an important tool for studies of genomic heterogeneity. Whole genome amplification (WGA is a key step in single-cell sequencing workflows and a multitude of methods have been introduced. Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA, Multiple Annealing and Looping Based Amplification Cycles (MALBAC, and the PicoPLEX single-cell WGA kit (NEB-WGA. We considered the effects of reaction gain on coverage uniformity, error rates and the level of background contamination. We compared the suitability of the different WGA methods for the detection of copy-number variations, for the detection of single-nucleotide polymorphisms and for de-novo genome assembly. No single method performed best across all criteria and significant differences in characteristics were observed; the choice of which amplifier to use will depend strongly on the details of the type of question being asked in any given experiment.

  5. Method for signal conditioning and data acquisition system, based on variable amplification and feedback technique

    Energy Technology Data Exchange (ETDEWEB)

    Conti, Livio, E-mail: livio.conti@uninettunouniversity.net [Facoltà di Ingegneria, Università Telematica Internazionale Uninettuno, Corso Vittorio Emanuele II 39, 00186 Rome, Italy INFN Sezione Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome (Italy); Sgrigna, Vittorio [Dipartimento di Matematica e Fisica, Università Roma Tre, 84 Via della Vasca Navale, I-00146 Rome (Italy); Zilpimiani, David [National Institute of Geophysics, Georgian Academy of Sciences, 1 M. Alexidze St., 009 Tbilisi, Georgia (United States); Assante, Dario [Facoltà di Ingegneria, Università Telematica Internazionale Uninettuno, Corso Vittorio Emanuele II 39, 00186 Rome, Italy INFN Sezione Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome (Italy)

    2014-08-21

    An original method of signal conditioning and adaptive amplification is proposed for data acquisition systems of analog signals, conceived to obtain a high resolution spectrum of any input signal. The procedure is based on a feedback scheme of the signal amplification with aim at maximizing the dynamic range and resolution of the data acquisition system. The paper describes the signal conditioning, digitization, and data processing procedures applied to an a priori unknown signal in order to enucleate its amplitude and frequency content for applications in different environments: on the ground, in space, or in the laboratory. An electronic board of the conditioning module has also been constructed and described. In the paper are also discussed the main fields of application and advantages of the method with respect to those known today.

  6. Method for signal conditioning and data acquisition system, based on variable amplification and feedback technique

    International Nuclear Information System (INIS)

    Conti, Livio; Sgrigna, Vittorio; Zilpimiani, David; Assante, Dario

    2014-01-01

    An original method of signal conditioning and adaptive amplification is proposed for data acquisition systems of analog signals, conceived to obtain a high resolution spectrum of any input signal. The procedure is based on a feedback scheme of the signal amplification with aim at maximizing the dynamic range and resolution of the data acquisition system. The paper describes the signal conditioning, digitization, and data processing procedures applied to an a priori unknown signal in order to enucleate its amplitude and frequency content for applications in different environments: on the ground, in space, or in the laboratory. An electronic board of the conditioning module has also been constructed and described. In the paper are also discussed the main fields of application and advantages of the method with respect to those known today

  7. Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies.

    Science.gov (United States)

    Mairinger, Fabian D; Walter, Robert Fh; Vollbrecht, Claudia; Hager, Thomas; Worm, Karl; Ting, Saskia; Wohlschläger, Jeremias; Zarogoulidis, Paul; Zarogoulidis, Konstantinos; Schmid, Kurt W

    2014-01-01

    Isothermal multiple displacement amplification (IMDA) can be a powerful tool in molecular routine diagnostics for homogeneous and sequence-independent whole-genome amplification of notably small tumor samples, eg, microcarcinomas and biopsies containing a small amount of tumor. Currently, this method is not well established in pathology laboratories. We designed a study to confirm the feasibility and convenience of this method for routine diagnostics with formalin-fixed, paraffin-embedded samples prepared by laser-capture microdissection. A total of 250 μg DNA (concentration 5 μg/μL) was generated by amplification over a period of 8 hours with a material input of approximately 25 cells, approximately equivalent to 175 pg of genomic DNA. In the generated DNA, a representation of all chromosomes could be shown and the presence of elected genes relevant for diagnosis in clinical samples could be proven. Mutational analysis of clinical samples could be performed without any difficulty and showed concordance with earlier diagnostic findings. We established the feasibility and convenience of IMDA for routine diagnostics. We also showed that small amounts of DNA, which were not analyzable with current molecular methods, could be sufficient for a wide field of applications in molecular routine diagnostics when they are preamplified with IMDA.

  8. Robust and efficient direct multiplex amplification method for large-scale DNA detection of blood samples on FTA cards

    International Nuclear Information System (INIS)

    Jiang Bowei; Xiang Fawei; Zhao Xingchun; Wang Lihua; Fan Chunhai

    2013-01-01

    Deoxyribonucleic acid (DNA) damage arising from radiations widely occurred along with the development of nuclear weapons and clinically wide application of computed tomography (CT) scan and nuclear medicine. All ionizing radiations (X-rays, γ-rays, alpha particles, etc.) and ultraviolet (UV) radiation lead to the DNA damage. Polymerase chain reaction (PCR) is one of the most wildly used techniques for detecting DNA damage as the amplification stops at the site of the damage. Improvements to enhance the efficiency of PCR are always required and remain a great challenge. Here we establish a multiplex PCR assay system (MPAS) that is served as a robust and efficient method for direct detection of target DNA sequences in genomic DNA. The establishment of the system is performed by adding a combination of PCR enhancers to standard PCR buffer, The performance of MPAS was demonstrated by carrying out the direct PCR amplification on l.2 mm human blood punch using commercially available primer sets which include multiple primer pairs. The optimized PCR system resulted in high quality genotyping results without any inhibitory effect indicated and led to a full-profile success rate of 98.13%. Our studies demonstrate that the MPAS provides an efficient and robust method for obtaining sensitive, reliable and reproducible PCR results from human blood samples. (authors)

  9. Identification of MYCN gene amplification in neuroblastoma using chromogenic in situ hybridization (CISH): an alternative and practical method.

    Science.gov (United States)

    Bhargava, Rohit; Oppenheimer, Orit; Gerald, William; Jhanwar, Suresh C; Chen, Beiyun

    2005-06-01

    Chromogenic in situ hybridization (CISH) is a recently developed technique, which utilizes the general principles of in situ hybridization and a detection system similar to immunohistochemistry. To assess the utility of CISH for analysis of MYCN gene amplification, we compared this assay with established diagnostic assays such as Southern blot analysis (SB) and fluorescent in situ hybridization (FISH). CISH was performed on 67 cases of neuroblastoma using tissue microarray (65 cases) and whole tissue sections (2 cases). Unequivocal, high-level amplification (> or =10 gene copies per tumor nucleus) was identified in 19 of 67 (28.4%) tumors. Two (3%) tumors showed low-level amplification (6-9 gene copies per tumor nucleus). No amplification was seen in 46 of 67 (68.6%) tumors. SB data were available in 44 tumors. Forty-one of the 44 tumors (93%) showed concordant results between CISH and SB. Three tumors showed MYCN amplification by CISH but no amplification by SB, most likely due to dilution effect of nonneoplastic tissue in the test samples. Two of these three tumors also showed MYCN amplification by FISH, and the third tumor was not analyzed by FISH. FISH data were available in total of 30 tumors. All 30 tumors showed concordant results between CISH and FISH for classifying a tumor as MYCN amplified or not amplified. We conclude that CISH is an accurate method for determining MYCN gene amplification, with added advantages that make it a more practically useful method.

  10. Chlamydia trachomatis infections in Greece: first prevalence study using nucleic acid amplification tests.

    Science.gov (United States)

    Levidiotou, S; Vrioni, G; Papadogeorgaki, H; Avdeliodi, K; Kada, H; Kaparos, G; Kouskouni, E; Fragouli, E; Legakis, N J

    2005-03-01

    The present retrospective study was initiated to determine the prevalence of Chlamydia trachomatis and to assess the risk factors for infection in adult women and men presenting to general practitioners, gynecologists, dermatologists, and family-planning centers in Greece. The study was carried out in four different Greek hospital centers using highly sensitive nucleic acid amplification techniques. Altogether, 16,834 women and 1,035 men were enrolled from October 1998 to April 2004. Two types of specimens were collected from each patient: cervical swabs from women, urethral swabs from men, and first-catch urine from women and men. All specimens were examined with the Cobas Amplicor C. trachomatis polymerase chain reaction assay (Roche Molecular Systems, Branchburg, NJ, USA) or the LC x C. trachomatis ligase chain reaction assay (Abbott Laboratories, Abbott Park, IL, USA). Demographic and behavioral data were collected by clinicians using a standardized questionnaire. A total of 704 (3.9%) patients were infected with C. trachomatis. The prevalence among female patients was 3.5% and that among male patients 11.2%. Among infected patients, 88% were under 30 years of age, 71% reported more than one sexual partner, and 91% reported a new sexual partner within the last year. In conclusion, the prevalence of C. trachomatis infection in Greece is low. Young age and new and multiple sexual partners within the last year were factors consistently associated with an increased risk of chlamydial infection.

  11. Transmission of Mycobacterium tuberculosis from patients who are nucleic acid amplification test- negative.

    Science.gov (United States)

    Xie, Yingda L; Cronin, Wendy A; Proschan, Michael; Oatis, Richard; Cohn, Silvia; Curry, Scott R; Golub, Jonathan E; Barry Iii, Clifton E; Dorman, Susan E

    2018-04-24

    Among adults with signs and symptoms of pulmonary tuberculosis (TB), recognition of transmissible TB has implications for airborne infection isolation and public health activities. Sputum smear-negative TB patients account for around one-fifth of tuberculosis transmission. The tuberculosis transmission risk of TB patients with negative results on nucleic acid amplification (NAA) testing of respiratory specimens has not been established. We sought to estimate the tuberculosis transmission risk of NAA test-negative TB patients. We retrospectively reviewed Maryland TB program data from 2004 to 2009 during which NAA testing by the Mycobacterium Tuberculosis Direct Test (MTD) was performed routinely. Patients with sputum Mycobacterium tuberculosis (M.tb) isolates having matching genotypes were assigned to clusters. Transmission sequence was approximated by collection order of individuals' first culture-positive specimens. Minimum transmission risks of NAA (MTD)-negative TB patients and of smear-negative TB patients were estimated based on individuals' positions within clusters. Among 809 patients with culture-confirmed TB, M.tb genotypes were available for 782 (96.7%). For NAA-negative TB patients the minimum transmission risk estimate was 5.1% (95% CI 0-11.4). For smear-negative TB patients the minimum transmission risk estimate was 11.2% (95% CI 7.2-15.3). Minimum transmission risk of NAA-negative TB patients was lower than that of smear-negative TB patients. However, transmission risk of NAA-negative TB patients appears to not be negligible.

  12. Rapid screening method for male DNA by using the loop-mediated isothermal amplification assay.

    Science.gov (United States)

    Kitamura, Masashi; Kubo, Seiji; Tanaka, Jin; Adachi, Tatsushi

    2017-08-12

    Screening for male-derived biological material from collected samples plays an important role in criminal investigations, especially those involving sexual assaults. We have developed a loop-mediated isothermal amplification (LAMP) assay targeting multi-repeat sequences of the Y chromosome for detecting male DNA. Successful amplification occurred with 0.5 ng of male DNA under isothermal conditions of 61 to 67 °C, but no amplification occurred with up to 10 ng of female DNA. Under the optimized conditions, the LAMP reaction initiated amplification within 10 min and amplified for 20 min. The LAMP reaction was sensitive at levels as low as 1-pg male DNA, and a quantitative LAMP assay could be developed because of the strong correlation between the reaction time and the amount of template DNA in the range of 10 pg to 10 ng. Furthermore, to apply the LAMP assay to on-site screening for male-derived samples, we evaluated a protocol using a simple DNA extraction method and a colorimetric intercalating dye that allows detection of the LAMP reaction by evaluating the change in color of the solution. Using this protocol, samples of male-derived blood and saliva stains were processed in approximately 30 min from DNA extraction to detection. Because our protocol does not require much hands-on time or special equipment, this LAMP assay promises to become a rapid and simple screening method for male-derived samples in forensic investigations.

  13. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests

    Science.gov (United States)

    Mauk, Michael G.; Song, Jinzhao; Liu, Changchun; Bau, Haim H.

    2018-01-01

    Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges (‘chips’) that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed. PMID:29495424

  14. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests

    Directory of Open Access Journals (Sweden)

    Michael G. Mauk

    2018-02-01

    Full Text Available Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC tests for resource-limited settings. Microfluidic cartridges (‘chips’ that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets is demonstrated. Low-cost detection and added functionality (data analysis, control, communication can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.

  15. Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification

    OpenAIRE

    Yi Wang; Yan Wang; Ai-Jing Ma; Dong-Xun Li; Li-Juan Luo; Dong-Xin Liu; Dong Jin; Kai Liu; Chang-Yun Ye

    2015-01-01

    We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61?65??C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primer...

  16. Trichomonas vaginalis Nucleic Acid Amplification Testing at an Urban HIV Clinic.

    Science.gov (United States)

    Muzny, Christina A; Burkholder, Greer A; Fry, Karen R; Austin, Erika L; Schwebke, Jane R

    2016-08-01

    Trichomonas vaginalis is the most common nonviral sexually transmitted infection. T. vaginalis nucleic acid amplification testing (NAAT) recently became available at the University of Alabama at Birmingham human immunodeficiency virus (HIV) clinic. The objective of this study was to determine the uptake of T. vaginalis NAAT testing among clinic providers during the first year of test availability in addition to T. vaginalis prevalence and predictors based on NAAT results. This was a retrospective review of HIV+ women and men ages ≥16 years at the University of Alabama at Birmingham HIV Clinic, including those receiving a T. vaginalis NAAT on a genitourinary specimen. Between August 2014 and August 2015, 3163 HIV+ patients were seen (768 women, 2395 men), of whom 861 (27.3%) received a T. vaginalis NAAT; 402 women (52.3%) and 459 men (19.2%). Among those with T. vaginalis NAAT results, 70 (17.4%) of 402 women and 12 (2.6%) of 459 men (9 men who have sex with women, 1 man who has sex with men, 2 unknown) tested positive. In adjusted analyses for women, age ≤40 years (odds ratio [OR], 2.93; 95% confidence interval [CI], 1.23-6.96), current cocaine use (OR, 4.86; 95% CI, 1.57-15.06), and CD4 vaginalis NAAT. For those with a positive T. vaginalis NAAT, treatment was prescribed for 65 (92.9%) of 70 women and 10 (83.3%) of 12 men. Initial uptake of T. vaginalis NAAT testing was modest at this HIV clinic yet identified a high prevalence among women tested. Emphasis on the need for testing in HIV+ women is necessary.

  17. One-Step Nucleic Acid Amplification in Breast Cancer Sentinel Lymph Node: A Single Institutional Experience and a Short Review.

    Science.gov (United States)

    Brambilla, Tatiana; Fiamengo, Barbara; Tinterri, Corrado; Testori, Alberto; Grassi, Massimo Maria; Sciarra, Amedeo; Abbate, Tommaso; Gatzemeier, Wolfgang; Roncalli, Massimo; Di Tommaso, Luca

    2015-01-01

    Sentinel lymph node (SLN) examination is a standard in breast cancer patients, with several methods employed along its 20 years history, the last one represented by one-step nucleic acid amplification (OSNA). The latter is a intra-operative molecular assay searching for CK19 mRNA as a surrogate of metastatic cells. Our 3 years experience with OSNA (1122 patients) showed results overlapping those recorded in the same institution with a morphological evaluation (930 patients) of SLN. In detail, the data of OSNA were almost identical to those observed with standard post-operative procedure in terms of patients with positive SLN (30%) and micrometastatic/macrometastatic involvement of SLN (respectively, 38-45 and 62-55%). By contrast, when OSNA was compared to the standard intraoperatory procedure, it was superior in terms of accuracy, prompting the use of this molecular assay as a very valid, and reproducible for intra-operative evaluation of SLN. Further possibilities prompting the use of OSNA range from adhesion to quality control programs, saving of medical time, ability to predict, during surgery, additional nodal metastasis, and molecular bio-banking.

  18. Culture confirmation of gonococcal infection by recall of subjects found to be positive by nucleic acid amplification tests in general practice

    DEFF Research Database (Denmark)

    Møller, Jens Kjølseth

    2010-01-01

    To evaluate a routine notification of general practitioners to recall nucleic acid amplification test (NAAT)-positive subjects for culture of Neisseria gonorrhoeae to confirm gonococcal infection in the community....

  19. Prospective evaluation of the Alere i Influenza A&B nucleic acid amplification versus Xpert Flu/RSV.

    Science.gov (United States)

    Nguyen Van, J C; Caméléna, F; Dahoun, M; Pilmis, B; Mizrahi, A; Lourtet, J; Behillil, S; Enouf, V; Le Monnier, A

    2016-05-01

    The rapid and accurate detection of influenza virus in respiratory specimens is required for optimal management of patients with acute respiratory infections. Because of the variability of the symptoms and the numerous other causes of influenza-like illness, the diagnosis of influenza cannot be made on the basis of clinical criteria alone. Thus, rapid influenza diagnostic tests have been developed such as the Alere i Influenza A&B isothermal nucleic acid assay. We prospectively evaluated the performance of the Alere i Influenza A&B assay in comparison with our routine Xpert Flu/RSV assay. Positive samples were subtyped according to the protocol from the National Influenza Center (Paris, France). A total of 96 respiratory nasal swab samples were analyzed: with both methods, 38 were positive and 56 were negative. Samples were prospectively collected from January 20 to April 8, 2015, from patient (86 adult and 10 pediatric patients) presenting with an influenza-like illness through the French influenza season. In comparison with the Xpert Flu/RSV assay, the overall sensitivity and specificity of the Alere i Influenza A&B assay were 95% and 100%, respectively. Our results indicate that the Alere i Influenza A&B assay has a good overall analytical performance and a high degree of concordance with the PCR-based Xpert Flu/RSV assay. The Alere i Influenza A&B isothermal nucleic acid amplification test is a powerful tool for influenza detection due to its high sensitivity and specificity as well as its ability to generate results within 15min. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Study of reconstruction methods for a time projection chamber with GEM gas amplification system

    Energy Technology Data Exchange (ETDEWEB)

    Diener, R.

    2006-12-15

    A new e{sup +}e{sup -} linear collider with an energy range up to 1TeV is planned in an international collaboration: the International Linear Collider (ILC). This collider will be able to do precision measurements of the Higgs particle and of physics beyond the Standard Model. In the Large Detector Concept (LDC) - which is one proposal for a detector at the ILC - a Time Projection Chamber (TPC) is foreseen as the main tracking device. To meet the requirements on the resolution and to be able to work in the environment at the ILC, the application of new gas amplification technologies in the TPC is necessary. One option is an amplification system based on Gas Electron Multipliers (GEMs). Due to the - in comparison with older technologies - small spatial width of the signals, this technology poses new requirements on the readout structures and the reconstruction methods. In this work, the performance and the systematics of different reconstruction methods have been studied, based on data measured with a TPC prototype in high magnetic fields of up to 4T and data from a Monte Carlo simulation. The latest results of the achievable point resolution are presented and their limitations have been investigated. (orig.)

  1. Study of reconstruction methods for a time projection chamber with GEM gas amplification system

    International Nuclear Information System (INIS)

    Diener, R.

    2006-12-01

    A new e + e - linear collider with an energy range up to 1TeV is planned in an international collaboration: the International Linear Collider (ILC). This collider will be able to do precision measurements of the Higgs particle and of physics beyond the Standard Model. In the Large Detector Concept (LDC) - which is one proposal for a detector at the ILC - a Time Projection Chamber (TPC) is foreseen as the main tracking device. To meet the requirements on the resolution and to be able to work in the environment at the ILC, the application of new gas amplification technologies in the TPC is necessary. One option is an amplification system based on Gas Electron Multipliers (GEMs). Due to the - in comparison with older technologies - small spatial width of the signals, this technology poses new requirements on the readout structures and the reconstruction methods. In this work, the performance and the systematics of different reconstruction methods have been studied, based on data measured with a TPC prototype in high magnetic fields of up to 4T and data from a Monte Carlo simulation. The latest results of the achievable point resolution are presented and their limitations have been investigated. (orig.)

  2. Locked nucleic acid inhibits amplification of contaminating DNA in real-time PCR

    DEFF Research Database (Denmark)

    Hummelshoj, Lone; Ryder, Lars P; Madsen, Hans O

    2005-01-01

    and real-time PCR, the addition of LNA showed blocking of the amplification of genomic XBP1 but not cDNA XBP1. To test the effect of melting temperature (Tm) on the LNA, we investigated the number of LNA nucleotides that could be replaced with DNA nucleotides and still retain the blocking activity. More...

  3. A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings.

    Directory of Open Access Journals (Sweden)

    Paul LaBarre

    2011-05-01

    Full Text Available Molecular assays targeted to nucleic acid (NA markers are becoming increasingly important to medical diagnostics. However, these are typically confined to wealthy, developed countries; or, to the national reference laboratories of developing-world countries. There are many infectious diseases that are endemic in low-resource settings (LRS where the lack of simple, instrument-free, NA diagnostic tests is a critical barrier to timely treatment. One of the primary barriers to the practicality and availability of NA assays in LRS has been the complexity and power requirements of polymerase chain reaction (PCR instrumentation (another is sample preparation.In this article, we investigate the hypothesis that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays. We assess the heater's equivalence to commercially available PCR instruments through the characterization of the temperature profiles produced, and a minimal method comparison. Versions of the prototype for several different isothermal techniques are presented.We demonstrate that an electricity-free heater based on exothermic chemical reactions and engineered phase change materials can successfully incubate isothermal NA amplification assays, and that the results of those assays are not significantly different from ones incubated in parallel in commercially available PCR instruments. These results clearly suggest the potential of the non-instrumented nucleic acid amplification (NINA heater for molecular diagnostics in LRS. When combined with other innovations in development that eliminate power requirements for sample preparation, cold reagent storage, and readout, the NINA heater will comprise part of a kit that should enable electricity-free NA testing for many important analytes.

  4. Colorimetric tests for diagnosis of filarial infection and vector surveillance using non-instrumented nucleic acid loop-mediated isothermal amplification (NINA-LAMP.

    Directory of Open Access Journals (Sweden)

    Catherine B Poole

    Full Text Available Accurate detection of filarial parasites in humans is essential for the implementation and evaluation of mass drug administration programs to control onchocerciasis and lymphatic filariasis. Determining the infection levels in vector populations is also important for assessing transmission, deciding when drug treatments may be terminated and for monitoring recrudescence. Immunological methods to detect infection in humans are available, however, cross-reactivity issues have been reported. Nucleic acid-based molecular assays offer high levels of specificity and sensitivity, and can be used to detect infection in both humans and vectors. In this study we developed loop-mediated isothermal amplification (LAMP tests to detect three different filarial DNAs in human and insect samples using pH sensitive dyes for enhanced visual detection of amplification. Furthermore, reactions were performed in a portable, non-instrumented nucleic acid amplification (NINA device that provides a stable heat source for LAMP. The efficacy of several strand displacing DNA polymerases were evaluated in combination with neutral red or phenol red dyes. Colorimetric NINA-LAMP assays targeting Brugia Hha I repeat, Onchocerca volvulus GST1a and Wuchereria bancrofti LDR each exhibit species-specificity and are also highly sensitive, detecting DNA equivalent to 1/10-1/5000th of one microfilaria. Reaction times varied depending on whether a single copy gene (70 minutes, O. volvulus or repetitive DNA (40 min, B. malayi and W. bancrofti was employed as a biomarker. The NINA heater can be used to detect multiple infections simultaneously. The accuracy, simplicity and versatility of the technology suggests that colorimetric NINA-LAMP assays are ideally suited for monitoring the success of filariasis control programs.

  5. Performance of different mono- and multiplex nucleic acid amplification tests on a multipathogen external quality assessment panel.

    Science.gov (United States)

    Loens, K; van Loon, A M; Coenjaerts, F; van Aarle, Y; Goossens, H; Wallace, P; Claas, E J C; Ieven, M

    2012-03-01

    An external quality assessment (EQA) panel consisting of a total of 48 samples in bronchoalveolar lavage (BAL) fluid or transport medium was prepared in collaboration with Quality Control for Molecular Diagnostics (QCMD) (www.qcmd.org). The panel was used to assess the proficiency of the three laboratories that would be responsible for examining the 6,000 samples to be collected in the GRACE Network of Excellence (www.grace-lrti.org). The main objective was to decide on the best-performing testing approach for the detection of influenza viruses A and B, parainfluenza virus types 1 to 3, respiratory syncytial virus (RSV), human metapneumovirus, coronavirus, rhinovirus, adenovirus, Chlamydophila pneumoniae, Mycoplasma pneumoniae, and Legionella pneumophila by nucleic acid amplification techniques (NAATs). Two approaches were chosen: (i) laboratories testing samples using their in-house procedures for extraction and amplification and (ii) laboratories using their in-house amplification procedures on centrally extracted samples. Furthermore, three commercially available multiplex NAAT tests-the ResPlex (Qiagen GmbH, Hilden, Germany), RespiFinder plus (PathoFinder, Maastricht, The Netherlands), and RespiFinder Smart 21 (PathoFinder) tests-were evaluated by examination of the same EQA panel by the manufacturer. No large differences among the 3 laboratories were noticed when the performances of the assays developed in-house in combination with the in-house extraction procedures were compared. Also, the extraction procedure (central versus local) had little effect on performance. However, large differences in amplification efficacy were found between the commercially available tests; acceptable results were obtained by using the PathoFinder assays.

  6. Loop-mediated isothermal amplification (LAMP) method for detection of genetically modified maize T25.

    Science.gov (United States)

    Xu, Junyi; Zheng, Qiuyue; Yu, Ling; Liu, Ran; Zhao, Xin; Wang, Gang; Wang, Qinghua; Cao, Jijuan

    2013-11-01

    The loop-mediated isothermal amplification (LAMP) assay indicates a potential and valuable means for genetically modified organism (GMO) detection especially for its rapidity, simplicity, and low cost. We developed and evaluated the specificity and sensitivity of the LAMP method for rapid detection of the genetically modified (GM) maize T25. A set of six specific primers was successfully designed to recognize six distinct sequences on the target gene, including a pair of inner primers, a pair of outer primers, and a pair of loop primers. The optimum reaction temperature and time were verified to be 65°C and 45 min, respectively. The detection limit of this LAMP assay was 5 g kg(-1) GMO component. Comparative experiments showed that the LAMP assay was a simple, rapid, accurate, and specific method for detecting the GM maize T25.

  7. Performance of nucleic acid amplification following extraction of 5 milliliters of whole blood for diagnosis of Mycobacterium tuberculosis bacteremia.

    Science.gov (United States)

    Crump, John A; Tuohy, Marion J; Morrissey, Anne B; Ramadhani, Habib O; Njau, Boniface N; Maro, Venance P; Reller, L Barth; Procop, Gary W

    2012-01-01

    To investigate the performance of a nucleic acid amplification test (NAAT) for the diagnosis of Mycobacterium tuberculosis bacteremia, 5-ml aliquots of blood were inoculated into bioMérieux mycobacterial (MB) bottles and incubated, and 5-ml aliquots of blood were extracted and tested by real-time PCR. Of 25 samples from patients with M. tuberculosis bacteremia, 9 (36.0%) were positive and 1 (1.5%) of 66 control samples was positive by NAAT. The NAAT shows promise, but modifications should focus on improving sensitivity.

  8. Multiplex Nucleic Acid Sequence-Based Amplification for Simultaneous Detection of Several Enteric Viruses in Model Ready-To-Eat Foods†

    Science.gov (United States)

    Jean, Julie; D'Souza, Doris H.; Jaykus, Lee-Ann

    2004-01-01

    Human enteric viruses are currently recognized as one of the most important causes of food-borne disease. Implication of enteric viruses in food-borne outbreaks can be difficult to confirm due to the inadequacy of the detection methods available. In this study, a nucleic acid sequence-based amplification (NASBA) method was developed in a multiplex format for the specific, simultaneous, and rapid detection of epidemiologically relevant human enteric viruses. Three previously reported primer sets were used in a single reaction for the amplification of RNA target fragments of 474, 371, and 165 nucleotides for the detection of hepatitis A virus and genogroup I and genogroup II noroviruses, respectively. Amplicons were detected by agarose gel electrophoresis and confirmed by electrochemiluminescence and Northern hybridization. Endpoint detection sensitivity for the multiplex NASBA assay was approximately 10−1 reverse transcription-PCR-detectable units (or PFU, as appropriate) per reaction. When representative ready-to-eat foods (deli sliced turkey and lettuce) were inoculated with various concentrations of each virus and processed for virus detection with the multiplex NASBA method, all three human enteric viruses were simultaneously detected at initial inoculum levels of 100 to 102 reverse transcription-PCR-detectable units (or PFU)/9 cm2 in both food commodities. The multiplex NASBA system provides rapid and simultaneous detection of clinically relevant food-borne viruses in a single reaction tube and may be a promising alternative to reverse transcription-PCR for the detection of viral contamination of foods. PMID:15528524

  9. Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods.

    Science.gov (United States)

    Jean, Julie; D'Souza, Doris H; Jaykus, Lee-Ann

    2004-11-01

    Human enteric viruses are currently recognized as one of the most important causes of food-borne disease. Implication of enteric viruses in food-borne outbreaks can be difficult to confirm due to the inadequacy of the detection methods available. In this study, a nucleic acid sequence-based amplification (NASBA) method was developed in a multiplex format for the specific, simultaneous, and rapid detection of epidemiologically relevant human enteric viruses. Three previously reported primer sets were used in a single reaction for the amplification of RNA target fragments of 474, 371, and 165 nucleotides for the detection of hepatitis A virus and genogroup I and genogroup II noroviruses, respectively. Amplicons were detected by agarose gel electrophoresis and confirmed by electrochemiluminescence and Northern hybridization. Endpoint detection sensitivity for the multiplex NASBA assay was approximately 10(-1) reverse transcription-PCR-detectable units (or PFU, as appropriate) per reaction. When representative ready-to-eat foods (deli sliced turkey and lettuce) were inoculated with various concentrations of each virus and processed for virus detection with the multiplex NASBA method, all three human enteric viruses were simultaneously detected at initial inoculum levels of 10(0) to 10(2) reverse transcription-PCR-detectable units (or PFU)/9 cm2 in both food commodities. The multiplex NASBA system provides rapid and simultaneous detection of clinically relevant food-borne viruses in a single reaction tube and may be a promising alternative to reverse transcription-PCR for the detection of viral contamination of foods.

  10. Detection of HIV-1 p24 Gag in plasma by a nanoparticle-based bio-barcode-amplification method.

    Science.gov (United States)

    Kim, Eun-Young; Stanton, Jennifer; Korber, Bette T M; Krebs, Kendall; Bogdan, Derek; Kunstman, Kevin; Wu, Samuel; Phair, John P; Mirkin, Chad A; Wolinsky, Steven M

    2008-06-01

    Detection of HIV-1 in patients is limited by the sensitivity and selectivity of available tests. The nanotechnology-based bio-barcode-amplification method offers an innovative approach to detect specific HIV-1 antigens from diverse HIV-1 subtypes. We evaluated the efficacy of this protein-detection method in detecting HIV-1 in men enrolled in the Chicago component of the Multicenter AIDS Cohort Study (MACS). The method relies on magnetic microparticles with antibodies that specifically bind the HIV-1 p24 Gag protein and nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the microparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated to remove the conjugated barcode DNA. The DNA barcodes (hundreds per target) were identified by a nanoparticle-based detection method that does not rely on PCR. Of 112 plasma samples from HIV-1-infected subjects, 111 were positive for HIV-1 p24 Gag protein (range: 0.11-71.5 ng/ml of plasma) by the bio-barcode-amplification method. HIV-1 p24 Gag protein was detected in only 23 out of 112 men by the conventional ELISA. A total of 34 uninfected subjects were negative by both tests. Thus, the specificity of the bio-barcode-amplification method was 100% and the sensitivity 99%. The bio-barcode-amplification method detected HIV-1 p24 Gag protein in plasma from all study subjects with less than 200 CD4(+) T cells/microl of plasma (100%) and 19 out of 20 (95%) HIV-1-infected men who had less than 50 copies/ml of plasma of HIV-1 RNA. In a separate group of 60 diverse international isolates, representative of clades A, B, C and D and circulating recombinant forms CRF01_AE and CRF02_AG, the bio-barcode-amplification method identified the presence of virus correctly. The bio-barcode-amplification method was superior to the conventional ELISA assay for the detection of HIV-1 p24 Gag protein in plasma with a breadth of coverage for diverse

  11. Comparison between quantitative nucleic acid sequence-based amplification, real-time reverse transcriptase PCR, and real-time PCR for quantification of Leishmania parasites

    NARCIS (Netherlands)

    van der Meide, Wendy; Guerra, Jorge; Schoone, Gerard; Farenhorst, Marit; Coelho, Leila; Faber, William; Peekel, Inge; Schallig, Henk

    2008-01-01

    DNA or RNA amplification methods for detection of Leishmania parasites have advantages regarding sensitivity and potential quantitative characteristics in comparison with conventional diagnostic methods but are often still not routinely applied. However, the use and application of molecular assays

  12. One-step nucleic acid amplification: the possible value in assessing sentinel lymph node metastasis during mastectomy

    Directory of Open Access Journals (Sweden)

    Hunter-Smith AE

    2018-01-01

    Full Text Available Alison E Hunter-Smith, Zenon Rayter Breast Surgery Unit, Bristol Breast Care Centre, North Bristol NHS Trust, Southmead Hospital, Westbury-on-Trym, Bristol, UK Abstract: Breast cancer is the most common cancer in women, worldwide, and 1,400 deaths per day are attributed to it. The success of national screening programs has seen breast cancers being diagnosed at an earlier stage. With conservative surgery to the breast demonstrating equivalent long-term outcomes, the last 10 years have seen a growing interest in the safety of less invasive management for the axilla in breast cancer patients. One-step nucleic acid amplification (OSNA is a validated, reliable, and efficient tool in identifying micro- and macro-metastases intraoperatively. It is the most widely used intraoperative analysis tool within the United Kingdom, and is employed by over 320 units across Europe and Asia. Recent evidence from the AMAROS, IBCSG 23-01, and ACOSOG Z0011 trials has changed surgical practice in managing the axilla of patients with breast cancer. We propose a clinical algorithm demonstrating the role of OSNA as an intraoperative analysis tool in today’s management of breast cancer as well as prospects for the future use of OSNA. Keywords: breast cancer, sentinel lymph node, intraoperative assessment, one-stop nucleic acid amplification, mastectomy

  13. Molecular detection of genotype II grass carp reovirus based on nucleic acid sequence-based amplification combined with enzyme-linked immunosorbent assay (NASBA-ELISA).

    Science.gov (United States)

    Zeng, Weiwei; Yao, Wei; Wang, Yingying; Li, Yingying; Bermann, Sven M; Ren, Yan; Shi, Cunbin; Song, Xinjian; Huang, Qiwen; Zheng, Shuchen; Wang, Qing

    2017-05-01

    Grass carp reovirus (GCRV) is the causative agent of the grass carp hemorrhagic disease that has resulted in severe economic losses in the grass carp (Ctenopharyngodon idella) farming industry in China. Early diagnosis and vaccine administration are important priorities for GCRV control. In this study, a nucleic acid sequence-based amplification with enzyme-linked immunosorbent assay (NASBA-ELISA) was developed for to detect genotype II GCRV (GCRV- II). Primers specifically targeting viral RNA genome segment 6 were utilized for amplification in an isothermal digoxigenin-labeling NASBA process, resulting in DIG-labeled RNA amplicons. The amplicons were hybridized to specific biotinylated DNA probes and the products were detected colorimetrically using horseradish peroxidase and a microplate reader. The new method is able to detect GCRV at 14 copies/μL within 5h and had a diagnostic sensitivity and a specificity of 100% when GCRV-II and non-target virus were tested. This NASBA-ELISA was evaluated using a panel of clinical samples (n=103) to demonstrate that it is a rapid, effective and sensitive method for GCRV detection in grass carp aquaculture. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Study of C-MYC amplification and expression in Iranian gastric cancer samples using CISH and IHC methods

    Directory of Open Access Journals (Sweden)

    Malihea Khaleghian

    2015-01-01

    Full Text Available Background: Gastric cancer is the fourth most frequent malignancy and the second cause of cancer-related mortality worldwide. It has been suggested that in gastric carcinogenesis, the C-MYC gene has an important function. The objective of this study is to establish the preference of Chromogenic in situ hybridization (CISH and Immunohistochemistry (IHC in the diagnosis and prognosis of gastric cancer. Materials and Methods: Samples comprised of 50 randomly selected patients of whom 40 were male and 10 female. To evaluate the MYC copy number and its protein expression, CISH and IHC analyses were performed for 50 gastric adenocarcinomas, in Iran. Results: The location of the tumor in 64% of the patients was the fundus, and in 72% of patients, the tumors were of a diffuse type; 22 samples showed no amplification, and 28 samples were with amplification. MYC immunoreactivity was observed in 13 samples. Twelve samples showed both MYC amplification and MYC immunoreactivity. In addition, among the 28 CISH+ samples, 12 samples had positive signals for IHC and 16 samples had negative signals for IHC. A majority of the IHC-negative patients had no amplification, but only one patient with IHC positive had no amplification. Conclusion: Our conclusion was that for the management and treatment of gastric cancer, and for special attention of clinicians, for prognosis and tumor progression, the CISH was a better and more feasible test than IHC, in regard to the sensitivity and specificity.

  15. Evaluation on the effects of ageing factor, sampling and preservation methods on Asiatic black bear (Ursus thibetanus noninvasive DNA amplification

    Directory of Open Access Journals (Sweden)

    Chih-Chin SHIH

    2017-11-01

    Full Text Available Noninvasive genetic sampling allows studying wildlife without having to catch, handle or even observe individuals. In this study, factors which may affect the quality of noninvasive samples of Asiatic black bear (Ursus thibetanus in the subtropical areas were identified. We collected hair and faecal samples from captive Asiatic black bears and quantitatively evaluated the effects of hair age (from fresh to 60 days, faeces age (from fresh to 14 days, faeces sampling locations (i.e. sample collected from either the surface, inside or a mixture of both the surface and inside of faeces, and faeces preservation methods (frozen or kept at room temperature in 95% ethanol on amplification success rates of mitochondrial DNA fragments of different sizes (450bp, 900bp, and 1600bp. The results showed that the amplification success rates decreased with sample age and amplicon size in both hair and faecal DNA. In subtropical environment, there was no significant difference between amplification success of DNA extracted from fresh and 7-day-old samples of either the hair or faeces. The amplification success rates were not influenced by sampling location of faeces. For faeces preserved in 95% ethanol, the amplification success appeared unaffected by frozen at -20 °C or kept at room temperature in shorter mtDNA fragments, but was significantly influenced when amplicon size was 1600bp. The results of this study will reinforce the optimization of noninvasive sampling approaches in Asiatic black bear research, especially in the subtropics.

  16. Dual-cyclical nucleic acid strand-displacement polymerization based signal amplification system for highly sensitive determination of p53 gene.

    Science.gov (United States)

    Xu, Jianguo; Wu, Zai-Sheng; Li, Hongling; Wang, Zhenmeng; Le, Jingqing; Zheng, Tingting; Jia, Lee

    2016-12-15

    In the present study, we proposed a novel dual-cyclical nucleic acid strand-displacement polymerization (dual-CNDP) based signal amplification system for highly sensitive determination of tumor suppressor genes. The system primarily consisted of a signaling hairpin probe (SHP), a label-free hairpin probe (LHP) and an initiating primer (IP). The presence of target DNA was able to induce one CNDP through continuous process of ligation, polymerization and nicking, leading to extensively accumulation of two nicked triggers (NT1 and NT2). Intriguingly, the NT1 could directly hybridize SHP, while the NT2 could act as the target analog to induce another CNDP. The resulting dual-CNDP contributed the striking signal amplification, and only a very weak blank noise existed since the ligation template of target was not involved. In this case, the target could be detected in a wide linear range (5 orders of magnitude), and a low detection limit (78 fM) was obtained, which is superior to most of the existing fluorescent methods. Moreover, the dual-CNDP sensing system provided a high selectivity towards target DNA against mismatched target and was successfully applied to analysis of target gene extracted from cancer cells or in human serum-contained samples, indicating its great potential for practical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Improved Method for Direct Detection of Environmental Microorganisms Using an Amplification of 16S rDNA Region

    Science.gov (United States)

    Tsujimura, M.; Akutsu, J.; Zhang, Z.; Sasaki, M.; Tajima, H.; Kawarabayasi, Y.

    2004-12-01

    The thermostable proteins or enzymes were expected to be capable to be utilized in many areas of industries. Many thermophilic microorganisms, which possess the thermostable proteins or enzymes, were identified from the extreme environment. However, many unidentified and uncultivable microorganisms are still remaining in the environment on the earth. It is generally said that the cultivable microorganisms are less than 1% of entire microorganisms living in the earth, remaining over 99% are still uncultivable. As an approach to the uncultivable microorganisms, the PCR amplification of 16S rDNA region using primer sets designed from the conserved region has been generally utilized for detection and community analysis of microorganism in the environment. However, the facts, that PCR amplification introduces the mutation in the amplified DNA fragment and efficiency of PCR amplification is depend on the sequences of primer sets, indicated that the improving of PCR analysis was necessary for more correct detection of microorganisms. As the result of evaluation for the quality of DNA polymerases, sequences of primers used for amplification and conditions of PCR amplification, the DNA polymerase, the primer set and the conditions for amplification, which did not amplify the DNA fragment from the DNA contaminated within the DNA polymerase itself, were successfully selected. Also the rate of mutation in the DNA fragment amplified was evaluated using this conditions and the genomic DNA from cultivable microbes as a template. The result indicated the rate of mutation introduced by PCR was approximately 0.1% to 0.125%. The improved method using these conditions and error rate calculated was applied for the analysis of microorganisms in the geothermal environment. The result indicated that four kinds of dominant microorganisms, including both of bacteria and archaea, were alive within soil in the hot spring in Tohoku Area. We would like to apply this improved method to detection

  18. Evaluation of a loop-mediated isothermal amplification (LAMP) method for rapid on-site detection of horse meat

    NARCIS (Netherlands)

    Aartse, Aafke; Scholtens-Toma, Ingrid; A, van der Hans J.G.; Boersma-Greve, Monique M.; Prins, Theo W.; Ginkel, van Leen A.; Kok, Esther J.; Bovee, Toine F.H.

    2017-01-01

    Detection of horse DNA by loop-mediated isothermal amplification (LAMP) seems one of the most promising methods to meet the criteria of fast, robust, cost efficient, specific, and sensitive on-site detection. In the present study an assessment of the specificity and sensitivity of the LAMP horse

  19. Rapid Detection of Prunus Necrotic Ringspot Virus by Reverse Transcription-cross-priming Amplification Coupled with Nucleic Acid Test Strip Cassette.

    Science.gov (United States)

    Huo, Ya-Yun; Li, Gui-Fen; Qiu, Yan-Hong; Li, Wei-Min; Zhang, Yong-Jiang

    2017-11-23

    Prunus necrotic ringspot virus (PNRSV) is one of the most devastating viruses to Prunus spp. In this study, we developed a diagnostic system RT-CPA-NATSC, wherein reverse transcription-cross-priming amplification (RT-CPA) is coupled with nucleic acid test strip cassette (NATSC), a vertical flow (VF) visualization, for PNRSV detection. The RT-CPA-NATSC assay targets the encoding gene of the PNRSV coat protein with a limit of detection of 72 copies per reaction and no cross-reaction with the known Prunus pathogenic viruses and viroids, demonstrating high sensitivity and specificity. The reaction is performed on 60 °C and can be completed less than 90 min with the prepared template RNA. Field sample test confirmed the reliability of RT-CPA-NATSC, indicating the potential application of this simple and rapid detection method in routine test of PNRSV.

  20. A rapid Salmonella detection method involving thermophilic helicase-dependent amplification and a lateral flow assay.

    Science.gov (United States)

    Du, Xin-Jun; Zhou, Tian-Jiao; Li, Ping; Wang, Shuo

    2017-08-01

    Salmonella is a major foodborne pathogen that is widespread in the environment and can cause serious human and animal disease. Since conventional culture methods to detect Salmonella are time-consuming and laborious, rapid and accurate techniques to detect this pathogen are critically important for food safety and diagnosing foodborne illness. In this study, we developed a rapid, simple and portable Salmonella detection strategy that combines thermophilic helicase-dependent amplification (tHDA) with a lateral flow assay to provide a detection result based on visual signals within 90 min. Performance analyses indicated that the method had detection limits for DNA and pure cultured bacteria of 73.4-80.7 fg and 35-40 CFU, respectively. Specificity analyses showed no cross reactions with Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Enterobacter aerogenes, Shigella and Campylobacter jejuni. The results for detection in real food samples showed that 1.3-1.9 CFU/g or 1.3-1.9 CFU/mL of Salmonella in contaminated chicken products and infant nutritional cereal could be detected after 2 h of enrichment. The same amount of Salmonella in contaminated milk could be detected after 4 h of enrichment. This tHDA-strip can be used for the rapid detection of Salmonella in food samples and is particularly suitable for use in areas with limited equipment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Colony-PCR Is a Rapid Method for DNA Amplification of Hyphomycetes

    Directory of Open Access Journals (Sweden)

    Georg Walch

    2016-04-01

    Full Text Available Fungal pure cultures identified with both classical morphological methods and through barcoding sequences are a basic requirement for reliable reference sequences in public databases. Improved techniques for an accelerated DNA barcode reference library construction will result in considerably improved sequence databases covering a wider taxonomic range. Fast, cheap, and reliable methods for obtaining DNA sequences from fungal isolates are, therefore, a valuable tool for the scientific community. Direct colony PCR was already successfully established for yeasts, but has not been evaluated for a wide range of anamorphic soil fungi up to now, and a direct amplification protocol for hyphomycetes without tissue pre-treatment has not been published so far. Here, we present a colony PCR technique directly from fungal hyphae without previous DNA extraction or other prior manipulation. Seven hundred eighty-eight fungal strains from 48 genera were tested with a success rate of 86%. PCR success varied considerably: DNA of fungi belonging to the genera Cladosporium, Geomyces, Fusarium, and Mortierella could be amplified with high success. DNA of soil-borne yeasts was always successfully amplified. Absidia, Mucor, Trichoderma, and Penicillium isolates had noticeably lower PCR success.

  2. Novel degenerate PCR method for whole genome amplification applied to Peru Margin (ODP Leg 201 subsurface samples

    Directory of Open Access Journals (Sweden)

    Amanda eMartino

    2012-01-01

    Full Text Available A degenerate PCR-based method of whole-genome amplification, designed to work fluidly with 454 sequencing technology, was developed and tested for use on deep marine subsurface DNA samples. The method, which we have called Random Amplification Metagenomic PCR (RAMP, involves the use of specific primers from Roche 454 amplicon sequencing, modified by the addition of a degenerate region at the 3’ end. It utilizes a PCR reaction, which resulted in no amplification from blanks, even after 50 cycles of PCR. After efforts to optimize experimental conditions, the method was tested with DNA extracted from cultured E. coli cells, and genome coverage was estimated after sequencing on three different occasions. Coverage did not vary greatly with the different experimental conditions tested, and was around 62% with a sequencing effort equivalent to a theoretical genome coverage of 14.10X. The GC content of the sequenced amplification product was within 2% of the predicted values for this strain of E. coli. The method was also applied to DNA extracted from marine subsurface samples from ODP Leg 201 site 1229 (Peru Margin, and results of a taxonomic analysis revealed microbial communities dominated by Proteobacteria, Chloroflexi, Firmicutes, Euryarchaeota, and Crenarchaeota, among others. These results were similar to those obtained previously for those samples; however, variations in the proportions of taxa show that community analysis can be sensitive to both the amplification technique used and the method of assigning sequences to taxonomic groups. Overall, we find that RAMP represents a valid methodology for amplifying metagenomes from low biomass samples.

  3. Novel Degenerate PCR Method for Whole-Genome Amplification Applied to Peru Margin (ODP Leg 201) Subsurface Samples

    Science.gov (United States)

    Martino, Amanda J.; Rhodes, Matthew E.; Biddle, Jennifer F.; Brandt, Leah D.; Tomsho, Lynn P.; House, Christopher H.

    2011-01-01

    A degenerate polymerase chain reaction (PCR)-based method of whole-genome amplification, designed to work fluidly with 454 sequencing technology, was developed and tested for use on deep marine subsurface DNA samples. While optimized here for use with Roche 454 technology, the general framework presented may be applicable to other next generation sequencing systems as well (e.g., Illumina, Ion Torrent). The method, which we have called random amplification metagenomic PCR (RAMP), involves the use of specific primers from Roche 454 amplicon sequencing, modified by the addition of a degenerate region at the 3′ end. It utilizes a PCR reaction, which resulted in no amplification from blanks, even after 50 cycles of PCR. After efforts to optimize experimental conditions, the method was tested with DNA extracted from cultured E. coli cells, and genome coverage was estimated after sequencing on three different occasions. Coverage did not vary greatly with the different experimental conditions tested, and was around 62% with a sequencing effort equivalent to a theoretical genome coverage of 14.10×. The GC content of the sequenced amplification product was within 2% of the predicted values for this strain of E. coli. The method was also applied to DNA extracted from marine subsurface samples from ODP Leg 201 site 1229 (Peru Margin), and results of a taxonomic analysis revealed microbial communities dominated by Proteobacteria, Chloroflexi, Firmicutes, Euryarchaeota, and Crenarchaeota, among others. These results were similar to those obtained previously for those samples; however, variations in the proportions of taxa identified illustrates well the generally accepted view that community analysis is sensitive to both the amplification technique used and the method of assigning sequences to taxonomic groups. Overall, we find that RAMP represents a valid methodology for amplifying metagenomes from low-biomass samples. PMID:22319519

  4. HER2 gene amplification in patients with prostate cancer: Evaluating a CISH-based method.

    Science.gov (United States)

    Sharifi, Nazanin; Salmaninejad, Arash; Ferdosi, Samira; Bajestani, Abolfazl Nesaei; Khaleghiyan, Malihe; Estiar, Mehrdad Asghari; Jamali, Mansour; Nowroozi, Mohammad Reza; Shakoori, Abbas

    2016-12-01

    Prostate cancer (PCa) is one of the most widespread malignancies in the world. The role of the human epidermal growth factor receptor 2 (HER2) in the pathogenesis and progression of human PCa remains poorly understood. In contradiction with breast cancer, studies on HER2 overexpression and gene amplification in PCa have produced varying results, although the HER2 oncogene has been implicated in the biology of numerous tumor types, and serves as a prognostic marker and therapeutic target in breast cancer. Technical challenges are considered the main reasons for data discrepancies. Amplification of the HER2 gene has previously been reported in PCa, in which it was associated with tumor progression. The present study aimed to evaluate the prevalence and clinical significance of HER2 amplification in PCa. A total of 32 biopsy samples obtained from human prostate adenocarcinomas were evaluated by chromogenic in situ hybridization (CISH) to determine the frequency of patients with HER2 gene amplifications. High copy numbers of HER2 were detected in 19 of the prostate tumors analyzed. The results of the present study suggested that, in patients without amplification of HER2, high levels of prostate-specific antigen or a high Gleason score were not significantly correlated with a high pathologic stage. Furthermore, amplification levels of the HER2 gene were directly associated with pathologic stage in patients with PCa. Therefore, the potential use of HER2 as a prognostic factor or therapeutic target for PCa warrants further study.

  5. Direct quantification of human cytomegalovirus immediate-early and late mRNA levels in blood of lung transplant recipients by competitive nucleic acid sequence-based amplification

    NARCIS (Netherlands)

    Greijer, AE; Verschuuren, EAM; Harmsen, MC; Dekkers, CAJ; Adriaanse, HMA; The, TH; Middeldorp, JM

    The dynamics of active human cytomegalovirus (HCMV) infection was monitored by competitive nucleic acid sequence-based amplification (NASBA) assays for quantification of IE1 (UL123) and pp67 (UL65) mRNA expression levels In the blood of patients after lung transplantation. RNA was isolated from 339

  6. Development and implementation of real-time nucleic acid amplification for the detection of enterovirus infections in comparison to rapid culture of various clinical specimens

    NARCIS (Netherlands)

    van Doornum, G J J; Schutten, Martin; Voermans, J; Guldemeester, G J J; Niesters, H G M

    2007-01-01

    Several real-time PCR and nucleic acid sequence-based amplification (NASBA) primer pairs and a modified real-time PCR primer pair for the detection of enteroviruses were compared. The modified real-time PCR primer pair was evaluated on clinical samples in comparison with cell culture using the

  7. Lab-on-capillary: a rapid, simple and quantitative genetic analysis platform integrating nucleic acid extraction, amplification and detection.

    Science.gov (United States)

    Fu, Yu; Zhou, Xiaoming; Xing, Da

    2017-12-05

    In this work, we describe for the first time a genetic diagnosis platform employing a polydiallyldimethylammonium chloride (PDDA)-modified capillary and a liquid-based thermalization system for rapid, simple and quantitative DNA analysis with minimal user interaction. Positively charged PDDA is modified on the inner surface of the silicon dioxide capillary by using an electrostatic self-assembly approach that allows the negatively charged DNA to be separated from the lysate in less than 20 seconds. The capillary loaded with the PCR mix is incorporated in the thermalization system, which can achieve on-site real-time PCR. This system is based on the circulation of pre-heated liquids in the chamber, allowing for high-speed thermalization of the capillary and fast amplification. Multiple targets can be simultaneously analysed with multiplex spatial melting. Starting with live Escherichia coli (E. coli) cells in milk, as a realistic sample, the current method can achieve DNA extraction, amplification, and detection within 40 min.

  8. Equipment-free nucleic acid extraction and amplification on a simple paper disc for point-of-care diagnosis of rotavirus A.

    Science.gov (United States)

    Ye, Xin; Xu, Jin; Lu, Lijuan; Li, Xinxin; Fang, Xueen; Kong, Jilie

    2018-08-14

    The use of paper-based methods for clinical diagnostics is a rapidly expanding research topic attracting a great deal of interest. Some groups have attempted to realize an integrated nucleic acid test on a single microfluidic paper chip, including extraction, amplification, and readout functions. However, these studies were not able to overcome complex modification and fabrication requirements, long turn-around times, or the need for sophisticated equipment like pumps, thermal cyclers, or centrifuges. Here, we report an extremely simple paper-based test for the point-of-care diagnosis of rotavirus A, one of the most common pathogens that causes pediatric gastroenteritis. This paper-based test could perform nucleic acid extraction within 5 min, then took 25 min to amplify the target sequence, and the result was visible to the naked eye immediately afterward or quantitative by the UV-Vis absorbance. This low-cost method does not require extra equipment and is easy to use either in a lab or at the point-of-care. The detection limit for rotavirus A was found to be 1 × 10 3 copies/mL. In addition, 100% sensitivity and specificity were achieved when testing 48 clinical stool samples. In conclusion, the present paper-based test fulfills the main requirements for a point-of-care diagnostic tool, and has the potential to be applied to disease prevention, control, and precision diagnosis. Copyright © 2018 Elsevier B.V. All rights reserved.

  9. Identifying the plant-associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery

    Energy Technology Data Exchange (ETDEWEB)

    Jackrel, Sara L. [Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street Chicago IL 60637 USA; Owens, Sarah M. [Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue Lemont IL 60439 USA; Gilbert, Jack A. [Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue Lemont IL 60439 USA; The Microbiome Center, Department of Surgery, The University of Chicago, 5841 S Maryland Ave Chicago IL 60637 USA; Pfister, Catherine A. [Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street Chicago IL 60637 USA

    2017-01-25

    Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robust method for assessing animal-associated microbiota, Proteobacterial 16S rRNA binds to the chloroplast-blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14-bp sequence in the Proteobacteria that matches the 17-bp chloroplast-blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14-bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle-blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n-mer oligonucleotides of each PNA sequence.

  10. Development and Comparison of a Rapid Isothermal Nucleic Acid Amplification Test for Typing of Herpes Simplex Virus Types 1 and 2 on a Portable Fluorescence Detector

    Science.gov (United States)

    Tong, Yanhong; McCarthy, Kaitlin; Kong, Huimin; Lemieux, Bertrand

    2013-01-01

    We have developed a rapid and simple molecular test, the IsoGlow HSV Typing assay, for the detection and typing of herpes simplex virus (type 1 and 2) from genital or oral lesions. Clinical samples suspended in viral transport mediums are simply diluted and then added to a helicase-dependent amplification master mix. The amplification and detection were performed on a portable fluorescence detector called the FireFly instrument. Detection of amplification products is based on end-point analysis using cycling probe technology. An internal control nucleic acid was included in the amplification master mix to monitor the presence of amplification inhibitors in the samples. Because the device has only two fluorescence detection channels, two strategies were developed and compared to detect the internal control template: internal control detected by melting curve analysis using a dual-labeled probe, versus internal control detection using end-point fluorescence release by a CPT probe at a lower temperature. Both have a total turnaround time of about 1 hour. Clinical performance relative to herpes viral culture was evaluated using 176 clinical specimens. Both formats of the IsoGlow HSV typing assay had sensitivities comparable to that of the Food and Drug Administration–cleared IsoAmp HSV (BioHelix Corp., Beverly MA) test and specificity for the two types of HSV comparable to that of ELVIS HSV (Diagnostic Hybrids, Athens, OH). PMID:22951487

  11. A service evaluation of the Gen-Probe APTIMA nucleic acid amplification test for Trichomonas vaginalis: should it change whom we screen for infection?

    Science.gov (United States)

    Hathorn, Emma; Ng, Andrea; Page, Matthew; Hodson, James; Gaydos, Charlotte; Ross, Jonathan D C

    2015-01-01

    Objective A service evaluation of the new Gen-Probe APTIMA nucleic acid amplification test was performed to determine the prevalence of Trichomonas vaginalis (TV) infection in a UK sexual health clinic and identify risk factors to inform an appropriate TV screening strategy. Method Unselected patients presenting with a new clinical episode were offered TV testing with Gen Probe transcription-mediated amplification (TV TMA) in addition to routine sexually transmitted infection screening. Asymptomatic females provided a self-collected vulvovaginal specimen and asymptomatic men a first-void urine sample. Symptomatic patients were examined and a urethral swab taken from men and two posterior vaginal swabs from females; one for culture and one for TV TMA testing. Demographic and clinical data were collected on all patients positive for TV infection and 100 randomly selected TV-negative controls. Results 3503 patients underwent TV TMA testing during the evaluation period. The prevalence of TV infection was 21/1483, 1.4% (95% CI 0.9% to 2.2%) in men and 72/2020, 3.6% (95% CI 2.8% to 4.5%) in women. The rate of TV positivity was higher in Black Caribbean patients compared with Caucasian patients (men 5.4% vs 0.1%, pwomen 9.0% vs 1.2%, pTV TMA detected an additional 16 infections (38%) in symptomatic women compared with culture. Conclusions While screening all patients with TV TMA will identify more TV infections, the UK prevalence remains low and this approach is unlikely to be cost effective. In addition to testing symptomatic patients, targeted testing of high-risk asymptomatic groups using TV TMA should be considered. PMID:25170162

  12. Linear and exponential TAIL-PCR: a method for efficient and quick amplification of flanking sequences adjacent to Tn5 transposon insertion sites.

    Science.gov (United States)

    Jia, Xianbo; Lin, Xinjian; Chen, Jichen

    2017-11-02

    Current genome walking methods are very time consuming, and many produce non-specific amplification products. To amplify the flanking sequences that are adjacent to Tn5 transposon insertion sites in Serratia marcescens FZSF02, we developed a genome walking method based on TAIL-PCR. This PCR method added a 20-cycle linear amplification step before the exponential amplification step to increase the concentration of the target sequences. Products of the linear amplification and the exponential amplification were diluted 100-fold to decrease the concentration of the templates that cause non-specific amplification. Fast DNA polymerase with a high extension speed was used in this method, and an amplification program was used to rapidly amplify long specific sequences. With this linear and exponential TAIL-PCR (LETAIL-PCR), we successfully obtained products larger than 2 kb from Tn5 transposon insertion mutant strains within 3 h. This method can be widely used in genome walking studies to amplify unknown sequences that are adjacent to known sequences.

  13. A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification.

    Directory of Open Access Journals (Sweden)

    Saharnaz Bigdeli

    Full Text Available Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroides cells were diluted in alginate polymer and sprayed into microdroplets using a fingertip aerosol sprayer. The encapsulated cells were lysed and subjected either to conventional PCR, or whole genome amplification using either multiple displacement amplification (MDA or a two-step PCR protocol. Microscopic examination after PCR showed that the lumen of the occupied microspheres contained fluorescently stained DNA product, but multiple displacement amplification with phi29 produced only a small number of polymerase colonies. The 2-step WGA protocol was successful in generating fluorescent material, and quantitative PCR from DNA extracted from aliquots of microspheres suggested that the copy number inside the microspheres was amplified up to 3 orders of magnitude. Microspheres containing fluorescent material were sorted by a dilution series and screened with a fluorescent plate reader to identify single microspheres. The DNA was extracted from individual isolates, re-amplified with full-length sequencing adapters, and then a single isolate was sequenced using the Illumina MiSeq platform. After filtering the reads, the only sequences that collectively matched a genome in the NCBI nucleotide database belonged to R. sphaeroides. This demonstrated that sequencing-ready DNA could be generated from the contents of a single microsphere without culturing. However, the 2-step WGA strategy showed limitations in terms of low genome coverage and an uneven frequency distribution of reads across the genome. This paper offers a simple method for embedding cells in alginate microspheres and performing PCR on isolated

  14. Nucleic acid detection system and method for detecting influenza

    Science.gov (United States)

    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. A cascade autocatalytic strand displacement amplification and hybridization chain reaction event for label-free and ultrasensitive electrochemical nucleic acid biosensing.

    Science.gov (United States)

    Chen, Zhiqiang; Liu, Ying; Xin, Chen; Zhao, Jikuan; Liu, Shufeng

    2018-04-23

    Herein, an autocatalytic strand displacement amplification (ASDA) strategy was proposed for the first time, which was further ingeniously coupled with hybridization chain reaction (HCR) event for the isothermal, label-free and multiple amplification toward nucleic acid detection. During the ASDA module, the target recognition opens the immobilized hairpin probe (IP) and initiates the annealing of the auxiliary DNA strand (AS) with the opened IP for the successive polymerization and nicking reaction in the presence of DNA polymerase and nicking endonuclease. This induces the target recycling and generation of a large amount of intermediate DNA sequences, which can be used as target analogy to execute the autocatalytic strand displacement amplification. Simultaneously, the introduced AS strand can propagate the HCR between two hairpins (H1 and H2) to form a linear DNA concatamer with cytosine (C)-rich loop region, which can facilitate the in-situ synthesis of silver nanoclusters (AgNCs) as electrochemical tags for further amplification toward target responses. With current cascade ASDA and HCR strategy, the detection of target DNA could be achieved with a low detection limit of about 0.16 fM and a good selectivity. The developed biosensor also exhibits the distinct advantages of flexibility and simplicity in probe design and biosensor fabrication, and label-free electrochemical detection, thus opens a promising avenue for the detection of nucleic acid with low abundance in bioanalysis and clinical biomedicine. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Direct method for the periodic amplification of a soliton in an optical fibre link with loss

    International Nuclear Information System (INIS)

    Li Lu; Xue Wenrui; Xu Zhiyong; Li Zhonghao; Zhou Guosheng

    2003-01-01

    A direct approach is applied to the periodic amplification of a soliton in an optical fibre link with loss. In a single soliton case, the adiabatic solution and first-order correction are given for the system. The apparent advantage of this direct approach is that it not only presents the slow evolution of soliton parameters, but also the perturbation-induced radiation, and can be easily used to investigate the system of dispersion management with periodically varying dispersion and other fields

  17. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. II. Isothermal signal amplification in process of DNA analysis by minisequencing].

    Science.gov (United States)

    Dmitrienko, E V; Khomiakova, E A; Pyshnaia; Bragin, A G; Vedernikov, V E; Pyshnyĭ, D V

    2010-01-01

    The isothermal amplification of reporter signal via limited probe extension (minisequencing) upon hybridization of nucleic acids has been studied. The intensity of reporter signal has been shown to increase due to enzymatic labeling of multiple probes upon consecutive hybridization with one DNA template both in homophase and heterophase assays using various kinds of detection signal: radioisotope label, fluorescent label, and enzyme-linked assay. The kinetic scheme of the process has been proposed and kinetic parameters for each step have been determined. The signal intensity has been shown to correlate with physicochemical characteristics of both complexes: probe/DNA and product/DNA. The maximum intensity has been observed at minimal difference between the thermodynamic stability of these complexes, provided the reaction temperature has been adjusted near their melting temperature values; rising or lowering the reaction temperature reduces the amount of reporting product. The signal intensity has been shown to decrease significantly upon hybridization with the DNA template containing single-nucleotide mismatches. Limited probe extension assay is useful not only for detection of DNA template but also for its quantitative characterization.

  18. Detecting asymptomatic Trichomonas vaginalis in females using the BD ProbeTec™ Trichomonas vaginalis Qx nucleic acid amplification test.

    Science.gov (United States)

    Lord, Emily; Newnham, Tana; Dorrell, Lucy; Jesuthasan, Gerald; Clarke, Lorraine; Jeffery, Katie; Sherrard, Jackie

    2017-03-01

    Trichomonas vaginalis (TV) rates in women are increasing and many are asymptomatic. Nucleic acid amplification tests (NAATs) are becoming the 'gold standard' for diagnosis. We aimed to establish our asymptomatic TV rates by testing all women attending Oxfordshire's Sexual Health service, regardless of symptoms, using the BD ProbeTec™ TV Q x NAATs (BDQ x ). During BDQ x 's verification process, the sensitivity and specificity were calculated using results of 220 endocervical samples from symptomatic women, compared with culture. BDQ x was subsequently implemented and prospectively evaluated over 6 months in female attendees. Wet mount microscopy was also performed in symptomatics. Demographic and clinical characteristics of those diagnosed were analysed. From 220 samples tested by BDQ x and culture: 5 were positive on both and one solely using BDQ x , giving a sensitivity and specificity of 100% and 99.53%, respectively. In the prospective cohort, of 5775 BDQ x tests, 33 (0.57%) were positive. 11/33 (33%) patients were asymptomatic. All patients diagnosed had risk factors: age >25 years (85%), residence in a deprived area (79%) and black ethnicity (21%). Despite BDQ x being highly sensitive and specific, with our low TV prevalence universal screening may not be justified. Targeted screening using local demographic data merits further investigation.

  19. Simultaneous amplification of two bacterial genes: more reliable method of Helicobacter pylori detection in microbial rich dental plaque samples.

    Science.gov (United States)

    Chaudhry, Saima; Idrees, Muhammad; Izhar, Mateen; Butt, Arshad Kamal; Khan, Ayyaz Ali

    2011-01-01

    Polymerase Chain reaction (PCR) assay is considered superior to other methods for detection of Helicobacter pylori (H. pylori) in oral cavity; however, it also has limitations when sample under study is microbial rich dental plaque. The type of gene targeted and number of primers used for bacterial detection in dental plaque samples can have a significant effect on the results obtained as there are a number of closely related bacterial species residing in plaque biofilm. Also due to high recombination rate of H. pylori some of the genes might be down regulated or absent. The present study was conducted to determine the frequency of H. pylori colonization of dental plaque by simultaneously amplifying two genes of the bacterium. One hundred dental plaque specimens were collected from dyspeptic patients before their upper gastrointestinal endoscopy and presence of H. pylori was determined through PCR assay using primers targeting two different genes of the bacterium. Eighty-nine of the 100 samples were included in final analysis. With simultaneous amplification of two bacterial genes 51.6% of the dental plaque samples were positive for H. pylori while this prevalence increased to 73% when only one gene amplification was used for bacterial identification. Detection of H. pylori in dental plaque samples is more reliable when two genes of the bacterium are simultaneously amplified as compared to one gene amplification only.

  20. Clostridium difficile Testing Algorithm: Is There a Difference in Patients Who Test Positive by Enzyme Immunoassay vs. Those Who Only Test Positive by Nucleic Acid Amplification Methodology?

    OpenAIRE

    Polak, Jonathan; Odili, Ogheneruona; Craver, Mary Ashleigh; Mayen, Anthony; Purrman, Kyle; Rahman, Asem; Sang, Charlie Joseph; Cook, Paul P

    2017-01-01

    Abstract Background Testing for Clostridium difficile infection (CDI) commonly involves checking for the presence of toxins A and B by enzyme immunoassay (EIA) or nucleic acid amplification (NAA). The former is very specific, but not very sensitive. The latter is very sensitive. Beginning in 2011, our hospital incorporated an algorithm that involved testing liquid stool specimens for glutamate dehydrogenase (GDH) and toxin by EIA. For discrepant results, the stool specimen was tested for the ...

  1. Comparison of DNA probe, PCR amplification, ELISA and culture methods for the rapid detection of Salmonella in poultry

    International Nuclear Information System (INIS)

    Qasem, J.A.; Al-Mouqati, S.; Rajkumar, G.

    2005-01-01

    The identification of Salmonella spp. from poultry meat was studied by comparing bacterial detection using the Gene-Trak colorimetric hybridization method, a PCR amplification kit and an Enzyme Linked Immunosorbent Assay (ELISA), and these methods were compared with the conventional methodology proposed by the United States Food and Drug Administration (US FDA) for detection of Salmonella in food samples. Forty positive and negative samples were studied. The three methods yielded similar results with levels of Salmonella greater than 10 CFU per sample, even when the samples were highly contaminated with competing bacteria. In contrast, 20 CFU of seed inoculum per sample was the lowest level of Salmonella detectable with all three methods and the standard culture method. The detection limits of the PCR and ELISA assays were 5 CFU/g after enrichment at 37 deg. C for 6 and 9 hours, respectively. Compared with conventional bacteriology, all three methods here demonstrated high sensitivity and specificity for Salmonella. (author)

  2. Detection of hepatitis A virus by the nucleic acid sequence-based amplification technique and comparison with reverse transcription-PCR.

    Science.gov (United States)

    Jean, J; Blais, B; Darveau, A; Fliss, I

    2001-12-01

    A nucleic acid sequence-based amplification (NASBA) technique for the detection of hepatitis A virus (HAV) in foods was developed and compared to the traditional reverse transcription (RT)-PCR technique. Oligonucleotide primers targeting the VP1 and VP2 genes encoding the major HAV capsid proteins were used for the amplification of viral RNA in an isothermal process resulting in the accumulation of RNA amplicons. Amplicons were detected by hybridization with a digoxigenin-labeled oligonucleotide probe in a dot blot assay format. Using the NASBA, as little as 0.4 ng of target RNA/ml was detected per comparison to 4 ng/ml for RT-PCR. When crude HAV viral lysate was used, a detection limit of 2 PFU (4 x 10(2) PFU/ml) was obtained with NASBA, compared to 50 PFU (1 x 10(4) PFU/ml) obtained with RT-PCR. No interference was encountered in the amplification of HAV RNA in the presence of excess nontarget RNA or DNA. The NASBA system successfully detected HAV recovered from experimentally inoculated samples of waste water, lettuce, and blueberries. Compared to RT-PCR and other amplification techniques, the NASBA system offers several advantages in terms of sensitivity, rapidity, and simplicity. This technique should be readily adaptable for detection of other RNA viruses in both foods and clinical samples.

  3. Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

    2016-01-01

    We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

  4. SIMPLIFIED DIAGNOSIS OF MALARIA INFECTION: GFM/PCR/ELISA A SIMPLIFIED NUCLEIC ACID AMPLIFICATION TECHNIQUE BY PCR/ELISA

    Directory of Open Access Journals (Sweden)

    Ricardo Luiz Dantas MACHADO

    1998-09-01

    Full Text Available We report an adaptation of a technique for the blood sample collection (GFM as well as for the extraction and amplification of Plasmodium DNA for the diagnosis of malaria infection by the PCR/ELISA. The method of blood sample collection requires less expertise and saves both time and money, thus reducing the cost by more than half. The material is also suitable for genetic analysis in either fresh or stored specimens prepared by this method.Relatamos a adaptação de uma técnica para coleta de amostras (MFV e outra para extração, amplificação de DNA de parasitas da malária para diagnóstico por PCR/ELISA. O método de coleta de amostras requer menos habilidade e economisa tempo e dinheiro, assim reduzindo a mais da metade o custo. O material é também adequado para análise genética em especimens frescos ou estocados, preparados por este método.

  5. Methods for preparation of deuterated amino acids

    International Nuclear Information System (INIS)

    Pshenichnikova, A.B.; Karnaukhova, E.N.; Zvonkova, E.N.

    1995-01-01

    The current state and prospects for the use of amino acids labeled with stable isotopes are considered. Methods for the preparation of deuterated amino acids, including synthetic, chemicoenzymatic, and biosynthetic ones, and deuterium exchange reactions are summarized. Problems in the preparation of optically pure amino acids are discussed. 120 refs., 15 figs

  6. Development of Lentivirus-Based Reference Materials for Ebola Virus Nucleic Acid Amplification Technology-Based Assays.

    Science.gov (United States)

    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.

  7. Development of Lentivirus-Based Reference Materials for Ebola Virus Nucleic Acid Amplification Technology-Based Assays.

    Directory of Open Access Journals (Sweden)

    Giada Mattiuzzo

    Full Text Available 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.

  8. Nucleic Acid Amplification Testing and Sequencing Combined with Acid-Fast Staining in Needle Biopsy Lung Tissues for the Diagnosis of Smear-Negative Pulmonary Tuberculosis.

    Directory of Open Access Journals (Sweden)

    Faming Jiang

    Full Text Available Smear-negative pulmonary tuberculosis (PTB is common and difficult to diagnose. In this study, we investigated the diagnostic value of nucleic acid amplification testing and sequencing combined with acid-fast bacteria (AFB staining of needle biopsy lung tissues for patients with suspected smear-negative PTB.Patients with suspected smear-negative PTB who underwent percutaneous transthoracic needle biopsy between May 1, 2012, and June 30, 2015, were enrolled in this retrospective study. Patients with AFB in sputum smears were excluded. All lung biopsy specimens were fixed in formalin, embedded in paraffin, and subjected to acid-fast staining and tuberculous polymerase chain reaction (TB-PCR. For patients with positive AFB and negative TB-PCR results in lung tissues, probe assays and 16S rRNA sequencing were used for identification of nontuberculous mycobacteria (NTM. The sensitivity, specificity, positive predictive value (PPV, negative predictive value (NPV, and diagnostic accuracy of PCR and AFB staining were calculated separately and in combination.Among the 220 eligible patients, 133 were diagnosed with TB (men/women: 76/57; age range: 17-80 years, confirmed TB: 9, probable TB: 124. Forty-eight patients who were diagnosed with other specific diseases were assigned as negative controls, and 39 patients with indeterminate final diagnosis were excluded from statistical analysis. The sensitivity, specificity, PPV, NPV, and accuracy of histological AFB (HAFB for the diagnosis of smear-negative were 61.7% (82/133, 100% (48/48, 100% (82/82, 48.5% (48/181, and 71.8% (130/181, respectively. The sensitivity, specificity, PPV, and NPV of histological PCR were 89.5% (119/133, 95.8% (46/48, 98.3% (119/121, and 76.7% (46/60, respectively, demonstrating that histological PCR had significantly higher accuracy (91.2% [165/181] than histological acid-fast staining (71.8% [130/181], P < 0.001. Parallel testing of histological AFB staining and PCR showed the

  9. Development of a loop-mediated isothermal amplification method for rapid mass-screening of sand flies for Leishmania infection.

    Science.gov (United States)

    Nzelu, Chukwunonso O; Gomez, Eduardo A; Cáceres, Abraham G; Sakurai, Tatsuya; Martini-Robles, Luiggi; Uezato, Hiroshi; Mimori, Tatsuyuki; Katakura, Ken; Hashiguchi, Yoshihisa; Kato, Hirotomo

    2014-04-01

    Entomological monitoring of Leishmania infection in leishmaniasis endemic areas offers epidemiologic advantages for predicting the risk and expansion of the disease, as well as evaluation of the effectiveness of control programs. In this study, we developed a highly sensitive loop-mediated isothermal amplification (LAMP) method for the mass screening of sand flies for Leishmania infection based on the 18S rRNA gene. The LAMP technique could detect 0.01 parasites, which was more sensitive than classical PCR. The method was robust and could amplify the target DNA within 1h from a crude sand fly template without DNA purification. Amplicon detection could be accomplished by the newly developed colorimetric malachite green (MG)--mediated naked eye visualization. Pre-addition of MG to the LAMP reaction solution did not inhibit amplification efficiency. The field applicability of the colorimetric MG-based LAMP assay was demonstrated with 397 field-caught samples from the endemic areas of Ecuador and eight positive sand flies were detected. The robustness, superior sensitivity, and ability to produce better visual discriminatory reaction products than existing LAMP fluorescence and turbidity assays indicated the field potential usefulness of this new method for surveillance and epidemiological studies of leishmaniasis in developing countries. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Malaria prevalence defined by microscopy, antigen detection, DNA amplification and total nucleic acid amplification in a malaria-endemic region during the peak malaria transmission season.

    Science.gov (United States)

    Waitumbi, John N; Gerlach, Jay; Afonina, Irina; Anyona, Samuel B; Koros, Joseph N; Siangla, Joram; Ankoudinova, Irina; Singhal, Mitra; Watts, Kate; Polhemus, Mark E; Vermeulen, Nicolaas M; Mahoney, Walt; Steele, Matt; Domingo, Gonzalo J

    2011-07-01

    To determine the malaria prevalence by microscopy, antigen detection and nucleic acid detection in a defined subpopulation in a Plasmodium falciparum-endemic region during the peak transmission season. Blood specimens were collected in a cross-sectional study involving children aged 5-10 years (n = 195) presenting with acute fever to two clinics in Western Kenya. All specimens underwent microscopy, HRP2 and aldolase antigen detection by enzyme immunoassay (EIA), parasite-specific DNA and total nucleic acid (RNA and DNA) by real-time PCR (qPCR) and reverse-transcriptase PCR (qRT-PCR). Microscopy detected 65/195 cases of malaria infection [95% confidence interval (CI) 52-78]. HRP2 and aldolase EIA had similar sensitivity levels detecting antigen in 65/195 (95% CI, 52-78) and 57/195 (95% CI, 45-70) cases. Discordants in antigen detection vs. microscopy occurred at Detection of total nucleic acid allowed a 3 log lower limit of detection than just DNA detection by real-time PCR in vitro. In clinical specimens, 114/195 (95% CI, 100-127) were qPCR positive (DNA), and 187/195 (95% CI, 179-191) were qRT-PCR positive (DNA plus RNA). The prevalence of submicroscopic malaria infection was significantly higher when detecting total nucleic acid than just DNA in this outpatient population during the high transmission season. Defining standards for submicroscopic infection will be important for control programmes, diagnostics development efforts and molecular epidemiology studies. © 2011 Blackwell Publishing Ltd.

  11. Comparison of in situ hybridization methods for the assessment of HER-2/neu gene amplification status in breast cancer using a tissue microarray.

    Science.gov (United States)

    Malicka-Durczak, Anna; Korski, Konstanty; Ibbs, Matthew

    2012-01-01

    This project compared HER-2/neu gene status in breast cancers, as demonstrated by FISH (fluorescent in situ hybridization) and CISH (chromogenic in situ hybridization) and using a tissue microarray (TMA). The study also aimed to show whether the TMA technique could be used in clinical diagnostics, rather than remain a scientific tool. A TMA was constructed using 121 breast cancer specimens, 6 cores from each specimen. Demonstration and assessment of HER-2/neu gene status was by FISH (Vysis Path) and CISH (DAKO Duo CISH). The 121 breast cancer specimens were divided into 3 groups by HER-2 status, as determined by immunohistochemistry. In the HER-2 negative group no amplification was observed in 36 out of 40 cases. 3 cases showed amplification by both methods and one by CISH alone. The equivocal HER-2 group showed no amplification in 30 out of 41 cases and amplification in 9 cases. One case was FISH negative CISH positive and one was discarded. In the HER-2 positive group, amplification was confirmed in 37 of the 40 cases by both methods. 3 cases were unsuitable for assessment. This study indicated that CISH is a sensitive alternative to FISH in detecting HER2 gene amplification and may replace FISH in HER2 testing. Good agreement was observed between methods (98.5% - 119 out of 121 cases). Furthermore, as only 4 out of 121 cases were unsuitable for assessment (no signal or missing TMA cores) - it may be feasible to use TMA in diagnostics.

  12. Nucleic Acid Amplification Testing and Sequencing Combined with Acid-Fast Staining in Needle Biopsy Lung Tissues for the Diagnosis of Smear-Negative Pulmonary Tuberculosis.

    Science.gov (United States)

    Jiang, Faming; Huang, Weiwei; Wang, Ye; Tian, Panwen; Chen, Xuerong; Liang, Zongan

    2016-01-01

    Smear-negative pulmonary tuberculosis (PTB) is common and difficult to diagnose. In this study, we investigated the diagnostic value of nucleic acid amplification testing and sequencing combined with acid-fast bacteria (AFB) staining of needle biopsy lung tissues for patients with suspected smear-negative PTB. Patients with suspected smear-negative PTB who underwent percutaneous transthoracic needle biopsy between May 1, 2012, and June 30, 2015, were enrolled in this retrospective study. Patients with AFB in sputum smears were excluded. All lung biopsy specimens were fixed in formalin, embedded in paraffin, and subjected to acid-fast staining and tuberculous polymerase chain reaction (TB-PCR). For patients with positive AFB and negative TB-PCR results in lung tissues, probe assays and 16S rRNA sequencing were used for identification of nontuberculous mycobacteria (NTM). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy of PCR and AFB staining were calculated separately and in combination. Among the 220 eligible patients, 133 were diagnosed with TB (men/women: 76/57; age range: 17-80 years, confirmed TB: 9, probable TB: 124). Forty-eight patients who were diagnosed with other specific diseases were assigned as negative controls, and 39 patients with indeterminate final diagnosis were excluded from statistical analysis. The sensitivity, specificity, PPV, NPV, and accuracy of histological AFB (HAFB) for the diagnosis of smear-negative were 61.7% (82/133), 100% (48/48), 100% (82/82), 48.5% (48/181), and 71.8% (130/181), respectively. The sensitivity, specificity, PPV, and NPV of histological PCR were 89.5% (119/133), 95.8% (46/48), 98.3% (119/121), and 76.7% (46/60), respectively, demonstrating that histological PCR had significantly higher accuracy (91.2% [165/181]) than histological acid-fast staining (71.8% [130/181]), P pulmonary tuberculosis. For patients with positive histological AFB and

  13. Method for production of dicarbonic acid anhydrides

    International Nuclear Information System (INIS)

    Mistr, A.; Necas, J.; Polak, V.

    1975-01-01

    A method is described of producing dicarboxylic acid anhydrides by the reaction of maleic acid anhydride with olefins. The synthesis is initiated by gamma radiation at a total dose of 10 4 to 10 6 rads in the presence of an organic solvent. The addition reactions of maleic acid anhydride to 1-hexadecene, 1-octene and cyclohexene with yields of 43%, 17% and 11%, respectively, are specified. (L.K.)

  14. Loop-Mediated Isothermal Amplification as a Fast Noninvasive Method of Helicobacter pylori Diagnosis.

    Science.gov (United States)

    Yari, Farideh; Abiri, Ramin; Aryan, Ehsan; Ahmadi Jouybari, Touraj; Navabi, Jafar; Alvandi, Amirhooshang

    2016-09-01

    Helicobacter pylori infection is etiologically associated with some important health problems such as gastric cancer. Because of the high clinical importance of H. pylori infection, development of a noninvasive test for the detection of H. pylori is desirable. In this study, a loop-mediated isothermal amplification (LAMP) targeted ureC of H. pylori was evaluated on 100 stool specimens and compared with a stool antigen test. Culture and rapid urease test were considered as gold standards. The overall detection rate of the fecal antigen test and LAMP was 58% and 82%, respectively. The analytical sensitivity of the fecal antigen test and LAMP was 500 and 10 H. pylori cells/g and 10 fg DNA/reaction, which is equal to six H. pylori genome. LAMP technique has been characterized by high sensitivity and low detection limit for the detection of H. pylori in stool specimen. Clinical diagnostic performance of LAMP was better than the stool antigen test. © 2015 Wiley Periodicals, Inc.

  15. Multiplex, rapid and sensitive isothermal detection of nucleic-acid sequence by endonuclease restriction-mediated real-time multiple cross displacement amplification

    Directory of Open Access Journals (Sweden)

    Yi eWang

    2016-05-01

    Full Text Available We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA, which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5’ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labelled at the 5’ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5’ end short sequences and their complementary sequences, which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 minutes, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

  16. A simple and rapid identification method for newly emerged porcine Deltacoronavirus with loop-mediated isothermal amplification

    Directory of Open Access Journals (Sweden)

    Fanfan Zhang

    2017-10-01

    Full Text Available Abstract Background Porcine Deltacoronavirus (PDCoV is a newly emerged enteropathogenic coronavirus that causes diarrhea and mortality in neonatal piglets. PDCoV has spread to many countries around the world, leading to significant economic losses in the pork industry. Therefore, a rapid and sensitive method for detection of PDCoV in clinical samples is urgently needed. Results In this study, we developed a single-tube one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP assay specific for nucleocapsid gene to diagnose and monitor PDCoV infections. The detection limit of RT-LAMP assay was 1 × 101 copies of PDCoV, which was approximately 100-fold more sensitive than gel-based one-step reverse transcription polymerase chain reaction (RT-PCR. This assay could specifically amplify PDCoV and had no cross amplification with porcine epidemic diarrhea virus (PEDV, transmissible gastroenteritis virus (TGEV, porcine kobuvirus (PKoV, porcine astrovirus (PAstV, porcine reproductive and respiratory syndrome virus (PRRSV, classic swine fever virus (CSFV, and porcine circovirus type 2 (PCV2. By screening a panel of clinical specimens (N = 192, this method presented a similar sensitivity with nested RT-PCR and was 1–2 log more sensitive than conventional RT-PCR in detection of PDCoV. Conclusions The RT-LAMP assay established in this study is a potentially valuable tool, especially in low-resource laboratories and filed settings, for a rapid diagnosis, surveillance, and molecular epidemiology investigation of PDCoV infections. To the best of our knowledge, this is the first work for detection of newly emerged PDCoV with LAMP technology.

  17. Development of a highly sensitive loop-mediated isothermal amplification (LAMP) method for the detection of Loa loa.

    Science.gov (United States)

    Fernández-Soto, Pedro; Mvoulouga, Prosper Obolo; Akue, Jean Paul; Abán, Julio López; Santiago, Belén Vicente; Sánchez, Miguel Cordero; Muro, Antonio

    2014-01-01

    The filarial parasite Loa loa, the causative agent of loiasis, is endemic in Central and Western Africa infecting 3-13 million people. L. loa has been associated with fatal encephalopathic reactions in high Loa-infected individuals receiving ivermectin during mass drug administration programs for the control of onchocerciasis and lymphatic filariasis. In endemic areas, the only diagnostic method routinely used is the microscopic examination of mid-day blood samples by thick blood film. Improved methods for detection of L. loa are needed in endemic regions with limited resources, where delayed diagnosis results in high mortality. We have investigated the use of a loop-mediated isothermal amplification (LAMP) assay to facilitate rapid, inexpensive, molecular diagnosis of loiasis. Primers for LAMP were designed from a species-specific repetitive DNA sequence from L. loa retrieved from GenBank. Genomic DNA of a L. loa adult worm was used to optimize the LAMP conditions using a thermocycler or a conventional heating block. Amplification of DNA in the LAMP mixture was visually inspected for turbidity as well as addition of fluorescent dye. LAMP specificity was evaluated using DNA from other parasites; sensitivity was evaluated using DNA from L. loa 10-fold serially diluted. Simulated human blood samples spiked with DNA from L. loa were also tested for sensitivity. Upon addition of fluorescent dye, all positive reactions turned green while the negative controls remained orange under ambient light. After electrophoresis on agarose gels, a ladder of multiple bands of different sizes could be observed in positive samples. The detection limit of the assay was found to be as little as 0.5 ag of L. loa genomic DNA when using a heating block. We have designed, for the first time, a highly sensitive LAMP assay for the detection of L. loa which is potentially adaptable for field diagnosis and disease surveillance in loiasis-endemic areas.

  18. Method for extraction and amplification of DNA from seeds and tubers

    African Journals Online (AJOL)

    Computer Department

    2013-04-10

    Apr 10, 2013 ... from 100 mg tissue) of high quality from seeds of maize, soybean, and cowpea, tubers of yam, tuberous ... designed to fix and store nucleic acids directly from fresh tissues pressed into ... thermal cycle conditions for PCR using various primer sets are given in .... The protocol does not use liquid nitrogen and.

  19. Chiral relay: a novel strategy for the control and amplification of enantioselectivity in chiral Lewis acid promoted reactions.

    Science.gov (United States)

    Corminboeuf, Olivier; Quaranta, Laura; Renaud, Philippe; Liu, Mei; Jasperse, Craig P; Sibi, Mukund P

    2003-01-03

    Chiral Lewis acid catalysis has emerged as one of the premiere method to control stereochemistry. Much effort has gone into the design of superior ligands with increasing steric extension to shield distant reactive sites. We report here an alternative and complementary approach based on a "chiral relay". This strategy focuses on the improved design of achiral templates which may relay and amplify the stereochemistry from ligands. The essence of this strategy is that the chiral Lewis acid would effectively convert an achiral template into a chiral non-racemic template. This approach combines the advantages of enantioselective catalysis (substoichiometric amount of the chiral inducer) with the ones of chiral auxiliary control (efficient and predictable stereocontrol).

  20. A modified phase-fitted and amplification-fitted Runge-Kutta-Nyström method for the numerical solution of the radial Schrödinger equation

    OpenAIRE

    Papadopoulos , D. F.; Anastassi , Z. A.; Simos , T. E.

    2010-01-01

    Abstract A new Runge-Kutta-Nystrom method, with phase-lag and amplification error of order infinity, for the numerical solution of the Schrodinger equation is developed in this paper. The new method is based on the Runge-Kutta-Nystrom method with fourth algebraic order, developed by Dormand, El-Mikkawy and Prince. Numerical illustrations indicate that the new method is much more efficient than other methods derived for the same purpose. phone: +30-210-9421510 (Simos, T. E.) ...

  1. Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method.

    Science.gov (United States)

    Honda, Shozo; Morichika, Keisuke; Kirino, Yohei

    2016-03-01

    RNA digestions catalyzed by many ribonucleases generate RNA fragments that contain a 2',3'-cyclic phosphate (cP) at their 3' termini. However, standard RNA-seq methods are unable to accurately capture cP-containing RNAs because the cP inhibits the adapter ligation reaction. We recently developed a method named cP-RNA-seq that is able to selectively amplify and sequence cP-containing RNAs. Here we describe the cP-RNA-seq protocol in which the 3' termini of all RNAs, except those containing a cP, are cleaved through a periodate treatment after phosphatase treatment; hence, subsequent adapter ligation and cDNA amplification steps are exclusively applied to cP-containing RNAs. cP-RNA-seq takes ∼6 d, excluding the time required for sequencing and bioinformatics analyses, which are not covered in detail in this protocol. Biochemical validation of the existence of cP in the identified RNAs takes ∼3 d. Even though the cP-RNA-seq method was developed to identify angiogenin-generating 5'-tRNA halves as a proof of principle, the method should be applicable to global identification of cP-containing RNA repertoires in various transcriptomes.

  2. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

    DEFF Research Database (Denmark)

    Hou, Yong; Wu, Kui; Shi, Xulian

    2015-01-01

    methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly...... performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level....

  3. Easy assessment of diversity in Jatropha curcas L. plants using two single-primer amplification reaction (SPAR) methods

    Energy Technology Data Exchange (ETDEWEB)

    Ranade, Shirish A; Srivastava, Anuj P; Srivastava, Jyoti; Tuli, Rakesh [PMB Division, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, U.P. (India); Rana, Tikam S [Plant Biodiversity and Conservation Biology Division, National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, U.P. (India)

    2008-06-15

    Jatropha curcas L. (physic nut) has drawn attention in recent years as a source of seed oil that can provide an economically viable substitute for diesel. Very little work on provenance trials and genetic resources of J. curcas L. has been reported so far. Though J. curcas grows widely in India and several collections of the plant are also maintained, pedigree and provenance records are not always available. This article reports our studies on the diversity amongst the accessions of J. curcas L., both amongst already held collections as well as from a few locations in the wild. Two single-primer amplification reaction (SPAR) methods were used for this purpose. The accessions from the North East were most distant from all other accessions in UPGMA analysis. The NBRI, Bhubaneshwar and Lalkuan accessions were more related to each other. The UPGMA tree clearly shows well-separated accession groups: NBRI, Bhubaneshwar, North East, Lalkuan and Outgroup. The study suggests that this relatively recently introduced plant species shows adequate genetic diversity in India and that the SPAR methods are useful for a rapid assessment of the same. The methods provide important tools for analyzing the diversity within the available collections to shortlist the parental lines for adaptability trials and further improvement of Jatropha plants. (author)

  4. Biomaterials in light amplification

    Science.gov (United States)

    Mysliwiec, Jaroslaw; Cyprych, Konrad; Sznitko, Lech; Miniewicz, Andrzej

    2017-03-01

    Biologically produced or inspired materials can serve as optical gain media, i.e. they can exhibit the phenomenon of light amplification. Some of these materials, under suitable dye-doping and optical pumping conditions, show lasing phenomena. The emerging branch of research focused on obtaining lasing action in highly disordered and highly light scattering materials, i.e. research on random lasing, is perfectly suited for biological materials. The use of biomaterials in light amplification has been extensively reported in the literature. In this review we attempt to report on progress in the development of biologically derived systems able to show the phenomena of light amplification and random lasing together with the contribution of our group to this field. The rich world of biopolymers modified with molecular aggregates and nanocrystals, and self-organized at the nanoscale, offers a multitude of possibilities for tailoring luminescent and light scattering properties that are not easily replicated in conventional organic or inorganic materials. Of particular importance and interest are light amplification and lasing, or random lasing studies in biological cells and tissues. In this review we will describe nucleic acids and their complexes employed as gain media due to their favorable optical properties and ease of manipulation. We will report on research conducted on various biomaterials showing structural analogy to nucleic acids such as fluorescent proteins, gelatins in which the first distributed feedback laser was realized, and also amyloids or silks, which, due to their dye-doped fiber-like structure, allow for light amplification. Other materials that were investigated in that respect include polysaccharides, like starch exhibiting favorable photostability in comparison to other biomaterials, and chitosan, which forms photonic crystals or cellulose. Light amplification and random lasing was not only observed in processed biomaterials but also in living

  5. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    Directory of Open Access Journals (Sweden)

    Yanagihara Kazuyoshi

    2009-06-01

    Full Text Available Abstract Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS, which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. Methods DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. Results DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20 of gastric cancer cell lines (8–18-fold amplification and 4.7% (4/86 of primary gastric tumors (8–50-fold amplification. KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild

  6. Evaluation of a loop-mediated isothermal amplification method for the detection of Listeria monocytogenes in dairy food

    Directory of Open Access Journals (Sweden)

    Erica Tirloni

    2017-12-01

    Full Text Available Objective of the present study was to test the performances of a loop-mediated isothermal amplification (LAMP-based method for the detection of Listeria monocytogenes, with particular focus on the dairy products. The specificity of the method was evaluated on 42 different Listeria spp. strains from collections, food and environmental samples. 100% (32 of 32 of the L. monocytogenes strains were correctly recognised, and none of other 10 Listeria spp. strains was misidentified. The sensitivity was evaluated on four L. monocytogenes strains from different sources. The instrument was able to detect 10-400 CFU/mL. The ability to detect low initial numbers of L. monocytogenes (0.3- 0.7 Log CFU/g was also evaluated, in duplicate, in pasteurised milk (whole and skimmed and dairy samples (fresh ricotta, crescenza, mascarpone, mozzarella, cottage cheese, cream cheese, taleggio, gorgonzola. The analysis was performed after 18, 24 and 48 h of incubation, and was coupled with the count of L. monocytogenes in the broth. Microbial loads were insufficient to achieve a positive result after 18 and 24 h in most of the samples; after 48 h, all the products, except taleggio and one gorgonzola sample, were identified as positive; the sensitivity of the method when applied to contaminated dairy foods was about 5 Log CFU/g. The LAMP method tested can be considered a very useful tool, as it is a costeffective and easy-functioning method. The preliminary data obtained should be confirmed with a validation process taking into account different food typologies.

  7. Neutralization method for a hydrofluoric acid release

    International Nuclear Information System (INIS)

    Williams, D.L.; Deacon, L.E.

    1976-01-01

    A laboratory investigation of methods for neutralizing a release at the hydrofluoric acid tank farm at the Portsmouth Gaseous Diffusion Plant has revealed that the best neutralization method incorporates the use of a lime/water slurry. In this method, settling of suspended solids in the liquid is enhanced by the application of sodium dodecyl sulfate, which causes immediate flocculation and settling. Dilution and expulsion of the supernatant liquid above the flocculated solids result in an effluent which meets the one part per million fluoride limit established by the U.S. Environmental Protection Agency. A fluoride specific ion electrode is used to determine fluoride concentration. This method presently is being adapted for use in the hydrofluoric acid tank farm and is being considered for use at the plant's fluorine generation facility. It could be adapted for use in any facility that contains fluoride in aqueous solution

  8. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    International Nuclear Information System (INIS)

    Mita, Hiroaki; Yanagihara, Kazuyoshi; Fujita, Masahiro; Hosokawa, Masao; Kusano, Masanobu; Sabau, Sorin Vasile; Tatsumi, Haruyuki; Imai, Kohzoh; Shinomura, Yasuhisa; Tokino, Takashi; Toyota, Minoru; Aoki, Fumio; Akashi, Hirofumi; Maruyama, Reo; Sasaki, Yasushi; Suzuki, Hiromu; Idogawa, Masashi; Kashima, Lisa

    2009-01-01

    Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS), which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20) of gastric cancer cell lines (8–18-fold amplification) and 4.7% (4/86) of primary gastric tumors (8–50-fold amplification). KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild-type KRAS resulted in the inhibition of cell growth and

  9. Evaluation of six nucleic acid amplification tests used for diagnosis of Neisseria gonorrhoeae in Russia compared with an international strictly validated real-time porA pseudogene polymerase chain reaction.

    Science.gov (United States)

    Shipitsyna, E; Zolotoverkhaya, E; Hjelmevoll, S O; Maximova, A; Savicheva, A; Sokolovsky, E; Skogen, V; Domeika, M; Unemo, M

    2009-11-01

    In Russia, laboratory diagnosis of gonorrhoea has been mainly based on microscopy only and, in some settings, relatively rare suboptimal culturing. In recent years, Russian developed and manufactured nucleic acid amplification tests (NAAT) have been implemented for routine diagnosis of Neisseria gonorrhoeae. However, these NAATs have never been validated to any international well-recognized diagnostic NAAT. This study aims to evaluate the performance characteristics of six Russian NAATs for N. gonorrhoeae diagnostics. In total, 496 symptomatic patients were included. Five polymerase chain reaction (PCR) assays and one real-time nucleic acid sequence based amplification (NASBA) assay, developed by three Russian companies, were evaluated on urogenital samples, i.e. cervical and first voided urine (FVU) samples from females (n = 319), urethral and FVU samples from males (n = 127), and extragenital samples, i.e. rectal and pharyngeal samples, from 50 additional female patients with suspicion of gonorrhoea. As reference method, an international strictly validated real-time porA pseudogene PCR was applied. The prevalence of N. gonorrhoeae was 2.7% and 16% among the patients providing urogenital and extragenital samples, respectively. The Russian NAATs and the reference method displayed high level of concordance (99.4-100%). The sensitivities, specificities, positive predictive values and negative predictive values of the Russian tests in different specimens were 66.7-100%, 100%, 100%, and 99.4-100%, respectively. Russian N. gonorrhoeae diagnostic NAATs comprise relatively good performance characteristics. However, larger studies are crucial and, beneficially, the Russian assays should also be evaluated to other international highly sensitive and specific, and ideally Food and Drug Administration approved, NAATs such as Aptima Combo 2 (Gen-Probe).

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

    Science.gov (United States)

    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 1 pM, 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Study of C-MYC amplification and expression in Iranian gastric cancer samples using CISH and IHC methods.

    Science.gov (United States)

    Khaleghian, Malihea; Jahanzad, Issa; Shakoori, Abbas; Ardalan, Farid Azmoudeh; Azimi, Cyrus

    2015-01-01

    Gastric cancer is the fourth most frequent malignancy and the second cause of cancer-related mortality worldwide. It has been suggested that in gastric carcinogenesis, the C-MYC gene has an important function. The objective of this study is to establish the preference of Chromogenic in situ hybridization (CISH) and Immunohistochemistry (IHC) in the diagnosis and prognosis of gastric cancer. Samples comprised of 50 randomly selected patients of whom 40 were male and 10 female. To evaluate the MYC copy number and its protein expression, CISH and IHC analyses were performed for 50 gastric adenocarcinomas, in Iran. The location of the tumor in 64% of the patients was the fundus, and in 72% of patients, the tumors were of a diffuse type; 22 samples showed no amplification, and 28 samples were with amplification. MYC immunoreactivity was observed in 13 samples. Twelve samples showed both MYC amplification and MYC immunoreactivity. In addition, among the 28 CISH+ samples, 12 samples had positive signals for IHC and 16 samples had negative signals for IHC. A majority of the IHC-negative patients had no amplification, but only one patient with IHC positive had no amplification. Our conclusion was that for the management and treatment of gastric cancer, and for special attention of clinicians, for prognosis and tumor progression, the CISH was a better and more feasible test than IHC, in regard to the sensitivity and specificity.

  12. The development and evaluation of a loop-mediated isothermal amplification (LAMP) method for detection of Babesia spp. infective to sheep and goats in China.

    Science.gov (United States)

    Guan, Guiquan; Chauvin, Alain; Luo, Jianxun; Inoue, Noboru; Moreau, Emmanuelle; Liu, Zhijie; Gao, Jinliang; Thekisoe, Oriel M M; Ma, Miling; Liu, Aihong; Dang, Zhisheng; Liu, Junlong; Ren, Qiaoyun; Jin, Yurong; Sugimoto, Chihiro; Yin, Hong

    2008-09-01

    The loop-mediated isothermal amplification (LAMP) reaction is a method that amplifies with high sensitivity, efficiency, and rapidity, deoxyribonucleic acid (DNA) under isothermal condition in simple incubators. Two primer sets for the LAMP method were designed using the nucleotide sequences of 18S rRNA gene of Babesia sp. BQ1 (Lintan) and Babesia sp. Xinjiang-2005 isolated in China. The primers were used to detect parasite DNA extracted from infected blood and purified parasites by LAMP. The specific ladder bands were amplified from the autologous genomic DNA of two Babesia species, respectively, and did not cross-react with the genomic DNA of Theileria sp. China 1, Theileria sp. China 2, B. bovis, Theileria sp. (Japan) and sheep. The LAMP was sensitive enough to detect 0.02 pg and 0.2 pg genomic DNA of Babesia sp. BQ1 (Lintan) and Babesia sp. Xinjiang-2005, respectively, from 10-fold serially diluted samples corresponding to the amount of DNA present in 50 microl of 0.000002% and 0.00002% parasitemic erythrocytes. Furthermore, DNA extracted from blood of intact (non-splenectomized) sheep experimentally infected with Babesia sp. BQ1 (Lintan) and Babesia sp. Xinjiang-2005 was amplified by the LAMP from week 1 to 9 and week 2 and 3 post-infection, respectively, demonstrating the high sensitivity of these primers. Of 365 samples collected from Gansu province, 14.3% (52/365) were positively detected by the LAMP. Of 145 samples collected on filter papers (Whatman) from the grazing sheep in Xinjiang province, 3.5% (5/145) were positive. These results show that the LAMP could be an alternative diagnostic tool for the detection of babesial infection in sheep and goats.

  13. Cavitation during the protein misfolding cyclic amplification (PMCA) method – The trigger for de novo prion generation?

    International Nuclear Information System (INIS)

    Haigh, Cathryn L.; Drew, Simon C.

    2015-01-01

    The protein misfolding cyclic amplification (PMCA) technique has become a widely-adopted method for amplifying minute amounts of the infectious conformer of the prion protein (PrP). PMCA involves repeated cycles of 20 kHz sonication and incubation, during which the infectious conformer seeds the conversion of normally folded protein by a templating interaction. Recently, it has proved possible to create an infectious PrP conformer without the need for an infectious seed, by including RNA and the phospholipid POPG as essential cofactors during PMCA. The mechanism underpinning this de novo prion formation remains unknown. In this study, we first establish by spin trapping methods that cavitation bubbles formed during PMCA provide a radical-rich environment. Using a substrate preparation comparable to that employed in studies of de novo prion formation, we demonstrate by immuno-spin trapping that PrP- and RNA-centered radicals are generated during sonication, in addition to PrP-RNA cross-links. We further show that serial PMCA produces protease-resistant PrP that is oxidatively modified. We suggest a unique confluence of structural (membrane-mimetic hydrophobic/hydrophilic bubble interface) and chemical (ROS) effects underlie the phenomenon of de novo prion formation by PMCA, and that these effects have meaningful biological counterparts of possible relevance to spontaneous prion formation in vivo. - Highlights: • Sonication during PMCA generates free radicals at the surface of cavitation bubbles. • PrP-centered and RNA-centered radicals are formed in addition to PrP-RNA adducts. • De novo prions may result from ROS and structural constraints during cavitation

  14. Cavitation during the protein misfolding cyclic amplification (PMCA) method – The trigger for de novo prion generation?

    Energy Technology Data Exchange (ETDEWEB)

    Haigh, Cathryn L., E-mail: chaigh@unimelb.edu.au [Department of Pathology, The University of Melbourne, Victoria 3010 (Australia); Drew, Simon C., E-mail: sdrew@unimelb.edu.au [Florey Department of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010 (Australia)

    2015-06-05

    The protein misfolding cyclic amplification (PMCA) technique has become a widely-adopted method for amplifying minute amounts of the infectious conformer of the prion protein (PrP). PMCA involves repeated cycles of 20 kHz sonication and incubation, during which the infectious conformer seeds the conversion of normally folded protein by a templating interaction. Recently, it has proved possible to create an infectious PrP conformer without the need for an infectious seed, by including RNA and the phospholipid POPG as essential cofactors during PMCA. The mechanism underpinning this de novo prion formation remains unknown. In this study, we first establish by spin trapping methods that cavitation bubbles formed during PMCA provide a radical-rich environment. Using a substrate preparation comparable to that employed in studies of de novo prion formation, we demonstrate by immuno-spin trapping that PrP- and RNA-centered radicals are generated during sonication, in addition to PrP-RNA cross-links. We further show that serial PMCA produces protease-resistant PrP that is oxidatively modified. We suggest a unique confluence of structural (membrane-mimetic hydrophobic/hydrophilic bubble interface) and chemical (ROS) effects underlie the phenomenon of de novo prion formation by PMCA, and that these effects have meaningful biological counterparts of possible relevance to spontaneous prion formation in vivo. - Highlights: • Sonication during PMCA generates free radicals at the surface of cavitation bubbles. • PrP-centered and RNA-centered radicals are formed in addition to PrP-RNA adducts. • De novo prions may result from ROS and structural constraints during cavitation.

  15. Application of a Real-time Reverse Transcription Loop Mediated Amplification Method to the Detection of Rabies Virus in Arctic Foxes in Greenland

    DEFF Research Database (Denmark)

    Wakeley, Philip; Johnson, Nicholas; Rasmussen, Thomas Bruun

    Reverse transcription loop mediated amplification (RT-LAMP) offers a rapid, isothermal method for amplification of virus RNA. In this study a panel of positive rabies virus samples originally prepared from arctic fox brain tissue was assessed for the presence of rabies viral RNA using a real time...... RT-LAMP. The method had previously been shown to work with samples from Ghana which clustered with cosmopolitan lineage rabies viruses but the assay had not been assessed using samples from animals infected with rabies from the arctic region. The assay is designed to amplify both cosmopolitan strains...... and arctic-like strains of classical rabies virus due to the primer design and is therefore expected to be universally applicable independent of region of the world where the virus is isolated. Of the samples tested all were found to be positive after incubation for 25 to 30 minutes. The method made use...

  16. Microfluidic method for rapid turbidimetric detection of the DNA of Mycobacterium tuberculosis using loop-mediated isothermal amplification in capillary tubes

    International Nuclear Information System (INIS)

    Rafati, Adele; Gill, Pooria

    2015-01-01

    We describe a microfluidic method for rapid isothermal turbidimetric detection of the DNA of Mycobacterium tuberculosis. Loop-mediated isothermal amplification is accomplished in capillary tubes for amplifying DNA in less than 15 min, and sensitivity and specificity were compared to conventional loop-mediated isothermal amplification (LAMP). The method can detect as little as 1 pg mL −1 DNA in a sample. Results obtained with clinical specimens indicated 90 % sensitivity and 95 % specificity for microfluidic LAMP in comparison to culture methods. No interference occurred due to the presence of nonspecific DNAs. The findings demonstrate the power of the new microfluidic LAMP test for rapid molecular detection of microorganisms even when using bare eyes. (author)

  17. A FISH-based method for assessment of HER-2 amplification status in breast cancer circulating tumor cells following CellSearch isolation

    Directory of Open Access Journals (Sweden)

    Frithiof H

    2016-11-01

    Full Text Available Henrik Frithiof,1 Kristina Aaltonen,1 Lisa Rydén2,3 1Division of Oncology and Pathology, 2Division of Surgery, Department of Clinical Sciences Lund, Lund University, Lund, 3Department of Surgery, Skåne University Hospital, Malmö, Sweden Introduction: Amplification of the HER-2/neu (HER-2 proto-oncogene occurs in 10%–15% of primary breast cancer, leading to an activated HER-2 receptor, augmenting growth of cancer cells. Tumor classification is determined in primary tumor tissue and metastatic biopsies. However, malignant cells tend to alter their phenotype during disease progression. Circulating tumor cell (CTC analysis may serve as an alternative to repeated biopsies. The Food and Drug Administration-approved CellSearch system allows determination of the HER-2 protein, but not of the HER-2 gene. The aim of this study was to optimize a fluorescence in situ hybridization (FISH-based method to quantitatively determine HER-2 amplification in breast cancer CTCs following CellSearch-based isolation and verify the method in patient samples. Methods: Using healthy donor blood spiked with human epidermal growth factor receptor 2 (HER-2-positive breast cancer cell lines, SKBr-3 and BT-474, and a corresponding negative control (the HER-2-negative MCF-7 cell line, an in vitro CTC model system was designed. Following isolation in the CellSearch system, CTC samples were further enriched and fixed on microscope slides. Immunocytochemical staining with cytokeratin and 4',6-diamidino-2'-phenylindole dihydrochloride identified CTCs under a fluorescence microscope. A FISH-based procedure was optimized by applying the HER2 IQFISH pharmDx assay for assessment of HER-2 amplification status in breast cancer CTCs. Results: A method for defining the presence of HER-2 amplification in single breast cancer CTCs after CellSearch isolation was established using cell lines as positive and negative controls. The method was validated in blood from breast cancer patients

  18. Iodometric microdetermination of phosphorus in organic compounds by use of An amplification reaction

    OpenAIRE

    Al Kubaisi, A. H. [عبد الله حسين الكبيسي; Farag, A. B.; Amin, R. R.

    1994-01-01

    A high chemical amplification method is described for the iodometric microdetermination of phosphorus in organic compounds. This method depends on combustion by the oxygen flask, absorption of the combustion products in distilled water and conversion to orthophosphoric acid with bromine water. The phosphoric acid produced is then allowed to react with sodium molybdate in acid medium to form phosphomolybdic acid which is extracted into a mixture of diethyl ether and pentanol (5:1, V/V), and ba...

  19. Rapid genome detection of Schmallenberg virus and bovine viral diarrhea virus by use of isothermal amplification methods and high-speed real-time reverse transcriptase PCR.

    Science.gov (United States)

    Aebischer, Andrea; Wernike, Kerstin; Hoffmann, Bernd; Beer, Martin

    2014-06-01

    Over the past few years, there has been an increasing demand for rapid and simple diagnostic tools that can be applied outside centralized laboratories by using transportable devices. In veterinary medicine, such mobile test systems would circumvent barriers associated with the transportation of samples and significantly reduce the time to diagnose important infectious animal diseases. Among a wide range of available technologies, high-speed real-time reverse transcriptase quantitative PCR (RT-qPCR) and the two isothermal amplification techniques loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) represent three promising candidates for integration into mobile pen-side tests. The aim of this study was to investigate the performance of these amplification strategies and to evaluate their suitability for field application. In order to enable a valid comparison, novel pathogen-specific assays have been developed for the detection of Schmallenberg virus and bovine viral diarrhea virus. The newly developed assays were evaluated in comparison with established standard RT-qPCR using samples from experimentally or field-infected animals. Even though all assays allowed detection of the target virus in less than 30 min, major differences were revealed concerning sensitivity, specificity, robustness, testing time, and complexity of assay design. These findings indicated that the success of an assay will depend on the integrated amplification technology. Therefore, the application-specific pros and cons of each method that were identified during this study provide very valuable insights for future development and optimization of pen-side tests. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  20. Polymerase spiral reaction (PSR): a novel, visual isothermal amplification method for detection of canine parvovirus 2 genomic DNA.

    Science.gov (United States)

    Gupta, Vikas; Chakravarti, Soumendu; Chander, Vishal; Majumder, Saurabh; Bhat, Shabir Ahmad; Gupta, Vivek Kumar; Nandi, Sukdeb

    2017-07-01

    Canine parvovirus-2 (CPV-2), which is ubiquitously distributed worldwide, causes severe and often fatal gastroenteritis in dogs. Accurate, differential and rapid diagnosis of canine parvoviral enteritis remains a challenge for clinicians. A recently developed isothermal amplification technique, polymerase spiral reaction (PSR), was optimized for the first time for a viral pathogen with reference recombinant plasmid standards from different CPV-2 antigenic variants (CPV-2, CPV-2a, CPV-2b and CPV-2c) and subsequently validated using clinical samples. Addition of chromogenic substrate SYBR Green I after the completion of the reaction resulted in bright green fluorescence in positive samples, while negative samples and a no-template control remained orange. These results were further substantiated through visualization of a laddering pattern of the PSR-amplified product in an agarose gel in positive cases and the absence of this pattern in no-template control and negative samples. The PSR assay was found to be highly specific, as it did not react with other putative canine pathogens (canine adenovirus 1 and canine distemper virus). The sensitivity of the newly developed PSR technique was compared with that of conventional PCR, real-time PCR and LAMP, using a serial tenfold dilution of canine parvovirus DNA. The detection limit of PSR was found to be at the femtogram level, which is comparable with that of real-time PCR and LAMP, which are ten times more sensitive than conventional PCR. The assay was validated using 90 clinical samples, of which 54 were found positive, while only 45 samples were positive in conventional PCR. This novel assay, which is fully compliant with the 'ASSURED' concept for disease diagnosis, provides a simple, rapid, specific, sensitive and cost-effective method for diagnosis of canine parvoviral enteritis in veterinary clinics.

  1. An efficient and high fidelity method for amplification, cloning and sequencing of complete tospovirus genomic RNA segments

    Science.gov (United States)

    Amplification and sequencing of the complete M- and S-RNA segments of Tomato spotted wilt virus and Impatiens necrotic spot virus as a single fragment is useful for whole genome sequencing of tospoviruses co-infecting a single host plant. It avoids issues associated with overlapping amplicon-based ...

  2. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    OpenAIRE

    Karolina Chwialkowska; Urszula Korotko; Joanna Kosinska; Iwona Szarejko; Miroslaw Kwasniewski

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing ...

  3. A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans.

    Science.gov (United States)

    Mauchline, T H; Mohan, S; Davies, K G; Schaff, J E; Opperman, C H; Kerry, B R; Hirsch, P R

    2010-05-01

    To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR-based diagnostic tool for P. penetrans. An optimized method to decontaminate endospores, release and purify DNA enabled multiple strand amplification. DNA purity was assessed by cloning and sequencing gyrB and 16S rRNA gene fragments obtained from PCR using generic primers. Samples indicated to be 100%P. penetrans by the gyrB assay were estimated at 46% using the 16S rRNA gene. No bias was detected on cloning and sequencing 12 housekeeping and sporulation gene fragments from amplified DNA. The detection limit by PCR with Pasteuria-specific 16S rRNA gene primers following multiple strand amplification of DNA extracted using the method was a single endospore. Generation of large quantities DNA will facilitate genomic sequencing of P. penetrans. Apparent differences in sample purity are explained by variations in 16S rRNA gene copy number in Eubacteria leading to exaggerated estimations of sample contamination. Detection of single endospores will facilitate investigations of P. penetrans molecular ecology. These methods will advance studies on P. penetrans and facilitate research on other obligate and fastidious micro-organisms where it is currently impractical to obtain DNA in sufficient quantity and quality.

  4. Development and application of loop-mediated isothermal amplification methods targeting the seM gene for detection of Streptococcus equi subsp. equi.

    Science.gov (United States)

    Hobo, Seiji; Niwa, Hidekazu; Oku, Kazuomi

    2012-03-01

    Loop-mediated isothermal amplification (LAMP) constitutes a potentially valuable diagnostic tool for rapid diagnosis of contagious diseases. In this study, we developed a novel LAMP method (seM-LAMP) to detect the seM gene of Streptococcus equi subsp. equi (S. equi), the causative agent of strangles in equids. The seM-LAMP successfully amplified the target sequence of the seM gene at 63°C within 60 min. The sensitivity of the seM-LAMP was slightly lower than the 2nd reaction of the seM semi-nested PCR. To evaluate the species specificity of the seM-LAMP, we tested 100 S. equi and 189 non-S. equi strains. Significant amplification of the DNA originating from S. equi was observed within 60 min incubation, but no amplification of non-S. equi DNA occurred. The results were identical to those of seM semi-nested PCR. To investigate the clinical usefulness of the methods, the seM-LAMP and the seM semi-nested PCR were used to screen 590 nasal swabs obtained during an outbreak of strangles. Both methods showed that 79 and 511 swabs were S. equi positive and negative, respectively, and the results were identical to those of the culture examination. These results indicate that the seM-LAMP is potentially useful for the reliable routine diagnosis of Streptococcus equi subsp. equi infections.

  5. A Simple Method for the Extraction, PCR-amplification, Cloning, and Sequencing of Pasteuria 16S rDNA from Small Numbers of Endospores.

    Science.gov (United States)

    Atibalentja, N; Noel, G R; Ciancio, A

    2004-03-01

    For many years the taxonomy of the genus Pasteuria has been marred with confusion because the bacterium could not be cultured in vitro and, therefore, descriptions were based solely on morphological, developmental, and pathological characteristics. The current study sought to devise a simple method for PCR-amplification, cloning, and sequencing of Pasteuria 16S rDNA from small numbers of endospores, with no need for prior DNA purification. Results show that DNA extracts from plain glass bead-beating of crude suspensions containing 10,000 endospores at 0.2 x 10 endospores ml(-1) were sufficient for PCR-amplification of Pasteuria 16S rDNA, when used in conjunction with specific primers. These results imply that for P. penetrans and P. nishizawae only one parasitized female of Meloidogyne spp. and Heterodera glycines, respectively, should be sufficient, and as few as eight cadavers of Belonolaimus longicaudatus with an average number of 1,250 endospores of "Candidatus Pasteuria usgae" are needed for PCR-amplification of Pasteuria 16S rDNA. The method described in this paper should facilitate the sequencing of the 16S rDNA of the many Pasteuria isolates that have been reported on nematodes and, consequently, expedite the classification of those isolates through comparative sequence analysis.

  6. A loop-mediated isothermal amplification method for a differential identification of Taenia tapeworms from human: application to a field survey.

    Science.gov (United States)

    Nkouawa, Agathe; Sako, Yasuhito; Li, Tiaoying; Chen, Xingwang; Nakao, Minoru; Yanagida, Tetsuya; Okamoto, Munehiro; Giraudoux, Patrick; Raoul, Francis; Nakaya, Kazuhiro; Xiao, Ning; Qiu, Jiamin; Qiu, Dongchuan; Craig, Philip S; Ito, Akira

    2012-12-01

    In this study, we applied a loop-mediated isothermal amplification method for identification of human Taenia tapeworms in Tibetan communities in Sichuan, China. Out of 51 proglottids recovered from 35 carriers, 9, 1, and 41 samples were identified as Taenia solium, Taenia asiatica and Taenia saginata, respectively. Same results were obtained afterwards in the laboratory, except one sample. These results demonstrated that the LAMP method enabled rapid identification of parasites in the field surveys, which suggested that this method would contribute to the control of Taenia infections in endemic areas. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  7. Method of purifying phosphoric acid after solvent extraction

    International Nuclear Information System (INIS)

    Kouloheris, A.P.; Lefever, J.A.

    1979-01-01

    A method of purifying phosphoric acid after solvent extraction is described. The phosphoric acid is contacted with a sorbent which sorbs or takes up the residual amount of organic carrier and the phosphoric acid separated from the organic carrier-laden sorbent. The method is especially suitable for removing residual organic carrier from phosphoric acid after solvent extraction uranium recovery. (author)

  8. Amplification factor variable amplifier

    NARCIS (Netherlands)

    Akitsugu, Oshita; Nauta, Bram

    2007-01-01

    PROBLEM TO BE SOLVED: To provide an amplification factor variable amplifier capable of achieving temperature compensation of an amplification factor over a wide variable amplification factor range. ; SOLUTION: A Gilbert type amplification factor variable amplifier 11 amplifies an input signal and

  9. Amplification factor variable amplifier

    NARCIS (Netherlands)

    Akitsugu, Oshita; Nauta, Bram

    2010-01-01

    PROBLEM TO BE SOLVED: To provide an amplification factor variable amplifier capable of achieving temperature compensation of an amplification factor over a wide variable amplification factor range. ;SOLUTION: A Gilbert type amplification factor variable amplifier 11 amplifies an input signal and can

  10. Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

    Directory of Open Access Journals (Sweden)

    Anja Gulliksen

    2012-01-01

    Full Text Available The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n=28 from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection.

  11. Chlamydia trachomatis infection positivity rates determined by nucleic acid amplification test in patients of hospitals in the northeastern region of Ukraine.

    Science.gov (United States)

    Belozorov, Alexei; Fedets, Olga; Chastii, Tatjana; Milutina, Elena; Sokol, Oksana; Grigorova, Ritsa; Unuchko, Sergey

    2017-12-01

    There are no accurate data regarding the prevalence of Chlamydia trachomatis infection in Ukraine. This study aims to estimate the prevalence in the northeastern region of the country through reviewing nucleic acid amplification test results in patients of medical institutions in the Kharkov region during 2014-2016. Samples from 6920 patients (5028 women and 1892 men) aged 12-76 years were tested. The overall positivity rate was 4.5% (95% CI 4.0-5.0): 3.9% (95% CI 3.4-4.5) in women and 6.1% (95% CI 5.1-7.3) in men. The highest prevalence was found in the 16-20 (8.5%, CI 6.3-11.4) and 21-25 (8.0%, CI 6.7-9.4) year age groups. The prevalence in men was higher than in women in all investigated groups. The results show the need for more attention to the prevention, diagnosis, and treatment of chlamydial infection in these age groups of women and men in this region.

  12. Detection and identification of occult HBV in blood donors in Taiwan using a commercial, multiplex, multi-dye nucleic acid amplification technology screening test.

    Science.gov (United States)

    Lin, K T; Chang, C L; Tsai, M H; Lin, K S; Saldanha, J; Hung, C M

    2014-02-01

    The ability of a new generation commercial, multiplex, multi-dye test from Roche, the cobas TaqScreen MPX test, version 2.0, to detect and identify occult HBV infections was evaluated using routine donor samples from Kaohsiung Blood Bank, Taiwan. A total of 5973 samples were tested by nucleic acid amplification technology (NAT); 5898 in pools of six, 66 in pools of less than six and nine samples individually. NAT-reactive samples were retested with alternative NAT tests, and follow-up samples from the donors were tested individually by NAT and for all the HBV serological markers. Eight NAT-only-reactive donors were identified, and follow-up samples were obtained from six of the donors. The results indicated that all eight donors had an occult HBV infection with viral loads <12 IU/ml. The cobas(®) TaqScreen MPX test, version 2.0, has an advantage over the current Roche blood screening test, the cobas TaqScreen MPX test, for screening donations in countries with a high prevalence of occult HBV infections since the uncertainty associated with identifying samples with very low viremia is removed by the ability of the test to identify the viral target in samples that are reactive with the cobas TaqScreen MPX test, version 2.0. © 2013 International Society of Blood Transfusion.

  13. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Neufeld, Josh D; Bodrossy, Levente; Stralis-Pavese, Nancy; McNamara, Niall P; Ostle, Nick; Briones, Maria J I; Murrell, J Colin

    2008-10-01

    Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

  14. Novel subtractive transcription-based amplification of mRNA (STAR method and its application in search of rare and differentially expressed genes in AD brains

    Directory of Open Access Journals (Sweden)

    Walker P Roy

    2006-11-01

    Full Text Available Abstract Background Alzheimer's disease (AD is a complex disorder that involves multiple biological processes. Many genes implicated in these processes may be present in low abundance in the human brain. DNA microarray analysis identifies changed genes that are expressed at high or moderate levels. Complementary to this approach, we described here a novel technology designed specifically to isolate rare and novel genes previously undetectable by other methods. We have used this method to identify differentially expressed genes in brains affected by AD. Our method, termed Subtractive Transcription-based Amplification of mRNA (STAR, is a combination of subtractive RNA/DNA hybridization and RNA amplification, which allows the removal of non-differentially expressed transcripts and the linear amplification of the differentially expressed genes. Results Using the STAR technology we have identified over 800 differentially expressed sequences in AD brains, both up- and down- regulated, compared to age-matched controls. Over 55% of the sequences represent genes of unknown function and roughly half of them were novel and rare discoveries in the human brain. The expression changes of nearly 80 unique genes were further confirmed by qRT-PCR and the association of additional genes with AD and/or neurodegeneration was established using an in-house literature mining tool (LitMiner. Conclusion The STAR process significantly amplifies unique and rare sequences relative to abundant housekeeping genes and, as a consequence, identifies genes not previously linked to AD. This method also offers new opportunities to study the subtle changes in gene expression that potentially contribute to the development and/or progression of AD.

  15. A universal colorimetry for nucleic acids and aptamer-specific ligands detection based on DNA hybridization amplification.

    Science.gov (United States)

    Li, Shuang; Shang, Xinxin; Liu, Jia; Wang, Yujie; Guo, Yingshu; You, Jinmao

    2017-07-01

    We present a universal amplified-colorimetric for detecting nucleic acid targets or aptamer-specific ligand targets based on gold nanoparticle-DNA (GNP-DNA) hybridization chain reaction (HCR). The universal arrays consisted of capture probe and hairpin DNA-GNP. First, capture probe recognized target specificity and released the initiator sequence. Then dispersed hairpin DNA modified GNPs were cross-linked to form aggregates through HCR events triggered by initiator sequence. As the aggregates accumulate, a significant red-to purple color change can be easily visualized by the naked eye. We used miRNA target sequence (miRNA-203) and aptamer-specific ligand (ATP) as target molecules for this proof-of-concept experiment. Initiator sequence (DNA2) was released from the capture probe (MNP/DNA1/2 conjugates) under the strong competitiveness of miRNA-203. Hairpin DNA (H1 and H2) can be complementary with the help of initiator DNA2 to form GNP-H1/GNP-H2 aggregates. The absorption ratio (A 620 /A 520 ) values of solutions were a sensitive function of miRNA-203 concentration covering from 1.0 × 10 -11  M to 9.0 × 10 -10  M, and as low as 1.0 × 10 -11  M could be detected. At the same time, the color changed from light wine red to purple and then to light blue have occurred in the solution. For ATP, initiator sequence (5'-end of DNA3) was released from the capture probe (DNA3) under the strong combination of aptamer-ATP. The present colorimetric for specific detection of ATP exhibited good sensitivity and 1.0 × 10 -8  M ATP could be detected. The proposed strategy also showed good performances for qualitative analysis and quantitative analysis of intracellular nucleic acids and aptamer-specific ligands. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Ultrasmall volume molecular isothermal amplification in microfluidic chip with advanced surface processing

    International Nuclear Information System (INIS)

    Huang Guoliang; Yang Xiaoyong; Ma Li; Yang Xu

    2011-01-01

    In this paper, we developed a metal micro-fluidic chip with advanced surface processing for ultra-small volume molecular isothermal amplification. This method takes advantages of the nucleic acid amplification with good stability and consistency, high sensitivity about 31 genomic DNA copies and bacteria specific gene identification. Based on the advanced surface processing, the bioreaction assays of nucleic acid amplification was dropped about 392nl in volume. A high numerical aperture confocal optical detection system was advanced to sensitively monitor the DNA amplification with low noise and high power collecting fluorescence near to the optical diffraction limit. A speedy nucleic acid isothermal amplification was performed in the ultra-small volume microfluidic chip, where the time at the inflexions of second derivative to DNA exponential amplified curves was brought forward and the sensitivity was improved about 65 folds to that of in current 25μl Ep-tube amplified reaction, which indicates a promising clinic molecular diagnostics in the droplet amplification.

  17. Development of a Reverse Transcription Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Subtype H7N9 Avian Influenza Virus

    Directory of Open Access Journals (Sweden)

    Hongmei Bao

    2014-01-01

    Full Text Available A novel influenza A (H7N9 virus has emerged in China. To rapidly detect this virus from clinical samples, we developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP method for the detection of the H7N9 virus. The minimum detection limit of the RT-LAMP assay was 0.01 PFU H7N9 virus, making this method 100-fold more sensitive to the detection of the H7N9 virus than conventional RT-PCR. The H7N9 virus RT-LAMP assays can efficiently detect different sources of H7N9 influenza virus RNA (from chickens, pigeons, the environment, and humans. No cross-reactive amplification with the RNA of other subtype influenza viruses or of other avian respiratory viruses was observed. The assays can effectively detect H7N9 influenza virus RNA in drinking water, soil, cloacal swab, and tracheal swab samples that were collected from live poultry markets, as well as human H7N9 virus, in less than 30 min. These results suggest that the H7N9 virus RT-LAMP assays were efficient, practical, and rapid diagnostic methods for the epidemiological surveillance and diagnosis of influenza A (H7N9 virus from different resource samples.

  18. Type-specific identification of anogenital herpes simplex virus infections by use of a commercially available nucleic acid amplification test.

    Science.gov (United States)

    Van Der Pol, Barbara; Warren, Terri; Taylor, Stephanie N; Martens, Mark; Jerome, Keith R; Mena, Leandro; Lebed, Joel; Ginde, Savita; Fine, Paul; Hook, Edward W

    2012-11-01

    Herpes infections are among the most common sexually transmitted infections (STI), but diagnostic methods for genital herpes have not kept pace with the movement toward molecular testing. Here, we describe an FDA-approved molecular assay that identifies and types herpes simplex virus (HSV) infections for use in routine clinical settings. Paired samples from anogenital lesions were tested using the BD ProbeTec HSV Q(x) (HSVQ(x)) system, HSV culture and, a laboratory-developed PCR assay. Family planning, obstetrics/gynecology (OB/GYN), or sexually transmitted disease (STD) clinics in the United States served as recruitment sites. Sensitivity and specificity estimates, head-to-head comparisons, measures of agreement, and latent-class analyses were performed to provide robust estimates of performance. A total of 508 participants (174 men and 334 women) with anogenital lesions were included; 260 HSV-2 and 73 HSV-1 infections were identified. No differences in test performance based on gender, clinic type, location of the lesion, or type of lesion were observed. The sensitivity of HSV-2 detection ranged from 98.4 to 100% depending on the analytical approach, while the specificity ranged from 80.6%, compared to the less sensitive culture method, to 97.0%, compared to PCR. For HSV-1, the sensitivity and specificity ranges were 96.7 to 100% and 95.1 to 99.4%, respectively. This assay may improve our ability to accurately diagnose anogenital lesions due to herpes infection.

  19. ONE STEP NUCLEIC ACID AMPLIFICATION IN BREAST CANCER SENTINEL LYMPH NODE.A SINGLE INSTITUTIONAL EXPERIENCE AND A SHORT REVIEW.

    Directory of Open Access Journals (Sweden)

    Tatiana eBrambilla

    2015-06-01

    Full Text Available Sentinel lymph node (SLN examination is a standard in breast cancer patients, with several methods employed along its 20-years history, the last one represented by OSNA. The latter is a intra-operative molecular assay searching for CK19 mRNA as a surrogate of metastatic cells. Our 3-years experience with OSNA (1122 patients showed results overlapping those recorded in the same Institution with a morphological evaluation (930 patients of SLN. In detail the data of OSNA were almost identical to those observed with standard post-operative procedure in terms of patients with positive SLN (30% and micrometastatic/macrometastatic involvement of SLN (respectively 38-45% and 62-55%. By contrast when OSNA was compared to the standard intra-operatory procedure it was superior in terms of accuracy, prompting the use of this molecular assay as a very valid and reproducible for intra-operative evaluation of SLN.Further possibilities prompting the use of OSNA range from adhesion to quality control programs, saving of medical time, ability to predict, during surgery, additional nodal metatastis and molecular bio-banking.

  20. Added benefit of nucleic acid amplification testing for the diagnosis of Trichomonas vaginalis among men and women attending a sexually transmitted diseases clinic.

    Science.gov (United States)

    Muzny, Christina A; Blackburn, Reaford J; Sinsky, Richard J; Austin, Erika L; Schwebke, Jane R

    2014-09-15

    Trichomonas vaginalis (TV) is the most common nonviral sexually transmitted infection (STI) in the world. However, TV is not a reportable STI and, with the exception of HIV-positive women, there are no guidelines for screening in women or men. The objective of this study was to determine the added value of nucleic acid amplification tests (NAATs) for detection of TV in men and women at high risk for infection as well as correlates of infection. This was a review of clinical and laboratory data of men and women presenting to the Jefferson County Department of Health Sexually Transmitted Diseases (STD) Clinic and receiving a TV NAAT. During 2012-2013, 6335 patients (3821 women and 2514 men) received a TV NAAT on endocervical, urethral, or urine specimens. Overall TV prevalence was 20.2%; 27.0% in women and 9.8% in men. Correlates of TV among men included age >40 years, African American race, and ≥5 polymorphonuclear cells per high-power field on urethral Gram stain. Age >40 years, African American race, leukorrhea on wet mount, elevated vaginal pH, positive whiff test, and concurrent gonococcal infection were positively associated with TV among women. TV NAAT detected approximately one-third more infections among women than wet mount alone. TV prevalence among men and women was high in this study, suggesting that both groups should be routinely screened, including those aged >40 years. Improved detection of TV by routine implementation of NAATs should result in better control of this common, treatable STI. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Effects of humic acid on DNA quantification with Quantifiler® Human DNA Quantification kit and short tandem repeat amplification efficiency.

    Science.gov (United States)

    Seo, Seung Bum; Lee, Hye Young; Zhang, Ai Hua; Kim, Hye Yeon; Shin, Dong Hoon; Lee, Soong Deok

    2012-11-01

    Correct DNA quantification is an essential part to obtain reliable STR typing results. Forensic DNA analysts often use commercial kits for DNA quantification; among them, real-time-based DNA quantification kits are most frequently used. Incorrect DNA quantification due to the presence of PCR inhibitors may affect experiment results. In this study, we examined the alteration degree of DNA quantification results estimated in DNA samples containing a PCR inhibitor by using a Quantifiler® Human DNA Quantification kit. For experiments, we prepared approximately 0.25 ng/μl DNA samples containing various concentrations of humic acid (HA). The quantification results were 0.194-0.303 ng/μl at 0-1.6 ng/μl HA (final concentration in the Quantifiler reaction) and 0.003-0.168 ng/μl at 2.4-4.0 ng/μl HA. Most DNA quantity was undetermined when HA concentration was higher than 4.8 ng/μl HA. The C (T) values of an internal PCR control (IPC) were 28.0-31.0, 36.5-37.1, and undetermined at 0-1.6, 2.4, and 3.2 ng/μl HA. These results indicate that underestimated DNA quantification results may be obtained in the DNA sample with high C (T) values of IPC. Thus, researchers should carefully interpret the DNA quantification results. We additionally examined the effects of HA on the STR amplification by using an Identifiler® kit and a MiniFiler™ kit. Based on the results of this study, it is thought that a better understanding of various effects of HA would help researchers recognize and manipulate samples containing HA.

  2. Investigation of an algorithm for anti HCV EIA reactivity in blood donor screening in Turkey in the absence of nucleic acid amplification screening.

    Science.gov (United States)

    Karakoc, Ayse Esra; Berkem, Rukiye; Irmak, Hasan; Demiroz, Ali Pekcan; Yenicesu, Idil; Ertugrul, Nigar; Arslan, Önder; Kemahli, Sabri; Yilmaz, Sevinc; Ozcebe, Osman; Kara, Abdurrahman; Ozet, Gulsum; Acikgoz, Ziya Cibali; Acikgoz, Tulin

    2017-10-01

    In this study we aimed to propose an algorithm for initial anti HCV EIA reactive blood donations in Turkey where nucleic acid amplification tests are not yet obligatory for donor screening. A total of 416 anti HCV screening test reactive donor samples collected from 13 blood centers from three cities in Turkey were tested in duplicate by Ortho HCV Ab Version 3.0 and Radim HCV Ab. All the repeat reactive samples were tested by INNO-LIA HCV Ab 3.0 or Chiron RIBA HCV 3.0 and Abbott Real Time HCV. Intra-assay correlations were calculated with Pearson r test. ROC analysis was used to study the relationship between EIA tests and the confirmatory tests. The number of repeat reactive results with Ortho EIA were 221 (53.1%) whereas that of microEIA, 62 (14.9%). Confirmed positivity rate was 14.6% (33/226) by RIBA and 10.6% (24/226) by NAT. Reactive PCR results were predicted with 100% sensitivity and 95% specificity with S/CO levels of 8.1 with Ortho EIA and 3.4 with microEIA. Repeat reactivity rates declined with a second HCV antibody assay. Samples repeat reactive with one HCV antibody test and negative with the other were all NAT negative. All the NAT reactive samples were RIBA positive. None of the RIBA indeterminate or negative samples were NAT reactive. Considering the threshold values for EIA kits determined by ROC analysis NAT was decided to be performed for the samples above the threshold value and a validated supplemental HCV antibody test for the samples below. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Methods to determine the transcriptomes of trypanosomes in mixtures with mammalian cells: the effects of parasite purification and selective cDNA amplification.

    Directory of Open Access Journals (Sweden)

    Julius Mulindwa

    2014-04-01

    Full Text Available Patterns of gene expression in cultured Trypanosoma brucei bloodstream and procyclic forms have been extensively characterized, and some comparisons have been made with trypanosomes grown to high parasitaemias in laboratory rodents. We do not know, however, to what extent these transcriptomes resemble those in infected Tsetse flies - or in humans or cattle, where parasitaemias are substantially lower. For clinical and field samples it is difficult to characterize parasite gene expression because of the large excess of host cell RNA. We have here examined two potential solutions to this problem for bloodstream form trypanosomes, assaying transcriptomes by high throughput cDNA sequencing (RNASeq. We first purified the parasites from blood of infected rats. We found that a red blood cell lysis procedure affected the transcriptome substantially more than purification using a DEAE cellulose column, but that too introduced significant distortions and variability. As an alternative, we specifically amplified parasite sequences from a mixture containing a 1000-fold excess of human RNA. We first purified polyadenylated RNA, then made trypanosome-specific cDNA by priming with a spliced leader primer. Finally, the cDNA was amplified using nested primers. The amplification procedure was able to produce samples in which 20% of sequence reads mapped to the trypanosome genome. Synthesis of the second cDNA strand with a spliced leader primer, followed by amplification, is sufficiently reproducible to allow comparison of different samples so long as they are all treated in the same way. However, SL priming distorted the abundances of the cDNA products and definitely cannot be used, by itself, to measure absolute mRNA levels. The amplification method might be suitable for clinical samples with low parasitaemias, and could also be adapted for other Kinetoplastids and to samples from infected vectors.

  4. Whole genome amplification of Chelex-extracted DNA from a single mite: a method for studying genetics of the predatory mite Phytoseiulus persimilis.

    Science.gov (United States)

    Konakandla, Bhanu; Park, Yoonseong; Margolies, David

    2006-01-01

    We developed and optimized a method using Chelex DNA extraction followed by whole genome amplification (WGA) to overcome problems conducting molecular genetic studies due to the limited amount of DNA obtainable from individual small organisms such as predatory mites. The DNA from a single mite, Phytoseiulus persimilis Athias-Henrot (Acari: Phytoseiidae), isolated in Chelex suspension was subjected to WGA. More than 1000-fold amplification of the DNA was achieved using as little as 0.03 ng genomic DNA template. The DNA obtained by the WGA was used for polymerase chain reaction followed by direct sequencing. From WGA DNA, nuclear DNA intergenic spacers ITS1 and ITS2 and a mitochondrial DNA 12S marker were tested in three different geographical populations of the predatory mite: California, the Netherlands, and Sicily. We found a total of four different alleles of the 12S in the Sicilian population, but no polymorphism was identified in the ITS marker. The combination of Chelex DNA extraction and WGA is thus shown to be a simple and robust technique for examining molecular markers for multiple loci by using individual mites. We conclude that the methods, Chelex extraction of DNA followed by WGA, provide a large quantity of DNA template that can be used for multiple PCR reactions useful for genetic studies requiring the genotypes of individual mites.

  5. A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters.

    Science.gov (United States)

    Kolm, Claudia; Martzy, Roland; Brunner, Kurt; Mach, Robert L; Krska, Rudolf; Heinze, Georg; Sommer, Regina; Reischer, Georg H; Farnleitner, Andreas H

    2017-06-20

    We report a novel molecular assay, based on helicase-dependent amplification (HDA), for the detection of enterococci as markers for fecal pollution in water. This isothermal assay targets the same Enterococcus 23S rRNA gene region as the existing quantitative polymerase chain reaction (qPCR) assays of U.S. Environmental Protection Agency Methods 1611 and 1609 but can be entirely performed on a simple heating block. The developed Enterococcus HDA assay successfully discriminated 15 enterococcal from 15 non-enterococcal reference strains and reliably detected 48 environmental isolates of enterococci. The limit of detection was 25 target copies per reaction, only 3 times higher than that of qPCR. The applicability of the assay was tested on 30 environmental water sample DNA extracts, simulating a gradient of fecal pollution. Despite the isothermal nature of the reaction, the HDA results were consistent with those of the qPCR reference. Given this performance, we conclude that the developed Enterococcus HDA assay has great potential as a qualitative molecular screening method for resource-limited settings when combined with compatible up- and downstream processes. This amplification strategy can pave the way for developing a new generation of rapid, low-cost, and field-deployable molecular diagnostic tools for water quality monitoring.

  6. Amplification of the epidermal growth factor receptor gene in glioblastoma: an analysis of the relationship between genotype and phenotype by CISH method.

    Science.gov (United States)

    Miyanaga, Tomomi; Hirato, Junko; Nakazato, Yoichi

    2008-04-01

    We examined epidermal growth factor receptor (EGFR) overexpression and EGFR gene amplification using immunohistochemistry (IHC) and chromogenic in situ hybridization (CISH) in 109 glioblastomas, including 98 primary glioblastomas and 11 secondary glioblastomas. EGFR overexpression and EGFR gene amplification were found in 33% and 24% of glioblastoma, respectively, and all of those cases were primary glioblastoma. Large ischemic necrosis was significantly more frequent in primary glioblastomas than in secondary glioblastomas (54% vs. 18%), but pseudopalisading necrosis was not (65% vs. 54%). EGFR gene amplification was detected significantly more frequently in cases with both types of necrosis. Although glioblastomas with EGFR gene amplification invariably exhibited EGFR overexpression at the level of the whole tumor, tumor cells with EGFR gene amplification did not always show EGFR overexpression at the level of individual tumor cells. Cases of "strong" EGFR overexpression on IHC could be regarded as having EGFR gene amplification, and cases without EGFR overexpression could not. Cases of "weak" EGFR overexpression should be tested with CISH to confirm the presence of EGFR gene amplification. We found that 54% of glioblastomas with EGFR gene amplification were composed of areas with and without EGFR gene amplification; however, there were no obvious differences in morphology between tumor cells with and without EGFR gene amplification. Although small cell architecture might be associated with EGFR gene amplification at the level of the whole tumor, it did not always suggest amplification of the EGFR gene at the level of individual tumor cells. In one case, it seemed to suggest that a clone with EGFR gene amplification may arise in pre-existing tumor tissue and extend into the surrounding area. In cases of overall EGFR amplification, CISH would be a useful tool to decide the tumor border in areas infiltrated by tumor cells.

  7. Evaluation of three methods of DNA extraction from paraffin-embedded material for the amplification of genomic DNA by means of the PCR technique

    Directory of Open Access Journals (Sweden)

    MESQUITA Ricardo Alves

    2001-01-01

    Full Text Available There are several protocols reported in the literature for the extraction of genomic DNA from formalin-fixed paraffin-embedded samples. Genomic DNA is utilized in molecular analyses, including PCR. This study compares three different methods for the extraction of genomic DNA from formalin-fixed paraffin-embedded (inflammatory fibrous hyperplasia and non-formalin-fixed (normal oral mucosa samples: phenol with enzymatic digestion, and silica with and without enzymatic digestion. The amplification of DNA by means of the PCR technique was carried out with primers for the exon 7 of human keratin type 14. Amplicons were analyzed by means of electrophoresis in an 8% polyacrylamide gel with 5% glycerol, followed by silver-staining visualization. The phenol/enzymatic digestion and the silica/enzymatic digestion methods provided amplicons from both tissue samples. The method described is a potential aid in the establishment of the histopathologic diagnosis and in retrospective studies with archival paraffin-embedded samples.

  8. Highly simplified lateral flow-based nucleic acid sample preparation and passive fluid flow control

    Science.gov (United States)

    Cary, Robert E.

    2015-12-08

    Highly simplified lateral flow chromatographic nucleic acid sample preparation methods, devices, and integrated systems are provided for the efficient concentration of trace samples and the removal of nucleic acid amplification inhibitors. Methods for capturing and reducing inhibitors of nucleic acid amplification reactions, such as humic acid, using polyvinylpyrrolidone treated elements of the lateral flow device are also provided. Further provided are passive fluid control methods and systems for use in lateral flow assays.

  9. Highly simplified lateral flow-based nucleic acid sample preparation and passive fluid flow control

    Energy Technology Data Exchange (ETDEWEB)

    Cary, Robert B.

    2018-04-17

    Highly simplified lateral flow chromatographic nucleic acid sample preparation methods, devices, and integrated systems are provided for the efficient concentration of trace samples and the removal of nucleic acid amplification inhibitors. Methods for capturing and reducing inhibitors of nucleic acid amplification reactions, such as humic acid, using polyvinylpyrrolidone treated elements of the lateral flow device are also provided. Further provided are passive fluid control methods and systems for use in lateral flow assays.

  10. Removal of plutonium from nitric acid-oxalic acid solutions using anion exchange method

    International Nuclear Information System (INIS)

    Kasar, U.M.; Pawar, S.M.; Joshi, A.R.

    1999-01-01

    An anion exchange method using Amberlyst A-26 (MP) resin was developed for removal of Pu from nitric acid-oxalic acid solutions without destroying oxalate. The method consists of sorption of Pu(IV) on Amberlyst A-26, a macroporous anion exchange resin, from nitric acid-oxalic acid medium in the presence of Al(NO 3 ) 3 . Pu(IV) breakthrough capacity of Amberlyst A-26 using synthetic feed solution was determined. (author)

  11. Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities.

    Science.gov (United States)

    Lee, Patrick K H; Men, Yujie; Wang, Shanquan; He, Jianzhong; Alvarez-Cohen, Lisa

    2015-02-03

    Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

  12. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes.

    Science.gov (United States)

    Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare . However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

  13. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    Directory of Open Access Journals (Sweden)

    Karolina Chwialkowska

    2017-11-01

    Full Text Available Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq. We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation

  14. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    Science.gov (United States)

    Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

  15. Novel Method of Lactic Acid Production by Electrodialysis Fermentation

    OpenAIRE

    Hongo, Motoyoshi; Nomura, Yoshiyuki; Iwahara, Masayoshi

    1986-01-01

    In lactic acid fermentation by Lactobacillus delbrueckii, the produced lactic acid affected the lactic acid productivity. Therefore, for the purpose of alleviating this inhibitory effect, an electrodialysis fermentation method which can continuously remove produced lactic acid from the fermentation broth was applied to this fermentation process. As a result, the continuation of fermentation activity was obtained, and the productivity was three times higher than in non-pH-controlled fermentati...

  16. Instant, Visual, and Instrument-Free Method for On-Site Screening of GTS 40-3-2 Soybean Based on Body-Heat Triggered Recombinase Polymerase Amplification.

    Science.gov (United States)

    Wang, Rui; Zhang, Fang; Wang, Liu; Qian, Wenjuan; Qian, Cheng; Wu, Jian; Ying, Yibin

    2017-04-18

    On-site monitoring the plantation of genetically modified (GM) crops is of critical importance in agriculture industry throughout the world. In this paper, a simple, visual and instrument-free method for instant on-site detection of GTS 40-3-2 soybean has been developed. It is based on body-heat recombinase polymerase amplification (RPA) and followed with naked-eye detection via fluorescent DNA dye. Combining with extremely simplified sample preparation, the whole detection process can be accomplished within 10 min and the fluorescent results can be photographed by an accompanied smart phone. Results demonstrated a 100% detection rate for screening of practical GTS 40-3-2 soybean samples by 20 volunteers under different ambient temperatures. This method is not only suitable for on-site detection of GM crops but also demonstrates great potential to be applied in other fields.

  17. Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification

    Directory of Open Access Journals (Sweden)

    Joojin Jeong

    2015-09-01

    Full Text Available The primary step for efficient control of viral diseases is the development of simple, rapid, and sensitive virus detection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR to demonstrate its advantages over RT-PCR. RT-LAMP reactions were conducted with or without a set of loop primers since one out of six primers showed PVX specificity. Based on real-time monitoring, RT-LAMP detected PVX around 30 min, compared to 120 min for RT-PCR. By adding a fluorescent reagent during the reaction, the extra step of visualization by gel electrophoresis was not necessary. RT-LAMP was conducted using simple inexpensive instruments and a regular incubator to evaluate whether RNA could be amplified at a constant temperature instead of using an expensive thermal cycler. This study shows the potential of RT-LAMP for the diagnosis of viral diseases and PVX epidemiology because of its simplicity and rapidness compared to RT-PCR.

  18. Hypochlorous Acid - Analytical Methods and Antimicrobial Activity ...

    African Journals Online (AJOL)

    Hypochlorous acid (HOCl) is produced by the human body's immune cells to fight infections. It is effective against a broad range of microorganisms. It is non-toxic, non-irritant and non-corrosive at proper usage concentrations. There are some available commercial products that contain HOCl. However, its low storage ...

  19. Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection

    NARCIS (Netherlands)

    Velders, Aldrik H.; Schoen, Cor; Saggiomo, Vittorio

    2018-01-01

    Objective: Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap

  20. Mutant fatty acid desaturase and methods for directed mutagenesis

    Science.gov (United States)

    Shanklin, John [Shoreham, NY; Whittle, Edward J [Greenport, NY

    2008-01-29

    The present invention relates to methods for producing fatty acid desaturase mutants having a substantially increased activity towards substrates with fewer than 18 carbon atom chains relative to an unmutagenized precursor desaturase having an 18 carbon chain length specificity, the sequences encoding the desaturases and to the desaturases that are produced by the methods. The present invention further relates to a method for altering a function of a protein, including a fatty acid desaturase, through directed mutagenesis involving identifying candidate amino acid residues, producing a library of mutants of the protein by simultaneously randomizing all amino acid candidates, and selecting for mutants which exhibit the desired alteration of function. Candidate amino acids are identified by a combination of methods. Enzymatic, binding, structural and other functions of proteins can be altered by the method.

  1. On-site detection of Xylella fastidiosa in host plants and in “spy insects” using the real-time loop-mediated isothermal amplification method

    Directory of Open Access Journals (Sweden)

    Thaer YASEEN

    2015-12-01

    Full Text Available A recent severe outbreak of Xylella fastidiosa associated with ‘olive quick decline syndrome’ (OQDS was reported in Apulia (Southern Italy. In this study an on-site real-time loop-mediated isothermal amplification (real-time LAMP was developed for detecting X. fastidiosa in host plants and insects. A marked simplification of the DNA extraction procedure was obtained by heating the samples in a portable Smart-Dart device and using an optimized enhancer reaction buffer. The connection to a tablet or Smartphone allowed to visualize the results of the reaction in real time. Compared to PCR and ELISA, with which it showed comparable results in terms of sensitivity and reliability in the X. fastidiosa detection, this simplified real-time LAMP procedure proved to be “user friendly”, displaying the advantages to be an on-site detection method of easy handling, rapid execution and low cost.

  2. [Establishment of a novel HLA genotyping method for preimplantation genetic diagnonis using multiple displacement amplification-polymerase chain reaction-sequencing based technique].

    Science.gov (United States)

    Zhang, Yinfeng; Luo, Haining; Zhang, Yunshan

    2015-12-01

    To establish a novel HLA genotyping method for preimplantation genetic diagnonis (PGD) using multiple displacement amplification-polymerase chain reaction-sequencing based technique (MDA-PCR-SBT). Peripheral blood samples and 76 1PN, 2PN, 3PN discarded embryos from 9 couples were collected. The alleles of HLA-A, B, DR loci were detected from the MDA product with the PCR-SBT method. The HLA genotypes of the parental peripheral blood samples were analyzed with the same protocol. The genotypes of specific HLA region were evaluated for distinguishing the segregation of haplotypes among the family members, and primary HLA matching was performed between the embryos. The 76 embryos were subjected to MDA and 74 (97.4%) were successfully amplified. For the 34 embryos from the single blastomere group, the amplification rate was 94.1%, and for the 40 embryos in the two blastomeres group, the rate was 100%. The dropout rates for DQ allele and DR allele were 1.3% and 0, respectively. The positive rate for MDA in the single blastomere group was 100%, with the dropout rates for DQ allele and DR allele being 1.5% and 0, respectively. The positive rate of MDA for the two blastomere group was 100%, with the dropout rates for both DQ and DR alleles being 0. The recombination rate of fetal HLA was 20.2% (30/148). Due to the improper classification and abnormal fertilized embryos, the proportion of matched embryos HLA was 20.3% (15/74),which was lower than the theoretical value of 25%. PGD with HLA matching can facilitate creation of a HLA-identical donor (saviour child) for umbilical cord blood or bone marrow stem cells for its affected sibling with a genetic disease. Therefore, preimplantation HLA matching may provide a tool for couples desiring to conceive a potential donor progeny for transplantation for its sibling with a life-threatening disorder.

  3. A unique dual recognition hairpin probe mediated fluorescence amplification method for sensitive detection of uracil-DNA glycosylase and endonuclease IV activities.

    Science.gov (United States)

    Wu, Yushu; Yan, Ping; Xu, Xiaowen; Jiang, Wei

    2016-03-07

    Uracil-DNA glycosylase (UDG) and endonuclease IV (Endo IV) play cooperative roles in uracil base-excision repair (UBER) and inactivity of either will interrupt the UBER to cause disease. Detection of UDG and Endo IV activities is crucial to evaluate the UBER process in fundamental research and diagnostic application. Here, a unique dual recognition hairpin probe mediated fluorescence amplification method was developed for sensitively and selectively detecting UDG and Endo IV activities. For detecting UDG activity, the uracil base in the probe was excised by the target enzyme to generate an apurinic/apyrimidinic (AP) site, achieving the UDG recognition. Then, the AP site was cleaved by a tool enzyme Endo IV, releasing a primer to trigger rolling circle amplification (RCA) reaction. Finally, the RCA reaction produced numerous repeated G-quadruplex sequences, which interacted with N-methyl-mesoporphyrin IX to generate an enhanced fluorescence signal. Alternatively, for detecting Endo IV activity, the uracil base in the probe was first converted into an AP site by a tool enzyme UDG. Next, the AP site was cleaved by the target enzyme, achieving the Endo IV recognition. The signal was then generated and amplified in the same way as those in the UDG activity assay. The detection limits were as low as 0.00017 U mL(-1) for UDG and 0.11 U mL(-1) for Endo IV, respectively. Moreover, UDG and Endo IV can be well distinguished from their analogs. This method is beneficial for properly evaluating the UBER process in function studies and disease prognoses.

  4. Evaluation of cost-effective total nucleic acids extraction protocols for cultured Mycobacterium tuberculosis; a comparison by PCR amplification of genes associated with drug resistance

    Directory of Open Access Journals (Sweden)

    Gyamfi Oti K

    2010-02-01

    Full Text Available Abstract Background The emergence of drug resistant strains of Mycobacterium tuberculosis complex has made the management of tuberculosis difficult. Also, Mycobacterium species has a peculiar cell wall, made of an impermeable complex structure rich in mycolate, making the lyses of its cell difficult. In order to apply a radio-labelled-probe based detection of mutations in selected genes leading to drug resistance, we concede that the evaluation and modifications of nucleic acid extraction protocols that are less sophisticated and less prone to contamination would be useful in the management of tuberculosis in a resource-constrained setting. Findings The average amount of nucleic acids was determined for different extraction treatments. High temperature treatment only, yielded the lowest amount of nucleic acids, i.e. 15.7 ± 3.2 μg. The average amount of nucleic acids obtained with the addition of TE and triton-X100, was 133.7 ± 8.9 μg, while that obtained with the addition of TE only, and TE and SDS were 68.4 ± 22.7 μg and 70.4 ± 20.3 μg respectively. Other treatments yielded 28.8 ± 6.7 μg, 32.5 ± 2.4 μg and 36.9 ± 15.5 μg. The average amount of nucleic acids obtained with high temperature treatment in TE, and that obtained by freezing prior to high temperature treatment, successfully amplified for the genes of interest (rpoB, KatG, rrs. Conclusion We strongly recommend the use of 1× TE buffer, and freezing and heating for improved lysis of cultured M. tuberculosis, and therefore, as an effective method for the preparation of M. tuberculosis nucleic acid useful for PCR.

  5. Colorimetric Method of Loop-Mediated Isothermal Amplification with the Pre-Addition of Calcein for Detecting Flavobacterium columnare and its Assessment in Tilapia Farms.

    Science.gov (United States)

    Suebsing, Rungkarn; Kampeera, Jantana; Sirithammajak, Sarawut; Withyachumnarnkul, Boonsirm; Turner, Warren; Kiatpathomchai, Wansika

    2015-03-01

    Flavobacterium columnare, the causative agent of columnaris disease in fish, affects many economically important freshwater fish species. A colorimetric method of loop-mediated isothermal amplification with the pre-addition of calcein (LAMP-calcein) was developed and used to detect the presence of F. columnare in farmed tilapia (Nile Tilapia Oreochromis niloticus and red tilapia [Nile Tilapia × Mozambique Tilapia O. mossambicus]) and rearing water. The detection method, based on a change in color from orange to green, could be performed within 45 min at 63°C. The method was highly specific, as it had no cross-detections with 14 other bacterial species, including other fish pathogens and two Flavobacterium species. The method has a minimum detection limit of 2.2 × 10(2) F. columnare CFU; thus, it is about 10 times more sensitive than conventional PCR. With this method, F. columnare was detected in gonad, gill, and blood samples from apparently healthy tilapia broodstock as well as in samples of fertilized eggs, newly hatched fry, and rearing water. The bacteria isolated from the blood were further characterized biochemically and found to be phenotypically identical to F. columnare. The amplified products from the LAMP-calcein method had 97% homology with the DNA sequence of F. columnare.

  6. Gallic Acid: Review of the Methods of Determination and Quantification.

    Science.gov (United States)

    Fernandes, Felipe Hugo Alencar; Salgado, Hérida Regina Nunes

    2016-05-03

    Gallic acid (3,4,5 trihydroxybenzoic acid) is a secondary metabolite present in most plants. This metabolite is known to exhibit a range of bioactivities including antioxidant, antimicrobial, anti-inflammatory, and anticancer. There are various methods to analyze gallic acid including spectrometry, chromatography, and capillary electrophoresis, among others. They have been developed to identify and quantify this active ingredient in most biological matrices. The aim of this article is to review the available information on analytical methods for gallic acid, as well as presenting the advantages and limitations of each technique.

  7. Acid aerosol measurement method intercomparisons: An outdoor smog chamber study

    International Nuclear Information System (INIS)

    Ellestad, T.G.; Barnes, H.M.; Kamens, R.M.; McDow, S.R.; Sickles, J.E. II; Hodson, L.L.; Waldman, J.M.; Randtke, S.J.; Lane, D.D.; Springston, S.R.; Koutrakis, P.; Thurston, G.D.

    1991-01-01

    A workshop on the measurement of acid aerosols indicated that the sampling methods in use had not been intercompared. Following two laboratory pilot studies, EPA sponsored tests in an outdoor smog chamber with a variety of test aerosols, including sulfuric acid only, photochemical smog with added sulfuric acid, photo-chemical smog with added sulfuric acid and dust, and dust followed by photochemical smog with added sulfuric acid. Two experiments of each type were conducted. Six groups, several of which were active in ambient acid aerosol measurements, participated by operating duplicate samplers for each experiment. Five groups employed a similar method, in which ammonia is removed from the sample stream by diffusion, particles are removed by Teflon filter, and hydrogen ion on the Teflon filter is determined by pH electrode. However, differences existed in the method's implementation among groups in physical design, flow rate, procedures, and analysis. The sixth group's method did not use a diffusion denuder for ammonia and had several other important differences. Besides hydrogen ion, seven other species were reported by most of the groups, including particle phase sulfate, ammonium, and nitrate, and gas phase sulfur dioxide, ammonia, nitric acid, and nitrous acid. Results of the inter-comparison will be presented

  8. Method for recovery of uranium from phosphoric acid

    International Nuclear Information System (INIS)

    Duarte Neto, J.

    1984-01-01

    The results of a method for recuperation of uranium from phosphoric acid by humid way are presented. The extracting mixture used was di-ethylhexylphosphoric acid (D 2 EHPA) and trioctylphosphine oxide (TOPO). An installation in micro-pilot scale was made to get and visualize data for continuous process. (M.A.C.) [pt

  9. MEANS AND METHODS FOR CLONING NUCLEIC ACID SEQUENCES

    NARCIS (Netherlands)

    Geertsma, Eric Robin; Poolman, Berend

    2008-01-01

    The invention provides means and methods for efficiently cloning nucleic acid sequences of interest in micro-organisms that are less amenable to conventional nucleic acid manipulations, as compared to, for instance, E.coli. The present invention enables high-throughput cloning (and, preferably,

  10. A method for the determination of D(-)-lactic acid

    NARCIS (Netherlands)

    Hamer, C.J.A. van den; Elias, R.W.

    A method for the determination of D(—)-lactic acid is described. An acetone powder from Escherichia coli B in the presence of methylene blue oxidizes D(—)-lactic specifically. Oxygen consumption in a Warburg apparatus was used as a measure of the D(—)-lactic acid.

  11. The method of quantitative determination of iodine in acetic acid

    International Nuclear Information System (INIS)

    Sukhomlinov, A.B.; Kalinchenko, N.B.

    1988-01-01

    Method for separate determination of J 2 and J - concentrations in acetic acid is suggested. Iodine concentration in acetic acid is determined by measuring potential of iodine-selective electrode first in the initial solution of acetic acid, where molecular iodine dissociation equals 0.5, and then in acetic acid, with alkali (NaOH) addition up to pH > 3, where molecular iodine dissociation equals 1. Determination is conducted in 5x10 -7 -5x10 -6 mol/l concentration range with relative standard deviation not more than 0.1. 1 fig

  12. A rapid and specific detection of pathogenic serovar Salmonella typhimurium by loop-mediated isothermal amplification method (LAMP

    Directory of Open Access Journals (Sweden)

    Hadi Ravan

    2017-09-01

    Discussion and conclusion: As a result of a high sensitivity and specificity of the method as well as its low cost per assay, it could be concluded that the present LAMP assay is a powerful, accurate, and efficient method for detecting pathogenic serovar Salmonella typhimurium in food-processing industries and diagnostic laboratories.

  13. Development of a reverse transcription loop-mediated isothermal amplification method for the rapid detection of avian influenza virus subtype H7.

    Science.gov (United States)

    Bao, Hongmei; Wang, Xiurong; Zhao, Yuhui; Sun, Xiaodong; Li, Yanbing; Xiong, Yongzhong; Chen, Hualan

    2012-01-01

    A rapid and sensitive reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the detection of the H7 avian influenza virus (H7 AIV) isotype was developed. The minimum detection limit of the RT-LAMP assay was 0.1-0.01 PFU per reaction for H7 AIV RNA, making this assay 100-fold more sensitive than the conventional RT-PCR method. This RT-LAMP assay also has the capacity to detect both high- and low-pathogenic H7 AIV strains. Using a pool of RNAs extracted from influenza viruses corresponding to all 15 HA subtypes (in addition to other avian pathogenic viruses), the RT-LAMP system was confirmed to amplify only H7 AIV RNA. Furthermore, specific pathogen free (SPF) chickens were infected artificially with H7 AIV, throat and cloacal swabs were collected, and viral shedding was examined using viral isolation, RT-PCR and RT-LAMP. Shedding was detected following viral isolation and RT-LAMP one day after infection, whereas viral detection using RT-PCR was effective only on day 3 post-infection. These results indicate that the RT-LAMP method could facilitate epidemiological surveillance and the rapid diagnosis of the avian influenza subtype H7. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Development of loop-mediated isothermal amplification and SYBR green real-time PCR methods for the detection of Citrus yellow mosaic badnavirus in citrus species.

    Science.gov (United States)

    Anthony Johnson, A M; Dasgupta, I; Sai Gopal, D V R

    2014-07-01

    Citrus yellow mosaic badnavirus (CMBV) is an important pathogen in southern India spread by infected citrus propagules. One of the measures to arrest the spread of CMBV is to develop methods to screen and certify citrus propagules as CMBV-free. The methods loop-mediated isothermal amplification (LAMP) and SYBR green real-time PCR (SGRTPCR) have been developed for the efficient detection of CMBV in citrus propagules. This paper compares the sensitivities of LAMP and SGRTPCR with polymerase chain reaction (PCR) for the detection of CMBV. Whereas PCR and LAMP were able to detect CMBV from a minimum of 10 ng of total DNA of infected leaf samples, SGRTPCR could detect the same from 1 ng of total DNA. Using SGRTPCR, the viral titres were estimated to be the highest in rough lemon and lowest in Nagpur Mandarin of the five naturally infected citrus species tested. The results will help in designing suitable strategies for the sensitive detection of CMBV from citrus propagules. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. The Development and Evaluation of a Loop-Mediated Isothermal Amplification Method for the Rapid Detection of Salmonella enterica serovar Typhi.

    Directory of Open Access Journals (Sweden)

    Fenxia Fan

    Full Text Available Typhoid fever remains a public health threat in many countries. A positive result in traditional culture is a gold-standard for typhoid diagnosis, but this method is time consuming and not sensitive enough for detection of samples containing a low copy number of the target organism. The availability of the loop-mediated isothermal amplification (LAMP assay, which offers high speed and simplicity in detection of specific targets, has vastly improved the diagnosis of numerous infectious diseases. However, little research efforts have been made on utilizing this approach for diagnosis of Salmonella enterica serovar Typhi by targeting a single and specific gene. In this study, a LAMP assay for rapid detection of S. Typhi based on a novel marker gene, termed STY2879-LAMP, was established and evaluated with real-time PCR (RT-PCR. The specificity tests showed that STY2879 could be amplified in all S. Typhi strains isolated in different years and regions in China, whereas no amplification was observable in non-typhoidal strains covering 34 Salmonella serotypes and other pathogens causing febrile illness. The detection limit of STY2879-LAMP for S. Typhi was 15 copies/reaction in reference plasmids, 200 CFU/g with simple heat-treatment of DNA extracted from simulated stool samples and 20 CFU/ml with DNA extracted from simulated blood samples, which was 10 fold more sensitive than the parallel RT-PCR control experiment. Furthermore, the sensitivity of STY2879-LAMP and RT-PCR combining the traditional culture enrichment method for simulated stool and blood spiked with lower S. Typhi count during the 10 h enrichment time was also determined. In comparison with LAMP, the positive reaction time for RT-PCR required additional 2-3 h enrichment time for either simulated stool or blood specimens. Therefore, STY2879-LAMP is of practical value in the clinical settings and has a good potential for application in developing regions due to its easy-to-use protocol.

  16. Method of recovering phosphoric acid type decontaminating electrolytes by electrodeposition

    International Nuclear Information System (INIS)

    Sasaki, Takashi; Wada, Koichi; Kobayashi, Toshio.

    1985-01-01

    Purpose: To recoving phosphoric acid type highly concentrated decontaminating liquid used for the electrolytic decontamination of contaminated equipments, components, etc in nuclear power plants or the like through electrodeposition by diaphragm electrolysis. Method: Before supplying phosphoric acid decontaminating liquid at high concentration used in the electrolytic decontaminating step to an electrodeposition recovering tank, phosphoric acid in the decontaminating electrolyte is extracted with solvents and decomposed liquid extracts (electrolyte reduced with the phosphoric acid component) are supplied to the cathode chamber of the electrodeposition recovering tank, where phosphoric acid is back-extracted with water from the solvents after extraction of phosphoric acid. Then, the back-extracted liquids (aqueous phosphoric acid solution scarcely containing metal ions) are sent to the anode chamber of the electrodeposition recovering tank. Metal ions in the liquid are captured by electrodeposition in the cathode chamber, as well as phosphoric acid in the liquids is concentrated to the initial concentration of the electrolyte in the anode chamber for reuse as the decontaminating electrolyte. As the phosphoric acid extracting agent used in the electrodeposition recovering step for the decontaminating electrolyte, water-insoluble and non-combustible tributyl phosphate (TBP) is most effective. (Horiuchi, T.)

  17. Easy method for the preparation of L (+) 2-amino 3-sulfino propionic acid (cysteine sulfinic acid)

    International Nuclear Information System (INIS)

    Emiliozzi, Romeo; Pichat, Louis

    1960-01-01

    Description of a new method of preparing cystine disulphoxide by oxidising cystine hydrochloride with a mixture of formic acid and hydrogen peroxide. Yield; 85 per cent. The disproportionation of cystine disulphoxide by ammonia gives 2-amino 3-sulfino propionic acid with a yield of 93 per cent. The method had been applied to the preparation of 35 S DL cysteine sulfinic acid. Reprint of a paper published in Bulletin de la Societe Chimique de France, no. 2653, 4. quarter 1959, p. 1887-1888 [fr

  18. Phenol-Sulfuric Acid Method for Total Carbohydrates

    Science.gov (United States)

    Nielsen, S. Suzanne

    The phenol-sulfuric acid method is a simple and rapid colorimetric method to determine total carbohydrates in a sample. The method detects virtually all classes of carbohydrates, including mono-, di-, oligo-, and polysaccharides. Although the method detects almost all carbohydrates, the absorptivity of the different carbohydrates varies. Thus, unless a sample is known to contain only one carbohydrate, the results must be expressed arbitrarily in terms of one carbohydrate.

  19. A new method for selectively enhancing hemisphere processing: voice frequency amplification influences the strength of attribute framing.

    Science.gov (United States)

    McCormick, Michael; Seta, John J

    2012-01-01

    An attribute framing effect occurs when positive or negative associations produced by positive or negative frames are mapped onto evaluations resulting in a more favourable evaluation for the positively framed attribute. We used a new voice frequency manipulation to differentially enhance right versus left hemisphere processing. In doing so we found a strong attribute framing effect when a speaker with a low-frequency voice enhanced the contextual processing style of the right hemisphere. However, a framing effect was not obtained when a speaker with a high-frequency voice enhanced the inferential/analytical processing style of the left hemisphere. At the theoretical level our results provide evidence that the contextual processing style of the right hemisphere is especially susceptible to associative implications, such as those found in attribute framing manipulations. At the applied level we provide a simple method for altering the effectiveness of persuasion messages.

  20. Method for enhancing amidohydrolase activity of fatty acid amide hydrolase

    Science.gov (United States)

    John, George; Nagarajan, Subbiah; Chapman, Kent; Faure, Lionel; Koulen, Peter

    2017-12-26

    A method for enhancing amidohydrolase activity of Fatty Acid Amide Hydrolase (FAAH) is disclosed. The method comprising administering a phenoxyacyl-ethanolamide that causes the enhanced activity. The enhanced activity can have numerous effects on biological organisms including, for example, enhancing the growth of certain seedlings.

  1. Method for enhancing amidohydrolase activity of fatty acid amide hydrolase

    Science.gov (United States)

    John, George; Nagarajan, Subbiah; Chapman, Kent; Faure, Lionel; Koulen, Peter

    2016-10-25

    A method for enhancing amidohydrolase activity of Fatty Acid Amide Hydrolase (FAAH) is disclosed. The method comprising administering a phenoxyacylethanolamide that causes the enhanced activity. The enhanced activity can have numerous effects on biological organisms including, for example, enhancing the growth of certain seedlings. The subject matter disclosed herein relates to enhancers of amidohydrolase activity.

  2. Method Development for Efficient Incorporation of Unnatural Amino Acids

    KAUST Repository

    Harris, Paul D.

    2014-04-01

    The synthesis of proteins bearing unnatural amino acids has the potential to enhance and elucidate many processes in biochemistry and molecular biology. There are two primary methods for site specific unnatural amino acid incorporation, both of which use the cell’s native protein translating machinery: in vitro chemical acylation of suppressor tRNAs and the use of orthogonal amino acyl tRNA synthetases. Total chemical synthesis is theoretically possible, but current methods severely limit the maximum size of the product protein. In vivo orthogonal synthetase methods suffer from the high cost of the unnatural amino acid. In this thesis I sought to address this limitation by increasing cell density, first in shake flasks and then in a bioreactor in order to increase the yield of protein per amount of unnatural amino acid used. In a parallel project, I used the in vitro chemical acylation system to incorporate several unnatural amino acids, key among them the fluorophore BODIPYFL, with the aim of producing site specifically fluorescently labeled protein for single molecule FRET studies. I demonstrated successful incorporation of these amino acids into the trial protein GFP, although incorporation was not demonstrated in the final target, FEN1. This also served to confirm the effectiveness of a new procedure developed for chemical acylation.

  3. Method Development for Efficient Incorporation of Unnatural Amino Acids

    KAUST Repository

    Harris, Paul D.

    2014-01-01

    The synthesis of proteins bearing unnatural amino acids has the potential to enhance and elucidate many processes in biochemistry and molecular biology. There are two primary methods for site specific unnatural amino acid incorporation, both of which use the cell’s native protein translating machinery: in vitro chemical acylation of suppressor tRNAs and the use of orthogonal amino acyl tRNA synthetases. Total chemical synthesis is theoretically possible, but current methods severely limit the maximum size of the product protein. In vivo orthogonal synthetase methods suffer from the high cost of the unnatural amino acid. In this thesis I sought to address this limitation by increasing cell density, first in shake flasks and then in a bioreactor in order to increase the yield of protein per amount of unnatural amino acid used. In a parallel project, I used the in vitro chemical acylation system to incorporate several unnatural amino acids, key among them the fluorophore BODIPYFL, with the aim of producing site specifically fluorescently labeled protein for single molecule FRET studies. I demonstrated successful incorporation of these amino acids into the trial protein GFP, although incorporation was not demonstrated in the final target, FEN1. This also served to confirm the effectiveness of a new procedure developed for chemical acylation.

  4. Method for distinctive estimation of stored acidity forms in acid mine wastes.

    Science.gov (United States)

    Li, Jun; Kawashima, Nobuyuki; Fan, Rong; Schumann, Russell C; Gerson, Andrea R; Smart, Roger St C

    2014-10-07

    Jarosites and schwertmannite can be formed in the unsaturated oxidation zone of sulfide-containing mine waste rock and tailings together with ferrihydrite and goethite. They are also widely found in process wastes from electrometallurgical smelting and metal bioleaching and within drained coastal lowland soils (acid-sulfate soils). These secondary minerals can temporarily store acidity and metals or remove and immobilize contaminants through adsorption, coprecipitation, or structural incorporation, but release both acidity and toxic metals at pH above about 4. Therefore, they have significant relevance to environmental mineralogy through their role in controlling pollutant concentrations and dynamics in contaminated aqueous environments. Most importantly, they have widely different acid release rates at different pHs and strongly affect drainage water acidity dynamics. A procedure for estimation of the amounts of these different forms of nonsulfide stored acidity in mining wastes is required in order to predict acid release rates at any pH. A four-step extraction procedure to quantify jarosite and schwertmannite separately with various soluble sulfate salts has been developed and validated. Corrections to acid potentials and estimation of acid release rates can be reliably based on this method.

  5. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification.

    Science.gov (United States)

    Yang, Qi; Franco, Christopher M M; Zhang, Wei

    2015-10-01

    Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.

  6. Differential expression analysis of balding and nonbalding dermal papilla microRNAs in male pattern baldness with a microRNA amplification profiling method.

    Science.gov (United States)

    Goodarzi, H R; Abbasi, A; Saffari, M; Fazelzadeh Haghighi, M; Tabei, M B; Noori Daloii, M R

    2012-05-01

      Male pattern baldness or androgenetic alopecia is a common disorder affecting almost 50% of men throughout their lifetime, with androgens and genetics having significant contributing aetiologies. In contrast to the positive regulatory effect of androgens on body hair growth, they are thought to alter scalp hair follicle behaviour pathophysiologically, leading to male pattern baldness. However, the exact mechanisms of this paradoxical action have not yet been elucidated. The role of microRNAs, a novel group of noncoding RNAs impacting almost every aspect of biology, health and human diseases, has been documented in hair follicle formation. In addition, their deregulation in cancer of the prostate, a target organ of androgens, has also been well established. To investigate the possible contribution of microRNAs in the pathophysiology of male pattern baldness. We initially screened microRNA expression profiles of balding and nonbalding hair follicle papillae with a sensitive microRNA cloning method, microRNA amplification profiling, and statistically analysed significant differentially expressed microRNAs in balding relative to nonbalding dermal papillae, with real-time polymerase chain reaction as a confirmatory method to quantify expression in eight individuals affected with the disorder.   We detected the significant upregulation of miR-221, miR-125b, miR-106a and miR-410 in balding papilla cells.   We found four microRNAs that could participate in the pathogenesis of male pattern baldness. Regarding the strong therapeutic potential of microRNAs and the easy accessibility of hair follicles for gene therapy, microRNAs are possible candidates for a new generation of revolutionary treatments. © 2011 The Authors. BJD © 2011 British Association of Dermatologists.

  7. Determination of antimicrobial resistance of Enterococcus strains isolated from pigs and their genotypic characterization by method of amplification of DNA fragments surrounding rare restriction sites (ADSRRS fingerprinting).

    Science.gov (United States)

    Nowakiewicz, Aneta; Ziółkowska, Grażyna; Trościańczyk, Aleksandra; Zięba, Przemysław; Gnat, Sebastian

    2017-03-01

    In this study, we analysed phenotypic resistance profiles and their reflection in the genomic profiles of Enterococcus spp. strains isolated from pigs raised on different farms. Samples were collected from five pig farms (n=90 animals) and tested for Enterococcus. MICs of 12 antimicrobials were determined using the broth microdilution method, and epidemiological molecular analysis of strains belonging to selected species (faecalis, faecium and hirae) was performed using the ADSRRS-fingerprinting (amplification of DNA fragments surrounding rare restriction sites) method with a few modifications. The highest percentage of strains was resistant to tetracycline (73.4 %), erythromycin and tylosin (42.5 %) and rifampin (25.2 %), and a large number of strains exhibited high-level resistance to both kanamycin (25.2 %) and streptomycin (27.6 %). The strains of E. faecalis, E. faecium and E. hirae (n=184) revealed varied phenotypic resistance profiles, among which as many as seven met the criteria for multidrug resistance (30.4 % of strains tested). ADSRRS-fingerprinting analysis produced 17 genotypic profiles of individual strains which were correlated with their phenotypic resistance profiles. Only E. hirae strains susceptible to all of the chemotherapeutics tested had two different ADSRRS profiles. Moreover, eight animals were carriers of more than one genotype belonging to the same Enterococcus spp., mainly E. faecalis. Given the possibility of transmission to humans of the high-resistance/multidrug resistance enterococci and the significant role of pigs as food animals in this process, it is necessary to introduce a multilevel control strategy by carrying out research on the resistance and molecular characteristics of indicator bacterial strains isolated from animals on individual farms.

  8. Native nucleic acid electrophoresis as an efficient alternative for genotyping method of influenza virus.

    Science.gov (United States)

    Pajak, Beata; Lepek, Krzysztof

    2014-01-01

    Influenza viruses are the worldwide major causative agents of human and animal acute respiratory infections. Some of the influenza subtypes have caused epidemics and pandemics among humans. The varieties of methods are available for the rapid isolation and identification of influenza viruses in clinical and environmental samples. Since nucleic acids amplification techniques such as RT-PCR have been adapted, fast and sensitive influenza type and subtype determination is possible. However, in some ambiguous cases other, more detailed assay might be desired. The genetic material of influenza virus is highly unstable and constantly mutates. It is known that single nucleotide polymorphisms (SNPs) results in resistance to commercially available anti-viral drugs. The genetic drift of the virus could also result in weakening of immune response to infection. Finally, in a substantial number of patients co-infection with various virus strains or types has been confirmed. Although the detection of co-infection or presence of minor genetic variants within flu-infected patients is not a routine procedure, a rapid and wide spectrum diagnostics of influenza virus infections could reveal an accurate picture of the disease and more importantly, is crucial for choosing the appropriate therapeutics and virus monitoring. Herein we present the evidences that native gel electrophoresis and MSSCP--a method based on multitemperature single strand conformation polymorphism could furnish a useful technique for minor variants, which escape discovery by conventional diagnostic assays.

  9. [Investigation of RNA viral genome amplification by multiple displacement amplification technique].

    Science.gov (United States)

    Pang, Zheng; Li, Jian-Dong; Li, Chuan; Liang, Mi-Fang; Li, De-Xin

    2013-06-01

    In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

  10. A method to attenuate U(VI) mobility in acidic waste plumes using humic acids

    Energy Technology Data Exchange (ETDEWEB)

    Wan, J.; Dong, W.; Tokunaga, T.K.

    2011-02-01

    Acidic uranium (U) contaminated plumes have resulted from acid-extraction of plutonium during the Cold War and from U mining and milling operations. A sustainable method for in-situ immobilization of U under acidic conditions is not yet available. Here, we propose to use humic acids (HAs) for in-situ U immobilization in acidic waste plumes. Our laboratory batch experiments show that HA can adsorb onto aquifer sediments rapidly, strongly and practically irreversibly. Adding HA greatly enhanced U adsorption capacity to sediments at pH below 5.0. Our column experiments using historically contaminated sediments from the Savannah River Site under slow flow rates (120 and 12 m/y) show that desorption of U and HA were non-detectable over 100 pore-volumes of leaching with simulated acidic groundwaters. Upon HA-treatment, 99% of the contaminant [U] was immobilized at pH < 4.5, compared to 5% and 58% immobilized in the control columns at pH 3.5 and 4.5, respectively. These results demonstrated that HA-treatment is a promising in-situ remediation method for acidic U waste plumes. As a remediation reagent, HAs are resistant to biodegradation, cost effective, nontoxic, and easily introducible to the subsurface.

  11. A GC-ECD method for estimation of free and bound amino acids, gamma-aminobutyric acid, salicylic acid, and acetyl salicylic acid from Solanum lycopersicum (L.).

    Science.gov (United States)

    Meher, Hari Charan; Gajbhiye, Vijay T; Singh, Ghanendra

    2011-01-01

    A gas chromatograph with electron capture detection method for estimation of selected metabolites--amino acids (free and bound), gamma-aminobutyric acid (GABA), salicylic acid (SA), and acetyl salicylic acid (ASA) from tomato--is reported. The method is based on nitrophenylation of the metabolites by 1-fluoro-2, 4-dinitrobenzene under aqueous alkaline conditions to form dinitophenyl derivatives. The derivatives were stable under the operating conditions of GC. Analysis of bound amino acids comprised perchloric acid precipitation of protein, alkylation (carboxymethylation) with iodoacetic acid, vapor-phase hydrolysis, and derivatization with 1-fluoro-2,4-dinitrobenzene in that order. The metabolites were resolved in 35 min, using a temperature-programmed run. The method is rapid, sensitive, and precise. It easily measured the typical amino acids (aspartate, asparagine, glutamate, glutamine, alanine, leucine, lysine, and phenylalanine) used for identification and quantification of a protein, resolved amino acids of the same mass (leucine and isoleucine), satisfactorily measured sulfur amino acid (methionine, cystine, and cysteine), and quantified GABA, SA, and ASA, as well. The developed method was validated for specificity, linearity, and precision. It has been applied and recommended for estimation of 25 metabolites from Solanum lycopersicum (L.).

  12. New Fpg probe chemistry for direct detection of recombinase polymerase amplification on lateral flow strips.

    Science.gov (United States)

    Powell, Michael L; Bowler, Frank R; Martinez, Aurore J; Greenwood, Catherine J; Armes, Niall; Piepenburg, Olaf

    2018-02-15

    Rapid, cost-effective and sensitive detection of nucleic acids has the ability to improve upon current practices employed for pathogen detection in diagnosis of infectious disease and food testing. Furthermore, if assay complexity can be reduced, nucleic acid amplification tests could be deployed in resource-limited and home use scenarios. In this study, we developed a novel Fpg (Formamidopyrimidine DNA glycosylase) probe chemistry, which allows lateral flow detection of amplification in undiluted recombinase polymerase amplification (RPA) reactions. The prototype nucleic acid lateral flow chemistry was applied to a human genomic target (rs1207445), Campylobacter jejuni 16S rDNA and two genetic markers of the important food pathogen E. coli O157:H7. All four assays have an analytical sensitivity between 10 and 100 copies DNA per amplification. Furthermore, the assay is performed with fewer hands-on steps than using the current RPA Nfo lateral flow method as dilution of amplicon is not required for lateral flow analysis. Due to the simplicity of the workflow, we believe that the lateral flow chemistry for direct detection could be readily adapted to a cost-effective single-use consumable, ideal for use in non-laboratory settings. Copyright © 2017. Published by Elsevier Inc.

  13. Layer-by-layer self-assembled nanostructured phthalocyaninatoiron(II)/SWCNT-poly(m-aminobenzenesulfonic acid) hybrid system on gold surface: Electron transfer dynamics and amplification of H{sub 2}O{sub 2} response

    Energy Technology Data Exchange (ETDEWEB)

    Pillay, Jeseelan [Molecular and Nanomaterials Electrochemistry laboratory, Department of Chemistry, University of Pretoria, Pretoria 0002 (South Africa); Ozoemena, Kenneth I. [Molecular and Nanomaterials Electrochemistry laboratory, Department of Chemistry, University of Pretoria, Pretoria 0002 (South Africa)], E-mail: kenneth.ozoemena@up.ac.za

    2009-09-01

    The fabrication of nanostructured platform of poly(m-aminobenzenesulfonic acid) functionalised single-walled carbon nanotubes (SWCNTs-PABS)-iron(II)phthalocyanine nanoparticles (nanoFePc) using layer-by-layer(LBL) self-assembly strategy is described. The substrate build-up, via strong electrostatic interaction, was monitored using atomic force microscopy (AFM) and electrochemical measurements. As the number of bilayers is increased, the electron transfer kinetics of the ferricyaninde/ferrocyanide redox probe is decreased, while the electrochemical reduction of H{sub 2}O{sub 2} at a constant concentration is amplified. The amplification of the electrochemical response to H{sub 2}O{sub 2} detection suggests that this type of electrode could provide an important nano-architectural sensing platform for the development of a sensor.

  14. Gene amplification in carcinogenesis

    Directory of Open Access Journals (Sweden)

    Lucimari Bizari

    2006-01-01

    Full Text Available Gene amplification increases the number of genes in a genome and can give rise to karyotype abnormalities called double minutes (DM and homogeneously staining regions (HSR, both of which have been widely observed in human tumors but are also known to play a major role during embryonic development due to the fact that they are responsible for the programmed increase of gene expression. The etiology of gene amplification during carcinogenesis is not yet completely understood but can be considered a result of genetic instability. Gene amplification leads to an increase in protein expression and provides a selective advantage during cell growth. Oncogenes such as CCND1, c-MET, c-MYC, ERBB2, EGFR and MDM2 are amplified in human tumors and can be associated with increased expression of their respective proteins or not. In general, gene amplification is associated with more aggressive tumors, metastases, resistance to chemotherapy and a decrease in the period during which the patient stays free of the disease. This review discusses the major role of gene amplification in the progression of carcinomas, formation of genetic markers and as possible therapeutic targets for the development of drugs for the treatment of some types of tumors.

  15. A field based detection method for Rose rosette virus using isothermal probe-based Reverse transcription-recombinase polymerase amplification assay.

    Science.gov (United States)

    Babu, Binoy; Washburn, Brian K; Ertek, Tülin Sarigül; Miller, Steven H; Riddle, Charles B; Knox, Gary W; Ochoa-Corona, Francisco M; Olson, Jennifer; Katırcıoğlu, Yakup Zekai; Paret, Mathews L

    2017-09-01

    Rose rosette disease, caused by Rose rosette virus (RRV; genus Emaravirus) is a major threat to the rose industry in the U.S. The only strategy currently available for disease management is early detection and eradication of the infected plants, thereby limiting its potential spread. Current RT-PCR based diagnostic methods for RRV are time consuming and are inconsistent in detecting the virus from symptomatic plants. Real-time RT-qPCR assay is highly sensitive for detection of RRV, but it is expensive and requires well-equipped laboratories. Both the RT-PCR and RT-qPCR cannot be used in a field-based testing for RRV. Hence a novel probe based, isothermal reverse transcription-recombinase polymerase amplification (RT-exoRPA) assay, using primer/probe designed based on the nucleocapsid gene of the RRV has been developed. The assay is highly specific and did not give a positive reaction to other viruses infecting roses belonging to both inclusive and exclusive genus. Dilution assays using the in vitro transcript showed that the primer/probe set is highly sensitive, with a detection limit of 1 fg/μl. In addition, a rapid technique for the extraction of viral RNA (rose varieties, collected from different states in the U.S. The entire process, including the extraction can be completed in 25min, with less sophisticated equipments. The developed assay can be used with high efficiency in large scale field testing for rapid detection of RRV in commercial nurseries and landscapes. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Study of the population dynamics of a mixed bacterial culture able to degrade cyanuric acid in a packed bed reactor, using RAPD (Random amplification of polymorphic DNA) technique

    International Nuclear Information System (INIS)

    Galindez-Najera, S.; Llamas-Martinez, M.; Ahuatzi-Chacon, D.; Ruiz-Ordaz, N.; Galindez-Mayer, C. J.

    2009-01-01

    Cyanuric acid is a biodegradation byproduct of triazinic compounds. Because of its low carbon to nitrogen ratio, a complementary carbon source is usually needed for its complete biodegradation. In this work, glucose was used as extra carbon source. Cyanuric hydrolase is the first enzyme in cyanuric acid (CA) catabolism, and is produced by a wide number of microorganisms. (Author)

  17. Social amplification of risk

    International Nuclear Information System (INIS)

    Kasperson, R.E.; Renn, O.; Slovic, P.; Kasperson, J.X.; Emani, S.

    1989-01-01

    The risks associated with radioactive and other hazardous waste disposal may be expected to interact with societal processes to enlarge or attenuate the consequences of risks and risk events. This article summarizes a conceptual framework that depicts the social amplification of risk. Using a data base of 128 hazard events that have occurred largely over the past ten years, the authors examine the role of physical consequences, media coverage, and public perceptions of risk in generating social and economic impacts. The analysis concludes that social amplification processes substantially shape the nature and magnitude of those impacts but also that such social amplification appears to be systematically related to characteristics of the risks and risk events

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

    Science.gov (United States)

    Noor, M Omair; Krull, Ulrich J

    2014-10-21

    important framework for the integration of QD-FRET methods with digital imaging for a ratiometric transduction of nucleic acid hybridization on a paper-based platform.

  19. Roka Listeria detection method using transcription mediated amplification to detect Listeria species in select foods and surfaces. Performance Tested Method(SM) 011201.

    Science.gov (United States)

    Hua, Yang; Kaplan, Shannon; Reshatoff, Michael; Hu, Ernie; Zukowski, Alexis; Schweis, Franz; Gin, Cristal; Maroni, Brett; Becker, Michael; Wisniewski, Michele

    2012-01-01

    The Roka Listeria Detection Assay was compared to the reference culture methods for nine select foods and three select surfaces. The Roka method used Half-Fraser Broth for enrichment at 35 +/- 2 degrees C for 24-28 h. Comparison of Roka's method to reference methods requires an unpaired approach. Each method had a total of 545 samples inoculated with a Listeria strain. Each food and surface was inoculated with a different strain of Listeria at two different levels per method. For the dairy products (Brie cheese, whole milk, and ice cream), our method was compared to AOAC Official Method(SM) 993.12. For the ready-to-eat meats (deli chicken, cured ham, chicken salad, and hot dogs) and environmental surfaces (sealed concrete, stainless steel, and plastic), these samples were compared to the U.S. Department of Agriculture/Food Safety and Inspection Service-Microbiology Laboratory Guidebook (USDA/FSIS-MLG) method MLG 8.07. Cold-smoked salmon and romaine lettuce were compared to the U.S. Food and Drug Administration/Bacteriological Analytical Manual, Chapter 10 (FDA/BAM) method. Roka's method had 358 positives out of 545 total inoculated samples compared to 332 positive for the reference methods. Overall the probability of detection analysis of the results showed better or equivalent performance compared to the reference methods.

  20. Development of rapid and simple method for DNA extraction from cannabis resin based on the evaluation of relative PCR amplification ability.

    Science.gov (United States)

    Yamamuro, Tadashi; Iwata, Yuko T; Segawa, Hiroki; Kuwayama, Kenji; Tsujikawa, Kenji; Kanamori, Tatsuyuki; Inoue, Hiroyuki

    2018-04-04

    In recent years, analysis of cannabis DNA has been increasingly used in forensic drug tests. However, in the case of cannabis resin, a processed marijuana product, complicated procedures are required for the extraction of clean DNA, as the presence of various impurities inhibits PCR amplification. Therefore, in this study, we attempted to identify the factors that would allow quick and simple DNA extraction from cannabis resin with a commercially available kit. We also constructed a simple assay system for comparing relative amplification efficiencies by end-point PCR and used it to evaluate the purity of the obtained DNA solutions. For extraction with a kit that contains a silica column, reducing the starting amount of resin, using the residue remaining after methanol extraction, dilution of the final solution, extraction with an equal amount of powdered activated carbon or an excess amount of polyvinylpolypyrrolidone, and the addition of an appropriate amount of polyvinylpyrrolidone to the solution after extraction were effective measures that improved amplification efficiency. Furthermore, the use of the most rapid alkaline extraction kit combined with the addition of powdered activated carbon allowed obtaining DNA solutions with sufficient amplification efficiency in about 10min. These findings should be useful for routine DNA analysis of cannabis resin during forensic examination. Copyright © 2018 Elsevier B.V. All rights reserved.

  1. chipPCR: an R package to pre-process raw data of amplification curves.

    Science.gov (United States)

    Rödiger, Stefan; Burdukiewicz, Michał; Schierack, Peter

    2015-09-01

    Both the quantitative real-time polymerase chain reaction (qPCR) and quantitative isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous real-time read-out technologies have been developed. Despite the continuous interest in amplification-based techniques, there are only few tools for pre-processing of amplification data. However, a transparent tool for precise control of raw data is indispensable in several scenarios, for example, during the development of new instruments. chipPCR is an R: package for the pre-processing and quality analysis of raw data of amplification curves. The package takes advantage of R: 's S4 object model and offers an extensible environment. chipPCR contains tools for raw data exploration: normalization, baselining, imputation of missing values, a powerful wrapper for amplification curve smoothing and a function to detect the start and end of an amplification curve. The capabilities of the software are enhanced by the implementation of algorithms unavailable in R: , such as a 5-point stencil for derivative interpolation. Simulation tools, statistical tests, plots for data quality management, amplification efficiency/quantification cycle calculation, and datasets from qPCR and qIA experiments are part of the package. Core functionalities are integrated in GUIs (web-based and standalone shiny applications), thus streamlining analysis and report generation. http://cran.r-project.org/web/packages/chipPCR. Source code: https://github.com/michbur/chipPCR. stefan.roediger@b-tu.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Methods of introducing nucleic acids into cellular DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lajoie, Marc J.; Gregg, Christopher J.; Mosberg, Joshua A.; Church, George M.

    2017-06-27

    A method of introducing a nucleic acid sequence into a cell is provided where the cell has impaired or inhibited or disrupted DnaG primase activity or impaired or inhibited or disrupted DnaB helicase activity, or larger or increased gaps or distance between Okazaki fragments or lowered or reduced frequency of Okazaki fragment initiation, or the cell has increased single stranded DNA (ssDNA) on the lagging strand of the replication fork including transforming the cell through recombination with a nucleic acid oligomer.

  3. Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification.

    Science.gov (United States)

    Xu, Jianguo; Zheng, Tingting; Le, Jingqing; Jia, Lee

    2017-11-20

    Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs). Moreover, it is excitingly found that the LS-MMB can be employed to exert intramolecular and intermolecular interactions for strand displacement amplification (SDA) without the involvement of any assistant probes; this therapy results in a really easy and rapid sensing system that provides an extremely low background noise and high target output signal. In this case, an excellent sensitivity and specificity to detect target gene down to picomolar level and resolution to even one nucleotide variation are achieved, respectively. In addition, the application potential for real genomic DNA analysis is realized. We envision that the probe of LS-MMB can act as a universal platform for biosensing and biomedical research.

  4. Acid pre-treatment method for in situ ore leaching

    International Nuclear Information System (INIS)

    Mallon, R.G.; Braun, R.L.

    1975-01-01

    An acid leaching method is described for the recovery of a desired element from a subterranean rubblized body of primary ore containing the element and also having associated therewith a carbonate mineral wherein the rubblized ore body is flooded with an aqueous acidic solution in order to release carbon dioxide from the associated carbonate mineral. After a substantial portion of the available carbon dioxide is released and removed from the ore body, as by venting to the atmosphere, an oxidizing gas is introduced into the flooded, rubblized ore to oxidize the ore and form an acid leach solution effective in the presence of the dissolved oxidizing gas to dissolve the ore and cause the desired element to go into solution. The leach solution is then circulated to the surface where the metal values are recovered therefrom

  5. An enzymatic signal amplification system for calorimetric studies of cellobiohydrolases

    DEFF Research Database (Denmark)

    Murphy, Leigh; Baumann, Martin Johannes; Borch, Kim

    2010-01-01

    amplification method has been developed to measure even slow hydrolytically active enzymes such as cellobiohydrolases. This method is explained in detail for the amplification of the heat signal by more than 130 times by using glucose oxidase and catalase. The kinetics of this complex coupled reaction system...

  6. Devices, systems, and methods for detecting nucleic acids using sedimentation

    Energy Technology Data Exchange (ETDEWEB)

    Koh, Chung-Yan; Schaff, Ulrich Y.; Sommer, Gregory J.

    2017-10-24

    Embodiments of the present invention are directed toward devices, systems, and method for conducting nucleic acid purification and quantification using sedimentation. In one example, a method includes generating complexes which bind to a plurality of beads in a fluid sample, individual ones of the complexes comprising a nucleic acid molecule such as DNA or RNA and a labeling agent. The plurality of beads including the complexes may be transported through a density media, wherein the density media has a density lower than a density of the beads and higher than a density of the fluid sample, and wherein the transporting occurs, at least in part, by sedimentation. Signal may be detected from the labeling agents of the complexes.

  7. Detection and Characterization of Viral Species/Subspecies Using Isothermal Recombinase Polymerase Amplification (RPA) Assays.

    Science.gov (United States)

    Glais, Laurent; Jacquot, Emmanuel

    2015-01-01

    Numerous molecular-based detection protocols include an amplification step of the targeted nucleic acids. This step is important to reach the expected sensitive detection of pathogens in diagnostic procedures. Amplifications of nucleic acid sequences are generally performed, in the presence of appropriate primers, using thermocyclers. However, the time requested to amplify molecular targets and the cost of the thermocycler machines could impair the use of these methods in routine diagnostics. Recombinase polymerase amplification (RPA) technique allows rapid (short-term incubation of sample and primers in an enzymatic mixture) and simple (isothermal) amplification of molecular targets. RPA protocol requires only basic molecular steps such as extraction procedures and agarose gel electrophoresis. Thus, RPA can be considered as an interesting alternative to standard molecular-based diagnostic tools. In this paper, the complete procedures to set up an RPA assay, applied to detection of RNA (Potato virus Y, Potyvirus) and DNA (Wheat dwarf virus, Mastrevirus) viruses, are described. The proposed procedure allows developing species- or subspecies-specific detection assay.

  8. Stainless steel welding method with excellent nitric acid corrosion resistance

    International Nuclear Information System (INIS)

    Matsushita, Yukinobu; Inazumi, Toru; Hyakubo, Tamako; Masamura, Katsumi.

    1996-01-01

    The present invention concerns a welding method for a stainless steel used in a circumstance being in contact with a highly oxidizing nitric acid solution such as nuclear fuel reprocessing facilities, upon welding 316 type austenite steel containing Mo while giving excellent nitric acid resistance. A method of TIG welding using a filler metal having a composition of C, Si, Mn, P, S, Ni, Cr, Mo and Cu somewhat different from a stainless steel mother material in which C, Si, Mn, P, S, Ni, Cr and Mo are specified comprises a step of TIG-welding the surface of the mother material and a step of TIG-welding the rear face of the mother material, in which the welding conditions for the rear face of the mother material are such that the distance between the surface of the outermost welding metal layer on the side of the surface of the mother material and the bottom of the groove is not less than 5mm, and an amount of welding heat is made constant. As a result, even if the method is used in a circumstance being in contact with a highly corrosive solution such as nitric acid, corrosion resistance is not degraded. (N.H.)

  9. Electrochemical quantification of some water soluble vitamins in commercial multi-vitamin using poly-amino acid caped by graphene quantum dots nanocomposite as dual signal amplification elements.

    Science.gov (United States)

    Shadjou, Nasrin; Hasanzadeh, Mohammad; Omari, Ali

    2017-12-15

    Rapid analyses of some water soluble vitamins (Vitamin B2, B9, and C) in commercial multi vitamins could be routinely performed in analytical laboratories. This study reports on the electropolymerization of a low toxic and biocompatible polymer "poly aspartic acid-graphene quantum dots" as a novel strategy for surface modification of glassy carbon electrode and preparation a new interface for measurement of selected vitamins in commercial multi vitamins. Electrochemical deposition, as a well-controlled synthesis procedure, has been used for subsequently layer-by-layer preparation of graphene quantum dots nanostructures on a poly aspartic acid using cyclic voltammetry techniques in the regime of -1.5 to 2 V. The field emission scanning electron microscopy indicated immobilization of graphene quantum dots onto poly aspartic acid film. The modified electrode possessed as an effective electroactivity for detection of water soluble vitamins by using cyclic voltammetry, chronoamperometry and differential pulse voltammetry. Enhancement of peak currents is ascribed to the fast heterogeneous electron transfer kinetics that arise from the synergistic coupling between the excellent properties of poly aspartic acid as semiconducting polymer, graphene quantum dots as high density of edge plane sites and chemical modification. Under the optimized analysis conditions, the prepared sensor for detection of VB2, VB9, and VC showed a low limit of quantification 0.22, 0.1, 0.1 μM, respectively. Copyright © 2017. Published by Elsevier Inc.

  10. Method for the treatment of mining gangue containing sulfuric acid

    Energy Technology Data Exchange (ETDEWEB)

    Minnick, L J; Smith, C L; Webster, W C

    1976-07-01

    Mining gangue is often heaped up on large, open-air dumps. By means of extraction and oxidation of the sulfuric elements contained, the environment is being negatively influenced, due to the sulfuric acids occuring. The method described converts the gangue into an ecologically agreeable material which can be used even in road construction. This is achieved by mixing the gangue with lime, a pozzolane active material and water, and by hardening the gangue at atmospheric pressure for several days. This method can be very cost-effective if fly ash is used as pozzolane-active material.

  11. Preparative method to obtain ursolic acid from Clinopodium revolutum

    Directory of Open Access Journals (Sweden)

    Michael Azael Ludeña Huaman

    2018-01-01

    Full Text Available A method to obtain ursolic acid (UA in an easy, fast, and economical way was proposed, having as raw material the medicinal plant Clinopodium revolutum from Peru. This plant is known and marketed as flor de arena or té indio. The selective recrystallization technique used was efficient due to UA crystals were obtained without the need for chromatographic purification methods neither the use of toxic solvents. The purity determined by HPLC is greater than 95%. Thus, the flor de arena becomes an important biosource of this compound.

  12. Telomerase Repeated Amplification Protocol (TRAP).

    Science.gov (United States)

    Mender, Ilgen; Shay, Jerry W

    2015-11-20

    Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al. , 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC - counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al. , 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is

  13. Earthquake acceleration amplification based on single microtremor test

    Science.gov (United States)

    Jaya Syahbana, Arifan; Kurniawan, Rahmat; Soebowo, Eko

    2018-02-01

    Understanding soil dynamics is needed to understand soil behaviour, including the parameters of earthquake acceleration amplification. Many researchers now conduct single microtremor tests to obtain amplification of velocity and natural periods of soil at test sites. However, these amplification parameters are rarely used, so a method is needed to convert the velocity amplification to acceleration amplification. This paper will discuss the proposed process of changing the value of amplification. The proposed method is to integrate the time histories of the synthetic earthquake acceleration of the soil surface under the deaggregation at that location so the time histories of the velocity earthquake will be obtained. Next is to conduct a “fitting curve” between amplification by a single microtremor test with amplification of the synthetic earthquake velocity time histories. After obtaining the fitting curve time histories of velocity, differentiation will be conducted to obtain fitting curve acceleration time histories. The final step after obtaining the fitting curve is to compare the acceleration of the “fitting curve” against the histories time of the acceleration of synthetic earthquake at bedrocks to obtain single microtremor acceleration amplification factor.

  14. New method for the determination of bile acid turnover using /sup 75/Se-homocholic acid taurine

    Energy Technology Data Exchange (ETDEWEB)

    Delhez, H.; Meerwaldt, J.H.; van den Berg, J.W.O.; van Blankenstein, M.

    1982-06-01

    The introduction of /sup 75/Se-homocholic acid taurine (/sup 75/SeHCAT) greatly facilitates the investigation of diarrhoea of unknown origin. By using gamma-labelled bile acids, daily faecal bile acid loss can be measured in total collected stools, thus circumventing laborious mixing and sampling. The /sup 75/SeHCAT method proved to be reliable for the determination of bile acid turnover, giving results identical to the established turnover method using /sup 14/C-taurocholic acid. The new method however, is simpler and faster.

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

    Science.gov (United States)

    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.

  16. A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers

    Science.gov (United States)

    Du, Yan; Hughes, Randall A.; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.; Li, Bingling

    2015-06-01

    Strand exchange nucleic acid circuitry can be used to transduce isothermal nucleic acid amplification products into signals that can be readable on an off-the-shelf glucometer. Loop-mediated isothermal amplification (LAMP) is limited by the accumulation of non-specific products, but nucleic acid circuitry can be used to probe and distinguish specific amplicons. By combining this high temperature isothermal amplification method with a thermostable invertase, we can directly transduce Middle-East respiratory syndrome coronavirus and Zaire Ebolavirus templates into glucose signals, with a sensitivity as low as 20-100 copies/μl, equating to atto-molar (or low zepto-mole). Virus from cell lysates and synthetic templates could be readily amplified and detected even in sputum or saliva. An OR gate that coordinately triggered on viral amplicons further guaranteed fail-safe virus detection. The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device.

  17. A Simple and Robust Method for Semi-Quantitative Detection of Human Papillomavirus Nucleic Acids (HPV Helps Oncological Clinicians to Assess the Severeness of HPV Cellular Changing

    Directory of Open Access Journals (Sweden)

    Florian Heirler

    2011-01-01

    Full Text Available A simple and robust method for the detection of nucleic acids of human papilloma virus (HPV has been developed. The assay exploits the excellent sensitivity and specificity of “nested” polymerase chain reaction (nPCR that is designed in the original single tube configuration to effectively prevent the carry-over contamination. This approach theoretically covers the amplification of all cancer developing genotypes currently known. The nPCR, paired with very simple nucleic acids isolation steps, is a real alternative to the standard method. This manuscript shows its capacity for routine use under clinical conditions. It is shown that the strategy is at least as sensitive as the standard two tube nPCR and the data are acceptably reproducible.

  18. [Colorimetric detection of HPV6 and HPV16 by loop mediated isothermal amplification].

    Science.gov (United States)

    Lu, Chun-bin; Luo, Le; Yang, Meng-jie; Nie, Kai; Wang, Miao; Ma, Xue-Jun

    2011-01-01

    A simple, rapid and sensitive colorimetric loop mediated isothermal amplification (LAMP) method was established to detect HPV6 and HPV 16 respectively. The method employed a set of four specially designed primers that recognized six distinct sequences of HPV6-E6 or HPV16-E7 for amplification of nucleic acid under isothermal conditions at 63 degrees C for one hour. The amplification process of LAMP was monitored by the addition of HNB (hydroxy naphthol blue) dye prior to amplification. A positive reaction was indicated by a color change from violet to sky blue and confirmed by real-time turbidimeter and agarose electrophoresis. Thirteen cervical swab samples having single infection with 13 different HPV genotypes were examined to evaluate the specificity. A serial dilution of a cloned plasmid containing HPV-E6 or HPV-E7 gene was examined to evaluate the sensitivity. The results showed that no cross-reaction with other HPV genotypes was observed. The colorimetric LAMP assay could achieve a sensitivity of 1000 copies, 10-20 times lower than that of real-time PCR. The assay was further evaluated with 62 clinical specimens and consistent results were obtained compared with the detection using Kai Pu HPV Genotyping Kit. We concluded that this colorimetric LAMP assay had potential usefulness for the rapid screening of the HPV6 or HPV16 infection in the laboratories and hospitals of provincial and municipal region in China.

  19. Loop mediated isothermal amplification: An innovative gene amplification technique for animal diseases

    Directory of Open Access Journals (Sweden)

    Pravas Ranjan Sahoo

    2016-05-01

    Full Text Available India being a developing country mainly depends on livestock sector for its economy. However, nowadays, there is emergence and reemergence of more transboundary animal diseases. The existing diagnostic techniques are not so quick and with less specificity. To reduce the economy loss, there should be a development of rapid, reliable, robust diagnostic technique, which can work with high degree of sensitivity and specificity. Loop mediated isothermal amplification assay is a rapid gene amplification technique that amplifies nucleic acid under an isothermal condition with a set of designed primers spanning eight distinct sequences of the target. This assay can be used as an emerging powerful, innovative gene amplification diagnostic tool against various pathogens of livestock diseases. This review is to highlight the basic concept and methodology of this assay in livestock disease.

  20. Loop mediated isothermal amplification: An innovative gene amplification technique for animal diseases.

    Science.gov (United States)

    Sahoo, Pravas Ranjan; Sethy, Kamadev; Mohapatra, Swagat; Panda, Debasis

    2016-05-01

    India being a developing country mainly depends on livestock sector for its economy. However, nowadays, there is emergence and reemergence of more transboundary animal diseases. The existing diagnostic techniques are not so quick and with less specificity. To reduce the economy loss, there should be a development of rapid, reliable, robust diagnostic technique, which can work with high degree of sensitivity and specificity. Loop mediated isothermal amplification assay is a rapid gene amplification technique that amplifies nucleic acid under an isothermal condition with a set of designed primers spanning eight distinct sequences of the target. This assay can be used as an emerging powerful, innovative gene amplification diagnostic tool against various pathogens of livestock diseases. This review is to highlight the basic concept and methodology of this assay in livestock disease.

  1. ESTIMATION OF AMPLIFICATION FACTOR IN EARTHQUAKE ENGINEERING

    Directory of Open Access Journals (Sweden)

    Nazarov Yuriy Pavlovich

    2015-03-01

    Full Text Available The authors are the developers of Odyssey Software (Eurosoft Co. for the analysis of seismological data and computing of seismic loads and their parameters. While communicating with the users of the software, the authors have revealed some uncertainty about both understanding of the term "amplification factor (AF" and calculation of the amplification factor using various methods. In this article, a simple example shows that the determination of the amplification factor as the ratio of the acceleration’s spectrum to the maximal acceleration is derived from the classical definition of AF in the form of the ratio of maximal dynamic displacement to the displacement by the action of static load. Deterministic and probabilistic ap-proaches for the calculating of the AF were discussed. There was an example of AFs calculation and their envelopes for translational and rotational components of seismic impact by using Odyssey Software.

  2. Amplification of hofmeister effect by alcohols.

    Science.gov (United States)

    Xu, Yun; Liu, Guangming

    2014-07-03

    We have demonstrated that Hofmeister effect can be amplified by adding alcohols to aqueous solutions. The lower critical solution temperature behavior of poly(N-isopropylacrylamide) has been employed as the model system to study the amplification of Hofmeister effect. The alcohols can more effectively amplify the Hofmeister effect following the series methanol alcohols and following the series d-sorbitol ≈ xylitol ≈ meso-erythritol alcohols. Our study reveals that the relative extent of amplification of Hofmeister effect is determined by the stability of the water/alcohol complex, which is strongly dependent on the chemical structure of alcohols. The more stable solvent complex formed via stronger hydrogen bonds can more effectively differentiate the anions through the anion-solvent complex interactions, resulting in a stronger amplification of Hofmeister effect. This study provides an alternative method to tune the relative strength of Hofmeister effect besides salt concentration.

  3. Risk Perception and Social Amplification

    International Nuclear Information System (INIS)

    Smith, R.E.

    2001-01-01

    This paper seeks to consider social amplification as it applies to risk perception. Perceptions of the magnitude of a risk are conditioned by issues such as the degree of uncertainty in probability and consequences, the nature of the consequences and the relative weightings placed on probability and consequences. Risk perceptions are also influenced by factors such as confidence in the operator of an industrial process, trust in the regulator and the perceived fairness of regulatory decision-making. Different people may hold different views about these issues and there may also be difficulties in communication. The paper identifies and discusses self-reinforcing mechanisms, which will be labelled 'lock-in' here. They appear to apply in many situations where social amplification is observed. Historically, the term 'lock-in' has been applied mainly in the technological context but, in this paper, four types of lock-in are identified, namely scientific/technological, economic, social and institutional lock-in. One type of lock-in tends to lead to the next and all are buttressed by people's general acceptance of the familiar, fear of the unknown and resistance to change. The regulator seeks to make decisions which achieve the common good rather than supporting or perpetuating any set of vested interests. In this regard the locked-in positions of stakeholders, whether organisations, interest groups, or individual members of the public, are obstacles and challenges. Existing methods of consultation are unsatisfactory in terms of achieving a proper and productive level of dialogue with stakeholders

  4. Amplification of cox2 (approximately 620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases.

    Science.gov (United States)

    Telle, Sabine; Thines, Marco

    2008-01-01

    During the past years an increasing number of studies have focussed on the use of herbarium specimens for molecular phylogenetic investigations and several comparative studies have been published. However, in the studies reported so far usually rather large amounts of material (typically around 100 mg) were sampled for DNA extraction. This equals an amount roughly equivalent to 8 cm(2) of a medium thick leaf. For investigating the phylogeny of plant pathogens, such large amounts of tissue are usually not available or would irretrievably damage the specimens. Through systematic comparison of 19 DNA extraction protocols applied to only 2 mg of infected leaf tissue and testing 15 different DNA polymerases, we could successfully amplify a mitochondrial DNA region (cox2; approximately 620 bp) from herbarium specimens well over a hundred years old. We conclude that DNA extraction and the choice of DNA polymerase are crucial factors for successful PCR amplification from small samples of historic herbarium specimens. Through a combination of suitable DNA extraction protocols and DNA polymerases, only a fraction of the preserved plant material commonly used is necessary for successful PCR amplification. This facilitates the potential use of a far larger number of preserved specimens for molecular phylogenetic investigation and provides access to a wealth of genetic information in preserved in specimens deposited in herbaria around the world without reducing their scientific or historical value.

  5. Method for production of petroselinic acid and OMEGA12 hexadecanoic acid in transgenic plants

    Science.gov (United States)

    Ohlrogge, John B.; Cahoon, Edgar B.; Shanklin, John; Somerville, Christopher R.

    1995-01-01

    The present invention relates to a process for producing lipids containing the fatty acid petroselinic acid in plants. The production of petroselinic acid is accomplished by genetically transforming plants which do not normally accumulate petroselinic acid with a gene for a .omega.12 desaturase from another species which does normally accumulate petroselinic acid.

  6. Cocrystal Screening of Ibuprofen with Oxalic Acid and Citric Acid via Grinding Method

    Science.gov (United States)

    Othman, M. F.; Anuar, N.; Rahman, S. Ad; Taifuddin, N. A. Ahmad

    2018-05-01

    Ibuprofen is a Class II Biological Safety Class (BSC) drugs used for relief of arthritis, as an analgesic and possesses the effect of antiplatelet. The major problem involves in ibuprofen is it has a low solubility and high permeability thus causes an unsatisfactory therapeutic effect to humans. Thus, in this work, alteration of ibuprofen’s physicochemical properties is conducted by means of cocrystallization technique. Co-crystallizations of ibuprofen were prepared with selected coformers using dry grinding and liquid assisted grinding (LAG) techniques in different molar ratios while ethanol and propanol were used as a solvent. The new crystalline forms were identified and characterized by differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD) and fourier transform infrared spectroscopy (FTIR). Analysis for Ibuprofen-Citric acid (IBP-CA) system, co-crystal was successfully formed in 1:2, 1:3, 2:1 and 3:1 molar ratios for neat grinding method although the co-crystal produced is unstable. Meanwhile, for Ibuprofen-Oxalic acid (IBP-OA) system, the co-crystal formation was identified only in 1:1, 1:2 and 1:3 molar ratios for the neat grinding method. LAG method shows that co-crystal formation was unsuccessful in both solvents for IBP-CA, while IBP-OA co-crystal was formed in the molar ratio 1:1, 2:1 and 3:1 in ethanol, and 2:1 and 3:1 in propanol.

  7. Properties of nanocellulose isolated from corncob residue using sulfuric acid, formic acid, oxidative and mechanical methods.

    Science.gov (United States)

    Liu, Chao; Li, Bin; Du, Haishun; Lv, Dong; Zhang, Yuedong; Yu, Guang; Mu, Xindong; Peng, Hui

    2016-10-20

    In this work, nanocellulose was extracted from bleached corncob residue (CCR), an underutilized lignocellulose waste from furfural industry, using four different methods (i.e. sulfuric acid hydrolysis, formic acid (FA) hydrolysis, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediated oxidation, and pulp refining, respectively). The self-assembled structure, morphology, dimension, crystallinity, chemical structure and thermal stability of prepared nanocellulose were investigated. FA hydrolysis produced longer cellulose nanocrystals (CNCs) than the one obtained by sulfuric acid hydrolysis, and resulted in high crystallinity and thermal stability due to its preferential degradation of amorphous cellulose and lignin. The cellulose nanofibrils (CNFs) with fine and individualized structure could be isolated by TEMPO-mediated oxidation. In comparison with other nanocellulose products, the intensive pulp refining led to the CNFs with the longest length and the thickest diameter. This comparative study can help to provide an insight into the utilization of CCR as a potential source for nanocellulose production. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Method of Identifying a Base in a Nucleic Acid

    Science.gov (United States)

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

    1999-01-01

    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.

  9. Optofluidic analysis system for amplification-free, direct detection of Ebola infection

    Science.gov (United States)

    Cai, H.; Parks, J. W.; Wall, T. A.; Stott, M. A.; Stambaugh, A.; Alfson, K.; Griffiths, A.; Mathies, R. A.; Carrion, R.; Patterson, J. L.; Hawkins, A. R.; Schmidt, H.

    2015-09-01

    The massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately, and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.

  10. Bright-field in situ hybridization for HER2 gene amplification in breast cancer using tissue microarrays: correlation between chromogenic (CISH) and automated silver-enhanced (SISH) methods with patient outcome.

    Science.gov (United States)

    Francis, Glenn D; Jones, Mark A; Beadle, Geoffrey F; Stein, Sandra R

    2009-06-01

    HER2 gene amplification or overexpression occurs in 15% to 25% of breast cancers and has implications for treatment and prognosis. The most commonly used methods for HER2 testing are fluorescence in situ hybridization (FISH) and immunohistochemistry. FISH is considered to be the reference standard and more accurately predicts response to trastuzumab, but is technically demanding, expensive, and requires specialized equipment. In situ hybridization is required to be eligible for adjuvant treatment with trastuzumab in Australia. Bright-field in situ hybridization is an alternative to FISH and uses a combination of in situ methodology and a peroxidase-mediated chromogenic substrate such as diaminobenzidine [chromogenic in situ hybridization (CISH)] or multimer technology coupled with enzyme metallography [silver-enhanced in situ hybridization (SISH)] to create a marker visible under bright-field microscopy. CISH was introduced into diagnostic testing in Australia in October 2006. SISH methodology is a more recent introduction into the testing repertoire. An evaluation of CISH and SISH performance to assess patient outcome were performed using tissue microarrays. Tissue microarrays were constructed in duplicate using material from 593 patients with invasive breast carcinoma and assessed using CISH and SISH. Gene amplification was assessed using the American Society of Clinical Oncology/College of American Pathologists guideline and Australian HER2 Advisory Board criteria (single probe: diploid, 1 to 2.5 copies/nucleus; polysomy >2.5 to 4 copies/nucleus; equivocal, >4 to 6 copies/nucleus; low-level amplification, >6 to 10 copies/nucleus and high-level amplification >10 copies/nucleus; dual probe HER2/CHR17 ratio: nonamplified 2.2). Results were informative for 337 tissue cores comprising 230 patient samples. Concordance rates were 96% for HER2 single probe CISH and SISH and 95.5% for single probe CISH and dual probe HER2/CHR17 SISH. Both bright-field methods correlated

  11. Evaluation of two loop-mediated isothermal amplification methods for the detection of Salmonella Enteritidis and Listeria monocytogenes in artificially contaminated ready-to-eat fresh products

    Directory of Open Access Journals (Sweden)

    Angeliki Birmpa

    2015-08-01

    Full Text Available In the present study, the effectiveness of two loop-mediated isothermal amplification (LAMP assays was evaluated. Samples of romaine lettuce, strawberries, cherry tomatoes, green onions and sour berries were inoculated with known dilutions (100-108 CFU/g of produce of S. Enteritidis and L. monocytogenes. With LAMP assay, pathogens can be detected in less than 60 min. The limits of detection of S. Enteritidis and L. monocytogenes depended on the food sample tested and on the presence of enrichment step. After enrichment steps, all food samples were found positive even at low initial pathogen levels. The developed LAMP, assays, are expected to become a valuable, robust, innovative, powerful, cheap and fast monitoring tool, which can be extensively used for routine analysis, and screening of contaminated foods by the food industry and the Public Food Health Authorities.

  12. PCR amplification on microarrays of gel immobilized oligonucleotides

    Science.gov (United States)

    Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

    2003-11-04

    The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

  13. Evaluation of methods to estimate the essential amino acids requirements of fish from the muscle amino acid profile

    Directory of Open Access Journals (Sweden)

    Álvaro José de Almeida Bicudo

    2014-03-01

    Full Text Available Many methods to estimate amino acid requirement based on amino acid profile of fish have been proposed. This study evaluates the methodology proposed by Meyer & Fracalossi (2005 and by Tacon (1989 to estimate amino acids requirement of fish, which do exempt knowledge on previous nutritional requirement of reference amino acid. Data on amino acid requirement of pacu, Piaractus mesopotamicus, were used to validate de accuracy of those methods. Meyer & Fracalossi's and Tacon's methodology estimated the lysine requirement of pacu, respectively, at 13 and 23% above requirement determined using dose-response method. The values estimated by both methods lie within the range of requirements determined for other omnivorous fish species, the Meyer & Fracalossi (2005 method showing better accuracy.

  14. Evidence of high-elevation amplification versus Arctic amplification.

    Science.gov (United States)

    Wang, Qixiang; Fan, Xiaohui; Wang, Mengben

    2016-01-12

    Elevation-dependent warming in high-elevation regions and Arctic amplification are of tremendous interest to many scientists who are engaged in studies in climate change. Here, using annual mean temperatures from 2781 global stations for the 1961-2010 period, we find that the warming for the world's high-elevation stations (>500 m above sea level) is clearly stronger than their low-elevation counterparts; and the high-elevation amplification consists of not only an altitudinal amplification but also a latitudinal amplification. The warming for the high-elevation stations is linearly proportional to the temperature lapse rates along altitudinal and latitudinal gradients, as a result of the functional shape of Stefan-Boltzmann law in both vertical and latitudinal directions. In contrast, neither altitudinal amplification nor latitudinal amplification is found within the Arctic region despite its greater warming than lower latitudes. Further analysis shows that the Arctic amplification is an integrated part of the latitudinal amplification trend for the low-elevation stations (≤500 m above sea level) across the entire low- to high-latitude Northern Hemisphere, also a result of the mathematical shape of Stefan-Boltzmann law but only in latitudinal direction.

  15. Determination of organic acids evolution during apple cider fermentation using an improved HPLC analysis method

    NARCIS (Netherlands)

    Zhang, H.; Zhou, F.; Ji, B.; Nout, M.J.R.; Fang, Q.; Zhang, Z.

    2008-01-01

    An efficient method for analyzing ten organic acids in food, namely citric, pyruvic, malic, lactic, succinic, formic, acetic, adipic, propionic and butyric acids, using HPLC was developed. Boric acid was added into the mobile phase to separate lactic and succinic acids, and a post-column buffer

  16. Efficient Audio Power Amplification - Challenges

    DEFF Research Database (Denmark)

    Andersen, Michael Andreas E.

    2005-01-01

    For more than a decade efficient audio power amplification has evolved and today switch-mode audio power amplification in various forms are the state-of-the-art. The technical steps that lead to this evolution are described and in addition many of the challenges still to be faced and where...

  17. Efficient audio power amplification - challenges

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, Michael A.E.

    2005-07-01

    For more than a decade efficient audio power amplification has evolved and today switch-mode audio power amplification in various forms are the state-of-the-art. The technical steps that lead to this evolution are described and in addition many of the challenges still to be faced and where extensive research and development are needed is covered. (au)

  18. Classification of human cancers based on DNA copy number amplification modeling

    Directory of Open Access Journals (Sweden)

    Knuutila Sakari

    2008-05-01

    Full Text Available Abstract Background DNA amplifications alter gene dosage in cancer genomes by multiplying the gene copy number. Amplifications are quintessential in a considerable number of advanced cancers of various anatomical locations. The aims of this study were to classify human cancers based on their amplification patterns, explore the biological and clinical fundamentals behind their amplification-pattern based classification, and understand the characteristics in human genomic architecture that associate with amplification mechanisms. Methods We applied a machine learning approach to model DNA copy number amplifications using a data set of binary amplification records at chromosome sub-band resolution from 4400 cases that represent 82 cancer types. Amplification data was fused with background data: clinical, histological and biological classifications, and cytogenetic annotations. Statistical hypothesis testing was used to mine associations between the data sets. Results Probabilistic clustering of each chromosome identified 111 amplification models and divided the cancer cases into clusters. The distribution of classification terms in the amplification-model based clustering of cancer cases revealed cancer classes that were associated with specific DNA copy number amplification models. Amplification patterns – finite or bounded descriptions of the ranges of the amplifications in the chromosome – were extracted from the clustered data and expressed according to the original cytogenetic nomenclature. This was achieved by maximal frequent itemset mining using the cluster-specific data sets. The boundaries of amplification patterns were shown to be enriched with fragile sites, telomeres, centromeres, and light chromosome bands. Conclusions Our results demonstrate that amplifications are non-random chromosomal changes and specifically selected in tumor tissue microenvironment. Furthermore, statistical evidence showed that specific chromosomal features

  19. Risk Perception and Social Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Smith, R.E. [Environment Agency (United Kingdom)

    2001-07-01

    This paper seeks to consider social amplification as it applies to risk perception. Perceptions of the magnitude of a risk are conditioned by issues such as the degree of uncertainty in probability and consequences, the nature of the consequences and the relative weightings placed on probability and consequences. Risk perceptions are also influenced by factors such as confidence in the operator of an industrial process, trust in the regulator and the perceived fairness of regulatory decision-making. Different people may hold different views about these issues and there may also be difficulties in communication. The paper identifies and discusses self-reinforcing mechanisms, which will be labelled 'lock-in' here. They appear to apply in many situations where social amplification is observed. Historically, the term 'lock-in' has been applied mainly in the technological context but, in this paper, four types of lock-in are identified, namely scientific/technological, economic, social and institutional lock-in. One type of lock-in tends to lead to the next and all are buttressed by people's general acceptance of the familiar, fear of the unknown and resistance to change. The regulator seeks to make decisions which achieve the common good rather than supporting or perpetuating any set of vested interests. In this regard the locked-in positions of stakeholders, whether organisations, interest groups, or individual members of the public, are obstacles and challenges. Existing methods of consultation are unsatisfactory in terms of achieving a proper and productive level of dialogue with stakeholders.

  20. Universal nucleic acids sample preparation method for cells, spores and their mixture

    Science.gov (United States)

    Bavykin, Sergei [Darien, IL

    2011-01-18

    The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

  1. Fast high-throughput method for the determination of acidity constants by capillary electrophoresis: I. Monoprotic weak acids and bases.

    Science.gov (United States)

    Fuguet, Elisabet; Ràfols, Clara; Bosch, Elisabeth; Rosés, Martí

    2009-04-24

    A new and fast method to determine acidity constants of monoprotic weak acids and bases by capillary zone electrophoresis based on the use of an internal standard (compound of similar nature and acidity constant as the analyte) has been developed. This method requires only two electrophoretic runs for the determination of an acidity constant: a first one at a pH where both analyte and internal standard are totally ionized, and a second one at another pH where both are partially ionized. Furthermore, the method is not pH dependent, so an accurate measure of the pH of the buffer solutions is not needed. The acidity constants of several phenols and amines have been measured using internal standards of known pK(a), obtaining a mean deviation of 0.05 pH units compared to the literature values.

  2. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics.

    Science.gov (United States)

    James, Ameh; Macdonald, Joanne

    2015-01-01

    Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA.

  3. Rapid detection of Brucella spp. using loop-mediated isothermal amplification (LAMP).

    Science.gov (United States)

    Chen, Shouyi; Li, Xunde; Li, Juntao; Atwill, Edward R

    2013-01-01

    Brucella spp. are facultative intracellular bacteria that cause zoonotic disease of brucellosis worldwide. Livestock that are most vulnerable to brucellosis include cattle, goats, and pigs. Brucella spp. cause serious health problems to humans and animals and economic losses to the livestock industry. Traditional methods for detection of Brucella spp. take 48-72 h (Kumar et al., J Commun Dis 29:131-137, 1997; Barrouin-Melo et al., Res Vet Sci 83:340-346, 2007) that do not meet the food industry's need of rapid detection. Therefore, there is an urgent need of fast, specific, sensitive, and inexpensive method for diagnosing of Brucella spp. Loop-mediated isothermal amplification (LAMP) is a method to amplify nucleic acid at constant temperatures. Amplification can be detected by visual detection, fluorescent stain, turbidity, and electrophoresis. We targeted at the Brucella-specific gene omp25 and designed LAMP primers for detection of Brucella spp. Amplification of DNA with Bst DNA polymerase can be completed at 65 °C in 60 min. Amplified products can be detected by SYBR Green I stain and 2.0% agarose gel electrophoresis. The LAMP method is feasible for detection of Brucella spp. from blood and milk samples.

  4. A maturation method of uranium content in resins with acid dissolution

    International Nuclear Information System (INIS)

    Liu Yang

    2010-01-01

    Acid dissolution method is that with intensively oxidation acid to decompose ion exchanging resins and dissolving U and Fe ion in water, then menstruate the U content by titration. Comparing with our current method of filtering wash, acid dissolution menstruation U can get more accurate result and take less time, use more simple device. (authors)

  5. Application of a precipitation method for uranium recovery from Abu-Zaabal phosphoric acid plant, egypt

    International Nuclear Information System (INIS)

    El-Hazek, N.M.T.; Hussein, E.M.

    1997-01-01

    Current industrial recovery of uranium from 30% phosphoric acid-produced by the dihydrate process-is based on solvent extraction method. Uranium recovery from concentrated phosphoric acid (45-52% P 2 O 5 ) produced by evaporation of the 30% acid or directly produced by the hemihydrate process, by solvent extraction is difficult to apply in practice. In addition to possible contamination of the acid by the organic solvents and/or their deterioration. This paper investigates the possibility of applying a precipitation method (Weterings and Janssen, 1985) for uranium recovery from both low (28% P 2 O 2 ) and high (48% P 2 O 5 ) concentration phosphoric acids produced by abu-Zaabal phosphoric acid plant (abu-Zaabal fertilizers and chemicals Co., Egypt). The 28% acid produced by H 2 SO 4 dihydrate method and the 48% acid produced by evaporation of the 28% acid

  6. Detection of biological molecules using chemical amplification and optical sensors

    Science.gov (United States)

    Van Antwerp, William Peter; Mastrototaro, John Joseph

    2000-01-01

    Methods are provided for the determination of the concentration of biological levels of polyhydroxylated compounds, particularly glucose. The methods utilize an amplification system that is an analyte transducer immobilized in a polymeric matrix, where the system is implantable and biocompatible. Upon interrogation by an optical system, the amplification system produces a signal capable of detection external to the skin of the patient. Quantitation of the analyte of interest is achieved by measurement of the emitted signal.

  7. Development of an allele-specific, loop-mediated, isothermal amplification method (AS-LAMP to detect the L1014F kdr-w mutation in Anopheles gambiae s. l.

    Directory of Open Access Journals (Sweden)

    Badolo Athanase

    2012-07-01

    Full Text Available Abstract Background Malaria control relies heavily on treated bed nets and indoor residual spraying with pyrethroid insecticides. Unfortunately, the resistance to pyrethroid insecticides, mainly due to the kdr mutation, is spreading in the main malaria vector Anopheles gambiae s.l., decreasing the insecticides’ efficacy. To manage the insecticide resistance rapidly and flexibly, simple and effective tools for the early detection of resistant mosquitoes are needed. This study aimed to develop an allele-specific, loop-mediated, isothermal amplification (AS-LAMP method to detect the West African-type kdr mutation (kdr-w; L1014F in field-collected mosquitoes. Methods DNA fragments of the wild-type and the mutated kdr gene were used to select the primers and develop the method. The primers were designed with the mutation at the 5’ end of the backward inner primer (BIP. The AS-LAMP method was compared to the AS-PCR method using the genomic DNA of 120 field-collected mosquitoes. Results The AS-LAMP method could discriminate between the wild-type homozygote, the heterozygote, and the kdr-w homozygote within 75 min. The AS-LAMP method has the advantage of being faster and at least as sensitive and specific as the AS-PCR method. Conclusions The AS-LAMP method can be used to detect the kdr mutation for quick decision-making, even in less well-equipped laboratories.

  8. Metabolic labeling of sialic acids in tissue culture cell lines: methods to identify substituted and modified radioactive neuraminic acids

    International Nuclear Information System (INIS)

    Diaz, S.; Varki, A.

    1985-01-01

    The parent sialic acid N-acetylneuraminic acid can be modified or substituted in various ways, giving rise to a family of more than 25 compounds. The definitive identification of these compounds has previously required isolation of nanomole amounts for mass spectrometry or NMR. We have explored the possibility of using the known metabolic precursors of the sialic acids, particularly N-acetyl-[6-3H]mannosamine, to label and identify various forms of sialic acids in tissue culture cells. Firstly, we defined several variables that affect the labeling of sialic acids with N-acetyl-[6-3H]mannosamine. Secondly, we have devised a simple screening method to identify cell lines that synthesize substituted or modified sialic acids. We next demonstrate that it is possible to definitively identify the natures of the various labeled sialic acids without the use of mass spectrometry, even though they are present only in tracer amounts. The methods used include paper chromatography, analytical de-O-acetylation, periodate release of the 9-3H as [3H]formaldehyde (which is subsequently converted to a specific 3H-labeled chromophore), acylneuraminate pyruvate lyase treatment with identification of [3H]acylmannosamines, gas-liquid chromatography with radioactive detection, and two new high-pressure liquid chromatography methods utilizing the amine-adsorption:ion suppression and ion-pair principles. The use of an internal N-acetyl-[4-14C]neuraminic acid standard in each of these methods assures precision and accuracy. The combined use of these methods now allows the identification of radioactive tracer amounts of the various types of sialic acids in well-defined populations of tissue culture cells; it may also allow the identification of hitherto unknown forms of sialic acids

  9. Pre-staining thin layer chromatography method for amino acid ...

    African Journals Online (AJOL)

    Jane

    2010-12-13

    Dec 13, 2010 ... inexpensive and the results obtained were clean and reproducible. However, it is suitable for the high throughput screening of amino acid-producing strains. Key words: Thin layer chromatography, pre-staining, amino acid detection. INTRODUCTION. Several analytical techniques have been often used for.

  10. Evaluation of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a screening method for the detection of influenza viruses in the fecal materials of water birds.

    Science.gov (United States)

    Yoshida, Hiromi; Sakoda, Yoshihiro; Endo, Mayumi; Motoshima, Masayuki; Yoshino, Fumi; Yamamoto, Naoki; Okamatsu, Masatoshi; Soejima, Takahiro; Senba, Syouhei; Kanda, Hidetoshi; Kida, Hiroshi

    2011-06-01

    Migratory water birds are a natural reservoir for influenza A viruses. Viruses replicate in the intestines of ducks and are shed with the fecal materials. Virus isolation from collected fecal materials, therefore, is an integral part of the surveillance of avian influenza in water birds. In the present study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) was assessed for its usefulness in detecting the RNA of influenza A viruses in fecal materials. It was found that, RT-LAMP specifically and sensitively detects the matrix gene of influenza A viruses. Influenza A viruses were isolated from the fecal materials in which viral RNA were detected by RT-LAMP in 35 min. The present findings indicate that RT-LAMP is useful as a high throughput screening method for field samples prior to virus isolation, allowing the processing of hundreds of samples per day.

  11. A Comparative Study of the Radical-scavenging Activity of the Phenolcarboxylic Acids Caffeic Acid, p-Coumaric Acid, Chlorogenic Acid and Ferulic Acid, With or Without 2-Mercaptoethanol, a Thiol, Using the Induction Period Method

    Directory of Open Access Journals (Sweden)

    Seiichiro Fujisawa

    2008-10-01

    Full Text Available Phenolcarboxylic acid antioxidants do not act in vivo as radical-scavengers in isolation, but rather together with GSH (glutathione, a coantioxidant, they constitute an intricate antioxidant network. Caffeic acid, p-coumaric acid, ferulic acid and chlorogenic acid with or without 2-mercaptoethanol (ME, as a substitute for GSH, was investigated by the induction period (IP method for polymerization of methyl methacrylate (MMA initiated by thermal decomposition of 2,2'-azobisisobutyronitrile (AIBN, a source of alkyl radicals, R. and benzoyl peroxide (BPO, a source of peroxy radicals, PhCOO. using differential scanning calorimetry (DSC. Upon PhCOO. radical scavenging, the stoichiometric factors (n, number of free radical trapped by one mole of antioxidant for caffeic acid, ferulic acid, p-coumaric acid and chlorogenic acid were 2.4, 1.8, 1.7 and 0.9, whereas upon R. radical scavenging, the corresponding values were 1.3, 1.2, 1.0 and 0.8, respectively. Antioxidants with n values close to 2 suggest the stepwise formation of semiquinone radicals and quinones. By contrast, those with n values close to 1 suggest the formation of dimers after single-electron oxidation, possibly due to recombination of corresponding aryloxy radicals. The ratio of the rate constant of inhibition to that of propagation (kinh/kp declined in the order chlorogenic acid > p-coumaric acid > ferulic acid > caffeic acid. The ratio of the observed IP for the phenolcarboxylic acid/2-mercapto-ethanol (ME mixture (1:1 molar ratio (A to the calculated IP (the simple sum of phenol acid antioxidant and ME (B was investigated. Upon R. scavenging, the caffeic acid or p-coumaric acid/ME mixture was A/B > 1, particularly the former was 1.2, suggesting a synergic effect. By contrast, upon PhCOO. scavenging, the corresponding mixture was A/B < 1, particularly the latter was 0.7, suggesting an antagonistic effect. Upon both radicals scavenging, the A/B for the ferulic acid or chlorogenic acid

  12. Influence of the esterification method on the quantification of olive oil fatty acids

    Directory of Open Access Journals (Sweden)

    Maria Cristina Milinsk

    2011-09-01

    Full Text Available To analyze fatty acids by gas chromatography, it is necessary to apply esterification procedures to convert fatty acids into more volatile compounds, such as fatty acid methyl esters (FAME. Esterification methods are usually subdivided into two categories: acidic catalysis and basic catalysis. Due to the possibility of obtaining different concentrations of fatty acids for the same sample as a function of the esterification method used, the efficiency of eight different esterification methods that involve acidic and basic catalysis in the quantitative determination of FAME in olive oil was verified. The selected methods were described by Metcalfe, 1966 (MET; Bannon, 1982 (BAN; Joseph and Ackman, 1992 (JAC; Hartman and Lago, 1973 (HLA; Jham, 1982 (JHA; ISO 5509, 1978 (ISO; Bannon, 1982 (BBA and Schuchardt and Lopes, 1988 (SLO. The results showed the efficiency of the esterification methods for the main saturated fatty acids that were present in the olive oil analyzed. The most efficient methods for the esterification of unsaturated fatty acids in the oils analyzed were JAC, ISO, and BBA. Nevertheless, the reagent BF3 in methanol, used in the JAC method, is extremely toxic. Thus, when the oil to be analyzed has low acidity, the basic catalysis methods ISO and BBA can be used instead, since they use inexpensive reagents of low toxicity. The results obtained showed that the choice of a method for the analysis of fatty acids also depends on the composition of the oil to be studied.

  13. Influence of low dose ionizing radiation on amplification and antitumor activity of LAK/TIL cells

    International Nuclear Information System (INIS)

    Liu Wei; Hou Dianjun; Qiao Jianwei; Shang Ximei; Li Jieqing

    2000-01-01

    Objective: To study the influence of low dose ionization on amplification and antitumor activity of LAK/TIL cells. Methods: TIL cells isolated from Lewis lung cancer tissues and LAK cells from spleen of tumor-bearing mouse were irradiated with different low doses of X-rays and were cultured after irradiation. Results: Low dose ionizing radiation improved the amplification volume of LAK/TIL cells, decreased the cell death ratio in amplification process, and increased the toxicity of LAK/TIL cells, Conclusions: Low dose ionizing radiation can result in amplification of biologically activated lymphocytes, and decreases the death ratio of the cells in amplification process

  14. Next generation Chirped Pulse Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Nees, J; Biswal, S; Mourou, G [Univ. Michigan, Center for Ultrafast Optical Science, Ann Arbor, MI (United States); Nishimura, Akihiko; Takuma, Hiroshi

    1998-03-01

    The limiting factors of Chirped Pulse Amplification (CPA) are discussed and experimental results of CPA in Yb:glass regenerative amplifier are given. Scaling of Yb:glass to the petawatt level is briefly discussed. (author)

  15. Validation of a multi-analyte HPLC-DAD method for determination of uric acid, creatinine, homovanillic acid, niacinamide, hippuric acid, indole-3-acetic acid and 2-methylhippuric acid in human urine.

    Science.gov (United States)

    Remane, Daniela; Grunwald, Soeren; Hoeke, Henrike; Mueller, Andrea; Roeder, Stefan; von Bergen, Martin; Wissenbach, Dirk K

    2015-08-15

    During the last decades exposure sciences and epidemiological studies attracts more attention to unravel the mechanisms for the development of chronic diseases. According to this an existing HPLC-DAD method for determination of creatinine in urine samples was expended for seven analytes and validated. Creatinine, uric acid, homovanillic acid, niacinamide, hippuric acid, indole-3-acetic acid, and 2-methylhippuric acid were separated by gradient elution (formate buffer/methanol) using an Eclipse Plus C18 Rapid Resolution column (4.6mm×100mm). No interfering signals were detected in mobile phase. After injection of blank urine samples signals for the endogenous compounds but no interferences were detected. All analytes were linear in the selected calibration range and a non weighted calibration model was chosen. Bias, intra-day and inter-day precision for all analytes were below 20% for quality control (QC) low and below 10% for QC medium and high. The limits of quantification in mobile phase were in line with reported reference values but had to be adjusted in urine for homovanillic acid (45mg/L), niacinamide 58.5(mg/L), and indole-3-acetic acid (63mg/L). Comparison of creatinine data obtained by the existing method with those of the developed method showing differences from -120mg/L to +110mg/L with a mean of differences of 29.0mg/L for 50 authentic urine samples. Analyzing 50 authentic urine samples, uric acid, creatinine, hippuric acid, and 2-methylhippuric acid were detected in (nearly) all samples. However, homovanillic acid was detected in 40%, niacinamide in 4% and indole-3-acetic acid was never detected within the selected samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Targeting helicase-dependent amplification products with an electrochemical genosensor for reliable and sensitive screening of genetically modified organisms.

    Science.gov (United States)

    Moura-Melo, Suely; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo J; Dos Santos Junior, J Ribeiro; da Silva Fonseca, Rosana A; Lobo-Castañón, Maria Jesús

    2015-08-18

    Cultivation of genetically modified organisms (GMOs) and their use in food and feed is constantly expanding; thus, the question of informing consumers about their presence in food has proven of significant interest. The development of sensitive, rapid, robust, and reliable methods for the detection of GMOs is crucial for proper food labeling. In response, we have experimentally characterized the helicase-dependent isothermal amplification (HDA) and sequence-specific detection of a transgene from the Cauliflower Mosaic Virus 35S Promoter (CaMV35S), inserted into most transgenic plants. HDA is one of the simplest approaches for DNA amplification, emulating the bacterial replication machinery, and resembling PCR but under isothermal conditions. However, it usually suffers from a lack of selectivity, which is due to the accumulation of spurious amplification products. To improve the selectivity of HDA, which makes the detection of amplification products more reliable, we have developed an electrochemical platform targeting the central sequence of HDA copies of the transgene. A binary monolayer architecture is built onto a thin gold film where, upon the formation of perfect nucleic acid duplexes with the amplification products, these are enzyme-labeled and electrochemically transduced. The resulting combined system increases genosensor detectability up to 10(6)-fold, allowing Yes/No detection of GMOs with a limit of detection of ∼30 copies of the CaMV35S genomic DNA. A set of general utility rules in the design of genosensors for detection of HDA amplicons, which may assist in the development of point-of-care tests, is also included. The method provides a versatile tool for detecting nucleic acids with extremely low abundance not only for food safety control but also in the diagnostics and environmental control areas.

  17. In situ synthesis carbonated hydroxyapatite layers on enamel slices with acidic amino acids by a novel two-step method.

    Science.gov (United States)

    Wu, Xiaoguang; Zhao, Xu; Li, Yi; Yang, Tao; Yan, Xiujuan; Wang, Ke

    2015-09-01

    In situ fabrication of carbonated hydroxyapatite (CHA) remineralization layer on an enamel slice was completed in a novel, biomimetic two-step method. First, a CaCO3 layer was synthesized on the surface of demineralized enamel using an acidic amino acid (aspartic acid or glutamate acid) as a soft template. Second, at the same concentration of the acidic amino acid, rod-like carbonated hydroxyapatite was produced with the CaCO3 layer as a sacrificial template and a reactant. The morphology, crystallinity and other physicochemical properties of the crystals were characterized using field emission scanning electron microscopy (FESEM), Fourier transform infrared spectrometry (FTIR), X-ray diffraction (XRD) and energy-dispersive X-ray analysis (EDAX), respectively. Acidic amino acid could promote the uniform deposition of hydroxyapatite with rod-like crystals via absorption of phosphate and carbonate ions from the reaction solution. Moreover, compared with hydroxyapatite crystals coated on the enamel when synthesized by a one-step method, the CaCO3 coating that was synthesized in the first step acted as an active bridge layer and sacrificial template. It played a vital role in orienting the artificial coating layer through the template effect. The results show that the rod-like carbonated hydroxyapatite crystals grow into bundles, which are similar in size and appearance to prisms in human enamel, when using the two-step method with either aspartic acid or acidic glutamate (20.00 mmol/L). Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Study of water nature in tungstoboric acid by thermochemical method

    International Nuclear Information System (INIS)

    Kosmodem'yanskaya, G.V.; Sadykova, M.M.; Spitsyn, V.I.

    1976-01-01

    The kinetics of the dehydration of the crystalline higher hydrates of tungstoboric acid (TBA) were studied. The dehydration of TBA shows first order behaviour. An appreciable proportion of the water in TBA is zeolitic water

  19. Materials and methods for efficient lactic acid production

    Science.gov (United States)

    Zhou, Shengde; Ingram, Lonnie O& #x27; Neal; Shanmugam, Keelnatham T; Yomano, Lorraine; Grabar, Tammy B; Moore, Jonathan C

    2013-04-23

    The present invention provides derivatives of Escherichia coli constructed for the production of lactic acid. The transformed E. coli of the invention are prepared by deleting the genes that encode competing pathways followed by a growth-based selection for mutants with improved performance. These transformed E. coli are useful for providing an increased supply of lactic acid for use in food and industrial applications.

  20. Amplification and Re-Generation of LNA-Modified Libraries

    DEFF Research Database (Denmark)

    Doessing, Holger; Hansen, Lykke H.; Veedu, Rakesh N.

    2012-01-01

    Locked nucleic acids (LNA) confer high thermal stability and nuclease resistance to oligonucleotides. The discovery of polymerases that accept LNA triphosphates has led us to propose a scheme for the amplification and re-generation of LNA-containing oligonucleotide libraries. Such libraries could...

  1. HER2 amplification, overexpression and score criteria in esophageal adenocarcinoma

    Science.gov (United States)

    Hu, Yingchuan; Bandla, Santhoshi; Godfrey, Tony E.; Tan, Dongfeng; Luketich, James D.; Pennathur, Arjun; Qiu, Xing; Hicks, David G.; Peters, Jeffrey; Zhou, Zhongren

    2011-01-01

    The HER2 oncogene was recently reported to be amplified and overexpressed in esophageal adenocarcinoma. However, the relationship of HER2 amplification in esophageal adenocarcinoma with prognosis has not been well defined. The scoring systems for clinically evaluating HER2 in esophageal adenocarcinoma are not established. The aims of the study were to establish a HER2 scoring system and comprehensively investigate HER2 amplification and overexpression in esophageal adenocarcinoma and its precursor lesion. Using a tissue microarray, containing 116 cases of esophageal adenocarcinoma, 34 cases of BE, 18 cases of low grade dysplasia and 15 cases of high grade dysplasia, HER2 amplification and overexpression were analyzed by HercepTest and CISH methods. The amplification frequency in an independent series of 116 esophageal adenocarcinoma samples was also analyzed using Affymetrix SNP 6.0 microarrays. In our studies, we have found that HER2 amplification does not associate with poor prognosis in total 232 esophageal adenocarcinoma patients by CISH and high density microarrays. We further confirm the similar frequency of HER2 amplification by CISH (18.10%; 21/116) and SNP 6.0 microarrays (16.4%, 19/116) in esophageal adenocarcinoma. HER2 protein overexpression was observed in 12.1 % (14/116) of esophageal adenocarcinoma and 6.67% (1/15) of HGD. No HER2 amplification or overexpression was identified in BE or LGD. All HER2 protein overexpression cases showed HER2 gene amplification. Gene amplification was found to be more frequent by CISH than protein overexpression in esophageal adenocarcinoma (18.10% vs 12.9%). A modified two-step model for esophageal adenocarcinoma HER-2 testing is recommend for clinical esophageal adenocarcinoma HER-2 trial. PMID:21460800

  2. A method for the automatic control method of the carbonation of alkylsalicylic acids

    Energy Technology Data Exchange (ETDEWEB)

    Manoilo, A M; Alekseev, A K; Antonov, V N; Gordash, Iu T; Mikhailov, Iu A; Vavilov, N E; Zvonarev, A P

    1980-03-17

    In the method for the automatic control of the process of carbonation of alkylsalicylic acids (in the production of alkylsalicylic additives for motor oils) by a hydrate of an oxide of alkali earth metal (AEM) and CO/sub 2/ in a medium of petroleum oil by changing the consumption of CO/sub 2/, oil, and AEM, for the purpose of reducing the consumption of the reagent with the preservation of the stability of the quality of the target product, the consumption of CO/sub 2/ is changed depending on the viscosity of the target product. With this, it is necessary the observe the equality of the unit of the ratio of the values of its viscosity, measured at two different velocites of the shift, and at an inclination of the given value from one, the supply of CO/sub 2//sup -/ is curtailed. The total consumption of oil and consumption of AEM is changed, in addition, proportionally to the change in the viscosity of alkylsalicylic acids. The method makes it possible to stabilize the concentration of the active substance and the general alkalinity of the carbonation product and to maintain the given properties with great accuracy, which improves the quality of the additives with economically valuable reagents and an increase in the productivity of the installation.

  3. Light amplification by seeded Kerr instability

    Science.gov (United States)

    Vampa, G.; Hammond, T. J.; Nesrallah, M.; Naumov, A. Yu.; Corkum, P. B.; Brabec, T.

    2018-02-01

    Amplification of femtosecond laser pulses typically requires a lasing medium or a nonlinear crystal. In either case, the chemical properties of the lasing medium or the momentum conservation in the nonlinear crystal constrain the frequency and the bandwidth of the amplified pulses. We demonstrate high gain amplification (greater than 1000) of widely tunable (0.5 to 2.2 micrometers) and short (less than 60 femtosecond) laser pulses, up to intensities of 1 terawatt per square centimeter, by seeding the modulation instability in an Y3Al5O12 crystal pumped by femtosecond near-infrared pulses. Our method avoids constraints related to doping and phase matching and therefore can occur in a wider pool of glasses and crystals even at far-infrared frequencies and for single-cycle pulses. Such amplified pulses are ideal to study strong-field processes in solids and highly excited states in gases.

  4. Radioimmunoassay compared to an enzymatic method for serum bile acid determination

    International Nuclear Information System (INIS)

    Samuelson, K.

    1980-01-01

    Radioimmunoassay (RIA) of cholic and chenodeoxycholic acid was compared to a total bile acid determination with 3α-hydroxysteroid dehydrogenase (3α HSD) and a gas liquid chromatographic (GLC) determination of individual bile acids. When sera from patients with increased bile acid concentration were analysed the results indicated a good correlation between GLC and the other methods. Analysis of sera from healthy subjects indicated a good correlation between GLC and RIA. No correlation existed between RIA and 3α-HSD when serum bile acids were analysed in healthy subjects partly due to the presence of varying amounts of secondary bile acids. (author)

  5. Estimation of solubility of organo-phosphorus extractants by P determination using molybdovanadophosphoric acid method

    International Nuclear Information System (INIS)

    Gill, J.S.; Kotekar, M.K.; Singh, H.

    2005-01-01

    Solvent extraction processes have been found to be suitable for uranium recovery from phosphoric acid. Various extractants like di-2-ethyl hexylphosphoric acid (D2EHPA), di-nonylphenyl phosphoric acid (DNPPA) and synergistic agents like tri-butyl phosphate (TBP), tri-octyl phosphine oxide (TOPO) have been used in liquid-liquid extraction of uranium from phosphoric acid. Contents of these organo-phosphorus compounds in aqueous raffinates need estimation for process requirements. Solubility of Tri-butyl phosphate (TBP) and Di-2-ethylhexyl phosphoric acid (D2EHPA) extractants have been determined in different media of water, oxalic acid (0.6M) and sulphuric acid (3.75M) solutions. These compounds were estimated by determining their phosphorus (P) contents employing molybdovanadophosphoric acid method, after digesting and solubalizing them in nitric and perchloric acid. (author)

  6. RNA amplification for successful gene profiling analysis

    Directory of Open Access Journals (Sweden)

    Wang Ena

    2005-07-01

    -specific, unbiased transcriptome wide amplification accurately maintains proportionality among all RNA species within a given specimen. This allows the utilization of clinical material obtained with minimally invasive methods such as fine needle aspirates (FNA or cytological washings for high throughput functional genomics studies. This review provides a comprehensive and updated discussion of the literature in the subject and critically discusses the main approaches, the pitfalls and provides practical suggestions for successful unbiased amplification of the whole transcriptome in clinical samples.

  7. Potassium hydroxide-ethylene diamine tetraacetic acid method for the rapid preparation of small-scale PCR template DNA from actinobacteria.

    Science.gov (United States)

    Sun, Zhibin; Huang, Yan; Wang, Yanzhuo; Zhao, Yuguo; Cui, Zhongli

    2014-01-01

    Genomic DNA extraction from Gram-positive bacteria is a laborious and time-consuming process. A rapid and convenient method was established to extract genomic DNA from a single colony as a PCR template. KOH-EDTA is used as a lysis buffer to disrupt the cell envelope, releasing genomic DNA, and Tris-HCl (pH = 4) is then added to neutralize the lysate. The lysate can be used directly as a template for PCR amplification. 16S rDNA was successfully amplified from Gram-positive bacteria from the genera of Bacillus, Streptomyces, Micromonospora, Nonomuraea, Microbispora, and Staphylococcus. Amplification of the trpB gene indicated that this method could also be applied to the amplification of functional genes. Compared to colony PCR methods without KOH-EDTA, this method is extremely fast and efficient, and it is applicable to high-throughput PCR amplifications.

  8. A Novel Loop-Mediated Isothermal Amplification (LAMP) Method for Detection of the JP2 Clone of Aggregatibacter actinomycetemcomitans in Subgingival Plaque

    DEFF Research Database (Denmark)

    Seki, M; Poulsen, Knud; Haubek, Dorte

    2008-01-01

    We developed a LAMP method that detects the JP2 clone of Aggregatibacter actinomycetemcomitans, which induces aggressive periodontitis in adolescents of North- and West-African descents. Being independent of special equipment this specific and sensitive method offers significant advantages...

  9. Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection.

    Science.gov (United States)

    Velders, Aldrik H; Schoen, Cor; Saggiomo, Vittorio

    2018-02-01

    Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap and easy, one-button device that can perform LAMP experiments. Here we show how to build and program an Arduino shield for a LAMP and detection of DNA. The here described Arduino Shield is cheap, easy to assemble, to program and use, it is battery operated and the detection of DNA is done by naked-eye so that it can be used in field.

  10. A review on methods of recovery of acid(s) from spent pickle liquor of steel industry.

    Science.gov (United States)

    Ghare, N Y; Wani, K S; Patil, V S

    2013-04-01

    Pickling is the process of removal of oxide layer and rust formed on metal surface. It also removes sand and corrosion products from the surface of metal. Acids such as sulfuric acid, hydrochloric acid are used for pickling. Hydrofluoric acid-Nitric acid mixture is used for stainless steel pickling. Pickling solutions are spent when acid concentration in pickling solutions decreases by 75-85%, which also has metal content up to 150-250 g/ dm3. Spent pickling liquor (SPL) should be dumped because the efficiency of pickling decreases with increasing content of dissolved metal in the bath. The SPL content depends on the plant of origin and the pickling method applied there. SPL from steel pickling in hot-dip galvanizing plants contains zinc(II), iron, traces of lead, chromium. and other heavy metals (max. 500 mg/dm3) and hydrochloric acid. Zinc(II) passes tothe spent solution after dissolution of this metal from zinc(II)-covered racks, chains and baskets used for transportation of galvanized elements. Unevenly covered zinc layers are usually removed in another pickling bath. Due to this, zinc(II) concentration increases even up to 110 g/dm3, while iron content may reach or exceed even 80 g/dm3 in the same solution. This review presents an overview on different aspects of generation and treatment of SPL with recourse to recovery of acid for recycling. Different processes are described in this review and higher weightage is given to membrane processes.

  11. Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing

    OpenAIRE

    Wang, Huiping; Kong, Fanrong; Sorrell, Tania C; Wang, Bin; McNicholas, Paul; Pantarat, Namfon; Ellis, David; Xiao, Meng; Widmer, Fred; Chen, Sharon CA

    2009-01-01

    Abstract Background Amino acid substitutions in the target enzyme Erg11p of azole antifungals contribute to clinically-relevant azole resistance in Candida albicans. A simple molecular method for rapid detection of ERG11 gene mutations would be an advantage as a screening tool to identify potentially-resistant strains and to track their movement. To complement DNA sequencing, we developed a padlock probe and rolling circle amplification (RCA)-based method to detect a series of mutations in th...

  12. A method for measuring fatty acid oxidation in C. elegans

    DEFF Research Database (Denmark)

    Elle, Ida Coordt; Rødkær, Steven Vestergaard; Fredens, Julius

    2012-01-01

    The nematode C. elegans has during the past decade proven to be a valuable model organism to identify and examine molecular mechanisms regulating lipid storage and metabolism. While the primary approach has been to identify genes and pathways conferring alterations in lipid accumulation, only a few...... recent studies have recognized the central role of fatty acid degradation in cellular lipid homeostasis. In the present study, we show how complete oxidation of fatty acids can be determined in live C. elegans by examining oxidation of tritium-labeled fatty acids to tritiated H2O that can be measured......, the present methodology can be used to delineate the role of specific genes and pathways in the regulation of β-oxidation in C. elegans....

  13. Comparison of critical methods developed for fatty acid analysis: A review.

    Science.gov (United States)

    Wu, Zhuona; Zhang, Qi; Li, Ning; Pu, Yiqiong; Wang, Bing; Zhang, Tong

    2017-01-01

    Fatty acids are important nutritional substances and metabolites in living organisms. These acids are abundant in Chinese herbs, such as Brucea javanica, Notopterygium forbesii, Isatis tinctoria, Astragalus membranaceus, and Aconitum szechenyianum. This review illustrates the types of fatty acids and their significant roles in the human body. Many analytical methods are used for the qualitative and quantitative evaluation of fatty acids. Some of the methods used to analyze fatty acids in more than 30 kinds of plants, drugs, and other samples are presented in this paper. These analytical methods include gas chromatography, liquid chromatography, near-infrared spectroscopy, and NMR spectroscopy. The advantages and disadvantages of these techniques are described and compared. This review provides a valuable reference for establishing methods for fatty acid determination. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. A Fast and Accurate UPLC Method for Analysis of Proteinogenic Amino Acids

    NARCIS (Netherlands)

    Meussen, B.J.; Zeeland, van A.N.T.; Bruins, M.E.; Sanders, J.P.M.

    2014-01-01

    A reliable and inexpensive method for the measurement of proteinogenic amino acids was developed. It allows the screening of large sample volumes that is important for current food and feed applications, but also for future biobased applications. The method is based on acid hydrolysis and automated

  15. Evaluation of Simple and Inexpensive High-Throughput Methods for Phytic Acid Determination

    DEFF Research Database (Denmark)

    Raboy, Victor; Johnson, Amy; Bilyeu, Kristin

    2017-01-01

    High-throughput/low-cost/low-tech methods for phytic acid determination that are sufficiently accurate and reproducible would be of value in plant genetics, crop breeding and in the food and feed industries. Variants of two candidate methods, those described by Vaintraub and Lapteva (Anal Biochem...... and legume flours regardless of endogenous phytic acid levels or matrix constituents....

  16. Preparation of high purification and food grade phosphoric acid from technical grade phosphoric acid by liquid-liquid detraction method

    International Nuclear Information System (INIS)

    Alimoradi, M.; Borji, F.; Kishani, A.

    2002-01-01

    Pay attention to increasing consumption of high purification and food grade phosphoric acid in various industries and food industries and on in on hand and lack of preparation between production and distribution of this products its purification is so vital. In this article of liquid-liquid extraction method with normal hexane-mixture of ammonia and acetone-diisopropyl alcohol and normal butanol solvents and these determination of distribution coefficient each one with ph-me try titration we can evaluate effectiveness and sufficiency each one. Because of proper coefficient distribution and its local production of normal butanol solvent and low price is the best solvent. To phosphoric acid modifying coefficient distribution for extraction of phosphoric acid we can add a little value sulfuric acid to the mixture and to remove flouride impurity we add a little Na 2 O. After extraction stage extracted phosphoric acid in the normal strips by evaluating with distilled water and then by passing the carbon active bed and following passes of cationic resine column and concentrated with vacuum distillation. Conclusion of this article is produce of phosphoric acid 85% w/w and food grade from impure phosphoric acid 52% w/w with technical grade

  17. Application of a precipitation method for uranium recovery from abu-zaabal phosphoric acid plant, Egypt

    International Nuclear Information System (INIS)

    El-hazek, N.M.T.; Hussein, E.M.

    1995-01-01

    Current industrial recovery of uranium from 30% phosphoric acid-produced by the dihydrate process-is based on solvent extraction method. Uranium recovery from concentrated phosphoric acid (45-52% p o5 ) produced by evaporation of the 30% acid or directly produced by the hemihydrate process, by solvent extraction is difficult to apply in practice. In addition to possible contamination of the acid by the organic solvents and/or their deterioration. This paper investigates the possibility of applying a precipitation method (Weterings and Janssen, 1985) for uranium recovery from both low (28% P 2 O 5 ) and high (48% P 2 O 5 ) concentration phosphoric acids produced by abu-zaabal phosphoric acid plant (Abuzaabal fertilizers and chemicals Co., Egypt). The 28% acid produced by H 2 SO 4 dihydrate method and the 48% acid produced by evaporation of the 28% acid The applied precipitation method depends on using NH 4 F as a uranium precipitant from both low and high concentration phosphoric acids in presence of acetone as a dispersing agent. All the relevant factors have been studied

  18. Method to produce furandicarboxylic acid (FDCA) from 5-hydroxymethylfurfural (HMF)

    Science.gov (United States)

    Dumesic, James A.; Motagamwala, Ali Hussain

    2017-04-11

    A process to produce furandicarboxylic acid (FDCA). The process includes the steps of reacting a C6 sugar-containing reactant in a reaction solution comprising a first organic solvent selected from the group consisting of beta-, gamma-, and delta-lactones, hydrofurans, hydropyrans, and combinations thereof, in the presence of an acid catalyst for a time and under conditions wherein at least a portion of the C6 sugar present in the reactant is converted to 5-(hydroxymethyl)furfural (HMF); oxidizing the HMF into FDCA with or without separating the HMF from the reaction solution; and extracting the FDCA by adding an aprotic organic solvent having a dipole moment of about 1.0 D or less to the reaction solution.

  19. NOx generation method from recovered nitric acid by electrolysis

    International Nuclear Information System (INIS)

    Suzuki, Y.; Shimizu, H.; Inoue, M.; Fujiso, M.; Shibuya, M.; Iwamoto, F.; Outou, Y.; Ochi, E.; Tsuyuki, T.

    1998-01-01

    An R and D has been conducted on an electrolytic NO x generation process utilizing recovered nitric acid from a PUREX reprocessing plant. The purpose of the study is to drastically reduce the amount of low-level-liquid waste(LLW). The research program phase-1, constituting mainly of electrochemical reaction mechanism study, material balance evaluation and process design study, finished in 1995. The results were presented in the previous papers). The research program phase-2 has started in 1995. The schedule is as follows: FY 1991-1994: Research program phase-1 Basic study using electrolysis equipment with 100-700 cm 2 electrodes FY 1995-1999: Research program phase-2 Process performance test by larger scale electrolysis equipment with 3.6 m 2 electrodes - pilot plant design (FY 1995) - pilot plant construction (FY 1996) - engineering data acquisition (FY 1997-1999). The process consists of many unit operations such as electrolysis, oxidation, nitric acid concentration, NO x compression and storage, NO x recovery, off-gas treatment and acid supplier. This paper outlines the pilot test plant. (author)

  20. Development of a cost-efficient novel method for rapid, concurrent genotyping of five common single nucleotide polymorphisms of the brain derived neurotrophic factor (BDNF) gene by tetra-primer amplification refractory mutation system.

    Science.gov (United States)

    Wang, Cathy K; Xu, Michael S; Ross, Colin J; Lo, Ryan; Procyshyn, Ric M; Vila-Rodriguez, Fidel; White, Randall F; Honer, William G; Barr, Alasdair M

    2015-09-01

    Brain derived neurotrophic factor (BDNF) is a molecular trophic factor that plays a key role in neuronal survival and plasticity. Single nucleotide polymorphisms (SNPs) of the BDNF gene have been associated with specific phenotypic traits in a large number of neuropsychiatric disorders and the response to psychotherapeutic medications in patient populations. Nevertheless, due to study differences and occasionally contrasting findings, substantial further research is required to understand in better detail the association between specific BDNF SNPs and these psychiatric disorders. While considerable progress has been made recently in developing advanced genotyping platforms of SNPs, many high-throughput probe- or array-based detection methods currently available are limited by high costs, slow processing times or access to advanced instrumentation. The polymerase chain reaction (PCR)-based, tetra-primer amplification refractory mutation system (T-ARMS) method is a potential alternative technique for detecting SNP genotypes efficiently, quickly, easily, and cheaply. As a tool in psychopathology research, T-ARMS was shown to be capable of detecting five common SNPs in the BDNF gene (rs6265, rs988748, rs11030104, 11757G/C and rs7103411), which are all SNPs with previously demonstrated clinical relevance to schizophrenia and depression. The present technique therefore represents a suitable protocol for many research laboratories to study the genetic correlates of BDNF in psychiatric disorders. Copyright Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  1. A method for the determination of ascorbic acid using the iron(II)-pyridine-dimethylglyoxime complex

    International Nuclear Information System (INIS)

    Arya, S. P.; Mahajan, M.

    1998-01-01

    A simple and rapid spectrophotometric method for the determination of ascorbic acid is proposed. Ascorbic acid reduces iron (III) to iron (II) which forms a red colored complex with dimethylglyoxime in the presence of pyridine. The absorbance of the resulting solution is measured at 514 nm and a linear relationship between absorbance and concentration of ascorbic acid is observed up to 14 μg ml -1 . Studies on the interference of substances usually associated with ascorbic acid have been carried out and the applicability of the method has been tested by analysing pharmaceutical preparations of vitamin C [it

  2. The development of precisely analytical method for the concentrated boric acid solution in the NPP systems

    Energy Technology Data Exchange (ETDEWEB)

    Sung, G. B.; Jung, K. H.; Kang, D. W. [KEPRI, Taejon (Korea, Republic of); Park, C. S. [KEPCO, Taejon (Korea, Republic of)

    1999-05-01

    Boric acid is used for reactivity control in nuclear reactors, which frequently results in leftover boric acid. This extra boric acid is stored in boric acid storage tank after the concentration process by boric acid evaporator. Apart from this excess, highly concentrated boric acid is stored in safety-related boric acid storage tank. Accordingly, proper maintenance of these boric acid is one of the greatest safety concerns. The solubility of boric acid decreases with decreasing temperature resulting in its precipitation. Consequently, the temperature of boric acid storage tanks is maintained at high temperature. The following analysis should be also performed at the similar temperature to prevent the formation of boric acid precipitation, which is difficult to achieve affecting the accuracy of analytical results. This paper presents a new sampling and measuring technique that makes up for the difficulties mentioned above and shows several advantages including improved reliability and short analysis time. This method is based on gravimetry and dilution method and is expected to be widely used in field application.

  3. [Individual Identification of Cartilage by Direct Amplification in Mass Disasters].

    Science.gov (United States)

    Wang, C H; Xu, C; Li, X Q; Wu, Y; Du, Z

    2017-06-01

    To explore the effectiveness of direct amplification for the STR analysis of cartilage, and to accelerate the effectiveness of disaster victim identification. Eighty-eight cartilage samples were directly amplified by PowerPle® 21 kit, and the results of genotyping were compared with that obtained by the magnetic beads method. In 88 cartilage samples, the STR genotypes were successfully detected from 84 samples by direct amplification and magnetic beads method, and both the results of genotyping by two method were consistent. Direct amplification with PowerPlex® 21 kit can be used for STR genotyping of cartilages. This method is operated easily and promptly, which has a potential application in the individual identification of mass disasters. Copyright© by the Editorial Department of Journal of Forensic Medicine

  4. Method of increasing efficiency of uranium sorption from acid pulp

    International Nuclear Information System (INIS)

    Parobek, P.; Hinterholzinger, O.; Baloun, S.; Homolka, V.; Vanek, J.; Vebr, Z.

    1989-01-01

    Acid pulp containing uranium is adjusted to pH 2.5 to 4 with alkaline agents, such as alkaline pulp, lime milk, finely ground limestone or soda, or a combination thereof. The treated pulp is put into contact with an ion exchanger whose pH has been adjuste to a range of 2.5 to 4. Partial pulp neutralization causes the hydrolysis of the iron present and an overall reduction in salt contents and a significant increase in the ion exchanger sorptio capacity and thus the overall sorption efficiency. The quality o the eluate and of the uranium concentrate improves. (B.S.)

  5. Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection.

    Directory of Open Access Journals (Sweden)

    Ahmed Abd El Wahed

    Full Text Available Over 2.5 billion people are exposed to the risk of contracting dengue fever (DF. Early diagnosis of DF helps to diminish its burden on public health. Real-time reverse transcription polymerase amplification assays (RT-PCR are the standard method for molecular detection of the dengue virus (DENV. Real-time RT-PCR analysis is not suitable for on-site screening since mobile devices are large, expensive, and complex. In this study, two RT-recombinase polymerase amplification (RT-RPA assays were developed to detect DENV1-4.Using two quantitative RNA molecular standards, the analytical sensitivity of a RT-RPA targeting the 3´non-translated region of DENV1-4 was found to range from 14 (DENV4 to 241 (DENV1-3 RNA molecules detected. The assay was specific and did not cross detect other Flaviviruses. The RT-RPA assay was tested in a mobile laboratory combining magnetic-bead based total nucleic acid extraction and a portable detection device in Kedougou (Senegal and in Bangkok (Thailand. In Kedougou, the RT-RPA was operated at an ambient temperature of 38 °C with auxiliary electricity tapped from a motor vehicle and yielded a clinical sensitivity and specificity of 98% (n=31 and 100% (n=23, respectively. While in the field trial in Bangkok, the clinical sensitivity and specificity were 72% (n=90 and 100%(n=41, respectively.During the first 5 days of infection, the developed DENV1-4 RT-RPA assays constitute a suitable accurate and rapid assay for DENV diagnosis. Moreover, the use of a portable fluorescence-reading device broadens its application potential to the point-of-care for outbreak investigations.

  6. Thin layer chromatographic method for the detection of uric acid: collaborative study.

    Science.gov (United States)

    Thrasher, J J; Abadie, A

    1978-07-01

    A collaborative study has been completed on an improved method for the detection and confirmation of uric acid from bird and insect excreta. The proposed method involves the lithium carbonate solubilization of the suspect excreta material, followed by butanol-methanol-water-acetic acid thin layer chromatography, and trisodium phosphate-phosphotungstic acid color development. The collaborative tests resulted in 100% detection of uric acid standard at the 50 ng level and 75% detection at the 20-25 ng level. No false positives were reported during tests of compounds similar to uric acid. The proposed method has been adopted official first action; the present official final action method, 44.161, will be retained for screening purposes.

  7. Evaluation of four novel isothermal amplification assays towards simple and rapid genotyping of chloroquine resistant Plasmodium falciparum.

    Science.gov (United States)

    Chahar, Madhvi; Anvikar, Anup; Dixit, Rajnikant; Valecha, Neena

    2018-07-01

    Loop mediated isothermal amplification (LAMP) assay is sensitive, prompt, high throughput and field deployable technique for nucleic acid amplification under isothermal conditions. In this study, we have developed and optimized four different visualization methods of loop-mediated isothermal amplification (LAMP) assay to detect Pfcrt K76T mutants of P. falciparum and compared their important features for one-pot in-field applications. Even though all the four tested LAMP methods could successfully detect K76T mutants of P. falciparum, however considering the time, safety, sensitivity, cost and simplicity, the malachite green and HNB based methods were found more efficient. Among four different visual dyes uses to detect LAMP products accurately, hydroxynaphthol blue and malachite green could produce long stable color change and brightness in a close tube-based approach to prevent cross-contamination risk. Our results indicated that the LAMP offers an interesting novel and convenient best method for the rapid, sensitive, cost-effective, and fairly user friendly tool for detection of K76T mutants of P. falciparum and therefore presents an alternative to PCR-based assays. Based on our comparative analysis, better field based LAMP visualization method can be chosen easily for the monitoring of other important drug targets (Kelch13 propeller region). Copyright © 2018 Elsevier Inc. All rights reserved.

  8. In situ synthesis carbonated hydroxyapatite layers on enamel slices with acidic amino acids by a novel two-step method

    International Nuclear Information System (INIS)

    Wu, Xiaoguang; Zhao, Xu; Li, Yi; Yang, Tao; Yan, Xiujuan; Wang, Ke

    2015-01-01

    In situ fabrication of carbonated hydroxyapatite (CHA) remineralization layer on an enamel slice was completed in a novel, biomimetic two-step method. First, a CaCO 3 layer was synthesized on the surface of demineralized enamel using an acidic amino acid (aspartic acid or glutamate acid) as a soft template. Second, at the same concentration of the acidic amino acid, rod-like carbonated hydroxyapatite was produced with the CaCO 3 layer as a sacrificial template and a reactant. The morphology, crystallinity and other physicochemical properties of the crystals were characterized using field emission scanning electron microscopy (FESEM), Fourier transform infrared spectrometry (FTIR), X-ray diffraction (XRD) and energy-dispersive X-ray analysis (EDAX), respectively. Acidic amino acid could promote the uniform deposition of hydroxyapatite with rod-like crystals via absorption of phosphate and carbonate ions from the reaction solution. Moreover, compared with hydroxyapatite crystals coated on the enamel when synthesized by a one-step method, the CaCO 3 coating that was synthesized in the first step acted as an active bridge layer and sacrificial template. It played a vital role in orienting the artificial coating layer through the template effect. The results show that the rod-like carbonated hydroxyapatite crystals grow into bundles, which are similar in size and appearance to prisms in human enamel, when using the two-step method with either aspartic acid or acidic glutamate (20.00 mmol/L). - Graphical abstract: FESEM images of enamel slices etched for 60 s and repaired by the two-step method with Glu concentration of 20.00 mmol/L. (A) The boundary (dotted line) of the repaired areas (b) and unrepaired areas (a). (Some selected areas of etched enamel slices were coated with a nail polish before the reaction, which was removed by acetone after the reaction); (B) high magnification image of Ga, (C) high magnification image of Gb. In situ fabrication of carbonated

  9. In situ synthesis carbonated hydroxyapatite layers on enamel slices with acidic amino acids by a novel two-step method

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Xiaoguang [Department of Pediatric Dentistry, The Hospital of Stomatology, Jilin University, Changchun 130021 (China); Zhao, Xu [College of Chemistry, Jilin University, Changchun 130021 (China); Li, Yi, E-mail: lyi99@jlu.edu.cn [Department of Pediatric Dentistry, The Hospital of Stomatology, Jilin University, Changchun 130021 (China); Yang, Tao [Department of Stomatology, Children' s Hospital of Changchun, 130051 (China); Yan, Xiujuan; Wang, Ke [Department of Pediatric Dentistry, The Hospital of Stomatology, Jilin University, Changchun 130021 (China)

    2015-09-01

    In situ fabrication of carbonated hydroxyapatite (CHA) remineralization layer on an enamel slice was completed in a novel, biomimetic two-step method. First, a CaCO{sub 3} layer was synthesized on the surface of demineralized enamel using an acidic amino acid (aspartic acid or glutamate acid) as a soft template. Second, at the same concentration of the acidic amino acid, rod-like carbonated hydroxyapatite was produced with the CaCO{sub 3} layer as a sacrificial template and a reactant. The morphology, crystallinity and other physicochemical properties of the crystals were characterized using field emission scanning electron microscopy (FESEM), Fourier transform infrared spectrometry (FTIR), X-ray diffraction (XRD) and energy-dispersive X-ray analysis (EDAX), respectively. Acidic amino acid could promote the uniform deposition of hydroxyapatite with rod-like crystals via absorption of phosphate and carbonate ions from the reaction solution. Moreover, compared with hydroxyapatite crystals coated on the enamel when synthesized by a one-step method, the CaCO{sub 3} coating that was synthesized in the first step acted as an active bridge layer and sacrificial template. It played a vital role in orienting the artificial coating layer through the template effect. The results show that the rod-like carbonated hydroxyapatite crystals grow into bundles, which are similar in size and appearance to prisms in human enamel, when using the two-step method with either aspartic acid or acidic glutamate (20.00 mmol/L). - Graphical abstract: FESEM images of enamel slices etched for 60 s and repaired by the two-step method with Glu concentration of 20.00 mmol/L. (A) The boundary (dotted line) of the repaired areas (b) and unrepaired areas (a). (Some selected areas of etched enamel slices were coated with a nail polish before the reaction, which was removed by acetone after the reaction); (B) high magnification image of Ga, (C) high magnification image of Gb. In situ fabrication of

  10. Nonspecific amplification of human DNA by Streptococcus pneumoniae LytA primer

    Directory of Open Access Journals (Sweden)

    Helen Hencida Thangamony

    2018-01-01

    Full Text Available Background: Determination of various analytical parameters is essential for the validation of primers used for in-house nucleic acid amplification tests. While standardising a high-resolution melt analysis (HRMA for detection of Streptococcus pneumoniae in acute pyogenic meningitis, we encountered non-specific amplification of certain base pair sequences of human DNA by Centers for Disease Control & Prevention, USA recommended S. pneumoniae LytA primer. Materials and Methods: HRMA was standardised using DNA extracted from an ATCC strain of S. pneumoniae using SP LytA F373 primer and Type-it HRMTM polymerase chain reaction kit in Rotor-Gene Q Thermal Cycler according to the manufacturer's instructions. Specificity of the primers was determined in dry and wet laboratory experiments against diverse related and unrelated microbial pathogens by HRMA and on DNA extracted from unspiked clinical samples negative for SP DNA. Sensitivity was determined by calculating lower limit of detection threshold in experiments with spiked samples. The amplicon from spiked experiments was sequenced and analysed through Gene Bank. Results: Our dry/wet laboratory experiments showed two separate curves and different Tm values indicating certain non-specific amplification by the primer. Basic Local Alignment Search Tool (BLAST analysis of the amplicon obtained in the spiked experiment showed sequences of human chromosome 20 associated with Homo sapiens protein tyrosine phosphatase, receptor type T gene. The problem was resolved by stopping the reaction at 30th Ct cycle and observing the Tm values. Conclusion: Since HRMA is done without a specific probe, one should be aware of non-specific amplifications while using primers for HRMA of human clinical samples.

  11. Method of improving the decontaminating efficiency of ruthenium in evaporating treatment of nitric acid

    International Nuclear Information System (INIS)

    Kubota, Kanya; Yamana, Hajime; Takeda, Seiichiro.

    1984-01-01

    Purpose: To significantly improve the ruthenium removing efficiency in a nitric acid solution in an acid recovery system for the recovery of nitric acid from nitric acid liquid wastes through evaporating condensation. Method: Upon evaporating treatment of nitric acid solution containing ruthenium by supplying and heating the solution to a nitric acid evaporating device, hydrazine is previously added to the nitric acid solution. Hydrazine and intermediate reaction product of hydrazine such as azide causes a reduction reaction with intermediate reaction product of ruthenium tetraoxide to suppress the oxidation of ruthenium and thereby improve the decontaminating efficiency of ruthenium. The amount of hydrazine to be added is preferably between 20 - 500 mg/l and most suitably between 200 - 2000 mg/l per one liter of the liquid in the evaporating device. (Seki, T.)

  12. Comparative study of different cooking methods on nutritional attributes and fatty acid profile of chicken meat

    International Nuclear Information System (INIS)

    Hussain, A. I.; Chatha, S. A. S.; Iqbal, T.; Zahoor, A. F.; Arshad, M. U.; Afzal, S.

    2013-01-01

    The effects of different cooking methods (boiling, grilling, frying and microwave roasting) on the nutritional quality of chicken meat were assessed by measuring quality parameters i.e. moisture, ash, protein, fat and fiber contents. The fatty acid composition of chicken fat was analyzed by GC-FID. The chicken fat was found to contain high levels of oleic acid (38.0-47.3%) followed by linolenic acid (13.3-28.0%) and palmitic acid (2.0-13.6%). Different cooking methods exhibited significant effect (p<=0.05) on the fatty acid composition and other nutritional parameters of meat samples. Generally, fried meat had lower saturated fatty acid contents. It can be concluded from this study that boiling and frying are healthy cooking practices while grilling and microwave roasting show some negative effects. (author)

  13. [Comparison of two nucleic acid extraction methods for norovirus in oysters].

    Science.gov (United States)

    Yuan, Qiao; Li, Hui; Deng, Xiaoling; Mo, Yanling; Fang, Ling; Ke, Changwen

    2013-04-01

    To explore a convenient and effective method for norovirus nucleic acid extraction from oysters suitable for long-term viral surveillance. Two methods, namely method A (glycine washing and polyethylene glycol precipitation of the virus followed by silica gel centrifugal column) and method B (protease K digestion followed by application of paramagnetic silicon) were compared for their performance in norovirus nucleic acid extraction from oysters. Real-time RT-PCR was used to detect norovirus in naturally infected oysters and in oysters with induced infection. The two methods yielded comparable positive detection rates for the samples, but the recovery rate of the virus was higher with method B than with method A. Method B is a more convenient and rapid method for norovirus nucleic acid extraction from oysters and suitable for long-term surveillance of norovirus.

  14. Genome position and gene amplification

    Czech Academy of Sciences Publication Activity Database

    Jirsová, Pavla; Snijders, A.M.; Kwek, S.; Roydasgupta, R.; Fridlyand, J.; Tokuyasu, T.; Pinkel, D.; Albertson, D. G.

    2007-01-01

    Roč. 8, č. 6 (2007), r120 ISSN 1474-760X Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * array comparative genomic hybridization * oncogene Subject RIV: BO - Biophysics Impact factor: 6.589, year: 2007

  15. Strand Invasion Based Amplification (SIBA®): a novel isothermal DNA amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte.

    Science.gov (United States)

    Hoser, Mark J; Mansukoski, Hannu K; Morrical, Scott W; Eboigbodin, Kevin E

    2014-01-01

    Isothermal nucleic acid amplification technologies offer significant advantages over polymerase chain reaction (PCR) in that they do not require thermal cycling or sophisticated laboratory equipment. However, non-target-dependent amplification has limited the sensitivity of isothermal technologies and complex probes are usually required to distinguish between non-specific and target-dependent amplification. Here, we report a novel isothermal nucleic acid amplification technology, Strand Invasion Based Amplification (SIBA). SIBA technology is resistant to non-specific amplification, is able to detect a single molecule of target analyte, and does not require target-specific probes. The technology relies on the recombinase-dependent insertion of an invasion oligonucleotide (IO) into the double-stranded target nucleic acid. The duplex regions peripheral to the IO insertion site dissociate, thereby enabling target-specific primers to bind. A polymerase then extends the primers onto the target nucleic acid leading to exponential amplification of the target. The primers are not substrates for the recombinase and are, therefore unable to extend the target template in the absence of the IO. The inclusion of 2'-O-methyl RNA to the IO ensures that it is not extendible and that it does not take part in the extension of the target template. These characteristics ensure that the technology is resistant to non-specific amplification since primer dimers or mis-priming are unable to exponentially amplify. Consequently, SIBA is highly specific and able to distinguish closely-related species with single molecule sensitivity in the absence of complex probes or sophisticated laboratory equipment. Here, we describe this technology in detail and demonstrate its use for the detection of Salmonella.

  16. Strand Invasion Based Amplification (SIBA®: a novel isothermal DNA amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte.

    Directory of Open Access Journals (Sweden)

    Mark J Hoser

    Full Text Available Isothermal nucleic acid amplification technologies offer significant advantages over polymerase chain reaction (PCR in that they do not require thermal cycling or sophisticated laboratory equipment. However, non-target-dependent amplification has limited the sensitivity of isothermal technologies and complex probes are usually required to distinguish between non-specific and target-dependent amplification. Here, we report a novel isothermal nucleic acid amplification technology, Strand Invasion Based Amplification (SIBA. SIBA technology is resistant to non-specific amplification, is able to detect a single molecule of target analyte, and does not require target-specific probes. The technology relies on the recombinase-dependent insertion of an invasion oligonucleotide (IO into the double-stranded target nucleic acid. The duplex regions peripheral to the IO insertion site dissociate, thereby enabling target-specific primers to bind. A polymerase then extends the primers onto the target nucleic acid leading to exponential amplification of the target. The primers are not substrates for the recombinase and are, therefore unable to extend the target template in the absence of the IO. The inclusion of 2'-O-methyl RNA to the IO ensures that it is not extendible and that it does not take part in the extension of the target template. These characteristics ensure that the technology is resistant to non-specific amplification since primer dimers or mis-priming are unable to exponentially amplify. Consequently, SIBA is highly specific and able to distinguish closely-related species with single molecule sensitivity in the absence of complex probes or sophisticated laboratory equipment. Here, we describe this technology in detail and demonstrate its use for the detection of Salmonella.

  17. By-product formation in repetitive PCR amplification of DNA libraries during SELEX.

    Science.gov (United States)

    Tolle, Fabian; Wilke, Julian; Wengel, Jesper; Mayer, Günter

    2014-01-01

    The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments. Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation and improving the success rate of aptamer selection.

  18. IMPEDANCE METHOD OF MEASURING OF THE TITRATABLE ACIDITY OF YOGURT

    Directory of Open Access Journals (Sweden)

    Miroslav Vasilev

    2016-10-01

    Full Text Available In the present work are analyzed studies related to changes in the active impedance component of the dairy environment caused by the flow of lactic fermentation and coagulation of casein in milk. The aim of this work was to determine the relationship between the relative change of titratable acidity and the relative change of active impedance component of the dairy environment with lactic fermentation, causing coagulation of the casein in milk. . The data were interpolated with cubic spline, visualizing how when the fat content increases, the electrical resistance increases too. All data, collected during the tests would complement and be used for solving the optimization problem to determine the time of completion of the coagulation in future work.

  19. Establishment of recombinase polymerase amplification assay for five hemorrhagic fever-related viruses

    Directory of Open Access Journals (Sweden)

    Xue-feng CAO

    2017-08-01

    Full Text Available Objective To establish a one-step recombinase polymerase amplification (RPA method for pathogen screening and rapid detection in the field targeting for five hemorrhagic fever related viruses (Zaire ebola virus, Sudan ebola virus, Marburg virus, Lassa virus and Yellow fever virus. Methods The specific nucleic acid (NA fragments of each virus were selected as target genes by genome sequence analysis, and the primers and probes for RPA assays were designed according to the sequence. A series of diluted template genes were used for RPA detection to determine the sensitivity. The hemorrhagic fever-related viral nucleic acids were used for RPA detection to determine the specificity. The amplification experiments were carried out at different temperature ranging from 37℃ to 42℃ to validate the reaction temperature range. Results The RPA reaction systems of the five hemorrhagic fever viruses could effectively amplify the target genes, the sensitivities were between 1.5×102 and 1.5×103 copies. No cross reactions existed with the other hemorrhagic fever-related viral genes. Meanwhile, RPA assay could effectively amplify the target genes at 37-42℃. Conclusion The isothermal RPA assays of five hemorrhagic fever viruses are established, which may amply target genes fast and react at a wide temperature range, and be potentially useful for in field pathogens detection. DOI: 10.11855/j.issn.0577-7402.2017.06.09

  20. Effects of the traditional method and an alternative parboiling process on the fatty acids, vitamin E, γ-oryzanol and phenolic acids of glutinous rice.

    Science.gov (United States)

    Thammapat, Pornpisanu; Meeso, Naret; Siriamornpun, Sirithon

    2016-03-01

    The impacts of traditional and alternative parboiling processes on the concentrations of fatty acids, tocopherol, tocotrienol, γ-oryzanol and phenolic acids in glutinous rice were investigated. Differences between the two methods were the soaking temperatures and the steaming methods. Results showed that parboiling processes significantly increased the concentrations of saturated fatty acids (SFA), mono-unsaturated fatty acids (MUFA), γ-oryzanol, γ-tocotrienol and total phenolic acids (TPA) in glutinous rice, while α-tocopherol, γ-tocopherol and polyunsaturated fatty acids (PUFA) decreased (p-oryzanol by three or fourfold compared with the level of γ-oryzanol in raw rice. Parboiling caused both adverse and favorable effects on phenolic acids content (p-oryzanol, hydrobenzoic acid, hydroxycinnamic acid and TPA compared to the traditional method. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. The comparison of techniques and methods for L-ascorbic acid determination in the fruits

    Directory of Open Access Journals (Sweden)

    Cvetković Biljana R.

    2012-01-01

    Full Text Available Vitamin C is an essential vitamin for human nutrition; with the L-ascorbic acid (AA being the active form of vitamin C. Hence, determination of the L-ascorbic acid in the natural and processed foods is very important. In the past, plenty of methods based on the reversible redox reaction of AA oxidation/DHA reduction were developed. Because of L-ascorbic acid instability in aqueous solutions, it is useful to analyze various types of extraction. The aim of this study is to compare three different methods and three different extractants for the L-ascorbic acid determination. Fruits (kiwi, lemon, orange, and grapefruit were purchased from a local market. The L-ascorbic acid in these four samples was determined by the three different methods: the AOAC, the HPLC method with three different types of extractions, and the colorimetric method using ascorbate-oxidase. For the HPLC measurements, one part of the fruits was extracted with distilled water, the second with potassium hydrogen phosphate, and the third with 3% meta-phosphoric acid (MPA in 8% acetic acid. The HPLC measurements of each sample were repeated three times, the AOAC titration was repeated five times, and in the calorimetric method three measurements were performed. The results were statistically evaluated related to sample basis. Statistical analysis shows that there is a significant difference between the results for all three methods of extraction for all samples, except for the grapefruit sample where no significant difference was observed between the results obtained after the buffer extraction (E2 and the metaphosphoric acid in acetic acid extraction (E3. Discriminative analysis for the HPLC determinations proves that there is a clear difference and defined border between the samples in relation to the methods of extraction during the HPLC determination.

  2. Controlled Microwave Heating Accelerates Rolling Circle Amplification.

    Science.gov (United States)

    Yoshimura, Takeo; Suzuki, Takamasa; Mineki, Shigeru; Ohuchi, Shokichi

    2015-01-01

    Rolling circle amplification (RCA) generates single-stranded DNAs or RNA, and the diverse applications of this isothermal technique range from the sensitive detection of nucleic acids to analysis of single nucleotide polymorphisms. Microwave chemistry is widely applied to increase reaction rate as well as product yield and purity. The objectives of the present research were to apply microwave heating to RCA and indicate factors that contribute to the microwave selective heating effect. The microwave reaction temperature was strictly controlled using a microwave applicator optimized for enzymatic-scale reactions. Here, we showed that microwave-assisted RCA reactions catalyzed by either of the four thermostable DNA polymerases were accelerated over 4-folds compared with conventional RCA. Furthermore, the temperatures of the individual buffer components were specifically influenced by microwave heating. We concluded that microwave heating accelerated isothermal RCA of DNA because of the differential heating mechanisms of microwaves on the temperatures of reaction components, although the overall reaction temperatures were the same.

  3. A direct method for the synthesis of orthogonally protected furyl- and thienyl- amino acids.

    Science.gov (United States)

    Hudson, Alex S; Caron, Laurent; Colgin, Neil; Cobb, Steven L

    2015-04-01

    The synthesis of unnatural amino acids plays a key part in expanding the potential application of peptide-based drugs and in the total synthesis of peptide natural products. Herein, we report a direct method for the synthesis of orthogonally protected 5-membered heteroaromatic amino acids.

  4. PCR method for the rapid detection and discrimination of Legionella spp. based on the amplification of pcs, pmtA, and 16S rRNA genes.

    Science.gov (United States)

    Janczarek, Monika; Palusińska-Szysz, Marta

    2016-05-01

    Legionella bacteria are organisms of public health interest due to their ability to cause pneumonia (Legionnaires' disease) in susceptible humans and their ubiquitous presence in water supply systems. Rapid diagnosis of Legionnaires' disease allows the use of therapy specific for the disease. L. pneumophila serogroup 1 is the most common cause of infection acquired in community and hospital environments. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this work, simplex and duplex PCR assays with the use of new molecular markers pcs and pmtA involved in phosphatidylcholine synthesis were specified for rapid and cost-efficient identification and distinguishing Legionella species. The sets of primers developed were found to be sensitive and specific for reliable detection of Legionella belonging to the eight most clinically relevant species. Among these, four primer sets I, II, VI, and VII used for duplex-PCRs proved to have the highest identification power and reliability in the detection of the bacteria. Application of this PCR-based method should improve detection of Legionella spp. in both clinical and environmental settings and facilitate molecular typing of these organisms.

  5. Social amplification of risk: An empirical study

    International Nuclear Information System (INIS)

    Burns, W.; Slovic, P.; Kasperson, R.; Kasperson, J.; Renn, O.; Emani, S.

    1990-09-01

    The social amplification of risk is a theoretical framework that addresses an important deficiency of formal risk assessment methods and procedures. Typically assessments of risk from technological mishaps have been based upon the expected number of people who could be killed or injured or the amount of property that might be damaged. The diverse and consequential impacts that followed in the aftermath of the Three Mile Island accident make it clear that risk assessments that exclude the role of public perceptions of risk will greatly underestimate the potential costs of certain types of hazards. The accident at Three Mile Island produced no direct fatalities and few, if any, expected deaths due to cancer, yet few other accidents in history have had such costly societal impacts. The experience of amplified impacts argues for the development of a broadened theoretical and methodological perspective capable of integrating technical assessment of risk with public perceptions. This report presents the results to date in an ongoing research effort to better understand the complex processes by which adverse events produce impacts. In particular this research attempts to construct a framework that can account for those events that have produced, or are capable of producing, greater societal impacts than would be forecast by traditional risk assessment methods. This study demonstrates that the social amplification of risk involves interactions between sophisticated technological hazards, public and private institutions, and subtle individual and public perceptions and behaviors. These factors, and the variables underlying the intricate processes of social amplification that occur in modern society, are not fully defined and clarified in this report. 19 refs., 9 figs., 10 tabs

  6. A rapid colorimetric screening method for vanillic acid and vanillin-producing bacterial strains.

    Science.gov (United States)

    Zamzuri, N A; Abd-Aziz, S; Rahim, R A; Phang, L Y; Alitheen, N B; Maeda, T

    2014-04-01

    To isolate a bacterial strain capable of biotransforming ferulic acid, a major component of lignin, into vanillin and vanillic acid by a rapid colorimetric screening method. For the production of vanillin, a natural aroma compound, we attempted to isolate a potential strain using a simple screening method based on pH change resulting from the degradation of ferulic acid. The strain Pseudomonas sp. AZ10 UPM exhibited a significant result because of colour changes observed on the assay plate on day 1 with a high intensity of yellow colour. The biotransformation of ferulic acid into vanillic acid by the AZ10 strain provided the yield (Yp/s ) and productivity (Pr ) of 1·08 mg mg(-1) and 53·1 mg L(-1) h(-1) , respectively. In fact, new investigations regarding lignin degradation revealed that the strain was not able to produce vanillin and vanillic acid directly from lignin; however, partially digested lignin by mixed enzymatic treatment allowed the strain to produce 30·7 mg l(-1) and 1·94 mg l(-1) of vanillic acid and biovanillin, respectively. (i) The rapid colorimetric screening method allowed the isolation of a biovanillin producer using ferulic acid as the sole carbon source. (ii) Enzymatic treatment partially digested lignin, which could then be utilized by the strain to produce biovanillin and vanillic acid. To the best of our knowledge, this is the first study reporting the use of a rapid colorimetric screening method for bacterial strains producing vanillin and vanillic acid from ferulic acid. © 2013 The Society for Applied Microbiology.

  7. Kinetics of degradation of ascorbic acid by cyclic voltammetry method

    Directory of Open Access Journals (Sweden)

    Grudić Veselinka V.

    2015-01-01

    Full Text Available Cyclic voltammetry was used to examine the kinetics of degradation of ascorbic acid (AA at different temperatures. It has been shown that the reduction of the concentration of AA in all temperatures follow the kinetics of the first order reaction. The rate constant of the oxidation reaction increases with temperature as follows: 5x10-5; 2x10-4; 1x10-3 and 3x10-3 min-1 at temperatures of 25°C, 35°C, 65°C and 90°C, respectively. The temperature dependence of the rate constant follows Arrhenius equation, and the value of activation energy of the reaction degradation is 48.2 kJ mol-1 . The effect of storage time at a temperature of 90 °C on AA content in fresh juice of green peppers was investigated. It was shown that AA oxidation reaction in the juice is also the first order reaction, while the lower rate constant in relation to the pure AA (5x10-3 min-1 indicates the influence of other substances present in peppers.

  8. The drying method affects the organic acid content of alfalfa forages

    Directory of Open Access Journals (Sweden)

    P. Pezzi

    2011-03-01

    Full Text Available Malic acid (the main organic acid contained in alfalfa; Callaway et al., 1997 is an important metabolite for ruminal microbial population since it improves the uptake of lactic acid by Selenomonas ruminantium (Evans and Martin, 1997 and Megasphaera elsdenii (Rossi and Piva, 1999. Several studies have shown the effect of adding malic acid to the diet of steers and dairy cows on ruminal fermentation (Martin et al., 1999; Martin et al., 2000 and animal performances (Krummrey et al., 1979; Stallcup, 1979; Kung et al., 1982. Aim of this study was the evaluation of the influence of drying method.......

  9. Noise reduction methods for nucleic acid and macromolecule sequencing

    Science.gov (United States)

    Schuller, Ivan K.; Di Ventra, Massimiliano; Balatsky, Alexander

    2018-05-08

    Methods, systems, and devices are disclosed for processing macromolecule sequencing data with substantial noise reduction. In one aspect, a method for reducing noise in a sequential measurement of a macromolecule comprising serial subunits includes cross-correlating multiple measured signals of a physical property of subunits of interest of the macromolecule, the multiple measured signals including the time data associated with the measurement of the signal, to remove or at least reduce signal noise that is not in the same frequency and in phase with the systematic signal contribution of the measured signals.

  10. Determination of humic acid in alkali leaching solution of uranium by spectophotrometry-COD method

    International Nuclear Information System (INIS)

    Feng Yu; An Wei; Chen Shusen

    2014-01-01

    It is one of the main causes of extraction emulsification or resin toxicosis during alkali leaching process in uranium metallurgy which organic matters including humic acid exist in lixiviums. In order to study the effect of humic acid in uranium metallurgy, a method for determination of content of humic acid in aqueous solution need to be established. Spectrophotometry is a simple and convenient method in humic acid analysis. However, accuracy of spectrophotometry can be reduced greatly because of interference of uranium and other elements in the humic acid solutions. Although chemical oxygen demand (COD) method is a common analysis way of organic matters in aqueous solutions, the concentration of humic acid cannot be directly measured. In this paper, COD method is related with spectrophotometry to avoid the interference of uranium and ensure the accurate analysis of humic acid. The results showed that the detection limit of the method was 1.78 mg/L and the recovery rate was 101.2%. (authors)

  11. Amplification-free liquid biopsy by fluorescence approach

    DEFF Research Database (Denmark)

    Uhd, Jesper; Okholm, Anders; Kjems, Jargen

    2017-01-01

    Liquid biopsy is an attractive new paradigm of modern cancer research and clinical oncology. Synergy of fluorescence microscopy with mutation specific molecular probes is a method that we developed for the detection of tumor related circulating DNA, ctDNA. The present detection methods of ctDNA...... samples include amplification-based techniques that have multiple challenges, are often time consuming and rather expensive. In this work, we successfully applied the hybridization assay and advanced microscopy for the reliable amplification-free detection and quantification of cancer associated mutations...... in ctDNA....

  12. Quantification of fatty acids in salmon fillets conserved by different methods

    Directory of Open Access Journals (Sweden)

    Renata Menoci Gonçalves

    2017-09-01

    Full Text Available Lipid contents and the composition of fatty acids of fillets from Chilean salmon (Salmo salar were determined under different conservation methods: fresh salmon, frozen salmon, water-conserved canned salmon and frozen salmon in long-term storage. Fatty acid contents were determined by gas chromatography. The fillets had high lipid levels, ranging between 9.71 and 12.86%. All samples presented high levels of monounsaturated fatty acids, between 363.69 and 425.30 mg g-1 of total lipids, followed by polyunsaturated fatty acids (294.46 - 342.45 mg g-1 of total lipids and saturated fatty acids (203.32 - 223.17 mg g-1 of total lipids. Although samples revealed different lipid contents, all proved to be great sources of omega-3 fatty acids, regardless of the manner of conservation.

  13. Determination of Dornic acidity as a method to select donor milk in a milk bank.

    Science.gov (United States)

    Vázquez-Román, Sara; Garcia-Lara, Nadia Raquel; Escuder-Vieco, Diana; Chaves-Sánchez, Fernando; De la Cruz-Bertolo, Javier; Pallas-Alonso, Carmen Rosa

    2013-02-01

    Dornic acidity may be an indirect measurement of milk's bacteria content and its quality. There are no uniform criteria among different human milk banks on milk acceptance criteria. The main aim of this study is to report the correlation between Dornic acidity and bacterial growth in donor milk in order to validate the Dornic acidity value as an adequate method to select milk prior to its pasteurization. From 105 pools, 4-mL samples of human milk were collected. Dornic acidity measurement and culture in blood and McConkey's agar cultures were performed. Based on Dornic acidity degrees, we classified milk into three quality categories: top quality (acidity pasteurize in a human milk bank based in quality and safety criteria.

  14. Macromechanical Parametric Amplification

    DEFF Research Database (Denmark)

    Neumeyer, Stefan

    between the two peaks can be altered. The first experimental bistable amplified steady-state responses are also reported. The derived analytical models and experimental setups can readily be extended to investigate other factors. Some of the results are also applicable to the more general field of systems...... for energy harvesting. Using analytical, numerical, and experimental methods, the thesis focuses on superthreshold pumping (above the systems parametric instability threshold), nonlinear effects, frequency response backbones, and frequency detuning effects for parametric amplifiers. Part one of the thesis...... covers superthreshold pumping and nonlinear effects. Superthresh-old pumping produces some useful characteristics. For instance, strong superthreshold pumping yields a high gain even though nonlinear effects tend to reduce it. In addition, a narrower excitation phase range is realized for which...

  15. Determination of haloacetic acids in water by ion chromatography--method development.

    Science.gov (United States)

    Lopez-Avila, V; Liu, Y; Charan, C

    1999-01-01

    The microextraction/ion chromatographic (IC) method developed in this study involves extraction of 9 haloacetic acids (HAAs) from aqueous samples (acidified with sulfuric acid to a pH of copper sulfate pentahydrate and sodium sulfate) with methyl tert-butyl ether (MTBE), back extraction into reagent water, and analysis by IC with conductivity detection. The separation column consists of an Ion Pac AG-11 (2 mm id x 50 mm length) guard column and an Ion Pac AS-11 (2 mm id x 250 mm length) analytical column, and the concentration column is a 4 mm id x 35 mm length Dionex TAC-LP column. Use of the 2 mm id Dionex AS-11 column improved detection limits especially for trichloracetic acid (TCAA), bromodichloroacetic acid (BDCAA), dibromochloroacetic acid (DBCAA), and tribromoacetic acid (TBAA). The peak interfering with BCAA elutes at the same retention time as nitrate; however, we have not confirmed the presence of nitrate. Stability studies indicate that HAAs are stable in water for at least 8 days when preserved with ammonium chloride at 100 mg/L and stored at 4 degrees C in the dark. At day 30, recoveries were still high (e.g., 92.1-106%) for dichloroacetic acid (DCAA), BCAA, dibromoacetic acid (DBAA), trichloroacetic acid (TCAA), BDCAA, and DBCAA. However, recoveries of monochloroacetic acid (MCAA), monobromoacetic acid (MBAA), and TBAA were only 54.6, 56.8, and 66.8%, respectively. Stability studies of HAAs in H2SO4-saturated MTBE indicate that all compounds except TBAA are stable for 48 h when stored at 4 degrees C in the dark. TBAA recoveries dropped to 47.1% after 6 h of storage and no TBAA was detected after 48 h of storage. The method described here is only preliminary and was tested in only one laboratory. Additional research is needed to improve method performance.

  16. Laser amplification in excited dielectrics

    Science.gov (United States)

    Winkler, Thomas; Haahr-Lillevang, Lasse; Sarpe, Cristian; Zielinski, Bastian; Götte, Nadine; Senftleben, Arne; Balling, Peter; Baumert, Thomas

    2018-01-01

    Wide-bandgap dielectrics such as glasses or water are transparent at visible and infrared wavelengths. This changes when they are exposed to ultrashort and highly intense laser pulses. Different interaction mechanisms lead to the appearance of various transient nonlinear optical phenomena. Using these, the optical properties of dielectrics can be controlled from the transparent to the metal-like state. Here we expand this range by a yet unexplored mechanism in excited dielectrics: amplification. In a two-colour pump-probe experiment, we show that a 400 nm femtosecond laser pulse is coherently amplified inside an excited sapphire sample on a scale of a few micrometres. Simulations strongly support the proposed two-photon stimulated emission process, which is temporally and spatially controllable. Consequently, we expect applications in all fields that demand strongly localized amplification.

  17. Measuring the amplification of attention

    OpenAIRE

    Blaser, Erik; Sperling, George; Lu, Zhong-Lin

    1999-01-01

    An ambiguous motion paradigm, in which the direction of apparent motion is determined by salience (i.e., the extent to which an area is perceived as figure versus ground), is used to assay the amplification of color by attention to color. In the red–green colored gratings used in these experiments, without attention instructions, salience depends on the chromaticity difference between colored stripes embedded in the motion sequence and the yellow background. Selective attention to red (or to ...

  18. Spheromak Impedance and Current Amplification

    International Nuclear Information System (INIS)

    Fowler, T K; Hua, D D; Stallard, B W

    2002-01-01

    It is shown that high current amplification can be achieved only by injecting helicity on the timescale for reconnection, τ REC , which determines the effective impedance of the spheromak. An approximate equation for current amplification is: dI TOR 2 /dt ∼ I 2 /τ REC - I TOR 2 /τ closed where I is the gun current, I TOR is the spheromak toroidal current and τ CLOSED is the ohmic decay time of the spheromak. Achieving high current amplification, I TOR >> I, requires τ REC CLOSED . For resistive reconnection, this requires reconnection in a cold zone feeding helicity into a hot zone. Here we propose an impedance model based on these ideas in a form that can be implemented in the Corsica-based helicity transport code. The most important feature of the model is the possibility that τ REC actually increases as the spheromak temperature increases, perhaps accounting for the ''voltage sag'' observed in some experiments, and a tendency toward a constant ratio of field to current, B ∝ I, or I TOR ∼ I. Program implications are discussed

  19. The development of quantitative determination method of organic acids in complex poly herbal extraction

    Directory of Open Access Journals (Sweden)

    I. L. Dyachok

    2016-08-01

    Full Text Available Aim. The development of sensible, economical and expressive method of quantitative determination of organic acids in complex poly herbal extraction counted on izovaleric acid with the use of digital technologies. Materials and methods. Model complex poly herbal extraction of sedative action was chosen as a research object. Extraction is composed of these medical plants: Valeriana officinalis L., Crataégus, Melissa officinalis L., Hypericum, Mentha piperita L., Húmulus lúpulus, Viburnum. Based on chemical composition of plant components, we consider that main pharmacologically active compounds, which can be found in complex poly herbal extraction are: polyphenolic substances (flavonoids, which are contained in Crataégus, Viburnum, Hypericum, Mentha piperita L., Húmulus lúpulus; also organic acids, including izovaleric acid, which are contained in Valeriana officinalis L., Mentha piperita L., Melissa officinalis L., Viburnum; the aminoacid are contained in Valeriana officinalis L. For the determination of organic acids content in low concentration we applied instrumental method of analysis, namely conductometry titration which consisted in the dependences of water solution conductivity of complex poly herbal extraction on composition of organic acids. Result. The got analytical dependences, which describes tangent lines to the conductometry curve before and after the point of equivalence, allow to determine the volume of solution expended on titration and carry out procedure of quantitative determination of organic acids in the digital mode. Conclusion. The proposed method enables to determine the point of equivalence and carry out quantitative determination of organic acids counted on izovaleric acid with the use of digital technologies, that allows to computerize the method on the whole.

  20. Signal amplification of microRNAs with modified strand displacement-based cycling probe technology.

    Science.gov (United States)

    Jia, Huning; Bu, Ying; Zou, Bingjie; Wang, Jianping; Kumar, Shalen; Pitman, Janet L; Zhou, Guohua; Song, Qinxin

    2016-10-24

    Micro ribose nucleic acids (miRNAs) play an important role in biological processes such as cell differentiation, proliferation and apoptosis. Therefore, miRNAs are potentially a powerful marker for monitoring cancer and diagnosis. Here, we present sensitive signal amplification for miRNAs based on modified cycling probe technology with strand displacement amplification. miRNA was captured by the template coupled with beads, and then the first cycle based on SDA was repeatedly extended to the nicking end, which was produced by the extension reaction of miRNA. The products generated by SDA are captured by a molecular beacon (MB), which is designed to initiate the second amplification cycle, with a similar principle to the cycling probe technology (CPT), which is based on repeated digestion of the DNA-RNA hybrid by the RNase H. After one sample enrichment and two steps of signal amplification, 0.1 pM of let-7a can be detected. The miRNA assay exhibits a great dynamic range of over 100 orders of magnitude and high specificity to clearly discriminate a single base difference in miRNA sequences. This isothermal amplification does not require any special temperature control instrument. The assay is also about signal amplification rather than template amplification, therefore minimising contamination issues. In addition, there is no need for the reverse transcription (RT) process. Thus the amplification is suitable for miRNA detection.

  1. Capillary electrophoresis method for the analysis of organic acids and amino acids in the presence of strongly alternating concentrations of aqueous lactic acid.

    Science.gov (United States)

    Laube, Hendrik; Boden, Jana; Schneider, Roland

    2017-07-01

    During the production of bio-based bulk chemicals, such as lactic acid (LA), organic impurities have to be removed to produce a ready-to-market product. A capillary electrophoresis method for the simultaneous detection of LA and organic impurities in less than 10 min was developed. LA and organic impurities were detected using a direct UV detection method with micellar background electrolyte, which consisted of borate and sodium dodecyl sulfate. We investigated the effects of electrolyte composition and temperature on the speed, sensitivity, and robustness of the separation. A few validation parameters, such as linearity, limit of detection, and internal and external standards, were evaluated under optimized conditions. The method was applied for the detection of LA and organic impurities, including tyrosine, phenylalanine, and pyroglutamic acid, in samples from a continuous LA fermentation process from post-extraction tapioca starch and yeast extract.

  2. Nucleic acid extraction, oligonucleotide probes and PCR methods

    International Nuclear Information System (INIS)

    Zhongtang Yu; Forster, R.J.

    2005-01-01

    Complex microbiomes of rumen and gastrointestinal tracts. Bacteria, fungi and protozoa, present in rumen and gastrointestinal (GI) tracts, interact with feed, with each other, and with their host animals, resulting in a complex symbiotic microbiota of distinctive composition and structure. Such microbiota is dynamic and highly responsive to a variety of biotic and abiotic factors, such as diet, feed additives, age, health and physiological status of the host animal, geographical locations, season and feeding regimen (reviewed in Ref. [39]). This symbiotic microbiota has been the focus of microbial research for over half a century in search for improved ruminant nutrition. Before the advent of molecular biology techniques, microorganisms in rumen and GI tracts, as in other habitats, were studied with cultivation-based techniques, which only allows for the isolation and characterization of a limited number of readily culturable species. As estimated, there are more than 400 species of bacteria and up to 100 species of protozoa and fungi inhabiting rumen and GI tracts. In human GI tracts, as much as 60% of these members cannot be isolated on agar plates and, thus, remain unknown. In ruminants, although it is not known, the culturable species of the microbiota are probably in the same range. Even among the culturable species, probably only some of them have been isolated and described. The application of cultivation-independent, more sensitive and accurate molecular techniques to the study of ruminal and GI microorganisms provided an alternative to directly examining the diversity and the community structure of ruminal and GI microbiota on the basis of genotypes, instead of phenotypes. Both polymerase chain reaction (PCR)-based methods, such as denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis, terminal restriction fragment length polymorphism, cloning and sequencing of PCR amplicons and amplified 16S ribosomal DNA restriction

  3. Sensitive real-time PCR detection of pathogenic Leptospira spp. and a comparison of nucleic acid amplification methods for the diagnosis of leptospirosis.

    Science.gov (United States)

    Waggoner, Jesse J; Balassiano, Ilana; Abeynayake, Janaki; Sahoo, Malaya K; Mohamed-Hadley, Alisha; Liu, Yuanyuan; Vital-Brazil, Juliana Magalhães; Pinsky, Benjamin A

    2014-01-01

    Bacteria of the genus Leptospira, the causative agents of leptospirosis, are categorized into pathogenic and non-pathogenic species. However, the benefit of using a clinical diagnostic that is specific for pathogenic species remains unclear. In this study, we present the development of a real-time PCR (rtPCR) for the detection of pathogenic Leptospira (the pathogenic rtPCR), and we perform a comparison of the pathogenic rtPCR with a published assay that detects all Leptospira species [the undifferentiated febrile illness (UFI) assay] and a reference 16S Leptospira rtPCR, which was originally designed to detect pathogenic species. For the pathogenic rtPCR, a new hydrolysis probe was designed for use with primers from the UFI assay, which targets the 16S gene. The pathogenic rtPCR detected Leptospira DNA in 37/37 cultured isolates from 5 pathogenic and one intermediate species. Two strains of the non-pathogenic L. biflexa produced no signal. Clinical samples from 65 patients with suspected leptospirosis were then tested using the pathogenic rtPCR and a reference Leptospira 16S rtPCR. All 65 samples had tested positive for Leptospira using the UFI assay; 62 (95.4%) samples tested positive using the pathogenic rtPCR (p = 0.24). Only 24 (36.9%) samples tested positive in the reference 16S rtPCR (pLeptospira species in 49/50 cases, including 3 cases that were only detected using the UFI assay. The pathogenic rtPCR displayed similar sensitivity to the UFI assay when testing clinical specimens with no difference in specificity. Both assays proved significantly more sensitive than a real-time molecular test used for comparison. Future studies are needed to investigate the clinical and epidemiologic significance of more sensitive Leptospira detection using these tests.

  4. An Alternative and Rapid Method for the Extraction of Nucleic Acids from Ixodid Ticks by Potassium Acetate Procedure

    Directory of Open Access Journals (Sweden)

    Islay Rodríguez

    2014-08-01

    Full Text Available Four variants of the potassium acetate procedure for DNA extraction from ixodid ticks at different stage of their life cycles were evaluated and compared with phenol-chloroform and ammonium hydroxide methods. The most rapid and most efficient variant was validated in the DNA extraction procedure from the engorged ticks collected from bovine, canine as well as from house ticks for the screening of Borrelia burgdorferi sensu lato, Anaplasma spp. and Babesia spp. The ammonium hydroxide procedure was used for non-engorged ticks. All the variants were efficient and allowed obtaining PCR-quality material according to the specific amplification of 16S rRNA gene fragment of the original tick. DNA extracted from the ticks under the study was tested by multiplex PCR for the screening of tick-borne pathogens. Anaplasma spp. and Babesia spp. amplification products were obtained from 29/48 extracts. Ammonium hydroxide protocol was not efficient for two extracts. Detection of amplification products from the PCR indicated that DNA had been successfully extracted. The potassium acetate procedure could be an alternative, rapid, and reliable method for DNA extraction from the ixodid ticks, mainly for poorly-resourced laboratories.

  5. A Novel Method for Fabricating Double Layers Porous Anodic Alumina in Phosphoric/Oxalic Acid Solution and Oxalic Acid Solution

    Directory of Open Access Journals (Sweden)

    Yanfang Xu

    2016-01-01

    Full Text Available A novel method for fabricating ordered double layers porous anodic alumina (DL-PAA with controllable nanopore size was presented. Highly ordered large pore layer with interpore distance of 480 nm was fabricated in phosphoric acid solution with oxalic acid addition at the potential of 195 V and the small pore layer was fabricated in oxalic acid solution at the potential from 60 to 100 V. Experimental results show that the thickness of large pore layer is linearly correlative with anodizing time, and pore diameter is linearly correlative with pore widening time. When the anodizing potential in oxalic acid solution was adjusted from 60 to 100 V, the small pore layers with continuously tunable interpore distance from 142 to 241 nm and pore density from 1.94×109 to 4.89×109 cm−2 were obtained. And the interpore distance and the pore density of small pore layers are closely correlative with the anodizing potential. The fabricated DL-PAA templates can be widely utilized for fabrication of ordered nanomaterials, such as superhydrophobic or gecko-inspired adhesive materials and metal or semiconductor nanowires.

  6. Modeling the amplification dynamics of human Alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    Dale J Hedges

    2005-09-01

    Full Text Available Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.

  7. Modeling the amplification dynamics of human alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.

  8. Isothermal Amplification for MicroRNA Detection: From the Test Tube to the Cell.

    Science.gov (United States)

    Deng, Ruijie; Zhang, Kaixiang; Li, Jinghong

    2017-04-18

    MicroRNAs (miRNAs) are a class of small noncoding RNAs that act as pivotal post-transcriptional regulators of gene expression, thus involving in many fundamental cellular processes such as cell proliferation, migration, and canceration. The detection of miRNAs has attracted significant interest, as abnormal miRNA expression is identified to contribute to serious human diseases such as cancers. Particularly, miRNAs in peripheral blood have recently been recognized as important biomarkers potential for liquid biopsy. Furthermore, as miRNAs are expressed heterogeneously in different cells, investigations into single-cell miRNA expression will be of great value for resolving miRNA-mediated regulatory circuits and the complexity and heterogeneity of miRNA-related diseases. Thus, the development of miRNA detection methods, especially for complex clinic samples and single cells is in great demand. In this Account, we will present recent progress in the design and application of isothermal amplification enabling miRNA detection transition from the test tube to the clinical sample and single cell, which will significantly advance our knowledge of miRNA functions and disease associations, as well as its translation in clinical diagnostics. miRNAs present a huge challenge in detection because of their extremely short length (∼22 nucleotides) and sequence homology (even with only single-nucleotide variation). The conventional golden method for nucleic acid detection, quantitative PCR (qPCR), is not amenable to directly detecting short RNAs and hardly enables distinguishing between miRNA family members with very similar sequences. Alternatively, isothermal amplification has emerged as a powerful method for quantification of nucleic acids and attracts broad interest for utilization in developing miRNA assays. Compared to PCR, isothermal amplification can be performed without precise control of temperature cycling and is well fit for detecting short RNA or DNA. We and other

  9. Analytical methods for 2,4-D (Dichlorophenoxyacetic acid) determination

    International Nuclear Information System (INIS)

    Martinez G, M.S.M.

    1999-01-01

    The 2,4-D herbicide is one of the main pesticides for controlling the bad grass in crops such as the water undergrowth. In Mexico the allowed bound of this pesticide is 0.05 mg/l in water of 2,4-D so it is required to have methods trusts and exacts, which can used in order to detected low concentration of it. In this work we show some for the conventional techniques and for establishing the 2,4-D concentrations. The UV-Vis spectrometer and liquids chromatography due that they are the most common used nowadays. Beside, we introduce a now developed technique, which is based on the neutronic activation analysis. Though use of the UV-Vis spectrometer technique it was possible target the concentrations interval between 1 and 200 mg/l. In the liquids chromatography interval was between 0.1 and 0.9, and by the neutronic activation analysis the interval was between 0.01 and 200 mg/l. (Author)

  10. Anisotropic amplification of proton transport in proton exchange membrane fuel cells

    Science.gov (United States)

    Thimmappa, Ravikumar; Fawaz, Mohammed; Devendrachari, Mruthyunjayachari Chattanahalli; Gautam, Manu; Kottaichamy, Alagar Raja; Shafi, Shahid Pottachola; Thotiyl, Musthafa Ottakam

    2017-07-01

    Though graphene oxide (GO) membrane shuttles protons under humid conditions, it suffer severe disintegration and anhydrous conditions lead to abysmal ionic conductivity. The trade-off between mechanical integrity and ionic conductivity challenge the amplification of GO's ionic transport under anhydrous conditions. We show anisotropic amplification of GO's ionic transport with a selective amplification of in plane contribution under anhydrous conditions by doping it with a plant extract, phytic acid (PA). The hygroscopic nature of PA stabilized interlayer water molecules and peculiar geometry of sbnd OH functionalities around saturated hydrocarbon ring anisotropically enhanced ionic transport amplifying the fuel cell performance metrics.

  11. Comparison of methods for the determination of reduced inorganic sulphur in acid sulphate soils

    International Nuclear Information System (INIS)

    Santomartino, S.L.

    1999-01-01

    Full text: The management of acid sulphate soils requires analytical methods that provide accurate data on the quantity of reduced inorganic sulphur within a soil, as it is this fraction that produces acid upon oxidation. This study uses sulphidic Coode Island Silt samples to compare common analytical methods including POCAS (Peroxide Oxidation-Combined Acidity and Sulphate) which consists of TSA (Total Sulphidic Acidity), S pos (Peroxide Oxidisable Sulphur), TOS (Total Oxidisable Sulphur) and chromium-reducible sulphur. The determination of total sulphur by Leco sulphur is strongly correlated with, but slightly less than, that analysed by XRF. Comparison of soil sulphide content by chromium-reducible sulphur, TSA and TOS methods indicates that TOS values are substantially higher than both other methods. The problem with the TOS method lies in the sulphate extraction procedure. Hot distilled water and HCI are commonly used as extractants, however hot distilled water fails to remove organic sulphur, thereby overestimating the sulphide content of the soil. Leco carbon analyses verify that a substantial proportion of organic matter exists within the samples. The HCI extraction process, which uses Ion Chromatography to analyse for sulphate, produces highly inaccurate results due to the interference of the sulphate peak by the chloride peak during analysis. An alternative method involving HCI extraction and XRF analysis of the soil residue is currently being undertaken. The use of KCI to extract sulphate generally produces values similar to the hot distilled water method. The sulphidic content measured by TSA is strongly correlated with, but slightly higher than that determined by the chromium-reducible sulphur method. This is attributed to the use of hydrogen peroxide in the TSA method, which oxidises organic matter to organic acids in addition to oxidising sulphides. These preliminary findings indicate that the chromium-reducible sulphur method is the most suitable

  12. Digital holographic amplification of interferograms in the Michelson interferometer using the phase-only LCOS modulator

    Science.gov (United States)

    Balbekin, Nikolay; Petrov, Nikolay; Pul'kin, Sergey; Shoev, Vladislav; Sevryugin, Alexander; Tursunov, Ibrohim; Venediktov, Dmitrii; Venediktov, Vladimir

    2017-10-01

    The method of amplification of hologram was applied to the so-called Rozhdestvenskiy hooks, that were obtained in the Rozhdestvenskiy interferometer (Michelson interferometer, combined with a grating spectrograph). In such a device the absorption lines reveal themselves as specific "hooks", whose curvature provides the information about the atomic oscillator force. The holographic amplification "smoothes" the hooks and thus makes their analysis much simpler.

  13. SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence

    Directory of Open Access Journals (Sweden)

    Zhou Yuan Wu

    2013-07-01

    Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

  14. Quantum tomography enhanced through parametric amplification

    Science.gov (United States)

    Knyazev, E.; Spasibko, K. Yu; Chekhova, M. V.; Khalili, F. Ya

    2018-01-01

    Quantum tomography is the standard method of reconstructing the Wigner function of quantum states of light by means of balanced homodyne detection. The reconstruction quality strongly depends on the photodetectors quantum efficiency and other losses in the measurement setup. In this article we analyze in detail a protocol of enhanced quantum tomography, proposed by Leonhardt and Paul [1] which allows one to reduce the degrading effect of detection losses. It is based on phase-sensitive parametric amplification, with the phase of the amplified quadrature being scanned synchronously with the local oscillator phase. Although with sufficiently strong amplification the protocol enables overcoming any detection inefficiency, it was so far not implemented in the experiment, probably due to the losses in the amplifier. Here we discuss a possible proof-of-principle experiment with a traveling-wave parametric amplifier. We show that with the state-of-the-art optical elements, the protocol enables high fidelity tomographic reconstruction of bright non-classical states of light. We consider two examples: bright squeezed vacuum and squeezed single-photon state, with the latter being a non-Gaussian state and both strongly affected by the losses.

  15. Cascade DNA nanomachine and exponential amplification biosensing.

    Science.gov (United States)

    Xu, Jianguo; Wu, Zai-Sheng; Shen, Weiyu; Xu, Huo; Li, Hongling; Jia, Lee

    2015-11-15

    DNA is a versatile scaffold for the assembly of multifunctional nanostructures, and potential applications of various DNA nanodevices have been recently demonstrated for disease diagnosis and treatment. In the current study, a powerful cascade DNA nanomachine was developed that can execute the exponential amplification of p53 tumor suppressor gene. During the operation of the newly-proposed DNA nanomachine, dual-cyclical nucleic acid strand-displacement polymerization (dual-CNDP) was ingeniously introduced, where the target trigger is repeatedly used as the fuel molecule and the nicked fragments are dramatically accumulated. Moreover, each displaced nicked fragment is able to activate the another type of cyclical strand-displacement amplification, increasing exponentially the value of fluorescence intensity. Essentially, one target binding event can induce considerable number of subsequent reactions, and the nanodevice was called cascade DNA nanomachine. It can implement several functions, including recognition element, signaling probe, polymerization primer and template. Using the developed autonomous operation of DNA nanomachine, the p53 gene can be quantified in the wide concentration range from 0.05 to 150 nM with the detection limit of 50 pM. If taking into account the final volume of mixture, the detection limit is calculated as lower as 6.2 pM, achieving an desirable assay ability. More strikingly, the mutant gene can be easily distinguished from the wild-type one. The proof-of-concept demonstrations reported herein is expected to promote the development and application of DNA nanomachine, showing great potential value in basic biology and medical diagnosis. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Evaluation of Scotchbond Multipurpose and maleic acid as alternative methods of bonding orthodontic brackets.

    Science.gov (United States)

    Olsen, M E; Bishara, S E; Damon, P; Jakobsen, J R

    1997-05-01

    Damage to the enamel surface during bonding and debonding of orthodontic brackets is a clinical concern. Alternative bonding methods that minimize enamel surface damage while maintaining a clinically useful bond strength is an aim of current research. The purpose of this study was to compare the effects on bond strength and bracket failure location of two adhesives (System 1+ and Scotchbond Multipurpose, 3M Dental Products Division) and two enamel conditioners (37% phosphoric acid and 10% maleic acid). Forty-eight freshly extracted human premolars were pumiced and divided into four groups of 12 teeth, and metal orthodontic brackets were attached to the enamel surface by one of four protocols: (1) System 1+ and phosphoric acid, (2) Scotchbond and phosphoric acid, (3) System 1+ and maleic acid, and (4) Scotchbond and maleic acid. After bracket attachment, the teeth were mounted in phenolic rings and stored in deionized water at 37 degrees C for 72 hours. A Zwick universal testing machine (Zwick GmbH & Co.) was used to determine shear bond strengths. The residual adhesive on the enamel surface was evaluated with the Adhesive Remnant Index. The analysis of variance was used to compare the four groups. Significance was predetermined at p adhesives on the enamel surfaces, revealed significant differences among the four groups (mean 2 = 0.005). A Duncan multiple range test revealed the difference occurred between the phosphoric acid and maleic acid groups, with maleic acid having bond failures at the enamel-adhesive interface. In conclusion, the use of Scotchbond Multipurpose and/or maleic acid does not significantly effect bond strength, however, the use of maleic acid resulted in an unfavorable bond failure location.

  17. Rapid and simultaneous detection of human hepatitis B virus and hepatitis C virus antibodies based on a protein chip assay using nano-gold immunological amplification and silver staining method

    Directory of Open Access Journals (Sweden)

    Wan Zhixiang

    2005-07-01

    Full Text Available Abstract Background Viral hepatitis due to hepatitis B virus and hepatitis C virus are major public health problems all over the world. Traditional detection methods including polymerase chain reaction (PCR-based assays and enzyme-linked immunosorbent assays (ELISA are expensive and time-consuming. In our assay, a protein chip assay using Nano-gold Immunological Amplification and Silver Staining (NIASS method was applied to detect HBV and HCV antibodies rapidly and simultaneously. Methods Chemically modified glass slides were used as solid supports (named chip, on which several antigens, including HBsAg, HBeAg, HBcAg and HCVAg (a mixture of NS3, NS5 and core antigens were immobilized respectively. Colloidal nano-gold labelled staphylococcal protein A (SPA was used as an indicator and immunogold silver staining enhancement technique was applied to amplify the detection signals, producing black image on array spots, which were visible with naked eyes. To determine the detection limit of the protein chip assay, a set of model arrays in which human IgG was spotted were structured and the model arrays were incubated with different concentrations of anti-IgG. A total of 305 serum samples previously characterized with commercial ELISA were divided into 4 groups and tested in this assay. Results We prepared mono-dispersed, spherical nano-gold particles with an average diameter of 15 ± 2 nm. Colloidal nano-gold-SPA particles observed by TEM were well-distributed, maintaining uniform and stable. The optimum silver enhancement time ranged from 8 to 12 minutes. In our assay, the protein chips could detect serum antibodies against HBsAg, HBeAg, HBcAg and HCVAg with the absence of the cross reaction. In the model arrays, the anti-IgG as low as 3 ng/ml could be detected. The data for comparing the protein chip assay with ELISA indicated that no distinct difference (P > 0.05 existed between the results determined by our assay and ELISA respectively. Conclusion

  18. Whole genome amplification in preimplantation genetic diagnosis*

    Science.gov (United States)

    Zheng, Ying-ming; Wang, Ning; Li, Lei; Jin, Fan

    2011-01-01

    Preimplantation genetic diagnosis (PGD) refers to a procedure for genetically analyzing embryos prior to implantation, improving the chance of conception for patients at high risk of transmitting specific inherited disorders. This method has been widely used for a large number of genetic disorders since the first successful application in the early 1990s. Polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) are the two main methods in PGD, but there are some inevitable shortcomings limiting the scope of genetic diagnosis. Fortunately, different whole genome amplification (WGA) techniques have been developed to overcome these problems. Sufficient DNA can be amplified and multiple tasks which need abundant DNA can be performed. Moreover, WGA products can be analyzed as a template for multi-loci and multi-gene during the subsequent DNA analysis. In this review, we will focus on the currently available WGA techniques and their applications, as well as the new technical trends from WGA products. PMID:21194180

  19. Development of a multiplex polymerase chain reaction-sequence-specific primer method for NKG2D and NKG2F single-nucleotide polymorphism typing using isothermal multiple displacement amplification products.

    Science.gov (United States)

    Kaewmanee, M; Phoksawat, W; Romphruk, A; Romphruk, A V; Jumnainsong, A; Leelayuwat, C

    2013-06-01

    Natural killer group 2 member D (NKG2D) on immune effector cells recognizes multiple stress-inducible ligands. NKG2D single-nucleotide polymorphism (SNP) haplotypes were related to the levels of cytotoxic activity of peripheral blood mononuclear cells. Indeed, these polymorphisms were also located in NKG2F. Isothermal multiple displacement amplification (IMDA) is used for whole genome amplification (WGA) that can amplify very small genomic DNA templates into microgram with whole genome coverage. This is particularly useful in the cases of limited amount of valuable DNA samples requiring multi-locus genotyping. In this study, we evaluated the quality and applicability of IMDA to genetic studies in terms of sensitivity, efficiency of IMDA re-amplification and stability of IMDA products. The smallest amount of DNA to be effectively amplified by IMDA was 200 pg yielding final DNA of approximately 16 µg within 1.5 h. IMDA could be re-amplified only once (second round of amplification), and could be kept for 5 months at 4°C and more than a year at -20°C without loosing genome coverage. The amplified products were used successfully to setup a multiplex polymerase chain reaction-sequence-specific primer for SNP typing of the NKG2D/F genes. The NKG2D/F multiplex polymerase chain reaction (PCR) contained six PCR mixtures for detecting 10 selected SNPs, including 8 NKG2D/F SNP haplotypes and 2 additional NKG2D coding SNPs. This typing procedure will be applicable in both clinical and research laboratories. Thus, our data provide useful information and limitations for utilization of genome-wide amplification using IMDA and its application for multiplex NKG2D/F typing. © 2013 John Wiley & Sons Ltd.

  20. Method for separating mono- and di-octylphenyl phosphoric acid esters

    International Nuclear Information System (INIS)

    Arnold, W.D. Jr.

    1977-01-01

    A method for separating mono-octylphenyl phosphoric acid ester and di-octylphenyl phosphoric acid ester from a mixture thereof comprises reacting the ester mixture with a source of lithium or sodium ions to form a mixture of the phosphate salts; contacting the salt mixture with an organic solvent which causes the dioctylphenyl phosphate salt to be dissolved in the organic solvent phase and the mono-octylphenyl phosphate salt to exist in a solid phase; separating the phases; recovering the phosphate salts from their respective phases; and acidifying the recovered salts to form the original phosphoric acid esters

  1. The effects of various preservation methods on fatty acid content of ...

    African Journals Online (AJOL)

    The effect of various preservation methods on fatty acid content of African catfish, (Clarias gariepinus) and Nile tilapia (Oreochromis niloticus) was investigated. Fresh fish samples were obtained from swimming pool end (Gamji Gate) of River Rino, Kaduna. Preservation methods investigated were: straight smoking (SS), ...

  2. Alternate method of source preparation for alpha spectrometry: No electrodeposition, no hydrofluoric acid

    International Nuclear Information System (INIS)

    Kurosaki, Hiromu; Mueller, Rebecca J.; Lambert, Susan B.; Rao, Govind R.

    2016-01-01

    An alternate method of preparing actinide alpha counting sources was developed in place of electrodeposition or lanthanide fluoride micro-precipitation. The method uses lanthanide hydroxide micro-precipitation to avoid the use of hazardous hydrofluoric acid. Lastly, it provides a quicker, simpler, and safer way of preparing actinide alpha counting sources in routine, production-type laboratories that process many samples daily.

  3. Alternate method of source preparation for alpha spectrometry: no electrodeposition, no hydrofluoric acid

    International Nuclear Information System (INIS)

    Hiromu Kurosaki; Lambert, S.B.; Rao, G.R.; Mueller, R.J.

    2017-01-01

    An alternate method of preparing actinide alpha counting sources was developed in place of electrodeposition or lanthanide fluoride micro-precipitation. The method uses lanthanide hydroxide micro-precipitation to avoid the use of hazardous hydrofluoric acid. It provides a quicker, simpler, and safer way of preparing actinide alpha counting sources in routine, production-type laboratories that process many samples daily. (author)

  4. Fast and Sensitive Method for Determination of Domoic Acid in Mussel Tissue

    Directory of Open Access Journals (Sweden)

    Elena Barbaro

    2016-01-01

    Full Text Available Domoic acid (DA, a neurotoxic amino acid produced by diatoms, is the main cause of amnesic shellfish poisoning (ASP. In this work, we propose a very simple and fast analytical method to determine DA in mussel tissue. The method consists of two consecutive extractions and requires no purification steps, due to a reduction of the extraction of the interfering species and the application of very sensitive and selective HILIC-MS/MS method. The procedural method was validated through the estimation of trueness, extract yield, precision, detection, and quantification limits of analytical method. The sample preparation was also evaluated through qualitative and quantitative evaluations of the matrix effect. These evaluations were conducted both on the DA-free matrix spiked with known DA concentration and on the reference certified material (RCM. We developed a very selective LC-MS/MS method with a very low value of method detection limit (9 ng g−1 without cleanup steps.

  5. Simple system for isothermal DNA amplification coupled to lateral flow detection.

    Directory of Open Access Journals (Sweden)

    Kristina Roskos

    Full Text Available Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP or the Exponential Amplification Reaction (EXPAR, both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden.

  6. Quantification of organic acids in beer by nuclear magnetic resonance (NMR)-based methods

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, J.E.A. [CICECO-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Erny, G.L. [CESAM - Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Barros, A.S. [QOPNAA-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Esteves, V.I. [CESAM - Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal); Brandao, T.; Ferreira, A.A. [UNICER, Bebidas de Portugal, Leca do Balio, 4466-955 S. Mamede de Infesta (Portugal); Cabrita, E. [Department of Chemistry, New University of Lisbon, 2825-114 Caparica (Portugal); Gil, A.M., E-mail: agil@ua.pt [CICECO-Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro (Portugal)

    2010-08-03

    The organic acids present in beer provide important information on the product's quality and history, determining organoleptic properties and being useful indicators of fermentation performance. NMR spectroscopy may be used for rapid quantification of organic acids in beer and different NMR-based methodologies are hereby compared for the six main acids found in beer (acetic, citric, lactic, malic, pyruvic and succinic). The use of partial least squares (PLS) regression enables faster quantification, compared to traditional integration methods, and the performance of PLS models built using different reference methods (capillary electrophoresis (CE), both with direct and indirect UV detection, and enzymatic essays) was investigated. The best multivariate models were obtained using CE/indirect detection and enzymatic essays as reference and their response was compared with NMR integration, either using an internal reference or an electrical reference signal (Electronic REference To access In vivo Concentrations, ERETIC). NMR integration results generally agree with those obtained by PLS, with some overestimation for malic and pyruvic acids, probably due to peak overlap and subsequent integral errors, and an apparent relative underestimation for citric acid. Overall, these results make the PLS-NMR method an interesting choice for organic acid quantification in beer.

  7. A highly sensitive kinetic spectrophotometric method for the determination of ascorbic Acid in pharmaceutical samples.

    Science.gov (United States)

    Shishehbore, Masoud Reza; Aghamiri, Zahra

    2014-01-01

    In this study, a new reaction system for quantitative determination of ascorbic acid was introduced. The developed method is based on inhibitory effect of ascorbic acid on the Orange G-bromate system. The change in absorbance was followed spectrophotometrically at 478 nm. The dependence of sensitivity on the reaction variables including reagents concentration, temperature and time was investigated. Under optimum experimental conditions, calibration curve was linear over the range 0.7 - 33.5 μg mL(-1) of ascorbic acid including two linear segments and the relative standard deviations (n = 6) for 5.0 and 20.0 μg mL(-1) of ascorbic acid were 1.08 and 1.02%, respectively. The limit of detection was 0.21 μg mL(-) (1) of ascorbic acid. The effect of diverse species was also investigated. The developed method was successfully applied for the determination of ascorbic acid in pharmaceutical samples. The results were in a good agreement with those of reference method.

  8. Quantification of organic acids in beer by nuclear magnetic resonance (NMR)-based methods

    International Nuclear Information System (INIS)

    Rodrigues, J.E.A.; Erny, G.L.; Barros, A.S.; Esteves, V.I.; Brandao, T.; Ferreira, A.A.; Cabrita, E.; Gil, A.M.

    2010-01-01

    The organic acids present in beer provide important information on the product's quality and history, determining organoleptic properties and being useful indicators of fermentation performance. NMR spectroscopy may be used for rapid quantification of organic acids in beer and different NMR-based methodologies are hereby compared for the six main acids found in beer (acetic, citric, lactic, malic, pyruvic and succinic). The use of partial least squares (PLS) regression enables faster quantification, compared to traditional integration methods, and the performance of PLS models built using different reference methods (capillary electrophoresis (CE), both with direct and indirect UV detection, and enzymatic essays) was investigated. The best multivariate models were obtained using CE/indirect detection and enzymatic essays as reference and their response was compared with NMR integration, either using an internal reference or an electrical reference signal (Electronic REference To access In vivo Concentrations, ERETIC). NMR integration results generally agree with those obtained by PLS, with some overestimation for malic and pyruvic acids, probably due to peak overlap and subsequent integral errors, and an apparent relative underestimation for citric acid. Overall, these results make the PLS-NMR method an interesting choice for organic acid quantification in beer.

  9. Direct amplification of casework bloodstains using the Promega PowerPlex(®) 21 PCR amplification system.

    Science.gov (United States)

    Gray, Kerryn; Crowle, Damian; Scott, Pam

    2014-09-01

    A significant number of evidence items submitted to Forensic Science Service Tasmania (FSST) are blood swabs or bloodstained items. Samples from these items routinely undergo phenol:chloroform:isoamyl alcohol organic extraction and quantitative Polymerase Chain Reaction (qPCR) testing prior to PowerPlex(®) 21 amplification. This multi-step process has significant cost and timeframe implications in a fiscal climate of tightening government budgets, pressure towards improved operating efficiencies, and an increasing emphasis on rapid techniques better supporting intelligence-led policing. Direct amplification of blood and buccal cells on cloth and Whatman FTA™ card with PowerPlex(®) 21 has already been successfully implemented for reference samples, eliminating the requirement for sample pre-treatment. Scope for expanding this method to include less pristine casework blood swabs and samples from bloodstained items was explored in an endeavour to eliminate lengthy DNA extraction, purification and qPCR steps for a wider subset of samples. Blood was deposited onto a range of substrates including those historically found to inhibit STR amplification. Samples were collected with micro-punch, micro-swab, or both. The potential for further fiscal savings via reduced volume amplifications was assessed by amplifying all samples at full and reduced volume (25 and 13μL). Overall success rate data showed 80% of samples yielded a complete profile at reduced volume, compared to 78% at full volume. Particularly high success rates were observed for the blood on fabric/textile category with 100% of micro-punch samples yielding complete profiles at reduced volume and 85% at full volume. Following the success of this trial, direct amplification of suitable casework blood samples has been implemented at reduced volume. Significant benefits have been experienced, most noticeably where results from crucial items have been provided to police investigators prior to interview of

  10. Laser amplification in excited dielectrics

    DEFF Research Database (Denmark)

    Winkler, Thomas; Haahr-Lillevang, Lasse; Sarpe, Cristian

    2018-01-01

    Wide-bandgap dielectrics such as glasses or water are transparent at visible and infrared wavelengths. This changes when they are exposed to ultrashort and highly intense laser pulses. Different interaction mechanisms lead to the appearance of various transient nonlinear optical phenomena. Using...... these, the optical properties of dielectrics can be controlled from the transparent to the metal-like state. Here we expand this range by a yet unexplored mechanism in excited dielectrics: amplification. In a two-colour pump-probe experiment, we show that a 400nm femtosecond laser pulse is coherently...

  11. Resonant primordial gravitational waves amplification

    Directory of Open Access Journals (Sweden)

    Chunshan Lin

    2016-01-01

    Full Text Available We propose a mechanism to evade the Lyth bound in models of inflation. We minimally extend the conventional single-field inflation model in general relativity (GR to a theory with non-vanishing graviton mass in the very early universe. The modification primarily affects the tensor perturbation, while the scalar and vector perturbations are the same as the ones in GR with a single scalar field at least at the level of linear perturbation theory. During the reheating stage, the graviton mass oscillates coherently and leads to resonant amplification of the primordial tensor perturbation. After reheating the graviton mass vanishes and we recover GR.

  12. c-myc Amplification Is Frequent in Esophageal Adenocarcinoma and Correlated with the Upregulation of VEGF-A Expression

    Directory of Open Access Journals (Sweden)

    Burkhard H.A. von Rahden

    2006-09-01

    Full Text Available BACKGROUND: Deregulation of c-myc plays a major role in the carcinogenesis of human malignancies. We investigated the amplification of the c-myc gene in a surgical series of Barrett cancers. METHODS: Primary resected esophageal (Barrett adenocarcinomas (n = 84 were investigated for c-myc amplification using chromogene in situ hybridization. Tumor samples were assembled in a tissue microarray. c-myc gene dosage was correlated with clinicopathologic parameters, including the survival and gene expression of cyclooxygenases (COX-1 and COX-2 and proangiogenic growth factors (VEGF-A and VEGF-C. RESULTS: The majority (70 of 84; 83.3% exhibited amplification of the c-myc gene. There were low-level amplifications in 63 (75.0% cases and high-level amplifications in 7 (8.3% cases. No amplification was found in 14 (16.7% cases. Tumors without c-myc amplification had lower VEGF-A, VEGF-C, and COX-2 expression levels than tumors with low-level and high-level c-myc amplification (statistically significant for VEGF-A; P = .0348. c-myc amplification was not correlated with clinicopathological parameters or survival. Only diffuse and mixed-type tumors, according to Lauren classification, exhibited c-myc amplifications more frequently (P = .0466. CONCLUSIONS: Amplifications of the c-myc gene are frequent in Barrett cancer. c-myc may be involved in the regulation of angiogenesis.

  13. Development and Validation of a HPTLC Method for Simultaneous Estimation of L-Glutamic Acid and γ-Aminobutyric Acid in Mice Brain.

    Science.gov (United States)

    Sancheti, J S; Shaikh, M F; Khatwani, P F; Kulkarni, Savita R; Sathaye, Sadhana

    2013-11-01

    A new robust, simple and economic high performance thin layer chromatographic method was developed for simultaneous estimation of L-glutamic acid and γ-amino butyric acid in brain homogenate. The high performance thin layer chromatographic separation of these amino acid was achieved using n-butanol:glacial acetic acid:water (22:3:5 v/v/v) as mobile phase and ninhydrin as a derivatising agent. Quantitation of the method was achieved by densitometric method at 550 nm over the concentration range of 10-100 ng/spot. This method showed good separation of amino acids in the brain homogenate with Rf value of L-glutamic acid and γ-amino butyric acid as 21.67±0.58 and 33.67±0.58, respectively. The limit of detection and limit of quantification for L-glutamic acid was found to be 10 and 20 ng and for γ-amino butyric acid it was 4 and 10 ng, respectively. The method was also validated in terms of accuracy, precision and repeatability. The developed method was found to be precise and accurate with good reproducibility and shows promising applicability for studying pathological status of disease and therapeutic significance of drug treatment.

  14. Photometric method for determination of acidity constants through integral spectra analysis.

    Science.gov (United States)

    Zevatskiy, Yuriy Eduardovich; Ruzanov, Daniil Olegovich; Samoylov, Denis Vladimirovich

    2015-04-15

    An express method for determination of acidity constants of organic acids, based on the analysis of the integral transmittance vs. pH dependence is developed. The integral value is registered as a photocurrent of photometric device simultaneously with potentiometric titration. The proposed method allows to obtain pKa using only simple and low-cost instrumentation. The optical part of the experimental setup has been optimized through the exclusion of the monochromator device. Thus it only takes 10-15 min to obtain one pKa value with the absolute error of less than 0.15 pH units. Application limitations and reliability of the method have been tested for a series of organic acids of various nature. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Photometric method for determination of acidity constants through integral spectra analysis

    Science.gov (United States)

    Zevatskiy, Yuriy Eduardovich; Ruzanov, Daniil Olegovich; Samoylov, Denis Vladimirovich

    2015-04-01

    An express method for determination of acidity constants of organic acids, based on the analysis of the integral transmittance vs. pH dependence is developed. The integral value is registered as a photocurrent of photometric device simultaneously with potentiometric titration. The proposed method allows to obtain pKa using only simple and low-cost instrumentation. The optical part of the experimental setup has been optimized through the exclusion of the monochromator device. Thus it only takes 10-15 min to obtain one pKa value with the absolute error of less than 0.15 pH units. Application limitations and reliability of the method have been tested for a series of organic acids of various nature.

  16. Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization.

    Science.gov (United States)

    Girard, Laurie D; Boissinot, Karel; Peytavi, Régis; Boissinot, Maurice; Bergeron, Michel G

    2015-02-07

    The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have high complexity and cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotide sequence-dependent segment and a unique "target sequence-independent" 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design

  17. Development of a recombinase polymerase amplification assay for Vibrio parahaemolyticus detection with an internal amplification control.

    Science.gov (United States)

    Yang, Huan-Lan; Wei, Shuang; Gooneratne, Ravi; Mutukumira, Anthony N; Ma, Xue-Jun; Tang, Shu-Ze; Wu, Xi-Yang

    2018-04-01

    A novel RPA-IAC assay using recombinase polymerase and an internal amplification control (IAC) for Vibrio parahaemolyticus detection was developed. Specific primers were designed based on the coding sequence for the toxR gene in V. parahaemolyticus. The recombinase polymerase amplification (RPA) reaction was conducted at a constant low temperature of 37 °C for 20 min. Assay specificity was validated by using 63 Vibrio strains and 10 non-Vibrio bacterial species. In addition, a competitive IAC was employed to avoid false-negative results, which co-amplified simultaneously with the target sequence. The sensitivity of the assay was determined as 3 × 10 3 CFU/mL, which is decidedly more sensitive than the established PCR method. This method was then used to test seafood samples that were collected from local markets. Seven out of 53 different raw seafoods were detected as V. parahaemolyticus-positive, which were consistent with those obtained using traditional culturing method and biochemical assay. This novel RPA-IAC assay provides a rapid, specific, sensitive, and more convenient detection method for V. parahaemolyticus.

  18. Clinical Characteristics and Outcome of Patients with Neuroblastoma Presenting Genomic Amplification of Loci Other than MYCN

    Science.gov (United States)

    Guimier, Anne; Ferrand, Sandrine; Pierron, Gaëlle; Couturier, Jérôme; Janoueix-Lerosey, Isabelle; Combaret, Valérie; Mosseri, Véronique; Thebaud, Estelle; Gambart, Marion; Plantaz, Dominique; Marabelle, Aurélien; Coze, Carole; Rialland, Xavier; Fasola, Sylvie; Lapouble, Eve; Fréneaux, Paul; Peuchmaur, Michel; Michon, Jean; Delattre, Olivier; Schleiermacher, Gudrun

    2014-01-01

    Background Somatically acquired genomic alterations with MYCN amplification (MNA) are key features of neuroblastoma (NB), the most common extra-cranial malignant tumour of childhood. Little is known about the frequency, clinical characteristics and outcome of NBs harbouring genomic amplification(s) distinct from MYCN. Methods Genomic profiles of 1100 NBs from French centres studied by array-CGH were re-examined specifically to identify regional amplifications. Patients were included if amplifications distinct from the MYCN locus were seen. A subset of NBs treated at Institut Curie and harbouring MNA as determined by array-CGH without other amplification was also studied. Clinical and histology data were retrospectively collected. Results In total, 56 patients were included and categorised into 3 groups. Group 1 (n = 8) presented regional amplification(s) without MNA. Locus 12q13-14 was a recurrent amplified region (4/8 cases). This group was heterogeneous in terms of INSS stages, primary localisations and histology, with atypical clinical features. Group 2 (n = 26) had MNA as well as other regional amplifications. These patients shared clinical features of those of a group of NBs MYCN amplified (Group 3, n = 22). Overall survival for group 1 was better than that of groups 2 and 3 (5 year OS: 87.5%±11% vs 34.9%±7%, log-rank p<0.05). Conclusion NBs harbouring regional amplification(s) without MNA are rare and seem to show atypical features in clinical presentation and genomic profile. Further high resolution genetic explorations are justified in this heterogeneous group, especially when considering these alterations as predictive markers for targeted therapy. PMID:25013904

  19. Estimation of Physical Properties of Amino Acids by Group-Contribution Method

    DEFF Research Database (Denmark)

    Jhamb, Spardha Virendra; Liang, Xiaodong; Gani, Rafiqul

    2018-01-01

    In this paper, we present group-contribution (GC) based property models for estimation of physical properties of amino acids using their molecular structural information. The physical properties modelled in this work are normal melting point (Tm), aqueous solubility (Ws), and octanol....../water partition coefficient (Kow) of amino acids. The developed GC-models are based on the published GC-method by Marrero and Gani (J. Marrero, R. Gani, Fluid Phase Equilib. 2001, 183-184, 183-208) with inclusion of new structural parameters (groups and molecular weight of compounds). The main objective...... of introducing these new structural parameters in the GC-model is to provide additional structural information for amino acids having large and complex structures and thereby improve predictions of physical properties of amino acids. The group-contribution values were calculated by regression analysis using...

  20. Resistive wall modes and error field amplification

    International Nuclear Information System (INIS)

    Boozer, Allen H.

    2003-01-01

    Resistive wall modes and the rapid damping of plasma rotation by the amplification of magnetic field errors are related physical phenomena that affect the performance of the advanced tokamak and spherical torus plasma confinement devices. Elements of our understanding of these phenomena and the code that is used to design the major experimental facilities are based on the electrical circuit representation of the response of the plasma to perturbations. Although the circuit representation of the plasma may seem heuristic, this representation can be rigorously obtained using Maxwell's equations and linearity for plasmas that evolve on a disparate time scale from that of external currents. These and related results are derived. In addition methods are given for finding the plasma information that the circuit representation requires using post-processors for codes that calculate perturbed plasma equilibria

  1. A Closed-tube Loop-Mediated Isothermal Amplification Assay for the Visual Endpoint Detection of Brucella spp. and Mycobacterium avium subsp. paratuberculosis.

    Science.gov (United States)

    Trangoni, Marcos D; Gioffré, Andrea K; Cravero, Silvio L

    2017-01-01

    LAMP (loop-mediated isothermal amplification) is an isothermal nucleic acid amplification technique that is characterized by its efficiency, rapidity, high yield of final product, robustness, sensitivity, and specificity, with the blueprint that it can be implemented in laboratories of low technological complexity. Despite the conceptual complexity underlying the mechanistic basis for the nucleic acid amplification, the technique is simple to use and the amplification and detection can be carried out in just one step. In this chapter, we present a protocol based on LAMP for the rapid identification of isolates of Brucella spp. and Mycobacterium avium subsp. paratuberculosis, two major bacterial pathogens in veterinary medicine.

  2. Pharmacokinetic Profiling of Conjugated Therapeutic Oligonucleotides: A High-Throughput Method Based Upon Serial Blood Microsampling Coupled to Peptide Nucleic Acid Hybridization Assay.

    Science.gov (United States)

    Godinho, Bruno M D C; Gilbert, James W; Haraszti, Reka A; Coles, Andrew H; Biscans, Annabelle; Roux, Loic; Nikan, Mehran; Echeverria, Dimas; Hassler, Matthew; Khvorova, Anastasia

    2017-12-01

    Therapeutic oligonucleotides, such as small interfering RNAs (siRNAs), hold great promise for the treatment of incurable genetically defined disorders by targeting cognate toxic gene products for degradation. To achieve meaningful tissue distribution and efficacy in vivo, siRNAs must be conjugated or formulated. Clear understanding of the pharmacokinetic (PK)/pharmacodynamic behavior of these compounds is necessary to optimize and characterize the performance of therapeutic oligonucleotides in vivo. In this study, we describe a simple and reproducible methodology for the evaluation of in vivo blood/plasma PK profiles and tissue distribution of oligonucleotides. The method is based on serial blood microsampling from the saphenous vein, coupled to peptide nucleic acid hybridization assay for quantification of guide strands. Performed with minimal number of animals, this method allowed unequivocal detection and sensitive quantification without the need for amplification, or further modification of the oligonucleotides. Using this methodology, we compared plasma clearances and tissue distribution profiles of two different hydrophobically modified siRNAs (hsiRNAs). Notably, cholesterol-hsiRNA presented slow plasma clearances and mainly accumulated in the liver, whereas, phosphocholine-docosahexaenoic acid-hsiRNA was rapidly cleared from the plasma and preferably accumulated in the kidney. These data suggest that the PK/biodistribution profiles of modified hsiRNAs are determined by the chemical nature of the conjugate. Importantly, the method described in this study constitutes a simple platform to conduct pilot assessments of the basic clearance and tissue distribution profiles, which can be broadly applied for evaluation of new chemical variants of siRNAs and micro-RNAs.

  3. Capillary electrophoresis method with UV-detection for analysis of free amino acids concentrations in food.

    Science.gov (United States)

    Omar, Mei Musa Ali; Elbashir, Abdalla Ahmed; Schmitz, Oliver J

    2017-01-01

    Simple and inexpensive capillary electrophoresis with UV-detection method (CE-UV) was optimized and validated for determination of six amino acids namely (alanine, asparagine, glutamine, proline, serine and valine) for Sudanese food. Amino acids in the samples were derivatized with 4-chloro-7-nitro-2,1,3-benzoxadiazole (NBD-Cl) prior to CE-UV analysis. Labeling reaction conditions (100mM borate buffer at pH 8.5, labeling reaction time 60min, temperature 70°C and NBD-Cl concentration 40mM) were systematically investigated. The optimal conditions for the separation were 100mM borate buffer at pH 9.7 and detected at 475nm. The method was validated in terms of linearity, limit of detection (LOD), limit of quantification (LOQ), precision (repeatability) (RSD%) and accuracy (recovery). Good linearity was achieved for all amino acids (r(2)>0.9981) in the concentration range of 2.5-40mg/L. The LODs in the range of 0.32-0.56mg/L were obtained. Recoveries of amino acids ranging from 85% to 108%, (n=3) were obtained. The validated method was successfully applied for the determination of amino acids for Sudanese food samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Citric acid facilitated thermal treatment: An innovative method for the remediation of mercury contaminated soil

    International Nuclear Information System (INIS)

    Ma, Fujun; Peng, Changsheng; Hou, Deyi; Wu, Bin; Zhang, Qian; Li, Fasheng; Gu, Qingbao

    2015-01-01

    Highlights: • Hg content was reduced to <1.5 mg/kg when treated at 400 °C with citric acid. • The treated soil retained most of its original soil physicochemical properties. • Proton provided by citric acid facilitates thermal removal of mercury. • This thermal treatment method is expected to reduce energy input by 35%. - Abstract: Thermal treatment is a promising technology for the remediation of mercury contaminated soils, but it often requires high energy input at heating temperatures above 600 °C, and the treated soil is not suitable for agricultural reuse. The present study developed a novel method for the thermal treatment of mercury contaminated soils with the facilitation of citric acid (CA). A CA/Hg molar ratio of 15 was adopted as the optimum dosage. The mercury concentration in soils was successfully reduced from 134 mg/kg to 1.1 mg/kg when treated at 400 °C for 60 min and the treated soil retained most of its original soil physiochemical properties. During the treatment process, CA was found to provide an acidic environment which enhanced the volatilization of mercury. This method is expected to reduce energy input by 35% comparing to the traditional thermal treatment method, and lead to agricultural soil reuse, thus providing a greener and more sustainable remediation method for treating mercury contaminated soil in future engineering applications.

  5. Analyses of Dynamics in Dairy Products and Identification of Lactic Acid Bacteria Population by Molecular Methods

    Directory of Open Access Journals (Sweden)

    Aytül Sofu

    2017-01-01

    Full Text Available Lactic acid bacteria (LAB with different ecological niches are widely seen in fermented meat, vegetables, dairy products and cereals as well as in fermented beverages. Lactic acid bacteria are the most important group of bacteria in dairy industry due to their probiotic characteristics and fermentation agents as starter culture. In the taxonomy of the lactic acid bacteria; by means of rep-PCR, which is the analysis of repetitive sequences that are based on 16S ribosomal RNA (rRNA gene sequence, it is possible to conduct structural microbial community analyses such as Restriction Fragment Length Polymorphism (RFLP analysis of DNA fragments of different sizes cut with enzymes, Random Amplified Polymorphic DNA (RAPD polymorphic DNA amplified randomly at low temperatures and Amplified Fragment-Length Polymorphism (AFLP-PCR of cut genomic DNA. Besides, in the recent years, non-culture-based molecular methods such as Pulse Field Gel Electrophoresis (PFGE, Denaturing Gradient Gel Electrophoresis (DGGE, Thermal Gradient Gel Electrophoresis (TGGE, and Fluorescence In-situ Hybridization (FISH have replaced classical methods once used for the identification of LAB. Identification of lactic acid bacteria culture independent regardless of the method will be one of the most important methods used in the future pyrosequencing as a Next Generation Sequencing (NGS techniques. This paper reviews molecular-method based studies conducted on the identification of LAB species in dairy products.

  6. A simple assay method for omega-oxidation of lauric acid by hepatic enzymes

    International Nuclear Information System (INIS)

    Giera, D.D.; van Lier, R.B.L.

    1990-01-01

    Routine assessment of hepatic ω-oxidation of fatty acids in toxicology studies requires a simpler method of enzymatic analysis than HPLC or TLC. A method depending upon selective solvent separation of 14 C-lauric acid and 14 C-11/12-hydroxy lauric acid was developed. Following enzymatic incubation and addition of 15% methanol to the acidified incubation mixtures, partitioning with an alkane solvent such as iso-octane, cyclohexane, or n-hexane separated the lauric acid substrate and ω-hydroxylated products into two immiscible phases. Approximately 98% of the substrate partitioned into the organic phase, and approximately 83% of the hydroxylated products partitioned into the aqueous phase. Subsequent quantitation of the enzymatic activity required only liquid scintillation counting of the aqueous phase. Hepatic homogenates from male rats treated with 0.01, 0.05, 0.125, and 0.25% clofibrate in the diet for 7 days had enzyme levels 1.3, 6.1, 11.1, and 15.9 times control values, respectively, when assayed by conventional TLC methods, and 1.3, 5.3, 12.3, and 15.3 times control values when assayed by the solvent extraction method. The data indicate that the selective solvent partitioning yields comparable precision and sensitivity to the more conventional TLC method when studying induction of hepatic microsomal enzymes

  7. Citric acid facilitated thermal treatment: An innovative method for the remediation of mercury contaminated soil

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Fujun [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Peng, Changsheng [The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100 (China); Hou, Deyi [Geotechnical and Environmental Research Group, Department of Engineering, University of Cambridge, Cambridge CB2 1PZ (United Kingdom); Wu, Bin; Zhang, Qian; Li, Fasheng [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Gu, Qingbao, E-mail: guqb@craes.org.cn [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China)

    2015-12-30

    Highlights: • Hg content was reduced to <1.5 mg/kg when treated at 400 °C with citric acid. • The treated soil retained most of its original soil physicochemical properties. • Proton provided by citric acid facilitates thermal removal of mercury. • This thermal treatment method is expected to reduce energy input by 35%. - Abstract: Thermal treatment is a promising technology for the remediation of mercury contaminated soils, but it often requires high energy input at heating temperatures above 600 °C, and the treated soil is not suitable for agricultural reuse. The present study developed a novel method for the thermal treatment of mercury contaminated soils with the facilitation of citric acid (CA). A CA/Hg molar ratio of 15 was adopted as the optimum dosage. The mercury concentration in soils was successfully reduced from 134 mg/kg to 1.1 mg/kg when treated at 400 °C for 60 min and the treated soil retained most of its original soil physiochemical properties. During the treatment process, CA was found to provide an acidic environment which enhanced the volatilization of mercury. This method is expected to reduce energy input by 35% comparing to the traditional thermal treatment method, and lead to agricultural soil reuse, thus providing a greener and more sustainable remediation method for treating mercury contaminated soil in future engineering applications.

  8. Determination of free acid by standard addition method in potassium thiocyanate

    International Nuclear Information System (INIS)

    1981-01-01

    An analytical method for determination of free acidity in all SRP process solutions has been developed. Free acidity was successfully determined in solutions of nitric acid and the nitrates of aluminum, chromium(III), iron(III), mercury(II), nickel(II), thorium, and uranium(VI), at metal-to-acid ratios <2.5. Sample requirements, instrumentation, and mode of operation are similar to those currently used in the Laboratories Department free acid procedures. The simple procedure would be suitable for automation and microprocessor control. The method consists of two additions of known increments of acid into a solution containing the sample aliquot (10 μmoles free acid) and 10 mL 1M potassium thiocyanate. The potential is determined in the initial solution and after each addition with a glass electrode and pH meter. The sample concentration is calculated by solution of three simultaneous Nernst equations. Two programs for this iterative computation are available: one written for the PDP-15 computer and another for a Hewlett-Packard 67 (or 97) programmable calculator. The accuracy of the result is verified by a slope that approximates the theoretical Nernst value. The relative standard deviation is <2.5%. This memorandum includes a survey of experiments with thermometric, pH, and Gran plot titrations in a variety of complexants, from which this particular system and technique logically evolved. The appendix includes a literature survey of sixty references, a discussion of the basic measurements, and a complete analytical procedure. The final step for completion of this RTA is training and consultation at the convenience of the Laboratories Department for demonstration of the method with process samples

  9. Different Chromatographic Methods for Simultaneous Determination of Mefenamic Acid and Two of Its Toxic Impurities.

    Science.gov (United States)

    Morcoss, Martha M; Abdelwahab, Nada S; Ali, Nouruddin W; Elsaady, Mohammed T

    2017-08-01

    Two sensitive, accurate and precise chromatographic methods mentioned as TLC-densitometric method and RP-HPLC-DAD method, were developed and validated for the simultaneous determination of mefenamic acid (MEF) and its two toxic impurities, benzoic acid (BA) and 2,3-dimethylaniline (DMA). In the proposed TLC-densitometric method a developing system consisting of chloroform:acetone:acetic acid:ammonia solution(70:30:2:2, v/v/v/v) was used, TLC aluminum plates 60 F254 was used as a stationary phase and the separated bands were UV-scanned at 225 nm. While the proposed RP-HPLC-DAD method depended on chromatographic separation on C18 column using 0.05 M KH2PO4 buffer: acetonitrile (40:60, v/v) as a mobile phase at constant flow rate of 1 mL/min with UV detection at 225 nm. Linear relationships were obtained in the ranges of 0.3-2, 0.3-2 and 0.3-1.8 μg/band (for TLC-densitometric method) and in the ranges of 7-50, 10-50 and 7-50 μg/mL (for HPLC-DAD method) for MEF, BA and DMA, respectively. Factors affecting the developed methods have been studied and optimized. Moreover ,the proposed methods were successfully applied for determination of the studied drug in its pharmaceutical dosage form. The methods showed no significance difference when compared with the reported method using F-test and Student's-t test. The low of detection and quantization limits of the proposed methods get them suitable for quality control and stability studies of MEF in pharmaceutical formulation. The developed methods have advantages of being more selective and sensitive than the published methods. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. By-Product Formation in Repetitive PCR Amplification of DNA Libraries during SELEX

    DEFF Research Database (Denmark)

    Tolle, Fabian; Wilke, Julian; Wengel, Jesper

    2014-01-01

    The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target-recogniz......The selection of nucleic acid aptamers is an increasingly important approach to generate specific ligands binding to virtually any molecule of choice. However, selection-inherent amplification procedures are prone to artificial by-product formation that prohibits the enrichment of target......-recognizing aptamers. Little is known about the formation of such by-products when employing nucleic acid libraries as templates. We report on the formation of two different forms of by-products, named ladder- and non-ladder-type observed during repetitive amplification in the course of in vitro selection experiments....... Based on sequence information and the amplification behaviour of defined enriched nucleic acid molecules we suppose a molecular mechanism through which these amplification by-products are built. Better understanding of these mechanisms might help to find solutions minimizing by-product formation...

  11. Multiple displacement amplification as an adjunct to PCR-based detection of Staphylococcus aureus in synovial fluid

    Directory of Open Access Journals (Sweden)

    Johnson Sandra

    2010-10-01

    Full Text Available Abstract Background Detection of bacterial nucleic acids in synovial fluid following total joint arthroplasty with suspected infection can be difficult; among other technical challenges, inhibitors in the specimens require extensive sample preparation and can diminish assay sensitivity even using polymerase chain reaction (PCR-based methods. To address this problem a simple protocol for prior use of multiple displacement amplification (MDA as an adjunct to PCR was established and tested on both purified S. aureus DNA as well as on clinical samples known to contain S. aureus nucleic acids. Findings A single round of MDA on purified nucleic acids resulted in a > 300 thousand-fold increase in template DNA on subsequent quantitative PCR (qPCR analysis. MDA use on clinical samples resulted in at least a 100-fold increase in sensitivity on subsequent qPCR and required no sample preparation other than a simple alkali/heat lysis step. Mixed samples of S. aureus DNA with a 103 - 104-fold excess of human genomic DNA still allowed for MDA amplification of the minor bacterial component to the threshold of detectability. Conclusion MDA is a promising technique that may serve to significantly enhance the sensitivity of molecular assays in cases of suspected joint infection while simultaneously reducing the specimen handling required.

  12. Handbook of methods for acid-deposition studies. Laboratory analyses for soil chemistry

    International Nuclear Information System (INIS)

    Blume, L.J.; Schumacher, P.W.; Schaffer, K.A.; Cappo, K.A.; Papp, M.L.

    1990-09-01

    The handbook describes methods used to process and analyze soil samples. It is intended as a guidance document for groups involved in acid deposition monitoring activities similar to those implemented by the Aquatic Effects Research Program of the National Acid Precipitation Assessment Program. These methods were developed for use in the Direct/Delayed Response Project, a component project of the Aquatic Effects Research Program within the Office of Ecological Processes and Effects Research. The program addresses the following issues relating to the effects of acid deposition on aquatic ecosystems: The extent and magnitude of past change; The change to be expected in the future under various deposition scenarios; The maximum rates of deposition below which further change is not expected; and The rate of change or recovery of aquatic ecosystems if deposition rates are decreased. Chemical and physical parameters were measured during the Direct/Delayed Response Project and are described in the document

  13. Effect of irradiation and cooking methods on ascorbic acid levels of four potato cultivars

    International Nuclear Information System (INIS)

    Shirsat, S.G.; Thomas, Paul

    1998-01-01

    The changes in reduced and total ascorbic acid (AA) contents in control and in tubers irradiated to 100 Gy gamma rays for sprout inhibition were studied by HPLC and iodophenol titrimetry methods in four potato cultivars as a function of storage at 15 degC and after cooking by different methods. Both reduced and total ascorbic acid levels decreased in control tubers during the first 3 months in storage recording respectively 22 to 35% and 26 to 45% losses depending on the cultivar. Irradiated tubers recorded additional losses of 5 to 10% and 6.5 to 13%, respectively in reduced and total ascorbic acid levels during the same period but remained in good marketable conditions. Cooking of tubers in boiling water showed maximum loss in vitamin C content, whereas pressure and microwave cooking recorded least losses. The magnitude of losses in reduced and total vitamin C during cooking was comparable in control and in irradiated tubers. (author)

  14. Experience of using heat citric acid disinfection method in central dialysis fluid delivery system.

    Science.gov (United States)

    Sakuma, Koji; Uchiumi, Nobuko; Sato, Sumihiko; Aida, Nobuhiko; Ishimatsu, Taketo; Igoshi, Tadaaki; Kodama, Yoshihiro; Hotta, Hiroyuki

    2010-09-01

    We applied the heat citric acid disinfection method in the main part of the central dialysis fluid delivery system (MPCDDS), which consists of a multiple-patient dialysis fluid supply unit, dialysis console units, and dialysis fluid piping. This disinfection method has been used for single-patient dialysis machines, but this is the first trial in the MPCDDS. We examined, by points of safety and disinfection effect, whether this disinfection method is comparable to conventional disinfection methods in Japan. The conventional disinfection method is a combination of two disinfectants, sodium hypochlorite and acetic acid, used separately for protein removal and decalcification. Consequently, total microbial counts and endotoxin concentrations fully satisfied the microbiological requirements for standard dialysis fluid of ISO 11663. From our results and discussion, this heat citric acid disinfection method is proved to be safe and reliable for MPCDDS. However, to satisfy the microbiological requirements for ultrapure dialysis fluid, further consideration for this method in MPCDDS including the reverse osmosis device composition and piping is necessary.

  15. Pregabalin and Tranexamic Acid Evaluation by Two Simple and Sensitive Spectrophotometric Methods

    Directory of Open Access Journals (Sweden)

    Nawab Sher

    2015-01-01

    Full Text Available This paper demonstrates colorimetric visible spectrophotometric quantification methods for amino acid, namely, tranexamic acid and pregabalin. Both drugs contain the amino group, and when they are reacted with 2,4-dinitrophenol and 2,4,6-trinitrophenol, they give rise to yellow colored complexes showing absorption maximum at 418 nm and 425 nm, respectively, based on the Lewis acid base reaction. Detailed optimization process and stoichiometric studies were conducted along with investigation of thermodynamic features, that is, association constant and standard free energy changes. The method was linear over the concentration range of 0.02–200 µgmL−1 with correlation coefficient of more than 0.9990 in all of the cases. Limit of detection was in range from 0.0041 to 0.0094 µgmL−1 and limit of quantification was in the range from 0.0137 to 0.0302 µgmL−1. Excellent recovery in Placebo spiked samples indicated that there is no interference from common excipients. The analytical methods under proposal were successfully applied to determine tranexamic acid and pregabalin in commercial products. t-test and F ratio were evaluated without noticeable difference between the proposed and reference methods.

  16. Determination of free acid by standard addition method in potassium thiocyanate

    International Nuclear Information System (INIS)

    Baumann, E.W.

    1982-06-01

    The free acid content of solutions containing hydrolyzable ions has been determined potentiometrically by a standard addition method. Two increments of acid are added to the sample in 1M potassium thiocyanate solution. The sample concentration is calculated by solution of three simultaneous Nernst equations. The method has been demonstrated for solutions containing Al 3+ , Cr 3+ , Fe 3+ , Hg 2+ , Ni 2+ , Th 4+ , or UO 2 2+ with a metal-to-acid ratio of < 2.5. The method is suitable for determination of 10 μmoles acid in 10 mL total volume. The accuracy can be judged from the agreement of the Nernst slopes found in the presence and absence of hydrolyzable ions. The relative standard deviation is < 2.5%. The report includes a survey of experiments with thermometric, pH, and Gran plot titrations in a variety of complexants, from which the method was evolved. Also included is a literature survey of sixty references, a discussion of the basic measurements, and a complete analytical procedure

  17. Determining surface areas of marine alga cells by acid-base titration method.

    Science.gov (United States)

    Wang, X; Ma, Y; Su, Y

    1997-09-01

    A new method for determining the surface area of living marine alga cells was described. The method uses acid-base titration to measure the surface acid/base amount on the surface of alga cells and uses the BET (Brunauer, Emmett, and Teller) equation to estimate the maximum surface acid/base amount, assuming that hydrous cell walls have carbohydrates or other structural compounds which can behave like surface Brönsted acid-base sites due to coordination of environmental H2O molecules. The method was applied to 18 diverse alga species (including 7 diatoms, 2 flagellates, 8 green algae and 1 red alga) maintained in seawater cultures. For the species examined, the surface areas of individual cells ranged from 2.8 x 10(-8) m2 for Nannochloropsis oculata to 690 x 10(-8) m2 for Dunaliella viridis, specific surface areas from 1,030 m2.g-1 for Dunaliella salina to 28,900 m2.g-1 for Pyramidomonas sp. Measurement accuracy was 15.2%. Preliminary studies show that the method may be more promising and accurate than light/electron microscopic measurements for coarse estimation of the surface area of living algae.

  18. New insights into the methodological issues of the indicator amino acid oxidation method in preterm neonates

    NARCIS (Netherlands)

    de Groof, F.; Huang, L.S.; Twisk, J.W.R.; Voortman, G.J.; Joemai, W.; Hau, C.H.; Schierbeek, H.; Chen, C.; Huang, Y.; van Goudoever, J.B.

    2013-01-01

    Background: We determined the effect of adaptation to the study diet on oxidation of the indicator amino acid and the required tracer washout time in preterms. Methods: Subjects received a study diet for 6 d that entailed a 50% reduction in leucine. Tracer studies using enterally infused [ 13

  19. Method of dissolving metal oxides with di- or polyphosphonic acid and a redundant

    Science.gov (United States)

    Horwitz, Earl P.; Chiarizia, Renato

    1996-01-01

    A method of dissolving metal oxides using a mixture of a di- or polyphosphonic acid and a reductant wherein each is present in a sufficient amount to provide a synergistic effect with respect to the dissolution of metal oxides and optionally containing corrosion inhibitors and pH adjusting agents.

  20. Ruminal Methane Production on Simple Phenolic Acids Addition in in Vitro Gas Production Method

    Directory of Open Access Journals (Sweden)

    A. Jayanegara

    2009-04-01

    Full Text Available Methane production from ruminants contributes to total global methane production, which is an important contributor to global warming. In this experiment, six sources of simple phenolic acids (benzoic, cinnamic, phenylacetic, caffeic, p-coumaric and ferulic acids at two different levels (2 and 5 mM added to hay diet were evaluated for their potential to reduce enteric methane production using in vitro Hohenheim gas production method. The measured variables were gas production, methane, organic matter digestibility (OMD, and short chain fatty acids (SCFA. The results showed that addition of cinnamic, caffeic, p-coumaric and ferulic acids at 5 mM significantly (P p-coumaric > ferulic > cinnamic. The addition of simple phenols did not significantly decrease OMD. Addition of simple phenols tends to decrease total SCFA production. It was concluded that methane decrease by addition of phenolic acids was relatively small, and the effect of phenolic acids on methane decrease depended on the source and concentration applied.

  1. Method for rapid detection and identification of chaetomium and evaluation of resistance to peracetic acid.

    Science.gov (United States)

    Nakayama, Motokazu; Hosoya, Kouichi; Tomiyama, Daisuke; Tsugukuni, Takashi; Matsuzawa, Tetsuhiro; Imanishi, Yumi; Yaguchi, Takashi

    2013-06-01

    In the beverage industry, peracetic acid has been increasingly used as a disinfectant for the filling machinery and environment due to merits of leaving no residue, it is safe for humans, and its antiseptic effect against fungi and endospores of bacteria. Recently, Chaetomium globosum and Chaetomium funicola were reported resistant to peracetic acid; however, little is known concerning the detail of peracetic acid resistance. Therefore, we assessed the peracetic acid resistance of the species of Chaetomium and related genera under identical conditions and made a thorough observation of the microstructure of their ascospores by transmission electron microscopy. The results of analyses revealed that C. globosum and C. funicola showed the high resistance to peracetic acid (a 1-D antiseptic effect after 900 s and 3-D antiseptic effect after 900 s) and had thick cell walls of ascospores that can impede the action mechanism of peracetic acid. We also developed specific primers to detect the C. globosum clade and identify C. funicola by using PCR to amplify the β-tubulin gene. PCR with the primer sets designed for C. globosum (Chae 4F/4R) and C. funicola (Cfu 2F/2R) amplified PCR products specific for the C. globosum clade and C. funicola, respectively. PCR with these two primer sets did not detect other fungi involved in food spoilage and environmental contamination. This detection and identification method is rapid and simple, with extremely high specificity.

  2. Multiscale image contrast amplification (MUSICA)

    Science.gov (United States)

    Vuylsteke, Pieter; Schoeters, Emile P.

    1994-05-01

    This article presents a novel approach to the problem of detail contrast enhancement, based on multiresolution representation of the original image. The image is decomposed into a weighted sum of smooth, localized, 2D basis functions at multiple scales. Each transform coefficient represents the amount of local detail at some specific scale and at a specific position in the image. Detail contrast is enhanced by non-linear amplification of the transform coefficients. An inverse transform is then applied to the modified coefficients. This yields a uniformly contrast- enhanced image without artefacts. The MUSICA-algorithm is being applied routinely to computed radiography images of chest, skull, spine, shoulder, pelvis, extremities, and abdomen examinations, with excellent acceptance. It is useful for a wide range of applications in the medical, graphical, and industrial area.

  3. Measuring the amplification of attention.

    Science.gov (United States)

    Blaser, E; Sperling, G; Lu, Z L

    1999-09-28

    An ambiguous motion paradigm, in which the direction of apparent motion is determined by salience (i.e., the extent to which an area is perceived as figure versus ground), is used to assay the amplification of color by attention to color. In the red-green colored gratings used in these experiments, without attention instructions, salience depends on the chromaticity difference between colored stripes embedded in the motion sequence and the yellow background. Selective attention to red (or to green) alters the perceived direction of motion and is found to be equivalent to increasing the physical redness (or greenness) by 25-117%, depending on the observer and color. Whereas attention to a color drastically alters the salience of that color, it leaves color appearance unchanged. A computational model, which embodies separate, parallel pathways for object perception and for salience, accounts for 99% of the variance of the experimental data.

  4. Development of growth rate measuring method for intracellular, parasitic acid-fast bacteria using radioisotopes

    International Nuclear Information System (INIS)

    Nakata, Noboru; Fukutomi, Yasuo

    1998-01-01

    To prevent and treat infections diseases caused by pathogenic acid-fast bacteria such as Mycobacterium leprae, Tubercle bacillus, it is important to elucidate the mechanisms of intracellular proliferations of these bacteria. This research project was started to make DNA library using a new constructed shuttle vector. Development of in vitro evaluation method for intracellular proliferation of mycobacterium and its transformed cells was attempted on the basis of Buddemeyer method. This method was able to precisely determine the metabolic activities as low as those in leprae and its modified method using 14 C-palmitic acid was highly sensitive and the results were obtainable in a shorter period. The generated CO 2 was satisfactorily absorbed into scintillator without using a filter paper. A new culture medium from which arginine, a NO-producing compound was eliminated was used to repress the sterilizing effects of NO, but the metabolic activities of leprae was not enhanced. (M.N.)

  5. Development of growth rate measuring method for intracellular, parasitic acid-fast bacteria using radioisotopes

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, Noboru; Fukutomi, Yasuo [National Inst. of Infectious Deseases, Tokyo (Japan)

    1998-02-01

    To prevent and treat infections diseases caused by pathogenic acid-fast bacteria such as Mycobacterium leprae, Tubercle bacillus, it is important to elucidate the mechanisms of intracellular proliferations of these bacteria. This research project was started to make DNA library using a new constructed shuttle vector. Development of in vitro evaluation method for intracellular proliferation of mycobacterium and its transformed cells was attempted on the basis of Buddemeyer method. This method was able to precisely determine the metabolic activities as low as those in leprae and its modified method using {sup 14}C-palmitic acid was highly sensitive and the results were obtainable in a shorter period. The generated CO{sub 2} was satisfactorily absorbed into scintillator without using a filter paper. A new culture medium from which arginine, a NO-producing compound was eliminated was used to repress the sterilizing effects of NO, but the metabolic activities of leprae was not enhanced. (M.N.)

  6. Effect of curd freezing and packaging methods on the organic acid contents of goat cheeses during storage

    Directory of Open Access Journals (Sweden)

    Pınar Balkir

    2011-09-01

    Full Text Available Effects of freezing and packaging methods on organic acid content of goat cheese during 12 weeks of storage were determined. Goat cheese milk curds were divided into two batches; one of the batches was directly processed in to goat cheese while the other was frozen at -18 °C and stored for six months and processed into cheese after being thawed. Cheese samples were packed in three parts and stored at 4 °C refrigerated control sample and at -18 °C for six months frozen experimental samples. Cheese samples were packed in three different packaging methods: aerobic, vacuum or modified atmosphere. Citric, malic, fumaric, acetic, lactic, pyruvic and propionic acids were analyzed using HPLC method after 1st, 3rd, 6th, 9th and 12th week of storage period. Lactic acid was the main organic acids while pyruvic acid had the lowest content in all cheese samples. Citric and fumaric acid levels of frozen samples increased during storage whereas malic, acetic, pyruvic and propionic acid amounts were decreased compared to the beginning of storage. Packaging methods and freezing process also effected lactic acid levels statistically (p<0.05. Fumaric, acetic and lactic acid concentration of refrigerated samples were increased but citric, malic and propionic acids decreased during storage. Pyruvic acid level did not change significantly. It was determined that organic acid concentrations were effected by freezing process, storage time and packaging methods significantly (p<0.05.

  7. Comparison of different extraction methods for giberelic acid obtention from corn (Zea mays L. germinated seeds

    Directory of Open Access Journals (Sweden)

    Juan David Rivera

    2017-05-01

    Full Text Available Corn (Zea mays L. is the second most cultivated cereal in the world and is use as raw material for different kind of industries. To date no reports about obtaining giberellic acid (GA3 from corn have been found. In the present study two methods for extracting solid samples were evaluated: lixiviation and dynamic sonication-assisted solvent extraction (DSASE, for obtaining giberellic acid from corn germinated seeds. In lixiviation, the physical method (agitation and sonication, solvent, and time were the parameters analyzed; while in DSASE the variables were: solvent, flow, and time. The most efficient technique was DSASE employing acetonitrile-formic acid 5% (80:20, v:v as solvent at a flow of 0.4 mL/min for 25,0 min, obtaining a concentration 30.012 mg/kg giberellic acid. The identification and quantification were performed by high performance liquid chromatography (HPLC with diode array detector (DAD. These results showed that dynamic sonication-assisted solvent extraction (DSASE is a novel and powerful alternative technique for obtaining giberellic acid, because of its high efficiency; low solvent consumption and simplicity in obtaining the extract.

  8. Study of 3-amino phenylboronic acid interactions with selected sugars by optical methods

    Energy Technology Data Exchange (ETDEWEB)

    Kur, Katarzyna; Przybyt, Małgorzata, E-mail: malgorzata.przybyt@p.lodz.pl; Miller, Ewa

    2017-03-15

    ABSTRACT: The interactions of 3-amino phenylboronic acid with six saccharides (glucose, galactose, fructose, maltose, sucrose and lactose) were studied by absorbance, steady-state fluorescence and time-resolved fluorescence measurements. 3-Amino phenylboronic acid fluorescence is quenched by formation of esters with saccharides. Results of the steady-state fluorescence measurements fulfil the Stern-Volmer equation and quenching constants increase with a growing pH. The greatest quenching constant was observed for fructose. From the dependence of absorbance and fluorescence on pH the exponents of acid-base dissociation constants pK{sub a} were calculated giving similar values for both methods. The esterification of the boronic group shifted the acid-base equilibrium towards lower pH. This shift is growing with increasing bonding strength between sugar and boronic group. At acidic and neutral pH the decay of 3-amino phenylboronic acid fluorescence is monoexponential. The lifetime is about 8.3 ns and is independent of pH as well as sugar type and concentration. In alkaline environments the decays become biexponential with a shorter component about 1 ns or less. The contribution of this component is growing with increasing pH and affinity of sugar towards boronic group. This shorter component can be attributed to the anionic form of 3-amino phenylboronic acid or its ester. The results of absorbance and fluorescence measurements indicate that the studied sugars can be ordered by their affinity to 3-amino phenylboronic acid as follows: fructose>galactose>glucose>maltose≈lactose>sucrose.

  9. Validation of nitrogen-nitrate analysis by the chromotropic acid method

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Ana Claudia O.; Matoso, Erika, E-mail: anaclaudia.oliveira@marinha.mil.br [Centro Tecnológico da Marinha em São Paulo (CTMSP/CEA), Iperó, SP (Brazil). Centro Experimental ARAMAR

    2017-07-01

    The problems caused by contamination of water bodies demand strict control of disposal in rivers, seas and oceans. Nitrate ion is present in agricultural inputs, which are applied to the soil to boost plant growth. However, excess or indiscriminate use of these products contaminates water bodies, triggering eutrophication of the aquatic ecosystems. Furthermore, due to diseases that can be caused by the ingestion of high levels of nitrate, such as methaemoglobinaemia, nitrate levels should be controlled in drinking waters and effluents. There are several methods for the determination of nitrate, being the chromotropic acid method a simple and low-cost solution. This method consists of acid addition into the sample in the presence of H{sub 2}SO{sub 4}. The absorbance related to the produced yellow color can be measured by a UV-Vis spectrophotometer at 410 nm. In a modified form, this method can be applied to different aqueous matrices by use of other reagents that eliminate interferences. The aim of this study was to validate the nitrate determination method in waters using chromotropic acid. This method is used in Laboratório Radioecológico (LARE) to analyze effluent to comply with Wastewater Controlling Program of Centro Tecnológico da Marinha em São Paulo – Centro Experimental ARAMAR (CTMSP-CEA). The correlation coefficient for the linearity test was 0.9997. The evaluated detection limit was relatively high (LD = 0.045 mgN/L), if compared to ion chromatography, for example, but enough to determine the presence of this ion, considering the maximum limit proposed by the current legislation. The chromotropic acid method showed to be a robust, accurate and precise method, according the parameters used in this work. (author)

  10. Validation of nitrogen-nitrate analysis by the chromotropic acid method

    International Nuclear Information System (INIS)

    Santos, Ana Claudia O.; Matoso, Erika

    2017-01-01

    The problems caused by contamination of water bodies demand strict control of disposal in rivers, seas and oceans. Nitrate ion is present in agricultural inputs, which are applied to the soil to boost plant growth. However, excess or indiscriminate use of these products contaminates water bodies, triggering eutrophication of the aquatic ecosystems. Furthermore, due to diseases that can be caused by the ingestion of high levels of nitrate, such as methaemoglobinaemia, nitrate levels should be controlled in drinking waters and effluents. There are several methods for the determination of nitrate, being the chromotropic acid method a simple and low-cost solution. This method consists of acid addition into the sample in the presence of H 2 SO 4 . The absorbance related to the produced yellow color can be measured by a UV-Vis spectrophotometer at 410 nm. In a modified form, this method can be applied to different aqueous matrices by use of other reagents that eliminate interferences. The aim of this study was to validate the nitrate determination method in waters using chromotropic acid. This method is used in Laboratório Radioecológico (LARE) to analyze effluent to comply with Wastewater Controlling Program of Centro Tecnológico da Marinha em São Paulo – Centro Experimental ARAMAR (CTMSP-CEA). The correlation coefficient for the linearity test was 0.9997. The evaluated detection limit was relatively high (LD = 0.045 mgN/L), if compared to ion chromatography, for example, but enough to determine the presence of this ion, considering the maximum limit proposed by the current legislation. The chromotropic acid method showed to be a robust, accurate and precise method, according the parameters used in this work. (author)

  11. Recombinant cells and organisms having persistent nonstandard amino acid dependence and methods of making them

    Science.gov (United States)

    Church, George M.; Mandell, Daniel J.; Lajoie, Marc J.

    2017-12-05

    Recombinant cells and recombinant organisms persistently expressing nonstandard amino acids (NSAAs) are provided. Methods of making recombinant cells and recombinant organisms dependent on persistently expressing NSAAs for survival are also provided. These methods may be used to make safe recombinant cells and recombinant organisms and/or to provide a selective pressure to maintain one or more reassigned codon functions in recombinant cells and recombinant organisms.

  12. Study of PVC membrane grafted by Acrylic Acid, Acrylonitrile and Acrylamide using preirradiation method

    International Nuclear Information System (INIS)

    Kattan, M.; Al-Kasseri, H.

    2015-03-01

    Grafting of acrylic acid, acrylamide and acrylonitrile onto poly vinyl chloride (PVC) films using gamma radiation has been carried out by both type direct and preirradiation methods. The effect of different parameter such as monomer concentration, inhibitor concentration, reaction temperature, reaction time and irradiation dose on the grafting yield were investigated. It was found that the grafting yield depends on these parameters. The grafting yield was strongly monomer dependent and grafting method: the highest was found for AAc by the preirradiation method. The samples were characterized by tensile strength measurement, swilling and ion uptake. The highest increase in swilling was observed on samples grafted with AAc by the preirradiation method.(author)

  13. Controlled Microwave Heating Accelerates Rolling Circle Amplification.

    Directory of Open Access Journals (Sweden)

    Takeo Yoshimura

    Full Text Available Rolling circle amplification (RCA generates single-stranded DNAs or RNA, and the diverse applications of this isothermal technique range from the sensitive detection of nucleic acids to analysis of single nucleotide polymorphisms. Microwave chemistry is widely applied to increase reaction rate as well as product yield and purity. The objectives of the present research were to apply microwave heating to RCA and indicate factors that contribute to the microwave selective heating effect. The microwave reaction temperature was strictly controlled using a microwave applicator optimized for enzymatic-scale reactions. Here, we showed that microwave-assisted RCA reactions catalyzed by either of the four thermostable DNA polymerases were accelerated over 4-folds compared with conventional RCA. Furthermore, the temperatures of the individual buffer components were specifically influenced by microwave heating. We concluded that microwave heating accelerated isothermal RCA of DNA because of the differential heating mechanisms of microwaves on the temperatures of reaction components, although the overall reaction temperatures were the same.

  14. Validation of ascorbic acid tablets of national production by igh-performance liquid chromatography method

    International Nuclear Information System (INIS)

    Rodriguez Hernandez, Yaslenis; Suarez Perez, Yania; Izquierdo Castro, Idalberto

    2009-01-01

    We validate an analytical method by high-performance liquid chromatography to determine ascorbic acid proportion in vitamin C tablets, which was designed as an alternative method to quality control and to follow-up of active principle chemical stability, since official techniques to quality control of ascorbic acid in tablets are not selective with degradation products. Method was modified according to that reported in USP 28, 2005 for analysis of injectable product. We used a RP-18 column of 250 x 4.6 mm 5 μm with a UV detector to 245 nm. Its validation was necessary for both objectives, considering parameters required for methods of I and II categories. This method was enough linear, exact, and precise in the rank of 100-300 μg/mL. Also, it was selective with remaining components of matrix and with the possible degradation products achieved in stressing conditions. Detection and quantification limits were estimated. When method was validated it was applied to ascorbic acid quantification in two batches of expired tablets and we detected a marked influence of container in active degradation principle after 12 months at room temperature. (Author)

  15. An online computer method for the potentiometric titration of mixtures of a strong and a weak acid

    NARCIS (Netherlands)

    Bos, M.

    1977-01-01

    A PDP-11 online computer method for the titration of mixtures or a strong and a weak acid is described.The method is based on multiparametric curve-fitting. One or the parameters found from the calculations is the dissociation constant of the weak acid, hence the method can be applied even when this

  16. Employment of a novel ultrasonic method to investigate high pressure phase transitions in oleic acid

    Science.gov (United States)

    Rostocki, A. J.; Siegoczyński, R. M.; Kiełczyński, P.; Szalewski, M.; Balcerzak, A.; Zduniak, M.

    2011-06-01

    In this work, the variation of sound velocity with hydrostatic pressure for oleic acid is evaluated up to 350 MPa. During the measurement, we identified the phase transformation of oleic acid and the presence of the hysteresis of the dependence of sound velocity on pressure. From the performed measurements, it can be seen that the dependence of sound velocity on pressure can be used to investigate phase transformations in natural oils. Ultrasonic waves were excited and detected using piezoelectric LiNbO3(Y-36 cut) 5 MHz transducers. The phase velocity of the longitudinal ultrasonic waves was measured using a cross-correlation method to evaluate the time of flight.

  17. Synthesis and sintering of nanocrystalline hydroxyapatite powders by citric acid sol-gel combustion method

    International Nuclear Information System (INIS)

    Han Yingchao; Li Shipu; Wang Xinyu; Chen Xiaoming

    2004-01-01

    The citric acid sol-gel combustion method has been used for the synthesis of nanocrystalline hydroxyapatite (HAP) powder from calcium nitrate, diammonium hydrogen phosphate and citric acid. The phase composition of HAP powder was characterized by X-ray powder diffraction analysis (XRD). The morphology of HAP powder was observed by transmission electron microscope (TEM). The HAP powder has been sintered into microporous ceramic in air at 1200 deg. C with 3 h soaking time. The microstructure and phase composition of the resulting HAP ceramic were characterized by scanning electron microscope (SEM) and XRD, respectively. The physical characterization of open porosity and flexural strength have also been carried out

  18. The Development of Analytical Method for the Determination of Azelaic Acid Content in Cosmetic Cream Products

    Science.gov (United States)

    Lusianti, E.; Wibowo, R.; Hudiyono, S.

    2018-01-01

    Azelaic acid is one of the substances that has anti-acne and skin lightening effects which is often added to cosmetics. In the acne treatment, the azelaic acid is generally used with a concentration of 20% in cream formulation and 15% in gel. The use at concentrations below 10% is not recommended because it does not work effectively. While the use of above 10% is categorized as a medical treatment. In Indonesia, the Head of the National Agency of Drug and Food Control (BPOM) has issued Regulation No. 18 of 2015 on the Technical Requirements of Cosmetics Ingredients Annex V stating that the azelaic acid is banned in cosmetics. However, until this research began the BPOM has not had a valid method to identify it in cosmetics. Consequently, surveillance of such ingredient in products is hard to do. In this research, the fatty acid standard analysis method of AOAC International was modified and validated to be used in the laboratory. The method of analysis involves heating the cream preparations dissolved with methanol and then added BF3-methanol catalyst, followed by extraction and analysis using GCMS. The validation of method shows that the calibration curve is linear with correlative value of 0.9997. The method is fairly sensitive with 0.02% detection limit, and fairly precision with relative standard deviation (RSD) of between 0.626-0.961% and fairly accurate which the recovery percentage is 99.85% at range 98.27-100.72%. In sum the results demonstrate that the method can be used as a routine analysis method for laboratory testing.

  19. A simple RP-HPLC method for related substances of zoledronic acid in pharmaceutical products

    Directory of Open Access Journals (Sweden)

    L. Maheswara Reddy

    2017-02-01

    Full Text Available A novel, selective and sensitive reverse phase-high performance liquid chromatography (RP-HPLC method has been developed for the validated estimation of imidazol-1-yl-acetic acid in zoledronic acid formulations. The separation was achieved on a 5 μ C18 column (250 × 4.6 mm using a mobile phase that consists of the buffer (4.5 g of di-potassium hydrogen phosphate anhydrous and 2.0 g of tetra butyl ammonium hydrogen sulphate (TBAHS in 1000 mL of water and methanol in the ratio of 900:100 v/v. The flow rate was maintained at 1.0 mL min−1. The detection of the constituents was done at 215 nm using a UV detector. The retention times of imidazol-1-yl-acetic acid and zoledronic acid were 7.2 and 10.2 min respectively. Recovery studies were satisfactory and the correlation coefficient, 0.999 indicates linearity of the method within the limits. The developed method can be applicable for regular qualitative analysis.

  20. Systematic evaluation of bias in microbial community profiles induced by whole genome amplification.

    NARCIS (Netherlands)

    Direito, S.; Zaura, E.; Little, M.; Ehrenfreund, P.; Roling, W.F.M.

    2014-01-01

    Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement

  1. Systematic evaluation of bias in microbial community profiles induced by whole genome amplification

    NARCIS (Netherlands)

    Direito, S.O.L.; Zaura, E.; Little, M.; Ehrenfreund, P.; Röling, W.F.M.

    2014-01-01

    Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement

  2. Effect of Hyaluronic Acid Incorporation Method on the Stability and Biological Properties of Polyurethane-Hyaluronic Acid Biomaterials

    Science.gov (United States)

    Ruiz, Amaliris; Rathnam, Kashmila R.; Masters, Kristyn S.

    2014-01-01

    The high failure rate of small diameter vascular grafts continues to drive the development of new materials and modification strategies that address this clinical problem, with biomolecule incorporation typically achieved via surface-based modification of various biomaterials. In this work, we examined whether the method of biomolecule incorporation (i.e., bulk vs. surface modification) into a polyurethane (PU) polymer impacted biomaterial performance in the context of vascular applications. Specifically, hyaluronic acid (HA) was incorporated into a poly(ether urethane) via bulk copolymerization or covalent surface tethering, and the resulting PU-HA materials characterized with respect to both physical and biological properties. Modification of PU with HA by either surface or bulk methods yielded materials that, when tested under static conditions, possessed no significant differences in their ability to resist protein adsorption, platelet adhesion, and bacterial adhesion, while supporting endothelial cell culture. However, only bulk-modified PU-HA materials were able to fully retain these characteristics following material exposure to flow, demonstrating a superior ability to retain the incorporated HA and minimize enzymatic degradation, protein adsorption, platelet adhesion, and bacterial adhesion. Thus, despite bulk methods rarely being implemented in the context of biomolecule attachment, these results demonstrate improved performance of PU-HA upon bulk, rather than surface, incorporation of HA. Although explored only in the context of PU-HA, the findings revealed by these experiments have broader implications for the design and evaluation of vascular graft modification strategies. PMID:24276670

  3. Analytical methods for analysis of neutron cross sections of amino acids and proteins

    International Nuclear Information System (INIS)

    Voi, Dante L.; Ferreira, Francisco de O.; Nunes, Rogerio Chaffin; Carvalheira, Luciana; Rocha, Hélio F. da

    2017-01-01

    Two unpublished analytical processes were developed at IEN-CNEN-RJ for the analysis of neutron cross sections of chemical compounds and complex molecules, the method of data parceling and grouping (P and G) and the method of data equivalence and similarity (E and S) of cross-sections. The former allows the division of a complex compound or molecule so that the parts can be manipulated to construct a value of neutron cross section for the compound or the entire molecule. The second method allows by comparison obtain values of neutron cross-sections of specific parts of the compound or molecule, as the amino acid radicals or its parts. The processes were tested for the determination of neutron cross-sections of the 20 human amino acids and a small database was built for future use in the construction of neutron cross-sections of proteins and other components of the human being cells, also in other industrial applications. (author)

  4. Analytical methods for analysis of neutron cross sections of amino acids and proteins

    Energy Technology Data Exchange (ETDEWEB)

    Voi, Dante L.; Ferreira, Francisco de O.; Nunes, Rogerio Chaffin; Carvalheira, Luciana, E-mail: dante@ien.gov.br, E-mail: fferreira@ien.gov.br, E-mail: Chaffin@ien.gov.br, E-mail: luciana@ien.gov.br [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Rocha, Hélio F. da, E-mail: helionutro@gmail.com.br [Universidade Federal do Rio de Janeiro (IPPMG/UFRJ), Rio de Janeiro, RJ (Brazil). Instituto de Pediatria

    2017-07-01

    Two unpublished analytical processes were developed at IEN-CNEN-RJ for the analysis of neutron cross sections of chemical compounds and complex molecules, the method of data parceling and grouping (P and G) and the method of data equivalence and similarity (E and S) of cross-sections. The former allows the division of a complex compound or molecule so that the parts can be manipulated to construct a value of neutron cross section for the compound or the entire molecule. The second method allows by comparison obtain values of neutron cross-sections of specific parts of the compound or molecule, as the amino acid radicals or its parts. The processes were tested for the determination of neutron cross-sections of the 20 human amino acids and a small database was built for future use in the construction of neutron cross-sections of proteins and other components of the human being cells, also in other industrial applications. (author)

  5. Added Value of HER-2 Amplification Testing by Multiplex Ligation-Dependent Probe Amplification in Invasive Breast Cancer

    Science.gov (United States)

    Kuijpers, Chantal C. H. J.; Moelans, Cathy B.; van Slooten, Henk-Jan; Horstman, Anja; Hinrichs, John W. J.; Al-Janabi, Shaimaa; van Diest, Paul J.; Jiwa, Mehdi

    2013-01-01

    Background HER-2 is a prognostic and predictive marker, but as yet no technique is perfectly able to identify patients likely to benefit from HER-2 targeted therapies. We aimed to prospectively assess the added value of first-line co-testing by IHC, and multiplex ligation-dependent probe amplification (MLPA) and chromogenic in situ hybridization (CISH). Methods As local validation, HER-2 MLPA and CISH were compared in 99 breast cancers. Next, we reviewed 937 invasive breast cancers, from 4 Dutch pathology laboratories, that were prospectively assessed for HER-2 by IHC and MLPA (and CISH in selected cases). Results The validation study demonstrated 100% concordance between CISH and MLPA, if both methods were assessable and conclusive (81.8% of cases). Significant variation regarding percentages IHC 0/1+ and 2+ cases was observed between the laboratories (pCISH was 98.1% (575/586) (Kappa = 0.94). Of the IHC 3+ cases, 6.7% failed to reveal gene amplification, whereas 0.8% of the IHC 0/1+ cases demonstrated gene amplification. Results remained discordant after retrospective review in 3/11 discordant cases. In the remaining 8 cases the original IHC score was incorrect or adapted after repeated IHC staining. Conclusions MLPA is a low-cost and quantitative high-throughput technique with near perfect concordance with CISH. The use of MLPA in routinely co-testing all breast cancers may reduce HER-2 testing variation between laboratories, may serve as quality control for IHC, will reveal IHC 0/1+ patients with gene amplification, likely responsive to trastuzumab, and identify IHC 3+ cases without gene amplification that may respond less well. PMID:24324739

  6. Added value of HER-2 amplification testing by multiplex ligation-dependent probe amplification in invasive breast cancer.

    Directory of Open Access Journals (Sweden)

    Chantal C H J Kuijpers

    Full Text Available BACKGROUND: HER-2 is a prognostic and predictive marker, but as yet no technique is perfectly able to identify patients likely to benefit from HER-2 targeted therapies. We aimed to prospectively assess the added value of first-line co-testing by IHC, and multiplex ligation-dependent probe amplification (MLPA and chromogenic in situ hybridization (CISH. METHODS: As local validation, HER-2 MLPA and CISH were compared in 99 breast cancers. Next, we reviewed 937 invasive breast cancers, from 4 Dutch pathology laboratories, that were prospectively assessed for HER-2 by IHC and MLPA (and CISH in selected cases. RESULTS: The validation study demonstrated 100% concordance between CISH and MLPA, if both methods were assessable and conclusive (81.8% of cases. Significant variation regarding percentages IHC 0/1+ and 2+ cases was observed between the laboratories (p<0.0001. Overall concordance between IHC and MLPA/CISH was 98.1% (575/586 (Kappa = 0.94. Of the IHC 3+ cases, 6.7% failed to reveal gene amplification, whereas 0.8% of the IHC 0/1+ cases demonstrated gene amplification. Results remained discordant after retrospective review in 3/11 discordant cases. In the remaining 8 cases the original IHC score was incorrect or adapted after repeated IHC staining. CONCLUSIONS: MLPA is a low-cost and quantitative high-throughput technique with near perfect concordance with CISH. The use of MLPA in routinely co-testing all breast cancers may reduce HER-2 testing variation between laboratories, may serve as quality control for IHC, will reveal IHC 0/1+ patients with gene amplification, likely responsive to trastuzumab, and identify IHC 3+ cases without gene amplification that may respond less well.

  7. Improved method to obtain pfaffic acid as a marker for quality control

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, Marili Villa Nova; Vedovello, Amanda; Rodrigues, Rodney Alexandre Ferreira; Montanari Junior, Ilio; Rehder, Vera Lucia Garcia, E-mail: rodney@cpqba.unicamp.br [Centro Pluridisciplinar de Pesquisas Quimicas, Biologicas e Agricolas, Universidade Estadual de Campinas, SP (Brazil)

    2013-09-01

    Pfaffic acid, a marker of Hebanthe eriantha (Brazilian ginseng), was first isolated in 1983 but is not yet commercially available. This lack of availability compromises the quality control of this plant and its derivatives. This paper proposes a process for pfaffic acid isolation from roots of H. eriantha at a purity suitable for analytical purposes. The steps involved in this process included extraction, hydrolysis, fractionation and purification by preparative HPLC. This process led to isolation of pfaffic acid with a chromatographic purity of 98.5% in a 0.25% yield from dried roots of H. eriantha; this yield is more than forty times higher than that of the current method in the literature. (author)

  8. Microbial transformation of tannin-rich substrate to gallic acid through co-culture method.

    Science.gov (United States)

    Banerjee, Rintu; Mukherjee, Gargi; Patra, Krushna Chandra

    2005-05-01

    Modified solid-state fermentation (MSSF) of tannin-rich substrate yielding tannase and gallic acid was carried out using a co-culture of the filamentous fungi, Rhizopus oryzae (RO IIT RB-13, NRRL 21498) and Aspergillus foetidus (GMRB013 MTCC 3557). Powdered fruits of Terminalia chebula and powdered pod cover of Caesalpinia digyna was used in the process and the different process parameters for maximum production of tannase and gallic acid by co-culture method were optimized through media engineering. MSSF was carried out at the optimum conditions of 30 degrees C and 80% relative humidity. The optimal pH and incubation period was 5.0 and 48 h respectively. Through the co-culture technique the maximum yield of tannase and gallic acid was found to be 41.3 U/ml and 94.8% respectively.

  9. Detection of biological molecules using boronate-based chemical amplification and optical sensors

    Science.gov (United States)

    Van Antwerp, William Peter; Mastrototaro, John Joseph; Lane, Stephen M.; Satcher, Jr., Joe H.; Darrow, Christopher B.; Peyser, Thomas A.; Harder, Jennifer

    1999-01-01

    Methods are provided for the determination of the concentration of biological levels of polyhydroxylated compounds, particularly glucose. The methods utilize an amplification system that is an analyte transducer immobilized in a polymeric matrix, where the system is implantable and biocompatible. Upon interrogation by an optical system, the amplification system produces a signal capable of detection external to the skin of the patient. Quantitation of the analyte of interest is achieved by measurement of the emitted signal.

  10. Development of Manufacturing Method of Highly Functional Material Gallic acid-CLA Ester Using Irradiation

    International Nuclear Information System (INIS)

    Cho, C. H.; Byun, M. W.; Jeong, I. Y.; Kim, D. H.

    2006-01-01

    Increasing interest and current trends for natural materials with various health beneficial functions by radiation (RT)-biotechnology (BT) fusion by developed countries. However, the information and development of new functional materials using the RT-BT fusion technology is still limited. The target material developed and manufactured by RT-BT fusion technology may have a multi-functional effect on human health and it can be applied for pharmaceutical materials as well as functional food ingredient. The market of functional new materials has been grown dramatically and a multi-functional material manufactured by RT-BT fusion technology may have a great economic impact for both the domestic and overseas market. Development of GA-CLA ester by chemical synthetic method. Transformation of linoleic acid to conjugated linoleic acid by irradiation. Identification and confirmation of the biological functions including antioxidative, cancer cell proliferation inhibition, anti-microbial, enhancement of immune response and lipid metabolism of GA-CLA ester. Increase industrial applicability of the new materials. Development of GA-CLA ester by chemical synthetic method(2 patents submitted). Development of the optimum methodology of GA-CLA and its derivative, octadeca-9,12-dienyl-3,4,5-trihydroxy benzoate). Identification and confirmation of biological activities of GA-CLA. Extramural funding from the Ministry of Commerce, Industry, and Energy subjected by gallic acid-fatty acid derivatives (205,000,000 Won). Provides the basic data for successful project 'Development of cosmeceutical and cosmetics using gallic acid fatty acid derivatives' funded by Ministry of Commerce, Industry, and Energy and collaboration with the Technology-invested venture company, SunBiotech, Co. and problem-solving for industrial application. Complete the patent procedure and publish the results to international or domestic peer-reviewed journals

  11. Methods for extraction and determination of phenolic acids in medicinal plants: a review.

    Science.gov (United States)

    Arceusz, Agnieszka; Wesolowski, Marek; Konieczynski, Pawel

    2013-12-01

    Phenolic acids constitute a group of potentially immunostimulating compounds. They occur in all medicinal plants and are widely used in phytotherapy and foods of plant origin. In recent years, phenolic acids have attracted much interest owing to their biological functions. This paper reviews the extraction and determination methods of phenolic acids in medicinal plants over the last 10 years. Although Soxhlet extraction and ultrasonic assisted extraction (UAE) are commonly used for the extraction of phenolic acids from plant materials, alternative techniques such as supercritical fluid extraction (SFE), and accelerated solvent extraction (ASE) can also be used. After extraction, phenolic acids are determined usually by liquid chromatography (LC) owing to the recent developments in this technique, especially when it is coupled with mass spectrometry (MS). Also detection systems are discussed, including UV-Vis, diode array, electrochemical and fluorimetric. Other popular techniques for the analysis of this group of secondary metabolites are gas chromatography coupled with mass spectrometry (GC-MS) and capillary electrophoresis (CE).

  12. Development of a method for determination of fatty acid using FT-IR spectroscopy

    Directory of Open Access Journals (Sweden)

    Dimas Augusto Morozin Zaia

    2011-05-01

    Full Text Available In the present paper a new methodology has been developed for determination of fatty acids in biological systems using FT-IR spectroscopy. For this method is not necessary chromophore reagent or pre sample preparation. Palmitic acid was chosen as standard, because it is found in several biological systems. The FT-IR spectrum of palmitic acid showed two absorption bands in the region of 2852 and 2920 cm-1 attributed to CH stretching. The results for these bands showed that the Beer-Lambert Law was followed in wide range of concentration of palmitic acid (14 to 257 mmol L-1. Potassium ferricyanide (K3[Fe(CN6] was used as internal standard. Several interferents were tested and only cholesterol, ferric chloride (higher concentration, mixture of amino acids for the band at 2919 cm-1 (higher concentration and triglyceride could be interferent if they appear in high concentration. Thus, this new methodology has advantage to be not expensive and simple.

  13. Screening method for detection of immediate amino acid decarboxylases--producing bacteria implicated in food poisoning.

    Science.gov (United States)

    Hussain, Husniza; Mohd Fuat, A R; Vimala, B; Ghazali, H M

    2011-08-01

    Assessment of amino acid decarboxylase activity can be conducted using tubed broth or plated agar. In this study, the test was carried out in microtitre plates containing lysine, ornithine, arginine, tyrosine, tryptophan, phenylalanine or histidine as biogenic amine precursors. Møller decarboxylase base broth (MDB) with or without 1% of a known amino acid were added to wells of a 96 well-microtitre plate. The wells were inoculated with Escherichia coli, Klebsiella pneumoniae, Acinetobacter anitratus or Staphylococcus aureus to the final concentration of 6.0 x 10(7) cfu/ml and incubated at 35ºC. The absorbance of the culture broth was read at 570 nm at 0, 1.0, 2.0, 3.0, 4.0, 5.5, 6.5 and 7.5 hour. Comparison of means of A'(570) between 0 hour and a specified incubation time was determined statistically. Positive decarboxylase activities were detected in the media inoculated with E. coli and K. pneumoniae in less than 6 hours. The current method is suitable for immediate producers of amino acid decarboxylase enzymes. It costs less as it uses less amino acid and it has the potential to be used for screening aliquots of food materials for amino acid decarboxylase activities.

  14. Comparison of acid leachate and fusion methods to determine plutonium and americium in environmental samples

    International Nuclear Information System (INIS)

    Smith, L.L.; Markun, F.; TenKate, T.

    1992-06-01

    The Analytical Chemistry Laboratory at Argonne National Laboratory performs radiochemical analyses for a wide variety of sites within the Department of Energy complex. Since the chemical history of the samples may vary drastically from site to site, the effectiveness of any analytical technique may also vary. This study compares a potassium fluoride-pyrosulfate fusion technique with an acid leachate method. Both normal and high-fired soils and vegetation samples were analyzed for both americium and plutonium. Results show both methods work well, except for plutonium in high-fired soils. Here the fusion method provides higher accuracy

  15. Validation of a One-Step Method for Extracting Fatty Acids from Salmon, Chicken and Beef Samples.

    Science.gov (United States)

    Zhang, Zhichao; Richardson, Christine E; Hennebelle, Marie; Taha, Ameer Y

    2017-10-01

    Fatty acid extraction methods are time-consuming and expensive because they involve multiple steps and copious amounts of extraction solvents. In an effort to streamline the fatty acid extraction process, this study compared the standard Folch lipid extraction method to a one-step method involving a column that selectively elutes the lipid phase. The methods were tested on raw beef, salmon, and chicken. Compared to the standard Folch method, the one-step extraction process generally yielded statistically insignificant differences in chicken and salmon fatty acid concentrations, percent composition and weight percent. Initial testing showed that beef stearic, oleic and total fatty acid concentrations were significantly lower by 9-11% with the one-step method as compared to the Folch method, but retesting on a different batch of samples showed a significant 4-8% increase in several omega-3 and omega-6 fatty acid concentrations with the one-step method relative to the Folch. Overall, the findings reflect the utility of a one-step extraction method for routine and rapid monitoring of fatty acids in chicken and salmon. Inconsistencies in beef concentrations, although minor (within 11%), may be due to matrix effects. A one-step fatty acid extraction method has broad applications for rapidly and routinely monitoring fatty acids in the food supply and formulating controlled dietary interventions. © 2017 Institute of Food Technologists®.

  16. Acidic deposition: State of science and technology. Report 14. Methods for projecting future changes in surface water acid-base chemistry. Final report

    International Nuclear Information System (INIS)

    Thornton, K.W.; Marmorek, D.; Ryan, P.F.; Heltcher, K.; Robinson, D.

    1990-09-01

    The objectives of the report are to: critically evaluate methods for projecting future effects of acidic deposition on surface water acid-base chemistry; review and evaluate techniques and procedures for analyzing projection uncertainty; review procedures for estimating regional lake and stream population attributes; review the U.S. Environmental Protection Agency (EPA) Direct/Delayed Response Project (DDRP) methodology for projecting the effects of acidic deposition on future changes in surface water acid-base chemistry; and present the models, uncertainty estimators, population estimators, and proposed approach selected to project the effects of acidic deposition on future changes in surface water acid-base chemistry in the NAPAP 1990 Integrated Assessment and discuss the selection rationale

  17. Studies on the interference of hydrofluoric acid and phosphoric acid in the determination of uranium using Ti(III) reduction method-biamperometry end point

    International Nuclear Information System (INIS)

    Shiny, T.S.; Rajalakshmi, A.; Phal, D.G.; Charyulu, M.M.; Ramakumar, K.L.

    2007-01-01

    Accurate and precise determination of uranium in nuclear materials is necessary for chemical quality control as well as for nuclear material accounting purposes. Different types of uranium samples are received for the measurements. Depending upon the nature of the sample dissolution procedure is selected. Mixed oxide samples of uranium and plutonium, for example, are dissolved in nitric acid containing hydrofluoric acid under IR lamp. The fluoride ions are removed by repeated evaporation of the solution. However, some fluoride ions are left in the solutions depending on the conditions of evaporation. Uranium samples and alloy samples are dissolved in dilute hydrochloric acid. The rate of dissolution depends on concentration of acid. Sometimes a mixture of hydrochloric acid and hydrofluoric acid is used for the dissolution metal alloy samples, which may contain silica. Another method of dissolution of these samples is using a mixture of phosphoric acid and 1% hydrofluoric acid. It is necessary to study the interference of hydrofluoric acid and phosphoric acid on the determination of uranium

  18. A method for the determination of ascorbic acid using the iron(II)-pyridine-dimethylglyoxime complex

    Energy Technology Data Exchange (ETDEWEB)

    Arya, S. P.; Mahajan, M. [Haryana, Kurukshetra Univ. (India). Dept. of Chemistry

    1998-05-01

    A simple and rapid spectrophotometric method for the determination of ascorbic acid is proposed. Ascorbic acid reduces iron (III) to iron (II) which forms a red colored complex with dimethylglyoxime in the presence of pyridine. The absorbance of the resulting solution is measured at 514 nm and a linear relationship between absorbance and concentration of ascorbic acid is observed up to 14 {mu}g ml{sup -1}. Studies on the interference of substances usually associated with ascorbic acid have been carried out and the applicability of the method has been tested by analysing pharmaceutical preparations of vitamin C. [Italiano] Si propone un rapido e semplice metodo spettrofotometrico per la determinazione dell`acido ascorbico. L`acido ascorbico riduce il ferro(III) a ferro(II) che forma con la dimetilgliossima, in presenza di piridina, un complesso colorato in rosso. L`assorbanza della soluzione risultante e` misurata a 514 nm e si ottiene una relazione lineare tra assorbanza e concentrazione dell`acido ascorbico fino a 14 {mu}g ml{sup -1}. Si sono condotti studi sugli interferenti usualmente associati all`acido ascorbico ed e` stata valutata l`applicabilita` del metodo all`analisi di preparati farmaceutici di vitamina C.

  19. Evaluation of Acoustic Cavitation in Terephthalic Acid Solutions Containing Gold Nanoparticles by the Spectrofluorometry Method

    Directory of Open Access Journals (Sweden)

    Ameneh Sazgarnia

    2012-01-01

    Full Text Available Background. When a liquid is irradiated with high intensity and low-frequency ultrasound, acoustic cavitation occurs. The existence of particles in a liquid provides nucleation sites for cavitation bubbles and leads to a decrease in the ultrasonic intensity threshold needed for cavitation onset. Materials and Methods. The study was designed to measure hydroxyl radicals in terephthalic acid solutions containing gold nanoparticles in a near field of a 1 MHz sonotherapy probe. The effect of ultrasound irradiation parameters containing mode of sonication and ultrasound intensity in hydroxyl radicals production have been investigated by the spectrofluorometry method. Results. Recorded fluorescence signal in terephthalic acid solution containing gold nanoparticles was higher than the terephthalic acid solution without gold nanoparticles. Also, the results showed that any increase in intensity of the sonication would be associated with an increase in the fluorescence intensity. Conclusion. Acoustic cavitation in the presence of gold nanoparticles has been introduced as a way for improving therapeutic effects on the tumors in sonodynamic therapy. Also, the terephthalic acid dosimetry is suitable for detecting and quantifying free hydroxyl radicals as a criterion of cavitation production over a certain range of conditions in medical ultrasound fields.

  20. Carbamazepine-Fumaric Acid Co-Crystal Screening Using Solution Based Method

    Directory of Open Access Journals (Sweden)

    Abd Rahim Syarifah

    2016-01-01

    Full Text Available Co-crystals is a multi-component system which connected by non-covalent interactions, present physically as a solid form under ambient conditions. Nowadays, co-crystal has becoming as an alternative approach to improve the bioavailability of poor water soluble drugs especially for a weakly ionisable groups or neutral compounds. In this study the co-crystal screening was carried out for carbamazepine (CBZ and fumaric acid (FUM co-crystal former (CCF using non-stoichiometric method (addition of CBZ to CCF saturated solution and stoichiometric method (evaporation of 1:1 molar ratio of CBZ to CCF in acetonitrile, ethyl acetate, propanol, ethanol and formic acid solvent systems. The crystals produced from the screening were characterized using Powder X-ray Diffraction (PXRD, Differential Scanning Calorimetry (DSC and Fourier Transform Infrared (FT-IR. The PXRD analysis had confirmed that the co-crystal was successfully formed in both methods for all of the solvent system studied with an exception to formic acid in the stoichiometric method where no crystal was found precipitate. The findings from this study revealed that Form A and Form B of CBZ-FUM co-crystal had been successfully formed from different solvent systems.

  1. Development of a nested polymerase chain reaction for amplification of a sequence of the p57 gene of Renibacterium salmoninarum that provides a highly sensitive method for detection of the bacterium in salmonid kidney

    Science.gov (United States)

    Chase, D.M.; Pascho, R.J.

    1998-01-01

    Nucleic acid-based assays have shown promise for diagnosing Renibacterium salmoninarum in tissues and body fluids of salmonids. DeVelopment of a nested polymerase chain reaction (PCR) method to detect a 320 bp DNA segment of the gene encoding the p57 protein of R. salmoninarum is described. Whereas a conventional PCR for a 383 bp segment of the p57 gene reliably detected 1000 R. salmoninarum cells per reaction in kidney tissue, the nested PCR detected as few as 10 R. salmoninarum per reaction in kidney tissue. Two DNA extraction methods for the nested PCR were compared and the correlation between replicate samples was generally higher in samples extracted by the QIAamp system compared with those extracted by the phenol/chloroform method. The specificity of the nested PCR was confirmed by testing DNA extracts of common bacterial fish pathogens and a panel of bacterial species reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA) and the fluorescent antibody test (FAT) for R. salmoninarum. Kidney samples from 74 naturally infected chinook Salmon were examined by the nested PCR, the ELISA, and the FAT, and the detected prevalences of R. salmoninarum were 61, 47, and 43%, respectively.

  2. Short-time maximum entropy method analysis of molecular dynamics simulation: Unimolecular decomposition of formic acid

    Science.gov (United States)

    Takahashi, Osamu; Nomura, Tetsuo; Tabayashi, Kiyohiko; Yamasaki, Katsuyoshi

    2008-07-01

    We performed spectral analysis by using the maximum entropy method instead of the traditional Fourier transform technique to investigate the short-time behavior in molecular systems, such as the energy transfer between vibrational modes and chemical reactions. This procedure was applied to direct ab initio molecular dynamics calculations for the decomposition of formic acid. More reactive trajectories of dehydrolation than those of decarboxylation were obtained for Z-formic acid, which was consistent with the prediction of previous theoretical and experimental studies. Short-time maximum entropy method analyses were performed for typical reactive and non-reactive trajectories. Spectrograms of a reactive trajectory were obtained; these clearly showed the reactant, transient, and product regions, especially for the dehydrolation path.

  3. Electrochemical method for producing a biodiesel mixture comprising fatty acid alkyl esters and glycerol

    Science.gov (United States)

    Lin, YuPo J; St. Martin, Edward J

    2013-08-13

    The present invention relates to an integrated method and system for the simultaneous production of biodiesel from free fatty acids (via esterification) and from triglycerides (via transesterification) within the same reaction chamber. More specifically, one preferred embodiment of the invention relates to a method and system for the production of biodiesel using an electrodeionization stack, wherein an ion exchange resin matrix acts as a heterogeneous catalyst for simultaneous esterification and transesterification reactions between a feedstock and a lower alcohol to produce biodiesel, wherein the feedstock contains significant levels of free fatty acid. In addition, because of the use of a heterogeneous catalyst, the glycerol and biodiesel have much lower salt concentrations than raw biodiesel produced by conventional transesterification processes. The present invention makes it much easier to purify glycerol and biodiesel.

  4. Purification of 2-oxo acid dehydrogenase multienzyme complexes from ox heart by a new method.

    OpenAIRE

    Stanley, C J; Perham, R N

    1980-01-01

    A new method is described that allows the parallel purification of the pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase multienzyme complexes from ox heart without the need for prior isolation of mitochondria. All the assayable activity of the 2-oxo acid dehydrogenase complexes in the disrupted tissue is made soluble by the inclusion of non-ionic detergents such as Triton X-100 or Tween-80 in the buffer used for the initial extraction of the enzyme complexes. The yields of the pyruvate...

  5. EFFECT OF COOKING METHODS ON AMINO ACIDS COMPOSITION OF CHICKEN MEAT

    OpenAIRE

    Thanaa Shehab

    2016-01-01

    Chicken meat is an important item in the Syrian diet. The increasing production of chickens and their potential in restaurants and food service operation implies the need for more detailed information regarding their quality and nutrient retention. Cooking methods have different effects on the values of nutrients of chicken. Therefore, this study was carried out to evaluate the effect of microwave cooking in amino acids composition of chicken meat (breast &thigh) as compared with some con...

  6. COMPARISON OF METHODS FOR ETHYLHEXYL 4-METHOXYCINNAMATE ACID ESTER OXIDATION IN WATER MEDIUM

    OpenAIRE

    Waldemar Studziński; Alicja Gackowska

    2017-01-01

    The aim of studies was to compare an impact of oxidizing agents on degradation of ethylhexyl 4-methoxycinnamate acid (EHMC). The oxidation reaction was carried out in the presence of sodium hypochlorite, hydrogen peroxide and ozone with/without UV radiation. EHMC degradation and analysis of products were performed using gas chromatograph coupled with mass spectrometry detector. The most effective method of EHMC degradation turned out to be ozonation with participation of UV radiation. In this...

  7. Simplified method for gravimetric determination of zirconium or hafnium with α-hydroxy carboxylic acids

    International Nuclear Information System (INIS)

    Barbieri, R.S.; Rocha, J.C.; Terra, V.R.; Marques Netto, A.

    1989-01-01

    The conditions for gravimetric determination of zirconium or hafnium by glicoloc acids derivatives were studied by thermogravimetric analysis. The method utilized shownd that after precipitation, washing and drying of precipitates at 150 o C, the resulting solid was weighed in the form of [M (RCH(OH)COO) 4 ] (M = Zr, Hf; R + C 6 H 5 , β-C 10 H 7 , p-BrC 6 H 4 ). (author)

  8. Modified method for zirconium or hafnium gravimetric determination with glycolic acid derivatives

    International Nuclear Information System (INIS)

    Barbieri, R.S.; Rocha, J.C.; Terra, V.R.; Marques Neto, A.

    1989-01-01

    The conditions for gravimetric determination of zirconium or hafnium by glicolic acid derivatives were studied by thermogravimetric analysis. The method utilized shown that after precipitation, washing and drying of precipitates at 150 0 C, the resulting solid was weighed in the form of [M{RCH(OH)COO} 4 ] (M = Zr,Hf;R = C 6 H 5 , β-C 10 H 7 ,p-BrC 6 H 4 ). (author) [pt

  9. Aspects on testing methods for acid attacks on concrete - further experiments

    International Nuclear Information System (INIS)

    Romben, L.

    1980-01-01

    The report presents a number of control experiments which have been performed to verify test procedures of the resistance of concrete and concrete products. A more detailed study of the calcium dissolution and the layer dissolution process has been performed. The mechanisms which control the rate of attack in the long term are discussed. The proposed method is intended for use in studying the resistance to attacks by acid water solutions. (G.B.)

  10. Error amplification to promote motor learning and motivation in therapy robotics.

    Science.gov (United States)

    Shirzad, Navid; Van der Loos, H F Machiel

    2012-01-01

    To study the effects of different feedback error amplification methods on a subject's upper-limb motor learning and affect during a point-to-point reaching exercise, we developed a real-time controller for a robotic manipulandum. The reaching environment was visually distorted by implementing a thirty degrees rotation between the coordinate systems of the robot's end-effector and the visual display. Feedback error amplification was provided to subjects as they trained to learn reaching within the visually rotated environment. Error amplification was provided either visually or through both haptic and visual means, each method with two different amplification gains. Subjects' performance (i.e., trajectory error) and self-reports to a questionnaire were used to study the speed and amount of adaptation promoted by each error amplification method and subjects' emotional changes. We found that providing haptic and visual feedback promotes faster adaptation to the distortion and increases subjects' satisfaction with the task, leading to a higher level of attentiveness during the exercise. This finding can be used to design a novel exercise regimen, where alternating between error amplification methods is used to both increase a subject's motor learning and maintain a minimum level of motivational engagement in the exercise. In future experiments, we will test whether such exercise methods will lead to a faster learning time and greater motivation to pursue a therapy exercise regimen.

  11. A new method for determining the acid number of biodiesel based on coulometric titration.

    Science.gov (United States)

    Barbieri Gonzaga, Fabiano; Pereira Sobral, Sidney

    2012-08-15

    A new method is proposed for determining the acid number (AN) of biodiesel using coulometric titration with potentiometric detection, basically employing a potentiostat/galvanostat and an electrochemical cell containing a platinum electrode, a silver electrode, and a combination pH electrode. The method involves a sequential application of a constant current between the platinum (cathode) and silver (anode) electrodes, followed by measuring the potential of the combination pH electrode, using an isopropanol/water mixture as solvent and LiCl as the supporting electrolyte. A preliminary evaluation of the new method, using acetic acid for doping a biodiesel sample, showed an average recovery of 100.1%. Compared to a volumetric titration-based method for determining the AN of several biodiesel samples (ranging from about 0.18 to 0.95 mg g(-1)), the new method produced statistically similar results with better repeatability. Compared to other works reported in the literature, the new method presented an average repeatability up to 3.2 times better and employed a sample size up to 20 times smaller. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. STATISTICAL EVALUATION OF AN ANALYTICAL GC/MS METHOD FOR THE DETERMINATION OF LONG CHAIN FATTY ACIDS

    Science.gov (United States)

    In-depth evaluation of an analytical method to detect and quantify long chain fatty acids (C8 - C16) at trace level concentrations (25-1000 µg/l) is presented. The method requires derivatization of the acids with methanolic boron trifluoride, separation, and...

  13. Benzoic acid derivatives: Evaluation of thermochemical properties with complementary experimental and computational methods

    International Nuclear Information System (INIS)

    Verevkin, Sergey P.; Zaitsau, Dzmitry H.; Emeĺyanenko, Vladimir N.; Stepurko, Elena N.; Zherikova, Kseniya V.

    2015-01-01

    Highlights: • Vapor pressures of benzoic acid derivatives were measured. • Sublimation enthalpies were derived and compared with the literature. • Thermochemical data tested for consistency using additivity rules and computations. • Contradiction between available enthalpies of sublimation was resolved. • Pairwise interactions of substituents on the benzene ring were derived. - Abstract: Molar sublimation enthalpies of the methyl- and methoxybenzoic acids were derived from the transpiration method, static method, and TGA. Thermochemical data available in the literature were collected, evaluated, and combined with own experimental results. This collection together with the new experimental results reported here has helped to resolve contradictions in the available enthalpy data and to recommend sets of sublimation and formation enthalpies for the benzoic acid derivatives. Gas-phase enthalpies of formation calculated with the G4 quantum-chemical method were in agreement with the experiment. Pairwise interactions of the methyl, methoxy, and carboxyl substituents on the benzene ring were derived and used for the development of simple group-additivity procedures for estimation of the vaporization enthalpies, gas-phase, and liquid-phase enthalpies of formation of substituted benzenes.

  14. Development of a method for the quantitation of chloro-, bromo-, and iodoacetic acids in alcoholic beverages.

    Science.gov (United States)

    Cardador, Maria Jose; Gallego, Mercedes

    2012-01-25

    Chloroacetic, bromoacetic, and iodoacetic acids can be found in alcoholic beverages when they are used as preservatives/stabilizers or as disinfectants. As they are toxic components, their addition is not permitted under European Union and U.S. regulations. To date, no sensitive methods are available, and those proposed are very laborious. This paper describes a sensitive and straightforward method for the determination of the three monohalogenated acetic acids (m-HAAs) in wines and beers using static headspace extraction coupled with gas chromatography-mass spectrometry. Prior to extraction, the target analytes were esterified to increase their volatility, and all parameters related to the extraction/methylation process were optimized to achieve high efficiency (>90%). The study examined the influence both of the ethanol concentration on the headspace partitioning and of the primary acids present in wine on the derivatization reaction of the m-HAAs. The proposed method allows the determination of these compounds at microgram per liter levels in alcoholic beverages.

  15. Benzoic acid derivatives: Evaluation of thermochemical properties with complementary experimental and computational methods

    Energy Technology Data Exchange (ETDEWEB)

    Verevkin, Sergey P., E-mail: sergey.verevkin@uni-rostock.de [Department of Physical Chemistry and Department “Science and Technology of Life, Light and Matter”, University of Rostock, D-18059 Rostock (Germany); Department of Physical Chemistry, Kazan Federal University, 420008 Kazan (Russian Federation); Zaitsau, Dzmitry H. [Department of Physical Chemistry, Kazan Federal University, 420008 Kazan (Russian Federation); Emeĺyanenko, Vladimir N. [Department of Physical Chemistry and Department “Science and Technology of Life, Light and Matter”, University of Rostock, D-18059 Rostock (Germany); Stepurko, Elena N. [Chemistry Faculty and Research Institute for Physical Chemical Problems, Belarusian State University, 220030 Minsk (Belarus); Zherikova, Kseniya V. [Nikolaev Institute of Inorganic Chemistry of Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk (Russian Federation)

    2015-12-20

    Highlights: • Vapor pressures of benzoic acid derivatives were measured. • Sublimation enthalpies were derived and compared with the literature. • Thermochemical data tested for consistency using additivity rules and computations. • Contradiction between available enthalpies of sublimation was resolved. • Pairwise interactions of substituents on the benzene ring were derived. - Abstract: Molar sublimation enthalpies of the methyl- and methoxybenzoic acids were derived from the transpiration method, static method, and TGA. Thermochemical data available in the literature were collected, evaluated, and combined with own experimental results. This collection together with the new experimental results reported here has helped to resolve contradictions in the available enthalpy data and to recommend sets of sublimation and formation enthalpies for the benzoic acid derivatives. Gas-phase enthalpies of formation calculated with the G4 quantum-chemical method were in agreement with the experiment. Pairwise interactions of the methyl, methoxy, and carboxyl substituents on the benzene ring were derived and used for the development of simple group-additivity procedures for estimation of the vaporization enthalpies, gas-phase, and liquid-phase enthalpies of formation of substituted benzenes.

  16. Optimization of extraction method and HPLC analysis of six caffeoylquinic acids in Pluchea indica leaves from different provenances in Thailand

    Directory of Open Access Journals (Sweden)

    Sumet Kongkiatpaiboon

    Full Text Available ABSTRACT Pluchea indica (L. Less., Asteraceae, is a medicinal plant which contains a high amount of phenolic compounds such as caffeoylquinic acid derivatives. The leaves have been traditionally used as a nerve tonic and extensively as herbal tea. This study aimed to develop and validate an HPLC method to quantitatively analyze six caffeoylquinic acid derivatives, viz. 3-O-caffeoylquinic acid, 4-O-caffeoylquinic acid, 5-O caffeoylquinic acid, 3,4-O-dicaffeoylquinic acid, 3,5-O-dicaffeoylquinic acid, and 4,5-O-dicaffeoylquinic acid in P. indica leaf extract. HPLC was carried out in a Hypersil BDS C18-column eluted with 0.5% acetic acid in water and methanol using gradient elution with a flow rate of 1 ml/min and detection at 326 nm. The method validation was performed to assure its linearity, precision, accuracy and limits of detection and quantitation. Several extraction techniques including maceration, decoction, digestion, Soxhlet extraction, and ultrasound extraction, were used to extract active constituents. The ultrasound extraction with 50% ethanol yielded the highest concentration of these caffeoylquinic acid derivatives in the P. indica leaf extract. Our developed HPLC method is simple and reliable for a routine analysis of the six caffeoylquinic acids in P. indica leaves and could potentially be applied to be used in commercial herbal products.

  17. Bayesian estimation for quantification by real-time polymerase chain reaction under a branching process model of the DNA molecules amplification process

    NARCIS (Netherlands)

    Lalam, N.; Jacob, C.

    2007-01-01

    The aim of Quantitative Polymerase Chain Reaction is to determine the initial amount X0 of specific nucleic acids from an observed trajectory of the amplification process, the amplification being achieved through successive replication cycles. This process depends on the efficiency fpngn of

  18. Small sample whole-genome amplification

    Science.gov (United States)

    Hara, Christine; Nguyen, Christine; Wheeler, Elizabeth; Sorensen, Karen; Arroyo, Erin; Vrankovich, Greg; Christian, Allen

    2005-11-01

    Many challenges arise when trying to amplify and analyze human samples collected in the field due to limitations in sample quantity, and contamination of the starting material. Tests such as DNA fingerprinting and mitochondrial typing require a certain sample size and are carried out in large volume reactions; in cases where insufficient sample is present whole genome amplification (WGA) can be used. WGA allows very small quantities of DNA to be amplified in a way that enables subsequent DNA-based tests to be performed. A limiting step to WGA is sample preparation. To minimize the necessary sample size, we have developed two modifications of WGA: the first allows for an increase in amplified product from small, nanoscale, purified samples with the use of carrier DNA while the second is a single-step method for cleaning and amplifying samples all in one column. Conventional DNA cleanup involves binding the DNA to silica, washing away impurities, and then releasing the DNA for subsequent testing. We have eliminated losses associated with incomplete sample release, thereby decreasing the required amount of starting template for DNA testing. Both techniques address the limitations of sample size by providing ample copies of genomic samples. Carrier DNA, included in our WGA reactions, can be used when amplifying samples with the standard purification method, or can be used in conjunction with our single-step DNA purification technique to potentially further decrease the amount of starting sample necessary for future forensic DNA-based assays.

  19. Privacy amplification for quantum key distribution

    International Nuclear Information System (INIS)

    Watanabe, Yodai

    2007-01-01

    This paper examines classical privacy amplification using a universal family of hash functions. In quantum key distribution, the adversary's measurement can wait until the choice of hash functions is announced, and so the adversary's information may depend on the choice. Therefore the existing result on classical privacy amplification, which assumes the independence of the choice from the other random variables, is not applicable to this case. This paper provides a security proof of privacy amplification which is valid even when the adversary's information may depend on the choice of hash functions. The compression rate of the proposed privacy amplification can be taken to be the same as that of the existing one with an exponentially small loss in secrecy of a final key. (fast track communication)

  20. Digital Droplet Multiple Displacement Amplification (ddMDA for Whole Genome Sequencing of Limited DNA Samples.

    Directory of Open Access Journals (Sweden)

    Minsoung Rhee

    Full Text Available Multiple displacement amplification (MDA is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet, ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

  1. EFFECT OF COOKING METHODS ON AMINO ACIDS COMPOSITION OF CHICKEN MEAT

    Directory of Open Access Journals (Sweden)

    Thanaa Shehab

    2016-01-01

    Full Text Available Chicken meat is an important item in the Syrian diet. The increasing production of chickens and their potential in restaurants and food service operation implies the need for more detailed information regarding their quality and nutrient retention. Cooking methods have different effects on the values of nutrients of chicken. Therefore, this study was carried out to evaluate the effect of microwave cooking in amino acids composition of chicken meat (breast &thigh as compared with some conventional methods, i.e. boiling, pressure and roasting

  2. Developing a rapid method for the determination of uranium in pure phosphoric acid and D2 EHPA

    International Nuclear Information System (INIS)

    Koudsi, Y.; Stas, J.; Al-Merey, R.; shaddoud, G.

    1996-02-01

    Arsenazo (III) used in titrate uranium spectrophotometrically in phosphoric acid after its extraction into organic phase. In this work we used arsenazo(III) to complex uranyl ion in pure phosphoric acid and in the aqueous phase. The spectrum of the complex shows that λ max is at 650 nm. The linearity of the method is corelated with acid molarity, it is (1 -4, 10 - 30, 10 - 40) ppm uranium for (0.2, 1, 2) M of phosphoric acid respectively. Uranium in D 2 EHPA stripped by phosphoric acid and then determined by this method. Also it has been applied to determine uranium in pure perchloric acid. The method is direct, rapid, very cheap and relatively accurate. (author)

  3. Rolling circle amplification of metazoan mitochondrialgenomes

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Lindberg, D.R.; Boore, J.L.

    2005-07-31

    Here we report the successful use of rolling circle amplification (RCA) for the amplification of complete metazoan mt genomes to make a product that is amenable to high-throughput genome sequencing techniques. The benefits of RCA over PCR are many and with further development and refinement of RCA, the sequencing of organellar genomics will require far less time and effort than current long PCR approaches.

  4. Rapid Newcastle Disease Virus Detection Based on Loop-Mediated Isothermal Amplification and Optomagnetic Readout

    DEFF Research Database (Denmark)

    Tian, Bo; Ma, Jing; Zardán Gómez de la Torre, Teresa

    2016-01-01

    Rapid and sensitive diagnostic methods based on isothermal amplification are ideal substitutes for PCR in out-of-lab settings. However, there are bottlenecks in terms of establishing low-cost and user-friendly readout methods for isothermal amplification schemes. Combining the high amplification...... efficiency of loop-mediated isothermal amplification (LAMP) with an optomagnetic nanoparticle-based readout system, we demonstrate ultrasensitive and rapid detection of Newcastle disease virus RNA. Biotinylated amplicons of LAMP and reverse transcription LAMP (RT-LAMP) bind to streptavidin-coated magnetic...... nanoparticles (MNPs) resulting in a dramatical increase in the hydrodynamic size of the MNPs. This increase was measured by an optomagnetic readout system and provided quantitative information on the amount of LAMP target sequence. Our assay resulted in a limit of detection of 10 aM of target sequence...

  5. Pentavalent Bismuth-Mediated Glycosylation Methods to Activate Sialic and Uronic Acids and the Incorporation of Sialic Acids Into Insulin

    Science.gov (United States)

    Kabotso, Daniel Elorm Kwame

    The negative charge at physiological pH of carboxylic acid-containing monosaccharides modulate the properties of many natural biomolecules such as oligosaccharides and glycoconjugates. Unfortunately, these altered electronic properties also make the incorporation of such acidic sugars more challenging as compared to the more commonly studied neutral sugars. Herein are reported the first demonstration of glycosylation reactions mediated by triphenylbis(1,1,1-trifluoromethanesulfonato)-bismuth with thioglycosides containing carboxylic acid substituents protected as esters. Unlike with many neutral sugar substrates, the addition of 1-propanethiol to the reactions proved critical to obtaining good yields of the desired glycosylation products using sialic acid, galacturonic acid, and glucuronic acid. The protocol was demonstrated to be amenable to automation using a liquid-handling platform. The consequences of artificially incorporating carboxylic-acid-containing sugars into proteins were tested by the design of a linker containing 1 to 4 sialic acids--a sugar found in many human proteins and brain tissues--that was attached via reductive amination of trityl thiopropylaldehyde at the phenyl alanine terminal end of the protein insulin produced through solid-phase peptide synthesis. Removal of the trityl group with neat trifluoroacetic acid furnished the thiol-free modified insulin that was ligated via a disulfide bond to the peptide scaffold bearing acetyl protected sialic acids. A 14-15% ammonium hydroxide solution was found to be effective in deprotecting the acetyl groups without degradation of the disulfide bond. In addition to maintaining the potency and bioactivity of insulin, the sialic acid-containing linker rendered insulin more resistant to aggregation due to heat and mechanical agitation compared to the unmodified protein.

  6. [A thin-layer chromatography method for determining the styrene metabolites mandelic and phenylglyoxylic acid in urine].

    Science.gov (United States)

    Gartzke, J; Burck, D

    1989-06-01

    A thin-layer chromatographic method is described for the determination of mandelic and phenyglyoxillic acid on silicagel (Silufol UV 254) after extraction from urine of styrene exposed workers. The quantitative determination was performed after eluting the spots. Phenylglyoxilic acid was measured at 255 nm and mandelic acid by derivative spectroscopically estimation of the .CH(OH).COOH -chromophore at 217 nm or by a three-wavelength mode, respectively. The recovery in urine was 80-104% for phenylglyoxilic acid and 99-105% for mandelic acid.

  7. Improved microscopical detection of acid-fast bacilli by the modified bleach method in lymphnode aspirates

    Directory of Open Access Journals (Sweden)

    Annam Vamseedhar

    2009-07-01

    Full Text Available Objectives: To improve the smear microscopy for detection of acid-fast bacilli (AFB in fine needle aspiration cytology (FNAC of lymph node using the bleach method and also to compare this with cytological diagnosis and the conventional Ziehl-Neelsen (ZN method. Study Design: In 99 consecutive patients with clinical suspicion of tuberculosis (TB presenting with lymphadenopathy, FNACs were performed. Smears from the aspirates were processed for routine cytology and the conventional ZN method. The remaining material in the needle hub and/or the syringe was used for the bleach method. The significance of the bleach method over the conventional ZN method and cytology was analyzed using the χ2 test. Results: Of 99 aspirates, 93 were studied and the remaining six were excluded from the study due to diagnosis of malignancy in 4.04% (4/6 and inadequate aspiration in 2.02% (2/6. Among the 93 aspirates, 33.33% (31/93 were positive for AFB on conventional ZN method, 41.94% (39/93 were indicative of TB on cytology and the smear positivity increased to 63.44% (59/93 on bleach method. Conclusion: The bleach method is simple, inexpensive and potent disinfectant, also limiting the risk of laboratory-acquired infections. The implementation of the bleach method clearly improves microscopic detection and can be a useful contribution to routine cytology.

  8. Effect of Cooking Method on the Proximate, Amino Acid and Fatty Acid Compositions of Clarias gariepinus and Oreochromis niloticus

    Directory of Open Access Journals (Sweden)

    Omolara Olusola Oluwaniyi

    2016-10-01

    Full Text Available The proximate, amino acid and fatty acid compositions of the fillet and oil from Clarias gariepinus (Catfish and Oreochromis niloticus (Tilapia were determined. The moisture content ranged from 76.27 % for catfish to 79.97 % for tilapia while the oil content ranged from 7.80 % for tilapia and 11.00 % for catfish. Ash content was in the range 8.03 – 9.16 % and the protein content was 15.83 - 18.48 %. Cooking – boiling, roasting or frying – resulted in a variation in the nutrient composition but with no significant effect on the amino acid composition except for the samples fried with palm oil which resulted in significantly reduced essential amino acids contents. All the fish samples – both fresh and processed – have amino acid scores less than 100, with lysine, threonine and the sulphur-containing amino acids being among the limiting amino acids. Both fish samples contain more unsaturated than saturated fatty acids.

  9. Critical Test of Some Computational Chemistry Methods for Prediction of Gas-Phase Acidities and Basicities.

    Science.gov (United States)

    Toomsalu, Eve; Koppel, Ilmar A; Burk, Peeter

    2013-09-10

    Gas-phase acidities and basicities were calculated for 64 neutral bases (covering the scale from 139.9 kcal/mol to 251.9 kcal/mol) and 53 neutral acids (covering the scale from 299.5 kcal/mol to 411.7 kcal/mol). The following methods were used: AM1, PM3, PM6, PDDG, G2, G2MP2, G3, G3MP2, G4, G4MP2, CBS-QB3, B1B95, B2PLYP, B2PLYPD, B3LYP, B3PW91, B97D, B98, BLYP, BMK, BP86, CAM-B3LYP, HSEh1PBE, M06, M062X, M06HF, M06L, mPW2PLYP, mPW2PLYPD, O3LYP, OLYP, PBE1PBE, PBEPBE, tHCTHhyb, TPSSh, VSXC, X3LYP. The addition of the Grimmes empirical dispersion correction (D) to B2PLYP and mPW2PLYP was evaluated, and it was found that adding this correction gave more-accurate results when considering acidities. Calculations with B3LYP, B97D, BLYP, B2PLYPD, and PBE1PBE methods were carried out with five basis sets (6-311G**, 6-311+G**, TZVP, cc-pVTZ, and aug-cc-pVTZ) to evaluate the effect of basis sets on the accuracy of calculations. It was found that the best basis sets when considering accuracy of results and needed time were 6-311+G** and TZVP. Among semiempirical methods AM1 had the best ability to reproduce experimental acidities and basicities (the mean absolute error (mae) was 7.3 kcal/mol). Among DFT methods the best method considering accuracy, robustness, and computation time was PBE1PBE/6-311+G** (mae = 2.7 kcal/mol). Four Gaussian-type methods (G2, G2MP2, G4, and G4MP2) gave similar results to each other (mae = 2.3 kcal/mol). Gaussian-type methods are quite accurate, but their downside is the relatively long computational time.

  10. Molecular cloning, characterization and expression of the caffeic acid O-methyltransferase (COMT) ortholog from kenaf (Hibiscus cannabinus)

    Science.gov (United States)

    We cloned the full-length of the gene putatively encoding caffeic acid O-methyltransferase (COMT) from kenaf (Hibiscus cannabinus L.) using degenerate primers and the RACE (rapid amplification of cDNA ends) method. Kenaf is an herbaceous and rapidly growing dicotyledonous plant with great potential ...

  11. Metal-ion induced amplification of three receptors from dynamic combinatorial libraries of peptide-hydrazones

    NARCIS (Netherlands)

    Roberts, Sarah L.; Furlan, Ricardo L.E.; Otto, Sijbren; Sanders, Jeremy K.M.

    2003-01-01

    Three building blocks of general structure (MeO)2CH–aromatic linker–Pro–amino acid–NHNH2 have been prepared and tested in acid-catalysed dynamic combinatorial libraries. Exposure of these libraries to LiI and NaI led to the amplification of three macrocyclic pseudopeptide receptors. The receptors

  12. New closed tube loop mediated isothermal amplification assay for prevention of product cross-contamination

    OpenAIRE

    Karthik, K.; Rathore, Rajesh; Thomas, Prasad; Arun, T.R.; Viswas, K.N.; Dhama, Kuldeep; Agarwal, R.K.

    2014-01-01

    Loop mediated isothermal amplification (LAMP) assay, a promising diagnostic test, has been developed for detection of different pathogens of human as well as animals. Various positive points support its use as a field level test but the major problem is product cross contamination leading to false positive results. Different methods were adopted by various researchers to control this false positive amplification due to cross contamination but all have their own advantages and disadvantages. A...

  13. Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions.

    Science.gov (United States)

    Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

    2017-02-14

    We present a novel method for the study of weak polyelectrolytes and general acid-base reactions in molecular dynamics and Monte Carlo simulations. The approach combines the advantages of the reaction ensemble and the Wang-Landau sampling method. Deprotonation and protonation reactions are simulated explicitly with the help of the reaction ensemble method, while the accurate sampling of the corresponding phase space is achieved by the Wang-Landau approach. The combination of both techniques provides a sufficient statistical accuracy such that meaningful estimates for the density of states and the partition sum can be obtained. With regard to these estimates, several thermodynamic observables like the heat capacity or reaction free energies can be calculated. We demonstrate that the computation times for the calculation of titration curves with a high statistical accuracy can be significantly decreased when compared to the original reaction ensemble method. The applicability of our approach is validated by the study of weak polyelectrolytes and their thermodynamic properties.

  14. Lactic Acid Fermentation, Urea and Lime Addition: Promising Faecal Sludge Sanitizing Methods for Emergency Sanitation.

    Science.gov (United States)

    Anderson, Catherine; Malambo, Dennis Hanjalika; Perez, Maria Eliette Gonzalez; Nobela, Happiness Ngwanamoseka; de Pooter, Lobke; Spit, Jan; Hooijmans, Christine Maria; de Vossenberg, Jack van; Greya, Wilson; Thole, Bernard; van Lier, Jules B; Brdjanovic, Damir

    2015-10-29

    In this research, three faecal sludge sanitizing methods-lactic acid fermentation, urea treatment and lime treatment-were studied for application in emergency situations. These methods were investigated by undertaking small scale field trials with pit latrine sludge in Blantyre, Malawi. Hydrated lime was able to reduce the E. coli count in the sludge to below the detectable limit within 1 h applying a pH > 11 (using a dosage from 7% to 17% w/w, depending faecal sludge alkalinity), urea treatment required about 4 days using 2.5% wet weight urea addition, and lactic acid fermentation needed approximately 1 week after being dosed with 10% wet weight molasses (2 g (glucose/fructose)/kg) and 10% wet weight pre-culture (99.8% pasteurised whole milk and 0.02% fermented milk drink containing Lactobacillus casei Shirota). Based on Malawian prices, the cost of sanitizing 1 m³ of faecal sludge was estimated to be €32 for lactic acid