Development of a quantitative recombinase polymerase amplification assay with an internal positive control.

PubMed

Crannell, Zachary A; Rohrman, Brittany; Richards-Kortum, Rebecca

2015-03-30

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.

Successful amplification of DNA aboard the International Space Station.

PubMed

Boguraev, Anna-Sophia; Christensen, Holly C; Bonneau, Ashley R; Pezza, John A; Nichols, Nicole M; Giraldez, Antonio J; Gray, Michelle M; Wagner, Brandon M; Aken, Jordan T; Foley, Kevin D; Copeland, D Scott; Kraves, Sebastian; Alvarez Saavedra, Ezequiel

2017-01-01

As the range and duration of human ventures into space increase, it becomes imperative that we understand the effects of the cosmic environment on astronaut health. Molecular technologies now widely used in research and medicine will need to become available in space to ensure appropriate care of astronauts. The polymerase chain reaction (PCR) is the gold standard for DNA analysis, yet its potential for use on-orbit remains under-explored. We describe DNA amplification aboard the International Space Station (ISS) through the use of a miniaturized miniPCR system. Target sequences in plasmid, zebrafish genomic DNA, and bisulfite-treated DNA were successfully amplified under a variety of conditions. Methylation-specific primers differentially amplified bisulfite-treated samples as would be expected under standard laboratory conditions. Our findings establish proof of concept for targeted detection of DNA sequences during spaceflight and lay a foundation for future uses ranging from environmental monitoring to on-orbit diagnostics.

Stochastic resonance in the majority vote model on regular and small-world lattices

NASA Astrophysics Data System (ADS)

Krawiecki, A.

2017-11-01

The majority vote model with two states on regular and small-world networks is considered under the influence of periodic driving. Monte Carlo simulations show that the time-dependent magnetization, playing the role of the output signal, exhibits maximum periodicity at nonzero values of the internal noise parameter q, which is manifested as the occurrence of the maximum of the spectral power amplification; the location of the maximum depends in a nontrivial way on the amplitude and frequency of the periodic driving as well as on the network topology. This indicates the appearance of stochastic resonance in the system as a function of the intensity of the internal noise. Besides, for low frequencies and for certain narrow ranges of the amplitudes of the periodic driving double maxima of the spectral power amplification as a function of q occur, i.e., stochastic multiresonance appears. The above-mentioned results quantitatively agree with those obtained from numerical simulations of the mean-field equations for the time-dependent magnetization. In contrast, analytic solutions for the spectral power amplification obtained from the latter equations using the linear response approximation deviate significanlty from the numerical results since the effect of the periodic driving on the system is not small even for vanishing amplitude.

Amplified total internal reflection: theory, analysis, and demonstration of existence via FDTD.

PubMed

Willis, Keely J; Schneider, John B; Hagness, Susan C

2008-02-04

The explanation of wave behavior upon total internal reflection from a gainy medium has defied consensus for 40 years. We examine this question using both the finite-difference time-domain (FDTD) method and theoretical analyses. FDTD simulations of a localized wave impinging on a gainy half space are based directly on Maxwell's equations and make no underlying assumptions. They reveal that amplification occurs upon total internal reflection from a gainy medium; conversely, amplification does not occur for incidence below the critical angle. Excellent agreement is obtained between the FDTD results and an analytical formulation that employs a new branch cut in the complex "propagation-constant" plane.

Measurement of hearing aid internal noise1

PubMed Central

Lewis, James D.; Goodman, Shawn S.; Bentler, Ruth A.

2010-01-01

Hearing aid equivalent input noise (EIN) measures assume the primary source of internal noise to be located prior to amplification and to be constant regardless of input level. EIN will underestimate internal noise in the case that noise is generated following amplification. The present study investigated the internal noise levels of six hearing aids (HAs). Concurrent with HA processing of a speech-like stimulus with both adaptive features (acoustic feedback cancellation, digital noise reduction, microphone directionality) enabled and disabled, internal noise was quantified for various stimulus levels as the variance across repeated trials. Changes in noise level as a function of stimulus level demonstrated that (1) generation of internal noise is not isolated to the microphone, (2) noise may be dependent on input level, and (3) certain adaptive features may contribute to internal noise. Quantifying internal noise as the variance of the output measures allows for noise to be measured under real-world processing conditions, accounts for all sources of noise, and is predictive of internal noise audibility. PMID:20370034

Internal validation of the GlobalFiler™ Express PCR Amplification Kit for the direct amplification of reference DNA samples on a high-throughput automated workflow.

PubMed

Flores, Shahida; Sun, Jie; King, Jonathan; Budowle, Bruce

2014-05-01

The GlobalFiler™ Express PCR Amplification Kit uses 6-dye fluorescent chemistry to enable multiplexing of 21 autosomal STRs, 1 Y-STR, 1 Y-indel and the sex-determining marker amelogenin. The kit is specifically designed for processing reference DNA samples in a high throughput manner. Validation studies were conducted to assess the performance and define the limitations of this direct amplification kit for typing blood and buccal reference DNA samples on various punchable collection media. Studies included thermal cycling sensitivity, reproducibility, precision, sensitivity of detection, minimum detection threshold, system contamination, stochastic threshold and concordance. Results showed that optimal amplification and injection parameters for a 1.2mm punch from blood and buccal samples were 27 and 28 cycles, respectively, combined with a 12s injection on an ABI 3500xL Genetic Analyzer. Minimum detection thresholds were set at 100 and 120RFUs for 27 and 28 cycles, respectively, and it was suggested that data from positive amplification controls provided a better threshold representation. Stochastic thresholds were set at 250 and 400RFUs for 27 and 28 cycles, respectively, as stochastic effects increased with cycle number. The minimum amount of input DNA resulting in a full profile was 0.5ng, however, the optimum range determined was 2.5-10ng. Profile quality from the GlobalFiler™ Express Kit and the previously validated AmpFlSTR(®) Identifiler(®) Direct Kit was comparable. The validation data support that reliable DNA typing results from reference DNA samples can be obtained using the GlobalFiler™ Express PCR Amplification Kit. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Natural genomic amplification of cholinesterase genes in animals.

PubMed

Chatonnet, Arnaud; Lenfant, Nicolas; Marchot, Pascale; Selkirk, Murray E

2017-08-01

Tight control of the concentration of acetylcholine at cholinergic synapses requires precise regulation of the number and state of the acetylcholine receptors, and of the synthesis and degradation of the neurotransmitter. In particular, the cholinesterase activity has to be controlled exquisitely. In the genome of the first experimental models used (man, mouse, zebrafish and drosophila), there are only one or two genes coding for cholinesterases, whereas there are more genes for their closest relatives the carboxylesterases. Natural amplification of cholinesterase genes was first found to occur in some cancer cells and in insect species subjected to evolutionary pressure by insecticides. Analysis of the complete genome sequences of numerous representatives of the various metazoan phyla show that moderate amplification of cholinesterase genes is not uncommon in molluscs, echinoderms, hemichordates, prochordates or lepidosauria. Amplification of acetylcholinesterase genes is also a feature of parasitic nematodes or ticks. In these parasites, over-production of cholinesterase-like proteins in secreted products and the saliva are presumed to have effector roles related to host infection. These amplification events raise questions about the role of the amplified gene products, and the adaptation processes necessary to preserve efficient cholinergic transmission. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms. © 2017 International Society for Neurochemistry.

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.

PubMed

Kimura, Yasumasa; Soma, Takahiro; Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J L; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays

PubMed Central

Kasahara, Naoko; Delobel, Diane; Hanami, Takeshi; Tanaka, Yuki; de Hoon, Michiel J. L.; Hayashizaki, Yoshihide; Usui, Kengo; Harbers, Matthias

2016-01-01

Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download. PMID:26863543

Development of an amorphous selenium based photoconductor and its application in a high-sensitivity photodetector (Conference Presentation)

NASA Astrophysics Data System (ADS)

Masuzawa, Tomoaki; Ebisudani, Taishi; Ochiai, Jun; Saito, Ichitaro; Yamada, Takatoshi; Chua, Daniel H. C.; Mimura, Hidenori; Okano, Ken

2016-09-01

Although present imaging devices are mostly silicon-based devices such as CMOS and CCD, these devices are reaching their sensitivity limit due to the band gap of silicon. Amorphous selenium (a-Se) is a promising candidate for high- sensitivity photo imaging devices, because of its low thermal noise, high spatial resolution, as well as adaptability to wide-area deposition. In addition, internal signal amplification is reported on a-Se based photodetectors, which enables a photodetector having effective quantum efficiency over 100 % against visible light. Since a-Se has sensitivity to UV and soft X-rays, the reported internal signal amplification should be applicable to UV and X-ray detection. However, application of the internal signal amplification required high voltage, which caused unexpected breakdown at the contact or thin-film transistor-based signal read-out. For this reason, vacuum devices having electron-beam read-out is proposed. The advantages of vacuum-type devices are vacuum insulation and its extremely low dark current. In this study, we present recent progresses in developing a-Se based photoconductive films and photodetector using nitrogen-doped diamond electron beam source as signal read-out. A novel electrochemical method is used to dope impurities into a-Se, turning the material from weak p-type to n-type. A p-n junction is formed within a-Se photoconductive film, which has increased the sensitivity of a-Se based photodetector. Our result suggests a possibility of high sensitivity photodetector that can potentially break the limit of silicon-based devices.

Development of a recombinase polymerase amplification assay for Vibrio parahaemolyticus detection with an internal amplification control.

PubMed

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.

Direct detection of MeV-scale dark matter utilizing germanium internal amplification for the charge created by the ionization of impurities

NASA Astrophysics Data System (ADS)

Mei, D.-M.; Wang, G.-J.; Mei, H.; Yang, G.; Liu, J.; Wagner, M.; Panth, R.; Kooi, K.; Yang, Y.-Y.; Wei, W.-Z.

2018-03-01

Light, MeV-scale dark matter (DM) is an exciting DM candidate that is undetectable by current experiments. A germanium (Ge) detector utilizing internal charge amplification for the charge carriers created by the ionization of impurities is a promising new technology with experimental sensitivity for detecting MeV-scale DM. We analyze the physics mechanisms of the signal formation, charge creation, charge internal amplification, and the projected sensitivity for directly detecting MeV-scale DM particles. We present a design for a novel Ge detector at helium temperature (˜ 4 K) enabling ionization of impurities from DM impacts. With large localized E-fields, the ionized excitations can be accelerated to kinetic energies larger than the Ge bandgap at which point they can create additional electron-hole pairs, producing intrinsic amplification to achieve an ultra-low energy threshold of ˜ 0.1 eV for detecting low-mass DM particles in the MeV scale. Correspondingly, such a Ge detector with 1 kg-year exposure will have high sensitivity to a DM-nucleon cross section of ˜ 5 × 10^{-45} cm2 at a DM mass of ˜ 10 MeV/c2 and a DM-electron cross section of ˜ 5 × 10^{-46} cm2 at a DM mass of ˜ 1 MeV/c^2.

Performance evaluation of radiation sensors with internal signal amplification based on the BJT effect

NASA Astrophysics Data System (ADS)

Bosisio, Luciano; Batignani, Giovanni; Bettarini, Stefano; Boscardin, Maurizio; Dalla Betta, Gian-Franco; Giacomini, Gabriele; Piemonte, Claudio; Verzellesi, Giovanni; Zorzi, Nicola

2006-11-01

Prototypes of ionizing radiation detectors with internal signal amplification based on the bipolar transistor effect have been fabricated at ITC-irst (Trento, Italy). Results from the electrical characterization and preliminary functional tests of the devices have been previously reported. Here, we present a more detailed investigation of the performance of this type of detector, with particular attention to their noise and rate limits. Measurements of the signal waveform and of the gain versus frequency dependence are performed by illuminating the devices with, respectively, pulsed or sinusoidally modulated IR light. Pulse height spectra of X-rays from an Am241 source have been taken with very simple front-end electronics (an LF351 operational amplifier) or by directly reading with an oscilloscope the voltage drop across a load resistor connected to the emitter. An equivalent noise charge (referred to input) of 380 electrons r.m.s. has been obtained with the first setup for a small device, with an active area of 0.5×0.5 mm2 and a depleted thickness of 0.6 mm. The corresponding power dissipation in the BJT was 17 μW. The performance limitations of the devices are discussed.

The Development and Use of Internal Amplification Controls (IACs) with DNA Profiling Kits for Forensic DNA Analysis.

PubMed

Zahra, Nathalie; Goodwin, William

2016-01-01

Biological samples recovered for forensic investigations are often degraded and/or have low amounts of DNA; in addition, in some instances the samples may be contaminated with chemicals that can act as PCR inhibitors. As a consequence this can make interpretation of the results challenging with the possibility of having partial profiles and false negative results. Because of the impact of DNA analysis on forensic investigations, it is important to monitor the process of DNA profiling, in particular the amplification reaction. In this chapter we describe a method for the in-house generation and use of internal amplification controls (IACs) with DNA profiling kits to monitor the success of the PCR proces. In the example we show the use of the SGM Plus® kit. These controls can also be used to aid the interpretation of the DNA profile.

The Prevalence of Human Papilloma Virus in Esophageal Squamous Cell Carcinoma

PubMed Central

Noori, Sadat; Monabati, Ahmad; Ghaderi, Abbasali

2012-01-01

Background: Carcinomas of esophagus, mostly squamous cell carcinomas, occur throughout the world. There are a number of suspected genetic or environmental etiologies. Human papilloma virus (HPV) is said to be a major etiology in areas with high incidence of esophageal carcinoma, while it is hardly detectable in low incidence regions. This study was designed to evaluate the prevalence of HPV in esophageal squamous cell carcinoma (ESCC) cases diagnosed in Pathology Department, Medical School, Shiraz University of Medical Sciences. Methods: DNA material for PCR amplification of HPV genome was extracted from formalin-fixed paraffin-embedded tissue blocks of 92 cases of ESCC, diagnosed during 20 years from 1982 to 2002. Polymerase chain reaction was performed for amplification and detection of common HPV and type specific HPV-16 and HPV-18 genomic sequences in the presence of positive control (HPV-18 and HPV positive biopsies of uterine exocervix) and additional internal controls i.e. beta-globin and cytotoxic T lymphocyte antigen 4 (CTLA4). Result: Good amplification of positive control and internal controls was observed. However, no amplification of HPV genome was observed. Conclusion: There is no association between HPV infection and the development of esophageal squamous cell carcinoma in the cases evaluated. PMID:23115442

Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for Campylobacter... of high-processivity polymerase with novel internal amplification controls for rapid and specific detection.

USDA-ARS?s Scientific Manuscript database

Although Campylobacter is an important food-borne human pathogen, there remains a lack of molecular diagnostic assays that are simple to use, cost-effective, and provide rapid results in research, clinical, or regulatory laboratories. Of the numerous Campylobacter assays that do exist, to our knowl...

ESR1 gene amplification in endometrial carcinomas: a clinicopathological analysis.

PubMed

Rahman, Mohammed Tanjimur; Nakayama, Kentaro; Rahman, Munmun; Ishikawa, Masako; Katagiri, Hiroshi; Katagiri, Atsuko; Ishibashi, Tomoka; Sato, Emi; Iida, Kouji; Ishikawa, Noriyuki; Nakayama, Naomi; Miyazaki, Kohji

2013-09-01

This study investigated the clinicopathological significance of estrogen receptor 1 (ESR1) gene amplification and its relationship to phosphatase and tensin homolog (PTEN), human epidermal growth factor receptor 2 (HER2), MutL homolog 1 (MLH1), p53, and AT rich interactive domain 1A (ARID1A) expression in endometrial carcinomas. ESR1 amplification and expression were assessed by fluorescence in situ hybridization and immunohistochemistry. Clinical data were collected by retrospective chart review. ESR1 amplification was identified in 13 out of 111 (11.7%) endometrial carcinomas. No significant association was observed between ESR1 amplification and International Federation of Gynecology and Obstetrics (FIGO) stage (p=0.17), histological grade (p=0.35), lymph node metastasis (p=0.51), or deep myometrial invasion (p=0.46). ESR1 amplification was independent of PTEN, p53, HER2, MLH1, and ARID1A protein expression. Patients without estrogen receptor (ER) or progesterone receptor (PR) expression had shorter progression-free and overall survival than those with ER or PR expression (p<0.01). ESR1 amplification is independent of known clinicopathological factors related to poor prognosis and PTEN, p53, HER2, MLH1, and ARID1A protein expression, suggesting ESR1 amplification may be an early event in endometrial carcinoma development.

Up-regulation of the G3PDH 'housekeeping' gene by estrogen.

PubMed

Galal, Nadia; El-Beialy, Waleed; Deyama, Yoshiaki; Yoshimura, Yoshitaka; Tei, Kanchu; Suzuki, Kuniaki; Totsuka, Yasunori

2010-01-01

Proteomic and genomic studies commonly involve the assessment of mRNA levels using reverse transcription-polymerase chain reaction (PCR) and real-time quantitative PCR. An internal standard RNA is fundamentally analyzed along with the investigated mRNA to document the specificity of the effect(s) on mRNA and to correct for inter-sample variations. In our studies implementing estrogen treatments on different cell lines, we initially used glyceraldehyde-3-phosphate dehydrogenase (G3PDH) as an internal standard. However, the results of PCR amplification demonstrated that 17β-estradiol enhanced the expression of the G3PDH gene, rendering it impossible to use G3PDH as an unbiased comparative control.

Identification of root rot fungi in nursery seedlings by nested multiplex PCR.

PubMed Central

Hamelin, R C; Bérubé, P; Gignac, M; Bourassa, M

1996-01-01

The internal transcribed spacer (ITS) of the ribosomal DNA (rDNA) subunit repeat was sequenced in 12 isolates of Cylindrocladium floridanum and 11 isolates of Cylindrocarpon destructans. Sequences were aligned and compared with ITS sequences of other fungi in GenBank. Some intraspecific variability was present within our collections of C. destructans but not in C. floridanum. Three ITS variants were identified within C. destructans, but there was no apparent association between ITS variants and host or geographic origin. Two internal primers were synthesized for the specific amplification of portions of the ITS for C. floridanum, and two primers were designed to amplify all three variants of C. destructans. The species-specific primers amplified PCR products of the expected length when tested with cultures of C, destructans and C. floridanum from white spruce, black spruce, Norway spruce, red spruce, jack pine, red pine, and black walnut from eight nurseries and three plantations in Quebec. No amplification resulted from PCR reactions on fungal DNA from 26 common contaminants of conifer roots. For amplifications directly from infected tissues, a nested primer PCR using two rounds of amplification was combined with multiplex PCR approach resulting in the amplification of two different species-specific PCR fragments in the same reaction. First, the entire ITS was amplified with one universal primer and a second primer specific to fungi; a second round of amplification was carried out with species-specific primers that amplified a 400-bp PCR product from C. destructans and a 328-bp product from C. floridanum. The species-specific fragments were amplified directly from infected roots from which one or the two fungi had been isolated. PMID:8899993

The focusing effect in backward Raman amplification in plasma

NASA Astrophysics Data System (ADS)

Li, Zhaoli; Peng, Hao; Zuo, Yanlei; Su, Jingxin; Yang, Suhui

2018-04-01

In this paper, the focusing effect on backward Raman amplification in plasma is investigated. A fluid model, used to simulate the backward Raman amplification and including the relativistic, ponderomotive, and thermal self-focusing and the mutual-focusing effect simultaneously, is proposed and investigated. The focusing effect is shown to severely distort the profile of the seed when the seed intensity was as high as 10 17 W/cm2. Reducing the plasma density can relax the focusing effect, but at the cost of decreasing the amplification efficiency. Changing the profile of the seed has a limited effect on mitigating the focusing effect. A Gaussian profile of the pump and a defocusing shape of the plasma density seem to be an effective way to mitigate the focusing effect without decreasing the amplification efficiency.

Real-time isothermal RNA amplification of toxic marine microalgae using preserved reagents on an integrated microfluidic platform.

PubMed

Tsaloglou, Maria-Nefeli; Laouenan, Florian; Loukas, Christos-Moritz; Monsalve, Lisandro Gabriel; Thanner, Christine; Morgan, Hywel; Ruano-López, Jesus M; Mowlem, Matthew C

2013-01-21

Quantitation of specific RNA sequences is a useful technique in marine biology that can elucidate cell abundance, speciation and viability, especially for early detection of harmful algal blooms. We are thus developing an integrated microfluidic system for cell concentration and lysis, RNA extraction/purification and quantitative RNA detection for environmental applications. The portable system is based on a microfluidic cartridge, or "lab-card", using a low-cost injection moulded device, with a laminated lid. Here we present real-time isothermal RNA amplification using reagent master-mixes preserved on-chip in a gel at 4 °C for up to eight months. We demonstrate quantitation by reference to an internal control in a competitive assay with 500 cell equivalents of the toxic microalga Karenia brevis. Annealing of primers, amplification at 41 °C and real-time fluorescence detection of the internal control and target using sequence-specific molecular beacons were all performed on-chip.

Laser light triggers increased Raman amplification in the regime of nonlinear Landau damping

PubMed Central

Depierreux, S.; Yahia, V.; Goyon, C.; Loisel, G.; Masson-Laborde, P. -E.; Borisenko, N.; Orekhov, A.; Rosmej, O.; Rienecker, T.; Labaune, C.

2014-01-01

Stimulated Raman backscattering (SRS) has many unwanted effects in megajoule-scale inertially confined fusion (ICF) plasmas. Moreover, attempts to harness SRS to amplify short laser pulses through backward Raman amplification have achieved limited success. In high-temperature fusion plasmas, SRS usually occurs in a kinetic regime where the nonlinear response of the Langmuir wave to the laser drive and its host of complicating factors make it difficult to predict the degree of amplification that can be achieved under given experimental conditions. Here we present experimental evidence of reduced Landau damping with increasing Langmuir wave amplitude and determine its effects on Raman amplification. The threshold for trapping effects to influence the amplification is shown to be very low. Above threshold, the complex SRS dynamics results in increased amplification factors, which partly explains previous ICF experiments. These insights could aid the development of more efficient backward Raman amplification schemes in this regime. PMID:24938756

Development and evaluation of an in-house single step loop-mediated isothermal amplification (SS-LAMP) assay for the detection of Mycobacterium tuberculosis complex in sputum samples from Moroccan patients.

PubMed

Bentaleb, El Mehdi; Abid, Mohammed; El Messaoudi, My Driss; Lakssir, Brahim; Ressami, El Mostafa; Amzazi, Saaïd; Sefrioui, Hassan; Ait Benhassou, Hassan

2016-09-27

Tuberculosis (TB) is a major global health problem and remains the leading cause of morbidity and mortality in developing countries. Routinely used TB diagnostic methods, in most endemic areas, are time-consuming, often less-sensitive, expensive and inaccessible to most patients. Therefore, there is an urgent need for the development of early, easy to use and effective diagnosis tools of TB, which can be effectively integrated into resource limited settings, to anticipate the early treatment and limit further spread of the disease. Over the last decade, Loop-mediated isothermal amplification (LAMP) assays have become a powerful tool for rapid diagnosis of infectious diseases because of the simplicity of device requirements. Indeed, LAMP is a simple, quick and cost effective Isothermal Nucleic Acid Amplification diagnostic test (INAAT) that has the potential to be used in TB endemic settings of resource-poor countries. In the present study, we have developed a simple and rapid TB molecular diagnostic test using a Single-Step Loop-mediated isothermal DNA amplification (SS-LAMP) method for the detection of Mycobacterium tuberculosis complex (MTBC) strains, with a simplified sample preparation procedure, eliminating DNA extraction prior to LAMP amplification, DNA initial denaturation and enzymatic inactivation steps during the amplification process. To perform our in-house SS-LAMP assay, a set of six specific primers was specifically designed to recognize eight distinct regions on the MTBC species-specific repetitive insertion sequence 6110 (IS6110). The amplification of the targeted DNA was carried out under isothermal conditions at 65 °C within 1 h. Our protocol was firstly optimized using 60 of confirmed MTBC isolates and a recombinant pGEMeasy-IS6110 vector for sensitivity testing. Thereafter, the assay was evaluated on liquefied sputum specimens collected from 157 Moroccan patients suspected of having TB. Our SS-LAMP developed assay was able to detect MTBC DNA directly from liquefied sputum samples without any prior DNA extraction, denaturation nor the final enzymatic inactivation step. When compared to routinely used Löwenstein Jensen (LJ) Culture method, our SS-LAMP assay is rapid and showed specificity and sensitivity of 99.14 % and 82.93 % respectively which are within the international standards. In addition, the limit of detection of our assay was found to be as little as 10 copies of bacterial DNA. To our knowledge, this is the first study using a single step LAMP (SS-LAMP) procedure as a rapid, easy to perform and cost effective testing for TB early detection. This innovative assay could be suitable for low-income countries with restricted health equipment facilities.

Discovery of a photoresponse amplification mechanism in compensated PN junctions

NASA Astrophysics Data System (ADS)

Zhou, Yuchun; Liu, Yu-Hsin; Rahman, Samia N.; Hall, David; Sham, L. J.; Lo, Yu-Hwa

2015-01-01

We report the experimental evidence of uncovering a photoresponse amplification mechanism in heavily doped, partially compensated silicon p-n junctions under very low bias voltage. We show that the observed photocurrent gain occurs at a bias that is more than an order of magnitude below the threshold voltage for conventional impact ionization. Moreover, contrary to the case of avalanche detectors and p-i-n diodes, the amplified photoresponse is enhanced rather than suppressed with increasing temperature. These distinctive characteristics lead us to hypothesize that the inelastic scattering between energetic electrons (holes) and the ionized impurities in the depletion and charge neutral regions of the p-n junction in a cyclic manner plays a significant role in the amplification process. Such an internal signal amplification mechanism, which occurs at much lower bias than impact ionization and favors room temperature over cryogenic temperature, makes it promising for practical device applications.

Detection of genetically modified organisms (GMOs) using isothermal amplification of target DNA sequences.

PubMed

Lee, David; La Mura, Maurizio; Allnutt, Theo R; Powell, Wayne

2009-02-02

The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR). Here we have applied the loop-mediated isothermal amplification (LAMP) method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene) junctions. We have tested the specificity and sensitivity of the technique for use in GMO studies. Results show that detection of 0.01% GMO in equivalent background DNA was possible and dilutions of template suggest that detection from single copies of the template may be possible using LAMP. This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection.

Discovery of a photoresponse amplification mechanism in compensated PN junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Yuchun; Rahman, Samia N.; Hall, David

2015-01-19

We report the experimental evidence of uncovering a photoresponse amplification mechanism in heavily doped, partially compensated silicon p-n junctions under very low bias voltage. We show that the observed photocurrent gain occurs at a bias that is more than an order of magnitude below the threshold voltage for conventional impact ionization. Moreover, contrary to the case of avalanche detectors and p-i-n diodes, the amplified photoresponse is enhanced rather than suppressed with increasing temperature. These distinctive characteristics lead us to hypothesize that the inelastic scattering between energetic electrons (holes) and the ionized impurities in the depletion and charge neutral regions ofmore » the p-n junction in a cyclic manner plays a significant role in the amplification process. Such an internal signal amplification mechanism, which occurs at much lower bias than impact ionization and favors room temperature over cryogenic temperature, makes it promising for practical device applications.« less

An integrated microfluidic sensor for real-time detection of RNA in seawater using preserved reagents

NASA Astrophysics Data System (ADS)

Tsaloglou, M.-N.; Loukas, C. M.; Ruano-López, J. M.; Morgan, H.; Mowlem, M. C.

2012-04-01

Quantitation of RNA sequences coding either for key metabolic proteins or highly conserved ribosomal subunits can provide insight on cell abundance, speciation and viability. Nucleic sequence-based amplification (NASBA) is an isothermal alternative to traditional nucleic acid amplification methods, such as quantitative PCR. We present here an integrated microfluidic sensor for cell concentration and lysis, RNA extraction/purification and quantitative RNA detection for environmental applications. The portable system uses pre-loaded reagents, stored as a gel on a disposable microfluidic cartridge, which is manufactured using low-cost injection moulding. The NASBA reaction is monitored real-time using a bespoke control unit which includes: an external fluorescence detector, three peristaltic micro-pumps, two heaters and temperature sensors, a battery, seven pin actuated micro-motors (or valve actuators), and an automatic cartridge insertion mechanism. The system has USB connectivity and none of the expensive components require replacing between reactions. Long-term storage of reagents is critically important for any diagnostic tool that will be used in the field, whether for medical or environmental analysis and has not been previously demonstrated for NASBA reagents on-chip. We have shown effective amplification, for as little as 500 cells of the toxic microalga Karenia brevis using reagents which had been preserved as a gel for 45 days. This is the first reported real-time isothermal RNA amplification using with on-chip preservation. Annealing of primers, amplification at 41 °C and real-time fluorescence detection using, also for the first time, an internal control and sequence-specific molecular beacons was all performed on our microfluidic sensor. Our results show excellent promise as a future quantitative tool of in situ phytoplankton analysis and other environmental applications, where long-term reagent storage and low power consumption is essential.

Loop-Mediated Isothermal Amplification for Detection of Endogenous Sad1 Gene in Cotton: An Internal Control for Rapid Onsite GMO Testing.

PubMed

Singh, Monika; Bhoge, Rajesh K; Randhawa, Gurinderjit

2018-04-20

Background : Confirming the integrity of seed samples in powdered form is important priorto conducting a genetically modified organism (GMO) test. Rapid onsite methods may provide a technological solution to check for genetically modified (GM) events at ports of entry. In India, Bt cotton is the commercialized GM crop with four approved GM events; however, 59 GM events have been approved globally. GMO screening is required to test for authorized GM events. The identity and amplifiability of test samples could be ensured first by employing endogenous genes as an internal control. Objective : A rapid onsite detection method was developed for an endogenous reference gene, stearoyl acyl carrier protein desaturase ( Sad1 ) of cotton, employing visual and real-time loop-mediated isothermal amplification (LAMP). Methods : The assays were performed at a constant temperature of 63°C for 30 min for visual LAMP and 62ºC for 40 min for real-time LAMP. Positive amplification was visualized as a change in color from orange to green on addition of SYBR ® Green or detected as real-time amplification curves. Results : Specificity of LAMP assays was confirmed using a set of 10 samples. LOD for visual LAMP was up to 0.1%, detecting 40 target copies, and for real-time LAMP up to 0.05%, detecting 20 target copies. Conclusions : The developed methods could be utilized to confirm the integrity of seed powder prior to conducting a GMO test for specific GM events of cotton. Highlights : LAMP assays for the endogenous Sad1 gene of cotton have been developed to be used as an internal control for onsite GMO testing in cotton.

S-band optical amplification by an internally generated pump in thulium ytterbium codoped fiber.

PubMed

Chang, Jun; Wang, Qing-Pu; Zhang, Xingyu; Liu, Zhejin; Liu, Zhaojun; Peng, Gang-Ding

2005-05-30

We propose a novel scheme in which Yb3+ codoping and a laser cavity are introduced in Tm3+ doped fiber to achieve efficient S-band optical amplification with a 980 nm pump source. This scheme makes it possible for conventional 980 nm pump sources for Er3+ doped fiber amplifiers to be used for S-band Tm3+ doped fiber amplifiers (TDFAs). By introducing a laser cavity into an amplifier, an internally generated pump from Yb3+ at a desirable wavelength for pumping Tm3+ could be produced. We establish and analyze, for the first time to our knowledge, a new theoretical model that takes into consideration both the internal lasing operation inside the optical amplification process and the energy transfer between the Tm3+ and the Yb3+ ions in TDFAs. Various situations such as Tm3+ doping concentration and cavity reflectivity have been investigated. The results show that high optical gain and high pump efficiency can be achieved by use of 980 nm sources. With a laser cavity of 1050 nm in Tm3+ and Yb3+ codoped fiber, for example, it is possible to achieve high optical gain of greater than 20 dB, a noise figure of approximately 5 dB in the wavelength range from 1450 to 1480 nm with a 0.3 W power at 980 nm pump source.

Diagnostic application of polymerase chain reaction for detection of Ehrlichia risticii in equine monocytic ehrlichiosis (Potomac horse fever).

PubMed

Biswas, B; Mukherjee, D; Mattingly-Napier, B L; Dutta, S K

1991-10-01

Genomic amplification by the polymerase chain reaction (PCR) was used to identify a unique genomic sequence of Ehrlichia risticii directly in DNA isolated from peripheral-blood buffy coat cells of E. risticii-infected horses (Potomac horse fever) and from infected cell cultures. A specific primer pair, selected from a cloned, species-specific, 1-kb DNA fragment of the E. risticii genome as a template, was used for the amplification of the target DNA of 247 bp. The optimal number of 40 PCR cycles, determined by analyzing an amplification profile obtained with a constant Taq polymerase concentration, was used to achieve maximum amplification of the E. risticii DNA segment. Efficient amplification of target DNA was achieved with specimens processed by either the phenol extraction or rapid lysis method. The specificity of the amplified DNA product was confirmed by the proper size (247 bp) and appropriate restriction enzyme cleavage pattern of the amplified target DNA, as well as by the specific hybridization signal obtained by using a PCR-amplified 185-bp internal DNA probe. A 10(5)- to 10(6)-fold amplification of target DNA, which allowed detection of E. risticii from as few as two to three infected cells in culture and from a very small volume of buffy coat cells from infected horses, was achieved. This PCR amplification procedure was found to be highly specific and sensitive for the detection of E. risticii for the study of Potomac horse fever.

Construction of Genetically Engineered Streptococcus gordonii Strains to Provide Control in QPCR Assays for Assessing Microbiological Quality in Recreational Water.

EPA Science Inventory

Quantitative PCR (QPCR) methods for beach monitoring by estimating abundance of Enterococcus spp. in recreational waters use internal, positive controls which address only the amplification of target DNA. In this study two internal, positive controls were developed to control for...

Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant-Associated Fungi.

PubMed

Ikenaga, Makoto; Tabuchi, Masakazu; Kawauchi, Tomohiro; Sakai, Masao

2016-09-29

The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant-associated fungi due to the similar homologies of sequences in primer-annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3' end of the primer-binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant-associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant-associated fungi.

Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant–Associated Fungi

PubMed Central

Ikenaga, Makoto; Tabuchi, Masakazu; Kawauchi, Tomohiro; Sakai, Masao

2016-01-01

The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant–associated fungi due to the similar homologies of sequences in primer–annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3′ end of the primer–binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant–associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant–associated fungi. PMID:27600711

Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence

PubMed Central

Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

2016-01-01

Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided. PMID:27146605

Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence.

PubMed

Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

2016-05-05

Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided.

Surface-mode-assisted amplification of radiative heat transfer between nanoparticles

NASA Astrophysics Data System (ADS)

Messina, Riccardo; Biehs, Svend-Age; Ben-Abdallah, Philippe

2018-04-01

We show that the radiative heat flux between two nanoparticles can be significantly amplified when they are placed in proximity of a planar substrate supporting a surface resonance. The amplification factor goes beyond two orders of magnitude in the case of dielectric nanoparticles, whereas it is lower in the case of metallic nanoparticles. We analyze how this effect depends on the frequency and on the particle-surface distance by clearly identifying the signature of the surface mode producing the amplification. Finally, we show how the presence of a graphene sheet on top of the substrate can modify the effect by making an amplification of two orders of magnitude possible also in the case of metallic nanoparticles. This long-range amplification effect should play an important role in the thermal relaxation dynamics of nanoparticle networks.

The SUMO Pathway Is Developmentally Regulated and Required for Programmed DNA Elimination in Paramecium tetraurelia† ‡

PubMed Central

Matsuda, Atsushi; Forney, James D.

2006-01-01

Extensive genome-wide remodeling occurs during the formation of the somatic macronuclei from the germ line micronuclei in ciliated protozoa. This process is limited to sexual reproduction and includes DNA amplification, chromosome fragmentation, and the elimination of internal segments of DNA. Our efforts to define the pathways regulating these events revealed a gene encoding a homologue of ubiquitin activating enzyme 2 (UBA2) that is upregulated at the onset of macronuclear development in Paramecium tetraurelia. Uba2 enzymes are known to activate the protein called small ubiquitin-related modifier (SUMO) that is covalently attached to target proteins. Consistent with this relationship, Northern analysis showed increased abundance of SUMO transcripts during sexual reproduction in Paramecium. RNA interference (RNAi) against UBA2 or SUMO during vegetative growth had little effect on cell survival or fission rates. In contrast, RNAi of mating cells resulted in failure to form a functional macronucleus. Despite normal amplification of the genome, excision of internal eliminated sequences was completely blocked. Additional experiments showed that the homologous UBA2 and SUMO genes in Tetrahymena thermophila are also upregulated during conjugation. These results provide evidence for the developmental regulation of the SUMO pathway in ciliates and suggest a key role for the pathway in controlling genome remodeling. PMID:16682458

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

PubMed

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.

Amplification of hofmeister effect by alcohols.

PubMed

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 < ethanol < 1-propanol < 2-propanol for the monohydric alcohols and following the series d-sorbitol ≈ xylitol ≈ meso-erythritol < glycerol < ethylene glycol < methanol for the polyhydric 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.

Quantitative PCR Method for Diagnosis of Citrus Bacterial Canker†

PubMed Central

Cubero, J.; Graham, J. H.; Gottwald, T. R.

2001-01-01

For diagnosis of citrus bacterial canker by PCR, an internal standard is employed to ensure the quality of the DNA extraction and that proper requisites exist for the amplification reaction. The ratio of PCR products from the internal standard and bacterial target is used to estimate the initial bacterial concentration in citrus tissues with lesions. PMID:11375206

Genomic Sequence of the WHO International Standard for Hepatitis A Virus RNA.

PubMed

Jenkins, Adrian; Minhas, Rehan; Morris, Clare; Berry, Neil

2018-05-10

The World Health Organization (WHO) international standard for hepatitis A virus (HAV) RNA nucleic acid assays was characterized by complete genome sequencing. The entire coding sequence and noncoding regions were assigned HAV genotype IB. This information will aid the design, development, and evaluation of HAV RNA amplification assays. Copyright © 2018 Jenkins et al.

The effect of voice amplification on occupational vocal dose in elementary school teachers.

PubMed

Gaskill, Christopher S; O'Brien, Shenendoah G; Tinter, Sara R

2012-09-01

Two elementary school teachers, one with and one without a history of vocal complaints, wore a vocal dosimeter all day at school for a 3-week period. In the second week, each teacher wore a portable voice amplifier. Each teacher showed a reduction in vocal intensity during the week of amplification, with a larger effect for the teacher with vocal difficulties. This teacher also showed a decrease in hourly vocal fold distance dose as measured by the dosimeter despite incurring longer phonation times. Fundamental frequency and vocal fold cycle dose did not appear to be affected by the use of amplification during the teaching day. Both teachers showed evidence of a possible moderate effect of adjusting vocal intensity in the week after amplification, possibly as a means to recalibrate their perceived vocal loudness. This study demonstrates the usefulness of both vocal dosimetry and amplification in monitoring and modifying vocal dose in an occupational setting and reinforces previous data suggesting the effectiveness of amplification in reducing the vocal load in schoolteachers. Implications of the data for future research regarding prevention and treatment of occupational voice disorders are discussed. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Use of Bacteriophage MS2 as an Internal Control in Viral Reverse Transcription-PCR Assays

PubMed Central

Dreier, Jens; Störmer, Melanie; Kleesiek, Knut

2005-01-01

Diagnostic systems based on reverse transcription (RT)-PCR are widely used for the detection of viral genomes in different human specimens. The application of internal controls (IC) to monitor each step of nucleic acid amplification is necessary to prevent false-negative results due to inhibition or human error. In this study, we designed various real-time RT-PCRs utilizing the coliphage MS2 replicase gene, which differ in detection format, amplicon size, and efficiency of amplification. These noncompetitive IC assays, using TaqMan, hybridization probe, or duplex scorpion probe techniques, were tested on the LightCycler and Rotorgene systems. In our approach, clinical specimens were spiked with the control virus to monitor the efficiency of extraction, reverse transcription, and amplification steps. The MS2 RT-PCR assays were applied for internal control when using a second target hepatitis C virus RNA in duplex PCR in blood donor screening. The 95% detection limit was calculated by probit analysis to 44.9 copies per PCR (range, 38.4 to 73.4). As demonstrated routinely, application of MS2 IC assays exhibits low variability and can be applied in various RT-PCR assays. MS2 phage lysates were obtained under standard laboratory conditions. The quantification of phage and template RNA was performed by plating assays to determine PFU or via real-time RT-PCR. High stability of the MS2 phage preparations stored at −20°C, 4°C, and room temperature was demonstrated. PMID:16145106

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.

PubMed

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).

Estimation of the interior parameters from Mars nutations and from Doppler measurements

NASA Astrophysics Data System (ADS)

Yseboodt, M.; Rivoldini, A.; Le Maistre, S.; Dehant, V. M. A.

2017-12-01

The presence of a liquid core inside Mars changes the nutations: the nutation amplitudes can be resonantly amplified because of a free mode, called the free core nutation (FCN).We quantify how the internal structure, in particular the size of the core, affects the nutation amplifications and the Doppler observable between a Martian lander and the Earth.Present day core size estimates suggest that the effect is the largest on the prograde semi-annual and retrograde ter-annual nutation.We solve the inverse problem assuming a given precision on the nutation amplifications provided by an extensive set of geodesy measurements and we estimate the precision on the core properties. Such measurements will be available in the near future thanks to the geodesy experiments RISE (InSight mission) and LaRa (ExoMars mission).We find that the precision on the core properties is very dependent on the proximity of the FCN period to the ter-annual forcing (-229 days) and the assumed a priori precision on the nutations.

Backward Raman amplification in the long-wavelength infrared

NASA Astrophysics Data System (ADS)

Johnson, L. A.; Gordon, D. F.; Palastro, J. P.; Hafizi, B.

2017-03-01

The wealth of work in backward Raman amplification in plasma has focused on the extreme intensity limit; however, backward Raman amplification may also provide an effective and practical mechanism for generating intense, broad bandwidth, long-wavelength infrared radiation (LWIR). An electromagnetic simulation coupled with a relativistic cold fluid plasma model is used to demonstrate the generation of picosecond pulses at a wavelength of 10 μm with terawatt powers through backward Raman amplification. The effects of collisional damping, Landau damping, pump depletion, and wave breaking are examined, as well as the resulting design considerations for an LWIR Raman amplifier.

Drastic disorder-induced reduction of signal amplification in scale-free networks.

PubMed

Chacón, Ricardo; Martínez, Pedro J

2015-07-01

Understanding information transmission across a network is a fundamental task for controlling and manipulating both biological and manmade information-processing systems. Here we show how topological resonant-like amplification effects in scale-free networks of signaling devices are drastically reduced when phase disorder in the external signals is considered. This is demonstrated theoretically by means of a starlike network of overdamped bistable systems, and confirmed numerically by simulations of scale-free networks of such systems. The taming effect of the phase disorder is found to be sensitive to the amplification's strength, while the topology-induced amplification mechanism is robust against this kind of quenched disorder in the sense that it does not significantly change the values of the coupling strength where amplification is maximum in its absence.

Effects of sound-field frequency modulation amplification on reducing teachers' sound pressure level in the classroom.

PubMed

Sapienza, C M; Crandell, C C; Curtis, B

1999-09-01

Voice problems are a frequent difficulty that teachers experience. Common complaints by teachers include vocal fatigue and hoarseness. One possible explanation for these symptoms is prolonged elevations in vocal loudness within the classroom. This investigation examined the effectiveness of sound-field frequency modulation (FM) amplification on reducing the sound pressure level (SPL) of the teacher's voice during classroom instruction. Specifically, SPL was examined during speech produced in a classroom lecture by 10 teachers with and without the use of sound-field amplification. Results indicated a significant 2.42-dB decrease in SPL with the use of sound-field FM amplification. These data support the use of sound-field amplification in the vocal hygiene regimen recommended to teachers by speech-language pathologists.

Observation of aftershocks of the 2003 Tokachi-Oki earthquake for estimation of local site effects

NASA Astrophysics Data System (ADS)

Yamanaka, Hiroaki; Motoki, Kentaro; Etoh, Kiminobu; Murayama, Masanari; Komaba, Nobuhiko

2004-03-01

Observation of aftershocks of the 2003 Tokachi-Oki earthquake was conducted in the southern part of the Tokachi basin in Hokkaido, Japan for estimation of local site effects. We installed accelerographs at 12 sites in Chokubetsu, Toyokoro, and Taiki areas, where large strong motion records were obtained during the main shock at stations of the K-NET and KiK-net. The stations of the aftershock observation are situated with different geological conditions and some of the sites were installed on Pleistocene layers as reference sites. The site amplifications are investigated using spectral ratio of S-waves from the aftershocks. The S-wave amplification factor is dominant at a period of about 1 second at the site near the KiK-net site in Toyokoro. This amplification fits well with calculated 1D amplification of S-wave in alluvial layers with a thickness of 50 meters. In addition to the site effects, we detected nonlinear amplification of the soft soils only during the main shock. The site effects at the strong motion site of the K-NET at Chokubetsu have a dominate peak at a period of 0.4 seconds. This amplification is due to soft soils having a thickness of about 13 meters. Contrary to the results at the two areas, site effects are not significantly different at the stations in the Taiki area, because of similarity on surface geological conditions.

Real-time correction of tsunami site effect by frequency-dependent tsunami-amplification factor

NASA Astrophysics Data System (ADS)

Tsushima, H.

2017-12-01

For tsunami early warning, I developed frequency-dependent tsunami-amplification factor and used it to design a recursive digital filter that can be applicable for real-time correction of tsunami site response. In this study, I assumed that a tsunami waveform at an observing point could be modeled by convolution of source, path and site effects in time domain. Under this assumption, spectral ratio between offshore and the nearby coast can be regarded as site response (i.e. frequency-dependent amplification factor). If the amplification factor can be prepared before tsunamigenic earthquakes, its temporal convolution to offshore tsunami waveform provides tsunami prediction at coast in real time. In this study, tsunami waveforms calculated by tsunami numerical simulations were used to develop frequency-dependent tsunami-amplification factor. Firstly, I performed numerical tsunami simulations based on nonlinear shallow-water theory from many tsuanmigenic earthquake scenarios by varying the seismic magnitudes and locations. The resultant tsunami waveforms at offshore and the nearby coastal observing points were then used in spectral-ratio analysis. An average of the resulted spectral ratios from the tsunamigenic-earthquake scenarios is regarded as frequency-dependent amplification factor. Finally, the estimated amplification factor is used in design of a recursive digital filter that can be applicable in time domain. The above procedure is applied to Miyako bay at the Pacific coast of northeastern Japan. The averaged tsunami-height spectral ratio (i.e. amplification factor) between the location at the center of the bay and the outside show a peak at wave-period of 20 min. A recursive digital filter based on the estimated amplification factor shows good performance in real-time correction of tsunami-height amplification due to the site effect. This study is supported by Japan Society for the Promotion of Science (JSPS) KAKENHI grant 15K16309.

Simultaneous use of multiplex ligation-dependent probe amplification assay and flow cytometric DNA ploidy analysis in patients with acute leukemia.

PubMed

Reyes-Núñez, Virginia; Galo-Hooker, Evelyn; Pérez-Romano, Beatriz; Duque, Ricardo E; Ruiz-Arguelles, Alejandro; Garcés-Eisele, Javier

2018-01-01

The aim of this work was to simultaneously use multiplex ligation-dependent probe amplification (MLPA) assay and flow cytometric DNA ploidy analysis (FPA) to detect aneuploidy in patients with newly diagnosed acute leukemia. MLPA assay and propidium iodide FPA were used to test samples from 53 consecutive patients with newly diagnosed acute leukemia referred to our laboratory for immunophenotyping. Results were compared by nonparametric statistics. The combined use of both methods significantly increased the rate of detection of aneuploidy as compared to that obtained by each method alone. The limitations of one method are somehow countervailed by the other and vice versa. MPLA and FPA yield different yet complementary information concerning aneuploidy in acute leukemia. The simultaneous use of both methods might be recommended in the clinical setting. © 2017 International Clinical Cytometry Society. © 2017 International Clinical Cytometry Society.

An improved assay for the determination of Huntington`s disease allele size

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reeves, C.; Klinger, K.; Miller, G.

1994-09-01

The hallmark of Huntington`s disease (HD) is the expansion of a polymorphic (CAG)n repeat. Several methods have been published describing PCR amplification of this region. Most of these assays require a complex PCR reaction mixture to amplify this GC-rich region. A consistent problem with trinucleotide repeat PCR amplification is the presence of a number of {open_quotes}stutter bands{close_quotes} which may be caused by primer or amplicon slippage during amplification or insufficient polymerase processivity. Most assays for HD arbitrarily select a particular band for diagnostic purposes. Without a clear choice for band selection such an arbitrary selection may result in inconsistent intra-more » or inter-laboratory findings. We present an improved protocol for the amplification of the HD trinucleotide repeat region. This method simplifies the PCR reaction buffer and results in a set of easily identifiable bands from which to determine allele size. HD alleles were identified by selecting bands of clearly greater signal intensity. Stutter banding was much reduced thus permitting easy identification of the most relevant PCR product. A second set of primers internal to the CCG polymorphism was used in selected samples to confirm allele size. The mechanism of action of N,N,N trimethylglycine in the PCR reaction is not clear. It may be possible that the minimal isostabilizing effect of N,N,N trimethylglycine at 2.5 M is significant enough to affect primer specificity. The use of N,N,N trimethylglycine in the PCR reaction facilitated identification of HD alleles and may be appropriate for use in other assays of this type.« less

Solid-Phase Nucleic Acid Sequence-Based Amplification and Length-Scale Effects during RNA Amplification.

PubMed

Ma, Youlong; Teng, Feiyue; Libera, Matthew

2018-06-05

Solid-phase oligonucleotide amplification is of interest because of possible applications to next-generation sequencing, multiplexed microarray-based detection, and cell-free synthetic biology. Its efficiency is, however, less than that of traditional liquid-phase amplification involving unconstrained primers and enzymes, and understanding how to optimize the solid-phase amplification process remains challenging. Here, we demonstrate the concept of solid-phase nucleic acid sequence-based amplification (SP-NASBA) and use it to study the effect of tethering density on amplification efficiency. SP-NASBA involves two enzymes, avian myeloblastosis virus reverse transcriptase (AMV-RT) and RNase H, to convert tethered forward and reverse primers into tethered double-stranded DNA (ds-DNA) bridges from which RNA - amplicons can be generated by a third enzyme, T7 RNA polymerase. We create microgels on silicon surfaces using electron-beam patterning of thin-film blends of hydroxyl-terminated and biotin-terminated poly(ethylene glycol) (PEG-OH, PEG-B). The tethering density is linearly related to the PEG-B concentration, and biotinylated primers and molecular beacon detection probes are tethered to streptavidin-activated microgels. While SP-NASBA is very efficient at low tethering densities, the efficiency decreases dramatically with increasing tethering density due to three effects: (a) a reduced hybridization efficiency of tethered molecular beacon detection probes; (b) a decrease in T7 RNA polymerase efficiency; (c) inhibition of T7 RNA polymerase activity by AMV-RT.

Children with Developmental Disabilities: The Effect of Sound Field Amplification on Word Identification.

ERIC Educational Resources Information Center

Flexer, Carol; And Others

1990-01-01

Using sound field amplification which increased the intensity of the teacher's voice by 10 decibels, 9 primary-level children with developmental disabilities made fewer errors on a word identification task, were more relaxed, and responded more quickly than without amplification. (Author/JDD)

Amplification of Genomic DNA for Decoy Receptor 3 Predicts Post-Resection Disease Recurrence in Breast Cancer Patients.

PubMed

Kanbayashi, Chizuko; Koyama, Yu; Ichikawa, Hiroshi; Sakata, Eiko; Hasegawa, Miki; Toshikawa, Chie; Manba, Naoko; Ikarashi, Mayuko; Kobayashi, Takashi; Minagawa, Masahiro; Kosugi, Shin-Ichi; Wakai, Toshifumi

2014-02-01

Decoy receptor 3 (DcR3), a member of the tumor necrosis factor receptor (TNFR) superfamily, shows inhibitory effects on Fas-mediated apoptosis. Currently, data are lacking on the correlation between DcR3 and the recurrence of breast cancer. The authors examined DcR3 mRNA expression and genomic amplification in breast cancer, and investigated the effect of DcR3 gene amplification on prognosis of patients. A total of 95 patients formed the basis of the current retrospective study. DcR3 mRNA expression in breast cancer tissues was examined by RNase protection assay and in situ hybridization. DcR3 gene amplification was examined by quantitative polymerase chain reaction. The correlation between DcR3 gene amplification status and clinicopathological factors was examined and also the relationship between DcR3-Amp and relapse and survival. The relative copy numbers of DcR3 genomic DNA correlated significantly with the levels of DcR3 mRNA expression (ρ = 0.755, P = 0.0067). In addition, lymphatic invasion correlated significantly with DcR3 gene amplification (P = 0.012). However, there was no correlation between the remaining clinicopathological factors and DcR3 gene amplification. In the univariate analysis, the recurrence-free survival (RFS) rate of patients who were positive for DcR3 gene amplification was significantly lower than that of patients who were negative for DcR3 gene amplification (P = 0.0271). Multivariate analysis showed that DcR3 gene amplification (P = 0.028) and disease stage (P < 0.001) remained significant independent predictors of RFS. DcR3 gene amplification was significantly correlated with lymphatic invasion, and also DcR3 gene amplification predicts recurrence after resection, which may be an important prognostic factor in breast cancer patients.

Frequent amplification of receptor tyrosine kinase genes in welldifferentiated/ dedifferentiated liposarcoma.

PubMed

Asano, Naofumi; Yoshida, Akihiko; Mitani, Sachiyo; Kobayashi, Eisuke; Shiotani, Bunsyo; Komiyama, Motokiyo; Fujimoto, Hiroyuki; Chuman, Hirokazu; Morioka, Hideo; Matsumoto, Morio; Nakamura, Masaya; Kubo, Takashi; Kato, Mamoru; Kohno, Takashi; Kawai, Akira; Kondo, Tadashi; Ichikawa, Hitoshi

2017-02-21

Well-differentiated liposarcoma (WDLPS) and dedifferentiated liposarcoma (DDLPS) are closely related tumors commonly characterized by MDM2/CDK4 gene amplification, and lack clinically effective treatment options when inoperable. To identify novel therapeutic targets, we performed targeted genomic sequencing analysis of 19 WDLPS and 37 DDLPS tumor samples using a panel of 104 cancer-related genes (NCC oncopanel v3) developed specifically for genomic testing to select suitable molecular targeted therapies. The results of this analysis indicated that these sarcomas had very few gene mutations and a high frequency of amplifications of not only MDM2 and CDK4 but also other genes. Potential driver mutations were found in only six (11%) samples; however, gene amplification events (other than MDM2 and CDK4 amplification) were identified in 30 (54%) samples. Receptor tyrosine kinase (RTK) genes in particular were amplified in 18 (32%) samples. In addition, growth of a WDLPS cell line with IGF1R amplification was suppressed by simultaneous inhibition of CDK4 and IGF1R, using palbociclib and NVP-AEW541, respectively. Combination therapy with CDK4 and RTK inhibitors may be an effective therapeutic option for WDLPS/DDLPS patients with RTK gene amplification.

Quantification of HIV-1 DNA using real-time recombinase polymerase amplification.

PubMed

Crannell, Zachary Austin; Rohrman, Brittany; Richards-Kortum, Rebecca

2014-06-17

Although recombinase polymerase amplification (RPA) has many advantages for the detection of pathogenic nucleic acids in point-of-care applications, RPA has not yet been implemented to quantify sample concentration using a standard curve. Here, we describe a real-time RPA assay with an internal positive control and an algorithm that analyzes real-time fluorescence data to quantify HIV-1 DNA. We show that DNA concentration and the onset of detectable amplification are correlated by an exponential standard curve. In a set of experiments in which the standard curve and algorithm were used to analyze and quantify additional DNA samples, the algorithm predicted an average concentration within 1 order of magnitude of the correct concentration for all HIV-1 DNA concentrations tested. These results suggest that quantitative RPA (qRPA) may serve as a powerful tool for quantifying nucleic acids and may be adapted for use in single-sample point-of-care diagnostic systems.

Evaluating Sound Field Amplification Technology in New Brunswick Schools

ERIC Educational Resources Information Center

Rubin, Rhonda; Aquino-Russell, Catherine; Flagg-Williams, Joan

2007-01-01

(Purpose) The purpose of this study was to investigate the effects of classroom sound field amplification on communication in kindergarten through grade 3 classrooms. (Methodology) Sixty classrooms were involved in the study; half of the classrooms were provided with sound field amplification. The flow of communication was measured through…

Pyrosequencing-based validation of a simple cell-suspension polymerase chain reaction assay for Campylobacter with application of high-processivity polymerase and novel internal amplification controls for rapid and specific detection.

PubMed

Oakley, Brian B; Line, J Eric; Berrang, Mark E; Johnson, Jessica M; Buhr, R Jeff; Cox, Nelson A; Hiett, Kelli L; Seal, Bruce S

2012-02-01

Although Campylobacter is an important food-borne human pathogen, there remains a lack of molecular diagnostic assays that are simple to use, cost-effective, and provide rapid results in research, clinical, or regulatory laboratories. Of the numerous Campylobacter assays that do exist, to our knowledge none has been empirically tested for specificity using high-throughput sequencing. Here we demonstrate the power of next-generation sequencing to determine the specificity of a widely cited Campylobacter-specific polymerase chain reaction (PCR) assay and describe a rapid method for direct cell suspension PCR to quickly and easily screen samples for Campylobacter. We present a specific protocol which eliminates the need for time-consuming and expensive genomic DNA extractions and, using a high-processivity polymerase, demonstrate conclusive screening of samples in <1 h. Pyrosequencing results show the assay to be extremely (>99%) sensitive, and spike-back experiments demonstrated a detection threshold of <10(2) CFU mL(-1). Additionally, we present 2 newly designed broad-range bacterial primer sets targeting the 23S rRNA gene that have wide applicability as internal amplification controls. Empirical testing of putative taxon-specific assays using high-throughput sequencing is an important validation step that is now financially feasible for research, regulatory, or clinical applications. Published by Elsevier Inc.

Site Amplification in the Central U.S.: Towards and understanding of factors influencing the site effect

NASA Astrophysics Data System (ADS)

Yassminh, R.; Sandvol, E. A.

2017-12-01

We have mapped site amplification using a Reverse Two Station (RTS) approach across much of the Central United States. We have found several unexpected results including a lack of amplification in Paleozoic basins such as the Illinois and Michigan basins. In general, we found that the amplification of high frequency regional waves is related to the topography. We also suggest that the HVSR spectra are primarily a function of the shallow velocity structure. The Central United States Seismic Observatory (CUSSO) is a vertical seismic array located adjacent to the central segment of the NMSZ. CUSSO data gives us the opportunity to understand the amplification of the ground motion at different depths within the uppermost crust. Simulating ground motions throughout the CUSSO borehole and examining the factors affecting the ground amplification, such as the velocity and thicknesses of the model layers and the source sizes, is an effective way to understand the role different factors playing in modifying the ground motion for both the local and regional seismic phases. We have used the spectral-element method (SEMs) with a 1D crustal velocity structure derived from logging data taken from CUSSO borehole. This model is comprised of near surface sediment layers and a Paleozoic basement. Utilizing the software package SPECFEM2D with virtual seismometers located on the surface and in the bottom of the different sediment layers, we have computed the true synthetic site amplification for frequencies between 0.01-3 Hz. For the local model, we have tested the sensitivity of the ground motion amplification to the source magnitude. For frequencies>0.6, the ground motions have been amplified with decreasing the magnitudes while for HZ<0.6 the the horizontal amplification increases with increasing the magnitudes. The effect of the velocity of the upper 30m was tested and the result shows that decreasing the Vs30m resulted in amplifying of the ground motion and decreasing of the resonant frequency. The velocity of the lower part of the sediment basin modifies the ground motion amplification and the result shows that increasing the velocity resulted in shifting the horizontal amplification peak frequency toward a lower frequency and increasing the amplification for frequencies >2Hz.

Investigation of major genetic alterations in neuroblastoma.

PubMed

Costa, Régis Afonso; Seuánez, Héctor N

2018-06-01

Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. This malignancy shows a wide spectrum of clinical outcome and its prognosis is conditioned by manifold biological and genetic factors. We investigated the tumor genetic profile and clinical data of 29 patients with NB by multiplex ligation-dependent probe amplification (MLPA) to assess therapeutic risk. In 18 of these tumors, MYCN status was assessed by fluorescence in situ hybridization (FISH). Copy number variation was also determined for confirming MLPA findings in two 6p loci. We found 2p, 7q and 17q gains, and 1p and 11q losses as the most frequent chromosome alterations in this cohort. FISH confirmed all cases of MYCN amplification detected by MLPA. In view of unexpected 6p imbalance, copy number variation of two 6p loci was assessed for validating MLPA findings. Based on clinical data and genetic profiles, patients were stratified in pretreatment risk groups according to international consensus. MLPA proved to be effective for detecting multiple genetic alterations in all chromosome regions as requested by the International Neuroblastoma Risk Group (INRG) for therapeutic stratification. Moreover, this technique proved to be cost effective, reliable, only requiring standard PCR equipment, and attractive for routine analysis. However, the observed 6p imbalances made PKHD1 and DCDC2 inadequate for control loci. This must be considered when designing commercial MLPA kits for NB. Finally, four patients showed a normal MLPA profile, suggesting that NB might have a more complex genetic pattern than the one assessed by presently available MLPA kits.

Strand displacement amplification as an in vitro model for rolling-circle replication: deletion formation and evolution during serial transfer.

PubMed Central

Walter, N G; Strunk, G

1994-01-01

Strand displacement amplification is an isothermal DNA amplification reaction based on a restriction endonuclease nicking its recognition site and a polymerase extending the nick at its 3' end, displacing the downstream strand. The reaction resembles rolling-circle replication of single-stranded phages and small plasmids. The displaced sense strand serves as target for an antisense reaction and vice versa, resulting in exponential growth and the autocatalytic nature of this in vitro reaction as long as the template is the limiting agent. We describe the optimization of strand displacement amplification for in vitro evolution experiments under serial transfer conditions. The reaction was followed and controlled by use of the fluorescent dye thiazole orange binding to the amplified DNA. We were able to maintain exponential growth conditions with a doubling time of 3.0 min throughout 100 transfers or approximately 350 molecular generations by using an automatic handling device. Homology of in vitro amplification with rolling-circle replication was mirrored by the occurring evolutionary processes. Deletion events most likely caused by a slipped mispairing mechanism as postulated for in vivo replication took place. Under our conditions, the mutation rate was high and a molecular quasi-species formed with a mutant lacking internal hairpin formation ability and thus outgrowing all other species under dGTP/dCTP deficiency. Images PMID:8058737

Organic field effect transistor with ultra high amplification

NASA Astrophysics Data System (ADS)

Torricelli, Fabrizio

2016-09-01

High-gain transistors are essential for the large-scale circuit integration, high-sensitivity sensors and signal amplification in sensing systems. Unfortunately, organic field-effect transistors show limited gain, usually of the order of tens, because of the large contact resistance and channel-length modulation. Here we show organic transistors fabricated on plastic foils enabling unipolar amplifiers with ultra-gain. The proposed approach is general and opens up new opportunities for ultra-large signal amplification in organic circuits and sensors.

Control of Brillouin short-pulse seed amplification by chirping the pump pulse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehmann, G.; Spatschek, K. H.

Seed amplification via Brillouin backscattering of a long pump pulse is considered. Similar to Raman amplification, several obstructive effects may occur during short-pulse Brillouin amplification. One is the spontaneous Raman backscattering of the pump before interacting with the seed. Preforming the plasma and/or chirping the pump will reduce unwanted pump backscattering. Optimized regions for low-loss pump propagation were proposed already in conjunction with Raman seed amplification. Hence, the influence of the chirp of the pump during Brillouin interaction with the seed becomes important and will be considered here. Both, the linear as well as the nonlinear evolution phases of themore » seed caused by Brillouin amplification under the action of a chirped pump are investigated. The amplification rate as well as the seed profiles are presented as function of the chirping rate. Also the dependence of superradiant scaling rates on the chirp parameter is discussed.« less

Parametric amplification in MoS2 drum resonator.

PubMed

Prasad, Parmeshwar; Arora, Nishta; Naik, A K

2017-11-30

Parametric amplification is widely used in diverse areas from optics to electronic circuits to enhance low level signals by varying relevant system parameters. Parametric amplification has also been performed in several micro-nano resonators including nano-electromechanical system (NEMS) resonators based on a two-dimensional (2D) material. Here, we report the enhancement of mechanical response in a MoS 2 drum resonator using degenerate parametric amplification. We use parametric pumping to modulate the spring constant of the MoS 2 resonator and achieve a 10 dB amplitude gain. We also demonstrate quality factor enhancement in the resonator with parametric amplification. We investigate the effect of cubic nonlinearity on parametric amplification and show that it limits the gain of the mechanical resonator. Amplifying ultra-small displacements at room temperature and understanding the limitations of the amplification in these devices is key for using these devices for practical applications.

Optimal energy growth in a stably stratified shear flow

NASA Astrophysics Data System (ADS)

Jose, Sharath; Roy, Anubhab; Bale, Rahul; Iyer, Krithika; Govindarajan, Rama

2018-02-01

Transient growth of perturbations by a linear non-modal evolution is studied here in a stably stratified bounded Couette flow. The density stratification is linear. Classical inviscid stability theory states that a parallel shear flow is stable to exponentially growing disturbances if the Richardson number (Ri) is greater than 1/4 everywhere in the flow. Experiments and numerical simulations at higher Ri show however that algebraically growing disturbances can lead to transient amplification. The complexity of a stably stratified shear flow stems from its ability to combine this transient amplification with propagating internal gravity waves (IGWs). The optimal perturbations associated with maximum energy amplification are numerically obtained at intermediate Reynolds numbers. It is shown that in this wall-bounded flow, the three-dimensional optimal perturbations are oblique, unlike in unstratified flow. A partitioning of energy into kinetic and potential helps in understanding the exchange of energies and how it modifies the transient growth. We show that the apportionment between potential and kinetic energy depends, in an interesting manner, on the Richardson number, and on time, as the transient growth proceeds from an optimal perturbation. The oft-quoted stabilizing role of stratification is also probed in the non-diffusive limit in the context of disturbance energy amplification.

EGFR amplification and expression in oral squamous cell carcinoma in young adults.

PubMed

Costa, V; Kowalski, L P; Coutinho-Camillo, C M; Begnami, M D; Calsavara, V F; Neves, J I; Kaminagakura, E

2018-07-01

The aim of this study was to investigate epidermal growth factor receptor (EGFR) gene alterations in two groups of patients with oral squamous cell carcinoma (OSCC) (a test group of subjects aged ≤40 years and a control group of subjects aged ≥50 years) and to associate the results with EGFR immunostaining, clinicopathological features, and the prognosis. Sixty cases of OSCC were selected (test group, n=21; control group, n=39). The tissue microarray technique was applied to ensure the uniformity of results. Gene amplification was analyzed by fluorescence in situ hybridization (FISH), and immunohistochemical staining for EGFR was analyzed using an automated imaging system. EGFR amplification was higher in the test group than in the control group (P=0.018) and was associated with advanced clinical stage (P=0.013), regardless of age. Patients with EGFR overexpression had worse survival rates, as did patients who had T3-T4 tumours and positive margins. EGFR overexpression has a negative impact on disease progression. Despite the higher amplification of EGFR in young adults, it does not significantly impact the survival rates of affected patients. Copyright © 2018 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Describing Site Amplification for Surface Waves in Realistic Basins

NASA Astrophysics Data System (ADS)

Bowden, D. C.; Tsai, V. C.

2017-12-01

Standard characterizations of site-specific site response assume a vertically-incident shear wave; given a 1D velocity profile, amplification and resonances can be calculated based on conservation of energy. A similar approach can be applied to surface waves, resulting in an estimate of amplification relative to a hard rock site that is different in terms of both amount of amplification and frequency. This prediction of surface-wave site amplification has been well validated through simple simulations, and in this presentation we explore the extent to which a 1D profile can explain observed amplifications in more realistic scenarios. Comparisons of various simple 2D and 3D simulations, for example, allow us to explore the effect of different basin shapes and the relative importance of effects such as focusing, conversion of wave-types and lateral surface wave resonances. Additionally, the 1D estimates for vertically-incident shear waves and for surface waves are compared to spectral ratios of historic events in deep sedimentary basins to demonstrate the appropriateness of the two different predictions. This difference in amplification responses between the wave types implies that a single measurement of site response, whether analytically calculated from 1D models or empirically observed, is insufficient for regions where surface waves play a strong role.

The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification.

PubMed

Jevtuševskaja, Jekaterina; Krõlov, Katrin; Tulp, Indrek; Langel, Ülo

2017-04-01

The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification Results: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.

A generalized leaky FxLMS algorithm for tuning the waterbed effect of feedback active noise control systems

NASA Astrophysics Data System (ADS)

Wu, Lifu; Qiu, Xiaojun; Guo, Yecai

2018-06-01

To tune the noise amplification in the feedback system caused by the waterbed effect effectively, an adaptive algorithm is proposed in this paper by replacing the scalar leaky factor of the leaky FxLMS algorithm with a real symmetric Toeplitz matrix. The elements in the matrix are calculated explicitly according to the noise amplification constraints, which are defined based on a simple but efficient method. Simulations in an ANC headphone application demonstrate that the proposed algorithm can adjust the frequency band of noise amplification more effectively than the FxLMS algorithm and the leaky FxLMS algorithm.

Isolation and amplification of genomic DNA from recalcitrant dried berries of black pepper (Piper nigrum L.)--a medicinal spice.

PubMed

Dhanya, K; Kizhakkayil, Jaleel; Syamkumar, S; Sasikumar, B

2007-10-01

Black pepper is an important medicinal spice traded internationally. The extraction of high quality genomic DNA for PCR amplification from dried black pepper is challenging because of the presence of the exceptionally large amount of oxidized polyphenolic compounds, polysaccharides and other secondary metabolites. Here we report a modified hexadecyl trimethyl ammonium bromide (CTAB) protocol by incorporating potassium acetate and a final PEG precipitation step to isolate PCR amplifiable genomic DNA from dried and powdered berries of black pepper. The protocol has trade implication as it will help in the PCR characterization of traded black peppers from different countries.

Generating ultra wide low-frequency gap for transverse wave isolation via inertial amplification effects

NASA Astrophysics Data System (ADS)

Li, Jingru; Li, Sheng

2018-02-01

Low-frequency transverse wave propagation plays a significant role in the out-of-plane vibration control. To efficiently attenuate the propagation of transverse waves at low-frequency range, this letter proposed a new type phononic beam by attaching inertial amplification mechanisms on it. The wave propagation of the beam with enhanced effective inertia is analyzed using the transfer matrix method. It is demonstrated that the low-frequency gap within inertial amplification effects can possess much wider bandwidth than using the local resonance method, thus is more suitable for designing applications to suppress transverse wave propagation.

HER2 and TOP2A amplification in a hospital-based cohort of breast cancer patients: associations with patient and tumor characteristics.

PubMed

Fasching, Peter A; Weihbrecht, Sebastian; Haeberle, Lothar; Gasparyan, Armen; Villalobos, Ivonne E; Ma, Yanling; Ekici, Arif B; Wachter, David L; Hartmann, Arndt; Beckmann, Matthias W; Slamon, Dennis J; Press, Michael F

2014-05-01

Gene amplification is an important factor for altered gene expression in breast cancers. TOP2A-amplification often occurs concomitantly with HER2 amplification, and it has been suggested to be predictive for the response to anthracycline chemotherapy. This study assessed the correlation between HER2 status and TOP2A co-amplification, the possible association of TOP2A single-nucleotide polymorphisms with the frequency of this co-amplification as well as confirmation of association with outcome. HER2 and TOP2A amplification were analyzed in a tissue microarray from a clinical cohort study. Additionally, a common genetic variant (rs13695) in the TOP2A gene was genotyped in germline DNA. HER2 gene amplification was compared with HER2-IHC findings assessed during clinical routine work, and the association between all the biomarkers analyzed and the clinical outcome was determined. As an exploratory aim, rs13695 genotypes were compared with TOP2A amplification status. HER2 amplification was seen in 101 of 628 (16.1 %) and TOP2A amplification in 32 (5.1 %) cancers. No TOP2A amplification occurred without HER2 co-amplification. HER2 amplification was found in 8, 13.6, and 55.1 % of patients with HER2-IHC 0/1+, 2+, and 3+ tumors, respectively. HER2-IHC was not associated with an effect on the prognosis, but HER2-FISH was. There was an association between the rs13695 genotype and TOP2A amplification status (P = 0.03). Although there was a significant correlation between HER2 status determined by IHC and HER2 by FISH, only HER2 gene amplification status by FISH was correlated with outcome indicating greater utility for FISH in routine clinical settings.

Experience with International Neuroblastoma Staging System and Pathology Classification

PubMed Central

Ikeda, H; Iehara, T; Tsuchida, Y; Kaneko, M; Hata, J; Naito, H; Iwafuchi, M; Ohnuma, N; Mugishima, H; Toyoda, Y; Hamazaki, M; Mimaya, J; Kondo, S; Kawa, K; Okada, A; Hiyama, E; Suita, S; Takamatsu, H

2002-01-01

The International Neuroblastoma Staging System and Pathology Classification were proposed in 1988 and in 1999, respectively, but their clinical value has not yet been fully studied in new patients. Six hundred and forty-four patients with neuroblastoma treated between January 1995 and December 1999 were analysed by these classifications. The 4-year overall survival rate of patients <12 months of age with INSS stages 1, 2A, 2B, 3 and 4S disease was 98.5%, which was significantly higher than the 73.1% rate in stage 4 patients <12 months (P<0.0001). When patients were ⩾12 months, the 4-year overall survival rate of patients with neuroblastoma at 1, 2A, 2B and 3 stages was 100% and that of patients at stage 4 was 48.5% (P<0.0001). As to the International Neuroblastoma Pathology Classification histology, the 4-year overall survival rate was 98.8% in patients with favourable histology and 60.7% in those with unfavourable histology in the <12 months group (P<0.0001). In the ⩾12 months group, the 4-year oral survival of patients with favourable histology was 95.3% and that of patients with unfavourable histology was 50.6% (P<0.0001). Among biological factors, MYCN amplification, DNA diploidy and 1p deletions were significantly associated with poor prognosis in patients <12 months, as were MYCN amplification and DNA diploidy in patients ⩾12 months of age. Multivariate analysis showed that the INSS stage (stage 4 vs other stages) and International Neuroblastoma Pathology Classification histology (unfavourable vs favourable) were significantly and independently associated with the survival of patients undergoing treatment, stratified by age, stage and MYCN amplification (P=0.0002 and P=0.0051, respectively). British Journal of Cancer (2002) 86, 1110–1116. DOI: 10.1038/sj/bjc/6600231 www.bjcancer.com © 2002 Cancer Research UK PMID:11953858

Lidar using the backscatter amplification effect

NASA Astrophysics Data System (ADS)

Razenkov, Igor A.; Banakh, Victor A.

2018-04-01

Experimental data proving the possibility of lidar measurement of the refractive turbulence strength based on the effect of backscatter amplification (BSA) are reported. It is shown that the values of the amplification factor correlate with the variance of random jitter of optical image of an incoherent light source depending on the value of the structure constant of the air refractive index turbulent fluctuations averaged over the probing path. This paper presents the results of measurements of the BSA factor in comparison with the simultaneous measurements of the BSA peak, which is very narrow and only occurs on the laser beam axis. It is constructed the range-time images of the derivative of the amplification factor gives a comprehensive picture of the location of turbulent zones and their temporal dynamics.

Development and evaluation of internal amplification controls for use in a real-time duplex PCR assay for detection of Campylobacter coli and Campylobacter jejuni.

PubMed

Randall, Luke; Lemma, Fabrizio; Rodgers, John; Vidal, Ana; Clifton-Hadley, Felicity

2010-02-01

A common problem of both conventional and real-time PCR assays is failure of DNA amplification due to the presence of inhibitory substances in samples. In view of this, our aim was to develop and evaluate internal amplification controls (IACs) for use with an existing duplex real-time PCR assay for Campylobacter coli and Campylobacter jejuni. Both competitive and non-competitive IACs were developed and evaluated. The competitive approach involved a DNA fragment of the coding region of the fish viral haemorrhagic septicaemia virus, flanked by the mapA PCR primers, whilst the non-competitive approach utilized an extra set of universal 16S rDNA primers. Both IAC-PCR assay types were evaluated using cultures of Campylobacter and chicken caecal content samples. Both IACs were sensitive to caecal inhibitors, making them suitable for detecting inhibition which could lead to false-negatives. Results showed that both IACs at optimum concentrations worked well without reducing the overall sensitivity of the PCR assay. Compared to culture, the optimized competitive IAC-PCR assay detected 45/47 positives (sensitivity 93.6 %, specificity 80.1 %); however, it had the advantage over culture in that it could detect mixed infections of C. coli and C. jejuni and was capable of giving a result for a sample within a day.

Telomerase Repeated Amplification Protocol (TRAP).

PubMed

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 analyzed by electrophoresis. TSNT is, an internal standard control, amplified by TS primer. NT is its own reverse primer, which is not a substrate for telomerase. These primers are used to identify false-negative results by if the gel lacks internal control bands.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ochs, I. E.; Bertelli, N.; Fisch, N. J.

Although lower hybrid waves are effective at driving currents in present-day tokamaks, they are expected to interact strongly with high-energy particles in extrapolating to reactors. In the presence of a radial alpha particle birth gradient, this interaction can take the form of wave amplification rather than damping. While it is known that this amplification more easily occurs when launching from the tokamak high-field side, the extent of this amplification has not been made quantitative. Here, by tracing rays launched from the high- field-side of a tokamak, the required radial gradients to achieve amplification are calculated for a temperature and densitymore » regime consistent with a hot-ion-mode fusion reactor. As a result, these simulations, while valid only in the linear regime of wave amplification, nonetheless illustrate the possibilities for wave amplification using high-field launch of the lower hybrid wave.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ochs, I. E.; Bertelli, N.; Fisch, N. J.

Although lower hybrid waves are effective at driving currents in present-day tokamaks, they are expected to interact strongly with high-energy particles in extrapolating to reactors. In the presence of a radial alpha particle birth gradient, this interaction can take the form of wave amplification rather than damping. While it is known that this amplification more easily occurs when launching from the tokamak high-field side, the extent of this amplification has not been made quantitative. Here, by tracing rays launched from the high-field-side of a tokamak, the required radial gradients to achieve amplification are calculated for a temperature and density regimemore » consistent with a hot-ion-mode fusion reactor. These simulations, while valid only in the linear regime of wave amplification, nonetheless illustrate the possibilities for wave amplification using high-field launch of the lower hybrid wave.« less

High-throughput amplification of mature microRNAs in uncharacterized animal models using polyadenylated RNA and stem-loop reverse transcription polymerase chain reaction.

PubMed

Biggar, Kyle K; Wu, Cheng-Wei; Storey, Kenneth B

2014-10-01

This study makes a significant advancement on a microRNA amplification technique previously used for expression analysis and sequencing in animal models without annotated mature microRNA sequences. As research progresses into the post-genomic era of microRNA prediction and analysis, the need for a rapid and cost-effective method for microRNA amplification is critical to facilitate wide-scale analysis of microRNA expression. To facilitate this requirement, we have reoptimized the design of amplification primers and introduced a polyadenylation step to allow amplification of all mature microRNAs from a single RNA sample. Importantly, this method retains the ability to sequence reverse transcription polymerase chain reaction (RT-PCR) products, validating microRNA-specific amplification. Copyright © 2014 Elsevier Inc. All rights reserved.

Recurrent amplification of RTEL1 and ABCA13 and its synergistic effect associated with clinicopathological data of gastric adenocarcinoma.

PubMed

Araújo, T M; Seabra, A D; Lima, E M; Assumpção, P P; Montenegro, R C; Demachki, S; Burbano, R M; Khayat, A S

2016-01-01

Despite progression in treatment of gastric cancer, prognosis of patients remains poor, in part due to the low rate of diagnosis during its early stages. This paradigm implies the necessity to identify molecular biomarkers for early gastric cancer diagnosis, as well as for disease monitoring, thus contributing to the development of new therapeutic approaches. In a previous study, performed by array-Comparative Genomic Hybridization, we described for the first time in literature recurrent amplification of RTEL1 and ABCA13 genes in gastric cancer. Thus, the aim of the present study was to validate recurrent amplification of RTEL1 and ABCA13 genes and associate CNV status with clinicopathological data. Results showed RTEL1 and ABCA13 amplification in 38 % of samples. Statistical analysis demonstrated that RTEL amplification is more common in older patients and more associated with intestinal type and ABCA13 amplification increases the risk of lymph node metastasis and is more common in men. Co-amplification of these genes showed a significant association with advanced staging. aCGH is a very useful tool for investigating novel genes associated with carcinogenesis and RTEL1 amplification may be important for the development of gastric cancer in older patients, besides being a probable event contributing for chromosomal instability in intestinal gastric carcinogenesis. ABCA13 amplification may have age-specific function and could be considered a useful marker for predicting lymph node metastasis in resected gastric cancer patients in early stage. Lastly, RTEL1 and ABCA13 synergistic effect may be considered as a putative marker for advanced staging in gastric cancer patients.

Electricity-free amplification and detection for molecular point-of-care diagnosis of HIV-1.

PubMed

Singleton, Jered; Osborn, Jennifer L; Lillis, Lorraine; Hawkins, Kenneth; Guelig, Dylan; Price, Will; Johns, Rachel; Ebels, Kelly; Boyle, David; Weigl, Bernhard; LaBarre, Paul

2014-01-01

In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens.

Electricity-Free Amplification and Detection for Molecular Point-of-Care Diagnosis of HIV-1

PubMed Central

Singleton, Jered; Osborn, Jennifer L.; Lillis, Lorraine; Hawkins, Kenneth; Guelig, Dylan; Price, Will; Johns, Rachel; Ebels, Kelly; Boyle, David; Weigl, Bernhard; LaBarre, Paul

2014-01-01

In resource-limited settings, the lack of decentralized molecular diagnostic testing and sparse access to centralized medical facilities can present a critical barrier to timely diagnosis, treatment, and subsequent control and elimination of infectious diseases. Isothermal nucleic acid amplification methods, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), are well-suited for decentralized point-of-care molecular testing in minimal infrastructure laboratories since they significantly reduce the complexity of equipment and power requirements. Despite reduced complexity, however, there is still a need for a constant heat source to enable isothermal nucleic acid amplification. This requirement poses significant challenges for laboratories in developing countries where electricity is often unreliable or unavailable. To address this need, we previously developed a low-cost, electricity-free heater using an exothermic reaction thermally coupled with a phase change material. This heater achieved acceptable performance, but exhibited considerable variability. Furthermore, as an enabling technology, the heater was an incomplete diagnostic solution. Here we describe a more precise, affordable, and robust heater design with thermal standard deviation <0.5°C at operating temperature, a cost of approximately US$.06 per test for heater reaction materials, and an ambient temperature operating range from 16°C to 30°C. We also pair the heater with nucleic acid lateral flow (NALF)-detection for a visual readout. To further illustrate the utility of the electricity-free heater and NALF-detection platform, we demonstrate sensitive and repeatable detection of HIV-1 with a ß-actin positive internal amplification control from processed sample to result in less than 80 minutes. Together, these elements are building blocks for an electricity-free platform capable of isothermal amplification and detection of a variety of pathogens. PMID:25426953

HER2 Amplification and HER2 Mutation Are Distinct Molecular Targets in Lung Cancers.

PubMed

Li, Bob T; Ross, Dara S; Aisner, Dara L; Chaft, Jamie E; Hsu, Meier; Kako, Severine L; Kris, Mark G; Varella-Garcia, Marileila; Arcila, Maria E

2016-03-01

Human epidermal growth factor receptor 2 gene (HER2 [also known as ERBB2]) alterations have been identified as oncogenic drivers and potential therapeutic targets in lung cancers. The molecular associations of HER2 gene amplification, mutation, and HER2 protein overexpression in lung cancers have not been distinctly defined. To explore these associations, Memorial Sloan Kettering Cancer Center and the University of Colorado combined their data on HER2 alterations in lung cancers. Tumor specimens from 175 patients with lung adenocarcinomas and no prior targeted therapy were evaluated for the presence of HER2 amplification and mutation and HER2 protein overexpression. Amplification was assessed by fluorescence in situ hybridization (FISH) and defined as an HER2-to-chromosome enumeration probe 17 ratio of at least 2.0. Mutation was assessed by fragment analysis, mass spectrometry genotyping, and Sanger sequencing. Overexpression was assessed by immunohistochemical (IHC) staining. The frequencies of HER2 amplification and mutation and HER2 overexpression were calculated and their overlap examined. HER2 amplification was detected by FISH in 5 of 175 cases (3%). HER2 mutation was detected in 4 of 148 specimens (3%), including three identical 12-base pair insertions (p.A775_G776insYVMA) and a 9-base pair insertion, all in exon 20. None of the HER2-mutant cases was amplified. HER2 overexpression (2+ or 3+) on IHC staining was not detected in the 25 specimens available for testing, and negative IHC staining correlated with the negative results according to FISH. HER2 mutations are not associated with HER2 amplification, thus suggesting a distinct entity and therapeutic target. HER2-positive lung cancer may not be an adequate term, and patient cohorts for the study of HER2-targeted agents should be defined by the specific HER2 alteration present. Copyright © 2015 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification.

PubMed

Janse, Ingmar; Hamidjaja, Raditijo A; Bok, Jasper M; van Rotterdam, Bart J

2010-12-08

Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum.

Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification

PubMed Central

2010-01-01

Background Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Results Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. Conclusions The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum PMID:21143837

Children's Books in Translation: Facts and Beliefs

ERIC Educational Resources Information Center

Orvig, Mary

1972-01-01

The distribution channels of children's books and the part played by translations within children's literature of different countries are neglected fields of research. Translation is the strongest link in an international chain which is constantly in need of amplification and reinforcement. (34 references) (Author/NH)

3D modeling of seismic waves propagation in the Israeli continental shelf: soft sediments, buried canyons and their effects.

NASA Astrophysics Data System (ADS)

Tsesarsky, M.; Volk, O.; Shani-Kadmiel, S.; Gvirtzman, Z.

2016-12-01

Sedimentary wedges underlay many coastal areas, specifically along passive continental margins. Although a large portion of the world`s population is concentrated along coastal areas, relatively few studies investigated the seismic hazard related to internal structure of these wedges. This is particularly important, when the passive margin is located in proximity to active plate boundaries. Sedimentry wedges have low angles compared to fault bounded basins, hence commonly treated using 1D methods. In various locations the sedimentary wedges are transected by deep buried canyons typically filled with sediments softer than their surrounding bedrock. Such structures are found is the Mediterranean coast of Israel. Here, a sedimentary wedge and buried canyons underlay some of the country's most densely populated regions. Seismic sources can be found both at sea and on land at epicentral distances ranging from 50 to 200 km. Although this region has a proven seismic record, it has, like many other parts of the world, limited instrumental coverage and long return periods. This makes assessment of ground motions in a future earthquake difficult and highlights the importance of non-instrumental methods. We employ numerical modeling (SW4 FD code) to study seismic ground motions and their amplification atop the sedimentary wedge and canyons. This goal is a part of a larger objective aiming at developing a systematic approach for distinction between individual contributions of basin structures to the highly complex overall basin response. We show that the sedimentary wedge and buried canyon both exhibit a unique response and modeling them as one-dimensional structures could significantly underestimate seismic hazard. The sedimentary wedge exhibit amplification ratios, relative to a horizontally layered model, up to a factor of 2. This is mainly due to the amplification of Rayleigh waves traveling into the wedge from its thin side. The buried canyon structure shows a simple, "easy to use" response with considerably high PGV values and amplification ratios of up to 3 along its axis. This response is due to a geometrical focusing effect caused by the convex shape of the canyon's floor. The canyon's response is significant even where the canyon is buried deep under the surface.

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

PubMed

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 HIV-1 subtypes. Because the bio-barcode-amplification method does not require enzymatic amplification, this method could be translated into a robust point-of-care test.

Spellbinding and crooning: sound amplification, radio, and political rhetoric in international comparative perspective, 1900-1945.

PubMed

Wijfjes, Huub

2014-01-01

This article researches in an interdisciplinary way the relationship of sound technology and political culture at the beginning of the twentieth century. It sketches the different strategies that politicians--Franklin D. Roosevelt, Adolf Hitler, Winston Churchill, and Dutch prime minister Hendrikus Colijn--found for the challenges that sound amplification and radio created for their rhetoric and presentation. Taking their different political styles into account, the article demonstrates that the interconnected technologies of sound amplification and radio forced a transition from a spellbinding style based on atmosphere and pathos in a virtual environment to "political crooning" that created artificial intimacy in despatialized simultaneity. Roosevelt and Colijn created the best examples of this political crooning, while Churchill and Hitler encountered problems in this respect. Churchill's radio successes profited from the special circumstances during the first period of World War II. Hitler's speeches were integrated into a radio regime trying to shape, with dictatorial powers, a national socialistic community of listeners.

Designing a Micromixer for Rolling Circle Amplification in Cancer Biomarker Detection

NASA Astrophysics Data System (ADS)

Altural, Hayriye

2015-03-01

Rolling circle amplification (RCA) is an alternative method to the Polymerase Chain Reaction based amplification for point-of-care (POC) diagnosis. In future personalized cancer diagnostic for POC applications, smaller, faster and cheaper methods are needed instead of costly and time-consuming laboratory tests. Microfluidic chips can perform the detection of cancer biomarkers within less analysis time, and provide for improvement in the sensitivity and specificity required for biochemical analysis as well. Rapid mixing is essential in the chips used in cancer diagnostic. The goal of this study is to design a micromixer for rapid RCA-based analysis and develop the assay time in cancer biomarker detection. By combining assays with micromixers, multi-step bioreactions in microfluidic chips may be achieved with minimal external control. Here, simulation results related to the micromixer are obtained by COMSOL software. The Scientific and Technological Research Council of Turkey (TUBITAK) is acknowledged for granting of H. Altural postdoctoral study in the framework of TUBITAK-BIDEB 2219-International Postdoctoral Research Scholarship Program.

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

PubMed

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

A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification.

PubMed

Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

2016-10-21

Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of "G-quadruplex" in lantern-like structures. Finally, the continuously enriched "G-quadruplex lanterns" were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10 -17 M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring.

A Label-Free and Sensitive Fluorescent Qualitative Assay for Bisphenol A Based on Rolling Circle Amplification/Exonuclease III-Combined Cascade Amplification

PubMed Central

Li, Xia; Song, Juan; Xue, Qing-Wang; You, Fu-Heng; Lu, Xia; Kong, Yan-Cong; Ma, Shu-Yi; Jiang, Wei; Li, Chen-Zhong

2016-01-01

Bisphenol A (BPA) detection in drinking water and food packaging materials has attracted much attention since the discovery that BPA can interfere with normal physiological processes and cause adverse health effects. Here, we constructed a label-free aptamer fluorescent assay for selective and sensitive detection of BPA based on the rolling circle amplification (RCA)/Exonuclease III (Exo III)-combined cascade amplification strategy. First, the duplex DNA probe (RP) with anti-BPA aptamer and trigger sequence was designed for BPA recognition and signal amplification. Next, under the action of BPA, the trigger probe was liberated from RP to initiate RCA reaction as primary amplification. Subsequently, the RCA products were used to trigger Exo III assisted secondary amplification with the help of hairpin probes, producing plenty of “G-quadruplex” in lantern-like structures. Finally, the continuously enriched “G-quadruplex lanterns” were lightened by zinc(II)-protoporphyrin IX (ZnPPIX) generating enhanced fluorescence signals. By integrating the primary RCA and secondary Exo III mediated cascade amplification strategy, this method displayed an excellent sensitivity with the detection limits of 5.4 × 10−17 M. In addition, the anti-BPA aptamer exhibits high recognition ability with BPA, guaranteeing the specificity of detection. The reporter signal probe (G-quadruplex with ZnPPIX) provides a label-free fluorescence signals readout without complicated labeling procedures, making the method simple in design and cost-effective in operation. Moreover, environmental samples analysis was also performed, suggesting that our strategy was reliable and had a great potential application in environmental monitoring. PMID:28335318

Alpha channeling with high-field launch of lower hybrid waves

DOE PAGES

Ochs, I. E.; Bertelli, N.; Fisch, N. J.

2015-11-04

Although lower hybrid waves are effective at driving currents in present-day tokamaks, they are expected to interact strongly with high-energy particles in extrapolating to reactors. In the presence of a radial alpha particle birth gradient, this interaction can take the form of wave amplification rather than damping. While it is known that this amplification more easily occurs when launching from the tokamak high-field side, the extent of this amplification has not been made quantitative. Here, by tracing rays launched from the high- field-side of a tokamak, the required radial gradients to achieve amplification are calculated for a temperature and densitymore » regime consistent with a hot-ion-mode fusion reactor. As a result, these simulations, while valid only in the linear regime of wave amplification, nonetheless illustrate the possibilities for wave amplification using high-field launch of the lower hybrid wave.« less

Wave Propagation and Amplification in the Cochlea—A Moderated Discussion

NASA Astrophysics Data System (ADS)

Chadwick, Richard S.; Grosh, Karl

2011-11-01

A discussion moderated by the authors on the topics "Wave Propagation in the Cochlea" and "The Cochlear Amplifier" was held on 21 July 2011 at the 11th International Mechanics of Hearing Workshop in Williamstown, Massachusetts. The paper provides an edited transcript of the session.

Genome amplification of single sperm using multiple displacement amplification.

PubMed

Jiang, Zhengwen; Zhang, Xingqi; Deka, Ranjan; Jin, Li

2005-06-07

Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 mul reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.

Influence of forced internal air circulation on airflow distribution and heat transfer in a gas double-dynamic solid-state fermentation bioreactor.

PubMed

Chen, Hongzhang; Qin, Lanzhi; Li, Hongqiang

2014-02-01

Internal air circulation affects the temperature field distribution in a gas double-dynamic solid-state fermentation bioreactor (GDSFB). To enhance heat transfer through strengthening internal air circulation in a GDSFB, we put an air distribution plate (ADP) into the bioreactor and studied the effects of forced internal air circulation on airflow, heat transfer, and cellulase activity of Trichoderma viride L3. Results showed that ADP could help form a steady and uniform airflow distribution, and with gas-guide tubes, air reversal was formed inside the bioreactor, thus resulting in a smaller temperature difference between medium and air by enhancing convective heat transfer inside the bioreactor. Using an ADP of 5.35 % aperture ratio caused a 1 °C decrease in the average temperature difference during the solid-state fermentation process of T. viride L3. Meanwhile, the cellulase activity of T. viride L3 increased by 13.5 %. The best heat-transfer effect was attained when using an ADP of 5.35 % aperture ratio and setting the fan power to 125 V (4.81 W) in the gas double-dynamic solid-state fermentation (GDSF) process. An option of suitable aperture ratio and fan power may be conducive to ADPs' industrial amplification.

Thermoelectric effects and magnetic field amplification in magnetogasdynamic turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.

1991-01-01

It will be shown that thermoelectric effects amplify magnetic fields in compressible magnetogasdynamic turbulence (though not nearly as much as occurs across a curved reently bowshock). The importance of this result lies in the recognition that thermoelectric effects (in addition to kinetic effects) provide a real mechanism for the amplification of magnetic field strength (and total energy dissipation through ohmic losses) in a compressible, turbulent plasma.

MET amplification as a potential therapeutic target in gastric cancer

PubMed Central

Kawakami, Hisato; Okamoto, Isamu; Arao, Tokuzo; Okamoto, Wataru; Matsumoto, Kazuko; Taniguchi, Hirokazu; Kuwata, Kiyoko; Yamaguchi, Haruka; Nishio, Kazuto; Nakagawa, Kazuhiko; Yamada, Yasuhide

2013-01-01

Our aim was to investigate both the prevalence of MET amplification in gastric cancer as well as the potential of this genetic alteration to serve as a therapeutic target in gastric cancer. MET amplification was assessed by initial screening with a PCR-based copy number assay followed by confirmatory FISH analysis in formalin-fixed, paraffin-embedded specimens of gastric cancer obtained at surgery. The effects of MET tyrosine kinase inhibitors (MET-TKIs) in gastric cancer cells with or without MET amplification were also examined. The median MET copy number in 266 cases of gastric cancer was 1.7, with a range of 0.41 to 21.3. We performed FISH analysis for the 15 cases with the highest MET copy numbers. MET amplification was confirmed in the four assessable cases with a MET copy number of at least 4, whereas MET amplification was not detected in those with a gene copy number of <4. The prevalence of MET amplification was thus 1.5% (4 out of 266 cases). Inhibition of MET by MET-TKIs resulted in the induction of apoptosis accompanied by attenuation of downstream MET signaling in gastric cancer cell lines with MET amplification but not in those without this genetic change. MET amplification identifies a small but clinically important subgroup of gastric cancer patients who are likely to respond to MET-TKIs. Furthermore, screening with a PCR-based copy number assay is an efficient way to reduce the number of patients requiring confirmation of MET amplification by FISH analysis. PMID:23327903

ZnOEP based phototransistor: signal amplification and light-controlled switch.

PubMed

Ji, Heng-Xing; Hu, Jin-Song; Wan, Li-Jun

2008-06-21

A phototransistor with a field-effect transistor configuration was fabricated using a single zinc octaethylporphyrin (ZnOEP) nanorod; the device showed ability in signal amplification and reversible light-controlled switching.

Laboratory Diagnosis of Zika Virus Infection.

PubMed

Landry, Marie Louise; St George, Kirsten

2017-01-01

-The rapid and accurate diagnosis of Zika virus infection is an international priority. -To review current recommendations, methods, limitations, and priorities for Zika virus testing. -Sources include published literature, public health recommendations, laboratory procedures, and testing experience. -Until recently, the laboratory diagnosis of Zika infection was confined to public health or research laboratories that prepared their own reagents, and test capacity has been limited. Furthermore, Zika cross-reacts serologically with other flaviviruses, such as dengue, West Nile, and yellow fever. Current or past infection, or even vaccination with another flavivirus, will often cause false-positive or uninterpretable Zika serology results. Detection of viral RNA during acute infection using nucleic acid amplification tests provides more specific results, and a number of commercial nucleic acid amplification tests have received emergency use authorization. In addition to serum, testing of whole blood and urine is recommended because of the higher vial loads and longer duration of shedding. However, nucleic acid amplification testing has limited utility because many patients are asymptomatic or present for testing after the brief period of Zika shedding has passed. Thus, the greatest need and most difficult challenge is development of accurate antibody tests for the diagnosis of recent Zika infection. Research is urgently needed to identify Zika virus epitopes that do not cross-react with other flavivirus antigens. New information is emerging at a rapid pace and, with ongoing public-private and international collaborations and government support, it is hoped that rapid progress will be made in developing robust and widely applicable diagnostic tools.

Comparison of the rolling circle amplification and ligase-dependent reaction methods for the identification of opportunistic Exophiala species.

PubMed

Kaplan, Engin; Ilkit, Macit; de Hoog, G Sybren

2017-10-26

We developed two ligase-dependent probe amplification assays based on rolling circle amplification (RCA) and the ligase-dependent reaction (LDR) to differentiate species of Exophiala targeting the rDNA internal transcribed spacer region. We focused on Exophiala dermatitidis and E. phaeomuriformis, two opportunistic inhabitants of indoor wet cells, and further detected E. heteromorpha, E. xenobiotica, and E. crusticola; 57 reference isolates representing the five species were tested. Depending on the RCA probes used, the sensitivity was 100%, and the specificity ranged from 3.7% to 88.6% (median: 46.1%). In contrast, the sensitivity and specificity of the LDR probes targeting the same isolates were 88.6-100% (median: 95.8%) and 95.4-100% (median: 97.7%), respectively. We analyzed 198 additional environmental isolates representing the same Exophiala species. Overall, the sensitivity and specificity of LDR ranged from 89.7% to 100% (median: 94.1%) and from 93.9% to 100% (median: 96.9%), respectively. The assessment of performance and validation of LDR probes using SYBR Green quantitative polymerase chain reaction revealed high reproducibility and an acceptable range limit, in line with the guidelines of the European Network of GMO Laboratories. In conclusion, the LDR assay was more reliable and less expensive than RCA for species-level identification of Exophiala isolates. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Amplification of Angular Rotations Using Weak Measurements

NASA Astrophysics Data System (ADS)

Magaña-Loaiza, Omar S.; Mirhosseini, Mohammad; Rodenburg, Brandon; Boyd, Robert W.

2014-05-01

We present a weak measurement protocol that permits a sensitive estimation of angular rotations based on the concept of weak-value amplification. The shift in the state of a pointer, in both angular position and the conjugate orbital angular momentum bases, is used to estimate angular rotations. This is done by an amplification of both the real and imaginary parts of the weak-value of a polarization operator that has been coupled to the pointer, which is a spatial mode, via a spin-orbit coupling. Our experiment demonstrates the first realization of weak-value amplification in the azimuthal degree of freedom. We have achieved effective amplification factors as large as 100, providing a sensitivity that is on par with more complicated methods that employ quantum states of light or extremely large values of orbital angular momentum.

The effect of classroom amplification on the signal-to-noise ratio in classrooms while class is in session.

PubMed

Larsen, Jeffery B; Blair, James C

2008-10-01

The purpose of this study was to measure the signal-to-noise ratios in classrooms while class was in session and students were interacting with the teacher and each other. Measurements of noise and reverberation were collected for 5 different classrooms in 3 different schools while class was in session. Activities taking place during the measurements were recorded to compare with sound level measures. The use of infrared classroom amplification was compared with no amplification. The results revealed that when classroom amplification was used, students heard the teacher's voice at a level that was an average of 13 dB above the noise floor as compared to an average of +2 dB above the noise floor without amplification.

Differential Item Functioning Amplification and Cancellation in a Reading Test

ERIC Educational Resources Information Center

Bao, Han; Dayton, C. Mitchell; Hendrickson, Amy B.

2009-01-01

When testlet effects and item idiosyncratic features are both considered to be the reasons of DIF in educational tests using testlets (Wainer & Kiely, 1987) or item bundles (Rosenbaum, 1988), it is interesting to investigate the phenomena of DIF amplification and cancellation due to the interactive effects of these two factors. This research…

Prevention effect of rare ginsenosides against stress-hormone induced MTOC amplification

PubMed Central

Lee, Jee-Hyun; Cheong, Kyu Jin; Jung, Youn-Sang; Woo, Tae-Gyun; Yoon, Min-Ho; Oh, Ah-Young; Kang, So-Mi; Lee, Chunghui; Sun, Hokeun; Hwang, Jihwan; Song, Gyu-Yong; Park, Bum-Joon

2016-01-01

Stress has been suggested as one of important cause of human cancer without molecular biological evidence. Thus, we test the effect of stress-related hormones on cell viability and mitotic fidelity. Similarly to estrogen, stress hormone cortisol and its relative cortisone increase microtubule organizing center (MTOC) number through elevated expression of γ-tubulin and provide the Taxol resistance to human cancer cell lines. However, these effects are achieved by glucocorticoid hormone receptor (GR) but not by estrogen receptor (ER). Since ginsenosides possess steroid-like structure, we hypothesized that it would block the stress or estrogen-induced MTOC amplification and Taxol resistance. Among tested chemicals, rare ginsenoside, CSH1 (Rg6) shows obvious effect on inhibition of MTOC amplification, γ-tubulin induction and Taxol resistance. Comparing to Fulvestant (FST), ER-α specific inhibitor, this chemical can block the cortisol/cortisone-induced MTOC deregulation as well as ER-α signaling. Our results suggest that stress hormone induced tumorigenesis would be achieved by MTOC amplification, and CSH1 would be useful for prevention of stress-hormone or steroid hormone-induced chromosomal instability. PMID:27147573

Raman amplification in the coherent wave-breaking regime.

PubMed

Farmer, J P; Pukhov, A

2015-12-01

In regimes far beyond the wave-breaking threshold of Raman amplification, we show that significant amplification can occur after the onset of wave breaking, before phase mixing destroys the coherent coupling between pump, probe, and plasma wave. Amplification in this regime is therefore a transient effect, with the higher-efficiency "coherent wave-breaking" (CWB) regime accessed by using a short, intense probe. Parameter scans illustrate the marked difference in behavior between below wave breaking, in which the energy-transfer efficiency is high but total energy transfer is low, wave breaking, in which efficiency is low, and CWB, in which moderate efficiencies allow the highest total energy transfer.

Topographical and geological amplification: case studies and engineering implications

USGS Publications Warehouse

Celebi, M.

1991-01-01

Topographical and geological amplification that occurred during past earthquakes are quantified using spectral ratios of recorded motions. Several cases are presented from the 1985 Chilean and Mexican earthquakes as well as the 1983 Coalinga (California) and 1987 Supersition Hills (California) earthquake. The strong motions recorded in Mexico City during the 1985 Michoacan earthquake are supplemented by ambient motions recorded within Mexico City to quantify the now well known resonating frequencies of the Mexico City lakebed. Topographical amplification in Canal Beagle (Chile), Coalinga and Superstition Hills (California) are quantified using the ratios derived from the aftershocks following the earthquakes. A special dense array was deployed to record the aftershocks in each case. The implications of both geological and topographical amplification are discussed in light of current code provisions. The observed geological amplifications has already influenced the code provisions. Suggestions are made to the effect that the codes should include further provisions to take the amplification due to topography into account. ?? 1991.

Effect of Arctic Amplification on Design Snow Loads in Alaska

DTIC Science & Technology

2016-09-01

ER D C/ CR RE L M P- 16 -1 Strategic Environmental Research and Development Program (SERDP) Effect of Arctic Amplification on Design...September 2016 Approved for public release; distribution is unlimited. The U.S. Army Engineer Research and Development Center (ERDC...acwc.sdp.sirsi.net/client/default. Strategic Environmental Research and Development Program (SERDP) ERDC/CRREL MP-16-1 September 2016 Effect of Arctic

Sound-Field Amplification to Increase Compliance to Directions in Students with ADHD

ERIC Educational Resources Information Center

Maag, John W.; Anderson, Jean M.

2007-01-01

This study determined the effects of sound-field amplification (SFA) on the speed with which students with attention deficit hyperactivity disorder (ADHD) followed teacher directions. A multiple baseline design was used with 3 elementary-aged students with ADHD to assess the effects of SFA across 4 types of directions: (a) task demand (e.g., get…

Detection of EGFR Gene Mutation by Mutation-oriented LAMP Method.

PubMed

Matsumoto, Naoyuki; Kumasaka, Akira; Ando, Tomohiro; Komiyama, Kazuo

2018-04-01

Epidermal growth factor receptor (EGFR) is a target of molecular therapeutics for non-small cell lung cancer. EGFR gene mutations at codons 746-753 promote constitutive EGFR activation and result in worst prognosis. However, these mutations augment the therapeutic effect of EGFR-tyrosine kinase inhibitor. Therefore, the detection of EGFR gene mutations is important for determining treatment planning. The aim of the study was to establish a method to detect EGFR gene mutations at codons 746-753. EGFR gene mutation at codons 746-753 in six cancer cell lines were investigated. A loop-mediated isothermal amplification (LAMP)-based procedure was developed, that employed peptide nucleic acid to suppress amplification of the wild-type allele. This mutation-oriented LAMP can amplify the DNA fragment of the EGFR gene with codons 746-753 mutations within 30 min. Moreover, boiled cells can work as template resources. Mutation oriented-LAMP assay for EGFR gene mutation is sensitive on extracted DNA. This procedure would be capable of detecting EGFR gene mutation in sputum, pleural effusion, broncho-alveolar lavage fluid or trans-bronchial lung biopsy by chair side. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification

PubMed Central

Maruyama, Toru; Yamagishi, Keisuke; Mori, Tetsushi; Takeyama, Haruko

2015-01-01

Whole genome amplification (WGA) is essential for obtaining genome sequences from single bacterial cells because the quantity of template DNA contained in a single cell is very low. Multiple displacement amplification (MDA), using Phi29 DNA polymerase and random primers, is the most widely used method for single-cell WGA. However, single-cell MDA usually results in uneven genome coverage because of amplification bias, background amplification of contaminating DNA, and formation of chimeras by linking of non-contiguous chromosomal regions. Here, we present a novel MDA method, termed droplet MDA, that minimizes amplification bias and amplification of contaminants by using picoliter-sized droplets for compartmentalized WGA reactions. Extracted DNA fragments from a lysed cell in MDA mixture are divided into 105 droplets (67 pL) within minutes via flow through simple microfluidic channels. Compartmentalized genome fragments can be individually amplified in these droplets without the risk of encounter with reagent-borne or environmental contaminants. Following quality assessment of WGA products from single Escherichia coli cells, we showed that droplet MDA minimized unexpected amplification and improved the percentage of genome recovery from 59% to 89%. Our results demonstrate that microfluidic-generated droplets show potential as an efficient tool for effective amplification of low-input DNA for single-cell genomics and greatly reduce the cost and labor investment required for determination of nearly complete genome sequences of uncultured bacteria from environmental samples. PMID:26389587

Parametric Amplification For Detecting Weak Optical Signals

NASA Technical Reports Server (NTRS)

Hemmati, Hamid; Chen, Chien; Chakravarthi, Prakash

1996-01-01

Optical-communication receivers of proposed type implement high-sensitivity scheme of optical parametric amplification followed by direct detection for reception of extremely weak signals. Incorporates both optical parametric amplification and direct detection into optimized design enhancing effective signal-to-noise ratios during reception in photon-starved (photon-counting) regime. Eliminates need for complexity of heterodyne detection scheme and partly overcomes limitations imposed on older direct-detection schemes by noise generated in receivers and by limits on quantum efficiencies of photodetectors.

Applications and suggested directions of transition research

NASA Technical Reports Server (NTRS)

Bushnell, Dennis L.

1989-01-01

This paper summarizes many of the applications of transition research having significant technological importance and suggests critical general areas for further research. Critical research requirements include identification and quantification of initial disturbance fields, disturbance internalization by inviscid and viscous flow fields and amplification in nonboundary-layer flows, along with elucidation of the roughness-induced destabilization physics.

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

Treesearch

Alena K. Oliver; Shawn P. Brown; Mac A. Callaham; Ari Jumpponen

2015-01-01

Rare taxa overwhelm metabarcoding data generated using next-generation sequencing (NGS). Low frequency Operational Taxonomic Units (OTUs) may be artifacts generated by PCR-amplification errors resulting from polymerase mispairing. We analyzed two Internal Transcribed Spacer 2 (ITS2) MiSeq libraries generated with proofreading (ThermoScientific Phusion

An experimental topographic amplification study at Los Alamos National Laboratory using ambient vibrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stolte, Andrew C.; Cox, Brady R.; Lee, Richard C.

An experimental study aimed at investigating potential topographic amplification of seismic waves was conducted on a 50-m-tall and 185-m-wide soft-rock ridge located at Los Alamos National Laboratory near Los Alamos, New Mexico. Ten portable broadband seismograph stations were placed in arrays across the ridge and left to record ambient vibration data for ~9 hours. Clear evidence of topographic amplification was observed by comparing spectral ratios calculated from ambient noise recordings at the toe, slope, and crest of the instrumented ridge. The inferred resonance frequency of the ridge obtained from the experimental recordings was found to agree well with several simplemore » estimates of the theoretical resonance frequency based on its geometry and stiffness. Results support the feasibility of quantifying the frequency range of topographic amplification solely using ambient vibrations, rather than strong or weak ground motions. Additionally, comparisons have been made between a number of widely used experimental methods for quantifying topographic effects, such as the standard spectral ratio, median reference method, and horizontal-to-vertical spectral ratio. As a result, differences in the amplification and frequency range of topographic effects indicated by these methods highlight the importance of choosing a reference condition that is appropriate for the site-specific conditions and goals associated with an experimental topographic amplification study.« less

An experimental topographic amplification study at Los Alamos National Laboratory using ambient vibrations

DOE PAGES

Stolte, Andrew C.; Cox, Brady R.; Lee, Richard C.

2017-03-14

An experimental study aimed at investigating potential topographic amplification of seismic waves was conducted on a 50-m-tall and 185-m-wide soft-rock ridge located at Los Alamos National Laboratory near Los Alamos, New Mexico. Ten portable broadband seismograph stations were placed in arrays across the ridge and left to record ambient vibration data for ~9 hours. Clear evidence of topographic amplification was observed by comparing spectral ratios calculated from ambient noise recordings at the toe, slope, and crest of the instrumented ridge. The inferred resonance frequency of the ridge obtained from the experimental recordings was found to agree well with several simplemore » estimates of the theoretical resonance frequency based on its geometry and stiffness. Results support the feasibility of quantifying the frequency range of topographic amplification solely using ambient vibrations, rather than strong or weak ground motions. Additionally, comparisons have been made between a number of widely used experimental methods for quantifying topographic effects, such as the standard spectral ratio, median reference method, and horizontal-to-vertical spectral ratio. As a result, differences in the amplification and frequency range of topographic effects indicated by these methods highlight the importance of choosing a reference condition that is appropriate for the site-specific conditions and goals associated with an experimental topographic amplification study.« less

Multiplex qPCR for reliable detection and differentiation of Burkholderia mallei and Burkholderia pseudomallei.

PubMed

Janse, Ingmar; Hamidjaja, Raditijo A; Hendriks, Amber C A; van Rotterdam, Bart J

2013-02-14

Burkholderia mallei and B. pseudomallei are two closely related species of highly virulent bacteria that can be difficult to detect. Pathogenic Burkholderia are endemic in many regions worldwide and cases of infection, sometimes brought by travelers from unsuspected regions, also occur elsewhere. Rapid, sensitive methods for identification of B. mallei and B. pseudomallei are urgently needed in the interests of patient treatment and epidemiological surveillance. Signature sequences for sensitive, specific detection of pathogenic Burkholderia based on published genomes were identified and a qPCR assay was designed and validated. A single-reaction quadruplex qPCR assay for the detection of pathogenic Burkholderia, which includes a marker for internal control of DNA extraction and amplification, was developed. The assay permits differentiation of B. mallei and B. pseudomallei strains, and probit analysis showed a very low detection limit. Use of a multicopy signature sequence permits detection of less than 1 genome equivalent per reaction. The new assay permits rapid detection of pathogenic Burkholderia and combines enhanced sensitivity, species differentiation, and inclusion of an internal control for both DNA extraction and PCR amplification.

Development of internally controlled duplex real-time NASBA diagnostics assays for the detection of microorganisms associated with bacterial meningitis.

PubMed

Clancy, Eoin; Coughlan, Helena; Higgins, Owen; Boo, Teck Wee; Cormican, Martin; Barrett, Louise; Smith, Terry J; Reddington, Kate; Barry, Thomas

2016-08-01

Three duplex molecular beacon based real-time Nucleic Acid Sequence Based Amplification (NASBA) assays have been designed and experimentally validated targeting RNA transcripts for the detection and identification of Haemophilus influenzae, Neisseria meningitidis and Streptococcus pneumoniae respectively. Each real-time NASBA diagnostics assay includes an endogenous non-competitive Internal Amplification Control (IAC) to amplify the splice variant 1 mRNA of the Homo sapiens TBP gene from human total RNA. All three duplex real-time NASBA diagnostics assays were determined to be 100% specific for the target species tested for. Also the Limits of Detection (LODs) for the H. influenzae, N. meningitidis and S. pneumoniae duplex real-time NASBA assays were 55.36, 0.99, and 57.24 Cell Equivalents (CE) respectively. These robust duplex real-time NASBA diagnostics assays have the potential to be used in a clinical setting for the rapid (<60min) specific detection and identification of the most prominent microorganisms associated with bacterial meningitis in humans. Copyright © 2016 Elsevier B.V. All rights reserved.

Performance of MgO:PPLN, KTA, and KNbO₃ for mid-wave infrared broadband parametric amplification at high average power.

PubMed

Baudisch, M; Hemmer, M; Pires, H; Biegert, J

2014-10-15

The performance of potassium niobate (KNbO₃), MgO-doped periodically poled lithium niobate (MgO:PPLN), and potassium titanyl arsenate (KTA) were experimentally compared for broadband mid-wave infrared parametric amplification at a high repetition rate. The seed pulses, with an energy of 6.5 μJ, were amplified using 410 μJ pump energy at 1064 nm to a maximum pulse energy of 28.9 μJ at 3 μm wavelength and at a 160 kHz repetition rate in MgO:PPLN while supporting a transform limited duration of 73 fs. The high average powers of the interacting beams used in this study revealed average power-induced processes that limit the scaling of optical parametric amplification in MgO:PPLN; the pump peak intensity was limited to 3.8  GW/cm² due to nonpermanent beam reshaping, whereas in KNbO₃ an absorption-induced temperature gradient in the crystal led to permanent internal distortions in the crystal structure when operated above a pump peak intensity of 14.4  GW/cm².

Distractor inhibition: principles of operation during selective attention.

PubMed

Wyatt, Natalie; Machado, Liana

2013-02-01

Research suggests that although target amplification acts as the main determinant of the efficacy of selective attention, distractor inhibition contributes under some circumstances. Here we aimed to gain insight into the operating principles that regulate the use of distractor inhibition during selective attention. The results suggest that, in contrast to target amplification, distractor inhibition does not onset earlier or strengthen in response to advance location information. Instead, when the location of the impending distractor was predictable, evidence of inhibitory processing weakened. Furthermore, the results suggest that distractor inhibition does not operate as a compensatory mechanism for target amplification, as evidenced by the lack of an increase in inhibitory effects when reliance on target amplification was disrupted. Unexpected emergence of inhibitory effects for improbable targets provided evidence that distractor inhibition was at work even when no inhibitory effects manifested. Overall, the pattern of inhibitory effects is interpreted as indicating that, although distractor inhibition mounts primarily reactively rather than preemptively, advance information can help prevent overreaction to the distractor. Of course, less overreaction reduces the chances of behavioral inhibitory effects manifesting even when distractor inhibition has contributed to selective attention; thus, interpreting an absence of inhibitory effects should be done cautiously. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Competitor internal standards for quantitative detection of mycoplasma DNA.

PubMed

Sidhu, M K; Rashidbaigi, A; Testa, D; Liao, M J

1995-05-01

Homologous internal controls were used as competitor DNA in the polymerase chain reaction for the quantitative detection of mycoplasma DNA. PCR primer sets were designed on the basis of the most conserved nucleotide sequences of the 16S rRNA gene of mycoplasma species. Amplification of this gene was examined in five different mycoplasma species: Mycoplasma orale, M. hyorhinus, M. synoviae, M. gallisepticum and M. pneumoniae. To evaluate the primers, a number of different cell lines were assayed for the detection of mycoplasma infections. All positive cell lines showed a distinct product on agarose gels while uninfected cells showed no DNA amplification. Neither bacterial nor eukaryotic DNA produced any cross-reaction with the primers used, thus confirming their specificity. Internal control DNA to be used for quantitation was constructed by modifying the sizes of the wild-type amplified products and cloning them in plasmid vectors. These controls used the same primer binding sites as the wild-type and the amplified products were differentiated by a size difference. The detection limits for all the mycoplasma species by competitive quantitative PCR were estimated to range from 4 to 60 genome copies per assay as determined by ethidium bromide-stained agarose gels. These internal standards also serve as positive controls in PCR-based detection of mycoplasma DNA, and therefore accidental contamination of test samples with wild-type positive controls can be eliminated. The quantitative PCR method developed will be useful in monitoring the progression and significance of mycoplasma in the disease process.

1D and 2D site amplification effects at Tarcento (Friuli, NE Italy), 30 years later

NASA Astrophysics Data System (ADS)

Cauzzi, Carlo; Faccioli, Ezio; Costa, Giovanni

2011-01-01

A temporary accelerometer network has been installed in Tarcento (Friuli, NE Italy), a small town heavily hit by the 1976-1977 Friuli earthquake sequence, as a part of an ongoing research project aimed at ground motion simulation and generation of shakemaps in the near-field of an earthquake. The network operated from October 2008 to April 2010 and consisted of three K2 accelerographs with internal Episensor, distributed over a linear array of about 1.5 km length. Tarcento town had been chosen, at the end of the 1970s, as the ideal site for a pilot microzonation study, the first of this kind in Italy, in which a substantial number of field (and laboratory) tests were carried out in order to assess the mechanical properties of local alluvium deposits and their complex (3D) geometrical configuration. The data from the temporary network, illustrated herein, allow for proper verification and review of some of the quantitative predictions formulated in the 1980 study. As argued in the discussion section, we also believe that the data are apt to provide valuable information of more general interest on the complex seismic response of alluvium-filled valleys, and we show therein how the observations can be interpreted in the light of presently available parametric simulation studies and simplified criteria for handling basin amplification effects.

Observational Evidence for Desert Amplification Using Multiple Satellite Datasets.

PubMed

Wei, Nan; Zhou, Liming; Dai, Yongjiu; Xia, Geng; Hua, Wenjian

2017-05-17

Desert amplification identified in recent studies has large uncertainties due to data paucity over remote deserts. Here we present observational evidence using multiple satellite-derived datasets that desert amplification is a real large-scale pattern of warming mode in near surface and low-tropospheric temperatures. Trend analyses of three long-term temperature products consistently confirm that near-surface warming is generally strongest over the driest climate regions and this spatial pattern of warming maximizes near the surface, gradually decays with height, and disappears in the upper troposphere. Short-term anomaly analyses show a strong spatial and temporal coupling of changes in temperatures, water vapor and downward longwave radiation (DLR), indicating that the large increase in DLR drives primarily near surface warming and is tightly associated with increasing water vapor over deserts. Atmospheric soundings of temperature and water vapor anomalies support the results of the long-term temperature trend analysis and suggest that desert amplification is due to comparable warming and moistening effects of the troposphere. Likely, desert amplification results from the strongest water vapor feedbacks near the surface over the driest deserts, where the air is very sensitive to changes in water vapor and thus efficient in enhancing the longwave greenhouse effect in a warming climate.

Incorporation of Dynamic SSI Effects in the Design Response Spectra

NASA Astrophysics Data System (ADS)

Manjula, N. K.; Pillai, T. M. Madhavan; Nagarajan, Praveen; Reshma, K. K.

2018-05-01

Many studies in the past on dynamic soil-structure interactions have revealed the detrimental and advantageous effects of soil flexibility. Based on such studies, the design response spectra of international seismic codes are being improved worldwide. The improvements required for the short period range of the design response spectra in the Indian seismic code (IS 1893:2002) are presented in this paper. As the recent code revisions has not incorporated the short period amplifications, proposals given in this paper are equally applicable for the latest code also (IS 1893:2016). Analyses of single degree of freedom systems are performed to predict the required improvements. The proposed modifications to the constant acceleration portion of the spectra are evaluated with respect to the current design spectra in Eurocode 8.

Development of a quantitative-competitive PCR for quantification of human cytomegalovirus load and comparison with antigenaemia, viraemia and pp67 RNA detection by nucleic acid sequence-based amplification.

PubMed

Bergallo, M; Costa, C; Tarallo, S; Daniele, R; Merlino, C; Segoloni, G P; Negro Ponzi, A; Cavallo, R

2006-06-01

The human cytomegalovirus (HCMV) is an important pathogen in immunocompromised patients, such as transplant recipients. The use of sensitive and rapid diagnostic assays can have a great impact on antiviral prophylaxis and therapy monitoring and diagnosing active disease. Quantification of HCMV DNA may additionally have prognostic value and guide routine management. The aim of this study was to develop a reliable internally-controlled quantitative-competitive PCR (QC-PCR) for the detection and quantification of HCMV DNA viral load in peripheral blood and compare it with other methods: the HCMV pp65 antigenaemia assay in leukocyte fraction, the HCMV viraemia, both routinely employed in our laboratory, and the nucleic acid sequence-based amplification (NASBA) for detection of HCMV pp67-mRNA. Quantitative-competitive PCR is a procedure for nucleic acid quantification based on co-amplification of competitive templates, the target DNA and a competitor functioning as internal standard. In particular, a standard curve is generated by amplifying 10(2) to 10(5) copies of target pCMV-435 plasmid with 10(4) copies of competitor pCMV-C plasmid. Clinical samples derived from 40 kidney transplant patients were tested by spiking 10(4) copies of pCMV-C into the PCR mix as internal control, and comparing results with the standard curve. Of the 40 patients studied, 39 (97.5%) were positive for HCMV DNA by QC-PCR. While the correlation between the number of pp65-positive cells and the number of HCMV DNA genome copies/mL and the former and the pp67mRNA-positivity were statistically significant, there was no significant correlation between HCMV DNA viral load assayed by QC-PCR and HCMV viraemia. The QC-PCR assay could detect from 10(2) to over 10(7) copies of HCMV DNA with a range of linearity between 10(2) and 10(5) genomes.

Control of the amplifications of large-band amplitude-modulated pulses in an Nd-glass amplifier chain

NASA Astrophysics Data System (ADS)

Videau, Laurent; Bar, Emmanuel; Rouyer, Claude; Gouedard, Claude; Garnier, Josselin C.; Migus, Arnold

1999-07-01

We study nonlinear effects in amplification of partially coherent pulses in a high power laser chain. We compare statistical models with experimental results for temporal and spatial effects. First we show the interplay between self-phase modulation which broadens spectrum bandwidth and gain narrowing which reduces output spectrum. Theoretical results are presented for spectral broadening and energy limitation in case of time-incoherent pulses. In a second part, we introduce spatial incoherence with a multimode optical fiber which provides a smoothed beam. We show with experimental result that spatial filter pinholes are responsible for additive energy losses in the amplification. We develop a statistical model which takes into account the deformation of the focused beam as a function of B integral. We estimate the energy transmission of the spatial filter pinholes and compare this model with experimental data. We find a good agreement between theory and experiments. As a conclusion, we present an analogy between temporal and spatial effects with spectral broadening and spectral filter. Finally, we propose some solutions to control energy limitations in smoothed pulses amplification.

Hearing Loss and Cognitive-Communication Test Performance of Long-Term Care Residents With Dementia: Effects of Amplification

ERIC Educational Resources Information Center

Hopper, Tammy; Slaughter, Susan E.; Hodgetts, Bill; Ostevik, Amberley; Ickert, Carla

2016-01-01

Purpose: The study aims were (a) to explore the relationship between hearing loss and cognitive-communication performance of individuals with dementia, and (b) to determine if hearing loss is accurately identified by long-term care (LTC) staff. The research questions were (a) What is the effect of amplification on cognitive-communication test…

Can Anomalous Amplification be Attained without Postselection?

PubMed

Martínez-Rincón, Julián; Liu, Wei-Tao; Viza, Gerardo I; Howell, John C

2016-03-11

We present a parameter estimation technique based on performing joint measurements of a weak interaction away from the weak-value-amplification approximation. Two detectors are used to collect full statistics of the correlations between two weakly entangled degrees of freedom. Without discarding of data, the protocol resembles the anomalous amplification of an imaginary-weak-value-like response. The amplification is induced in the difference signal of both detectors allowing robustness to different sources of technical noise, and offering in addition the advantages of balanced signals for precision metrology. All of the Fisher information about the parameter of interest is collected. A tunable phase controls the strength of the amplification response. We experimentally demonstrate the proposed technique by measuring polarization rotations in a linearly polarized laser pulse. We show that in the presence of technical noise the effective sensitivity and precision of a split detector is increased when compared to a conventional continuous-wave balanced detection technique.

Can Anomalous Amplification be Attained without Postselection?

NASA Astrophysics Data System (ADS)

Martínez-Rincón, Julián; Liu, Wei-Tao; Viza, Gerardo I.; Howell, John C.

2016-03-01

We present a parameter estimation technique based on performing joint measurements of a weak interaction away from the weak-value-amplification approximation. Two detectors are used to collect full statistics of the correlations between two weakly entangled degrees of freedom. Without discarding of data, the protocol resembles the anomalous amplification of an imaginary-weak-value-like response. The amplification is induced in the difference signal of both detectors allowing robustness to different sources of technical noise, and offering in addition the advantages of balanced signals for precision metrology. All of the Fisher information about the parameter of interest is collected. A tunable phase controls the strength of the amplification response. We experimentally demonstrate the proposed technique by measuring polarization rotations in a linearly polarized laser pulse. We show that in the presence of technical noise the effective sensitivity and precision of a split detector is increased when compared to a conventional continuous-wave balanced detection technique.

Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.

PubMed Central

Hofmann, H P; Limmer, S; Hornung, V; Sprinzl, M

1997-01-01

RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA. PMID:9409620

Specific detection of Xanthomonas axonopodis pv. dieffenbachiae in anthurium (Anthurium andreanum) tissues by nested PCR.

PubMed

Robène-Soustrade, Isabelle; Laurent, Philippe; Gagnevin, Lionel; Jouen, Emmanuel; Pruvost, Olivier

2006-02-01

Efficient control of Xanthomonas axonopodis pv. dieffenbachiae, the causal agent of anthurium bacterial blight, requires a sensitive and reliable diagnostic tool. A nested PCR test was developed from a sequence-characterized amplified region marker identified by randomly amplified polymorphic DNA PCR for the detection of X. axonopodis pv. dieffenbachiae. Serological and pathogenicity tests were performed concurrently with the nested PCR test with a large collection of X. axonopodis pv. dieffenbachiae strains that were isolated worldwide and are pathogenic to anthurium and/or other aroids. The internal primer pair directed amplification of the expected product (785 bp) for all 70 X. axonopodis pv. dieffenbachiae strains pathogenic to anthurium tested and for isolates originating from syngonium and not pathogenic to anthurium. This finding is consistent with previous studies which indicated that there is a high level of relatedness between strains from anthurium and strains from syngonium. Strains originating from the two host genera can be distinguished by restriction analysis of the amplification product. No amplification product was obtained with 98 strains of unrelated phytopathogenic bacteria or saprophytic bacteria from the anthurium phyllosphere, except for a weak signal obtained for one X. axonopodis pv. allii strain. Nevertheless, restriction enzyme analysis permitted the two pathovars to be distinguished. The detection threshold obtained with pure cultures or plant extracts (10(3) CFU ml(-1)) allowed detection of the pathogen from symptomless contaminated plants. This test could be a useful diagnostic tool for screening propagation stock plant material and for monitoring international movement of X. axonopodis pv. dieffenbachiae.

Comparison of Three Different Sensitive Assays for Hepatitis B Virus DNA in Monitoring of Responses to Antiviral Therapy

PubMed Central

Chan, Henry L. Y.; Leung, Nancy W. Y.; Lau, Tracy C. M.; Wong, May L.; Sung, Joseph J. Y.

2000-01-01

The aim of our study was to compare the performances of two new hepatitis B virus (HBV) DNA assays, a cross-linking assay (NAXCOR) and a hybrid-capture amplification assay (Digene), versus the widely used branched-DNA (bDNA) assay (Chiron) in the monitoring of HBV DNA levels during antiviral treatment. Serial serum samples from 12 chronically HBV infected patients undergoing a phase II trial of an antiviral drug, 2′,3′-dideoxy-5-fluoro-3′-thiacytidine (FTC), were studied. A total of 96 serum samples were tested for HBV DNA using the cross-linking, hybrid-capture amplification, and bDNA assays. In the comparison of the cross-linking and bDNA assays, concordant results were found in 77 (80.3%) samples, no significant difference was found between the median log10 HBV DNA levels (6.66 versus 7.17 meq/ml), and the results of the two assays were closely correlated (r = 0.95). In the comparison of the hybrid-capture amplification and bDNA assays, concordant results were found in 79 (82.3%) samples, no significant difference was found between the median log10 HBV DNA levels (6.98 versus 6.99 meq/ml), and the results of the two assays were closely correlated (r = 0.99). Six (6.3%) samples by the cross-linking assay and 10 (10.4%) samples by the bDNA assay required retesting because of unacceptably high within-run coefficients of variance. No sample required retesting in the hybrid-capture amplification assay according to the internal validation. In conclusion, the cross-linking and hybrid-capture amplification assays were as sensitive as the bDNA assay for HBV DNA detection and can be recommended for monitoring of HBV DNA levels during antiviral treatment. PMID:10970358

Limits on amplification by Aharonov-Albert-Vaidman weak measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koike, Tatsuhiko; Tanaka, Saki

2011-12-15

We analyze the amplification by the Aharonov-Albert-Vaidman weak quantum measurement on a Sagnac interferometer [Dixon et al., Phys. Rev. Lett. 102, 173601 (2009)] up to all orders of the coupling strength between the measured system and the measuring device. The amplifier transforms a small tilt of a mirror into a large transverse displacement of the laser beam. The conventional analysis has shown that the measured value is proportional to the weak value, so that the amplification can be made arbitrarily large in the cost of decreasing output laser intensity. It is shown that the measured displacement and the amplification factormore » are in fact not proportional to the weak value and rather vanish in the limit of infinitesimal output intensity. We derive the optimal overlap of the pre- and postselected states with which the amplification become maximum. We also show that the nonlinear effects begin to arise in the performed experiments so that any improvements in the experiment, typically with an amplification greater than 100, should require the nonlinear theory in translating the observed value to the original displacement.« less

Simple method for production of internal control DNA for Mycobacterium tuberculosis polymerase chain reaction assays.

PubMed Central

deWit, D; Wootton, M; Allan, B; Steyn, L

1993-01-01

A simple method for the production of internal control DNA for two well-established Mycobacterium tuberculosis polymerase chain reaction assays is described. The internal controls were produced from Mycobacterium kansasii DNA with the same primers but at a lower annealing temperature than that used in the standard assays. In both assays, therefore, the internal control DNA has the same primer-binding sequences at the target DNA. One-microgram quantities of internal control DNA which was not contaminated with target DNA could easily be produced by this method. The inclusion of the internal control in the reaction mixture did not affect the efficiency of amplification of the target DNA. The method is simple and rapid and should be adaptable to most M. tuberculosis polymerase chain reaction assays. Images PMID:8370752

Nanoparticles Affect PCR Primarily via Surface Interactions with PCR Components: Using Amino-Modified Silica-Coated Magnetic Nanoparticles as a Main Model.

PubMed

Bai, Yalong; Cui, Yan; Paoli, George C; Shi, Chunlei; Wang, Dapeng; Shi, Xianming

2015-06-24

Nanomaterials have been widely reported to affect the polymerase chain reaction (PCR). However, many studies in which these effects were observed were not comprehensive, and many of the proposed mechanisms have been primarily speculative. In this work, we used amino-modified silica-coated magnetic nanoparticles (ASMNPs, which can be collected very easily using an external magnetic field) as a model and compared them with gold nanoparticles (AuNPs, which have been studied extensively) to reveal the mechanisms by which nanoparticles affect PCR. We found that nanoparticles affect PCR primarily by binding to PCR components: (1) inhibition, (2) specifity, and (3) efficiency and yield of PCR are impacted. (1) Excess nanomaterials inhibit PCR by adsorbing to DNA polymerase, Mg(2+), oligonucleotide primers, or DNA templates. Nanoparticle surface-active groups are particularly important to this effect. (2, a) Nanomaterials do not inhibit nonspecific amplification products caused by false priming as previously surmised. It was shown that relatively low concentrations of nanoparticles inhibited the amplification of long amplicons, and increasing the amount of nanoparticles inhibited the amplification of short amplicons. This concentration phenomenon appears to be the result of the formation of "joints" upon the adsorption of ASMNPs to DNA templates. (b) Nanomaterials are able to inhibit nonspecific amplification products due to incomplete amplification by preferably adsorbing single-stranded incomplete amplification products. (3) Some types of nanomaterials, such as AuNPs, enhance the efficiency and yield of PCR because these types of nanoparticles can adsorb to single-stranded DNA more strongly than to double-stranded DNA. This behavior assists in the rapid and thorough denaturation of double-stranded DNA templates. Therefore, the interaction between the surface of nanoparticles and PCR components is sufficient to explain most of the effects of nanoparticles on PCR.

Voice amplification as a means of reducing vocal load for elementary music teachers.

PubMed

Morrow, Sharon L; Connor, Nadine P

2011-07-01

Music teachers are over four times more likely than classroom teachers to develop voice disorders and greater than eight times more likely to have voice-related problems than the general public. Research has shown that individual voice-use parameters of phonation time, fundamental frequency and vocal intensity, as well as vocal load as calculated by cycle dose and distance dose are significantly higher for music teachers than their classroom teacher counterparts. Finding effective and inexpensive prophylactic measures to decrease vocal load for music teachers is an important aspect for voice preservation for this group of professional voice users. The purpose of this study was to determine the effects of voice amplification on vocal intensity and vocal load in the workplace as measured using a KayPENTAX Ambulatory Phonation Monitor (APM) (KayPENTAX, Lincoln Park, NJ). Seven music teachers were monitored for 1 workweek using an APM to determine average vocal intensity (dB sound pressure level [SPL]) and vocal load as calculated by cycle dose and distance dose. Participants were monitored a second week while using a voice amplification unit (Asyst ChatterVox; Asyst Communications Company, Inc., Indian Creek, IL). Significant decreases in mean vocal intensity of 7.00-dB SPL (P<0.001) were found using amplification, along with significant decreases (P=0.001) in cycle dose and distance dose. In addition, mean phonation time was found to decrease using amplification (P=0.023). These data suggest that voice amplification may be an effective intervention to decrease the potentially damaging vocal loads experienced by elementary music teachers in the classroom. Copyright © 2011 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

The effects of host diversity on vector-borne disease: the conditions under which diversity will amplify or dilute the disease risk.

PubMed

Miller, Ezer; Huppert, Amit

2013-01-01

Multihost vector-borne infectious diseases form a significant fraction of the global infectious disease burden. In this study we explore the relationship between host diversity, vector behavior, and disease risk. To this end, we have developed a new dynamic model which includes two distinct host species and one vector species with variable preferences. With the aid of the model we were able to compute the basic reproductive rate, R 0, a well-established measure of disease risk that serves as a threshold parameter for disease outbreak. The model analysis reveals that the system has two different qualitative behaviors: (i) the well-known dilution effect, where the maximal R0 is obtained in a community which consists a single host (ii) a new amplification effect, denoted by us as diversity amplification, where the maximal R0 is attained in a community which consists both hosts. The model analysis extends on previous results by underlining the mechanism of both, diversity amplification and the dilution, and specifies the exact conditions for their occurrence. We have found that diversity amplification occurs where the vector prefers the host with the highest transmission ability, and dilution is obtained when the vector does not show any preference, or it prefers to bite the host with the lower transmission ability. The mechanisms of dilution and diversity amplification are able to account for the different and contradictory patterns often observed in nature (i.e., in some cases disease risk is increased while in other is decreased when the diversity is increased). Implication of the diversity amplification mechanism also challenges current premises about the interaction between biodiversity, climate change, and disease risk and calls for retrospective thinking in planning intervention policies aimed at protecting the preferred host species.

Improving Mobile Phone Speech Recognition by Personalized Amplification: Application in People with Normal Hearing and Mild-to-Moderate Hearing Loss.

PubMed

Kam, Anna Chi Shan; Sung, John Ka Keung; Lee, Tan; Wong, Terence Ka Cheong; van Hasselt, Andrew

In this study, the authors evaluated the effect of personalized amplification on mobile phone speech recognition in people with and without hearing loss. This prospective study used double-blind, within-subjects, repeated measures, controlled trials to evaluate the effectiveness of applying personalized amplification based on the hearing level captured on the mobile device. The personalized amplification settings were created using modified one-third gain targets. The participants in this study included 100 adults of age between 20 and 78 years (60 with age-adjusted normal hearing and 40 with hearing loss). The performance of the participants with personalized amplification and standard settings was compared using both subjective and speech-perception measures. Speech recognition was measured in quiet and in noise using Cantonese disyllabic words. Subjective ratings on the quality, clarity, and comfortableness of the mobile signals were measured with an 11-point visual analog scale. Subjective preferences of the settings were also obtained by a paired-comparison procedure. The personalized amplification application provided better speech recognition via the mobile phone both in quiet and in noise for people with hearing impairment (improved 8 to 10%) and people with normal hearing (improved 1 to 4%). The improvement in speech recognition was significantly better for people with hearing impairment. When the average device output level was matched, more participants preferred to have the individualized gain than not to have it. The personalized amplification application has the potential to improve speech recognition for people with mild-to-moderate hearing loss, as well as people with normal hearing, in particular when listening in noisy environments.

Differential impact of ionic and coordinate covalent chromium (Cr)-DNA binding on DNA replication.

PubMed

Fornsaglio, Jamie L; O'Brien, Travis J; Patierno, Steven R

2005-11-01

The reactive species produced by the reduction of Cr(VI), particularly Cr(III), can form both ionic and coordinate covalent complexes with DNA. These Cr(III)-DNA interactions consist of Cr-DNA monoadducts, Cr-DNA ternary adducts, and Cr-DNA interstrand cross-links (Cr-ICLs), the latter of which are DNA polymerase arresting lesions (PALs). We sought to determine the impact of Cr-DNA interactions on the formation of replication blocking lesions in S. cerevisiae using a PCR-based method. We found that target sequence (TS) amplification using DNA isolated from Cr(VI)-treated yeast actually increased as a function of Cr(VI) concentration. Moreover, the enhanced TS amplification was reproduced in vitro using Cr(III)-treated DNA. In contrast, PCR amplification of TS from DNA isolated from yeast exposed to equitoxic doses of the inorganic DNA cross-linking agent cisplatin (CDDP), was decreased in a concentration-dependent manner. This paradox suggested that a specific Cr-DNA interaction, such as an ionic Cr-DNA complex, was responsible for the enhanced TS amplification, thereby masking the replication-blocking effect of certain ternary Cr-DNA adducts (i.e. interstrand cross-links). To test this possibility, we removed ionically associated Cr from the DNA using salt extraction prior to PCR analysis. This procedure obviated the increased amplification and revealed a dose-dependent decrease in TS amplification and an increase in Cr-PALs. These data from DNA analyzed ex vivo after treatment of intact cells indicate that ionic interactions of Cr with DNA result in increased DNA amplification whereas coordinate-covalent Cr-DNA complexes lead to formation of Cr-PALs. Thus, these results suggest that treatment of living cells with Cr(VI) leads to two modes of Cr-binding, which may have conflicting effects on DNA replication.

Comparisons of Low-Strain Amplification at Soft-Sediment, Hard-Rock, Topographic, and Fault-Zone Sites in the Hayward Fault Zone, California

NASA Astrophysics Data System (ADS)

Catchings, R.; Strayer, L. M.; Goldman, M.

2014-12-01

We used a temporary network of approximately 600 seismographs to record a seismic source generated by the collapse of a 13-story building near the active trace of the Hayward Fault. These data allow us to evaluate variations in ground shaking across a series of 30 2-km-long radial arrays centered on the seismic source. Individual seismographs were spaced at 200-m intervals, forming a series of 360°concentric arrays around the seismic source. The data show variations in amplification caused by (1) soft sediments within the East Bay alluvial plain (EBAP), (2) hard rocks within the East Bay hills (EBH), (3) low-velocity rocks within the Hayward Fault zone (HFZ), and (4) topography. Given that ground shaking varies strongly with distance from the source, the concentric arrays allowed us to measure variations in ground shaking as a function of azimuth at fixed distances from the source. On individual linear profiles within the concentric arrays, we observed decreases in peak ground velocity (PGV) across the HFZ and other faults within the EBH. However, for a given distance from the source, we observe four to five fold amplification from the EBAP sites compared to most sites in the EBH. Topographic and fault-zone amplification effects within the EBH, however, are greater than the EBAP sediment amplification. Thus, for future earthquakes, shaking at many sites within the EBH may be significantly stronger than many sites within the EBAP. These observations suggest amplification can be expected in unconsolidated sediments, but topographic and fault-zone amplification can be larger. This confirms the importance of site effects for hazard mitigation and in interpreting MMI for future and historical earthquakes.

Null expectations for disease dynamics in shrinking habitat: dilution or amplification?

PubMed Central

McCallum, Hamish I.; Gillespie, Thomas R.

2017-01-01

As biodiversity declines with anthropogenic land-use change, it is increasingly important to understand how changing biodiversity affects infectious disease risk. The dilution effect hypothesis, which points to decreases in biodiversity as critical to an increase in infection risk, has received considerable attention due to the allure of a win–win scenario for conservation and human well-being. Yet some empirical data suggest that the dilution effect is not a generalizable phenomenon. We explore the response of pathogen transmission dynamics to changes in biodiversity that are driven by habitat loss using an allometrically scaled multi-host model. With this model, we show that declining habitat, and thus declining biodiversity, can lead to either increasing or decreasing infectious-disease risk, measured as endemic prevalence. Whether larger habitats, and thus greater biodiversity, lead to a decrease (dilution effect) or increase (amplification effect) in infection prevalence depends upon the pathogen transmission mode and how host competence scales with body size. Dilution effects were detected for most frequency-transmitted pathogens and amplification effects were detected for density-dependent pathogens. Amplification effects were also observed over a particular range of habitat loss in frequency-dependent pathogens when we assumed that host competence was greatest in large-bodied species. By contrast, only amplification effects were observed for density-dependent pathogens; host competency only affected the magnitude of the effect. These models can be used to guide future empirical studies of biodiversity–disease relationships across gradients of habitat loss. The type of transmission, the relationship between host competence and community assembly, the identity of hosts contributing to transmission, and how transmission scales with area are essential factors to consider when elucidating the mechanisms driving disease risk in shrinking habitat. This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications'. PMID:28438921

Null expectations for disease dynamics in shrinking habitat: dilution or amplification?

PubMed

Faust, Christina L; Dobson, Andrew P; Gottdenker, Nicole; Bloomfield, Laura S P; McCallum, Hamish I; Gillespie, Thomas R; Diuk-Wasser, Maria; Plowright, Raina K

2017-06-05

As biodiversity declines with anthropogenic land-use change, it is increasingly important to understand how changing biodiversity affects infectious disease risk. The dilution effect hypothesis, which points to decreases in biodiversity as critical to an increase in infection risk, has received considerable attention due to the allure of a win-win scenario for conservation and human well-being. Yet some empirical data suggest that the dilution effect is not a generalizable phenomenon. We explore the response of pathogen transmission dynamics to changes in biodiversity that are driven by habitat loss using an allometrically scaled multi-host model. With this model, we show that declining habitat, and thus declining biodiversity, can lead to either increasing or decreasing infectious-disease risk, measured as endemic prevalence. Whether larger habitats, and thus greater biodiversity, lead to a decrease (dilution effect) or increase (amplification effect) in infection prevalence depends upon the pathogen transmission mode and how host competence scales with body size. Dilution effects were detected for most frequency-transmitted pathogens and amplification effects were detected for density-dependent pathogens. Amplification effects were also observed over a particular range of habitat loss in frequency-dependent pathogens when we assumed that host competence was greatest in large-bodied species. By contrast, only amplification effects were observed for density-dependent pathogens; host competency only affected the magnitude of the effect. These models can be used to guide future empirical studies of biodiversity-disease relationships across gradients of habitat loss. The type of transmission, the relationship between host competence and community assembly, the identity of hosts contributing to transmission, and how transmission scales with area are essential factors to consider when elucidating the mechanisms driving disease risk in shrinking habitat.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'. © 2017 The Author(s).

Detection of Listeria monocytogenes by using the polymerase chain reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bessesen, M.T.; Luo, Q.; Blaser, M.J.

1990-09-01

A method was developed for detection of Listeria monocytogens by polymerase chain reaction amplification followed by agarose gel electrophoresis or dot blot analysis with {sup 32}P-labeled internal probe. The technique identified 95 of 95 L. monocytogenes strains, 0 of 12 Listeria strains of other species, and 0 of 12 non-Listeria strains.

The effects of density gradients on the convective amplification of upper hybrid waves in the magnetosphere

NASA Technical Reports Server (NTRS)

Engel, J.; Kennel, C.

1985-01-01

Intense (at least 10 mV/m) electrostatic plasma waves have been detected near the upper hybrid frequency between + or -50 deg MLAT during recent GEOS-1 crossings. Wave growth rate and convective amplification calculations were carried out in order to explain the occurrence of intense upper hybrid (IUH) events over such a wide range of latitudes. The effects of wave refractions were taken into account in the convective amplification calculations. Specific results are presented for the upper hybrid wave growth of an IUH event occurring at 10 deg MLAT. It is shown that a density gradient may be necessary to explain the observed amplification at 10 deg MLAT. At the equator, however, the long scale length of the magnetic field gradient enables large amplitudes to be attained without a density gradient. The results of a UH ray tracing analysis are discussed within the framework of current theories concerning magnetospheric continuum radiation.

Noiseless intensity amplification of repetitive signals by coherent addition using the temporal Talbot effect

PubMed Central

Maram, Reza; Van Howe, James; Li, Ming; Azaña, José

2014-01-01

Amplification of signal intensity is essential for initiating physical processes, diagnostics, sensing, communications and measurement. During traditional amplification, the signal is amplified by multiplying the signal carriers through an active gain process, requiring the use of an external power source. In addition, the signal is degraded by noise and distortions that typically accompany active gain processes. We show noiseless intensity amplification of repetitive optical pulse waveforms with gain from 2 to ~20 without using active gain. The proposed method uses a dispersion-induced temporal self-imaging (Talbot) effect to redistribute and coherently accumulate energy of the original repetitive waveforms into fewer replica waveforms. In addition, we show how our passive amplifier performs a real-time average of the wave-train to reduce its original noise fluctuation, as well as enhances the extinction ratio of pulses to stand above the noise floor. Our technique is applicable to repetitive waveforms in any spectral region or wave system. PMID:25319207

Evidence that selected amplification of a bacterial lac frameshift allele stimulates Lac(+) reversion (adaptive mutation) with or without general hypermutability.

PubMed Central

Slechta, E Susan; Liu, Jing; Andersson, Dan I; Roth, John R

2002-01-01

In the genetic system of Cairns and Foster, a nongrowing population of an E. coli lac frameshift mutant appears to specifically accumulate Lac(+) revertants when starved on medium including lactose (adaptive mutation). This behavior has been attributed to stress-induced general mutagenesis in a subpopulation of starved cells (the hypermutable state model). We have suggested that, on the contrary, stress has no direct effect on mutability but favors only growth of cells that amplify their leaky mutant lac region (the amplification mutagenesis model). Selection enhances reversion primarily by increasing the mutant lac copy number within each developing clone on the selection plate. The observed general mutagenesis is attributed to a side effect of growth with an amplification-induction of SOS by DNA fragments released from a tandem array of lac copies. Here we show that the S. enterica version of the Cairns system shows SOS-dependent general mutagenesis and behaves in every way like the original E. coli system. In both systems, lac revertants are mutagenized during selection. Eliminating the 35-fold increase in mutation rate reduces revertant number only 2- to 4-fold. This discrepancy is due to continued growth of amplification cells until some clones manage to revert without mutagenesis solely by increasing their lac copy number. Reversion in the absence of mutagenesis is still dependent on RecA function, as expected if it depends on lac amplification (a recombination-dependent process). These observations support the amplification mutagenesis model. PMID:12136002

Inverse four-wave-mixing and self-parametric amplification effect in optical fibre

PubMed Central

Turitsyn, Sergei K.; Bednyakova, Anastasia E.; Fedoruk, Mikhail P.; Papernyi, Serguei B.; Clements, Wallace R.L.

2015-01-01

An important group of nonlinear processes in optical fibre involves the mixing of four waves due to the intensity dependence of the refractive index. It is customary to distinguish between nonlinear effects that require external/pumping waves (cross-phase modulation and parametric processes such as four-wave mixing) and self-action of the propagating optical field (self-phase modulation and modulation instability). Here, we present a new nonlinear self-action effect, self-parametric amplification (SPA), which manifests itself as optical spectrum narrowing in normal dispersion fibre, leading to very stable propagation with a distinctive spectral distribution. The narrowing results from an inverse four-wave mixing, resembling an effective parametric amplification of the central part of the spectrum by energy transfer from the spectral tails. SPA and the observed stable nonlinear spectral propagation with random temporal waveform can find applications in optical communications and high power fibre lasers with nonlinear intra-cavity dynamics. PMID:26345290

The influrence of an optical receiving system on statistical characteristics of a lidar signal

NASA Technical Reports Server (NTRS)

Zuev, A. E.; Banakh, V. A.; Mironov, V. L.

1986-01-01

The effects connected with correlation of direct and backward waves propagating through the same randomly inhomogeneous media can be observed along the path with refection in a turbulent atmosphere. In particular, the mean intensity of the reflected wave can increase in comparison with the wave propagating in the forward direction at a doubled distance; the intensity fluctuations can become stronger. These effects depend on the strength of optical turbulence, as well as on the diffraction sizes of the exit apertures of the source and the reflector. However, the focusing of radiation reflected with a receiving telescope leads, in some cases, to the fact that the dependence of amplification effects on the parameters becomes essentially different. This should be taken into account when alayzing the lidar signals. The effect of backscattering amplification and amplification of the intensity fluctuations is discussed.

Amplification, attenuation, and dispersion of sound in inhomogeneous flows

NASA Technical Reports Server (NTRS)

Kentzer, C. P.

1975-01-01

First order effects of gradients in nonuniform potential flows of a compressible gas are included in a dispersion relation for sound waves. Three nondimensional numbers, the ratio of the change in the kinetic energy in one wavelength to the thermal energy of the gas, the ratio of the change in the total energy in one wavelength to the thermal energy, and the ratio of the dillatation frequency (the rate of expansion per unit volume) to the acoustic frequency, play a role in the separation of the effects of flow gradients into isotropic and anisotropic effects. Dispersion and attenuation (or amplification) of sound are found to be proportional to the wavelength for small wavelength, and depend on the direction of wave propagation relative to flow gradients. Modification of ray acoustics for the effects of flow gradients is suggested, and conditions for amplification and attenuation of sound are discussed.

Quantum amplification and quantum optical tapping with squeezed states and correlated quantum states

NASA Technical Reports Server (NTRS)

Ou, Z. Y.; Pereira, S. F.; Kimble, H. J.

1994-01-01

Quantum fluctuations in a nondegenerate optical parametric amplifier (NOPA) are investigated experimentally with a squeezed state coupled into the internal idler mode of the NOPA. Reductions of the inherent quantum noise of the amplifier are observed with a minimum noise level 0.7 dB below the usual noise level of the amplifier with its idler mode in a vacuum state. With two correlated quantum fields as the amplifier's inputs and proper adjustment of the gain of the amplifier, it is shown that the amplifier's intrinsic quantum noise can be completely suppressed so that noise-free amplification is achieved. It is also shown that the NOPA, when coupled to either a squeezed state or a nonclassically correlated state, can realize quantum tapping of optical information.

Site effects in Port-au-Prince (Haiti) from the analysis of spectral ratio and numerical simulations.

USGS Publications Warehouse

St. Fleur, Sadrac; Bertrand, Etienne; Courboulex, Francoise; Mercier de Lépinay, Bernard; Deschamps, Anne; Hough, Susan E.; Cultrera, Giovanna; Boisson, Dominique; Prepetit, Claude

2016-01-01

To provide better insight into seismic ground motion in the Port‐au‐Prince metropolitan area, we investigate site effects at 12 seismological stations by analyzing 78 earthquakes with magnitude smaller than 5 that occurred between 2010 and 2013. Horizontal‐to‐vertical spectral ratio on earthquake recordings and a standard spectral ratio were applied to the seismic data. We also propose a simplified lithostratigraphic map and use available geotechnical and geophysical data to construct representative soil columns in the vicinity of each station that allow us to compute numerical transfer functions using 1D simulations. At most of the studied sites, spectral ratios are characterized by weak‐motion amplification at frequencies above 5 Hz, in good agreement with the numerical transfer functions. A mismatch between the observed amplifications and simulated response at lower frequencies shows that the considered soil columns could be missing a deeper velocity contrast. Furthermore, strong amplification between 2 and 10 Hz linked to local topographic features is found at one station located in the south of the city, and substantial amplification below 5 Hz is detected near the coastline, which we attribute to deep and soft sediments as well as the presence of surface waves. We conclude that for most investigated sites in Port‐au‐Prince, seismic amplifications due to site effects are highly variable but seem not to be important at high frequencies. At some specific locations, however, they could strongly enhance the low‐frequency content of the seismic ground shaking. Although our analysis does not consider nonlinear effects, we thus conclude that, apart from sites close to the coast, sediment‐induced amplification probably had only a minor impact on the level of strong ground motion, and was not the main reason for the high level of damage in Port‐au‐Prince.

Word Recognition and Learning: Effects of Hearing Loss and Amplification Feature

PubMed Central

Stewart, Elizabeth C.; Willman, Amanda P.; Odgear, Ian S.

2017-01-01

Two amplification features were examined using auditory tasks that varied in stimulus familiarity. It was expected that the benefits of certain amplification features would increase as the familiarity with the stimuli decreased. A total of 20 children and 15 adults with normal hearing as well as 21 children and 17 adults with mild to severe hearing loss participated. Three models of ear-level devices were selected based on the quality of the high-frequency amplification or the digital noise reduction (DNR) they provided. The devices were fitted to each participant and used during testing only. Participants completed three tasks: (a) word recognition, (b) repetition and lexical decision of real and nonsense words, and (c) novel word learning. Performance improved significantly with amplification for both the children and the adults with hearing loss. Performance improved further with wideband amplification for the children more than for the adults. In steady-state noise and multitalker babble, performance decreased for both groups with little to no benefit from amplification or from the use of DNR. When compared with the listeners with normal hearing, significantly poorer performance was observed for both the children and adults with hearing loss on all tasks with few exceptions. Finally, analysis of across-task performance confirmed the hypothesis that benefit increased as the familiarity of the stimuli decreased for wideband amplification but not for DNR. However, users who prefer DNR for listening comfort are not likely to jeopardize their ability to detect and learn new information when using this feature. PMID:29169314

Pressure waves in a supersaturated bubbly magma

USGS Publications Warehouse

Kurzon, I.; Lyakhovsky, V.; Navon, O.; Chouet, B.

2011-01-01

We study the interaction of acoustic pressure waves with an expanding bubbly magma. The expansion of magma is the result of bubble growth during or following magma decompression and leads to two competing processes that affect pressure waves. On the one hand, growth in vesicularity leads to increased damping and decreased wave amplitudes, and on the other hand, a decrease in the effective bulk modulus of the bubbly mixture reduces wave velocity, which in turn, reduces damping and may lead to wave amplification. The additional acoustic energy originates from the chemical energy released during bubble growth. We examine this phenomenon analytically to identify conditions under which amplification of pressure waves is possible. These conditions are further examined numerically to shed light on the frequency and phase dependencies in relation to the interaction of waves and growing bubbles. Amplification is possible at low frequencies and when the growth rate of bubbles reaches an optimum value for which the wave velocity decreases sufficiently to overcome the increased damping of the vesicular material. We examine two amplification phase-dependent effects: (1) a tensile-phase effect in which the inserted wave adds to the process of bubble growth, utilizing the energy associated with the gas overpressure in the bubble and therefore converting a large proportion of this energy into additional acoustic energy, and (2) a compressive-phase effect in which the pressure wave works against the growing bubbles and a large amount of its acoustic energy is dissipated during the first cycle, but later enough energy is gained to amplify the second cycle. These two effects provide additional new possible mechanisms for the amplification phase seen in Long-Period (LP) and Very-Long-Period (VLP) seismic signals originating in magma-filled cracks.

Use of an internal control in a nested-PCR assay for Mycoplasma hyopneumoniae detection and quantification in tracheobronchiolar washings from pigs.

PubMed

Verdin, E; Kobisch, M; Bové, J M; Garnier, M; Saillard, C

2000-12-01

We have previously reported a nested PCR assay for the detection of Mycoplasma hyopneumoniae directly in tracheobronchiolar washings from living pigs in field conditions. Here, we describe the construction and use of an internal control to monitor the presence of PCR inhibitors. A PCR modified target DNA was constructed by insertion of a small DNA fragment into the M. hyopneumoniae specific DNA target. We have demonstrated that the internal control failed to be amplified in only three tracheobronchiolar washings samples out of the 362 tested. This control molecule was inserted in a Spiroplasma citri derived plasmid vector and introduced into S. citri cells by electroporation. After a few passages we ensured that the recombinant plasmid became inserted into the genome of S. citri. PCR amplification of the DNA of this transformed S. citri strain using nested PCR primers led to amplification of a 900-bp fragment which can be discriminated from the M. hyopneumoniae PCR product 700 bp. The S. citri transformants with the integrated internal control were added to the tracheobronchiolar washings prior to PCR and used as an internal control to check the efficiency of sample processing, and to demonstrate the presence of inhibitors. Furthermore, we have been able to estimate the number of mycoplasma cells in the tracheobronchiolar washings. Quantitation was performed by comparing the PCR signal intensity of the specific M. hyopneumoniae template with known concentrations of the S. citri competitor. The titer in tracheobronchiolar washings ranged approximatively from 10(4)to 10(8)M. hyopneumoniae cells per ml of clinical specimen. Quantitative PCR can be a useful tool for monitoring the progression of M. hyopneumoniae in the disease process. Copyright 2000 Academic Press.

Comparison of Real-Time PCR, Reverse Transcriptase Real-Time PCR, Loop-Mediated Isothermal Amplification, and the FDA Conventional Microbiological Method for the Detection of Salmonella spp. in Produce ▿ †

PubMed Central

Zhang, Guodong; Brown, Eric W.; González-Escalona, Narjol

2011-01-01

Contamination of foods, especially produce, with Salmonella spp. is a major concern for public health. Several methods are available for the detection of Salmonella in produce, but their relative efficiency for detecting Salmonella in commonly consumed vegetables, often associated with outbreaks of food poisoning, needs to be confirmed. In this study, the effectiveness of three molecular methods for detection of Salmonella in six produce matrices was evaluated and compared to the FDA microbiological detection method. Samples of cilantro (coriander leaves), lettuce, parsley, spinach, tomato, and jalapeno pepper were inoculated with Salmonella serovars at two different levels (105 and <101 CFU/25 g of produce). The inoculated produce was assayed by the FDA Salmonella culture method (Bacteriological Analytical Manual) and by three molecular methods: quantitative real-time PCR (qPCR), quantitative reverse transcriptase real-time PCR (RT-qPCR), and loop-mediated isothermal amplification (LAMP). Comparable results were obtained by these four methods, which all detected as little as 2 CFU of Salmonella cells/25 g of produce. All control samples (not inoculated) were negative by the four methods. RT-qPCR detects only live Salmonella cells, obviating the danger of false-positive results from nonviable cells. False negatives (inhibition of either qPCR or RT-qPCR) were avoided by the use of either a DNA or an RNA amplification internal control (IAC). Compared to the conventional culture method, the qPCR, RT-qPCR, and LAMP assays allowed faster and equally accurate detection of Salmonella spp. in six high-risk produce commodities. PMID:21803916

Development and Evaluation of a Novel Multicopy-Element-Targeting Triplex PCR for Detection of Mycobacterium avium subsp. paratuberculosis in Feces

PubMed Central

Garrido, Joseba M.; Molina, Elena; Geijo, María V.; Elguezabal, Natalia; Vázquez, Patricia; Juste, Ramón A.

2014-01-01

The enteropathy called paratuberculosis (PTB), which mainly affects ruminants and has a worldwide distribution, is caused by Mycobacterium avium subsp. paratuberculosis. This disease significantly reduces the cost-effectiveness of ruminant farms, and therefore, reliable and rapid detection methods are needed to control the spread of the bacterium in livestock and in the environment. The aim of this study was to identify a specific and sensitive combination of DNA extraction and amplification to detect M. avium subsp. paratuberculosis in feces. Negative bovine fecal samples were inoculated with increasing concentrations of two different bacterial strains (field and reference) to compare the performance of four extraction and five amplification protocols. The best results were obtained using the JohnePrep and MagMax extraction kits combined with an in-house triplex real-time PCR designed to detect IS900, ISMap02 (an insertion sequence of M. avium subsp. paratuberculosis present in 6 copies per genome), and an internal amplification control DNA simultaneously. These combinations detected 10 M. avium subsp. paratuberculosis cells/g of spiked feces. The triplex PCR detected 1 fg of genomic DNA extracted from the reference strain K10. The performance of the robotized version of the MagMax extraction kit combined with the IS900 and ISMap02 PCR was further evaluated using 615 archival fecal samples from the first sampling of nine Friesian cattle herds included in a PTB control program and followed up for at least 4 years. The analysis of the results obtained in this survey demonstrated that the diagnostic method was highly specific and sensitive for the detection of M. avium subsp. paratuberculosis in fecal samples from cattle and a very valuable tool to be used in PTB control programs. PMID:24727272

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

PubMed

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 plants with large and complex genomes.

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

PubMed Central

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 plants with large and complex genomes. PMID:29250096

Amplification in the rehabilitation of unilateral deafness: speech in noise and directional hearing effects with bone-anchored hearing and contralateral routing of signal amplification.

PubMed

Lin, Li-Mei; Bowditch, Stephen; Anderson, Michael J; May, Bradford; Cox, Kenneth M; Niparko, John K

2006-02-01

Vibromechanical stimulation with a semi-implantable bone conductor (Entific BAHA device) overcomes some of the head-shadow effects in unilateral deafness. What specific rehabilitative benefits are observed when the functional ear exhibits normal hearing versus moderate sensorineural hearing loss (SNHL)? The authors conducted a prospective trial of subjects with unilateral deafness in a tertiary care center. This study comprised adults with unilateral deafness (pure-tone average [PTA] > 90 dB; Sp.D. < 20%) and either normal monaural hearing (n = 18) or moderate SNHL (PTA = 25-50 dB: Sp.D. > 75%) in the contralateral functional ear (n = 5). Subjects were fit with contralateral routing of signal (CROS) devices for 1 month and tested before (mastoid) implantation, fitting, and testing with a bone-anchored hearing aid (BAHA). Outcome measures were: 1) subjective benefit; 2) source localization tests (Source Azimuth Identification in Noise Test [SAINT]); 3) speech discrimination in quiet and in noise assessed with Hearing In Noise Test (HINT) protocols. There was consistent satisfaction with BAHA amplification and poor acceptance of CROS amplification. General directional hearing decreased with CROS use and was unchanged by BAHA and directional microphone aids. Relative to baseline and CROS, BAHA produced significantly better speech recognition in noise. Twenty-two of 23 subjects followed up in this study continue to use their BAHA device over an average follow-up period of 30.24 months (range, 51-12 months). BAHA amplification on the side of a deaf ear yields greater benefit in subjects with monaural hearing than does CROS amplification. Advantages likely related to averting the interference of speech signals delivered to the better ear, as occurs with conventional CROS amplification, while alleviating the negative head-shadow effects of unilateral deafness. The advantages of head-shadow reduction in enhancing speech recognition with noise in the hearing ear outweigh disadvantages inherent in head-shadow reduction that can occur by introducing noise from the deaf side. The level of hearing impairment correlates with incremental benefit provided by the BAHA. Patients with a moderate SNHL in the functioning ear perceived greater increments in benefit, especially in background noise, and demonstrated greater improvements in speech understanding with BAHA amplification.

Soil amplification with a strong impedance contrast: Boston, Massachusetts

USGS Publications Warehouse

Baise, Laurie G.; Kaklamanos, James; Berry, Bradford M; Thompson, Eric M.

2016-01-01

In this study, we evaluate the effect of strong sediment/bedrock impedance contrasts on soil amplification in Boston, Massachusetts, for typical sites along the Charles and Mystic Rivers. These sites can be characterized by artificial fill overlying marine sediments overlying glacial till and bedrock, where the depth to bedrock ranges from 20 to 80 m. The marine sediments generally consist of organic silts, sand, and Boston Blue Clay. We chose these sites because they represent typical foundation conditions in the city of Boston, and the soil conditions are similar to other high impedance contrast environments. The sediment/bedrock interface in this region results in an impedance ratio on the order of ten, which in turn results in a significant amplification of the ground motion. Using stratigraphic information derived from numerous boreholes across the region paired with geologic and geomorphologic constraints, we develop a depth-to-bedrock model for the greater Boston region. Using shear-wave velocity profiles from 30 locations, we develop average velocity profiles for sites mapped as artificial fill, glaciofluvial deposits, and bedrock. By pairing the depth-to-bedrock model with the surficial geology and the average shear-wave velocity profiles, we can predict soil amplification in Boston. We compare linear and equivalent-linear site response predictions for a soil layer of varying thickness over bedrock, and assess the effects of varying the bedrock shear-wave velocity (VSb) and quality factor (Q). In a moderate seismicity region like Boston, many earthquakes will result in ground motions that can be modeled with linear site response methods. We also assess the effect of bedrock depth on soil amplification for a generic soil profile in artificial fill, using both linear and equivalent-linear site response models. Finally, we assess the accuracy of the model results by comparing the predicted (linear site response) and observed site response at the Northeastern University (NEU) vertical seismometer array during the 2011 M 5.8 Mineral, Virginia, earthquake. Site response at the NEU vertical array results in amplification on the order of 10 times at a period between 0.7-0.8 s. The results from this study provide evidence that the mean short-period and mean intermediate-period amplification used in design codes (i.e., from the Fa and Fv site coefficients) may underpredict soil amplification in strong impedance contrast environments such as Boston.

Localized damage caused by topographic amplification during the 2010 M7.0 Haiti earthquake

USGS Publications Warehouse

Hough, S.E.; Altidor, J.R.; Anglade, D.; Given, D.; Janvier, M.G.; Maharrey, J.Z.; Meremonte, M.; Mildor, B.S.-L.; Prepetit, C.; Yong, A.

2010-01-01

Local geological conditions, including both near-surface sedimentary layers and topographic features, are known to significantly influence ground motions caused by earthquakes. Microzonation maps use local geological conditions to characterize seismic hazard, but commonly incorporate the effect of only sedimentary layers. Microzonation does not take into account local topography, because significant topographic amplification is assumed to be rare. Here we show that, although the extent of structural damage in the 2010 Haiti earthquake was primarily due to poor construction, topographic amplification contributed significantly to damage in the district of Petionville, south of central Port-au-Prince. A large number of substantial, relatively well-built structures situated along a foothill ridge in this district sustained serious damage or collapse. Using recordings of aftershocks, we calculate the ground motion response at two seismic stations along the topographic ridge and at two stations in the adjacent valley. Ground motions on the ridge are amplified relative to both sites in the valley and a hard-rock reference site, and thus cannot be explained by sediment-induced amplification. Instead, the amplitude and predominant frequencies of ground motion indicate the amplification of seismic waves by a narrow, steep ridge. We suggest that microzonation maps can potentially be significantly improved by incorporation of topographic effects. ?? 2010 Macmillan Publishers Limited. All rights reserved.

Ultrasensitive electrochemical aptasensor for ochratoxin A based on two-level cascaded signal amplification strategy.

PubMed

Yang, Xingwang; Qian, Jing; Jiang, Ling; Yan, Yuting; Wang, Kan; Liu, Qian; Wang, Kun

2014-04-01

Ochratoxin A (OTA) has a number of toxic effects to both humans and animals, so developing sensitive detection method is of great importance. Herein, we describe an ultrasensitive electrochemical aptasensor for OTA based on the two-level cascaded signal amplification strategy with methylene blue (MB) as a redox indicator. In this method, capture DNA, aptamers, and reporter DNA functionalized-gold nanoparticles (GNPs) were immobilized on the electrode accordingly, where GNPs were used as the first-level signal enhancer. To receive the more sensitive response, a larger number of guanine (G)-rich DNA was bound to the GNPs' surface to provide abundant anchoring sites for MB to achieve the second-level signal amplification. By employing this novel strategy, an ~8.5 (±0.3) fold amplification in signal intensity was obtained. Afterward, OTA was added to force partial GNPs/G-rich DNA to release from the sensing interface and thus decreased the electrochemical response. An effective sensing range from 2.5pM to 2.5nM was received with an extremely low detection limit of 0.75 (±0.12) pM. This amplification strategy has the potential to be the main technology for aptamer-based electrochemical biosensor in a variety of fields. Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed

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.

A simple, rapid, cost-effective and sensitive method for detection of Salmonella in environmental and pecan samples.

PubMed

Dobhal, S; Zhang, G; Rohla, C; Smith, M W; Ma, L M

2014-10-01

PCR is widely used in the routine detection of foodborne human pathogens; however, challenges remain in overcoming PCR inhibitors present in some sample matrices. The objective of this study was to develop a simple, sensitive, cost-effective and rapid method for processing large numbers of environmental and pecan samples for Salmonella detection. This study was also aimed at validation of a new protocol for the detection of Salmonella from in-shell pecans. Different DNA template preparation methods, including direct boiling, prespin, multiple washing and commercial DNA extraction kits, were evaluated with pure cultures of Salmonella Typhimurium and with enriched soil, cattle feces and in-shell pecan each spiked individually with Salmonella Typhimurium. PCR detection of Salmonella was conducted using invA and 16S rRNA gene (internal amplification control) specific primers. The effect of amplification facilitators, including bovine serum albumin (BSA), polyvinylpyrrolidone (PVP), polyethylene glycol (PEG) and gelatin on PCR sensitivity, was also evaluated. Conducting a prespin of sample matrices in combination with the addition of 0·4% (w/v) BSA and 1% (w/v) PVP in PCR mix was the simplest, most rapid, cost-effective and sensitive method for PCR detection of Salmonella, with up to 40 CFU Salmonella per reaction detectable in the presence of over 10(9 ) CFU ml(-1) of background micro-organisms from enriched feces soil or pecan samples. The developed method is rapid, cost-effective and sensitive for detection of Salmonella from different matrices. This study provides a method with broad applicability for PCR detection of Salmonella in complex sample matrices. This method has a potential for its application in different research arenas and diagnostic laboratories. © 2014 The Society for Applied Microbiology.

Phase-preserving wavefront amplification at 590 nm by stimulated Raman scattering

NASA Astrophysics Data System (ADS)

Wick, D. V.; Gruneisen, M. T.; Peterson, P. R.

1998-03-01

This paper presents an experimental demonstration of high-gain optical-wavefront amplification by stimulated Raman scattering near the D 1 resonance in atomic sodium vapor. Single-pass weak-field gain of nearly 400 is achieved with only 800 mW of pump power. Through judicious focusing, the weak wavefront is confined to the central region of the focused pump wave where saturation of the dispersion profile minimizes phase distortions due to self-focusing effects. Phase-preserving amplification is demonstrated by interferometric measurements of an amplified TEM 00 wavefront.

A novel real time PCR assay using melt curve analysis for ivory identification.

PubMed

Kitpipit, Thitika; Penchart, Kitichaya; Ouithavon, Kanita; Satasook, Chutamas; Linacre, Adrian; Thanakiatkrai, Phuvadol

2016-10-01

Demand for ivory and expansion of human settlements have resulted in a rapid decline in the number of elephants. Enforcement of local and international laws and regulations requires identification of the species from which any ivory, or ivory products, originated. Further geographical assignment of the dead elephant from which the ivory was taken can assist in forensic investigations. In this study, a real-time PCR assay using melt curve analysis was developed and fully validated for forensic use. The presence or absence of three Elephantidae-specific and elephant species-specific melting peaks was used to identify the elephant species. Using 141 blood and ivory samples from the three extant elephant species, the assay demonstrated very high reproducibility and accuracy. The limit of detection was as low as 0.031ng of input DNA for conventional amplification and 0.002ng for nested amplification. Both DNA concentrations are typically encountered in forensic casework, especially for degraded samples. No cross-reactivity was observed for non-target species. Evaluation of direct amplification and nested amplification demonstrated the assay's flexibility and capability of analyzing low-template DNA samples and aged samples. Additionally, blind trial testing showed the assay's suitability application in real casework. In conclusion, wildlife forensic laboratories could use this novel, quick, and low-cost assay to help combat the continuing poaching crises leading to the collapse of elephant numbers in the wild. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A signal-on electrochemical aptasensor for ultrasensitive detection of endotoxin using three-way DNA junction-aided enzymatic recycling and graphene nanohybrid for amplification

NASA Astrophysics Data System (ADS)

Bai, Lijuan; Chai, Yaqin; Pu, Xiaoyun; Yuan, Ruo

2014-02-01

Endotoxin, also known as lipopolysaccharide (LPS), is able to induce a strong immune response on its internalization into mammalian cells. To date, aptamer-based biosensors for LPS detection have been rarely reported. This work describes a new signal-on electrochemical aptasensor for the ultrasensitive detection of LPS by combining the three-way DNA hybridization process and nanotechnology-based amplification. With the help of DNA1 (associated with the concentration of target LPS), the capture probe hybridizes with DNA1 and the assistant probe to open its hairpin structure and form a ternary ``Y'' junction structure. The DNA1 can be released from the structure in the presence of nicking endonuclease to initiate the next hybridization process. Then a great deal of cleaved capture probe produced in the cyclic process can bind with DNA2-nanocomposite, which contains the electroactive toluidine blue (Tb) with the amplification materials graphene (Gra) and gold nanoparticles (AuNPs). Thus, an enhanced electrochemical signal can be easily read out. With the cascade signal amplification, this newly designed protocol provides an ultrasensitive electrochemical detection of LPS down to the femtogram level (8.7 fg mL-1) with a linear range of 6 orders of magnitude (from 10 fg mL-1 to 50 ng mL-1). Moreover, the high sensitivity and specificity make this method versatile for the detection of other biomolecules by changing the corresponding sequences of the capture probe and the assistant probe.

Quantifying the uncertainty in site amplification modeling and its effects on site-specific seismic-hazard estimation in the upper Mississippi embayment and adjacent areas

USGS Publications Warehouse

Cramer, C.H.

2006-01-01

The Mississippi embayment, located in the central United States, and its thick deposits of sediments (over 1 km in places) have a large effect on earthquake ground motions. Several previous studies have addressed how these thick sediments might modify probabilistic seismic-hazard maps. The high seismic hazard associated with the New Madrid seismic zone makes it particularly important to quantify the uncertainty in modeling site amplification to better represent earthquake hazard in seismic-hazard maps. The methodology of the Memphis urban seismic-hazard-mapping project (Cramer et al., 2004) is combined with the reference profile approach of Toro and Silva (2001) to better estimate seismic hazard in the Mississippi embayment. Improvements over previous approaches include using the 2002 national seismic-hazard model, fully probabilistic hazard calculations, calibration of site amplification with improved nonlinear soil-response estimates, and estimates of uncertainty. Comparisons are made with the results of several previous studies, and estimates of uncertainty inherent in site-amplification modeling for the upper Mississippi embayment are developed. I present new seismic-hazard maps for the upper Mississippi embayment with the effects of site geology incorporating these uncertainties.

Effects of Amplification, Speechreading, and Classroom Environments on Reception of Speech

ERIC Educational Resources Information Center

Blair, James C.

1977-01-01

Compared with 18 hard-of-hearing students (7 to 14-years-old) were two sources of amplification (binaural ear-level hearing aids and R F auditory training units with environmental microphones on) in "ideal" and "typical" classroom noise levels, with and without visual speechreading cues provided. (Author/IM)

Real-time DNA Amplification and Detection System Based on a CMOS Image Sensor.

PubMed

Wang, Tiantian; Devadhasan, Jasmine Pramila; Lee, Do Young; Kim, Sanghyo

2016-01-01

In the present study, we developed a polypropylene well-integrated complementary metal oxide semiconductor (CMOS) platform to perform the loop mediated isothermal amplification (LAMP) technique for real-time DNA amplification and detection simultaneously. An amplification-coupled detection system directly measures the photon number changes based on the generation of magnesium pyrophosphate and color changes. The photon number decreases during the amplification process. The CMOS image sensor observes the photons and converts into digital units with the aid of an analog-to-digital converter (ADC). In addition, UV-spectral studies, optical color intensity detection, pH analysis, and electrophoresis detection were carried out to prove the efficiency of the CMOS sensor based the LAMP system. Moreover, Clostridium perfringens was utilized as proof-of-concept detection for the new system. We anticipate that this CMOS image sensor-based LAMP method will enable the creation of cost-effective, label-free, optical, real-time and portable molecular diagnostic devices.

N-Myc knockdown and apigenin treatment controlled growth of malignant neuroblastoma cells having N-Myc amplification

PubMed Central

Hossain, Md. Motarab; Banik, Naren L.; Ray, Swapan K.

2013-01-01

Malignant neuroblastomas mostly occur in children and are frequently associated with N-Myc amplification. Oncogene amplification, which is selective increase in copy number of the oncogene, provides survival advantages in solid tumors including malignant neuroblastoma. We have decreased expression of N-Myc oncogene using short hairpin RNA (shRNA) plasmid to increase anti-tumor efficacy of the isoflavonoid apigenin (APG) in human malignant neuroblastoma SK-N-DZ and SK-N-BE2 cell lines that harbor N-Myc amplification. N-Myc knockdown induced morphological and biochemical features of neuronal differentiation. Combination of N-Myc knockdown and APG most effectively induced morphological and biochemical features of apoptotic death. This combination therapy also prevented cell migration and decreased N-Myc driven survival, angiogenic, and invasive factors. Collectively, N-Myc knockdown and APG treatment is a promising strategy for controlling the growth of human malignant neuroblastoma cell lines that harbor N-Myc amplification. PMID:23941992

N-Myc knockdown and apigenin treatment controlled growth of malignant neuroblastoma cells having N-Myc amplification.

PubMed

Hossain, Md Motarab; Banik, Naren L; Ray, Swapan K

2013-10-15

Malignant neuroblastomas mostly occur in children and are frequently associated with N-Myc amplification. Oncogene amplification, which is selective increase in copy number of the oncogene, provides survival advantages in solid tumors including malignant neuroblastoma. We have decreased expression of N-Myc oncogene using short hairpin RNA (shRNA) plasmid to increase anti-tumor efficacy of the isoflavonoid apigenin (APG) in human malignant neuroblastoma SK-N-DZ and SK-N-BE2 cell lines that harbor N-Myc amplification. N-Myc knockdown induced morphological and biochemical features of neuronal differentiation. Combination of N-Myc knockdown and APG most effectively induced morphological and biochemical features of apoptotic death. This combination therapy also prevented cell migration and decreased N-Myc driven survival, angiogenic, and invasive factors. Collectively, N-Myc knockdown and APG treatment is a promising strategy for controlling the growth of human malignant neuroblastoma cell lines that harbor N-Myc amplification. © 2013 Elsevier B.V. All rights reserved.

Resonant- and avalanche-ionization amplification of laser-induced plasma in air

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yue; Zhang, Zhili, E-mail: zzhang24@utk.edu; Jiang, Naibo

2014-10-14

Amplification of laser-induced plasma in air is demonstrated utilizing resonant laser ionization and avalanche ionization. Molecular oxygen in air is ionized by a low-energy laser pulse employing (2 + 1) resonance-enhanced multi-photon ionization (REMPI) to generate seed electrons. Subsequent avalanche ionization of molecular oxygen and nitrogen significantly amplifies the laser-induced plasma. In this plasma-amplification effect, three-body attachments to molecular oxygen dominate the electron-generation and -loss processes, while either nitrogen or argon acts as the third body with low electron affinity. Contour maps of the electron density within the plasma obtained in O₂/N₂ and O₂/Ar gas mixtures are provided to showmore » relative degrees of plasma amplification with respect to gas pressure and to verify that the seed electrons generated by O₂ 2 + 1 REMPI are selectively amplified by avalanche ionization of molecular nitrogen in a relatively low-pressure condition (≤100 Torr). Such plasma amplification occurring in air could be useful in aerospace applications at high altitude.« less

Development and evaluation of probe based real time loop mediated isothermal amplification for Salmonella: A new tool for DNA quantification.

PubMed

Mashooq, Mohmad; Kumar, Deepak; Niranjan, Ankush Kiran; Agarwal, Rajesh Kumar; Rathore, Rajesh

2016-07-01

A one step, single tube, accelerated probe based real time loop mediated isothermal amplification (RT LAMP) assay was developed for detecting the invasion gene (InvA) of Salmonella. The probe based RT LAMP is a novel method of gene amplification that amplifies nucleic acid with high specificity and rapidity under isothermal conditions with a set of six primers. The whole procedure is very simple and rapid, and amplification can be obtained in 20min. Detection of gene amplification was accomplished by amplification curve, turbidity and addition of DNA binding dye at the end of the reaction results in colour difference and can be visualized under normal day light and in UV. The sensitivity of developed assay was found 10 fold higher than taqman based qPCR. The specificity of the RT LAMP assay was validated by the absence of any cross reaction with other members of enterobacteriaceae family and other gram negative bacteria. These results indicate that the probe based RT LAMP assay is extremely rapid, cost effective, highly specific and sensitivity and has potential usefulness for rapid Salmonella surveillance. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Nucleic acid tool enzymes-aided signal amplification strategy for biochemical analysis: status and challenges.

PubMed

Qing, Taiping; He, Dinggeng; He, Xiaoxiao; Wang, Kemin; Xu, Fengzhou; Wen, Li; Shangguan, Jingfang; Mao, Zhengui; Lei, Yanli

2016-04-01

Owing to their highly efficient catalytic effects and substrate specificity, the nucleic acid tool enzymes are applied as 'nano-tools' for manipulating different nucleic acid substrates both in the test-tube and in living organisms. In addition to the function as molecular scissors and molecular glue in genetic engineering, the application of nucleic acid tool enzymes in biochemical analysis has also been extensively developed in the past few decades. Used as amplifying labels for biorecognition events, the nucleic acid tool enzymes are mainly applied in nucleic acids amplification sensing, as well as the amplification sensing of biorelated variations of nucleic acids. With the introduction of aptamers, which can bind different target molecules, the nucleic acid tool enzymes-aided signal amplification strategies can also be used to sense non-nucleic targets (e.g., ions, small molecules, proteins, and cells). This review describes and discusses the amplification strategies of nucleic acid tool enzymes-aided biosensors for biochemical analysis applications. Various analytes, including nucleic acids, ions, small molecules, proteins, and cells, are reviewed briefly. This work also addresses the future trends and outlooks for signal amplification in nucleic acid tool enzymes-aided biosensors.

The Fitness Consequences of Aneuploidy Are Driven by Condition-Dependent Gene Effects

PubMed Central

Sunshine, Anna B.; Payen, Celia; Ong, Giang T.; Liachko, Ivan; Tan, Kean Ming; Dunham, Maitreya J.

2015-01-01

Aneuploidy is a hallmark of tumor cells, and yet the precise relationship between aneuploidy and a cell’s proliferative ability, or cellular fitness, has remained elusive. In this study, we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. We found that aneuploid clones rise to high population frequencies in nutrient-limited evolution experiments and show increased fitness relative to wild type. Direct competition experiments confirmed that three out of four aneuploid events isolated from evolved populations were themselves sufficient to improve fitness. To expand the scope beyond this small number of exemplars, we created a genome-wide collection of >1,800 diploid yeast strains, each containing a different telomeric amplicon (Tamp), ranging in size from 0.4 to 1,000 kb. Using pooled competition experiments in nutrient-limited chemostats followed by high-throughput sequencing of strain-identifying barcodes, we determined the fitness effects of these >1,800 Tamps under three different conditions. Our data revealed that the fitness landscape explored by telomeric amplifications is much broader than that explored by single-gene amplifications. As also observed in the evolved clones, we found the fitness effects of most Tamps to be condition specific, with a minority showing common effects in all three conditions. By integrating our data with previous work that examined the fitness effects of single-gene amplifications genome-wide, we found that a small number of genes within each Tamp are centrally responsible for each Tamp’s fitness effects. Our genome-wide Tamp screen confirmed that telomeric amplifications identified in laboratory-evolved populations generally increased fitness. Our results show that Tamps are mutations that produce large, typically condition-dependent changes in fitness that are important drivers of increased fitness in asexually evolving populations. PMID:26011532

Evaluation of single-nucleotide polymorphisms as internal controls in prenatal diagnosis of fetal blood groups.

PubMed

Doescher, Andrea; Petershofen, Eduard K; Wagner, Franz F; Schunter, Markus; Müller, Thomas H

2013-02-01

Determination of fetal blood groups in maternal plasma samples critically depends on adequate amplification of fetal DNA. We evaluated the routine inclusion of 52 single-nucleotide polymorphisms (SNPs) as internal reference in our polymerase chain reaction (PCR) settings to obtain a positive internal control for fetal DNA. DNA from 223 plasma samples of pregnant women was screened for RHD Exons 3, 4, 5, and 7 in a multiplex PCR including 52 SNPs divided into four primer pools. Amplicons were analyzed by single-base extension and the GeneScan method in a genetic analyzer. Results of D screening were compared to standard RHD genotyping of amniotic fluid or real-time PCR of fetal DNA from maternal plasma. The vast majority of all samples (97.8%) demonstrated differences in maternal and fetal SNP patterns when tested with four primer pools. These differences were not observed in less than 2.2% of the samples most probably due to an extraction failure for adequate amounts of fetal DNA. Comparison of the fetal genotypes with independent results did not reveal a single false-negative case among samples (n = 42) with positive internal control and negative fetal RHD typing. Coamplification of 52 SNPs with RHD-specific sequences for fetal blood group determination introduces a valid positive control for the amplification of fetal DNA to avoid false-negative results. This new approach does not require a paternal blood sample. It may also be applicable to other assays for fetal genotyping in maternal blood samples. © 2012 American Association of Blood Banks.

Tip-enhanced fluorescence with radially polarized illumination for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA

NASA Astrophysics Data System (ADS)

Wei, Shih-Chung; Chuang, Tsung-Liang; Wang, Da-Shin; Lu, Hui-Hsin; Gu, Frank X.; Sung, Kung-Bin; Lin, Chii-Wann

2015-02-01

A tip nanobiosensor for monitoring DNA replication was presented. The effects of excitation power and polarization on tip-enhanced fluorescence (TEF) were assessed with the tip immersed in fluorescein isothiocyanate solution first. The photon count rose on average fivefold with radially polarized illumination at 50 mW. We then used polymerase-functionalized tips for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA. The amplicon-SYBR Green I complex was detected and compared to real-time loop-mediated isothermal amplification. The signals of the reaction using 4 and 0.004 ng/μl templates were detected 10 and 30 min earlier, respectively. The results showed the potential of TEF in developing a nanobiosensor for real-time DNA amplification.

Error amplification to promote motor learning and motivation in therapy robotics.

PubMed

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.

Nonlinear Brillouin amplification of finite-duration seeds in the strong coupling regime

NASA Astrophysics Data System (ADS)

Lehmann, G.; Spatschek, K. H.

2013-07-01

Parametric plasma processes received renewed interest in the context of generating ultra-intense and ultra-short laser pulses up to the exawatt-zetawatt regime. Both Raman as well as Brillouin amplifications of seed pulses were proposed. Here, we investigate Brillouin processes in the one-dimensional (1D) backscattering geometry with the help of numerical simulations. For optimal seed amplification, Brillouin scattering is considered in the so called strong coupling (sc) regime. Special emphasis lies on the dependence of the amplification process on the finite duration of the initial seed pulses. First, the standard plane-wave instability predictions are generalized to pulse models, and the changes of initial seed pulse forms due to parametric instabilities are investigated. Three-wave-interaction results are compared to predictions by a new (kinetic) Vlasov code. The calculations are then extended to the nonlinear region with pump depletion. Generation of different seed layers is interpreted by self-similar solutions of the three-wave interaction model. Similar to Raman amplification, shadowing of the rear layers by the leading layers of the seed occurs. The shadowing is more pronounced for initially broad seed pulses. The effect is quantified for Brillouin amplification. Kinetic Vlasov simulations agree with the three-wave interaction predictions and thereby affirm the universal validity of self-similar layer formation during Brillouin seed amplification in the strong coupling regime.

Evaluation of the efficacy of constitutional array-based comparative genomic hybridization in the diagnosis of aneuploidy using genomic and amplified DNA.

PubMed

Tan, Niap H; Palmer, Rodger; Wang, Rubin

2010-02-01

Array-based comparative genomic hybridization (array CGH) is a new molecular technique that has the potential to revolutionize cytogenetics. However, use of high resolution array CGH in the clinical setting is plagued by the problem of widespread copy number variations (CNV) in the human genome. Constitutional microarray, containing only clones that interrogate regions of known constitutional syndromes, may circumvent the dilemma of detecting CNV of unknown clinical significance. The present study investigated the efficacy of constitutional microarray in the diagnosis of trisomy. Test samples included genomic DNA from trisomic cell lines, amplification products of 50 ng of genomic DNA and whole genome amplification products of single cells. DNA amplification was achieved by means of multiple displacement amplification (MDA) over 16 h. The trisomic and sex chromosomes copy number imbalances in the genomic DNA were correctly identified by the constitutional microarrays. However, there was a failure to detect the trisomy in the amplification products of 50 ng of genomic DNA and whole genome amplification products of single cells. Using carefully selected clones, Spectral Genomics constitutional microarray was able to detect the chromosomal copy number imbalances in genomic DNA without the confounding effects of CNV. The diagnostic failure in amplified DNA samples could be attributed to the amplification process. The MDA duration of 16 h generated excessive amount of biases and shortening the duration might minimize the problem.

Ultrasensitive and rapid detection of β-conglutin combining aptamers and isothermal recombinase polymerase amplification.

PubMed

Jauset-Rubio, Miriam; Sabaté Del Río, Jonathan; Mairal, Teresa; Svobodová, Markéta; El-Shahawi, Mohammad S; Bashammakh, Abdulaziz S; Alyoubi, Abdulrahman O; O'Sullivan, Ciara K

2017-01-01

Lupin is increasingly being used in a variety of food products due to its nutritional, functional and nutraceutical properties. However, several examples of severe and even fatal food-associated anaphylaxis due to lupin inhalation or ingestion have been reported, resulting in the lupin subunit β-conglutin, being defined as the Lup an 1 allergen by the International Union of Immunological Societies (IUIS) in 2008. Here, we report an innovative method termed aptamer-recombinase polymerase amplification (Apta-RPA) exploiting the affinity and specificity of a DNA aptamer selected against the anaphylactic β-conglutin allergen termed β-conglutin binding aptamer II (β-CBA II), facilitating ultrasensitive detection via isothermal amplification. Combining magnetic beads as the solid phase with Apta-RPA detection, the total assay time was reduced from 210 min to just 25 min, with a limit of detection of 3.5 × 10 -11  M, demonstrating a rapid and ultrasensitive generic methodology that can be used with any aptamer. Future work will focus on further simplification of the assay to a lateral flow format. Graphical Abstract Schematic representation of the rapid and novel bead-based Apta-RPA assay.

Simultaneous detection and differentiation of three Potyviridae viruses by a multiplex TaqMan real time RT-PCR assay

USDA-ARS?s Scientific Manuscript database

A multiplex TaqMan real time RT-PCR was developed for detection and differentiation of Sweet potato virus G, Sweet potato latent virus and Sweet potato mild mottle virus in one tube. Amplification and detection of a fluorogenic cytochrome oxidase gene was included as an internal control. The assay w...

Development of Multiplex Real-time PCR with Internal Amplification Control for Simultaneous Detection of Salmonella and Cronobacter sakazakii in Powdered Infant Formula.

USDA-ARS?s Scientific Manuscript database

Contamination of powdered infant formula (PIF) by the bacteria Cronobacter sakazakii and Salmonella enterica was deemed a matter of great concern by the World Health Organization and the Food and Agriculture Organization of the United Nations in 2004. Therefore, we developed a rapid and sensitive m...

Progressive age-dependence and frequency difference in the effect of gap junctions on active cochlear amplification and hearing.

PubMed

Zong, Liang; Chen, Jin; Zhu, Yan; Zhao, Hong-Bo

2017-07-22

Mutations of Connexin 26 (Cx26, GJB2), which is a predominant gap junction isoform in the cochlea, can induce high incidence of nonsyndromic hearing loss. We previously found that targeted-deletion of Cx26 in supporting Deiters cells and outer pillar cells in the cochlea can influence outer hair cell (OHC) electromotility and reduce active cochlear amplification leading to hearing loss, even though there are no gap junction connexin expressions in the auditory sensory hair cells. Here, we further report that hearing loss and the reduction of active amplification in the Cx26 targeted-deletion mice are progressive and different at high and low frequency regions, first occurring in the high frequency region and then progressively extending to the middle and low frequency regions with mouse age increased. The speed of hearing loss extending was fast in the basal high frequency region and slow in the apical low frequency region, showing a logarithmic function with mouse age. Before postnatal day 25, there were no significant hearing loss and the reduction of active cochlear amplification in the low frequency region. Hearing loss and the reduction of active cochlear amplification also had frequency difference, severe and large in the high frequency regions. These new data indicate that the effect of gap junction on active cochlear amplification is progressive, but, consistent with our previous report, exists in both high and low frequency regions in adulthood. These new data also suggest that cochlear gap junctions may have an important role in age-related hearing loss. Copyright © 2017 Elsevier Inc. All rights reserved.

DHFR and MSH3 co-amplification in childhood acute lymphoblastic leukaemia, in vitro and in vivo.

PubMed

Matheson, Elizabeth C; Hogarth, Linda A; Case, Marian C; Irving, Julie A E; Hall, Andrew G

2007-06-01

The MSH3 and dihydrofolate reductase (DHFR) genes, located on chromosome 5, share a common promoter but are divergently transcribed. Dysregulation of the mismatch repair (MMR) pathway has been found to occur in cell line models due to co-amplification of MSH3 as a coincident effect of DHFR amplification, acquired as a mechanism generating resistance to methotrexate (MTX). The increased levels of MSH3 perturbed MutSalpha function resulting in hypermutability and increased resistance to thiopurines, drugs whose cytotoxic effects are triggered by MutSalpha. The relevance of this phenomenon in clinical samples is unknown but is extremely pertinent in childhood acute lymphoblastic leukaemia (ALL) in which children are exposed for prolonged periods to both MTX and thiopurines such that a single amplification event involving both the DHFR and the MSH3 genes may cause chemotherapeutic resistance to both agents. Thus, we have generated a leukaemic cell line (PreB697) and a normal human lymphoblastoid cell line (TK6) that are resistant to a pharmacologically relevant dose of MTX and show that while increased DHFR levels result in MTX resistance, the associated increased levels of MSH3 are insufficient to perturb MutSalpha functionality, in terms of MMR capacity or 6-thioguanine sensitivity. In addition, we show that although low-level DHFR amplification occurs alone in a significant number of samples, both at disease onset and relapse, co-amplification of both MSH3 and DHFR is rarely found in primary ALL samples, even after prolonged MTX therapy and is not at a sufficiently high level to perturb MMR function.

Nonlinear and linear site response and basin effects in Seattle for the M 6.8 Nisqually, Washington, earthquake

USGS Publications Warehouse

Frankel, A.D.; Carver, D.L.; Williams, R.A.

2002-01-01

We used recordings of the M 6.8 Nisqually earthquake and its ML 3.4 aftershock to study site response and basin effects for 35 locations in Seattle, Washington. We determined site amplification from Fourier spectral ratios of the recorded horizontal ground motions, referenced to a soft-rock site. Soft-soil sites (generally National Earthquake Hazard Reduction Program [NEHRP] class E) on artificial fill and young alluvium have the largest 1-Hz amplifications (factors of 3-7) for both the mainshock and aftershock. These amplifications are correlated with areas of higher damage from the mainshock to major buildings and liquefaction. There are several indications of nonlinear response at the soft-soil sites for the mainshock ground motions, despite relatively modest peak accelerations in the S waves of 15%-22%g. First, the mainshock spectral ratios do not show amplification at 2-8 Hz as do the aftershock spectral ratios. Spectral peaks at frequencies below 2 Hz generally occur at lower frequencies for the mainshock spectral ratios than for the aftershock ratios. At one soft-soil site, there is a clear shift of the resonant frequency to a lower frequency for the mainshock compared with the aftershock. The frequency of this resonance increases in the coda of the mainshock record, indicating that the site response during the weaker motions of the coda is more linear than that of the initial S wave. Three of the soft-soil sites display cusped, one-sided mainshock accelerograms after the S wave. These soft-soil sites also show amplification at 10-20 Hz in the S wave, relative to the rock site, that is not observed for the aftershock. The cusped waveforms and 10-20-Hz amplification are symptomatic of nonlinear response at the soft-soil sites. These sites had nearby liquefaction. The largest amplifications for 0.5 Hz occur at soft-soil sites on the southern portion of the Seattle Basin. Stiff-soil sites (NEHRP classes D and C) on Pleistocene-age glacial deposits display similar spectral amplification for the mainshock and aftershock, indicating approximately linear response. The stiff-soil sites generally have moderate amplification (factors of 1.1-2.4) at 0.5 and 1 Hz. Amplifications at 1 and 5 Hz for all sites generally increase with decreasing shear-wave velocity measured in the top 30 m (Vs 30). However, larger amplifications at 0.5 and 1 Hz for sites with similar Vs 30 values are observed for sites in the Seattle Basin, illustrating the amplification from the deeper (>30 m) sediments and the contribution from basin surface waves. Record sections for the mainshock and aftershock show that basin surface waves produce the peak velocities for many of the sites in the Seattle Basin and often dominate the amplitude at 1 Hz and lower frequencies.

CCNE1 amplification is associated with aggressive potential in endometrioid endometrial carcinomas.

PubMed

Nakayama, Kentaro; Rahman, Mohammed Tanjimur; Rahman, Munmun; Nakamura, Kohei; Ishikawa, Masako; Katagiri, Hiroshi; Sato, Emi; Ishibashi, Tomoka; Iida, Kouji; Ishikawa, Noriyuki; Kyo, Satoru

2016-02-01

The clinicopathological significance of amplification was investigated of the gene encoding cyclin E (CCNE1) and we assessed whether CCNE1 was a potential target in endometrioid endometrial carcinomas. CCNE1 amplification and CCNE1 or F-box and WD repeat domain-containing 7 (FBXW7) expression in endometrial endometrioid carcinoma was assessed by immunohistochemistry and fluorescence in situ hybridization. CCNE1 knockdown by small interfering RNA (siRNA) was used to assess the CCNE1 function. The results showed that CCNE1 amplification was present in 9 (8.3%) of 108 endometrial carcinomas. CCNE1 amplification was correlated with high histological grade (Grade 3; p=0.0087) and lymphovascular space invasion (p=0.0258). No significant association was observed between CCNE1 amplification and FIGO stage (p=0.851), lymph node metastasis (p=0.078), body mass index (p=0.265), deep myometrial invasion (p=0.256), menopausal status (p=0.289) or patient age (p=0.0817). CCNE1 amplification was significantly correlated with shorter progression-free and overall survival (p=0.0081 and 0.0073, respectively). CCNE1 protein expression or loss of FBXW7 expression in endometrial endometrioid carcinoma tended to be correlated with shorter progression-free and overall survival; however, this difference was not statistically significant. Multivariate analysis showed that CCNE1 amplification was an independent prognostic factor for overall survival but not for progression-free survival (P=0.0454 and 0.2175, respectively). Profound growth inhibition was observed in siRNA-transfected cancer cells with endogenous CCNE1 overexpression compared with that in cancer cells having low CCNE1 expression. CCNE1 amplification was independent of p53, HER2, MLH1 and ARID1A expression but dependent on PTEN expression in endometrial carcinomas. These findings indicated that CCNE1 amplification was critical for the survival of endometrial endometrioid carcinomas. Furthermore, the effects of CCNE1 knockdown were dependent on the CCNE1 expression status, suggesting that CCNE1-targeted therapy may be beneficial for patients with endometrial endometrioid carcinoma having CCNE1 amplification.

CCNE1 amplification is associated with aggressive potential in endometrioid endometrial carcinomas

PubMed Central

NAKAYAMA, KENTARO; RAHMAN, MOHAMMED TANJIMUR; RAHMAN, MUNMUN; NAKAMURA, KOHEI; ISHIKAWA, MASAKO; KATAGIRI, HIROSHI; SATO, EMI; ISHIBASHI, TOMOKA; IIDA, KOUJI; ISHIKAWA, NORIYUKI; KYO, SATORU

2016-01-01

The clinicopathological significance of amplification was investigated of the gene encoding cyclin E (CCNE1) and we assessed whether CCNE1 was a potential target in endometrioid endometrial carcinomas. CCNE1 amplification and CCNE1 or F-box and WD repeat domain-containing 7 (FBXW7) expression in endometrial endometrioid carcinoma was assessed by immunohistochemistry and fluorescence in situ hybridization. CCNE1 knockdown by small interfering RNA (siRNA) was used to assess the CCNE1 function. The results showed that CCNE1 amplification was present in 9 (8.3%) of 108 endometrial carcinomas. CCNE1 amplification was correlated with high histological grade (Grade 3; P=0.0087) and lymphovascular space invasion (P=0.0258). No significant association was observed between CCNE1 amplification and FIGO stage (P=0.851), lymph node metastasis (P=0.078), body mass index (P=0.265), deep myometrial invasion (P=0.256), menopausal status (P=0.289) or patient age (P=0.0817). CCNE1 amplification was significantly correlated with shorter progression-free and overall survival (P=0.0081 and 0.0073, respectively). CCNE1 protein expression or loss of FBXW7 expression in endometrial endometrioid carcinoma tended to be correlated with shorter progression-free and overall survival; however, this difference was not statistically significant. Multivariate analysis showed that CCNE1 amplification was an independent prognostic factor for overall survival but not for progression-free survival (P=0.0454 and 0.2175, respectively). Profound growth inhibition was observed in siRNA-transfected cancer cells with endogenous CCNE1 overexpression compared with that in cancer cells having low CCNE1 expression. CCNE1 amplification was independent of p53, HER2, MLH1 and ARID1A expression but dependent on PTEN expression in endometrial carcinomas. These findings indicated that CCNE1 amplification was critical for the survival of endometrial endometrioid carcinomas. Furthermore, the effects of CCNE1 knockdown were dependent on the CCNE1 expression status, suggesting that CCNE1-targeted therapy may be beneficial for patients with endometrial endometrioid carcinoma having CCNE1 amplification. PMID:26647729

Specific detection of Angiostrongylus cantonensis in the snail Achatina fulica using a loop-mediated isothermal amplification (LAMP) assay.

PubMed

Liu, Chun-Yan; Song, Hui-Qun; Zhang, Ren-Li; Chen, Mu-Xin; Xu, Min-Jun; Ai, Lin; Chen, Xiao-Guang; Zhan, Xi-Mei; Liang, Shao-Hui; Yuan, Zi-Guo; Lin, Rui-Qing; Zhu, Xing-Quan

2011-08-01

Angiostrongylus cantonensis, a rat lungworm, can cause eosinophilic meningitis and angiostrongyliasis in humans following ingestion of contaminated foods or intermediate/paratenic hosts with infective larvae. The snail Achatina fulica is one of the important intermediate hosts of A. cantonensis and is commonly eaten by humans in some countries. In the present study, we developed a loop-mediated isothermal amplification (LAMP) method for the specific detection of A. cantonensis in Ac. fulica. Primers for LAMP were designed based on the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA (rDNA) of A. cantonensis. Specificity tests showed that only the products of A. cantonensis were detected when DNA samples of A. cantonensis and the heterologous control samples Anisakis simplex s.s, Trichuris trichiura, Toxocara canis, Trichinella spiralis and Ascaris lumbricoides were amplified by LAMP. Sensitivity evaluation indicated that the LAMP assay is 10 times more sensitive than the conventional polymerase chain reaction (PCR) assay. The established LAMP assay is rapid, inexpensive and easy to be performed. It can be used in clinical applications for rapid and sensitive detection of A. cantonensis in snails, which has implications for the effective control of angiostrongyliasis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Validation of internal controls for extraction and amplification of nucleic acids from enteric viruses in water samples.

PubMed

Hata, Akihiko; Katayama, Hiroyuki; Kitajima, Masaaki; Visvanathan, Chettiyappan; Nol, Chea; Furumai, Hiroaki

2011-07-01

Inhibitors that reduce viral nucleic acid extraction efficiency and interfere with cDNA synthesis and/or polymerase activity affect the molecular detection of viruses in aquatic environments. To overcome these significant problems, we developed a methodology for assessing nucleic acid yields and DNA amplification efficiencies for environmental water samples. This involved adding particles of adenovirus type 5 and murine norovirus and newly developed primer-sharing controls, which are amplified with the same primer pairs and result in the same amplicon sizes as the targets, to these samples. We found that nucleic acid loss during the extraction process, rather than reverse transcription-PCR (RT-PCR) inhibition, more significantly attributed to underestimation of the presence of viral genomes in the environmental water samples tested in this study. Our success rate for satisfactorily amplifying viral RNAs and DNAs by RT-PCR was higher than that for obtaining adequate nucleic acid preparations. We found that inhibitory properties were greatest when we used larger sample volumes. A magnetic silica bead-based RNA extraction method effectively removed inhibitors that interfere with viral nucleic acid extraction and RT-PCR. To our knowledge, this is the first study to assess the inhibitory properties of environmental water samples by using both control virus particles and primer-sharing controls.

Genus Level Identification of Mycobacteria from Clinical Specimens by Using an Easy-To-Handle Mycobacterium-Specific PCR Assay

PubMed Central

Stauffer, Fritz; Haber, Heinrich; Rieger, Armin; Mutschlechner, Robert; Hasenberger, Petra; Tevere, Vincent J.; Young, Karen K. Y.

1998-01-01

An easy-to-handle Mycobacterium-specific PCR assay for detection of the presence of a wide range of mycobacterial species in clinical samples was evaluated. The performance of the genus probe was compared with the performance of probes specific for Mycobacterium tuberculosis and Mycobacterium avium and with that of standard culture. In addition, the utility of an internal control in monitoring amplification inhibitors was studied. Of 545 respiratory and 325 nonrespiratory specimens (a total of 870 specimens), 58 (6.7%) showed the presence of amplification inhibitors, as determined by a negative result for the internal control. Of these 58 specimens, 31 (53%) were stool specimens; other material, even citrate blood after lysis of erythrocytes, did not pose a problem with regard to inhibition of PCR amplification. Eighty-one of the remaining 812 specimens had a positive Mycobacterium culture result. Of these culture-positive specimens, 58 (71.6%) showed a positive result with the Mycobacterium genus-specific probe. Seventy-two samples had a positive result with the Mycobacterium-specific probe but a negative culture result. Of these 72 samples, 26 samples were regarded as true positive, either because the M. tuberculosis- or M. avium-specific probe was also positive at the same time or because other specimens from the same patient taken at the same time were culture positive. The sensitivity of the Mycobacterium-specific probe was 78.5% and the specificity was 93.5%. This study showed that pretesting of clinical specimens for mycobacteria to the genus level with a Mycobacterium-specific probe offers the routine clinical laboratory the possibility of detecting tuberculous and nontuberculous mycobacteria with one test. Furthermore, specimens testing positive with the genus-specific probe can be immediately identified with species-specific probes. PMID:9508282

Plasmonically amplified bioassay - Total internal reflection fluorescence vs. epifluorescence geometry.

PubMed

Hageneder, Simone; Bauch, Martin; Dostalek, Jakub

2016-08-15

This paper investigates plasmonic amplification in two commonly used optical configurations for fluorescence readout of bioassays - epifluorescence (EPF) and total internal reflection fluorescence (TIRF). The plasmonic amplification in the EPF configuration was implemented by using crossed gold diffraction grating and Kretschmann geometry of attenuated total reflection method (ATR) was employed in the TIRF configuration. Identical assay, surface architecture for analyte capture, and optics for the excitation, collection and detection of emitted fluorescence light intensity were used in both TIRF and EPF configurations. Simulations predict that the crossed gold diffraction grating (EPF) can amplify the fluorescence signal by a factor of 10(2) by the combination of surface plasmon-enhanced excitation and directional surface plasmon-coupled emission in the red part of spectrum. This factor is about order of magnitude higher than that predicted for the Kretschmann geometry (TIRF) which only took advantage of the surface plasmon-enhanced excitation. When applied for the readout of sandwich interleukin 6 (IL-6) immunoassay, the plasmonically amplified EPF geometry designed for Alexa Fluor 647 labels offered 4-times higher fluorescence signal intensity compared to TIRF. Interestingly, both geometries allowed reaching the same detection limit of 0.4pM despite of the difference in the fluorescence signal enhancement. This is attributed to inherently lower background of fluorescence signal for TIRF geometry compared to that for EPF which compensates for the weaker fluorescence signal enhancement. The analysis of the inflammation biomarker IL-6 in serum at medically relevant concentrations and the utilization of plasmonic amplification for the fluorescence measurement of kinetics of surface affinity reactions are demonstrated for both EPF and TIRF readout. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Internal Light Source-Driven Photoelectrochemical 3D-rGO/Cellulose Device Based on Cascade DNA Amplification Strategy Integrating Target Analog Chain and DNA Mimic Enzyme.

PubMed

Lan, Feifei; Liang, Linlin; Zhang, Yan; Li, Li; Ren, Na; Yan, Mei; Ge, Shenguang; Yu, Jinghua

2017-11-01

In this work, a chemiluminescence-driven collapsible greeting card-like photoelectrochemical lab-on-paper device (GPECD) with hollow channel was demonstrated, in which target-triggering cascade DNA amplification strategy was ingeniously introduced. The GPECD had the functions of reagents storage and signal collection, and the change of configuration could control fluidic path, reaction time and alterations in electrical connectivity. In addition, three-dimentional reduced graphene oxide affixed Au flower was in situ grown on paper cellulose fiber for achieving excellent conductivity and biocompatibility. The cascade DNA amplification strategy referred to the cyclic formation of target analog chain and its trigger action to hybridization chain reaction (HCR), leading to the formation of numerous hemin/G-quadruplex DNA mimic enzyme with the presence of hemin. Subjected to the catalysis of hemin/G-quadruplex, the strong chemiluminiscence of luminol-H 2 O 2 system was obtained, which then was used as internal light source to excite photoactive materials realizing the simplification of instrument. In this analyzing process, thrombin served as proof-of-concept, and the concentration of target was converted into the DNA signal output by the specific recognition of aptamer-protein and target analog chain recycling. The target analog chain was produced in quantity with the presence of target, which further triggered abundant HCR and introduced hemin/G-quadruplex into the system. The photocurrent signal was obtained after the nitrogen-doped carbon dots sensitized ZnO was stimulated by chemiluminescence. The proposed GPECD exhibited excellent specificity and sensitivity toward thrombin with a detection limit of 16.7 fM. This judiciously engineered GPECD paved a luciferous way for detecting other protein with trace amounts in bioanalysis and clinical biomedicine.

Light absorption by coated nano-sized carbonaceous particles

NASA Astrophysics Data System (ADS)

Gangl, Martin; Kocifaj, Miroslav; Videen, Gorden; Horvath, Helmuth

The optical properties of strongly absorbing soot particles coated by transparent material are investigated experimentally and described by several modeling approaches. Soot is produced by spark discharge and passed through a Sinclair-La Mer generator where non-absorbing carnauba wax is condensed onto it to obtain internal soot-wax mixtures in a controlled way. Measurements of the extinction and volume scattering coefficient show an amplification of absorption by a factor of approximately 1.8. This behavior was described by different approaches of internally mixed materials for the modal diameters of the measured size distributions: concentric-sphere model, effective medium approximations and heterogeneous ellipsoids. The concentric-sphere model describes the absorption increase quantitatively; and hence, it is chosen to be applied to the entire particle population in the size distribution. The growth of the soot particles by condensing wax is described by a simplified growth model to estimate the different contributions of several soot particle diameters to the overall absorption cross-section.

Four photon parametric amplification. [in unbiased Josephson junction

NASA Technical Reports Server (NTRS)

Parrish, P. T.; Feldman, M. J.; Ohta, H.; Chiao, R. Y.

1974-01-01

An analysis is presented describing four-photon parametric amplification in an unbiased Josephson junction. Central to the theory is the model of the Josephson effect as a nonlinear inductance. Linear, small signal analysis is applied to the two-fluid model of the Josephson junction. The gain, gain-bandwidth product, high frequency limit, and effective noise temperature are calculated for a cavity reflection amplifier. The analysis is extended to multiple (series-connected) junctions and subharmonic pumping.

Directional amplifier in an optomechanical system with optical gain

NASA Astrophysics Data System (ADS)

Jiang, Cheng; Song, L. N.; Li, Yong

2018-05-01

Directional amplifiers are crucial nonreciprocal devices in both classical and quantum information processing. Here we propose a scheme for realizing a directional amplifier between optical and microwave fields based on an optomechanical system with optical gain, where an active optical cavity and two passive microwave cavities are coupled to a common mechanical resonator via radiation pressure. The two passive cavities are coupled via hopping interaction to facilitate the directional amplification between the active and passive cavities. We obtain the condition of achieving optical directional amplification and find that the direction of amplification can be controlled by the phase differences between the effective optomechanical couplings. The effects of the gain rate of the active cavity and the effective coupling strengths on the maximum gain of the amplifier are discussed. We show that the noise added to this amplifier can be greatly suppressed in the large cooperativity limit.

Disinhibition of the extracellular-signal-regulated kinase restores the amplification of circadian rhythms by lithium in cells from bipolar disorder patients.

PubMed

McCarthy, Michael J; Wei, Heather; Landgraf, Dominic; Le Roux, Melissa J; Welsh, David K

2016-08-01

Bipolar disorder (BD) is characterized by depression, mania, and circadian rhythm abnormalities. Lithium, a treatment for BD stabilizes mood and increases circadian rhythm amplitude. However, in fibroblasts grown from BD patients, lithium has weak effects on rhythm amplitude compared to healthy controls. To understand the mechanism by which lithium differentially affects rhythm amplitude in BD cells, we investigated the extracellular-signal-regulated kinase (ERK) and related signaling molecules linked to BD and circadian rhythms. In fibroblasts from BD patients, controls and mice, we assessed the contribution of the ERK pathway to lithium-induced circadian rhythm amplification. Protein analyses revealed low phospho-ERK1/2 (p-ERK) content in fibroblasts from BD patients vs. Pharmacological inhibition of ERK1/2 by PD98059 attenuated the rhythm amplification effect of lithium, while inhibition of two related kinases, c-Jun N-terminal kinase (JNK), and P38 did not. Knockdown of the transcription factors CREB and EGR-1, downstream effectors of ERK1/2, reduced baseline rhythm amplitude, but did not alter rhythm amplification by lithium. In contrast, ELK-1 knockdown amplified rhythms, an effect that was not increased further by the addition of lithium, suggesting this transcription factor may regulate the effect of lithium on amplitude. Augmentation of ERK1/2 signaling through DUSP6 knockdown sensitized NIH3T3 cells to rhythm amplification by lithium. In BD fibroblasts, DUSP6 knockdown reversed the BD rhythm phenotype, restoring the ability of lithium to increase amplitude in these cells. We conclude that the inability of lithium to regulate circadian rhythms in BD may reflect reduced ERK activity, and signaling through ELK-1. Published by Elsevier B.V.

Loop-Mediated Isothermal Amplification for Salmonella Detection in Food and Feed: Current Applications and Future Directions

PubMed Central

Yang, Qianru; Domesle, Kelly J.

2018-01-01

Abstract Loop-mediated isothermal amplification (LAMP) has become a powerful alternative to polymerase chain reaction (PCR) for pathogen detection in clinical specimens and food matrices. Nontyphoidal Salmonella is a zoonotic pathogen of significant food and feed safety concern worldwide. The first study employing LAMP for the rapid detection of Salmonella was reported in 2005, 5 years after the invention of the LAMP technology in Japan. This review provides an overview of international efforts in the past decade on the development and application of Salmonella LAMP assays in a wide array of food and feed matrices. Recent progress in assay design, platform development, commercial application, and method validation is reviewed. Future perspectives toward more practical and wider applications of Salmonella LAMP assays in food and feed testing are discussed. PMID:29902082

Development of the polymerase chain reaction for diagnosis of chancroid.

PubMed Central

Chui, L; Albritton, W; Paster, B; Maclean, I; Marusyk, R

1993-01-01

The published nucleotide sequences of the 16S rRNA gene of Haemophilus ducreyi were used to develop primer sets and probes for the diagnosis of chancroid by polymerase chain reaction (PCR) DNA amplification. One set of broad specificity primers yielded a 303-bp PCR product from all bacteria tested. Two 16-base probes internal to this sequence were species specific for H. ducreyi when tested with 12 species of the families Pasteurellaceae and Enterobacteriaceae. The two probes in combination with the broad specificity primers were 100% sensitive with 51 strains of H. ducreyi isolated from six continents over a 15-year period. The direct detection of H. ducreyi from 100 clinical specimens by PCR showed a sensitivity of 83 to 98% and a specificity of 51 to 67%, depending on the number of amplification cycles. Images PMID:8458959

The Impact of Sound-Field Amplification in Mainstream Cross-Cultural Classrooms: Part 2 Teacher and Child Opinions

ERIC Educational Resources Information Center

Massie, Robyn; Dillon, Harvey

2006-01-01

This article presents teachers' and children's views of the effectiveness of sound-field amplification intervention. The rating scale, Teacher Opinions re Performance in Classrooms (TOPIC) provided information on teacher perceptions regarding changes in student performance in unamplified "OFF" and amplified "ON" listening conditions. The teachers…

Analogous pleiotropic effects of insecticide resistance genotypes in peach-potato aphids and houseflies.

PubMed

Foster, S P; Young, S; Williamson, M S; Duce, I; Denholm, I; Devine, G J

2003-08-01

We show that single-point mutations conferring target-site resistance (kdr) to pyrethroids and DDT in aphids and houseflies, and gene amplification conferring metabolic resistance (carboxylesterase) to organophosphates and carbamates in aphids, can have deleterious pleiotropic effects on fitness. Behavioural studies on peach-potato aphids showed that a reduced response to alarm pheromone was associated with both gene amplification and the kdr target-site mutation. In this species, gene amplification was also associated with a decreased propensity to move from senescing leaves to fresh leaves at low temperature. Housefly genotypes possessing the identical kdr mutation were also shown to exhibit behavioural differences in comparison with susceptible insects. In this species, resistant individuals showed no positional preference along a temperature gradient while susceptible genotypes exhibited a strong preference for warmer temperatures.

Impulse-induced optimum signal amplification in scale-free networks.

PubMed

Martínez, Pedro J; Chacón, Ricardo

2016-04-01

Optimizing information transmission across a network is an essential task for controlling and manipulating generic information-processing systems. Here, we show how topological amplification effects in scale-free networks of signaling devices are optimally enhanced when the impulse transmitted by periodic external signals (time integral over two consecutive zeros) is maximum. This is demonstrated theoretically by means of a star-like network of overdamped bistable systems subjected to generic zero-mean periodic signals and confirmed numerically by simulations of scale-free networks of such systems. Our results show that the enhancer effect of increasing values of the signal's impulse is due to a correlative increase of the energy transmitted by the periodic signals, while it is found to be resonant-like with respect to the topology-induced amplification mechanism.

Variability of site response in Seattle, Washington

USGS Publications Warehouse

Hartzell, S.; Carver, D.; Cranswick, E.; Frankel, A.

2000-01-01

Ground motion from local earthquakes and the SHIPS (Seismic Hazards Investigation in Puget Sound) experiment is used to estimate site amplification factors in Seattle. Earthquake and SHIPS records are analyzed by two methods: (1) spectral ratios relative to a nearby site on Tertiary sandstone, and (2) a source/site spectral inversion technique. Our results show site amplifications between 3 and 4 below 5 Hz for West Seattle relative to Tertiary rock. These values are approximately 30% lower than amplification in the Duwamish Valley on artificial fill, but significantly higher than the calculated range of 2 to 2.5 below 5 Hz for the till-covered hills east of downtown Seattle. Although spectral amplitudes are only 30% higher in the Duwamish Valley compared to West Seattle, the duration of long-period ground motion is significantly greater on the artificial fill sites. Using a three-dimensional displacement response spectrum measure that includes the effects of ground-motion duration, values in the Duwamish Valley are 2 to 3 times greater than West Seattle. These calculations and estimates of site response as a function of receiver azimuth point out the importance of trapped surface-wave energy within the shallow, low-velocity, sedimentary layers of the Duwamish Valley. One-dimensional velocity models yield spectral amplification factors close to the observations for till sites east of downtown Seattle and the Duwamish Valley, but underpredict amplifications by a factor of 2 in West Seattle. A two-dimensional finite-difference model does equally well for the till sites and the Duwamish Valley and also yields duration estimates consistent with the observations for the Duwamish Valley. The two-dimensional model, however, still underpredicts amplification in West Seattle by up to a factor of 2. This discrepancy is attributed to 3D effects, including basin-edge-induced surface waves and basin-geometry-focusing effects, caused by the proximity of the Seattle thrust fault and the sediment-filled Seattle basin.

Geometric Effects on the Amplification of First Mode Instability Waves

NASA Technical Reports Server (NTRS)

Kirk, Lindsay C.; Candler, Graham V.

2013-01-01

The effects of geometric changes on the amplification of first mode instability waves in an external supersonic boundary layer were investigated using numerical techniques. Boundary layer stability was analyzed at Mach 6 conditions similar to freestream conditions obtained in quiet ground test facilities so that results obtained in this study may be applied to future test article design to measure first mode instability waves. The DAKOTA optimization software package was used to optimize an axisymmetric geometry to maximize the amplification of the waves at first mode frequencies as computed by the 2D STABL hypersonic boundary layer stability analysis tool. First, geometric parameters such as nose radius, cone half angle, vehicle length, and surface curvature were examined separately to determine the individual effects on the first mode amplification. Finally, all geometric parameters were allowed to vary to produce a shape optimized to maximize the amplification of first mode instability waves while minimizing the amplification of second mode instability waves. Since first mode waves are known to be most unstable in the form of oblique wave, the geometries were optimized using a broad range of wave frequencies as well as a wide range of oblique wave angles to determine the geometry that most amplifies the first mode waves. Since first mode waves are seen most often in flows with low Mach numbers at the edge of the boundary layer, the edge Mach number for each geometry was recorded to determine any relationship between edge Mach number and the stability of first mode waves. Results indicate that an axisymmetric cone with a sharp nose and a slight flare at the aft end under the Mach 6 freestream conditions used here will lower the Mach number at the edge of the boundary layer to less than 4, and the corresponding stability analysis showed maximum first mode N factors of 3.

An isothermal based recombinase polymerase amplification assay for rapid, sensitive and robust indexing of citrus yellow mosaic virus.

PubMed

Kumar, P V; Sharma, S K; Rishi, N; Ghosh, D K; Baranwal, V K

Management of viral diseases relies on definite and sensitive detection methods. Citrus yellow mosaic virus (CYMV), a double stranded DNA virus of the genus Badnavirus, causes yellow mosaic disease in citrus plants. CYMV is transmitted through budwood and requires a robust and simplified indexing protocol for budwood certification programme. The present study reports development and standardization of an isothermal based recombinase polymerase amplification (RPA) assay for a sensitive, rapid, easy, and cost-effective method for detection and diagnosis of CYMV. Two different oligonucleotide primer sets were designed from ORF III (coding for polyprotein) and ORF II (coding for virion associated protein) regions of CYMV to perform amplification assays. Comparative evaluation of RPA, PCR and immuno-capture recombinase polymerase amplification (IC-RPA) based assays were done using purified DNA and plant crude sap. CYMV infection was efficiently detected from the crude sap in RPA and IC-RPA assays. The primer set used in RPA was specific and did not show any cross-amplification with banana streak MY virus (BSMYV), another Badnavirus species. The results from the present study indicated that RPA assay can be used easily in routine indexing of citrus planting material. To the best of our knowledge, this is the first report on development of a rapid and simplified isothermal detection assay for CYMV and can be utilized as an effective technique in quarantine and budwood certification process.

A Simple Power Law Governs Many Sensory Amplifications and Multisensory Enhancements.

PubMed

Billock, Vincent A; Havig, Paul R

2018-05-16

When one sensory response occurs in the presence of a different sensory stimulation, the sensory response is often amplified. The variety of sensory enhancement data tends to obscure the underlying rules, but it has long been clear that weak signals are usually amplified more than strong ones (the Principle of Inverse Effectiveness). Here we show that for many kinds of sensory amplification, the underlying law is simple and elegant: the amplified response is a power law of the unamplified response, with a compressive exponent that amplifies weak signals more than strong. For both psychophysics and cortical electrophysiology, for both humans and animals, and for both sensory integration and enhancement within a sense, gated power law amplification (amplification of one sense triggered by the presence of a different sensory signal) is often sufficient to explain sensory enhancement.

Heralded noiseless amplification for single-photon entangled state with polarization feature

NASA Astrophysics Data System (ADS)

Wang, Dan-Dan; Jin, Yu-Yu; Qin, Sheng-Xian; Zu, Hao; Zhou, Lan; Zhong, Wei; Sheng, Yu-Bo

2018-03-01

Heralded noiseless amplification is a promising method to overcome the transmission photon loss in practical noisy quantum channel and can effectively lengthen the quantum communication distance. Single-photon entanglement is an important resource in current quantum communications. Here, we construct two single-photon-assisted heralded noiseless amplification protocols for the single-photon two-mode entangled state and single-photon three-mode W state, respectively, where the single-photon qubit has an arbitrary unknown polarization feature. After the amplification, the fidelity of the single-photon entangled state can be increased, while the polarization feature of the single-photon qubit can be well remained. Both the two protocols only require the linear optical elements, so that they can be realized under current experimental condition. Our protocols may be useful in current and future quantum information processing.

Amplification through chaotic synchronization in spatially extended beam-plasma systems

NASA Astrophysics Data System (ADS)

Moskalenko, Olga I.; Frolov, Nikita S.; Koronovskii, Alexey A.; Hramov, Alexander E.

2017-12-01

In this paper, we have studied the relationship between chaotic synchronization and microwave signal amplification in coupled beam-plasma systems. We have considered a 1D particle-in-cell numerical model of unidirectionally coupled beam-plasma oscillatory media being in the regime of electron pattern formation. We have shown the significant gain of microwave oscillation power in coupled beam-plasma media being in the different regimes of generation. The discovered effect has a close connection with the chaotic synchronization phenomenon, so we have observed that amplification appears after the onset of the complete time scale synchronization regime in the analyzed coupled spatially extended systems. We have also provided the numerical study of physical processes in the chain of beam-plasma systems leading to the chaotic synchronization and the amplification of microwave oscillations power, respectively.

Amplification and polarization of supernovae by gravitational lensing

NASA Technical Reports Server (NTRS)

Schneider, P.; Wagoner, Robert V.

1987-01-01

The gravitational lensing of supernovae by individual masses which could comprise the dark matter is analyzed. Detailed predictions of the amplification and polarization are presented, including effects of a galactic environment. Their time dependence is produced by the expansion of the supernovae beam within the lens. The fraction of supernovae which might thus be identified as being lensed in surveys at proposed limiting magnitudes is estimated. These two effects could provide the only known unique signature of microlensing.

Study of DNA extraction methods for use in loop-mediated isothermal amplification detection of single resting cysts in the toxic dinoflagellates Alexandrium tamarense and A. catenella.

PubMed

Nagai, Satoshi; Yamamoto, Keigo; Hata, Naotugu; Itakura, Shigeru

2012-09-01

In a previous study, we experienced instable amplification and a low amplification success in loop-mediated isothermal amplification (LAMP) reactions from naturally occurring vegetative cells or resting cysts of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella. In this study, we examined 4 methods for extracting DNA from single resting cysts of A. tamarense and A. catenella to obtain more stable and better amplification success and to facilitate unambiguous detection using the LAMP method. Apart from comparing the 4 different DNA extraction methods, namely, (1) boiling in Tris-EDTA (TE) buffer, (2) heating at 65 °C in hexadecyltrimethylammonium bromide buffer, (3) boiling in 0.5% Chelex buffer, and (4) boiling in 5% Chelex buffer, we also examined the need for homogenization to crush the resting cysts before DNA extraction in each method. Homogenization of resting cysts was found to be essential for DNA extraction in all 4 methods. The detection time was significantly shorter in 5% Chelex buffer than in the other buffers and the amplification success was 100% (65/65), indicating the importance of DNA extraction and the effectiveness of 5% Chelex buffer in the Alexandrium LAMP. Copyright © 2012 Elsevier B.V. All rights reserved.

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection.

PubMed

Barreda-García, Susana; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo J; Lobo-Castañón, María Jesús

2018-01-01

Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed. Graphical Abstract Expanding the analytical toolbox for the detection of DNA sequences specific of pathogens with isothermal helicase dependent amplification (HDA).

Use of Multiple Displacement Amplification as Pre-polymerase Chain Reaction (Pre-PCR) to amplify genomic DNA of siphonapterids preserved for long periods in scientific collections.

PubMed

Avelar, Daniel M; Linardi, Pedro M

2010-09-15

The recently developed Multiple Displacement Amplification technique (MDA) allows for the production of a large quantity of high quality genomic DNA from low amounts of the original DNA. The goal of this study was to evaluate the performance of the MDA technique to amplify genomic DNA of siphonapterids that have been stored for long periods in 70% ethanol at room temperature. We subjected each DNA sample to two different methodologies: (1) amplification of mitochondrial 16S sequences without MDA; (2) amplification of 16S after MDA. All the samples obtained from these procedures were then sequenced. Only 4 samples (15.4%) subjected to method 1 showed amplification. In contrast, the application of MDA (method 2) improved the performance substantially, with 24 samples (92.3%) showing amplification, with significant difference. Interestingly, one of the samples successfully amplified with this method was originally collected in 1909. All of the sequenced samples displayed satisfactory results in quality evaluations (Phred ≥ 20) and good similarities, as identified with the BLASTn tool. Our results demonstrate that the use of MDA may be an effective tool in molecular studies involving specimens of fleas that have traditionally been considered inadequately preserved for such purposes.

Use of Multiple Displacement Amplification as Pre-polymerase Chain Reaction (Pre-PCR) to amplify genomic DNA of siphonapterids preserved for long periods in scientific collections

PubMed Central

2010-01-01

The recently developed Multiple Displacement Amplification technique (MDA) allows for the production of a large quantity of high quality genomic DNA from low amounts of the original DNA. The goal of this study was to evaluate the performance of the MDA technique to amplify genomic DNA of siphonapterids that have been stored for long periods in 70% ethanol at room temperature. We subjected each DNA sample to two different methodologies: (1) amplification of mitochondrial 16S sequences without MDA; (2) amplification of 16S after MDA. All the samples obtained from these procedures were then sequenced. Only 4 samples (15.4%) subjected to method 1 showed amplification. In contrast, the application of MDA (method 2) improved the performance substantially, with 24 samples (92.3%) showing amplification, with significant difference. Interestingly, one of the samples successfully amplified with this method was originally collected in 1909. All of the sequenced samples displayed satisfactory results in quality evaluations (Phred ≥ 20) and good similarities, as identified with the BLASTn tool. Our results demonstrate that the use of MDA may be an effective tool in molecular studies involving specimens of fleas that have traditionally been considered inadequately preserved for such purposes. PMID:20840790

On the behavior of site effects in Central Mexico (the Mexican Volcanic Belt - MVB), based on records of shallow earthquakes that occurred in the zone between 1998 and 2011

NASA Astrophysics Data System (ADS)

Clemente-Chavez, A.; Zúñiga, F. R.; Lermo, J.; Figueroa-Soto, A.; Valdés, C.; Montiel, M.; Chavez, O.; Arroyo, M.

2013-11-01

The Mexican Volcanic Belt (MVB) is a seismogenic zone that transects the central part of Mexico with an east-west orientation. The risk and hazard seismic of this seismogenic zone has not been studied at detail due to the scarcity of instrumental data as well as because seismicity in the continental regimen of Central Mexico is not too frequent, however, it is known that there are precedents of large earthquakes (Mw > 6.0) that have taken place in this zone. The Valley of Mexico City (VM) is the sole zone, within the MVB, which has been studied in detail; mainly focusing on the ground amplification during large events such as the 1985 subduction earthquake that occurred in Michoacan. The purpose of this article is to analyze the behavior of site effects in the MVB zone based on records of shallow earthquakes (data not reported before) that occurred in the zone between 1998 and 2011. We present a general overview of site effects on the MVB, a classification of the stations in order to reduce the uncertainty in the data to obtain attenuation parameters in future works, and some comparisons between the information presented here and that presented in previous studies. A regional evaluation of site effects and Fourier Acceleration Spectrum (FAS) shape was estimated based on 80 records of 22 shallow earthquakes within the MVB zone. Data of 25 stations were analyzed. Site effects were estimated by using the Horizontal-to-Vertical Spectral Ratio (HVSR) methodology. The results show that seismic waves are less amplified in the northeast sites of the MVB with respect to the rest of the zone and that it is possible to classify two groups of stations: (1) stations with Negligible Site Amplification (NSA) and (2) stations with Significant Site Amplification (SSA). Most of the sites in the first group showed small (< 3) amplifications while the second group showed amplifications ranging from 4 to 6.5 at frequencies of about 0.35, 0.75, 15 and 23 Hz. With these groups of stations, average levels of amplification were contrasted for the first time with those caused by the subduction zone earthaquakes. With respect to the FAS shapes, most of them showed similarities at similar epicentral distances. Finally, some variations of site effects were found when compared to those obtained in previous studies on different seismicity regions. These variations were attributed to the location of the source. These aspects help to advance the understanding about the amplification behavior and of the expected seismic risk on the Central Mexico due to large earthquakes within the MVB seismogenic zone.

On the behavior of site effects in central Mexico (the Mexican volcanic belt - MVB), based on records of shallow earthquakes that occurred in the zone between 1998 and 2011

NASA Astrophysics Data System (ADS)

Clemente-Chavez, A.; Zúñiga, F. R.; Lermo, J.; Figueroa-Soto, A.; Valdés, C.; Montiel, M.; Chavez, O.; Arroyo, M.

2014-06-01

The Mexican volcanic belt (MVB) is a seismogenic zone that transects the central part of Mexico with an east-west orientation. The seismic risk and hazard of this seismogenic zone has not been studied in detail due to the scarcity of instrumental data as well as because seismicity in the continental regime of central Mexico is not too frequent. However, it is known that there are precedents of large earthquakes (Mw > 6.0) that have taken place in this zone. The valley of Mexico City (VM) is the sole zone, within the MVB, that has been studied in detail. Studies have mainly focused on the ground amplification during large events such as the 1985 subduction earthquake that occurred off coast of Michoacán. The purpose of this article is to analyze the behavior of site effects in the MVB zone based on records of shallow earthquakes (data not reported before) that occurred in the zone between 1998 and 2011. We present a general overview of site effects in the MVB, a classification of the stations in order to reduce the uncertainty in the data when obtaining attenuation parameters in future works, as well as some comparisons between the information presented here and that presented in previous studies. A regional evaluation of site effects and Fourier acceleration spectrum (FAS) shape was estimated based on 80 records of 22 shallow earthquakes within the MVB zone. Data of 25 stations were analyzed. Site effects were estimated by using the horizontal-to-vertical spectral ratio (HVSR) methodology. The results show that seismic waves are less amplified in the northeast sites of the MVB with respect to the rest of the zone and that it is possible to classify two groups of stations: (1) stations with negligible site amplification (NSA) and (2) stations with significant site amplification (SSA). Most of the sites in the first group showed small (<3) amplifications while the second group showed amplifications ranging from 4 to 6.5 at frequencies of about 0.35, 0.75, 15 and 23 Hz. With these groups of stations, average levels of amplification were contrasted for the first time with those caused by the subduction zone earthquakes. With respect to the FAS shapes, most of them showed similarities at similar epicentral distances. Finally, some variations of site effects were found when compared to those obtained in previous studies on different seismicity regions. These variations were attributed to the location of the source. These aspects help to advance the understanding about the amplification behavior and of the expected seismic risk on central Mexico due to large earthquakes within the MVB seismogenic zone.

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

PubMed

Schwartz, Alanna; Baidjoe, Amrish; Rosenthal, Philip J; Dorsey, Grant; Bousema, Teun; Greenhouse, Bryan

2015-05-01

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 investigated the effects of storage conditions, length of storage, and DNA extraction methods on amplification via three PCR-based assays using field samples and laboratory controls. Samples stored as DBS for 2 or more years at ambient temperature showed a significant loss of sensitivity that increased with time; after 10 years only 10% samples with parasite densities > 1,000 parasites/μL were detectable by nested polymerase chain reaction (PCR). Conversely, DBS and extracted DNA stored at -20°C showed no loss of sensitivity with time. Samples with low parasite densities amplified more successfully with saponin/Chelex compared with spin-column-based extraction, though the latter method performed better on samples with higher parasite densities stored for 2 years at ambient temperature. DNA extracted via both methods was stable after 20 freeze-thaw cycles. Our results suggest that DBS should be stored at -20°C or extracted immediately, especially if anticipating 2 or more years of storage. © The American Society of Tropical Medicine and Hygiene.

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

PubMed Central

Schwartz, Alanna; Baidjoe, Amrish; Rosenthal, Philip J.; Dorsey, Grant; Bousema, Teun; Greenhouse, Bryan

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 investigated the effects of storage conditions, length of storage, and DNA extraction methods on amplification via three PCR-based assays using field samples and laboratory controls. Samples stored as DBS for 2 or more years at ambient temperature showed a significant loss of sensitivity that increased with time; after 10 years only 10% samples with parasite densities > 1,000 parasites/μL were detectable by nested polymerase chain reaction (PCR). Conversely, DBS and extracted DNA stored at −20°C showed no loss of sensitivity with time. Samples with low parasite densities amplified more successfully with saponin/Chelex compared with spin-column-based extraction, though the latter method performed better on samples with higher parasite densities stored for 2 years at ambient temperature. DNA extracted via both methods was stable after 20 freeze-thaw cycles. Our results suggest that DBS should be stored at −20°C or extracted immediately, especially if anticipating 2 or more years of storage. PMID:25758652

Next-Level ShakeZoning for Earthquake Hazard Definition in Nevada

NASA Astrophysics Data System (ADS)

Louie, J. N.; Savran, W. H.; Flinchum, B. A.; Dudley, C.; Prina, N.; Pullammanappallil, S.; Pancha, A.

2011-12-01

We are developing "Next-Level ShakeZoning" procedures tailored for defining earthquake hazards in Nevada. The current Federally sponsored tools- the USGS hazard maps and ShakeMap, and FEMA HAZUS- were developed as statistical summaries to match earthquake data from California, Japan, and Taiwan. The 2008 Wells and Mogul events in Nevada showed in particular that the generalized statistical approach taken by ShakeMap cannot match actual data on shaking from earthquakes in the Intermountain West, even to first order. Next-Level ShakeZoning relies on physics and geology to define earthquake shaking hazards, rather than statistics. It follows theoretical and computational developments made over the past 20 years, to capitalize on detailed and specific local data sets to more accurately model the propagation and amplification of earthquake waves through the multiple geologic basins of the Intermountain West. Excellent new data sets are now available for Las Vegas Valley. Clark County, Nevada has completed the nation's very first effort to map earthquake hazard class systematically through an entire urban area using Optim's SeisOpt° ReMi technique, which was adapted for large-scale data collection. Using the new Parcel Map in computing shaking in the Valley for scenario earthquakes is crucial for obtaining realistic predictions of ground motions. In an educational element of the project, a dozen undergraduate students have been computing 50 separate earthquake scenarios affecting Las Vegas Valley, using the Next-Level ShakeZoning process. Despite affecting only the upper 30 meters, the Vs30 geotechnical shear-velocity from the Parcel Map shows clear effects on 3-d shaking predictions computed so far at frequencies from 0.1 Hz up to 1.0 Hz. The effect of the Parcel Map on even the 0.1-Hz waves is prominent even with the large mismatch of wavelength to geotechnical depths. Amplifications and de-amplifications affected by the Parcel Map exceed a factor of two, and are highly dependent on the particular scenario. As well, Parcel Map amplification effects extend into areas not characterized in the Parcel Map. The fully 3-d Next-Level ShakeZoning scenarios show many areas of shaking amplification and de-amplification that USGS ShakeMap scenarios cannot predict. For example, the Frenchman Mountain scenario shows PGV of the two approaches within 15% of each other near the source, but upwards of 200% relative amplification or de-amplification, depending on location, throughout Las Vegas Valley.

Flux amplification in helicity injected spherical tori

NASA Astrophysics Data System (ADS)

Tang, X. Z.; Boozer, A. H.

2005-04-01

An important measure of the effective current drive by helicity injection into spheromaks and spherical tori is provided by the flux amplification factor, defined as the ratio between the closed poloidal flux in the relaxed mean field and the initial injector vacuum poloidal flux. Flux amplification in magnetic helicity injection is governed by a resonant behavior for Taylor-relaxed plasmas satisfying j =kB. Under the finite net toroidal flux constraint in a spherical torus (ST), the constrained linear resonance k1c is upshifted substantially from the primary Jensen-Chu resonance k1 that was known to be responsible for flux amplification in spheromak formation. Standard coaxial helicity injection into a ST operates at large M, with M the characteristic dimensionless parameter defined as the ratio between the toroidal flux in the discharge chamber and the injector poloidal flux. Meaningful flux amplification for ST plasmas is limited by a critical kr at which edge toroidal field reverses its direction. The kr is downshifted from k1 by a small amount inversely proportional to M. The maximum flux amplification factor Ar≡A(k=kr) scales linearly with M. At the other end of k, substantial flux amplification A(k =ko)˜1 becomes available for ko that scales inversely proportional to M, a significant departure from that in spheromak formation. These important parameters follow the inequality ko

Failed PCR of Ganoderma type specimens affects nomenclature.

PubMed

Paterson, R R M; Lima, N

2015-06-01

The nomenclature of Ganoderma used as a Chinese medicine is debated. A group of researchers could not amplify the DNA of type specimens and concluded the DNA was degraded irreparably. New topotypes were used as the type specimens which was premature. The use of internal amplification controls is recommended to determine if other factors were involved as alternative explanations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Multiplex Allele-Specific Amplification from Whole Blood for Detecting Multiple Polymorphisms Simultaneously

PubMed Central

Zhu, Jianjie; Chen, Lanxin; Mao, Yong; Zhou, Huan

2013-01-01

Allele-specific amplification on the basis of polymerase chain reaction (PCR) has been widely used for single-nucleotide polymorphism (SNP) genotyping. However, the extraction of PCR-compatible genomic DNA from whole blood is usually required. This process is complicated and tedious, and is prone to cause cross-contamination between samples. To facilitate direct PCR amplification from whole blood without the extraction of genomic DNA, we optimized the pH value of PCR solution and the concentrations of magnesium ions and facilitator glycerol. Then, we developed multiplex allele-specific amplifications from whole blood and applied them to a case–control study. In this study, we successfully established triplex, five-plex, and eight-plex allele-specific amplifications from whole blood for determining the distribution of genotypes and alleles of 14 polymorphisms in 97 gastric cancer patients and 141 healthy controls. Statistical analysis results showed significant association of SNPs rs9344, rs1799931, and rs1800629 with the risk of gastric cancer. This method is accurate, time-saving, cost-effective, and easy-to-do, especially suitable for clinical prediction of disease susceptibility. PMID:23072573

Recombinase Polymerase Amplification (RPA) of CaMV-35S Promoter and nos Terminator for Rapid Detection of Genetically Modified Crops

PubMed Central

Xu, Chao; Li, Liang; Jin, Wujun; Wan, Yusong

2014-01-01

Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37–42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15–25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops. PMID:25310647

Dual signal amplification for highly sensitive electrochemical detection of uropathogens via enzyme-based catalytic target recycling.

PubMed

Su, Jiao; Zhang, Haijie; Jiang, Bingying; Zheng, Huzhi; Chai, Yaqin; Yuan, Ruo; Xiang, Yun

2011-11-15

We report an ultrasensitive electrochemical approach for the detection of uropathogen sequence-specific DNA target. The sensing strategy involves a dual signal amplification process, which combines the signal enhancement by the enzymatic target recycling technique with the sensitivity improvement by the quantum dot (QD) layer-by-layer (LBL) assembled labels. The enzyme-based catalytic target DNA recycling process results in the use of each target DNA sequence for multiple times and leads to direct amplification of the analytical signal. Moreover, the LBL assembled QD labels can further enhance the sensitivity of the sensing system. The coupling of these two effective signal amplification strategies thus leads to low femtomolar (5fM) detection of the target DNA sequences. The proposed strategy also shows excellent discrimination between the target DNA and the single-base mismatch sequences. The advantageous intrinsic sequence-independent property of exonuclease III over other sequence-dependent enzymes makes our new dual signal amplification system a general sensing platform for monitoring ultralow level of various types of target DNA sequences. Copyright © 2011 Elsevier B.V. All rights reserved.

Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops.

PubMed

Xu, Chao; Li, Liang; Jin, Wujun; Wan, Yusong

2014-10-10

Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37-42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15-25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops.

High amplification levels of MDM2 and CDK4 correlate with poor outcome in patients with dedifferentiated liposarcoma: A cytogenomic microarray analysis of 47 cases.

PubMed

Ricciotti, Robert W; Baraff, Aaron J; Jour, George; Kyriss, McKenna; Wu, Yu; Liu, Yuhua; Li, Shao-Chun; Hoch, Benjamin; Liu, Yajuan J

2017-12-01

Dedifferentiated liposarcoma (DDLS) is characterized at the molecular level by amplification of genes within 12q13-15 including MDM2 and CDK4. However, other than FNCLCC grade, prognostic markers are limited. We aim to identify molecular prognostic markers for DDLS to help risk stratify patients. To this end, we studied 49 cases of DDLS in our institutional archives and performed cytogenomic microarray analysis on 47 cases. Gene copy numbers for 12 loci were evaluated and correlated with outcome data retrieved from our institutional electronic medical records. Using cut point analysis and comparison of Kaplan-Meier survival curves by log rank tests, high amplification levels of MDM2 (>38 copies) and CDK4 (>30 copies) correlated with decreased disease free survival (DFS) (P = .0168 and 0.0169 respectively) and disease specific survival (DSS) (P = .0082 and 0.0140 respectively). Additionally, MDM2 and CDK4 showed evidence of a synergistic effect so that each additional copy of one enhances the effect on prognosis of each additional copy of the other for decreased DFS (P = .0227, 0.1% hazard). High amplification of JUN (>16 copies) also correlated with decreased DFS (P = .0217), but not DSS. The presence of copy number alteration at 3q29 correlated with decreased DSS (P = .0192). The presence of >10 mitoses per 10 high power fields and FNCLCC grade 3 also correlated with decreased DFS (P = .0310 and 0.0254 respectively). MDM2 and CDK4 gene amplification levels, along with JUN amplification and copy alterations at 3q29, can be utilized for predicting outcome in patients with DDLS. Published by Elsevier Inc.

HPV-18 E6 mutants reveal p53 modulation of viral DNA amplification in organotypic cultures

PubMed Central

Kho, Eun-Young; Wang, Hsu-Kun; Banerjee, N. Sanjib; Broker, Thomas R.; Chow, Louise T.

2013-01-01

Human papillomaviruses (HPVs) amplify in differentiated strata of a squamous epithelium. The HPV E7 protein destabilizes the p130/retinoblastoma susceptibility protein family of tumor suppressors and reactivates S-phase reentry, thereby facilitating viral DNA amplification. The high-risk HPV E6 protein destabilizes the p53 tumor suppressor and many other host proteins. However, the critical E6 targets relevant to viral DNA amplification have not been identified, because functionally significant E6 mutants are not stably maintained in transfected cells. Using Cre-loxP recombination, which efficiently generates HPV genomic plasmids in transfected primary human keratinocytes, we have recapitulated a highly productive infection of HPV-18 in organotypic epithelial cultures. By using this system, we now report the characterization of four HPV-18 E6 mutations. An E6 null mutant accumulated high levels of p53 and amplified very poorly. p53 siRNA or ectopic WT E6 partially restored amplification, whereas three missense E6 mutations that did not effectively destabilize p53 complemented the null mutant poorly. Unexpectedly, in cis, two of the missense mutants amplified, albeit to a lower extent than the WT and only in cells with undetectable p53. These observations and others implicate p53 and additional host proteins in regulating viral DNA amplification and also suggest an inhibitory effect of E6 overexpression. We show that high levels of viral DNA amplification are critical for late protein expression and report several previously undescribed viral RNAs, including bicistronic transcripts predicted to encode E5 and L2 or an alternative form of E1^E4 and L1. PMID:23572574

Sin Nombre Virus and Rodent Species Diversity: A Test of the Dilution and Amplification Hypotheses

PubMed Central

Clay, Christine A.; Lehmer, Erin M.; Jeor, Stephen St.; Dearing, M. Denise

2009-01-01

Background Species diversity is proposed to greatly impact the prevalence of pathogens. Two predominant hypotheses, the “Dilution Effect” and the “Amplification Effect”, predict divergent outcomes with respect to the impact of species diversity. The Dilution Effect predicts that pathogen prevalence will be negatively correlated with increased species diversity, while the Amplification Effect predicts that pathogen prevalence will be positively correlated with diversity. For many host-pathogen systems, the relationship between diversity and pathogen prevalence has not be empirically examined. Methodology/Principal Findings We tested the Dilution and Amplification Effect hypotheses by examining the prevalence of Sin Nombre virus (SNV) with respect to diversity of the nocturnal rodent community. SNV is directly transmitted primarily between deer mice (Peromyscus maniculatus). Using mark-recapture sampling in the Spring and Fall of 2003–2005, we measured SNV prevalence in deer mice at 16 landscape level sites (3.1 hectares each) that varied in rodent species diversity. We explored several mechanisms by which species diversity may affect SNV prevalence, including reduced host density, reduced host persistence, the presence of secondary reservoirs and community composition. We found a negative relationship between species diversity and SNV prevalence in deer mice, thereby supporting the Dilution Effect hypothesis. Deer mouse density and persistence were lower at sites with greater species diversity; however, only deer mouse persistence was positively correlated with SNV prevalence. Pinyon mice (P. truei) may serve as dilution agents, having a negative effect on prevalence, while kangaroo rats (Dipodomys ordii), may have a positive effect on the prevalence of SNV, perhaps through effects on deer mouse behavior. Conclusions/Significance While previous studies on host-pathogen systems have found patterns of diversity consistent with either the Dilution or Amplification Effects, the mechanisms by which species diversity influences prevalence have not been investigated. Our study indicates that changes in host persistence, coupled with interspecific interactions, are important mechanisms through which diversity may influence patterns of pathogens. Our results reveal the complexity of rodent community interactions with respect to SNV dynamics. PMID:19649283

On-chip electrical detection of parallel loop-mediated isothermal amplification with DG-BioFETs for the detection of foodborne bacterial pathogens

USDA-ARS?s Scientific Manuscript database

The use of field effect transistors (FETs) as the transduction element for the detection of DNA amplification reactions will enable portable and inexpensive nucleic acid analysis. Transistors used as biological sensors,or BioFETs, minimize the cost and size of detection platforms by leveraging fabri...

Optical Pattern Recognition With Self-Amplification

NASA Technical Reports Server (NTRS)

Liu, Hua-Kuang

1994-01-01

In optical pattern recognition system with self-amplification, no reference beam used in addressing mode. Polarization of laser beam and orientation of photorefractive crystal chosen to maximize photorefractive effect. Intensity of recognition signal is orders of magnitude greater than other optical correlators. Apparatus regarded as real-time or quasi-real-time optical pattern recognizer with memory and reprogrammability.

Real-time PCR assays using internal controls for quantitation of HPV-16 and beta-globin DNA in cervicovaginal lavages.

PubMed

Lefevre, Jonas; Hankins, Catherine; Pourreaux, Karina; Voyer, Hélène; Coutlée, François

2003-12-01

High-risk human papillomavirus 16 (HPV-16) DNA viral load has been measured with real-time PCR assays by amplifying HPV-16 and a human gene. However, these assays have not used internal controls (ICs) to screen for the presence of inhibitors contained in samples. To quantitate HPV-16 DNA and cell content with real-time PCR, ICs for HPV-16 DNA and beta-globin were synthesised and used to control for inhibition. The assays were sensitive and linear over 5 logs. Good reproducibility was achieved with inter-run coefficients of variation of 23% (10(2) HPV-16 copies), 12% (10(4) HPV-16 copies), 17% (274 beta-globin DNA copies) and 7% (27,400 beta-globin DNA copies). Samples containing 56,800,000, 306,000, 18,000, and 4,070 HPV-16 copies/microg of cellular DNA were tested blindly and estimated to contain 48,800,000, 479,000, 20,300, and 6,620 HPV-16 copies/microg of DNA (mean ratio of measured to expected viral load of 1.27+/-0.32). Inhibition of amplification of HPV-16 and beta-globin ICs by six samples known to contain PCR inhibitors was variable: four inhibited both ICs while two inhibited only the HPV-16 IC. The use of internal controls with real-time PCR for HPV-16 quantitation allows to screen for the presence of inhibitors that do not affect equally primer-driven genomic amplification.

Icotinib in Patients with Pretreated Advanced Esophageal Squamous Cell Carcinoma with EGFR Overexpression or EGFR Gene Amplification: A Single-Arm, Multicenter Phase 2 Study.

PubMed

Huang, Jing; Fan, Qingxia; Lu, Ping; Ying, Jianming; Ma, Changwu; Liu, Wei; Liu, Ying; Tan, Fenlai; Sun, Yan

2016-06-01

Epidermal growth factor receptor (EGFR) has been reported to be overexpressed and amplified in a high percentage of patients with esophageal squamous cell carcinoma (ESCC). The activity of icotinib, an EGFR tyrosine kinase inhibitor, was assessed in previously treated ESCC with EGFR overexpression or amplification. For this phase 2, single-arm, multicenter trial undertaken at six hospitals in China, we included Chinese patients with previously treated, histologically confirmed advanced ESCC and EGFR overexpression (immunohistochemical staining sore of 3+) or amplification (positive fluorescence in situ hybridization result). These patients received oral icotinib (250 mg, three times daily).The primary end point was the proportion of patients with objective responses as assessed by an independent radiology review committee. Between December 5, 2013, and May 28, 2015, a total of 281 patients were screened. Fifty-four eligible patients were enrolled. Nine responses were observed, including one complete response and eight partial responses, and 16 patients had stable disease, resulting in a 16.7% objective response rate (95% confidence interval [CI]: 6.7-26.6) and 46.3% disease control rate (95% CI: 33.0-59.6). The median progression-free survival and overall survival times were 52 (95% CI: 40-95) days and 153 (95% CI: 139-218) days, respectively. A total of 43 patients experienced at least one adverse event, but most were only grade 1 to 2 in severity. The most frequent was rash (48.1%), followed by diarrhea (22.2%). Icotinib showed favorable activity in patients with advanced, previously treated ESCC with EGFR overexpression or amplification. These findings suggest further research into EGFR overexpression or amplification for selecting responsive patients. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Direct PCR amplification of DNA from human bloodstains, saliva, and touch samples collected with microFLOQ® swabs.

PubMed

Ambers, Angie; Wiley, Rachel; Novroski, Nicole; Budowle, Bruce

2018-01-01

Previous studies have shown that nylon flocked swabs outperform traditional fiber swabs in DNA recovery due to their innovative design and lack of internal absorbent core to entrap cellular materials. The microFLOQ ® Direct swab, a miniaturized version of the 4N6 FLOQSwab ® , has a small swab head that is treated with a lysing agent which allows for direct amplification and DNA profiling from sample collection to final result in less than two hours. Additionally, the microFLOQ ® system subsamples only a minute portion of a stain and preserves the vast majority of the sample for subsequent testing or re-analysis, if desired. The efficacy of direct amplification of DNA from dilute bloodstains, saliva stains, and touch samples was evaluated using microFLOQ ® Direct swabs and the GlobalFiler™ Express system. Comparisons were made to traditional methods to assess the robustness of this alternate workflow. Controlled studies with 1:19 and 1:99 dilutions of bloodstains and saliva stains consistently yielded higher STR peak heights than standard methods with 1ng input DNA from the same samples. Touch samples from common items yielded single source and mixed profiles that were consistent with primary users of the objects. With this novel methodology/workflow, no sample loss occurs and therefore more template DNA is available during amplification. This approach may have important implications for analysis of low quantity and/or degraded samples that plague forensic casework. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Spectral amplification models for response spectrum addressing the directivity effect

NASA Astrophysics Data System (ADS)

Moghimi, Saed; Akkar, Sinan

2017-04-01

Ground motions with forward directivity effects are known with their significantly large spectral ordinates in medium-to-long periods. The large spectral ordinates stem from the impulsive characteristics of the forward directivity ground motions. The quantification of these spectral amplifications requires the identification of major seismological parameters that play a role in their generation. After running a suite of probabilistic seismic hazard analysis, Moghimi and Akkar (2016) have shown that fault slip rate, fault characteristic magnitude, fault-site geometry as well as mean annual exceedance rate are important parameters that determine the level of spectral amplification due to directivity. These parameters are considered to develop two separate spectral amplification equations in this study. The proposed equations rely on Shahi and Baker (SHB11; 2011) and Chiou and Spudich (CHS13; Spudic et al., 2013) narrow-band forward directivity models. The presented equations only focus on the estimation of maximum spectral amplifications that occur at the ends of the fault segments. This way we eliminate the fault-site parameter in our equations for simplification. The proposed equations show different trends due to differences in the narrow-band directivity models of SHB11 and CHS13. The equations given in this study can form bases for describing forward directivity effects in seismic design codes. REFERENCES Shahi. S., Baker, J.W. (2011), "An Empirically Calibrated Framework for Including the Effects of Near-Fault Directivity in Probabilistic Seismic Hazard Analysis", Bulletin of the Seismological Society of America, 101(2): 742-755. Spudich, P., Watson-Lamprey, J., Somerville, P., Bayless, J., Shahi, S. K., Baker, J. W., Rowshandel, B., and Chiou, B. (2013), "Final Report of the NGA-West2 Directivity Working Group", PEER Report 2013/09. Moghimi. S., Akkar, S. (2016), "Implications of Forward Directivity Effects on Design Ground Motions", Seismological Society of America, Annual meeting, 2016, Reno, Nevada, 87:2B Pg. 464

Amplification or suppression: Social networks and the climate change-migration association in rural Mexico.

PubMed

Nawrotzki, Raphael J; Riosmena, Fernando; Hunter, Lori M; Runfola, Daniel M

2015-11-01

Increasing rates of climate migration may be of economic and national concern to sending and destination countries. It has been argued that social networks - the ties connecting an origin and destination - may operate as "migration corridors" with the potential to strongly facilitate climate change-related migration. This study investigates whether social networks at the household and community levels amplify or suppress the impact of climate change on international migration from rural Mexico. A novel set of 15 climate change indices was generated based on daily temperature and precipitation data for 214 weather stations across Mexico. Employing geostatistical interpolation techniques, the climate change values were linked to 68 rural municipalities for which sociodemographic data and detailed migration histories were available from the Mexican Migration Project. Multi-level discrete-time event-history models were used to investigate the effect of climate change on international migration between 1986 and 1999. At the household level, the effect of social networks was approximated by comparing the first to the last move, assuming that through the first move a household establishes internal social capital. At the community level, the impact of social capital was explored through interactions with a measure of the proportion of adults with migration experience. The results show that rather than amplifying , social capital may suppress the sensitivity of migration to climate triggers, suggesting that social networks could facilitate climate change adaptation in place.

NONLINEAR OPTICAL EFFECTS AND FIBER OPTICS: Pulsed neodymium amplifier with phase conjugation and direct amplification

NASA Astrophysics Data System (ADS)

Basov, N. G.; Efimkov, V. F.; Zubarev, I. G.; Kolobrodov, V. V.; Pastukhov, S. A.; Smirnov, M. G.; Sobolev, V. B.

1988-12-01

A study was made of the characteristics of an amplifier containing neodymium-activated silicate rods, 45 mm in diameter, used in direct amplification and phase conjugation systems. At low output energies the divergence of the output radiation in the presence of a phase-conjugating mirror was half ( ~ 10- 4 rad) that in the case of direct amplification. An increase in the output power caused the divergence to rise more rapidly in the presence of a phase-conjugating mirror, which was tentatively attributed to an earlier manifestation of large-scale self-focusing. Output energies of 130 J in the case of direct amplification and 80 J in the presence of a phase-conjugating mirror were obtained when the output pulse duration was ~ 2 ns and the fraction of the total energy contained within an angle of ~ 10- 4 rad was ~ 0.3.

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

PubMed Central

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

Phase sensitive amplification in integrated waveguides (Conference Presentation)

NASA Astrophysics Data System (ADS)

Schroeder, Jochen B.; Zhang, Youngbin; Husko, Chad A.; LeFrancois, Simon; Eggleton, Benjamin J.

2017-02-01

Phase sensitive amplification (PSA) is an attractive technology for integrated all-optical signal processing, due to it's potential for noiseless amplification, phase regeneration and generation of squeezed light. In this talk I will review our results on implementing four-wave-mixing based PSA inside integrated photonic devices. In particular I will discuss PSA in chalcogenide ridge waveguides and silicon slow-light photonic crystals. We achieve PSA in both pump- and signal-degenerate schemes with maximum extinction ratios of 11 (silicon) and 18 (chalcogenide) dB. I will further discuss the influence of two-photon absorption and free carrier effects on the performance of silicon-based PSAs.

Protocol for the use of a rapid real-time PCR method for the detection of HIV-1 proviral DNA using double-stranded primer.

PubMed

Pau, Chou-Pong; Wells, Susan K; Granade, Timothy C

2012-01-01

This chapter describes a real-time PCR method for the detection of HIV-1 proviral DNA in whole blood samples using a novel double-stranded primer system. The assay utilizes a simple commercially available DNA extraction method and a rapid and easy-to-perform real-time PCR protocol to consistently detect a minimum of four copies of HIV-1 group M proviral DNA in as little as 90 min after sample (whole blood) collection. Co-amplification of the human RNase P gene serves as an internal control to monitor the efficiency of both the DNA extraction and amplification. Once the assay is validated properly, it may be suitable as an alternative confirmation test for HIV-1 infections in a variety of HIV testing venues including the mother-to-child transmission testing sites, clinics, and diagnostic testing centers.

Real-time monitoring of rolling-circle amplification using a modified molecular beacon design

PubMed Central

Nilsson, Mats; Gullberg, Mats; Dahl, Fredrik; Szuhai, Karoly; Raap, Anton K.

2002-01-01

We describe a method to monitor rolling-circle replication of circular oligonucleotides in dual-color and in real-time using molecular beacons. The method can be used to study the kinetics of the polymerization reaction and to amplify and quantify circularized oligonucleotide probes in a rolling-circle amplification (RCA) reaction. Modified molecular beacons were made of 2′-O-Me-RNA to prevent 3′ exonucleolytic degradation by the polymerase used. Moreover, the complement of one of the stem sequences of the molecular beacon was included in the RCA products to avoid fluorescence quenching due to inter-molecular hybridization of neighboring molecular beacons hybridizing to the concatemeric polymerization product. The method allows highly accurate quantification of circularized DNA over a broad concentration range by relating the signal from the test DNA circle to an internal reference DNA circle reporting in a distinct fluorescence color. PMID:12136114

Single molecule sequencing of the M13 virus genome without amplification

PubMed Central

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X.; Yan, Qin; Deem, Michael W.; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias. PMID:29253901

Single molecule sequencing of the M13 virus genome without amplification.

PubMed

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X; Yan, Qin; Deem, Michael W; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

Rapid and Inexpensive Screening of Genomic Copy Number Variations Using a Novel Quantitative Fluorescent PCR Method

PubMed Central

Han, Joan C.; Elsea, Sarah H.; Pena, Heloísa B.; Pena, Sérgio Danilo Junho

2013-01-01

Detection of human microdeletion and microduplication syndromes poses significant burden on public healthcare systems in developing countries. With genome-wide diagnostic assays frequently inaccessible, targeted low-cost PCR-based approaches are preferred. However, their reproducibility depends on equally efficient amplification using a number of target and control primers. To address this, the recently described technique called Microdeletion/Microduplication Quantitative Fluorescent PCR (MQF-PCR) was shown to reliably detect four human syndromes by quantifying DNA amplification in an internally controlled PCR reaction. Here, we confirm its utility in the detection of eight human microdeletion syndromes, including the more common WAGR, Smith-Magenis, and Potocki-Lupski syndromes with 100% sensitivity and 100% specificity. We present selection, design, and performance evaluation of detection primers using variety of approaches. We conclude that MQF-PCR is an easily adaptable method for detection of human pathological chromosomal aberrations. PMID:24288428

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

PubMed

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.

Factors affecting genotyping success in giant panda fecal samples.

PubMed

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong; Zhang, He-Min

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH -20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at -20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates ( P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ragan, Eric D; Bowman, Doug A; Scerbo, Siroberto

Virtual reality (VR) systems have been proposed for use in numerous training scenarios, such as room clearing, which require the trainee to maintain spatial awareness. But many VR training systems lack a fully surrounding display, requiring trainees to use a combination of physical and virtual turns to view the environment, thus decreasing spatial awareness. One solution to this problem is to amplify head rotations, such that smaller physical turns are mapped to larger virtual turns, allowing trainees to view the surrounding environment with head movements alone. For example, in a multi-monitor system covering only a 90-degree field of regard, headmore » rotations could be amplified four times to allow the user to see the entire 360-degree surrounding environment. This solution is attractive because it can be used with lower-cost VR systems and does not require virtual turning. However, the effects of amplified head rotations on spatial awareness and training transfer are not well understood. We hypothesized that small amounts of amplification might be tolerable, but that larger amplifications might cause trainees to become disoriented and to have decreased task performance and training transfer. In this paper, we will present our findings from an experiment designed to investigate these hypotheses. The experiment placed users in a virtual warehouse and asked them to move from room to room, counting objects placed around them in space. We varied the amount of amplification applied during these trials, and also varied the type of display used (head-mounted display or CAVE). We measured task performance and spatial awareness. We then assessed training transfer in an assessment environment with a fully surrounding display and no amplification. The results of this study will inform VR training system developers about the potential negative effects of using head rotation amplification and contribute to more effective VR training system design.« less

Factors affecting genotyping success in giant panda fecal samples

PubMed Central

Zhu, Ying; Liu, Hong-Yi; Yang, Hai-Qiong; Li, Yu-Dong

2017-01-01

Fecal samples play an important role in giant panda conservation studies. Optimal preservation conditions and choice of microsatellites for giant panda fecal samples have not been established. In this study, we evaluated the effect of four factors (namely, storage type (ethanol (EtOH), EtOH −20 °C, 2-step storage medium, DMSO/EDTA/Tris/salt buffer (DETs) and frozen at −20 °C), storage time (one, three and six months), fragment length, and repeat motif of microsatellite loci) on the success rate of microsatellite amplification, allelic dropout (ADO) and false allele (FA) rates from giant panda fecal samples. Amplification success and ADO rates differed between the storage types. Freezing was inferior to the other four storage methods based on the lowest average amplification success and the highest ADO rates (P < 0.05). The highest microsatellite amplification success was obtained from either EtOH or the 2-step storage medium at three storage time points. Storage time had a negative effect on the average amplification of microsatellites and samples stored in EtOH and the 2-step storage medium were more stable than the other three storage types. We only detected the effect of repeat motif on ADO and FA rates. The lower ADO and FA rates were obtained from tri- and tetra-nucleotide loci. We suggest that freezing should not be used for giant panda fecal preservation in microsatellite studies, and EtOH and the 2-step storage medium should be chosen on priority for long-term storage. We recommend candidate microsatellite loci with longer repeat motif to ensure greater genotyping success for giant panda fecal studies. PMID:28560107

RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection.

PubMed

Takahashi, Hirokazu; Ohkawachi, Masahiko; Horio, Kyohei; Kobori, Toshiro; Aki, Tsunehiro; Matsumura, Yukihiko; Nakashimada, Yutaka; Okamura, Yoshiko

2018-05-17

RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3'-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes. When padlock probes are hybridized to the target RNA molecule, they are converted to the circular form by SplintR ligase. Subsequently, RNase H creates nick sites only in the hybridized RNA sequence, and single-stranded DNA is finally synthesized from the nick site by phi29 DNA polymerase. This method could specifically detect at least 10 fmol of the target RNA molecule without reverse transcription. Moreover, this method detected GFP mRNA present in 10 ng of total RNA isolated from Escherichia coli without background DNA amplification. Therefore, this method can potentially detect almost all types of RNA molecules without reverse transcription and reveal full-length sequence information.

Amplification of thermostable lipase genes fragment from thermogenic phase of domestic waste composting process

NASA Astrophysics Data System (ADS)

Nurhasanah, Nurbaiti, Santi; Madayanti, Fida; Akhmaloka

2015-09-01

Lipases are lipolytic enzymes, catalyze the hydrolysis of fatty acid ester bonds of triglycerides to produce free fatty acids and glycerol. The enzyme is widely used in various fields of biotechnological industry. Hence, lipases with unique properties (e.g.thermostable lipase) are still being explored by variation methods. One of the strategy is by using metagenomic approach to amplify the gene directly from environmental sample. This research was focused on amplification of lipase gene fragment directly from the thermogenic phase of domestic waste composting in aerated trenches. We used domestic waste compost from waste treatment at SABUGA, ITB for the sample. Total chromosomal DNA were directly extracted from several stages at thermogenic phase of compost. The DNA was then directly used as a template for amplification of thermostable lipase gene fragments using a set of internal primers namely Flip-1a and Rlip-1a that has been affixed with a GC clamp in reverse primer. The results showed that the primers amplified the gene from four stages of thermogenic phase with the size of lipase gene fragment of approximately 570 base pairs (bp). These results were further used for Denaturing Gradient Gel Electrophoresis (DGGE) analysis to determine diversity of thermostable lipase gene fragments.

Social amplification of wildfire risk: The role of social interactions and information sources

Treesearch

Hannah Brenkert-Smith; Katherine L. Dickinson; Patricia A. Champ; Nicholas Flores

2013-01-01

Wildfire is a persistent and growing threat across much of the western United States. Understanding how people living in fire-prone areas perceive this threat is essential to the design of effective risk management policies. Drawing on the social amplification of risk framework, we develop a conceptual model of wildfire risk perceptions that incorporates the social...

Comparison of Five Modeling Approaches to Quantify and Estimate the Effect of Clouds on the Radiation Amplification Factor (RAF) for Solar Ultraviolet Radiation

EPA Science Inventory

A generally accepted value for the Radiation Amplification Factor (RAF), with respect to the erythemal action spectrum for sunburn of human skin, is −1.1, indicating that a 1.0% increase in stratospheric ozone leads to a 1.1% decrease in the biologically damaging UV radiation in ...

Effect of Arctic Amplification on Design Snow Loads in Alaska

DTIC Science & Technology

2016-09-01

snow water equivalent UFC Unified Facilities Criteria UTC Coordinated Universal Time Keywords: Alaska, Arctic amplification, climate change...extreme value analysis, snow loads, snow water equivalent , SWE Acknowledgements: This work was conducted with support from the Strategic... equivalent (SWE) of the snowpack. We acquired SWE data from a number of sources that provide automatic or manual observations, reanalysis data, or

The Efficiency of Magnetic Field Amplification at Shocks by Turbulence

NASA Technical Reports Server (NTRS)

Ji, Suoqing; Oh, S. Peng; Ruszkowsi, M.; Markevitch, M.

2016-01-01

Turbulent dynamo field amplification has often been invoked to explain the strong field strengths in thin rims in supernova shocks (approx.100 micrograms) and in radio relics in galaxy clusters (approx. micrograms). We present high-resolution magnetohydrodynamic simulations of the interaction between pre-shock turbulence, clumping and shocks, to quantify the conditions under which turbulent dynamo amplification can be significant. We demonstrate numerically converged field amplification which scales with Alfven Mach number, B/B0 varies as MA, up to MA approx.150.This implies that the post-shock field strength is relatively independent of the seed field. Amplification is dominated by compression at low MA, and stretching (turbulent amplification) at high MA. For high MA, the B-field grows exponentially and saturates at equipartition with turbulence, while the vorticity jumps sharply at the shock and subsequently decays; the resulting field is orientated predominately along the shock normal (an effect only apparent in 3D and not 2D). This agrees with the radial field bias seen in supernova remnants. By contrast, for low MA, field amplification is mostly compressional, relatively modest, and results in a predominantly perpendicular field. The latter is consistent with the polarization seen in radio relics. Our results are relatively robust to the assumed level of gas clumping. Our results imply that the turbulent dynamo may be important for supernovae, but is only consistent with the field strength, and not geometry, for cluster radio relics. For the latter, this implies strong pre-existing B-fields in the ambient cluster outskirts.

Optimization of strand displacement amplification-sensitized G-quadruplex DNAzyme-based sensing system and its application in activity detection of uracil-DNA glycosylase.

PubMed

Du, Yi-Chen; Jiang, Hong-Xin; Huo, Yan-Fang; Han, Gui-Mei; Kong, De-Ming

2016-03-15

As an isothermal nucleic acid amplification technique, strand displacement amplification (SDA) reaction has been introduced in G-quadruplex DNAzyme-based sensing system to improve the sensing performance. To further provide useful information for the design of SDA-amplified G-quadruplex DNAzyme-based sensors, the effects of nicking site number in SDA template DNA were investigated. With the increase of the nicking site number from 1 to 2, enrichment of G-quadruplex DNAzyme by SDA is changed from a linear amplification to an exponential amplification, thus greatly increasing the amplification efficiency and subsequently improving the sensing performance of corresponding sensing system. The nicking site number cannot be further increased because more nicking sites might result in high background signals. However, we demonstrated that G-quadruplex DNAzyme enrichment efficiency could be further improved by introducing a cross-triggered SDA strategy, in which two templates each has two nicking sites are used. To validate the proposed cross-triggered SDA strategy, we used it to develop a sensing platform for the detection of uracil-DNA glycosylase (UDG) activity. The sensor enables sensitive detection of UDG activity in the range of 1 × 10(-4)-1 U/mL with a detection limit of 1 × 10(-4)U/mL. Copyright © 2015 Elsevier B.V. All rights reserved.

Cascade Signal Amplification Based on Copper Nanoparticle-Reported Rolling Circle Amplification for Ultrasensitive Electrochemical Detection of the Prostate Cancer Biomarker.

PubMed

Zhu, Ye; Wang, Huijuan; Wang, Lin; Zhu, Jing; Jiang, Wei

2016-02-03

An ultrasensitive and highly selective electrochemical assay was first attempted by combining the rolling circle amplification (RCA) reaction with poly(thymine)-templated copper nanoparticles (CuNPs) for cascade signal amplification. As proof of concept, prostate specific antigen (PSA) was selected as a model target. Using a gold nanoparticle (AuNP) as a carrier, we synthesized the primer-AuNP-aptamer bioconjugate for signal amplification by increasing the primer/aptamer ratio. The specific construction of primer-AuNP-aptamer/PSA/anti-PSA sandwich structure triggered the effective RCA reaction, in which thousands of tandem poly(thymine) repeats were generated and directly served as the specific templates for the subsequent CuNP formation. The signal readout was easily achieved by dissolving the RCA product-templated CuNPs and detecting the released copper ions with differential pulse stripping voltammetry. Because of the designed cascade signal amplification strategy, the newly developed method achieved a linear range of 0.05-500 fg/mL, with a remarkable detection limit of 0.020 ± 0.001 fg/mL PSA. Finally, the feasibility of the developed method for practical application was investigated by analyzing PSA in the real clinical human serum samples. The ultrasensitivity, specificity, convenience, and capability for analyzing the clinical samples demonstrate that this method has great potential for practical disease diagnosis applications.

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

PubMed Central

Bokulich, Nicholas A.

2013-01-01

Ultra-high-throughput sequencing (HTS) of fungal communities has been restricted by short read lengths and primer amplification bias, slowing the adoption of newer sequencing technologies to fungal community profiling. To address these issues, we evaluated the performance of several common internal transcribed spacer (ITS) primers and designed a novel primer set and work flow for simultaneous quantification and species-level interrogation of fungal consortia. Primer comparison and validation were predicted in silico and by sequencing a “mock community” of mixed yeast species to explore the challenges of amplicon length and amplification bias for reconstructing defined yeast community structures. The amplicon size and distribution of this primer set are smaller than for all preexisting ITS primer sets, maximizing sequencing coverage of hypervariable ITS domains by very-short-amplicon, high-throughput sequencing platforms. This feature also enables the optional integration of quantitative PCR (qPCR) directly into the HTS preparatory work flow by substituting qPCR with these primers for standard PCR, yielding quantification of individual community members. The complete work flow described here, utilizing any of the qualified primer sets evaluated, can rapidly profile mixed fungal communities and capably reconstructed well-characterized beer and wine fermentation fungal communities. PMID:23377949

Development of a real-time PCR assay with an internal amplification control for detection of Gram-negative histamine-producing bacteria in fish.

PubMed

Bjornsdottir-Butler, Kristin; Jones, Jessica L; Benner, Ronald; Burkhardt, William

2011-05-01

Prompt detection of bacteria that contribute to scombrotoxin (histamine) fish poisoning can aid in the detection of potentially toxic fish products and prevent the occurrence of illness. We report development of the first real-time PCR method for rapid detection of Gram-negative histamine-producing bacteria (HPB) in fish. The real-time PCR assay was 100% inclusive for detecting high-histamine producing isolates and did not detect any of the low- or non-histamine producing isolates. The efficiency of the assay with/without internal amplification control ranged from 96-104% and in the presence of background flora and inhibitory matrices was 92/100% and 73-96%, respectively. This assay was used to detect HPB from naturally contaminated yellowfin tuna, bluefish, and false albacore samples. Photobacterium damselae (8), Plesiomonas shigelloides (2), Shewanella sp. (1), and Morganella morganii (1) were subsequently isolated from the real-time PCR positive fish samples. These results indicate that the real-time PCR assay developed in this study is a rapid and sensitive method for detecting high-HPB. The assay may be adapted for quantification of HPB, either directly or with an MPN-PCR method. Copyright © 2010. Published by Elsevier Ltd.

Internal amplification controls have not been employed in fungal PCR hence potential false negative results.

PubMed

Paterson, R R M

2007-01-01

Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage.

Turbulence and wave particle interactions in solar-terrestrial plasmas

NASA Technical Reports Server (NTRS)

Dulk, G. A.; Goldman, M. V.; Toomre, J.

1985-01-01

Activities in the following study areas are reported: (1) particle and wave processes in solar flares; (2) solar convection zone turbulence; and (3) solar radiation emission. To investigate the amplification of cyclotron maser radiation in solar flares, a radio frequency. (RF) heating model was developed for the corona surrounding the energy release site. Then nonlinear simulations of compressible convection display prominent penetration by plumes into regions of stable stratification at the base of the solar convection zone, leading to the excitation of internal gravity waves there. Lastly, linear saturation of electron-beam-driven Langmuir waves by ambient density fluctuations, nonlinear saturation by strong turbulence processes, and radiation emission mechanisms are examined. An additional section discusses solar magnetic fields and hydromagnetic waves in inhomogeneous media, and the effect of magnetic fields on stellar oscillation.

Spin noise amplification and giant noise in optical microcavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryzhov, I. I.; Poltavtsev, S. V.; Kozlov, G. G.

2015-06-14

When studying the spin-noise-induced fluctuations of Kerr rotation in a quantum-well microcavity, we have found a dramatic increase of the noise signal (by more than two orders of magnitude) in the vicinity of anti-crossing of the polariton branches. The effect is explained by nonlinear optical instability of the microcavity giving rise to the light-power-controlled amplification of the polarization noise signal. In the framework of the developed model of built-in amplifier, we also interpret the nontrivial spectral and intensity-related properties of the observed noise signal below the region of anti-crossing of polariton branches. The discovered effect of optically controllable amplification ofmore » broadband polarization signals in microcavities in the regime of optical instability may be of interest for detecting weak oscillations of optical anisotropy in fundamental research and for other applications in optical information processing.« less

Effects of exercise on central aortic pressure before and after treatment with renin-angiotensin system blockade in patients with hypertension.

PubMed

Lacy, Peter S; Brunel, Patrick; Baschiera, Fabio; Botha, Jaco; Williams, Bryan

2015-12-01

Brachial blood pressure increases with exercise and an excessive rise predicts increased cardiovascular risk. Measurement of brachial blood pressure alone may exaggerate the true blood pressure elevation due to exercise-induced change to pressure amplification. Whether blood pressure-lowering treatment modulates pressure amplification during exercise is unknown. Thirty-two participants with stage 1-2 hypertension (mean age 59.2 years) received eight weeks' blood pressure lowering with either aliskiren (300mg, n=16) or valsartan (320mg, n=16). Brachial and central aortic pressure (CASP) were measured non-invasively during treadmill exercise (Bruce protocol) at baseline, after eight weeks' treatment and 48 hours following treatment withdrawal. The rise in brachial blood pressure with exercise exceeded the rise in CASP, indicative of enhanced pressure amplification. Eight weeks' treatment elicited similar reductions in brachial blood pressure and CASP which did not differ between rest and peak exercise (p>0.05). The exercise-induced increase in systolic pressure amplification did not differ between baseline and following eight weeks' treatment (p>0.05). These effects remained unchanged following treatment withdrawal. Blood pressure lowering does not directly influence the relationship between aortic and brachial pressure either at rest or during exercise in patients with hypertension, other than through proportionate lowering of both pressures. These effects remained unchanged 48 hours after a simulated missed medication dose. © The Author(s) 2014.

Effect of Error Augmentation on Brain Activation and Motor Learning of a Complex Locomotor Task

PubMed Central

Marchal-Crespo, Laura; Michels, Lars; Jaeger, Lukas; López-Olóriz, Jorge; Riener, Robert

2017-01-01

Up to date, the functional gains obtained after robot-aided gait rehabilitation training are limited. Error augmenting strategies have a great potential to enhance motor learning of simple motor tasks. However, little is known about the effect of these error modulating strategies on complex tasks, such as relearning to walk after a neurologic accident. Additionally, neuroimaging evaluation of brain regions involved in learning processes could provide valuable information on behavioral outcomes. We investigated the effect of robotic training strategies that augment errors—error amplification and random force disturbance—and training without perturbations on brain activation and motor learning of a complex locomotor task. Thirty-four healthy subjects performed the experiment with a robotic stepper (MARCOS) in a 1.5 T MR scanner. The task consisted in tracking a Lissajous figure presented on a display by coordinating the legs in a gait-like movement pattern. Behavioral results showed that training without perturbations enhanced motor learning in initially less skilled subjects, while error amplification benefited better-skilled subjects. Training with error amplification, however, hampered transfer of learning. Randomly disturbing forces induced learning and promoted transfer in all subjects, probably because the unexpected forces increased subjects' attention. Functional MRI revealed main effects of training strategy and skill level during training. A main effect of training strategy was seen in brain regions typically associated with motor control and learning, such as, the basal ganglia, cerebellum, intraparietal sulcus, and angular gyrus. Especially, random disturbance and no perturbation lead to stronger brain activation in similar brain regions than error amplification. Skill-level related effects were observed in the IPS, in parts of the superior parietal lobe (SPL), i.e., precuneus, and temporal cortex. These neuroimaging findings indicate that gait-like motor learning depends on interplay between subcortical, cerebellar, and fronto-parietal brain regions. An interesting observation was the low activation observed in the brain's reward system after training with error amplification compared to training without perturbations. Our results suggest that to enhance learning of a locomotor task, errors should be augmented based on subjects' skill level. The impacts of these strategies on motor learning, brain activation, and motivation in neurological patients need further investigation. PMID:29021739

The media and genetically modified foods: evidence in support of social amplification of risk.

PubMed

Frewer, Lynn J; Miles, Susan; Marsh, Roy

2002-08-01

Empirical examinations of the "social amplification of risk" framework are rare, partly because of the difficulties in predicting when conditions likely to result in amplification effects will occur. This means that it is difficult to examine changes in risk perception that are contemporaneous with increases and/or decreases in social or media discussion of the risks associated with a particular risk event. However, the collection of attitude data before, during, and after the increased reporting of the risks of genetically modified food in the United Kingdom (spring 1999) has demonstrated that people's risk perceptions do increase and decrease in line with what might be expected upon examination of the amplification and attenuation mechanisms integral to the framework. Perceptions of benefit, however, appeared to be permanently depressed by negative reporting about genetically modified food. Trust in regulatory institutions with responsibility for protecting the public was not affected. It was concluded that the social amplification of risk framework is a useful framework for beginning to explain the potential impact on risk perceptions of a risk event, particularly if that risk event is presented to the public as a new hazard occurring in a crisis context.

Tunable Fano resonance using weak-value amplification with asymmetric spectral response as a natural pointer

NASA Astrophysics Data System (ADS)

Singh, Ankit K.; Ray, Subir K.; Chandel, Shubham; Pal, Semanti; Gupta, Angad; Mitra, P.; Ghosh, N.

2018-05-01

Weak measurement enables faithful amplification and high-precision measurement of small physical parameters and is under intensive investigation as an effective tool in metrology and for addressing foundational questions in quantum mechanics. Here we demonstrate weak-value amplification using the asymmetric spectral response of Fano resonance as the pointer arising naturally in precisely designed metamaterials, namely, waveguided plasmonic crystals. The weak coupling between the polarization degree of freedom and the spectral response of Fano resonance arises due to a tiny shift in the asymmetric spectral response between two orthogonal linear polarizations. By choosing the preselected and postselected polarization states to be nearly mutually orthogonal, we observe both real and imaginary weak-value amplifications manifested as a spectacular shift of the Fano-resonance peak and narrowing (or broadening) of the resonance linewidth, respectively. The remarkable control and tunability of Fano resonance in a single device enabled by weak-value amplification may enhance active Fano-resonance-based applications in the nano-optical domain. In general, weak measurements using Fano-type spectral response broadens the domain of applicability of weak measurements using natural spectral line shapes as a pointer in a wide range of physical systems.

Ultrasensitive Visual Detection of HIV DNA Biomarkers via a Multi-amplification Nanoplatform.

PubMed

Long, Yuyin; Zhou, Cuisong; Wang, Congmin; Cai, Honglian; Yin, Cuiyun; Yang, Qiufang; Xiao, Dan

2016-04-01

Methodologies to detect disease biomarkers at ultralow concentrations can potentially improve the standard of living. A facile and label-free multi-amplification strategy is proposed for the ultrasensitive visual detection of HIV DNA biomarkers in real physiological media. This multi-amplification strategy not only exhibits a signficantly low detection limit down to 4.8 pM but also provides a label-free, cost-effective and facile technique for visualizing a few molecules of nucleic acid analyte with the naked eye. Importantly, the biosensor is capable of discriminating single-based mismatch lower than 5.0 nM in human serum samples. Moreover, the visual sensing platform exhibits excellent specificity, acceptable reusability and a long-term stability. All these advantages could be attributed to the nanofibrous sensing platform that 1) has a high surface-area-to-volume provided by electrospun nanofibrous membrane, and 2) combines glucose oxidase (GOx) biocatalysis, DNAzyme-catalyzed colorimetric reaction and catalytic hairpin assembly (CHA) recycling amplification together. This multi-amplification nanoplatform promises label-free and visual single-based mismatch DNA monitoring with high sensitivity and specificity, suggesting wide applications that range from virus detection to genetic disease diagnosis.

Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification

PubMed Central

2010-01-01

Background Reverse phase protein arrays (RPPA) emerged as a useful experimental platform to analyze biological samples in a high-throughput format. Different signal detection methods have been described to generate a quantitative readout on RPPA including the use of fluorescently labeled antibodies. Increasing the sensitivity of RPPA approaches is important since many signaling proteins or posttranslational modifications are present at a low level. Results A new antibody-mediated signal amplification (AMSA) strategy relying on sequential incubation steps with fluorescently-labeled secondary antibodies reactive against each other is introduced here. The signal quantification is performed in the near-infrared range. The RPPA-based analysis of 14 endogenous proteins in seven different cell lines demonstrated a strong correlation (r = 0.89) between AMSA and standard NIR detection. Probing serial dilutions of human cancer cell lines with different primary antibodies demonstrated that the new amplification approach improved the limit of detection especially for low abundant target proteins. Conclusions Antibody-mediated signal amplification is a convenient and cost-effective approach for the robust and specific quantification of low abundant proteins on RPPAs. Contrasting other amplification approaches it allows target protein detection over a large linear range. PMID:20569466

Reversible Gating of Plasmonic Coupling for Optical Signal Amplification.

PubMed

Khoury, Christopher G; Fales, Andrew M; Vo-Dinh, Tuan

2016-07-20

Amplification of optical signals is useful for a wide variety of applications, ranging from data signal transmission to chemical sensing and biomedical diagnostics. One such application in chemical sensing is surface-enhanced Raman scattering (SERS), an important technique for increasing the Raman signal using the plasmonic effect of enhanced electromagnetic fields associated with metallic nanostructures. One of the most important limitations of SERS-based amplification is the difficulty to reproducibly control the SERS signal. Here, we describe the design and implementation of a unique hybrid system capable of producing reversible gating of plasmonic coupling for Raman signal amplification. The hybrid system is composed of two subsystems: (1) colloidal magneto-plasmonic nanoparticles for SERS enhancement and (2) a micromagnet substrate with an externally applied magnetic field to modulate the colloidal nanoparticles. For this proof of concept demonstration, the nanoparticles were labeled with a Raman-active dye, and it was shown that the detected SERS signal could be reproducibly modulated by controlling the externally applied magnetic field. The developed system provides a simple, robust, inexpensive, and reusable device for SERS signal modulation. These properties will open up new possibilities for optical signal amplification and gating as well for high-throughput, reproducible SERS detection.

New Downhole Strong-Motion Data Recorded at Tarzana Array

NASA Astrophysics Data System (ADS)

Graizer, V.; Shakal, A.; Haddadi, H.

2001-12-01

Significantly amplified ground accelerations at the Tarzana station were recorded during many, but not all, earthquakes (e.g., Shakal et al., 1988). Peak horizontal ground acceleration at the Tarzana station during the M7.1 Hector Mine earthquake was almost twice as large as the accelerations recorded at nearby stations. After the Northridge earthquake the California Strong Motion Instrumentation Program (CSMIP) significantly increased instrumentation at Tarzana to study the unusual site amplification effect. Current instrumentation at Tarzana consists of an accelerograph at the top of Tarzana hill (Tarzana - Cedar Hill B), a downhole instrument at 60 m depth, and an accelerograph at the foot of the hill (Tarzana - Clubhouse), 180 m from the Cedar Hill B station. The original station, Tarzana - Cedar Hill Nursery A, was lost in 1999 due to construction. Thirteen events, including the Hector Mine earthquake, were simultaneously recorded by these instruments at Tarzana. The downhole instrument (A) was used as a reference site to compare the amplification effects at the top of Tarzana hill (B) and at the foot of the hill (C). Spectral amplification from the bottom of the hole to the top of the hill (B/A) and to the foot of the hill (C/A) is similar along the component parallel to the strike of Tarzana hill. But B/A is almost double C/A along the component transverse to the strike of the hill in period range from 0.04 to 0.8 sec (1.2 to 25 Hz). Comparison of the response spectra demonstrates clear directional site response resonance (perpendicular to the strike of the hill) at Tarzana. In contrast to accelerations recorded during the Mw 7.1 Hector Mine earthquake (high frequency part of seismic signal), displacements (relatively low frequency part of seismic signal) demonstrate almost no site amplification from the bottom of the hole to the surface (B/A) at periods greater than 1.5 sec, in either direction. Ground displacements at other CSMIP downhole arrays which recorded the Hector Mine earthquake also demonstrate almost no near-surface site amplification at long periods. Comparison of empirical and theoretical site amplification effects at Tarzana was performed using SHAKE91 modeling motion separately in the longitudinal and transverse directions. The source of the site amplification that produces large motions at Tarzana is still under investigation. The topography, shear-wave velocity profile and three-dimensional structure of the site apparently all contribute to the higher amplification of ground motion at the Tarzana site. The studies of Tarzana were co-funded by CSMIP and by the National Science Foundation (NSF) through the Resolution of Site Response Issues from the Northridge Earthquake Project (ROSRINE).

Amplification of intrinsic fluctuations by the Lorenz equations

NASA Astrophysics Data System (ADS)

Fox, Ronald F.; Elston, T. C.

1993-07-01

Macroscopic systems (e.g., hydrodynamics, chemical reactions, electrical circuits, etc.) manifest intrinsic fluctuations of molecular and thermal origin. When the macroscopic dynamics is deterministically chaotic, the intrinsic fluctuations may become amplified by several orders of magnitude. Numerical studies of this phenomenon are presented in detail for the Lorenz model. Amplification to macroscopic scales is exhibited, and quantitative methods (binning and a difference-norm) are presented for measuring macroscopically subliminal amplification effects. In order to test the quality of the numerical results, noise induced chaos is studied around a deterministically nonchaotic state, where the scaling law relating the Lyapunov exponent to noise strength obtained for maps is confirmed for the Lorenz model, a system of ordinary differential equations.

Physical principles of the amplification of electromagnetic radiation due to negative electron masses in a semiconductor superlattice

NASA Astrophysics Data System (ADS)

Shorokhov, A. V.; Pyataev, M. A.; Khvastunov, N. N.; Hyart, T.; Kusmartsev, F. V.; Alekseev, K. N.

2015-02-01

In a superlattice placed in crossed static electric and magnetic fields, under certain conditions, the inversion of electron population can appear at which the average energy of electrons is above the middle of the mini-band and the effective mass of the electron is negative. This is the implementation of the negative effective mass amplifier and generator (NEMAG) in the superlattice. It can result in the amplification and generation of terahertz radiation even in the absence of negative differential conductivity.

A simple and rapid method for detection of Trypanosoma evansi in the dromedary camel using a nested polymerase chain reaction

PubMed Central

Aradaib, Imadeldin E; Majid, Ali A

2006-01-01

A nested polymerase chain reaction (nPCR)-based assay, was developed and evaluated for rapid detection of Trypanosoma evansi in experimentally infected mice and naturally infected camels (Camelus dromedarius). Four oligonucleotide primers (TE1, TE2, TE3 and TE4), selected from nuclear repetitive gene of T. evansi, were designed and used for PCR amplifications. The first amplification, using a pair of outer primers TE1 and TE2, produced a 821-bp primary PCR product from T. evansi DNA. The second amplification, using nested (internal) pair of primers TE3 and TE4, produced a 270-bp PCR product. T. evansi DNAs extracted from blood samples of experimentally infected mice and naturally infected Sudanese breed of dromedary camels were detected by this nested PCR-based assay. The nested primers TE3 and TE4 increased the sensitivity of the PCR assay and as little as 10 fg of T. evansi DNA (equivalent to a single copy of the putative gene of the parasite) was amplified and visualized onto ethidium bromide-stained agarose gels. Amplification products were not detected when the PCR-based assay was applied to DNA from other blood parasites including Thieleria annulata, Babesia bigemina or nucleic acid free samples. Application of this nPCR-based assay to clinical samples resulted in direct detection of T. evansi from a variety of tissue samples collected from experimentally infected mice and blood from naturally infected camels. The described nPCR-based assay provides a valuable tool to study the epidemiology of T. evansi infection in camels and other susceptible animal populations. PMID:16712737

Functional characterization of the 19q12 amplicon in grade III breast cancers

PubMed Central

2012-01-01

Introduction The 19q12 locus is amplified in a subgroup of oestrogen receptor (ER)-negative grade III breast cancers. This amplicon comprises nine genes, including cyclin E1 (CCNE1), which has been proposed as its 'driver'. The aim of this study was to identify the genes within the 19q12 amplicon whose expression is required for the survival of cancer cells harbouring their amplification. Methods We investigated the presence of 19q12 amplification in a series of 313 frozen primary breast cancers and 56 breast cancer cell lines using microarray comparative genomic hybridisation (aCGH). The nine genes mapping to the smallest region of amplification on 19q12 were silenced using RNA interference in phenotypically matched breast cancer cell lines with (MDA-MB-157 and HCC1569) and without (Hs578T, MCF7, MDA-MB-231, ZR75.1, JIMT1 and BT474) amplification of this locus. Genes whose silencing was selectively lethal in amplified cells were taken forward for further validation. The effects of cyclin-dependent kinase 2 (CDK2) silencing and chemical inhibition were tested in cancer cells with and without CCNE1 amplification. Results 19q12 amplification was identified in 7.8% of ER-negative grade III breast cancer. Of the nine genes mapping to this amplicon, UQCRFS1, POP4, PLEKHF1, C19ORF12, CCNE1 and C19ORF2 were significantly over-expressed when amplified in primary breast cancers and/or breast cancer cell lines. Silencing of POP4, PLEKHF1, CCNE1 and TSZH3 selectively reduced cell viability in cancer cells harbouring their amplification. Cancer cells with CCNE1 amplification were shown to be dependent on CDK2 expression and kinase activity for their survival. Conclusions The 19q12 amplicon may harbour more than a single 'driver', given that expression of POP4, PLEKHF1, CCNE1 and TSZH3 is required for the survival of cancer cells displaying their amplification. The observation that cancer cells harbouring CCNE1 gene amplification are sensitive to CDK2 inhibitors provides a rationale for the testing of these chemical inhibitors in a subgroup of patients with ER-negative grade III breast cancers. PMID:22433433

Point of care diagnosis of multiple schistosome parasites: Species-specific DNA detection in urine by loop-mediated isothermal amplification (LAMP).

PubMed

Lodh, Nilanjan; Mikita, Kei; Bosompem, Kwabena M; Anyan, William K; Quartey, Joseph K; Otchere, Joseph; Shiff, Clive J

2017-09-01

Schistosomes are easily transmitted and high chance of repeat infection, so if control strategies based on targeted mass drug administration (MDA) are to succeed it is essential to have a test that is sensitive, accurate and simple to use. It is known and regularly demonstrated that praziquantel does not always eliminate an infection so in spite of the successes of control programs a residual of the reservoir survives to re-infect snails. The issue of diagnostic sensitivity becomes more critical in the assessment of program effectiveness. While serology, such as antigen capture tests might improve sensitivity, it has been shown that the presence of species-specific DNA fragments will indicate, most effectively, the presence of active parasites. Polymerase chain reaction (PCR) can amplify and detect DNA from urine residue captured on Whatman No. 3 filter paper that is dried after filtration. Previously we have detected S. mansoni and S. haematobium parasite-specific small repeat DNA fragment from filtered urine on filter paper by PCR. In the current study, we assessed the efficacy of detection of 86 urine samples for either or both schistosome parasites by PCR and loop-mediated isothermal amplification (LAMP) that were collected from a low to moderate transmission area in Ghana. Two different DNA extraction methods, standard extraction kit and field usable LAMP-PURE kit were also evaluated by PCR and LAMP amplification. With S. haematobium LAMP amplification for both extractions showed similar sensitivity and specificity when compared with PCR amplification (100%) verified by gel electrophoresis. For S. mansoni sensitivity was highest for LAMP amplification (100%) for standard extraction than PCR and LAMP with LAMP-PURE (99% and 94%). The LAMP-PURE extraction produced false negatives, which require further investigation for this field usable extraction kit. Overall high positive and negative predictive values (90% - 100%) for both species demonstrated a highly robust approach. The LAMP approach is close to point of care use and equally sensitive and specific to detection of species-specific DNA by PCR. LAMP can be an effective means to detect low intensity infection due to its simplicity and minimal DNA extraction requirement. This will enhance the effectiveness of surveillance and MDA control programs of schistosomiasis. Copyright © 2017 Elsevier B.V. All rights reserved.

Aided Electrophysiology Using Direct Audio Input: Effects of Amplification and Absolute Signal Level

PubMed Central

Billings, Curtis J.; Miller, Christi W.; Tremblay, Kelly L.

2016-01-01

Purpose This study investigated (a) the effect of amplification on cortical auditory evoked potentials (CAEPs) at different signal levels when signal-to-noise ratios (SNRs) were equated between unaided and aided conditions, and (b) the effect of absolute signal level on aided CAEPs when SNR was held constant. Method CAEPs were recorded from 13 young adults with normal hearing. A 1000-Hz pure tone was presented in unaided and aided conditions with a linear analog hearing aid. Direct audio input was used, allowing recorded hearing aid noise floor to be added to unaided conditions to equate SNRs between conditions. An additional stimulus was created through scaling the noise floor to study the effect of signal level. Results Amplification resulted in delayed N1 and P2 peak latencies relative to the unaided condition. An effect of absolute signal level (when SNR was constant) was present for aided CAEP area measures, such that larger area measures were found at higher levels. Conclusion Results of this study further demonstrate that factors in addition to SNR must also be considered before CAEPs can be used to clinically to measure aided thresholds. PMID:26953543

Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA).

PubMed

Palmirotta, Raffaele; Lovero, Domenica; Silvestris, Erica; Felici, Claudia; Quaresmini, Davide; Cafforio, Paola; Silvestris, Franco

2017-01-01

Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS). However, the sequence of these molecular techniques is time-consuming and may also favor operator-dependent errors, related to the procedures themselves that, as in the case of the WGA technique, might affect downstream molecular analyses. A preliminary approach of molecular analysis by NGS on a model of CTCs without previous WGA procedural step was performed. We set-up an artificial sample obtained by spiking the SK-MEL-28 melanoma cell line in normal donor peripheral whole blood. Melanoma cells were first enriched using an AutoMACS® (Miltenyi) cell separator and then isolated as single and pooled CTCs by DEPArray™ System (Silicon Biosystems). NGS analysis, using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies) with the Ion Torrent PGM™ system (Life Technologies), was performed on the SK-MEL-28 cell pellet, a single CTC previously processed with WGA and on 1, 2, 4 and 8 recovered CTCs without WGA pre-amplification. NGS directly carried out on CTCs without WGA showed the same mutations identified in SK-MEL-28 cell line pellet, with a considerable efficiency and avoiding the errors induced by the WGA procedure. We identified a cost-effective, time-saving and reliable methodological approach that could improve the analytical accuracy of the liquid biopsy and appears promising in studying CTCs from cancer patients for both research and clinical purposes. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

A Gammaherpesviral Internal Repeat Contributes to Latency Amplification

PubMed Central

Thakur, Nagendra N.; El-Gogo, Susanne; Steer, Beatrix; Freimüller, Klaus; Waha, Andreas; Adler, Heiko

2007-01-01

Background Gammaherpesviruses cause important infections of humans, in particular in immunocompromised patients. The genomes of gammaherpesviruses contain variable numbers of internal repeats whose precise role for in vivo pathogenesis is not well understood. Methodology/Principal Findings We used infection of laboratory mice with murine gammaherpesvirus 68 (MHV-68) to explore the biological role of the 40 bp internal repeat of MHV-68. We constructed several mutant viruses partially or completely lacking this repeat. Both in vitro and in vivo, the loss of the repeat did not substantially affect lytic replication of the mutant viruses. However, the extent of splenomegaly, which is associated with the establishment of latency, and the number of ex vivo reactivating and genome positive splenocytes were reduced. Since the 40 bp repeat is part of the hypothetical open reading frame (ORF) M6, it might function as part of M6 or as an independent structure. To differentiate between these two possibilities, we constructed an N-terminal M6STOP mutant, leaving the repeat structure intact but rendering ORF M6 unfunctional. Disruption of ORF M6 did neither affect lytic nor latent infection. In contrast to the situation in lytically infected NIH3T3 cells, the expression of the latency-associated genes K3 and ORF72 was reduced in the latently infected murine B cell line Ag8 in the absence of the 40 bp repeat. Conclusions/Significance These data suggest that the 40 bp repeat contributes to latency amplification and might be involved in the regulation of viral gene expression. PMID:17710133

Simple procedures to obtain exogenous internal controls for use in RT-PCR detection of bovine pestiviruses.

PubMed

Golemba, Marcelo D; Parreño, Viviana; Jones, Leandro R

2008-06-01

Pestiviruses are ubiquitous pathogens of cattle and frequent adventitious viruses in biologicals. Furthermore, it has been suggested that these agents might be related to infantile gastroenteritis and microencephaly. Since the virus is highly prevalent in fetal bovine serum, the risk of contamination is high in most laboratories. Thus, the implementation of detection methods in all laboratories is of worth. Despite continuous surveillance, these agents have been detected in cell lines, fetal bovine serum, live and inactivated animal and human vaccines and interferon for human use. In this report, DNA and RNA internal controls (ICs) which can be implemented in laboratories with minimal equipment are described. The developed standards can be added before RNA purification, allowing to monitor all steps of the protocol (viral RNA extraction, reverse transcription and cDNA amplification). It is shown that inhibitory effects that could lead to decreased sensitivity can be minimized by controlling the amount of mimic molecules added to the samples. A method to avoid the problem of DNA traces present in in vitro transcribed RNA preparations is provided.

Detection device for hazardous materials

DOEpatents

Partin, Judy K.; Grey, Alan E.

1994-01-01

A detection device that is activated by the interaction of a hazardous chcal with a coating interactive with said chemical on an optical fiber thereby reducing the amount of light passing through the fiber to a light detector. A combination of optical filters separates the light into a signal beam and a reference beam which after detection, appropriate amplification, and comparison with preset internal signals, activates an alarm means if a predetermined level of contaminant is observed.

Active Control of Radiated Sound with Integrated Piezoelectric Composite Structures. Volume 3: Appendices (Concl.)

DTIC Science & Technology

1998-11-06

after many iterations of analysis , development, construction and testing was found to provide amplification ratios of around 250:1 and generate...IEEE International Symposium on Application of Ferroelectrics 2, 767-770 (1996). 11. "A Comparative Analysis of Piezoelectric Bending Mode Actuators...Active 95, 359-368, Newport Beach, CA(1995) 21. "Multiple Reference Feedforward Active Noise Control. Part I. Analysis and Simulation of Behavior," Y

Detection device for hazardous materials

DOEpatents

Partin, Judy K.; Grey, Alan E.

1994-04-05

A detection device that is activated by the interaction of a hazardous chcal with a coating interactive with said chemical on an optical fiber thereby reducing the amount of light passing through the fiber to a light detector. A combination of optical filters separates the light into a signal beam and a reference beam which after detection, appropriate amplification, and comparison with preset internal signals, activates an alarm means if a predetermined level of contaminant is observed.

Attributing Contributions of Climate Feedbacks to the Seasonal Cycle of Surface Warming due to CO2 Increase

NASA Astrophysics Data System (ADS)

Sejas, S.; Cai, M.

2012-12-01

Surfing warming due to CO2 doubling is a robust feature of coupled general circulation models (GCM), as noted in the IPCC AR4 assessment report. In this study, the contributions of different climate feedbacks to the magnitude, spatial distribution, and seasonality of the surface warming is examined using data from NCAR's CCSM4. In particular, a focus is placed on polar regions to see which feedbacks play a role in polar amplification and its seasonal pattern. A new climate feedback analysis method is used to isolate the surface warming or cooling contributions of both radiative and non-radiative (dynamical) climate feedbacks to the total (actual) surface temperature change given by the CCSM4. These contributions (or partial surface temperature changes) are additive and their total is approximately equal to the actual surface temperature change. What is found is that the effects of CO2 doubling alone warms the surface throughout with a maximum in polar regions, which indicates the CO2 forcing alone has a degree of polar warming amplification. Water vapor feedback is a positive feedback throughout but is most responsible for the surface warming found in the tropics. Polar warming amplification is found to be strongest away from summer (especially in NH), which is primarily caused by a positive feedback due to cloud feedbacks but with the surface temperature change due to the CO2 forcing alone and the ocean dynamics and storage feedback also playing an important role. Contrary to popular belief, surface albedo feedback (SAF) does not account for much of the polar amplification. SAF tries to amplify polar warming, but in summer. No major polar amplification is seen in summer for the actual surface temperature, so SAF is not the feedback responsible for polar amplification. This is actually a consequence of the ocean dynamics and storage feedback, which negates the effects of SAF to a large degree.

Computation of ground motion amplification in Kolkata megacity (India) using finite-difference method for seismic microzonation

NASA Astrophysics Data System (ADS)

Shiuly, Amit; Kumar, Vinay; Narayan, Jay

2014-06-01

This paper presents the ground motion amplification scenario along with fundamental frequency (F 0) of sedimentary deposit for the seismic microzonation of Kolkata City, situated on the world's largest delta island with very soft soil deposit. A 4th order accurate SH-wave viscoelastic finite-difference algorithm is used for computation of response of 1D model for each borehole location. Different maps, such as for F 0, amplification at F 0, average spectral amplification (ASA) in the different frequency bandwidth of earthquake engineering interest are developed for a variety of end-users communities. The obtained ASA of the order of 3-6 at most of the borehole locations in a frequency range of 0.25-10.0 Hz reveals that Kolkata City may suffer severe damage even during a moderate earthquake. Further, unexpected severe damage to collapse of multi-storey buildings may occur in localities near Hoogly River and Salt Lake area due to double resonance effects during distant large earthquakes.

Optimizing direct amplification of forensic commercial kits for STR determination.

PubMed

Caputo, M; Bobillo, M C; Sala, A; Corach, D

2017-04-01

Direct DNA amplification in forensic genotyping reduces analytical time when large sample sets are being analyzed. The amplification success depends mainly upon two factors: on one hand, the PCR chemistry and, on the other, the type of solid substrate where the samples are deposited. We developed a workflow strategy aiming to optimize times and cost when starting from blood samples spotted onto diverse absorbent substrates. A set of 770 blood samples spotted onto Blood cards, Whatman ® 3 MM paper, FTA™ Classic cards, and Whatman ® Grade 1 was analyzed by a unified working strategy including a low-cost pre-treatment, a PCR amplification volume scale-down, and the use of the 3500 Genetic Analyzer as the analytical platform. Samples were analyzed using three different commercial multiplex STR direct amplification kits. The efficiency of the strategy was evidenced by a higher percentage of high-quality profiles obtained (over 94%), a reduced number of re-injections (average 3.2%), and a reduced amplification failure rate (lower than 5%). Average peak height ratio among different commercial kits was 0.91, and the intra-locus balance showed values ranging from 0.92 to 0.94. A comparison with previously reported results was performed demonstrating the efficiency of the proposed modifications. The protocol described herein showed high performance, producing optimal quality profiles, and being both time and cost effective. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

PubMed

Wu, Jieying; Gao, Weimin; Zhang, Weiwen; Meldrum, Deirdre R

2011-01-01

Limitation in sample quality and quantity is one of the big obstacles for applying metatranscriptomic technologies to explore gene expression and functionality of microbial communities in natural environments. In this study, several amplification methods were evaluated for whole-transcriptome amplification of deep-sea microbial samples, which are of low cell density and high impurity. The best amplification method was identified and incorporated into a complete protocol to isolate and amplify deep-sea microbial samples. In the protocol, total RNA was first isolated by a modified method combining Trizol (Invitrogen, CA) and RNeasy (QIAGEN, CA) method, amplified with a WT-Ovation™ Pico RNA Amplification System (NuGEN, CA), and then converted to double-strand DNA from single-strand cDNA with a WT-Ovation™ Exon Module (NuGEN, CA). The products from the whole-transcriptome amplification of deep-sea microbial samples were assessed first through random clone library sequencing. The BLAST search results showed that marine-based sequences are dominant in the libraries, consistent with the ecological source of the samples. The products were then used for next-generation Roche GS FLX Titanium sequencing to obtain metatranscriptome data. Preliminary analysis of the metatranscriptomic data showed good sequencing quality. Although the protocol was designed and demonstrated to be effective for deep-sea microbial samples, it should be applicable to similar samples from other extreme environments in exploring community structure and functionality of microbial communities. Copyright © 2010 Elsevier B.V. All rights reserved.

Empirical Site Amplification Factors Incorporating Soil Nonlinearity in Taiwan

NASA Astrophysics Data System (ADS)

Kuo, C. H.; Chung, C. H.; Che-Min, L.; Huang, J. Y.; Wen, K. L.

2017-12-01

Characteristics of site amplifications caused by both crustal and subduction earthquakes are important in Taiwan. For example, seismic waves were amplified and led to significant building damages in the Taipei Basin by the 1986 Hualien offshore (subduction interface) and the 1999 Chi-Chi earthquakes (crustal), for which the epicentral distances were about 100 km. To understand local site amplifications in Taiwan, empirical site amplification factors for horizontal ground motions are studied using recently constructed strong motion and site databases for the free-field TSMIP stations in Taiwan. Records of large magnitude earthquakes of ML larger than six from 1994 to 2014 were selected for this study. Site amplification factors at site conditions with Vs30 of 120 m/s to 1500 m/s and base accelerations up to 0.7g were inferred from intensity ratios of station pairs within specific distances. The reference site condition is assumed as Vs30 of 760 m/s (B/C boundary). Preliminary results indicate: 1. Soil nonlinearity is more obviously at short periods (PGA, Sa0.3) than long periods (PGV, Sa1.0). 2. Soil nonlinearity is significant for stations belong to site classes of B, C, D, and E in Taiwan. 3. Effect of station-pair distance is seen at short periods (PGA and Sa0.3). 4. No significant different is found in site amplifications of crustal and subduction earthquakes. The result could be a reference for the Fa and Fv in Taiwan's building code.

Detection of KIT Genotype in Pigs by TaqMan MGB Real-Time Quantitative Polymerase Chain Reaction.

PubMed

Li, Xiuxiu; Li, Xiaoning; Luo, Rongrong; Wang, Wenwen; Wang, Tao; Tang, Hui

2018-05-01

The dominant white phenotype in domestic pigs is caused by two mutations in the KIT gene: a 450 kb duplication containing the entire KIT gene together with flanking sequences and one splice mutation with a G:A substitution in intron 17. The purpose of this study was to establish a simple, rapid method to determine KIT genotype in pigs. First, to detect KIT copy number variation (CNV), primers for exon 2 of the KIT gene, along with a TaqMan minor groove binder (MGB) probe, were designed. The single-copy gene, estrogen receptor (ESR), was used as an internal control. A real-time fluorescence-based quantitative PCR (FQ-PCR) protocol was developed to accurately detect KIT CNVs. Second, to detect the splice mutation ratio of the G:A substitution in intron 17, a 175 bp region, including the target mutation, was amplified from genomic DNA. Based on the sequence of the resulting amplified fragment, an MGB probe set was designed to detect the ratio of splice mutation to normal using FQ-PCR. A series of parallel amplification curves with the same internal distances were obtained using gradually diluted DNA as templates. The CT values among dilutions were significantly different (p < 0.001) and the coefficients of variation from each dilution were low (from 0.13% to 0.26%). The amplification efficiencies for KIT and ESR were approximately equal, indicating ESR was an appropriate control gene. Furthermore, use of the MGB probe set resulted in detection of the target mutation at a high resolution and stability; standard curves illustrated that the amplification efficiencies of KIT1 (G) and KIT2 (A) were approximately equal (98.8% and 97.2%). In conclusion, a simple, rapid method, with high specificity and stability, for the detection of the KIT genotype in pigs was established using TaqMan MGB probe real-time quantitative PCR.

Parametric amplification in a resonant sensing array

NASA Astrophysics Data System (ADS)

Yie, Zi; Miller, Nicholas J.; Shaw, Steven W.; Turner, Kimberly L.

2012-03-01

We demonstrate parametric amplification of a multidegree of freedom resonant mass sensing array via an applied base motion containing the appropriate frequency content and phases. Applying parametric forcing in this manner is simple and aligns naturally with the vibrational properties of the sensing structure. Using this technique, we observe an increase in the quality factors of the coupled array resonances, which provides an effective means of improving device sensitivity.

PHYSICAL EFFECTS OCCURRING DURING GENERATION AND AMPLIFICATION OF LASER RADIATION: Reversal of the contrast of optical radiation in round-trip amplifiers with a phase conjugation mirror

NASA Astrophysics Data System (ADS)

Afanas'ev, Anatolii A.; Samson, B. A.

1989-02-01

A description is given of a method for inversion of the contrast of optical radiation in a round-trip amplifier with a phase conjugation mirror and a phase nonreciprocal element. The system can be used to achieve high powers of contrast-reversed radiation because of compensation of phase distortions introduced by amplification.

A multivariate test of disease risk reveals conditions leading to disease amplification.

PubMed

Halliday, Fletcher W; Heckman, Robert W; Wilfahrt, Peter A; Mitchell, Charles E

2017-10-25

Theory predicts that increasing biodiversity will dilute the risk of infectious diseases under certain conditions and will amplify disease risk under others. Yet, few empirical studies demonstrate amplification. This contrast may occur because few studies have considered the multivariate nature of disease risk, which includes richness and abundance of parasites with different transmission modes. By combining a multivariate statistical model developed for biodiversity-ecosystem-multifunctionality with an extensive field manipulation of host (plant) richness, composition and resource supply to hosts, we reveal that (i) host richness alone could not explain most changes in disease risk, and (ii) shifting host composition allowed disease amplification, depending on parasite transmission mode. Specifically, as predicted from theory, the effect of host diversity on parasite abundance differed for microbes (more density-dependent transmission) and insects (more frequency-dependent transmission). Host diversity did not influence microbial parasite abundance, but nearly doubled insect parasite abundance, and this amplification effect was attributable to variation in host composition. Parasite richness was reduced by resource addition, but only in species-rich host communities. Overall, this study demonstrates that multiple drivers, related to both host community and parasite characteristics, can influence disease risk. Furthermore, it provides a framework for evaluating multivariate disease risk in other systems. © 2017 The Author(s).

Point of care nucleic acid detection of viable pathogenic bacteria with isothermal RNA amplification based paper biosensor

NASA Astrophysics Data System (ADS)

Liu, Hongxing; Xing, Da; Zhou, Xiaoming

2014-09-01

Food-borne pathogens such as Listeria monocytogenes have been recognized as a major cause of human infections worldwide, leading to substantial health problems. Food-borne pathogen identification needs to be simpler, cheaper and more reliable than the current traditional methods. Here, we have constructed a low-cost paper biosensor for the detection of viable pathogenic bacteria with the naked eye. In this study, an effective isothermal amplification method was used to amplify the hlyA mRNA gene, a specific RNA marker in Listeria monocytogenes. The amplification products were applied to the paper biosensor to perform a visual test, in which endpoint detection was performed using sandwich hybridization assays. When the RNA products migrated along the paper biosensor by capillary action, the gold nanoparticles accumulated at the designated Test line and Control line. Under optimized experimental conditions, as little as 0.5 pg/μL genomic RNA from Listeria monocytogenes could be detected. The whole assay process, including RNA extraction, amplification, and visualization, can be completed within several hours. The developed method is suitable for point-of-care applications to detect food-borne pathogens, as it can effectively overcome the false-positive results caused by amplifying nonviable Listeria monocytogenes.

Assessment of primer/template mismatch effects on real-time PCR amplification of target taxa for GMO quantification.

PubMed

Ghedira, Rim; Papazova, Nina; Vuylsteke, Marnik; Ruttink, Tom; Taverniers, Isabel; De Loose, Marc

2009-10-28

GMO quantification, based on real-time PCR, relies on the amplification of an event-specific transgene assay and a species-specific reference assay. The uniformity of the nucleotide sequences targeted by both assays across various transgenic varieties is an important prerequisite for correct quantification. Single nucleotide polymorphisms (SNPs) frequently occur in the maize genome and might lead to nucleotide variation in regions used to design primers and probes for reference assays. Further, they may affect the annealing of the primer to the template and reduce the efficiency of DNA amplification. We assessed the effect of a minor DNA template modification, such as a single base pair mismatch in the primer attachment site, on real-time PCR quantification. A model system was used based on the introduction of artificial mismatches between the forward primer and the DNA template in the reference assay targeting the maize starch synthase (SSIIb) gene. The results show that the presence of a mismatch between the primer and the DNA template causes partial to complete failure of the amplification of the initial DNA template depending on the type and location of the nucleotide mismatch. With this study, we show that the presence of a primer/template mismatch affects the estimated total DNA quantity to a varying degree.

The effectiveness of robotic training depends on motor task characteristics.

PubMed

Marchal-Crespo, Laura; Rappo, Nicole; Riener, Robert

2017-12-01

Previous research suggests that the effectiveness of robotic training depends on the motor task to be learned. However, it is still an open question which specific task's characteristics influence the efficacy of error-modulating training strategies. Motor tasks can be classified based on the time characteristics of the task, in particular the task's duration (discrete vs. continuous). Continuous tasks require movements without distinct beginning or end. Discrete tasks require fast movements that include well-defined postures at the beginning and the end. We developed two games, one that requires a continuous movement-a tracking task-and one that requires discrete movements-a fast reaching task. We conducted an experiment with thirty healthy subjects to evaluate the effectiveness of three error-modulating training strategies-no guidance, error amplification (i.e., repulsive forces proportional to errors) and haptic guidance-on self-reported motivation and learning of the continuous and discrete games. Training with error amplification resulted in better motor learning than haptic guidance, besides the fact that error amplification reduced subjects' interest/enjoyment and perceived competence during training. Only subjects trained with error amplification improved their performance after training the discrete game. In fact, subjects trained without guidance improved the performance in the continuous game significantly more than in the discrete game, probably because the continuous task required greater attentional levels. Error-amplifying training strategies have a great potential to provoke better motor learning in continuous and discrete tasks. However, their long-lasting negative effects on motivation might limit their applicability in intense neurorehabilitation programs.

Preparation of His-tagged armored RNA phage particles as a control for real-time reverse transcription-PCR detection of severe acute respiratory syndrome coronavirus.

PubMed

Cheng, Yangjian; Niu, Jianjun; Zhang, Yongyou; Huang, Jianwei; Li, Qingge

2006-10-01

Armored RNA has been increasingly used as both an external and internal positive control in nucleic acid-based assays for RNA virus. In order to facilitate armored RNA purification, a His6 tag was introduced into the loop region of the MS2 coat protein, which allows the exposure of multiple His tags on the surface during armored RNA assembly. The His-tagged armored RNA particles were purified to homogeneity and verified to be free of DNA contamination in a single run of affinity chromatography. A fragment of severe acute respiratory syndrome coronavirus (SARS-CoV) genome targeted for SARS-CoV detection was chosen for an external positive control preparation. A plant-specific gene sequence was chosen for a universal noncompetitive internal positive control preparation. Both controls were purified by Co2+ affinity chromatography and were included in a real-time reverse transcription-PCR assay for SARS-CoV. The noncompetitive internal positive control can be added to clinical samples before RNA extraction and enables the identification of potential inhibitive effects without interfering with target amplification. The external control could be used for the quantification of viral loads in clinical samples.

How long time will we go with linear seismology?

NASA Astrophysics Data System (ADS)

Marmureanu, Gheorghe; Cioflan, Carmen; Marmureanu, Alexandru; Apostol, Bogdan

2013-04-01

Motto: The nonlinear seismology is the rule, The linear seismology is the exception. Paraphrasing Tullio Levi-Civita The leading question is: how many cities, villages, metropolitan areas etc. in seismic regions are constructed on rock sites? Most of them are located on alluvial deposits/ sediments, on Quaternary layers or in river valleys. In last book written by Peter M. Shearer, Professor of Geophysics at University of California, we can find, in total, only 12 rows about non-linear seismology(page 176).Among others are the following conclusions:(i)-Strong ground accelerations from large earthquakes can produce a non-linear response in shallow soils; (ii)-When a non-linear site response is present, then the shaking from large earthquakes cannot be predicted by simple scaling of records from small earthquakes; (iii)-This is an active area of research in strong motion and engineering seismology. On the other hand, Aki wrote: Nonlinear amplification at sediments sites appears to be more pervasive than seismologists used to think…Any attempt at seismic zonation must take into account the local site condition and this nonlinear amplification(Aki, A., Local Site Effects on Weak and Strong Ground Motion, Tectonophysics,218,93-111,1993). The difficulty to seismologists in demonstrating the nonlinear site effects has been due to the effect being overshadowed by the overall patterns of shock generation and propagation. In other words, the seismological detection of the nonlinear site effects requires a simultaneous understanding and separating of the effects of earthquake source, propagation path and local geological site conditions. To see the actual influence of nonlinearity of the whole system (seismic source-path propagation-local geological structure) the authors used to study the response spectra because they are the last in this chain and, of course, that they are the ones who are taken into account in seismic design of all structures Stress-strain relationships for soils are usually nonlinear, soil stiffness decreases and internal damping increases with increasing shear strain during of strong earthquakes. There is a strong nonlinear dependence of the spectral amplification factors(SAF) on earthquake magnitude for all seismic stations on Romanian territory on extra-Carpathian area (Iasi, Bacau, Focsani, Bucharest etc.). Median values of SAF for last strong Vrancea earthquakes are decreasing from 4.16(May 31,1990;Mw=6.4),to 3.63 (May 30,1990;Mw=6.9) and to 3.26 (August 30, 1986; Mw=7.1) .The novelty and the complexity degree comes from the fact that for first time, the final decision for NPP Cernavoda site was also based on local strong nonlinear spectral amplifications for strong earthquakes and used in last "STRESS TEST" asked by IAEA Vienna in 2011. The present analysis indicates that the effect of nonlinearity could be very important and if the analysis is made for peak accelerations, it is 48.87% and for stronger earthquakes it will be bigger. The authors are coming with new recorded data which will open up a new challenge for seismologists studying nonlinear site effects in 2-D and 3-D irregular geological structures, leading them to a fascinating research subject in earth physics(Aki,1993, p.108,idem),in nonlinear seismology and,finally, in a real evaluation of earthquake risk and loss estimates.

The Effect of Sedimentary Basins on Through-Passing Short-Period Surface Waves

NASA Astrophysics Data System (ADS)

Feng, L.; Ritzwoller, M. H.

2017-12-01

Surface waves propagating through sedimentary basins undergo elastic wave field complications that include multiple scattering, amplification, the formation of secondary wave fronts, and subsequent wave front healing. Unless these effects are accounted for accurately, they may introduce systematic bias to estimates of source characteristics, the inference of the anelastic structure of the Earth, and ground motion predictions for hazard assessment. Most studies of the effects of basins on surface waves have centered on waves inside the basins. In contrast, we investigate wave field effects downstream from sedimentary basins, with particular emphasis on continental basins and propagation paths, elastic structural heterogeneity, and Rayleigh waves at 10 s period. Based on wave field simulations through a recent 3D crustal and upper mantle model of East Asia, we demonstrate significant Rayleigh wave amplification downstream from sedimentary basins in eastern China such that Ms measurements obtained on the simulated wave field vary by more than a magnitude unit. We show that surface wave amplification caused by basins results predominantly from elastic focusing and that amplification effects produced through 3D basin models are reproduced using 2D membrane wave simulations through an appropriately defined phase velocity map. The principal characteristics of elastic focusing in both 2D and 3D simulations include (1) retardation of the wave front inside the basins; (2) deflection of the wave propagation direction; (3) formation of a high amplitude lineation directly downstream from the basin bracketed by two low amplitude zones; and (4) formation of a secondary wave front. Finally, by comparing the impact of elastic focusing with anelastic attenuation, we argue that on-continent sedimentary basins are expected to affect surface wave amplitudes more strongly through elastic focusing than through the anelastic attenuation.

Effect of saliva stabilisers on detection of porcine reproductive and respiratory syndrome virus in oral fluid by quantitative reverse transcriptase real-time PCR.

PubMed

Decorte, Inge; Van der Stede, Yves; Nauwynck, Hans; De Regge, Nick; Cay, Ann Brigitte

2013-08-01

This study evaluated the effect of extraction-amplification methods, storage temperature and saliva stabilisers on detection of porcine reproductive and respiratory syndrome virus (PRRSV) RNA by quantitative reverse transcriptase real-time PCR (qRT-PCR) in porcine oral fluid. The diagnostic performance of different extraction-amplification methods was examined using a dilution series of oral fluid spiked with PRRSV. To determine RNA stability, porcine oral fluid, with or without commercially available saliva stabilisers, was spiked with PRRSV, stored at 4°C or room temperature and tested for the presence of PRRSV RNA by qRT-PCR. PRRSV RNA could be detected in oral fluid using all extraction-amplification combinations, but the limit of detection varied amongst different combinations. Storage temperature and saliva stabilisers had an effect on the stability of PRRSV RNA, which could only be detected for 7 days when PRRSV spiked oral fluid was kept at 4°C or stabilised at room temperature with a commercial mRNA stabiliser. Copyright © 2013 Elsevier Ltd. All rights reserved.

A theoretical study for the propagation of rolling noise over a porous road pavement

NASA Astrophysics Data System (ADS)

Keung Lui, Wai; Ming Li, Kai

2004-07-01

A simplified model based on the study of sound diffracted by a sphere is proposed for investigating the propagation of noise in a hornlike geometry between porous road surfaces and rolling tires. The simplified model is verified by comparing its predictions with the published numerical and experimental results of studies on the horn amplification of sound over a road pavement. In a parametric study, a point monopole source is assumed to be localized on the surface of a tire. In the frequency range of interest, a porous road pavement can effectively reduce the level of amplified sound due to the horn effect. It has been shown that an increase in the thickness and porosity of a porous layer, or the use of a double layer of porous road pavement, attenuates the horn amplification of sound. However, a decrease in the flow resistivity of a porous road pavement does little to reduce the horn amplification of sound. It has also been demonstrated that the horn effect over a porous road pavement is less dependent on the angular position of the source on the surface of tires.

Amplification or suppression: Social networks and the climate change—migration association in rural Mexico

PubMed Central

Riosmena, Fernando; Hunter, Lori M.; Runfola, Daniel M.

2015-01-01

Increasing rates of climate migration may be of economic and national concern to sending and destination countries. It has been argued that social networks – the ties connecting an origin and destination – may operate as “migration corridors” with the potential to strongly facilitate climate change-related migration. This study investigates whether social networks at the household and community levels amplify or suppress the impact of climate change on international migration from rural Mexico. A novel set of 15 climate change indices was generated based on daily temperature and precipitation data for 214 weather stations across Mexico. Employing geostatistical interpolation techniques, the climate change values were linked to 68 rural municipalities for which sociodemographic data and detailed migration histories were available from the Mexican Migration Project. Multi-level discrete-time event-history models were used to investigate the effect of climate change on international migration between 1986 and 1999. At the household level, the effect of social networks was approximated by comparing the first to the last move, assuming that through the first move a household establishes internal social capital. At the community level, the impact of social capital was explored through interactions with a measure of the proportion of adults with migration experience. The results show that rather than amplifying, social capital may suppress the sensitivity of migration to climate triggers, suggesting that social networks could facilitate climate change adaptation in place. PMID:26692656

Miniaturized isothermal nucleic acid amplification, a review.

PubMed

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.

The histone acetyltransferases CBP and Chameau integrate developmental and DNA replication programs in Drosophila ovarian follicle cells

PubMed Central

McConnell, Kristopher H.; Dixon, Michael; Calvi, Brian R.

2012-01-01

DNA replication origin activity changes during development. Chromatin modifications are known to influence the genomic location of origins and the time during S phase that they initiate replication in different cells. However, how chromatin regulates origins in concert with cell differentiation remains poorly understood. Here, we use developmental gene amplification in Drosophila ovarian follicle cells as a model to investigate how chromatin modifiers regulate origins in a developmental context. We find that the histone acetyltransferase (HAT) Chameau (Chm) binds to amplicon origins and is partially required for their function. Depletion of Chm had relatively mild effects on origins during gene amplification and genomic replication compared with previous knockdown of its ortholog HBO1 in human cells, which has severe effects on origin function. We show that another HAT, CBP (Nejire), also binds amplicon origins and is partially required for amplification. Knockdown of Chm and CBP together had a more severe effect on nucleosome acetylation and amplicon origin activity than knockdown of either HAT alone, suggesting that these HATs collaborate in origin regulation. In addition to their local function at the origin, we show that Chm and CBP also globally regulate the developmental transition of follicle cells into the amplification stages of oogenesis. Our results reveal a complexity of origin epigenetic regulation by multiple HATs during development and suggest that chromatin modifiers are a nexus that integrates differentiation and DNA replication programs. PMID:22951641

Weak Value Amplification of a Post-Selected Single Photon

NASA Astrophysics Data System (ADS)

Hallaji, Matin

Weak value amplification (WVA) is a measurement technique in which the effect of a pre- and post-selected system on a weakly interacting probe is magnified. In this thesis, I present the first experimental observation of WVA of a single photon. We observed that a signal photon --- sent through a polarization interferometer and post-selected by photodetection in the almost-dark port --- can act like eight photons. The effect of this single photon is measured as a nonlinear phase shift on a separate laser beam. The interaction between the two is mediated by a sample of laser- cooled 85Rb atoms. Electromagnetically induced transparency (EIT) is used to enhance the nonlinearity and overcome resonant absorption. I believe this work to be the first demonstration of WVA where a deterministic interaction is used to entangle two distinct optical systems. In WVA, the amplification is contingent on discarding a large portion of the original data set. While amplification increases measurement sensitivity, discarding data worsens it. Questioning whether these competing effects conspire to improve or diminish measurement accuracy has resulted recently in controversy. I address this question by calculating the maximum amount of information achievable with the WVA technique. By comparing this information to that achievable by the standard technique, where no post-selection is employed, I show that the WVA technique can be advantageous under a certain class of noise models. Finally, I propose a way to optimally apply the WVA technique.

Numerical investigations of non-collinear optical parametric chirped pulse amplification for Laguerre-Gaussian vortex beam

NASA Astrophysics Data System (ADS)

Xu, Lu; Yu, Lianghong; Liang, Xiaoyan

2016-04-01

We present for the first time a scheme to amplify a Laguerre-Gaussian vortex beam based on non-collinear optical parametric chirped pulse amplification (OPCPA). In addition, a three-dimensional numerical model of non-collinear optical parametric amplification was deduced in the frequency domain, in which the effects of non-collinear configuration, temporal and spatial walk-off, group-velocity dispersion and diffraction were also taken into account, to trace the dynamics of the Laguerre-Gaussian vortex beam and investigate its critical parameters in the non-collinear OPCPA process. Based on the numerical simulation results, the scheme shows promise for implementation in a relativistic twisted laser pulse system, which will diversify the light-matter interaction field.

Strong nonlinear dependence of the spectral amplification factors of deep Vrancea earthquakes magnitude

NASA Astrophysics Data System (ADS)

Marmureanu, Gheorghe; Ortanza Cioflan, Carmen; Marmureanu, Alexandru

2010-05-01

Nonlinear effects in ground motion during large earthquakes have long been a controversial issue between seismologists and geotechnical engineers. Aki wrote in 1993:"Nonlinear amplification at sediments sites appears to be more pervasive than seismologists used to think…Any attempt at seismic zonation must take into account the local site condition and this nonlinear amplification( Local site effects on weak and strong ground motion, Tectonophysics,218,93-111). In other words, the seismological detection of the nonlinear site effects requires a simultaneous understanding of the effects of earthquake source, propagation path and local geological site conditions. The difficulty for seismologists in demonstrating the nonlinear site effects has been due to the effect being overshadowed by the overall patterns of shock generation and path propagation. The researchers from National Institute for Earth Physics ,in order to make quantitative evidence of large nonlinear effects, introduced the spectral amplification factor (SAF) as ratio between maximum spectral absolute acceleration (Sa), relative velocity (Sv) , relative displacement (Sd) from response spectra for a fraction of critical damping at fundamental period and peak values of acceleration(a-max),velocity (v-max) and displacement (d-max),respectively, from processed strong motion record and pointed out that there is a strong nonlinear dependence on earthquake magnitude and site conditions.The spectral amplification factors(SAF) are finally computed for absolute accelerations at 5% fraction of critical damping (β=5%) in five seismic stations: Bucharest-INCERC(soft soils, quaternary layers with a total thickness of 800 m);Bucharest-Magurele (dense sand and loess on 350m); Cernavoda Nuclear Power Plant site (marl, loess, limestone on 270 m) Bacau(gravel and loess on 20m) and Iassy (loess, sand, clay, gravel on 60 m) for last strong and deep Vrancea earthquakes: March 4,1977 (MGR =7.2 and h=95 km);August 30,1986(MGR =7.0 and h=130 km);May 30,1990 (MGR =6.7 and h=90 km) and May 31,1990 (MGR =6.1 and h=87 km). With a view to understand the characteristics of nonlinear soil behavior and the nonlinearity in the seismology and the influence to hazard and risk assessment ,this study examined the ways that nonlinearity would expected to appear on strong motion records made on Romania territory during to last Vrancea earthquake. The effect on nonlinearity is very large. For example, if we maintain the same amplification factor (SAF=5.8942) as for relatively strong earthquake on May 31,1990 with magnitude Ms =6,1 then at Bacau seismic station for earthquake on May 30,1990 (MGR =6.7) the peak acceleration has to be a*max =0.154g( +14.16%) and the actual recorded was only, a max =0.135g. Also, for Vrancea earthquake on August 30,1986, the peak acceleration has to be a*max=0.107g (+45,57%), instead of real value of 0.0736 g recorded at Bacau seismic station. More, the spectral amplification factors(SAF) are function of earthquake magnitude and there is a strong nonlinear dependence of the SAF of earthquake magnitude. The median values of SAF of the last strong Vrancea earthquakes for damping 5% are: 4.16; 3.63 and 3.26 corresponding to May 31,1990 Vrancea earthquake (Ms=6.1),May 30,1990 Vrancea earthquake(Ms=6.7),respectively, August 30,1986 Vrancea one(Ms=7.0). At the same seismic station, for example at Bacau, for 5% damping, SAF for accelerations is 5.22 for May 31,1990 earthquake (Ms =6.1);4.32 for May 30,1990 earthquake (Ms =6.7) and 3,94 for August 30,1986 one (Ms=7.0) etc. Finally, it will be made a comment in connection to U.S. Atomic Energy Commission-Regulatory Guide 1.60 on "Design Response Spectra for seismic design of nuclear power plants " to see spectral amplification factors for deep Vrancea earthquakes are larger and different.

The effect of a jet stream on the generation of mountain wave-induced mean flows and turbulence near the tropopause

NASA Astrophysics Data System (ADS)

Dörnbrack, Andreas; Sharman, Robert

2015-04-01

Observational evidence indicates a higher incidence of turbulence near the tropopause, especially over mountainous terrain. Previous work by McHugh and Sharman (2013) indicate this may be due to nonlinear amplification of topographically-induced gravity waves as they impinge on the tropopause. However, that study did not consider nonlinear topography amplification effects, nor did it consider the more realistic case of a jet stream in the vicinity of the tropopause. This study extends the McHugh and Sharman study by considering these effects using fully nonlinear simulations with the jet modeled as a sech**2 profile. Sensitivity studies are performed to study such effects as the location of the nose of the jet relative to the tropopause height, the jet width, the height of the tropopause, and the size and shape of the obstacle. Momentum and energy flux profiles are used to deduce those configurations most conducive to gravity wave amplification, breakdown and turbulence near the tropopause. McHugh J., Sharman R., 2013: Generation of mountain wave-induced mean flows and turbulence near the tropopause. Q. J. R. Meteorol. Soc. 139: 1632-1642. DOI:10.1002/qj.2035

Successful isolation and PCR amplification of DNA from National Institute of Standards and Technology herbal dietary supplement standard reference material powders and extracts.

PubMed

Cimino, Matthew T

2010-03-01

Twenty-four herbal dietary supplement powder and extract reference standards provided by the National Institute of Standards and Technology (NIST) were investigated using three different commercially available DNA extraction kits to evaluate DNA availability for downstream nucleotide-based applications. The material included samples of Camellia, Citrus, Ephedra, Ginkgo, Hypericum, Serenoa, And Vaccinium. Protocols from Qiagen, MoBio, and Phytopure were used to isolate and purify DNA from the NIST standards. The resulting DNA concentration was quantified using SYBR Green fluorometry. Each of the 24 samples yielded DNA, though the concentration of DNA from each approach was notably different. The Phytopure method consistently yielded more DNA. The average yield ratio was 22 : 3 : 1 (ng/microL; Phytopure : Qiagen : MoBio). Amplification of the internal transcribed spacer II region using PCR was ultimately successful in 22 of the 24 samples. Direct sequencing chromatograms of the amplified material suggested that most of the samples were comprised of mixtures. However, the sequencing chromatograms of 12 of the 24 samples were sufficient to confirm the identity of the target material. The successful extraction, amplification, and sequencing of DNA from these herbal dietary supplement extracts and powders supports a continued effort to explore nucleotide sequence-based tools for the authentication and identification of plants in dietary supplements. (c) Georg Thieme Verlag KG Stuttgart . New York.

The C-module-binding factor supports amplification of TRE5-A retrotransposons in the Dictyostelium discoideum genome.

PubMed

Bilzer, Annika; Dölz, Heike; Reinhardt, Alexander; Schmith, Anika; Siol, Oliver; Winckler, Thomas

2011-01-01

Retrotransposable elements are molecular parasites that have invaded the genomes of virtually all organisms. Although retrotransposons encode essential proteins to mediate their amplification, they also require assistance by host cell-encoded machineries that perform functions such as DNA transcription and repair. The retrotransposon TRE5-A of the social amoeba Dictyostelium discoideum generates a notable amount of both sense and antisense RNAs, which are generated from element-internal promoters, located in the A module and the C module, respectively. We observed that TRE5-A retrotransposons depend on the C-module-binding factor (CbfA) to maintain high steady-state levels of TRE5-A transcripts and that CbfA supports the retrotransposition activity of TRE5-A elements. The carboxy-terminal domain of CbfA was found to be required and sufficient to mediate the accumulation of TRE5-A transcripts, but it did not support productive retrotransposition of TRE5-A. This result suggests different roles for CbfA protein domains in the regulation of TRE5-A retrotransposition frequency in D. discoideum cells. Although CbfA binds to the C module in vitro, the factor regulates neither C-module nor A-module promoter activity in vivo. We speculate that CbfA supports the amplification of TRE5-A retrotransposons by suppressing the expression of an as yet unidentified component of the cellular posttranscriptional gene silencing machinery.

Quantification of HER2/neu gene amplification by competitive pcr using fluorescent melting curve analysis.

PubMed

Lyon, E; Millson, A; Lowery, M C; Woods, R; Wittwer, C T

2001-05-01

Molecular detection methods for HER2/neu gene amplification include fluorescence in situ hybridization (FISH) and competitive PCR. We designed a quantitative PCR system utilizing fluorescent hybridization probes and a competitor that differed from the HER2/neu sequence by a single base change. Increasing twofold concentrations of competitor were coamplified with DNA from cell lines with various HER2/neu copy numbers at the HER2/neu locus. Competitor DNA was distinguished from the HER2/neu sequence by a fluorescent hybridization probe and melting curve analysis on a fluorescence-monitoring thermal cycler. The percentages of competitor to target peak areas on derivative fluorescence vs temperature curves were used to calculate copy number. Real-time monitoring of the PCR reaction showed comparable relative areas throughout the log phase and during the PCR plateau, indicating that only end-point detection is necessary. The dynamic range was over two logs (2000-250 000 competitor copies) with CVs < 20%. Three cell lines (MRC-5, T-47D, and SK-BR-3) were determined to have gene doses of 1, 3, and 11, respectively. Gene amplification was detected in 3 of 13 tumor samples and was correlated with conventional real-time PCR and FISH analysis. Use of relative peak areas allows gene copy numbers to be quantified against an internal competitive control in < 1 h.

MYC protein expression and genetic alterations have prognostic impact in patients with diffuse large B-cell lymphoma treated with immunochemotherapy

PubMed Central

Valera, Alexandra; López-Guillermo, Armando; Cardesa-Salzmann, Teresa; Climent, Fina; González-Barca, Eva; Mercadal, Santiago; Espinosa, Íñigo; Novelli, Silvana; Briones, Javier; Mate, José L.; Salamero, Olga; Sancho, Juan M.; Arenillas, Leonor; Serrano, Sergi; Erill, Nadina; Martínez, Daniel; Castillo, Paola; Rovira, Jordina; Martínez, Antonio; Campo, Elias; Colomo, Luis

2013-01-01

MYC alterations influence the survival of patients with diffuse large B-cell lymphoma. Most studies have focused on MYC translocations but there is little information regarding the impact of numerical alterations and protein expression. We analyzed the genetic alterations and protein expression of MYC, BCL2, BCL6, and MALT1 in 219 cases of diffuse large B-cell lymphoma. MYC rearrangement occurred as the sole abnormality (MYC single-hit) in 3% of cases, MYC and concurrent BCL2 and/or BCL6 rearrangements (MYC double/triple-hit) in 4%, MYC amplifications in 2% and MYC gains in 19%. MYC single-hit, MYC double/triple-hit and MYC amplifications, but not MYC gains or other gene rearrangements, were associated with unfavorable progression-free survival and overall survival. MYC protein expression, evaluated using computerized image analysis, captured the unfavorable prognosis of MYC translocations/amplifications and identified an additional subset of patients without gene alterations but with similar poor prognosis. Patients with tumors expressing both MYC/BCL2 had the worst prognosis, whereas those with double-negative tumors had the best outcome. High MYC expression was associated with shorter overall survival irrespectively of the International Prognostic Index and BCL2 expression. In conclusion, MYC protein expression identifies a subset of diffuse large B-cell lymphoma with very poor prognosis independently of gene alterations and other prognostic parameters. PMID:23716551

MYC protein expression and genetic alterations have prognostic impact in patients with diffuse large B-cell lymphoma treated with immunochemotherapy.

PubMed

Valera, Alexandra; López-Guillermo, Armando; Cardesa-Salzmann, Teresa; Climent, Fina; González-Barca, Eva; Mercadal, Santiago; Espinosa, Iñigo; Novelli, Silvana; Briones, Javier; Mate, José L; Salamero, Olga; Sancho, Juan M; Arenillas, Leonor; Serrano, Sergi; Erill, Nadina; Martínez, Daniel; Castillo, Paola; Rovira, Jordina; Martínez, Antonio; Campo, Elias; Colomo, Luis

2013-10-01

MYC alterations influence the survival of patients with diffuse large B-cell lymphoma. Most studies have focused on MYC translocations but there is little information regarding the impact of numerical alterations and protein expression. We analyzed the genetic alterations and protein expression of MYC, BCL2, BCL6, and MALT1 in 219 cases of diffuse large B-cell lymphoma. MYC rearrangement occurred as the sole abnormality (MYC single-hit) in 3% of cases, MYC and concurrent BCL2 and/or BCL6 rearrangements (MYC double/triple-hit) in 4%, MYC amplifications in 2% and MYC gains in 19%. MYC single-hit, MYC double/triple-hit and MYC amplifications, but not MYC gains or other gene rearrangements, were associated with unfavorable progression-free survival and overall survival. MYC protein expression, evaluated using computerized image analysis, captured the unfavorable prognosis of MYC translocations/amplifications and identified an additional subset of patients without gene alterations but with similar poor prognosis. Patients with tumors expressing both MYC/BCL2 had the worst prognosis, whereas those with double-negative tumors had the best outcome. High MYC expression was associated with shorter overall survival irrespectively of the International Prognostic Index and BCL2 expression. In conclusion, MYC protein expression identifies a subset of diffuse large B-cell lymphoma with very poor prognosis independently of gene alterations and other prognostic parameters.

More antitumor efficacy of the PI3K inhibitor GDC-0941 in breast cancer with PIK3CA mutation or HER2 amplification status in vitro.

PubMed

Zheng, Jie; Wang, Huan; Yao, Jia; Zou, Xianjin

2014-01-01

PIK3CA is probably the most commonly mutated kinase in several malignant tumors. Activation of class I phosphatidylinositol 3' kinase (PI3K) regulates tumor proliferation, survival, etc. This study sought to identify whether the pan-inhibitor has more antitumor efficacy in breast cancer cells with PIK3CA Mutation or HER2 amplification than basal-like cancer cells. The proliferation of breast cancer cells was measured by MTT assay in the presence of GDC-0941. Afterwards, we determined the visible changes in signaling in the PI3K/AKT/mTOR pathway. Finally, we examined GDC-0941 effects on cell cycle, apoptosis and motility. GDC-0941 exhibited excellent inhibition on three cell lines with PIK3CA mutation or HER2 amplification. In addition, GDC-0941 resulted in decreased Akt activity. GDC-0941 downregulated the key components of the cell cycle machinery, such as cyclin D1, upregulated the apoptotic markers and inhibited cell motility on three cell lines with PIK3CA Mutation or HER2 amplification. Antitumor activity of GDC-0941 treatment amongst tumor cell lines with PIK3CA mutation and HER2 amplification may have clinical utility in patients with these oncogenic alterations.

An Evidence-Based Systematic Review of Amplitude Compression in Hearing Aids for School-Age Children With Hearing Loss

PubMed Central

McCreery, Ryan W.; Venediktov, Rebecca A.; Coleman, Jaumeiko J.; Leech, Hillary M.

2013-01-01

Purpose Two clinical questions were developed: one addressing the comparison of linear amplification with compression limiting to linear amplification with peak clipping, and the second comparing wide dynamic range compression with linear amplification for outcomes of audibility, speech recognition, speech and language, and self- or parent report in children with hearing loss. Method Twenty-six databases were systematically searched for studies addressing a clinical question and meeting all inclusion criteria. Studies were evaluated for methodological quality, and effect sizes were reported or calculated when possible. Results The literature search resulted in the inclusion of 8 studies. All 8 studies included comparisons of wide dynamic range compression to linear amplification, and 2 of the 8 studies provided comparisons of compression limiting versus peak clipping. Conclusions Moderate evidence from the included studies demonstrated that audibility was improved and speech recognition was either maintained or improved with wide dynamic range compression as compared with linear amplification. No significant differences were observed between compression limiting and peak clipping on outcomes (i.e., speech recognition and self-/parent report) reported across the 2 studies. Preference ratings appear to be influenced by participant characteristics and environmental factors. Further research is needed before conclusions can confidently be drawn. PMID:22858616

Graphene Nanoprobes for Real-Time Monitoring of Isothermal Nucleic Acid Amplification.

PubMed

Li, Fan; Liu, Xiaoguo; Zhao, Bin; Yan, Juan; Li, Qian; Aldalbahi, Ali; Shi, Jiye; Song, Shiping; Fan, Chunhai; Wang, Lihua

2017-05-10

Isothermal amplification is an efficient way to amplify DNA with high accuracy; however, the real-time monitoring for quantification analysis mostly relied on expensive and precisely designed probes. In the present study, a graphene oxide (GO)-based nanoprobe was used to real-time monitor the isothermal amplification process. The interaction between GO and different DNA structures was systematically investigated, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), DNA 3-helix, and long rolling circle amplification (RCA) and hybridization chain reaction (HCR) products, which existed in one-, two-, and three-dimensional structures. It was found that the high rigid structures exhibited much lower affinity with GO than soft ssDNA, and generally the rigidity was dependent on the length of targets and the hybridization position with probe DNA. On the basis of these results, we successfully monitored HCR amplification process, RCA process, and the enzyme restriction of RCA products with GO nanoprobe; other applications including the detection of the assembly/disassembly of DNA 3-helix structures were also performed. Compared to the widely used end-point detection methods, the GO-based sensing platform is simple, sensitive, cost-effective, and especially in a real-time monitoring mode. We believe such studies can provide comprehensive understandings and evocation on design of GO-based biosensors for broad application in various fields.

Enhanced solid-phase recombinase polymerase amplification and electrochemical detection.

PubMed

Del Río, Jonathan Sabaté; Lobato, Ivan Magriñà; Mayboroda, Olena; Katakis, Ioanis; O'Sullivan, Ciara K

2017-05-01

Recombinase polymerase amplification (RPA) is an elegant method for the rapid, isothermal amplification of nucleic acids. Here, we elucidate the optimal surface chemistry for rapid and efficient solid-phase RPA, which was fine-tuned in order to obtain a maximum signal-to-noise ratio, defining the optimal DNA probe density, probe-to-lateral spacer ratio (1:0, 1:1, 1:10 and 1:100) and length of a vertical spacer of the probe as well as investigating the effect of different types of lateral spacers. The use of different labelling strategies was also examined in order to reduce the number of steps required for the analysis, using biotin or horseradish peroxidase-labelled reverse primers. Optimisation of the amplification temperature used and the use of surface blocking agents were also pursued. The combination of these changes facilitated a significantly more rapid amplification and detection protocol, with a lowered limit of detection (LOD) of 1 · 10 -15 M. The optimised protocol was applied to the detection of Francisella tularensis in real samples from hares and a clear correlation with PCR and qPCR results observed and the solid-phase RPA demonstrated to be capable of detecting 500 fM target DNA in real samples. Graphical abstract Relative size of thiolated lateral spacers tested versus the primer and the uvsx recombinase protein.

Comparison of Two Digital Stethoscopes with the Traditional Stethoscope Used on International Space Station

NASA Technical Reports Server (NTRS)

Rasbury, Jack; Bascal, Kira; Ownby, Matt; McCulley, Phyllis; Paul, Bonnie

2004-01-01

A traditional stethoscope is currently flown on the International Space Station (ISS). The background noise on the ISS is much higher than a normal exam room, and the literature shows that traditional stethoscopes are unable to function effectively in high noise environments. Digital stethoscopes provide amplification which improves the audibility in a quiet environment. This study is designed to determine if digital stethoscopes offer any advantage over traditional stethoscopes in being able to identify normal and abnormal sounds in the ISS noise environment. Methods: An ISS noise simulation facility was created to reproduce ISS noise profiles by modifying pink noise with a software-based graphic equalizer. The files were played in a continuous loop on a computer, amplified through a high-end stereo system and adjusted using a sound level meter. Nine caregiver analogues were given the same auscultation lesson received by astronauts. They began testing by becoming familiar with normal and abnormal sounds on a Student Auscultation Manikin . They then used two digital stethoscopes and a traditional stethoscope identical to the one flown on the ISS to auscultate the manikin sounds in the noise facility. They identified the sounds on a questionnaire and picked which of the three stethoscopes they preferred. Results: Evaluators displayed equivalent accuracy in sound identification when using either the 3M model 4000 digital stethoscope or traditional stethoscope. However, the 3M was preferred 2 to 1 by the evaluators, primarily because of additional amplification of the sounds. Discussion: Although our results show that the current ISS stethoscope and the "best-of-breed" digital stethoscope provide essentially the same auscultation utility, the latter has the advantage of recording and transmitting sounds to a remote physician. Since the astronaut caregivers are non-physiCians, this capability may be worth the additional expense and effort needed to certify the digital stethoscope for flight.

Evaluation of commercial kit based on loop-mediated isothermal amplification for rapid detection of low levels of uninjured and injured Salmonella on duck meat, bean sprouts, and fishballs in Singapore.

PubMed

Lim, Hazel Sin Yue; Zheng, Qianwang; Miks-Krajnik, Marta; Turner, Matthew; Yuk, Hyun-Gyun

2015-06-01

The objective of this study was to evaluate performance of the commercial kit based on loop-mediated isothermal amplification (LAMP) in comparison with the International Organization for Standardization method for detecting uninjured and sublethally injured Salmonella cells artificially inoculated at levels of 10(0) and 10(1) CFU/25 g on raw duck wing, raw mung bean sprouts, and processed fishballs. Injured cells were prepared by a heat treatment for duck wings and fishball samples and a chlorine treatment for bean sprout samples. Additionally, a validation study was performed on naturally contaminated food samples sold in Singapore. A total of 110 samples of each commodity were analyzed in this study. Regardless of inoculum levels, the detection by the commercial LAMP kit showed 100% sensitivity and specificity for both inoculated and uninoculated samples compared with the International Organization for Standardization method, with the exception of bean sprout samples. Only 20% of bean sprout samples inoculated with 10(0) CFU/25 g injured Salmonella cells were positive by using the commercial LAMP-based kit. However, all negative samples became positive following a secondary enrichment in Rappaport-Vassiliadis medium with soy broth or after concentration by centrifugation. These results suggest that secondary enrichment or centrifugation should be considered as an additional step to increase the sensitivity of the commercial LAMP-based kit with low numbers of injured target cells in samples with high background microflora (such as mung bean sprouts). The validation study also showed that the commercial LAMP-based kit provided 91% sensitivity and 95% specificity for naturally contaminated samples. Thus, this study demonstrates that the commercial LAMP-based kit might be a cost-effective method, as this system could provide rapid, accurate detection of both uninjured and injured Salmonella cells on raw duck wings, raw mung bean sprouts, and processed fishballs in less than 26 h.

Turbulent boundary layers subjected to multiple curvatures and pressure gradients

NASA Technical Reports Server (NTRS)

Bandyopadhyay, Promode R.; Ahmed, Anwar

1993-01-01

The effects of abruptly applied cycles of curvatures and pressure gradients on turbulent boundary layers are examined experimentally. Two two-dimensional curved test surfaces are considered: one has a sequence of concave and convex longitudinal surface curvatures and the other has a sequence of convex and concave curvatures. The choice of the curvature sequences were motivated by a desire to study the asymmetric response of turbulent boundary layers to convex and concave curvatures. The relaxation of a boundary layer from the effects of these two opposite sequences has been compared. The effect of the accompaying sequences of pressure gradient has also been examined but the effect of curvature dominates. The growth of internal layers at the curvature junctions have been studied. Measurements of the Gortler and corner vortex systems have been made. The boundary layer recovering from the sequence of concave to convex curvature has a sustained lower skin friction level than in that recovering from the sequence of convex to concave curvature. The amplification and suppression of turbulence due to the curvature sequences have also been studied.

Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime

NASA Astrophysics Data System (ADS)

Caré, Bertrand R.; Soula, Hédi A.

2013-01-01

Many types of membrane receptors are found to be organized as clusters on the cell surface. We investigate the potential effect of such receptor clustering on the intracellular signal transduction stage. We consider a canonical pathway with a membrane receptor (R) activating a membrane-bound intracellular relay protein (G). We use Monte Carlo simulations to recreate biochemical reactions using different receptor spatial distributions and explore the dynamics of the signal transduction. Results show that activation of G by R is severely impaired by R clustering, leading to an apparent blunted biological effect compared to control. Paradoxically, this clustering decreases the half maximal effective dose (ED50) of the transduction stage, increasing the apparent affinity. We study an example of inter-receptor interaction in order to account for possible compensatory effects of clustering and observe the parameter range in which such interactions slightly counterbalance the loss of activation of G. The membrane receptors’ spatial distribution affects the internal stages of signal amplification, suggesting a functional role for membrane domains and receptor clustering independently of proximity-induced receptor-receptor interactions.

RNA signal amplifier circuit with integrated fluorescence output.

PubMed

Akter, Farhima; Yokobayashi, Yohei

2015-05-15

We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.

Stimulated Raman amplification, oscillation, and linewidth in barium nitrate

NASA Technical Reports Server (NTRS)

McCray, Christopher J.; Chyba, Thomas H.

1998-01-01

Measurements of Raman gain in a Ba(NO3)2 crystal are reported at 532 nm using a Raman oscillator/amplifier arrangement for differential absorption lidar measurements of ozone. The experimentally determined gain coefficient will be compared with theoretical results. The effect of single and multi-longitudinal mode pumping upon the amplification process will be discussed. Measurement of the Raman linewidth for 1st 2nd and 3d stokes shifts arc presented.

Systematic Site Characterization at Seismic Stations combined with Empirical Spectral Modeling: critical data for local hazard analysis

NASA Astrophysics Data System (ADS)

Michel, Clotaire; Hobiger, Manuel; Edwards, Benjamin; Poggi, Valerio; Burjanek, Jan; Cauzzi, Carlo; Kästli, Philipp; Fäh, Donat

2016-04-01

The Swiss Seismological Service operates one of the densest national seismic networks in the world, still rapidly expanding (see http://www.seismo.ethz.ch/monitor/index_EN). Since 2009, every newly instrumented site is characterized following an established procedure to derive realistic 1D VS velocity profiles. In addition, empirical Fourier spectral modeling is performed on the whole network for each recorded event with sufficient signal-to-noise ratio. Besides the source characteristics of the earthquakes, statistical real time analyses of the residuals of the spectral modeling provide a seamlessly updated amplification function w.r. to Swiss rock conditions at every station. Our site characterization procedure is mainly based on the analysis of surface waves from passive experiments and includes cross-checks of the derived amplification functions with those obtained through spectral modeling. The systematic use of three component surface-wave analysis, allowing the derivation of both Rayleigh and Love waves dispersion curves, also contributes to the improved quality of the retrieved profiles. The results of site characterisation activities at recently installed strong-motion stations depict the large variety of possible effects of surface geology on ground motion in the Alpine context. Such effects range from de-amplification at hard-rock sites to amplification up to a factor of 15 in lacustrine sediments with respect to the Swiss reference rock velocity model. The derived velocity profiles are shown to reproduce observed amplification functions from empirical spectral modeling. Although many sites are found to exhibit 1D behavior, our procedure allows the detection and qualification of 2D and 3D effects. All data collected during the site characterization procedures in the last 20 years are gathered in a database, implementing a data model proposed for community use at the European scale through NERA and EPOS (www.epos-eu.org). A web stationbook derived from it can be accessed through the interface www.stations.seismo.ethz.ch.

Does the Arctic Amplification peak this decade?

NASA Astrophysics Data System (ADS)

Martin, Torge; Haine, Thomas W. N.

2017-04-01

Temperatures rise faster in the Arctic than on global average, a phenomenon known as Arctic Amplification. While this is well established from observations and model simulations, projections of future climate (here: RCP8.5) with models of the Coupled Model Intercomparison Project phase 5 (CMIP5) also indicate that the Arctic Amplification has a maximum. We show this by means of an Arctic Amplification factor (AAF), which we define as the ratio of Arctic mean to global mean surface air temperature (SAT) anomalies. The SAT anomalies are referenced to the period 1960-1980 and smoothed by a 30-year running mean. For October, the multi-model ensemble-mean AAF reaches a maximum in 2017. The maximum moves however to later years as Arctic winter progresses: for the autumn mean SAT (September to November) the maximum AAF is found in 2028 and for winter (December to February) in 2060. Arctic Amplification is driven, amongst others, by the ice-albedo feedback (IAF) as part of the more general surface albedo feedback (involving clouds, snow cover, vegetation changes) and temperature effects (Planck and lapse-rate feedbacks). We note that sea ice retreat and the associated warming of the summer Arctic Ocean are not only an integral part of the IAF but are also involved in the other drivers. In the CMIP5 simulations, the timing of the AAF maximum coincides with the period of fastest ice retreat for the respective month. Presence of at least some sea ice is crucial for the IAF to be effective because of the contrast in surface albedo between ice and open water and the need to turn ocean warming into ice melt. Once large areas of the Arctic Ocean are ice-free, the IAF should be less effective. We thus hypothesize that the ice retreat significantly affects AAF variability and forces a decline of its magnitude after at least half of the Arctic Ocean is ice-free and the ice cover becomes basically seasonal.

Effects of Instantaneous Multiband Dynamic Compression on Speech Intelligibility

NASA Astrophysics Data System (ADS)

Herzke, Tobias; Hohmann, Volker

2005-12-01

The recruitment phenomenon, that is, the reduced dynamic range between threshold and uncomfortable level, is attributed to the loss of instantaneous dynamic compression on the basilar membrane. Despite this, hearing aids commonly use slow-acting dynamic compression for its compensation, because this was found to be the most successful strategy in terms of speech quality and intelligibility rehabilitation. Former attempts to use fast-acting compression gave ambiguous results, raising the question as to whether auditory-based recruitment compensation by instantaneous compression is in principle applicable in hearing aids. This study thus investigates instantaneous multiband dynamic compression based on an auditory filterbank. Instantaneous envelope compression is performed in each frequency band of a gammatone filterbank, which provides a combination of time and frequency resolution comparable to the normal healthy cochlea. The gain characteristics used for dynamic compression are deduced from categorical loudness scaling. In speech intelligibility tests, the instantaneous dynamic compression scheme was compared against a linear amplification scheme, which used the same filterbank for frequency analysis, but employed constant gain factors that restored the sound level for medium perceived loudness in each frequency band. In subjective comparisons, five of nine subjects preferred the linear amplification scheme and would not accept the instantaneous dynamic compression in hearing aids. Four of nine subjects did not perceive any quality differences. A sentence intelligibility test in noise (Oldenburg sentence test) showed little to no negative effects of the instantaneous dynamic compression, compared to linear amplification. A word intelligibility test in quiet (one-syllable rhyme test) showed that the subjects benefit from the larger amplification at low levels provided by instantaneous dynamic compression. Further analysis showed that the increase in intelligibility resulting from a gain provided by instantaneous compression is as high as from a gain provided by linear amplification. No negative effects of the distortions introduced by the instantaneous compression scheme in terms of speech recognition are observed.

Increased expression of Solute carrier family 12 member 5 via gene amplification contributes to tumour progression and metastasis and associates with poor survival in colorectal cancer

PubMed Central

Xu, Lixia; Li, Xiaoxing; Cai, Muyan; Chen, Jinna; Li, Xiangchun; Wu, William K K; Kang, Wei; Tong, Joanna; To, Ka-Fai; Guan, Xin-Yuan; Sung, Joseph J Y; Chan, Francis K L; Yu, Jun

2016-01-01

Objective Using whole genome sequencing, we identified gene amplification of solute carrier family 12 member 5 (SLC12A5) located at 20q13.12 in colorectal cancer (CRC). We analysed its amplification, overexpression, biological effects and prognostic significance in CRC. Design SLC12A5 amplification status was evaluated by fluorescence in situ hybridisation (FISH). The effects of SLC12A5 re-expression or knockdown were determined in proliferation, apoptosis, invasion and metastasis assays. SLC12A5 target genes and related pathways were identified by reporter activity and cDNA microarray analyses. Clinical impact of SLC12A5 overexpression was assessed in 195 patients with CRC. Results Amplification of SLC12A5 was verified in 78 out of 191 (40.8%) patients with primary CRC by FISH, which was positively correlated with its protein overexpression (p<0.001). Biofunctional investigation of SLC12A5 revealed that SLC12A5 significantly increased cell proliferation, G1-S cell cycle transition, invasion/migration abilities, but suppressed apoptosis in vitro and promoted xenograft tumour growth as well as lung metastasis in vivo. The antiapoptosis effect by SLC12A5 was mediated through inhibiting apoptosis-inducing factor and endonuclease G-dependent apoptotic signalling pathway; and the pro-metastasis role was by regulating key elements of the matrix architecture, including matrix metallopeptidase and fibronectin. After a median follow-up of 50.16 months, multivariate analysis revealed that patients with SLC12A5 protein overexpression had a significant decrease in overall survival. Kaplan–Meier survival curves showed that SLC12A5 overexpression was significantly associated with shortened survival in patients with CRC. Conclusions SLC12A5 plays a pivotal oncogenic role in colorectal carcinogenesis; its overexpression is an independent prognostic factor of patients with CRC. PMID:25947013

Optomechanical transistor with mechanical gain

NASA Astrophysics Data System (ADS)

Zhang, X. Z.; Tian, Lin; Li, Yong

2018-04-01

We study an optomechanical transistor, where an input field can be transferred and amplified unidirectionally in a cyclic three-mode optomechanical system. In this system, the mechanical resonator is coupled simultaneously to two cavity modes. We show that it only requires a finite mechanical gain to achieve the nonreciprocal amplification. Here the nonreciprocity is caused by the phase difference between the linearized optomechanical couplings that breaks the time-reversal symmetry of this system. The amplification arises from the mechanical gain, which provides an effective phonon bath that pumps the mechanical mode coherently. This effect is analogous to the stimulated emission of atoms, where the probe field can be amplified when its frequency is in resonance with that of the anti-Stokes transition. We show that by choosing optimal parameters, this optomechanical transistor can reach perfect unidirectionality accompanied with strong amplification. In addition, the presence of the mechanical gain can result in ultralong delay in the phase of the probe field, which provides an alternative to controlling light transport in optomechanical systems.

A Novel Real-Time PCR for Listeria monocytogenes That Monitors Analytical Performance via an Internal Amplification Control

PubMed Central

Rodríguez-Lázaro, David; Pla, Maria; Scortti, Mariela; Monzó, Héctor J.; Vázquez-Boland, José A.

2005-01-01

We describe a novel quantitative real-time (Q)-PCR assay for Listeria monocytogenes based on the coamplification of a target hly gene fragment and an internal amplification control (IAC). The IAC is a chimeric double-stranded DNA containing a fragment of the rapeseed BnACCg8 gene flanked by the hly-specific target sequences. This IAC is detected using a second TaqMan probe labeled with a different fluorophore, enabling the simultaneous monitoring of the hly and IAC signals. The hly-IAC assay had a specificity and sensitivity of 100%, as assessed using 49 L. monocytogenes isolates of different serotypes and 96 strains of nontarget bacteria, including 51 Listeria isolates. The detection and quantification limits were 8 and 30 genome equivalents, and the coefficients for PCR linearity (R2) and efficiency (E) were 0.997 and 0.80, respectively. We tested the performance of the hly-IAC Q-PCR assay using various broth media and food matrices. Fraser and half-Fraser media, raw pork, and raw or cold-smoked salmon were strongly PCR-inhibitory. This Q-PCR assay for L. monocytogenes, the first incorporating an IAC to be described for quantitative detection of a food-borne pathogen, is a simple and robust tool facilitating the identification of false negatives or underestimations of contamination loads due to PCR failure. PMID:16332910

Two methods for construction of internal amplification controls for the detection of Escherichia coli O157 by polymerase chain reaction.

PubMed

Abdulmawjood, A; Roth, S; Bülte, M

2002-10-01

For the detection of food born bacteria by polymerase chain reaction (PCR) in food products, an internal amplification control (IAC) is required in order to prevent false negative results that might be caused by PCR inhibitors. In the present study, two IACs were constructed using two different methods. These IACs were designed in a way that the same primer pair can be used to amplify the target DNA and coamplify the IAC. The first IAC with a size of approximately 200 bp was constructed by deleting a part of the amplicon of the original target DNA (500 bp) between the two primer sites to produce an IAC smaller than the target DNA. The second IAC with a size of approximately 600 bp was synthesized in a one step PCR reaction. The primers used in this reaction possessed 5' over-hanging ends, which were identical to the primers used in the diagnostic reaction, whereas their 3' ends were complementary to the (pUC19) predetermined DNA sequence of defined length and sequence. The concentration of IACs appeared to be critical. Too much IAC DNA template would out-compete the target DNA template, thus giving a false negative result. However the use of an optimal IAC concentration increased the reliability of the PCR assays and appeared to be useful for food diagnostics.

Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation

PubMed Central

Kuwahara, Tomomi; Yamashita, Atsushi; Hirakawa, Hideki; Nakayama, Haruyuki; Toh, Hidehiro; Okada, Natsumi; Kuhara, Satoru; Hattori, Masahira; Hayashi, Tetsuya; Ohnishi, Yoshinari

2004-01-01

Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major species, Bacteroides thetaiotaomicron (BT), concentrates within the colon. We find corresponding differences in their genomes, based on determination of the genome sequence of BF and comparative analysis with BT. Both species have acquired two mechanisms that contribute to their dominance among the colonic microbiota: an exceptional capability to use a wide range of dietary polysaccharides by gene amplification and the capacity to create variable surface antigenicities by multiple DNA inversion systems. However, the gene amplification for polysaccharide assimilation is more developed in BT, in keeping with its internal localization. In contrast, external antigenic structures can be changed more systematically in BF. Thereby, at the mucosal surface, where microbes encounter continuous attack by host defenses, BF evasion of the immune system is favored, and its colonization and infectious potential are increased. PMID:15466707

Amplification of ST50 gene using dry-reagent-based polymerase chain reaction for the detection of Salmonella typhi.

PubMed

Aziah, Ismail; Ravichandran, Manickam; Ismail, Asma

2007-12-01

Conventional polymerase chain reaction (PCR) testing requires many pipetting steps and has to be transported and stored in cold chain. To overcome these limitations, we designed a ready-to-use PCR test for Salmonella typhi using PCR reagents, primers against the ST50 gene of S. typhi, a built-in internal amplification control (IAC), and gel loading dye mixed and freeze-dried in a single tube. The 2-step dry-reagent-based assay was used to amplify a 1238-bp target gene and an 810-bp IAC gene from 73 BACTEC blood culture broths (33 true positives for S. typhi and 40 true negatives for non-S. typhi). The sensitivity, specificity, positive predictive value, and negative predictive value of the PCR assay were 87.9%, 100%, 100%, and 90.9%, respectively. We suggest that this rapid 2-step PCR test could be used for the rapid diagnosis of typhoid fever.

Parametric resonance in tunable superconducting cavities

NASA Astrophysics Data System (ADS)

Wustmann, Waltraut; Shumeiko, Vitaly

2013-05-01

We develop a theory of parametric resonance in tunable superconducting cavities. The nonlinearity introduced by the superconducting quantum interference device (SQUID) attached to the cavity and damping due to connection of the cavity to a transmission line are taken into consideration. We study in detail the nonlinear classical dynamics of the cavity field below and above the parametric threshold for the degenerate parametric resonance, featuring regimes of multistability and parametric radiation. We investigate the phase-sensitive amplification of external signals on resonance, as well as amplification of detuned signals, and relate the amplifier performance to that of linear parametric amplifiers. We also discuss applications of the device for dispersive qubit readout. Beyond the classical response of the cavity, we investigate small quantum fluctuations around the amplified classical signals. We evaluate the noise power spectrum both for the internal field in the cavity and the output field. Other quantum-statistical properties of the noise are addressed such as squeezing spectra, second-order coherence, and two-mode entanglement.

Rapid and sensitive identification of the herbal tea ingredient Taraxacum formosanum using loop-mediated isothermal amplification.

PubMed

Lai, Guan-Hua; Chao, Jung; Lin, Ming-Kuem; Chang, Wen-Te; Peng, Wen-Huang; Sun, Fang-Chun; Lee, Meng-Shiunn; Lee, Meng-Shiou

2015-01-09

Taraxacum formosanum (TF) is a medicinal plant used as an important component of health drinks in Taiwan. In this study, a rapid, sensitive and specific loop-mediated isothermal amplification (LAMP) assay for authenticating TF was established. A set of four specific LAMP primers was designed based on the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA (nrDNA) of TF. LAMP amplicons were successfully amplified and detected when purified genomic DNA of TF was added in the LAMP reaction under isothermal condition (65 °C) within 45 min. These specific LAMP primers have high specificity and can accurately discriminate Taraxacum formosanum from other adulterant plants; 1 pg of genomic DNA was determined to be the detection limit of the LAMP assay. In conclusion, using this novel approach, TF and its misused plant samples obtained from herbal tea markets were easily identified and discriminated by LAMP assay for quality control.

Rapid and Sensitive Identification of the Herbal Tea Ingredient Taraxacum formosanum Using Loop-Mediated Isothermal Amplification

PubMed Central

Lai, Guan-Hua; Chao, Jung; Lin, Ming-Kuem; Chang, Wen-Te; Peng, Wen-Huang; Sun, Fang-Chun; Lee, Meng-Shiunn; Lee, Meng-Shiou

2015-01-01

Taraxacum formosanum (TF) is a medicinal plant used as an important component of health drinks in Taiwan. In this study, a rapid, sensitive and specific loop-mediated isothermal amplification (LAMP) assay for authenticating TF was established. A set of four specific LAMP primers was designed based on the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA (nrDNA) of TF. LAMP amplicons were successfully amplified and detected when purified genomic DNA of TF was added in the LAMP reaction under isothermal condition (65 °C) within 45 min. These specific LAMP primers have high specificity and can accurately discriminate Taraxacum formosanum from other adulterant plants; 1 pg of genomic DNA was determined to be the detection limit of the LAMP assay. In conclusion, using this novel approach, TF and its misused plant samples obtained from herbal tea markets were easily identified and discriminated by LAMP assay for quality control. PMID:25584616

A split recognition mode combined with cascade signal amplification strategy for highly specific, sensitive detection of microRNA.

PubMed

Wang, Rui; Wang, Lei; Zhao, Haiyan; Jiang, Wei

2016-12-15

MicroRNAs (miRNAs) are vital for many biological processes and have been regarded as cancer biomarkers. Specific and sensitive detection of miRNAs is essential for cancer diagnosis and therapy. Herein, a split recognition mode combined with cascade signal amplification strategy is developed for highly specific and sensitive detection of miRNA. The split recognition mode possesses two specific recognition processes, which are based on toehold-mediated strand displacement reaction (TSDR) and direct hybridization reaction. Two recognition probes, hairpin probe (HP) with overhanging toehold domain and assistant probe (AP), are specially designed. Firstly, the toehold domain of HP and AP recognize part of miRNA simultaneously, accompanied with TSDR to unfold the HP and form the stable DNA Y-shaped junction structure (YJS). Then, the AP in YJS can further act as primer to initiate strand displacement amplification, releasing numerous trigger sequences. Finally, the trigger sequences hybridize with padlock DNA to initiate circular rolling circle amplification and generate enhanced fluorescence responses. In this strategy, the dual recognition effect of split recognition mode guarantees the excellent selectivity to discriminate let-7b from high-homology sequences. Furthermore, the high amplification efficiency of cascade signal amplification guarantees a high sensitivity with the detection limit of 3.2 pM and the concentration of let-7b in total RNA sample extracted from Hela cells is determined. These results indicate our strategy will be a promising miRNA detection strategy in clinical diagnosis and disease treatment. Copyright © 2016 Elsevier B.V. All rights reserved.

Bacteriophage Amplification-Coupled Detection and Identification of Bacterial Pathogens

NASA Astrophysics Data System (ADS)

Cox, Christopher R.; Voorhees, Kent J.

Current methods of species-specific bacterial detection and identification are complex, time-consuming, and often require expensive specialized equipment and highly trained personnel. Numerous biochemical and genotypic identification methods have been applied to bacterial characterization, but all rely on tedious microbiological culturing practices and/or costly sequencing protocols which render them impractical for deployment as rapid, cost-effective point-of-care or field detection and identification methods. With a view towards addressing these shortcomings, we have exploited the evolutionarily conserved interactions between a bacteriophage (phage) and its bacterial host to develop species-specific detection methods. Phage amplification-coupled matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to rapidly detect phage propagation resulting from species-specific in vitro bacterial infection. This novel signal amplification method allowed for bacterial detection and identification in as little as 2 h, and when combined with disulfide bond reduction methods developed in our laboratory to enhance MALDI-TOF-MS resolution, was observed to lower the limit of detection by several orders of magnitude over conventional spectroscopy and phage typing methods. Phage amplification has been combined with lateral flow immunochromatography (LFI) to develop rapid, easy-to-operate, portable, species-specific point-of-care (POC) detection devices. Prototype LFI detectors have been developed and characterized for Yersinia pestis and Bacillus anthracis, the etiologic agents of plague and anthrax, respectively. Comparable sensitivity and rapidity was observed when phage amplification was adapted to a species-specific handheld LFI detector, thus allowing for rapid, simple, POC bacterial detection and identification while eliminating the need for bacterial culturing or DNA isolation and amplification techniques.

Dynamics and control of DNA sequence amplification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marimuthu, Karthikeyan; Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu; Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054

2014-10-28

DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reactionmore » are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.« less

Prognostic relevance of Fédération Nationale des Centres de Lutte Contre le Cancer grade and MDM2 amplification levels in dedifferentiated liposarcoma: a study of 50 cases.

PubMed

Jour, George; Gullet, Ashley; Liu, Mingdong; Hoch, Benjamin L

2015-01-01

Dedifferentiated liposarcoma represents a form of liposarcoma composed of a non-lipogenic sarcoma associated with well-differentiated liposarcoma. The prognostic significance of histological grading of the dedifferentiated component remains to be elucidated due to vague grading criteria employed in previous studies. Molecular markers of tumor behavior, including amplification levels of murine double minute-2 (MDM2) and cyclin-dependent kinase-4 (CDK4) genes, have been explored in a limited number of cases. Here we investigate whether 'Fédération Nationale des Centres de Lutte Contre le Cancer' (FNCLCC) grade and MDM2 gene amplification levels have prognostic value in dedifferentiated liposarcoma in terms of local recurrence and disease-specific survival. Fifty cases were retrieved, reviewed and FNCLCC grade was scored for the dedifferentiated component. Testing for MDM2 gene amplification was performed by fluorescence in situ hybridization. Amplification was categorized as high level (≥20 copies) and as low level (<20 copies). Follow-up data was obtained through chart review. Log-rank test and Cox proportional hazard models were used to determine the effect of grade and level of MDM2 amplification on outcomes. Our series includes 50 patients (male n=28, female n=22) with an average age of 63 years (range, 28-88) and a median follow-up of 28 months (range, 2-120). Tumors were graded as grade 1 (6%), grade 2 (58%), and grade 3 (36%). When adjusted for age, sex, site, tumor size, and margin status, grade 3 patients had a higher recurrence rate than grades 1 and 2 (HR=2.07, 95% CI: 1.24, 7.62; P=0.015). Patients with high-level MDM2 amplification had higher recurrence rate on univariate analysis (P=0.028), but not on multivariate analysis (HR=1.69, 95% CI: 0.73, 3.94; P=0.221). FNCLCC grade 3 dedifferentiation confers a worse prognosis in dedifferentiated liposarcoma in terms of local recurrence. MDM2 amplification level remains a useful diagnostic tool in dedifferentiated liposarcoma, but has no prognostic value in terms of local recurrence.

High amplification of FGFR1 gene is a delayed poor prognostic factor in early stage ESCC patients

PubMed Central

Song, Qi; Liu, Yalan; Jiang, Dongxian; Wang, Haixing; Huang, Jie; Xu, Yifan; Sujie, Akesu; Zeng, Haiying; Xu, Chen; Hou, Yingyong

2017-01-01

Amplification of the fibroblast growth factor receptor 1 (FGFR1) is believed to predict response to FGFR inhibitors. The aim of this study was to investigate the frequency and the prognostic impact of FGFR1 amplification in patients with resected esophageal squamous cell carcinoma (ESCC) by using fluorescent in situ hybridization. Microarrayed paraffin embedded blocks were constructed, and the cohort of tissues came from 506 patients with ESCC. FGFR1 high amplification (FGFR1high) was defined by an FGFR1/centromere 8 ratio of ≥ 2.0, or average number of FGFR1 signals/tumor cell nucleus ≥ 6.0, or percentage of tumor cells containing ≥ 15 FGFR1 signals, or large cluster in ≥ 10% of cancer cells. FGFR1 low amplification was defined by ≥ 5 FGFR1 signals in ≥ 50% of cancer cells. Kaplan-Meier curves with log-rank tests and Cox proportional hazards model were used to analyze patients’ survival. Among 506 patients, high amplification, low amplification, and disomy were detected in 8.7%, 3.6% and 87.7%, respectively. In general, the FGFR1high group trended towards worse disease-free survival (DFS) and overall survival (OS) compared to the FGFR1 low amplification/disomy (FGFR1low/disomy) group (DFS, P=0.108; OS, P=0.112), but this trend was amplified for patients with DFS ≥ 30 months (DFS, P=0.009; OS, P=0.007). Furthermore, when patients were stratified into stage I-II and stage III-IV, the FGFR1high group directly presented with adverse DFS and OS than the FGFR1low/disomy group in stage I-II patients (DFS, P=0.019; OS, P=0.034), especially with DFS ≥ 30 months (DFS, P=0.002; OS, P=0.001). However, for patients in stage III-IV, FGFR1high had no effect on prognosis regardless of DFS time. FGFR1high occurs in a minority of ESCC, and it predicts delayed poor prognosis in stage I and II ESCC patients. PMID:29088806

Free circulating nucleic acids in plasma and serum as a novel approach to the use of internal controls in real time PCR based detection.

PubMed

Karataylı, Ersin; Altunoğlu, Yasemin Çelik; Karataylı, Senem Ceren; Yurdaydın, Cihan; Bozdayı, A Mithat

2014-10-01

Internal controls (ICs), are the main components of any real-time PCR based amplification methods, which are co-purified and co-amplified with the actual target. The existence of free circulating nucleic acids in plasma and serum (CNAPS) has been known for many years. The aim of this study was to verify whether CNAPS can be used as ICs in real-time PCR based detection and quantification of DNA or RNA targets in plasma and serum samples. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a housekeeping gene, was chosen at random as CNAPS to serve as an intrinsic internal control in two different real-time PCR based quantification models in plasma and serum. Viral loads of hepatitis B virus (HBV) DNA and hepatitis delta virus (HDV) RNA were quantified as actual targets in parallel to GAPDH as IC in a total of 519 serum or plasma samples including 21 healthy controls, 202 positive chronic hepatitis delta patients, 37 chronic hepatitis C patients, 168 chronic hepatitis B patients, 52 patients with hepatocellular carcinoma, and 39 patients with non-alcoholic steatohepatitis/non-alcoholic fatty liver disease. GAPDH levels did not show significant variance in different patient groups and yielded positive signals in all 519 patients with persistent cycle threshold (CT) values 27.85±1.57 (mean±standard deviation (SD)). Reproducibility of the GAPDH amplification in HDV RNA and HBV DNA quantifications was shown with a SD value of CT ranging from 0.42 to 2.14 (mean SD; 1.18) and 0.24 to 1.75 (mean SD; 1.03), respectively. In conclusion, the freely circulating nucleic acids can clearly be used as internal controls for real-time PCR based detection and quantification of any RNA and mainly DNA targets (pathogens) in serum or plasma and this simply excludes the compulsory external addition of any IC molecules into the reaction. Copyright © 2014 Elsevier B.V. All rights reserved.

Extrachromosomal oncogene amplification drives tumor evolution and genetic heterogeneity

PubMed Central

Turner, Kristen M.; Deshpande, Viraj; Beyter, Doruk; Koga, Tomoyuki; Rusert, Jessica; Lee, Catherine; Li, Bin; Arden, Karen; Ren, Bing; Nathanson, David A.; Kornblum, Harley I.; Taylor, Michael D.; Kaushal, Sharmeela; Cavenee, Webster K.; Wechsler-Reya, Robert; Furnari, Frank B.; Vandenberg, Scott R.; Rao, P. Nagesh; Wahl, Geoffrey M.; Bafna, Vineet; Mischel, Paul S.

2017-01-01

Human cells have twenty-three pairs of chromosomes but in cancer, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ECDNA), whose frequency and functional significance are not understood1–4. We performed whole genome sequencing, structural modeling and cytogenetic analyses of 17 different cancer types, including 2572 metaphases, and developed ECdetect to conduct unbiased integrated ECDNA detection and analysis. ECDNA was found in nearly half of human cancers varying by tumor type, but almost never in normal cells. Driver oncogenes were amplified most commonly on ECDNA, elevating transcript level. Mathematical modeling predicted that ECDNA amplification elevates oncogene copy number and increases intratumoral heterogeneity more effectively than chromosomal amplification, which we validated by quantitative analyses of cancer samples. These results suggest that ECDNA contributes to accelerated evolution in cancer. PMID:28178237

Use of a nested PCR-enzyme immunoassay with an internal control to detect Chlamydophila psittaci in turkeys

PubMed Central

Van Loock, Marnix; Verminnen, Kristel; Messmer, Trudy O; Volckaert, Guido; Goddeeris, Bruno M; Vanrompay, Daisy

2005-01-01

Background Laboratory diagnosis of Chlamydophila psittaci, an important turkey respiratory pathogen, is difficult. To facilitate the diagnosis, a nested PCR-enzyme immunoassay (PCR-EIA) was developed to detect the Cp. psittaci outer membrane protein A (ompA) gene in pharyngeal swabs. Methods The fluorescein-biotin labelled PCR products were immobilized on streptavidin-coated microtiter plates and detected with anti-fluorescein peroxidase conjugate and a colorimetric substrate. An internal inhibition control was included to rule out the presence of inhibitors of DNA amplification. The diagnostic value of the ompA nested PCR-EIA in comparison to cell culture and a 16S-rRNA based nested PCR was assessed in pharyngeal turkey swabs from 10 different farms experiencing respiratory disease. Results The sensitivity of the nested PCR-EIA was established at 0.1 infection forming units (IFU). Specificity was 100%. The ompA nested PCR-EIA was more sensitive than the 16S-rRNA based nested PCR and isolation, revealing 105 out of 200 (52.5%) positives against 13 and 74 for the latter two tests, respectively. Twenty-nine (23.8%) out of 122 ompA PCR-EIA negatives showed the presence of inhibitors of DNA amplification, although 27 of them became positive after diluting (1/10) the specimens in PCR buffer or after phenol-chloroform extraction and subsequent ethanol precipitation. Conclusion The present study stresses the need for an internal control to confirm PCR true-negatives and demonstrates the high prevalence of chlamydiosis in Belgian turkeys and its potential zoonotic risk. The ompA nested PCR-EIA described here is a rapid, highly sensitive and specific diagnostic assay and will help to facilitate the diagnosis of Cp. psittaci infections in both poultry and man. PMID:16185353

Calibration of BK Virus Nucleic Acid Amplification Testing to the 1st WHO International Standard for BK Virus

PubMed Central

Tan, Susanna K.; Milligan, Stephen; Sahoo, Malaya K.; Taylor, Nathaniel

2017-01-01

ABSTRACT Significant interassay variability in the quantification of BK virus (BKV) DNA precludes establishing broadly applicable thresholds for the management of BKV infection in transplantation. The 1st WHO International Standard for BKV (primary standard) was introduced in 2016 as a common calibrator for improving the harmonization of BKV nucleic acid amplification testing (NAAT) and enabling comparisons of biological measurements worldwide. Here, we evaluated the Altona RealStar BKV assay (Altona) and calibrated the results to the international unit (IU) using the Exact Diagnostics BKV verification panel, a secondary standard traceable to the primary standard. The primary and secondary standards on Altona had nearly identical linear regression equations (primary standard, Y = 1.05X − 0.28, R2 = 0.99; secondary standard, Y = 1.04X − 0.26, R2 = 0.99) and conversion factors (primary standard, 1.11 IU/copy; secondary standard, 1.09 IU/copy). A comparison of Altona with a laboratory-developed BKV NAAT assay in IU/ml versus copies/ml using Passing-Bablok regression revealed similar regression lines, no proportional bias, and improvement in the systematic bias (95% confidence interval of intercepts: copies/ml, −0.52 to −1.01; IU/ml, 0.07 to −0.36). Additionally, Bland-Altman analyses revealed a clinically significant reduction of bias when results were reported in IU/ml (IU/ml, −0.10 log10; copies/ml, −0.70 log10). These results indicate that the use of a common calibrator improved the agreement between the two assays. As clinical laboratories worldwide use calibrators traceable to the primary standard to harmonize BKV NAAT results, we anticipate improved interassay comparisons with a potential for establishing broadly applicable quantitative BKV DNA load cutoffs for clinical practice. PMID:28053213

Quantification of Campylobacter spp. in pig feces by direct real-time PCR with an internal control of extraction and amplification.

PubMed

Leblanc-Maridor, Mily; Garénaux, Amélie; Beaudeau, François; Chidaine, Bérangère; Seegers, Henri; Denis, Martine; Belloc, Catherine

2011-04-01

The rapid and direct quantification of Campylobacter spp. in complex substrates like feces or environmental samples is crucial to facilitate epidemiological studies on Campylobacter in pig production systems. We developed a real-time PCR assay for detecting and quantifying Campylobacter spp. directly in pig feces with the use of an internal control. Campylobacter spp. and Yersinia ruckeri primers-probes sets were designed and checked for specificity with diverse Campylobacter, related organisms, and other bacterial pathogens before being used in field samples. The quantification of Campylobacter spp. by the real-time PCR then was realized on 531 fecal samples obtained from experimentally and naturally infected pigs; the numeration of Campylobacter on Karmali plate was done in parallel. Yersinia ruckeri, used as bacterial internal control, was added to the samples before DNA extraction to control DNA-extraction and PCR-amplification. The sensitivity of the PCR assay was 10 genome copies. The established Campylobacter real-time PCR assay showed a 7-log-wide linear dynamic range of quantification (R²=0.99) with a detection limit of 200 Colony Forming Units of Campylobacter per gram of feces. A high correlation was found between the results obtained by real-time PCR and those by culture at both qualitative and quantitative levels. Moreover, DNA extraction followed by real-time PCR reduced the time needed for analysis to a few hours (within a working day). In conclusion, the real-time PCR developed in this study provides new tools for further epidemiological surveys to investigate the carriage and excretion of Campylobacter by pigs. Copyright © 2011 Elsevier B.V. All rights reserved.

Re-Evaluation of the PBAN Receptor Molecule: Characterization of PBANR Variants Expressed in the Pheromone Glands of Moths

PubMed Central

Lee, Jae Min; Hull, J. Joe; Kawai, Takeshi; Goto, Chie; Kurihara, Masaaki; Tanokura, Masaru; Nagata, Koji; Nagasawa, Hiromichi; Matsumoto, Shogo

2011-01-01

Sex pheromone production in most moths is initiated following pheromone biosynthesis activating neuropeptide receptor (PBANR) activation. PBANR was initially cloned from pheromone glands (PGs) of Helicoverpa zea and Bombyx mori. The B. mori PBANR is characterized by a relatively long C-terminus that is essential for ligand-induced internalization, whereas the H. zea PBANR has a shorter C-terminus that lacks features present in the B. mori PBANR critical for internalization. Multiple PBANRs have been reported to be concurrently expressed in the larval CNS of Heliothis virescens. In the current study, we sought to examine the prevalence of multiple PBANRs in the PGs of three moths and to ascertain their potential functional relevance. Multiple PBANR variants (As, A, B, and C) were cloned from the PGs of all species examined with PBANR-C the most highly expressed. Alternative splicing of the C-terminal coding sequence of the PBAN gene gives rise to the variants, which are distinguishable only by the length and composition of their respective C-terminal tails. Transient expression of fluorescent PBANR chimeras in insect cells revealed that PBANR-B and PBANR-C localized exclusively to the cell surface while PBANR-As and PBANR-A exhibited varying degrees of cytosolic localization. Similarly, only the PBANR-B and PBANR-C variants underwent ligand-induced internalization. Taken together, our results suggest that PBANR-C is the principal receptor molecule involved in PBAN signaling regardless of moth species. The high GC content of the C-terminal coding sequence in the B and C variants, which makes amplification using conventional polymerases difficult, likely accounts for previous “preferential” amplification of PBANR-A like receptors from other species. PMID:22654850

The evolution of inducible defence.

PubMed

Harvell, C D

1990-01-01

Defences against parasites are characterized by inducible, amplifiable responses, often with a memory component. Inducible defences with similar properties are common in a variety of other types of interactions, for example many aquatic invertebrates produce inducible structural defences against their predators and competitors. Most inducible defences have the following properties: (1) a threshold of activation; (2) an amplification of response with increasing stimulus; (3) a memory component. Specificity, amplification and memory are the basis for defining a defence as 'immune' (Klein, 1982), and these properties are present in both the vertebrate and invertebrate internal defence responses to pathogens. Invertebrates differ in the absence of immunoglobulins and therefore in reduced specificity. Although the reduced specificity of invertebrate internal defence systems is often viewed as proof of their 'primitiveness', the differences in defence systems of vertebrates and invertebrates may be more related to their respective selection regimes than to phylogeny. The syngeneic recognition system of vertebrates functions to recognize small departures from self, such as would arise from neoplasia. Are vertebrates under more intense selection from neoplasia, perhaps due to a greater incidence of hormonal imbalance or hypersensitivity reactions? The invertebrate internal defence systems are all less discriminating than the vertebrate, but there are marked differences in degree of discrimination depending on whether the group is colonial or not. Even the phyla of colonial animals with quite simple body plans, the sponges and cnidarians, have a more discriminating recognition system than the phyla of solitary animals with more complex body plans, such as the molluscs and arthropods. The primary effectors of all invertebrate responses to parasites are encapsulation and phagocytosis, although in some phyla there are specific antibacterial proteins than can also be induced.(ABSTRACT TRUNCATED AT 250 WORDS)

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

PubMed

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.

Synergistic Activation upon MET and ALK Coamplification Sustains Targeted Therapy in Sarcomatoid Carcinoma, a Deadly Subtype of Lung Cancer.

PubMed

Pelosi, Giuseppe; Gasparini, Patrizia; Conte, Davide; Fabbri, Alessandra; Perrone, Federica; Tamborini, Elena; Pupa, Serenella M; Ciravolo, Valentina; Caserini, Roberto; Rossi, Giulio; Cavazza, Alberto; Papotti, Mauro; Nakatani, Yukio; Maisonneuve, Patrick; Pastorino, Ugo; Sozzi, Gabriella

2016-05-01

Genetic alterations suitable for targeted therapy are poorly known issues in pulmonary sarcomatoid carcinoma (PSC), an uncommon and life-threatening family of non-small cell lung cancers. Ninety-eight PSCs were assessed for MNNG HOS Transforming gene (MET) and anaplastic lymphoma receptor tyrosine kinase gene (ALK) status by fluorescence in situ hybridization (FISH) and for relevant protein expression by immunohistochemical analysis, also taking advantage of phosphorylated (p-) antibodies. Moreover, levels of ALK and MET mRNA were also determined by real-time polymerase chain reaction and Western blot analysis for downstream activation pathways involving p-MET, p-protein kinase B, p-mitogen-activated protein kinase, p-SRC proto-oncogene tyrosine-protein kinase, and p-focal adhesion kinase (p-FAK). MET amplification was detected by FISH in 25 of 98 PSCs (25.6%) and ALK amplification (but not the relevant rearrangement) was found in 16 of 98 (16.3%), with all ALK-amplified tumors also showing MET amplification (p < 0.0001). Nine PSCs, however, showed MET amplification without any ALK gene alteration. ALK protein expression was always lacking, whereas MET and p-MET were confined to the relevant amplified tumors only. Increased levels of ALK and MET mRNA were detectable in tumors with no direct relationship between mRNA content, protein expression, or alterations detected by FISH. Western blot assays showed complete activation of downstream signal pathways up to p-SRC proto-oncogene tyrosine-protein kinase, and p-focal adhesion kinase recruitment in MET and ALK-coamplified tumors only, whereas isolated MET amplification, MET and ALK borderline amplification (5%-10% of tumor cells with ≥15 copies of the relevant gene), or negative tumors showing eusomy or chromosome polysomy were confined to p-mitogen-activated protein kinase, p-protein kinase B, and/or p-MET activation. Multivariate survival analysis pushed a higher percentage of MET altered cells or a higher value of MET copy gain per cell to marginally emerge for overall survival (p = 0.140) and disease-free survival (p = 0.060), respectively. ALK and MET seemed to act as synergistic, nonrandom coactivators of downstream signal when coamplified in a subset of patients with PSC, thus likely suggesting a combined mechanism of oncogene addiction. These alterations could be a suitable target for therapy based on specific inhibitors. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Accurate modeling of high-repetition rate ultrashort pulse amplification in optical fibers

PubMed Central

Lindberg, Robert; Zeil, Peter; Malmström, Mikael; Laurell, Fredrik; Pasiskevicius, Valdas

2016-01-01

A numerical model for amplification of ultrashort pulses with high repetition rates in fiber amplifiers is presented. The pulse propagation is modeled by jointly solving the steady-state rate equations and the generalized nonlinear Schrödinger equation, which allows accurate treatment of nonlinear and dispersive effects whilst considering arbitrary spatial and spectral gain dependencies. Comparison of data acquired by using the developed model and experimental results prove to be in good agreement. PMID:27713496

Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steven, Blaire; Hesse, Cedar; Soghigian, John

The use of rRNA/DNA ratios derived from surveys of rRNA sequences in RNA and DNA extracts is an appealing but poorly validated approach to infer the activity status of environmental microbes. To improve the interpretation of rRNA/DNA ratios, we performed simulations to investigate the effects of community structure, rRNA amplification, and sampling depth on the accuracy of rRNA/DNA ratios in classifying bacterial populations as “active” or “dormant.” Community structure was an insignificant factor. In contrast, the extent of rRNA amplification that occurs as cells transition from dormant to growing had a significant effect (P < 0.0001) on classification accuracy, withmore » misclassification errors ranging from 16 to 28%, depending on the rRNA amplification model. The error rate increased to 47% when communities included a mixture of rRNA amplification models, but most of the inflated error was false negatives (i.e., active populations misclassified as dormant). Sampling depth also affected error rates (P < 0.001). Inadequate sampling depth produced various artifacts that are characteristic of rRNA/DNA ratios generated from real communities. These data show important constraints on the use of rRNA/DNA ratios to infer activity status. Whereas classification of populations as active based on rRNA/DNA ratios appears generally valid, classification of populations as dormant is potentially far less accurate.« less

Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant

DOE PAGES

Steven, Blaire; Hesse, Cedar; Soghigian, John; ...

2017-03-31

The use of rRNA/DNA ratios derived from surveys of rRNA sequences in RNA and DNA extracts is an appealing but poorly validated approach to infer the activity status of environmental microbes. To improve the interpretation of rRNA/DNA ratios, we performed simulations to investigate the effects of community structure, rRNA amplification, and sampling depth on the accuracy of rRNA/DNA ratios in classifying bacterial populations as “active” or “dormant.” Community structure was an insignificant factor. In contrast, the extent of rRNA amplification that occurs as cells transition from dormant to growing had a significant effect (P < 0.0001) on classification accuracy, withmore » misclassification errors ranging from 16 to 28%, depending on the rRNA amplification model. The error rate increased to 47% when communities included a mixture of rRNA amplification models, but most of the inflated error was false negatives (i.e., active populations misclassified as dormant). Sampling depth also affected error rates (P < 0.001). Inadequate sampling depth produced various artifacts that are characteristic of rRNA/DNA ratios generated from real communities. These data show important constraints on the use of rRNA/DNA ratios to infer activity status. Whereas classification of populations as active based on rRNA/DNA ratios appears generally valid, classification of populations as dormant is potentially far less accurate.« less

Recovery of viral RNA and infectious foot-and-mouth disease virus from positive lateral-flow devices.

PubMed

Fowler, Veronica L; Bankowski, Bartlomiej M; Armson, Bryony; Di Nardo, Antonello; Valdazo-Gonzalez, Begoña; Reid, Scott M; Barnett, Paul V; Wadsworth, Jemma; Ferris, Nigel P; Mioulet, Valérie; King, Donald P

2014-01-01

Foot-and-mouth disease Virus (FMDV) is an economically important, highly contagious picornavirus that affects both wild and domesticated cloven hooved animals. In developing countries, the effective laboratory diagnosis of foot-and-mouth disease (FMD) is often hindered by inadequate sample preservation due to difficulties in the transportation and storage of clinical material. These factors can compromise the ability to detect and characterise FMD virus in countries where the disease is endemic. Furthermore, the high cost of sending infectious virus material and the biosecurity risk it presents emphasises the need for a thermo-stable, non-infectious mode of transporting diagnostic samples. This paper investigates the potential of using FMDV lateral-flow devices (LFDs) for dry transportation of clinical samples for subsequent nucleic acid amplification, sequencing and recovery of infectious virus by electroporation. FMDV positive samples (epithelial suspensions and cell culture isolates) representing four FMDV serotypes were applied to antigen LFDs: after which it was possible to recover viral RNA that could be detected using real-time RT-PCR. Using this nucleic acid, it was also possible to recover VP1 sequences and also successfully utilise protocols for amplification of complete FMD virus genomes. It was not possible to recover infectious FMDV directly from the LFDs, however following electroporation into BHK-21 cells and subsequent cell passage, infectious virus could be recovered. Therefore, these results support the use of the antigen LFD for the dry, non-hazardous transportation of samples from FMD endemic countries to international reference laboratories.

Development and application of reverse transcription loop-mediated isothermal amplification for detecting live Shewanella putrefaciens in preserved fish sample.

PubMed

Li, Chenghua; Ying, Qi; Su, Xiurong; Li, Taiwu

2012-04-01

Given that live Shewanella putrefaciens is one of the major causes of spoilage for aquatic products even in chill storage, the rapid and accurate detection process is the first priority. In the present study, a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) detecting assay was developed by targeting internal transcribed spacer (ITS) sequence between 16S and 23S rRNA. At the same time, a new procaryotic mRNA isolation strategy was also established by introducing a polyA tail to RNA during cDNA synthesis step. Under the optimal reaction time (60 min) and temperature (64.1 °C), S. putrefaciens could be specially identified from a variety of other tested bacteria by RT-LAMP. The sensitivity analysis showed that RT-LAMP could be identified as lower as 5.4 copies per reaction, which is over 200-fold higher than that of standard PCR (1.08 × 10³ copies per reaction). The method could be effectively identified S. putrefaciens in artificially contaminated or spoilaged fish samples with dose-dependent manners. To our knowledge, this is the first report using RT-LAMP assay to detect live S. putrefaciens in fish. The study provided a rapid and accurate detection method for live bacteria in aquatic food and established a new procaryotic mRNA isolation strategy at the same time, which will be useful for food preservation. © 2012 Institute of Food Technologists®

Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations

NASA Astrophysics Data System (ADS)

Samoilov, Michael; Plyasunov, Sergey; Arkin, Adam P.

2005-02-01

Stochastic effects in biomolecular systems have now been recognized as a major physiologically and evolutionarily important factor in the development and function of many living organisms. Nevertheless, they are often thought of as providing only moderate refinements to the behaviors otherwise predicted by the classical deterministic system description. In this work we show by using both analytical and numerical investigation that at least in one ubiquitous class of (bio)chemical-reaction mechanisms, enzymatic futile cycles, the external noise may induce a bistable oscillatory (dynamic switching) behavior that is both quantitatively and qualitatively different from what is predicted or possible deterministically. We further demonstrate that the noise required to produce these distinct properties can itself be caused by a set of auxiliary chemical reactions, making it feasible for biological systems of sufficient complexity to generate such behavior internally. This new stochastic dynamics then serves to confer additional functional modalities on the enzymatic futile cycle mechanism that include stochastic amplification and signaling, the characteristics of which could be controlled by both the type and parameters of the driving noise. Hence, such noise-induced phenomena may, among other roles, potentially offer a novel type of control mechanism in pathways that contain these cycles and the like units. In particular, observations of endogenous or externally driven noise-induced dynamics in regulatory networks may thus provide additional insight into their topology, structure, and kinetics. network motif | signal transduction | chemical reaction | synthetic biology | systems biology

Heterogeneous distribution of alectinib in neuroblastoma xenografts revealed by matrix-assisted laser desorption ionization mass spectrometry imaging: a pilot study.

PubMed

Ryu, Shoraku; Hayashi, Mitsuhiro; Aikawa, Hiroaki; Okamoto, Isamu; Fujiwara, Yasuhiro; Hamada, Akinobu

2018-01-01

The penetration of the anaplastic lymphoma kinase (ALK) inhibitor alectinib in neuroblastomas and the relationship between alectinib and ALK expression are unknown. The aim of this study was to perform a quantitative investigation of the inter- and intra-tumoural distribution of alectinib in different neuroblastoma xenograft models using matrix-assisted laser desorption ionization MS imaging (MALDI-MSI). The distribution of alectinib in NB1 (ALK amplification) and SK-N-FI (ALK wild-type) xenograft tissues was analysed using MALDI-MSI. The abundance of alectinib in tumours and intra-tumoural areas was quantified using ion signal intensities from MALDI-MSI after normalization by correlation with LC-MS/MS. The distribution of alectinib was heterogeneous in neuroblastomas. The penetration of alectinib was not significantly different between ALK amplification and ALK wide-type tissues using both LC-MS/MS concentrations and MSI intensities. Normalization with an internal standard increased the quantitative property of MSI by adjusting for the ion suppression effect. The distribution of alectinib in different intra-tumoural areas can alternatively be quantified from MS images by correlation with LC-MS/MS. The penetration of alectinib into tumour tissues may not be homogenous or influenced by ALK expression in the early period after single-dose administration. MALDI-MSI may prove to be a valuable pharmaceutical method for elucidating the mechanism of action of drugs by clarifying their microscopic distribution in heterogeneous tissues. © 2017 The British Pharmacological Society.

Amplification volume reduction on DNA database samples using FTA™ Classic Cards.

PubMed

Wong, Hang Yee; Lim, Eng Seng Simon; Tan-Siew, Wai Fun

2012-03-01

The DNA forensic community always strives towards improvements in aspects such as sensitivity, robustness, and efficacy balanced with cost efficiency. Therefore our laboratory decided to study the feasibility of PCR amplification volume reduction using DNA entrapped in FTA™ Classic Card and to bring cost savings to the laboratory. There were a few concerns the laboratory needed to address. First, the kinetics of the amplification reaction could be significantly altered. Second, an increase in sensitivity might affect interpretation due to increased stochastic effects even though they were pristine samples. Third, statics might cause FTA punches to jump out of its allocated well into another thus causing sample-to-sample contamination. Fourth, the size of the punches might be too small for visual inspection. Last, there would be a limit to the extent of volume reduction due to evaporation and the possible need of re-injection of samples for capillary electrophoresis. The laboratory had successfully optimized a reduced amplification volume of 10 μL for FTA samples. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Development and validation of the AmpFℓSTR® Identifiler® Direct PCR Amplification Kit: a multiplex assay for the direct amplification of single-source samples.

PubMed

Wang, Dennis Y; Chang, Chien-Wei; Lagacé, Robert E; Oldroyd, Nicola J; Hennessy, Lori K

2011-07-01

The AmpFℓSTR(®) Identifiler(®) Direct PCR Amplification Kit is a new short tandem repeat multiplex assay optimized to allow the direct amplification of single-source blood and buccal samples on FTA(®) card without the need for sample purification and quantification. This multiplex assay has been validated according to the FBI/National Standards and SWGDAM guidelines. Validation results revealed that slight variations in primer concentration, master mix component concentration, and thermal cycling parameters did not affect the performance of the chemistry. The assay's sensitivity was demonstrated by amplifying known amounts of white blood cells spotted onto FTA(®) cards, and the assay's specificity was verified by establishing minimal cross-reactivity with nonhuman DNA. No effect on the age of the sample stored on the FTA(®) substrate was observed and full concordance was established in the population study. These findings of the validation study support the use of the Identifiler(®) Direct Kit for forensic standards and database samples genotyping. © 2011 American Academy of Forensic Sciences.

Development of Reverse Transcription Thermostable Helicase-Dependent DNA Amplification for the Detection of Tomato Spotted Wilt Virus.

PubMed

Wu, Xinghai; Chen, Chanfa; Xiao, Xizhi; Deng, Ming Jun

2016-11-01

A protocol for the reverse transcription-helicase-dependent amplification (RT-HDA) of isothermal DNA was developed for the detection of tomato spotted wilt virus (TSWV). Specific primers, which were based on the highly conserved region of the N gene sequence in TSWV, were used for the amplification of virus's RNA. The LOD of RT-HDA, reverse transcriptase-loop-mediated isothermal amplification (RT-LAMP), and reverse transcriptase-polymerase chain reaction (RT-PCR) assays were conducted using 10-fold serial dilution of RNA eluates. TSWV sensitivity in RT-HDA and RT-LAMP was 4 pg RNA compared with 40 pg RNA in RT-PCR. The specificity of RT-HDA for TSWV was high, showing no cross-reactivity with other tomato and Tospovirus viruses including cucumber mosaic virus (CMV), tomato black ring virus (TBRV), tomato mosaic virus (ToMV), or impatiens necrotic spot virus (INSV). The RT-HDA method is effective for the detection of TSWV in plant samples and is a potential tool for early and rapid detection of TSWV.

Optimization of noise in non-integrated instrumentation amplifier for the amplification of very low electrophysiological [corrected] signals. Case of electro cardio graphic signals (ECG).

PubMed

Ngounou, Guy Merlin; Kom, Martin

2014-12-01

In this paper we present an instrumentation amplifier with discrete elements and optimized noise for the amplification of very low signals. In amplifying signals of very weak amplitude, the noise can completely absorb these signals if the used amplifier does not present the optimal guarantee to minimize the noise. Based on related research and re-viewing of recent patents Journal of Medical Systems, 30:205-209, 2006, we suggest an approach of noise reduction in amplification much more thoroughly than re-viewing of recent patents and we deduce from it the general criteria necessary and essential to achieve this optimization. The comparison of these criteria with the provisions adopted in practice leads to the inadequacy of conventional amplifiers for effective noise reduction. The amplifier we propose is an instrumentation amplifier with active negative feedback and optimized noise for the amplification of signals with very low amplitude. The application of this method in the case of electro cardio graphic signals (ECG) provides simulation results fully in line with forecasts.

Optimized thermal amplification in a radiative transistor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prod'homme, Hugo; Ordonez-Miranda, Jose; Ezzahri, Younes, E-mail: younes.ezzahri@univ-poitiers.fr

The thermal performance of a far-field radiative transistor made up of a VO{sub 2} base in between a blackbody collector and a blackbody emitter is theoretically studied and optimized. This is done by using the grey approximation on the emissivity of VO{sub 2} and deriving analytical expressions for the involved heat fluxes and transistor amplification factor. It is shown that this amplification factor can be maximized by tuning the base temperature close to its critical one, which is determined by the temperature derivative of the VO{sub 2} emissivity and the equilibrium temperatures of the collector and emitter. This maximization ismore » the result of the presence of two bi-stable temperatures appearing during the heating and cooling processes of the VO{sub 2} base and enables a thermal switching (temperature jump) characterized by a sizeable variation of the collector-to-base and base-to-emitter heat fluxes associated with a slight change of the applied power to the base. This switching effect leads to the optimization of the amplification factor and therefore it could be used for thermal modulation purposes.« less

Enhanced sequencing coverage with digital droplet multiple displacement amplification

PubMed Central

Sidore, Angus M.; Lan, Freeman; Lim, Shaun W.; Abate, Adam R.

2016-01-01

Sequencing small quantities of DNA is important for applications ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associated mutations. To obtain sufficient quantities of DNA for sequencing, the small amount of starting material must be amplified significantly. However, existing methods often yield errors or non-uniform coverage, reducing sequencing data quality. Here, we describe digital droplet multiple displacement amplification, a method that enables massive amplification of low-input material while maintaining sequence accuracy and uniformity. The low-input material is compartmentalized as single molecules in millions of picoliter droplets. Because the molecules are isolated in compartments, they amplify to saturation without competing for resources; this yields uniform representation of all sequences in the final product and, in turn, enhances the quality of the sequence data. We demonstrate the ability to uniformly amplify the genomes of single Escherichia coli cells, comprising just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of unamplified material. Digital droplet multiple displacement amplification provides a simple and effective method for amplifying minute amounts of DNA for accurate and uniform sequencing. PMID:26704978

Direct and quantitative detection of HIV-1 RNA in human plasma with a branched DNA signal amplification assay.

PubMed

Urdea, M S; Wilber, J C; Yeghiazarian, T; Todd, J A; Kern, D G; Fong, S J; Besemer, D; Hoo, B; Sheridan, P J; Kokka, R

1993-11-01

To determine the relative effect of sample matrix on the quantitation of HIV RNA in plasma. Two HIV-positive specimens were diluted into five and 10 different HIV-negative plasma samples, respectively. Branched DNA signal amplification technology and reverse-transcriptase polymerase chain reaction were used to measure the viral load. In one sample the viral load by polymerase chain reaction ranged from undetectable to 1.9 x 10(5) copies/ml, and the branched DNA results ranged from 2.6 x 10(4) to 4.2 x 10(4) HIV RNA equivalent/ml. In the other sample the corresponding figures were 6.3 x 10(4) to 5.5 x 10(5) copies/ml and 5.7 x 10(4) to 7.5 x 10(4) HIV RNA equivalents/ml. In contrast to reverse-transcriptase polymerase chain reaction the branched DNA signal amplification assay does not require a separate extraction step or enzymatic amplification of the target. Therefore this measurement is less affected by the sample matrix and the signal generated is directly proportional to the viral load.

Towards in vivo amplification: Overcoming hurdles in the use of hematopoietic stem cells in transplantation and gene therapy

PubMed Central

Nagree, Murtaza S; López-Vásquez, Lucía; Medin, Jeffrey A

2015-01-01

With the advent of safer and more efficient gene transfer methods, gene therapy has become a viable solution for many inherited and acquired disorders. Hematopoietic stem cells (HSCs) are a prime cell compartment for gene therapy aimed at correcting blood-based disorders, as well as those amenable to metabolic outcomes that can effect cross-correction. While some resounding clinical successes have recently been demonstrated, ample room remains to increase the therapeutic output from HSC-directed gene therapy. In vivo amplification of therapeutic cells is one avenue to achieve enhanced gene product delivery. To date, attempts have been made to provide HSCs with resistance to cytotoxic drugs, to include drug-inducible growth modules specific to HSCs, and to increase the engraftment potential of transduced HSCs. This review aims to summarize amplification strategies that have been developed and tested and to discuss their advantages along with barriers faced towards their clinical adaptation. In addition, next-generation strategies to circumvent current limitations of specific amplification schemas are discussed. PMID:26730268

Contextual amplification or attenuation of the impact of pubertal timing on Mexican-origin boys' mental health symptoms.

PubMed

White, Rebecca M B; Deardorff, Julianna; Liu, Yu; Gonzales, Nancy A

2013-12-01

To examine the role of neighborhood contextual variation in the putative association between pubertal timing and internalizing and externalizing symptoms among Mexican-origin boys. In a sample of seventh-grade Mexican-origin boys (N = 353; x¯age=12.8years) we assessed a range of secondary sexual characteristics, internalizing, and externalizing symptoms. Reports on all secondary sexual characteristics were collapsed and age-standardized to represent total pubertal timing. We also distinguished between the timing of physical changes driven by adrenal versus gonadal maturation. Boys' residential addresses were geocoded and American Community Survey data were used to describe neighborhoods along two dimensions: ethnic concentration and socioeconomic disadvantage. Three years later (in 10th grade) we re-assessed internalizing and externalizing symptoms. We examined the moderating influence of neighborhood ethnic concentration and neighborhood socioeconomic disadvantage on the prospective associations between puberty timing (total, gonadal, adrenal) and internalizing and externalizing symptoms. Earlier total pubertal timing predicted increases in externalizing symptoms, but only when Mexican-origin boys lived in neighborhoods low on ethnic concentration. Total timing results for externalizing symptoms were replicated for adrenal timing. Furthermore, early adrenal timing predicted increases in internalizing symptoms, but again, only when boys lived in neighborhoods low on ethnic concentration. No effects were observed for gonadal timing specifically. Early pubertal timing, especially advanced physical changes initiated and regulated by adrenal maturation, have important implications for Mexican-origin boys' internalizing and externalizing symptoms, but these implications depend on neighborhood characteristics. Ethnically concentrated neighborhoods are protective for early-maturing Mexican-origin boys. Copyright © 2013 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

On the Horn Effect of a Tyre/road Interface, Part i: Experiment and Computation

NASA Astrophysics Data System (ADS)

Graf, R. A. G.; Kuo, C.-Y.; Dowling, A. P.; Graham, W. R.

2002-09-01

Near the tyre/road contact area, the road surface and the tyre belt form a horn-like geometry, which provides a significant amplification mechanism for sound sources. Measurements have been carried out on a stationary tyre placed on a plane surface in an otherwise anechoic chamber. Following the reciprocal theorem a microphone was placed in the road surface near the contact patch and a white noise source was used in the far field. The amplification by the horn effect can then be determined as a function of frequency for an array of microphone positions relative to the contact patch and the centre of the tyre. These experimental measurements show that the horn effect is responsible for about 10-20dB increase in noise level. The amplification function shows a distinct interference pattern for higher frequencies and is independent of the longitudinal source position for low frequencies and source positions close to the contact patch. Numerical calculations using the indirect boundary element method have been carried out. These show excellent agreement with the measurements in the frequency regime of the BEM, i.e., up to 2500 Hz. The dependence of the horn effect on primary geometrical parameters such as the effect of the radius of curvature of the shoulders, the load and the width of the tyre has been investigated experimentally and numerically. The broad features of the horn effect are given by the cylindrical geometry of the tyre. The rounded edges of the tyre tend to increase the levels of the minima and shift them to higher frequencies, while slightly decreasing the levels of the maxima. Shape variations due to load can be accounted for by correcting the source distance to the edge of the formed contact patch. The amplification at low frequencies increases with width, the results collapsing onto a single curve as a function of the dimensionless width ω / λ.

Laboratory Study of Topographic Effects on the Near-surface Tornado Flow Field

NASA Astrophysics Data System (ADS)

Razavi, Alireza; Sarkar, Partha P.

2018-03-01

To study topographic effects on the near-surface tornado flow field, the Iowa State University tornado simulator was used to simulate a translating tornado passing over three different two-dimensional topographies: a ridge, an escarpment and a valley. The effect of the translation speed on maximum horizontal wind speeds is observed for translation speeds of 0.15 and 0.50 m s^{-1} , with the lower value resulting in a larger maximum horizontal wind speed. The tornado translation over the three topographies with respect to flat terrain is assessed for changes in: (a) the maximum horizontal wind speeds in terms of the flow-amplification factor; (b) the maximum aerodynamic drag in terms of the tornado speed-up ratio; (c) the maximum duration of exposure at any location to high wind speeds of a specific range in terms of the exposure amplification factor. Results show that both the maximum wind amplification factor of 14%, as well as the maximum speed-up ratio of 14%, occur on the ridge. For all topographies, the increase in aerodynamic drag is observed to be maximized for low-rise buildings, which illustrates the importance of the vertical profiles of the horizontal wind speed near the ground. The maximum exposure amplification factors, estimated for the range of wind speeds corresponding to the EF2 (50-60 m s^{-1} ) and EF3 (61-75 m s^{-1}) scales, are 86 and 110% for the ridge, 4 and 60% for the escarpment and - 6 and 47% for the valley, respectively.

Interference effects in a cavity for optical amplification

NASA Astrophysics Data System (ADS)

Cardimona, D. A.; Alsing, P. M.

2009-08-01

In space situational awareness scenarios, the objects needed to be characterized and identified are usually quite far away and quite dim. Thus, optical detectors need to be able to sense these very dim optical signals. Quantum interference in a three-level system can lead to amplification of optical signals. If we put a three-level system into a cavity tuned to the frequency of an incoming optical signal, we anticipate the amplification possibilities should be increased proportional to the quality factor of the cavity. Our vision is to utilize quantum dots in photonic crystal cavities, but as a stepping stone we first investigate a simple three-level system in a free-space optical cavity. We investigate quantum interference and classical interference effects when a three-level system interacts with both a cavity field mode and an external driving field mode. We find that under certain circumstances the cavity field evolves to be equal in magnitude to, but 180° out-of-phase with the external pump field when the pump field frequency equals the cavity frequency. At this point the resonance fluorescence from the atom in the cavity goes to zero due to a purely classical interference effect between the two out-of-phase fields. This is quite different from the quantum interference that occurs under the right circumstances, when the state populations are coherently driven into a linear combination that is decoupled from any applied field - and population is trapped in the excited states, thus allowing for a population inversion and an amplification of incoming optical signals.

Effects of antihypertensive drugs on central blood pressure in humans: a preliminary observation.

PubMed

Agnoletti, Davide; Zhang, Yi; Borghi, Claudio; Blacher, Jacques; Safar, Michel E

2013-08-01

Central blood pressure (BP) is considered a better predictor of cardiovascular events than brachial BP. Modifications of central, beyond brachial BP, can be assessed by pressure amplification, a potential new cardiovascular risk factor. Comparison between drugs' effect on central hemodynamics has been poorly studied. Our aim was to assess the hemodynamic effect of a 12-week treatment with amlodipine 5mg, or candesartan 8mg, or indapamide sustained-release 1.5mg, in comparison with placebo. We analyzed 145 out-patients with essential hypertension in primary prevention enrolled in the Natrilix SR Versus Candesartan and Amlodipine in the Reduction of Systolic Blood Pressure in Hypertensive Patients (X-CELLENT) study, a multicenter, randomized, double-blinded, placebo-controlled trial. Arterial stiffness, central BP, pressure amplification, and wave reflection were measured by applanation tonometry. Baseline characteristics of patients were homogeneous between groups. After treatment, we found that active drugs produced similar reduction of both central and peripheral BPs, with no significant interdrug differences (all P < 0.05; excluded peripheral pulse pressure, compared with placebo). Second, amlodipine (1.9% ± 15.3%), candesartan (3.0% ± 14.6%) and indapamide (4.1% ± 14.4%) all increased pulse pressure amplification, but only indapamide was statistically different from placebo (P = 0.02). Finally, no significant changes were observed on pulse wave velocity, heart rate, and augmentation index. The 3 antihypertensive drugs similarly reduced peripheral and central BP, as compared with placebo, but a significant increase in pulse pressure amplification was obtained only with indapamide, independently of arterial stiffness modifications. 3283161 by BIOPHARMA.

Experimental approach for estimating seismic amplification effects at the top of a ridge and their implication on ground motion predictions: the case of Narni (Central Italy).

NASA Astrophysics Data System (ADS)

Lovati, Sara; Bakavoli, Mohammad; Massa, Marco; Ferretti, Gabriele; Pacor, Francesca; Paolucci, Roberto

2010-05-01

From March to September 2009 a dense velocimetric network was installed in correspondence of Narni, a little village in central Italy, built on the top of a massive limestone ridge. The network was planned with the aim to investigate possible local site effects due to the morphology of the ridge, characterized by slopes ranging from 22° to 35° and a maximum difference of quota between top and bottom of 230 m. Three stations were installed at the base of the hill and other 7 monitored the crest. A remarkable dataset was obtained, composed by about 700 earthquakes, the great amount of which occurred after the 06th April 2009, Mw 6.3, L'Aquila earthquake. Site amplifications related to the ridge morphological features were investigated through empirical techniques with and without reference site, computing Spectral Standard Ratio, SSR and Horizontal to Vertical spectral ratio, HVSR. Directional spectral analyses were also performed . The agreement between the results coming from HVSR and SSR techniques allows us to assess with reliability a clear amplification effect for frequencies ranging between 3 and 5 Hz for all stations installed on the crest: in particular, SSR results show an amplification level with respect to the reference station up to 4.5. The highest amplification level (almost double) were observed when the direction perpendicular to the main elongation of the ridge is taken into account. Finally, considering the L'Aquila events with Mw > 4.5 and merging the information coming from the reference and non-reference site techniques, it was possible to recognize further amplification effects, at frequency lower than 1 Hz, probably related not to the morphology of the area but to source and/or polarization effects. Bidimensional numerical simulations were then computed in order to compare the results coming from the experiment with those obtained through numerical modeling. A hybrid finite-boundary element method based on code named HYBRID has been used for modeling. The model has been excited by SV and P Ricker wavelet in order to extract transform functions. The medium assumed to have a linear elastic constitutive behavior. All calculations were performed in time domain using direct boundary element method. The amplification patterns both in time and frequency domain were derived and similarities and discrepancies between the results were discussed. At last, considering only local events (epicentral distance R <= 30 km), empirical ground motion predictive equations, calibrated for maximum horizontal peak ground acceleration, PGA, velocity, PGV, and acceleration response spectra (SA, 5% damping) up to 1s, were carried out with the only aim to estimate topographical corrective coefficients. The results show significant corrective term values (between 0.35 and 0.48 in logarithmic scale) for the spectral ordinates between 0.2 s and 0.3 s. These results, in agreement to those obtained from the spectral analyses, suggest that the introduction of a topographic site class in the calculation of predictive models might probably reduce the inter-station variability for stations installed in correspondence of topographic irregularities, often included in reference-rock classes.

Evidence of high-elevation amplification versus Arctic amplification

NASA Astrophysics Data System (ADS)

Wang, Qixiang; Fan, Xiaohui; Wang, Mengben

2016-01-01

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.

Evidence of high-elevation amplification versus Arctic amplification

PubMed Central

Wang, Qixiang; Fan, Xiaohui; Wang, Mengben

2016-01-01

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. PMID:26753547

Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation.

PubMed

Sarkar, A; Beard, D A; Franza, B R

2006-07-01

The effects of binding on the phosphorylation-dephosphorylation cycle (PDPC) - one of the key components of the signal transduction processes - is analyzed based on a mathematical model. The model shows that binding of proteins, forming a complex, diminishes the ultrasensitivity of the PDPC to the differences in activity between kinase and phosphatase in the cycle. It is also found that signal amplification depends upon the strength of the binding affinity of the protein (phosphorylated or dephosphorylated) to other proteins . It is also observed that the amplification of signal is not only dependent on phosphorylation potential but also on binding properties and resulting adjustments in binding energies.

Topoisomerase expression and amplification in solid tumours: Analysis of 24,262 patients

PubMed Central

Heestand, Gregory M.; Schwaederle, Maria; Gatalica, Zoran; Arguello, David; Kurzrock, Razelle

2017-01-01

Background Topoisomerase I (TOPO1) and topoisomerase IIα (TOP2A) are specific targets of multiple chemotherapy drugs. Increased expression of TOPO1 protein and amplification of the TOP2A gene have been associated with treatment response in colorectal and breast cancers, respectively. TOPO1 and TOP2A may be potential therapeutic targets in other malignancies as well. Summary of methods We analysed TOPO1 protein expression and TOP2A gene amplification in patients (n = 24,262 specimens) with diverse cancers. Since HER2 and TOP2A co-amplification have been investigated for predictive value regarding anthracycline benefit, we analysed specimens for HER2 amplification as well. Results Overexpressed TOPO1 protein was present in 51% of the tumours. Four percent of the tumours had TOP2A amplification, with gallbladder tumours and gastroesophageal/oesophageal tumours having rates over 10%. Overall, 4903 specimens were assessed for both TOP2A and HER2 amplification; 129 (2.6%) had co-amplification. High rates (>40%) of HER2 amplification were seen in patients with TOP2A amplification in breast, ovarian, gastroesophageal/oesophageal and pancreatic cancer. Conclusion Our data indicate that increased TOPO1 expression and TOP2A amplification, as well as HER2 co-alterations, are present in multiple malignancies. The implications of these observations regarding sensitivity to chemotherapy not traditionally administered to these tumour types merits investigation. PMID:28728050

PMS2 gene mutational analysis: direct cDNA sequencing to circumvent pseudogene interference.

PubMed

Wimmer, Katharina; Wernstedt, Annekatrin

2014-01-01

The presence of highly homologous pseudocopies can compromise the mutation analysis of a gene of interest. In particular, when using PCR-based strategies, pseudogene co-amplification has to be effectively prevented. This is often achieved by using primers designed to be parental gene specific according to the reference sequence and by applying stringent PCR conditions. However, there are cases in which this approach is of limited utility. For example, it has been shown that the PMS2 gene exchanges sequences with one of its pseudogenes, named PMS2CL. This results in functional PMS2 alleles containing pseudogene-derived sequences at their 3'-end and in nonfunctional PMS2CL pseudogene alleles that contain gene-derived sequences. Hence, the paralogues cannot be distinguished according to the reference sequence. This shortcoming can be effectively circumvented by using direct cDNA sequencing. This approach is based on the selective amplification of PMS2 transcripts in two overlapping 1.6-kb RT-PCR products. In addition to avoiding pseudogene co-amplification and allele dropout, this method has also the advantage that it allows to effectively identify deletions, splice mutations, and de novo retrotransposon insertions that escape the detection of most DNA-based mutation analysis protocols.

Parametric amplification in quasi-PT symmetric coupled waveguide structures

NASA Astrophysics Data System (ADS)

Zhong, Q.; Ahmed, A.; Dadap, J. I.; Osgood, R. M., Jr.; El-Ganainy, R.

2016-12-01

The concept of non-Hermitian parametric amplification was recently proposed as a means to achieve an efficient energy conversion throughout the process of nonlinear three wave mixing in the absence of phase matching. Here we investigate this effect in a waveguide coupler arrangement whose characteristics are tailored to introduce passive PT symmetry only for the idler component. By means of analytical solutions and numerical analysis, we demonstrate the utility of these novel schemes and obtain the optimal design conditions for these devices.

Molecular Biological Studies on the Biogenesis of Human Cholinesterases in vivo and as Directed by Cloned Cholinesterase DNA Sequences

DTIC Science & Technology

1990-10-24

amplifications. A considerable body of information, accumulated over the years, demonstrates cytotoxic and mutogenic effects for OP poisons. Pesticide -induced...occupational exposure to pesticides (306). However, the damage may not be limited to these high-risk groups of humans, since pesticide residues were found in...with amplification of the HER-2/neu oncogene. Science 235: 177-182 (1987). 296 Ahmed, F.; Hart, R.; Lewis, N. Pesticide induced DNA damage and its

Comparison of sensor structures for the signal amplification of surface plasmon resonance immunoassay using enzyme precipitation

NASA Astrophysics Data System (ADS)

Yang, Chih-Tsung; Thierry, Benjamin

2015-12-01

Surface plasmon resonance (SPR) biosensing has been successfully applied for the label-free detection of a broad range of bioanalytes ranging from bacteria, cell, exosome, protein and nucleic acids. When it comes to the detection of small molecules or analytes found at low concentration, amplification schemes are desirable to enhance binding signals and in turn increase sensitivity. A number of SPR signal amplification schemes have been developed and validated; however, little effort has been devoted to understanding the effect of the SPR sensor structures on the amplification of binding signals and therefore on the overall sensing performance. The physical phenomenon of long-range SPR (LRSPR) relies on the propagation of coupled surface plasmonic waves on the opposite sides of a nanoscale-thick noble metal film suspended between two dielectrics with similar refractive indices. Importantly, as compared with commonly used conventional SPR (cSPR), LRSPR is not only characterized by a longer penetration depth of the plasmonic waves in the analyzed medium but also by a greater sensitivity to bulk refractive index changes. In this work, an immunoassay signal amplification platform based on horseradish peroxidase (HRP) catalyzed precipitation was utilized to investigate the sensing performance with regards to cSPR and LRSPR. The enzymatic precipitation of 3, 3'-diaminobenzidine tetrahydrochloride (DAB)/H2O2 was used to amplify SPR signals. The structure-function relationship of cSPR and LRSPR sensors is presented for both standard refractometric measurements and the enzymatic precipitation scheme. Experimental data shows that despite its inherent higher sensitivity to bulk refractive index changes and higher figure of merit, LRSPR was characterized by a lower angular sensitivity in the model enzymatic amplification scheme used here.

Selective whole genome amplification for resequencing target microbial species from complex natural samples.

PubMed

Leichty, Aaron R; Brisson, Dustin

2014-10-01

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with <6.7-fold amplification of the background. SWGA-treated genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

Potential for an Arctic-breeding migratory bird to adjust spring migration phenology to Arctic amplification.

PubMed

Lameris, Thomas K; Scholten, Ilse; Bauer, Silke; Cobben, Marleen M P; Ens, Bruno J; Nolet, Bart A

2017-10-01

Arctic amplification, the accelerated climate warming in the polar regions, is causing a more rapid advancement of the onset of spring in the Arctic than in temperate regions. Consequently, the arrival of many migratory birds in the Arctic is thought to become increasingly mismatched with the onset of local spring, consequently reducing individual fitness and potentially even population levels. We used a dynamic state variable model to study whether Arctic long-distance migrants can advance their migratory schedules under climate warming scenarios which include Arctic amplification, and whether such an advancement is constrained by fuel accumulation or the ability to anticipate climatic changes. Our model predicts that barnacle geese Branta leucopsis suffer from considerably reduced reproductive success with increasing Arctic amplification through mistimed arrival, when they cannot anticipate a more rapid progress of Arctic spring from their wintering grounds. When geese are able to anticipate a more rapid progress of Arctic spring, they are predicted to advance their spring arrival under Arctic amplification up to 44 days without any reproductive costs in terms of optimal condition or timing of breeding. Negative effects of mistimed arrival on reproduction are predicted to be somewhat mitigated by increasing summer length under warming in the Arctic, as late arriving geese can still breed successfully. We conclude that adaptation to Arctic amplification may rather be constrained by the (un)predictability of changes in the Arctic spring than by the time available for fuel accumulation. Social migrants like geese tend to have a high behavioural plasticity regarding stopover site choice and migration schedule, giving them the potential to adapt to future climate changes on their flyway. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Hearing aid fitting for visual and hearing impaired patients with Usher syndrome type IIa.

PubMed

Hartel, B P; Agterberg, M J H; Snik, A F; Kunst, H P M; van Opstal, A J; Bosman, A J; Pennings, R J E

2017-08-01

Usher syndrome is the leading cause of hereditary deaf-blindness. Most patients with Usher syndrome type IIa start using hearing aids from a young age. A serious complaint refers to interference between sound localisation abilities and adaptive sound processing (compression), as present in today's hearing aids. The aim of this study was to investigate the effect of advanced signal processing on binaural hearing, including sound localisation. In this prospective study, patients were fitted with hearing aids with a nonlinear (compression) and linear amplification programs. Data logging was used to objectively evaluate the use of either program. Performance was evaluated with a speech-in-noise test, a sound localisation test and two questionnaires focussing on self-reported benefit. Data logging confirmed that the reported use of hearing aids was high. The linear program was used significantly more often (average use: 77%) than the nonlinear program (average use: 17%). The results for speech intelligibility in noise and sound localisation did not show a significant difference between type of amplification. However, the self-reported outcomes showed higher scores on 'ease of communication' and overall benefit, and significant lower scores on disability for the new hearing aids when compared to their previous hearing aids with compression amplification. Patients with Usher syndrome type IIa prefer a linear amplification over nonlinear amplification when fitted with novel hearing aids. Apart from a significantly higher logged use, no difference in speech in noise and sound localisation was observed between linear and nonlinear amplification with the currently used tests. Further research is needed to evaluate the reasons behind the preference for the linear settings. © 2016 The Authors. Clinical Otolaryngology Published by John Wiley & Sons Ltd.

Development of loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Penicillium nordicum in dry-cured meat products.

PubMed

Ferrara, M; Perrone, G; Gallo, A; Epifani, F; Visconti, A; Susca, A

2015-06-02

The need of powerful diagnostic tools for rapid, simple, and cost-effective detection of food-borne fungi has become very important in the area of food safety. Currently, several isothermal nucleic acid amplification methods have been developed as an alternative to PCR-based analyses. Loop-mediated isothermal amplification (LAMP) is one of these innovative methods; it requires neither gel electrophoresis to separate and visualize the products nor expensive laboratory equipment and it has been applied already for detection of pathogenic organisms. In the current study, we developed a LAMP assay for the specific detection of Penicillium nordicum, the major causative agent of ochratoxin A contamination in protein-rich food, especially dry-cured meat products. The assay was based on targeting otapksPN gene, a key gene in the biosynthesis of ochratoxin A (OTA) in P. nordicum. Amplification of DNA during the reaction was detected directly in-tube by color transition of hydroxynaphthol blue from violet to sky blue, visible to the naked eye, avoiding further post amplification analyses. Only DNAs isolated from several P. nordicum strains led to positive results and no amplification was observed from non-target OTA and non OTA-producing strains. The assay was able to detect down to 100 fg of purified targeted genomic DNA or 10(2) conidia/reaction within 60 min. The LAMP assay for detection and identification of P. nordicum was combined with a rapid DNA extraction method set up on serially diluted conidia, providing an alternative rapid, specific and sensitive DNA-based method suitable for application directly "on-site", notably in key steps of dry-cured meat production. Copyright © 2015 Elsevier B.V. All rights reserved.

Colocalization recognition-activated cascade signal amplification strategy for ultrasensitive detection of transcription factors.

PubMed

Zhu, Desong; Wang, Lei; Xu, Xiaowen; Jiang, Wei

2017-03-15

Transcription factors (TFs) bind to specific double-stranded DNA (dsDNA) sequences in the regulatory regions of genes to regulate the process of gene transcription. Their expression levels sensitively reflect cell developmental situation and disease state. TFs have become potential diagnostic markers and therapeutic targets of cancers and some other diseases. Hence, high sensitive detection of TFs is of vital importance for early diagnosis of diseases and drugs development. The traditional exonucleases-assisted signal amplification methods suffered from the false positives caused by incomplete digestion of excess recognition probes. Herein, based on a new recognition way-colocalization recognition (CR)-activated dual signal amplification, an ultrasensitive fluorescent detection strategy for TFs was developed. TFs-induced the colocalization of three split recognition components resulted in noticeable increases of local effective concentrations and hybridization of three split components, which activated the subsequent cascade signal amplification including strand displacement amplification (SDA) and exponential rolling circle amplification (ERCA). This strategy eliminated the false positive influence and achieved ultra-high sensitivity towards the purified NF-κB p50 with detection limit of 2.0×10 -13 M. Moreover, NF-κB p50 can be detected in as low as 0.21ngμL -1 HeLa cell nuclear extracts. In addition, this proposed strategy could be used for the screening of NF-κB p50 activity inhibitors and potential anti-NF-κB p50 drugs. Finally, our proposed strategy offered a potential method for reliable detection of TFs in medical diagnosis and treatment research of cancers and other related diseases. Copyright © 2016 Elsevier B.V. All rights reserved.

Amplification of the 20q Chromosomal Arm Occurs Early in Tumorigenic Transformation and May Initiate Cancer

PubMed Central

Buganim, Yosef; Solomon, Hilla; Goldfinger, Naomi; Hovland, Randi; Ke, Xi-Song; Oyan, Anne M.; Kalland, Karl-H.; Rotter, Varda; Domany, Eytan

2011-01-01

Duplication of chromosomal arm 20q occurs in prostate, cervical, colon, gastric, bladder, melanoma, pancreas and breast cancer, suggesting that 20q amplification may play a causal role in tumorigenesis. According to an alternative view, chromosomal imbalance is mainly a common side effect of cancer progression. To test whether a specific genomic aberration might serve as a cancer initiating event, we established an in vitro system that models the evolutionary process of early stages of prostate tumor formation; normal prostate cells were immortalized by the over-expression of human telomerase catalytic subunit hTERT, and cultured for 650 days till several transformation hallmarks were observed. Gene expression patterns were measured and chromosomal aberrations were monitored by spectral karyotype analysis at different times. Several chromosomal aberrations, in particular duplication of chromosomal arm 20q, occurred early in the process and were fixed in the cell populations, while other aberrations became extinct shortly after their appearance. A wide range of bioinformatic tools, applied to our data and to data from several cancer databases, revealed that spontaneous 20q amplification can promote cancer initiation. Our computational model suggests that 20q amplification induced deregulation of several specific cancer-related pathways including the MAPK pathway, the p53 pathway and Polycomb group factors. In addition, activation of Myc, AML, B-Catenin and the ETS family transcription factors was identified as an important step in cancer development driven by 20q amplification. Finally we identified 13 "cancer initiating genes", located on 20q13, which were significantly over-expressed in many tumors, with expression levels correlated with tumor grade and outcome suggesting that these genes induce the malignant process upon 20q amplification. PMID:21297939

Simple potential model for interaction of dark particles with massive bodies

NASA Astrophysics Data System (ADS)

Takibayev, Nurgali

2018-01-01

A simple model for interaction of dark particles with matter based on resonance behavior in a three-body system is proposed. The model describes resonant amplification of effective interaction between two massive bodies at large distances between them. The phenomenon is explained by catalytic action of dark particles rescattering at a system of two heavy bodies which are understood here as the big stellar objects. Resonant amplification of the effective interaction between the two heavy bodies imitates the increase in their mass while their true gravitational mass remains unchanged. Such increased interaction leads to more pronounced gravitational lensing of bypassing light. It is shown that effective interaction between the heavy bodies is changed at larger distances and can transform into repulsive action.

The G1 phase Cdks regulate the centrosome cycle and mediate oncogene-dependent centrosome amplification

PubMed Central

2011-01-01

Because centrosome amplification generates aneuploidy and since centrosome amplification is ubiquitous in human tumors, a strong case is made for centrosome amplification being a major force in tumor biogenesis. Various evidence showing that oncogenes and altered tumor suppressors lead to centrosome amplification and aneuploidy suggests that oncogenes and altered tumor suppressors are a major source of genomic instability in tumors, and that they generate those abnormal processes to initiate and sustain tumorigenesis. We discuss how altered tumor suppressors and oncogenes utilize the cell cycle regulatory machinery to signal centrosome amplification and aneuploidy. PMID:21272329

A norovirus detection architecture based on isothermal amplification and expanded genetic systems.

PubMed

Yaren, Ozlem; Bradley, Kevin M; Moussatche, Patricia; Hoshika, Shuichi; Yang, Zunyi; Zhu, Shu; Karst, Stephanie M; Benner, Steven A

2016-11-01

Noroviruses are the major cause of global viral gastroenteritis with short incubation times and small inoculums required for infection. This creates a need for a rapid molecular test for norovirus for early diagnosis, in the hope of preventing the spread of the disease. Non-chemists generally use off-the shelf reagents and natural DNA to create such tests, suffering from background noise that comes from adventitious DNA and RNA (collectively xNA) that is abundant in real biological samples, especially feces, a common location for norovirus. Here, we create an assay that combines artificially expanded genetic information systems (AEGIS, which adds nucleotides to the four in standard xNA, pairing orthogonally to A:T and G:C) with loop-mediated isothermal amplification (LAMP) to amplify norovirus RNA at constant temperatures, without the power or instrument requirements of PCR cycling. This assay was then validated using feces contaminated with murine norovirus (MNV). Treating stool samples with ammonia extracts the MNV RNA, which is then amplified in an AEGIS-RT-LAMP where AEGIS segments are incorporated both into an internal LAMP primer and into a molecular beacon stem, the second lowering background signaling noise. This is coupled with RNase H nicking during sample amplification, allowing detection of as few as 10 copies of noroviral RNA in a stool sample, generating a fluorescent signal visible to human eye, all in a closed reaction vessel. Copyright © 2016 Elsevier B.V. All rights reserved.

The C-Module-Binding Factor Supports Amplification of TRE5-A Retrotransposons in the Dictyostelium discoideum Genome ▿

PubMed Central

Bilzer, Annika; Dölz, Heike; Reinhardt, Alexander; Schmith, Anika; Siol, Oliver; Winckler, Thomas

2011-01-01

Retrotransposable elements are molecular parasites that have invaded the genomes of virtually all organisms. Although retrotransposons encode essential proteins to mediate their amplification, they also require assistance by host cell-encoded machineries that perform functions such as DNA transcription and repair. The retrotransposon TRE5-A of the social amoeba Dictyostelium discoideum generates a notable amount of both sense and antisense RNAs, which are generated from element-internal promoters, located in the A module and the C module, respectively. We observed that TRE5-A retrotransposons depend on the C-module-binding factor (CbfA) to maintain high steady-state levels of TRE5-A transcripts and that CbfA supports the retrotransposition activity of TRE5-A elements. The carboxy-terminal domain of CbfA was found to be required and sufficient to mediate the accumulation of TRE5-A transcripts, but it did not support productive retrotransposition of TRE5-A. This result suggests different roles for CbfA protein domains in the regulation of TRE5-A retrotransposition frequency in D. discoideum cells. Although CbfA binds to the C module in vitro, the factor regulates neither C-module nor A-module promoter activity in vivo. We speculate that CbfA supports the amplification of TRE5-A retrotransposons by suppressing the expression of an as yet unidentified component of the cellular posttranscriptional gene silencing machinery. PMID:21076008

8 x 120 Gb/s unrepeatered transmission over 444 km (76.6 dB) using distributed Raman amplification and ROPA without discrete amplification.

PubMed

Chang, Do Il; Pelouch, Wayne; Patki, Pallavi; McLaughlin, John

2011-12-12

Unrepeatered transmission of 8 x 120 Gb/s over 444.2 km (76.6 dB) and multi-rate transmission of 8 x 120 Gb/s and 9 x 10.7 Gb/s over a 75.4 dB span have been demonstrated with off-line digital processing for the coherent 120 Gb/s channels. Transmission of 2 x 120 Gb/s with 7 x 12.5 Gb/s over 78 dB is also demonstrated with a real-time ASIC processor. All transmission results have been achieved using standard effective-area pure-silica-core fiber using forward and backward distributed Raman amplification and remotely-pumped erbium fiber. ASIC real-time processed results match well with off-line processing. © 2011 Optical Society of America

Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio

PubMed Central

Clausson, Carl-Magnus; Arngården, Linda; Ishaq, Omer; Klaesson, Axel; Kühnemund, Malte; Grannas, Karin; Koos, Björn; Qian, Xiaoyan; Ranefall, Petter; Krzywkowski, Tomasz; Brismar, Hjalmar; Nilsson, Mats; Wählby, Carolina; Söderberg, Ola

2015-01-01

Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes. PMID:26202090

Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR

PubMed Central

Miner, Brooks E.; Stöger, Reinhard J.; Burden, Alice F.; Laird, Charles D.; Hansen, R. Scott

2004-01-01

PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular ‘batch-stamps’ that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes. PMID:15459281

Weak Value Amplification is Suboptimal for Estimation and Detection

NASA Astrophysics Data System (ADS)

Ferrie, Christopher; Combes, Joshua

2014-01-01

We show by using statistically rigorous arguments that the technique of weak value amplification does not perform better than standard statistical techniques for the tasks of single parameter estimation and signal detection. Specifically, we prove that postselection, a necessary ingredient for weak value amplification, decreases estimation accuracy and, moreover, arranging for anomalously large weak values is a suboptimal strategy. In doing so, we explicitly provide the optimal estimator, which in turn allows us to identify the optimal experimental arrangement to be the one in which all outcomes have equal weak values (all as small as possible) and the initial state of the meter is the maximal eigenvalue of the square of the system observable. Finally, we give precise quantitative conditions for when weak measurement (measurements without postselection or anomalously large weak values) can mitigate the effect of uncharacterized technical noise in estimation.

Signal persistence and amplification in cancer development and possible, related opportunities for novel therapies.

PubMed

Ford, Shea A; Blanck, George

2015-01-01

Research in cancer biology has been largely driven by experimental approaches whereby discreet inputs are used to assess discreet outputs, for example, gene-knockouts to assess cancer occurrence. However, cancer hallmarks are only rarely, if ever, exclusively dependent on discreet regulatory processes. Rather, cancer-related regulatory factors affect multiple cancer hallmarks. Thus, novel approaches and paradigms are needed for further advances. Signal pathway persistence and amplification, rather than signal pathway activation resulting from an on/off switch, represent emerging paradigms for cancer research, closely related to developmental regulatory paradigms. In this review, we address both mechanisms and effects of signal pathway persistence and amplification in cancer settings; and address the possibility that hyper-activation of pro-proliferative signal pathways in certain cancer settings could be exploited for therapy. Copyright © 2014. Published by Elsevier B.V.

Psychological correlates and psychiatric morbidity in patients with Dhat syndrome

PubMed Central

Grover, Sandeep; Gupta, Sunil; Avasthi, Ajit

2015-01-01

Aim: The aim of this study was to examine psychological factors in the form of somatosensory amplification, alexithymia and hypochondriasis in patients with Dhat syndrome. Secondary aims of the study were: (1) To evaluate the influence of psychiatric comorbidity on the psychological correlates; (2) to compare the prevalence of psychological correlates in those with Dhat syndrome and in those with depression and somatoform disorders. Materials and Methods: A total of 106 subjects diagnosed with Dhat syndrome as per International Classification of Diseases-10 (ICD-10) criteria were assessed on Toronto Alexithymia Scale (TAS-20), Somatosensory Amplification Scale (SSAS) and Whitely Index (WI). Psychiatric comorbidity was diagnosed as per ICD-10. Data on 50 patients with depression and 119 patients with somatoform disorder was used for comparison. Results: The age at onset of Dhat syndrome was 22.54 (standard deviation [SD] - 7.5) years, and duration of illness was 5.04 (SD - 4.2) years. Depressive disorders were diagnosed in 13.2%, anxiety disorders in 15.1%, erectile dysfunction in 14.2% and premature ejaculation in 17% of cases. The mean SSAS total score was 23.12 (SD - 7.99), mean total TAS-20 score was 63.3 (SD - 13.3) and mean WI score was 8.23 (SD - 2.7). About two third of the patients had alexithymia (n = 67; 63.2%) and hypochondriasis (n = 69; 65.1%). Comparison of the psychological correlates between those with Dhat syndrome alone (n = 59) and those with comorbid psychiatric disorder (n = 47) revealed no significant differences. Patients with only Dhat syndrome had significantly higher scores for somatosensory amplification when compared with those with somatoform disorders, but no difference was seen between those with depression and Dhat syndrome alone. Compared to patients with Dhat syndrome alone, those with depression had higher prevalence of alexithymia and hypochondriasis. Conclusion: There are differences in the prevalence of somatosensory amplification, hypochondriasis and alexithymia between those with Dhat syndrome alone and those with depression and somatoform disorders. PMID:26600578

Development of Rapid Isothermal Amplification Assays for Detection of Phytophthora spp. in Plant Tissue.

PubMed

Miles, Timothy D; Martin, Frank N; Coffey, Michael D

2015-02-01

Several isothermal amplification techniques recently have been developed that are tolerant of inhibitors present in many plant extracts, which can reduce the need for obtaining purified DNA for running diagnostic assays. One such commercially available technique that has similarities with real-time polymerase chain reaction (PCR) for designing primers and a labeled probe is recombinase polymerase amplification (RPA). This technology was used to develop two simple and rapid approaches for detection of Phytophthora spp.: one genus-specific assay multiplexed with a plant internal control and the other species-specific assays for Phytophthora ramorum and P. kernoviae. All assays were tested for sensitivity (ranging from 3 ng to 1 fg of DNA) and specificity using DNA extracted from more than 136 Phytophthora taxa, 21 Pythium spp., 1 Phytopythium sp., and a wide range of plant species. The lower limit of linear detection using purified DNA was 200 to 300 fg of DNA in all pathogen RPA assays. Six different extraction buffers were tested for use during plant tissue maceration and the assays were validated in the field by collecting 222 symptomatic plant samples from over 50 different hosts. Only 56 samples were culture positive for Phytophthora spp. whereas 91 were positive using the Phytophthora genus-specific RPA test and a TaqMan real-time PCR assay. A technique for the generation of sequencing templates from positive RPA amplifications to confirm species identification was also developed. These RPA assays have added benefits over traditional technologies because they are rapid (results can be obtained in as little as 15 min), do not require DNA extraction or extensive training to complete, use less expensive portable equipment than PCR-based assays, and are significantly more specific than current immunologically based methods. This should provide a rapid, field-deployable capability for pathogen detection that will facilitate point-of-sample collection processing, thereby reducing the time necessary for accurate diagnostics and making management decisions.

Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control.

PubMed

Kesanakurti, Prasad; Belton, Mark; Saeed, Hanaa; Rast, Heidi; Boyes, Ian; Rott, Michael

2016-10-01

The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS). Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

FAST: Rapid determinations of antibiotic susceptibility phenotypes using label-free cytometry.

PubMed

Huang, Tzu-Hsueh; Tzeng, Yih-Ling; Dickson, Robert M

2018-05-07

Sepsis, a life-threatening immune response to blood infections (bacteremia), has a ∼30% mortality rate and is the 10th leading cause of US hospital deaths. The typical bacterial loads in adult septic patients are ≤100 bacterial cells (colony forming units, CFU) per ml blood, while pediatric patients exhibit only ∼1000 CFU/ml. Due to the low numbers, bacteria must be propagated through ∼24-hours blood cultures to generate sufficient CFUs for diagnosis and further analyses. Herein, we demonstrate that, unlike other rapid post-blood culture antibiotic susceptibility tests (ASTs), our phenotypic approach can drastically accelerate ASTs for the most common sepsis-causing gram-negative pathogens by circumventing long blood culture-based amplification. For all blood isolates of multi-drug resistant pathogens investigated (Escherichia coli, Klebsiella pneumoniae, and Acinetobacter nosocomialis), effective antibiotic(s) were readily identified within the equivalent of 8 hours from initial blood draw using <0.5 mL of adult blood per antibiotic. These methods should drastically improve patient outcomes by significantly reducing time to actionable treatment information and reduce the incidence of antibiotic resistance. © 2018 International Society for Advancement of Cytometry. © 2018 International Society for Advancement of Cytometry.

Enhanced stimulated emission in ZnO thin films using microdisk top-down structuring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nomenyo, K.; Kostcheev, S.; Lérondel, G.

2014-05-05

Microdisks were fabricated in zinc oxide (ZnO) thin films using a top-down approach combining electron beam lithography and reactive ion etching. These microdisk structured thin films exhibit a stimulated surface emission between 3 and 7 times higher than that from a reference film depending on the excitation power density. Emission peak narrowing, reduction in lasing threshold and blue-shifting of the emission wavelength were observed along with enhancement in the emitted intensity. Results indicate that this enhancement is due to an increase in the internal quantum efficiency combined with an amplification of the stimulated emission. An analysis in terms of waveguidingmore » is presented in order to explain these effects. These results demonstrate that very significant gains in emission can be obtained through conventional microstructuration without the need for more onerous top-down nanostructuration techniques.« less

High-performance passive microwave survey on Josephson Junctions

NASA Technical Reports Server (NTRS)

Denisov, A. G.; Radzikhovsky, V. N.; Kudeliya, A. M.

1995-01-01

The quasi-optical generations of images of objects with their internal structure in millimeter (MM) and submillimeter (SMM) bands is one of prime problems of modern radioelectronics. The main advantage of passive MM imaging systems in comparison with visible and infrared (IR) systems is small attenuation of signals in fog, cloud, smoke, dust and other obscurants. However, at a panoramic scanning of space the observation time lengthens and thereby the information processing rate becomes restricted so that single-channel system cannot image in real time. Therefore we must use many radiometers in parallel to reduce the observation time. Such system must contain receiving sensors as pixels in multibeam antenna. The use of Josephson Junctions (JJ) for this purpose together with the cryoelectronic devices like GaAs FET (field effect transistors) or SQUIDS for signal amplifications after JJ is of particular interest in this case.

Three-dimensional drift kinetic response of high-β plasmas in the DIII-D tokamak.

PubMed

Wang, Z R; Lanctot, M J; Liu, Y Q; Park, J-K; Menard, J E

2015-04-10

A quantitative interpretation of the experimentally measured high-pressure plasma response to externally applied three-dimensional (3D) magnetic field perturbations, across the no-wall Troyon β limit, is achieved. The self-consistent inclusion of the drift kinetic effects in magnetohydrodynamic (MHD) modeling [Y. Q. Liu et al., Phys. Plasmas 15, 112503 (2008)] successfully resolves an outstanding issue of the ideal MHD model, which significantly overpredicts the plasma-induced field amplification near the no-wall limit, as compared to experiments. The model leads to quantitative agreement not only for the measured field amplitude and toroidal phase but also for the measured internal 3D displacement of the plasma. The results can be important to the prediction of the reliable plasma behavior in advanced fusion devices, such as ITER [K. Ikeda, Nucl. Fusion 47, S1 (2007)].

Clinical Characteristics and Outcome of Patients with Neuroblastoma Presenting Genomic Amplification of Loci Other than MYCN

PubMed Central

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

Coupling p+n Field-Effect Transistor Circuits for Low Concentration Methane Gas Detection

PubMed Central

Zhou, Xinyuan; Yang, Liping; Bian, Yuzhi; Ma, Xiang; Chen, Yunfa

2018-01-01

Nowadays, the detection of low concentration combustible methane gas has attracted great concern. In this paper, a coupling p+n field effect transistor (FET) amplification circuit is designed to detect methane gas. By optimizing the load resistance (RL), the response to methane of the commercial MP-4 sensor can be magnified ~15 times using this coupling circuit. At the same time, it decreases the limit of detection (LOD) from several hundred ppm to ~10 ppm methane, with the apparent response of 7.0 ± 0.2 and voltage signal of 1.1 ± 0.1 V. This is promising for the detection of trace concentrations of methane gas to avoid an accidental explosion because its lower explosion limit (LEL) is ~5%. The mechanism of this coupling circuit is that the n-type FET firstly generates an output voltage (VOUT) amplification process caused by the gate voltage-induced resistance change of the FET. Then, the p-type FET continues to amplify the signal based on the previous VOUT amplification process. PMID:29509659

Coupling p+n Field-Effect Transistor Circuits for Low Concentration Methane Gas Detection.

PubMed

Zhou, Xinyuan; Yang, Liping; Bian, Yuzhi; Ma, Xiang; Han, Ning; Chen, Yunfa

2018-03-06

Nowadays, the detection of low concentration combustible methane gas has attracted great concern. In this paper, a coupling p+n field effect transistor (FET) amplification circuit is designed to detect methane gas. By optimizing the load resistance ( R L ), the response to methane of the commercial MP-4 sensor can be magnified ~15 times using this coupling circuit. At the same time, it decreases the limit of detection (LOD) from several hundred ppm to ~10 ppm methane, with the apparent response of 7.0 ± 0.2 and voltage signal of 1.1 ± 0.1 V. This is promising for the detection of trace concentrations of methane gas to avoid an accidental explosion because its lower explosion limit (LEL) is ~5%. The mechanism of this coupling circuit is that the n-type FET firstly generates an output voltage ( V OUT ) amplification process caused by the gate voltage-induced resistance change of the FET. Then, the p-type FET continues to amplify the signal based on the previous V OUT amplification process.

Rapid and Sensitive Detection of Norovirus Genomes in Oysters by a Two-Step Isothermal Amplification Assay System Combining Nucleic Acid Sequence-Based Amplification and Reverse Transcription-Loop-Mediated Isothermal Amplification Assays▿

PubMed Central

Fukuda, Shinji; Sasaki, Yukie; Seno, Masato

2008-01-01

We developed a two-step isothermal amplification assay system, which achieved the detection of norovirus (NoV) genomes in oysters with a sensitivity similar to that of reverse transcription-seminested PCR. The time taken for the amplification of NoV genomes from RNA extracts was shortened to about 3 h. PMID:18456857

Angiotensin-converting enzyme 2 amplification limited to the circulation does not protect mice from development of diabetic nephropathy.

PubMed

Wysocki, Jan; Ye, Minghao; Khattab, Ahmed M; Fogo, Agnes; Martin, Aline; David, Nicolae Valentin; Kanwar, Yashpal; Osborn, Mark; Batlle, Daniel

2017-06-01

Blockers of the renin-angiotensin system are effective in the treatment of experimental and clinical diabetic nephropathy. An approach different from blocking the formation or action of angiotensin II (1-8) that could also be effective involves fostering its degradation. Angiotensin-converting enzyme 2 (ACE2) is a monocarboxypeptidase that cleaves angiotensin II (1-8) to form angiotensin (1-7). Therefore, we examined the renal effects of murine recombinant ACE2 in mice with streptozotocin-induced diabetic nephropathy as well as that of amplification of circulating ACE2 using minicircle DNA delivery prior to induction of experimental diabetes. This delivery resulted in a long-term sustained and profound increase in serum ACE2 activity and enhanced ability to metabolize an acute angiotensin II (1-8) load. In mice with streptozotocin-induced diabetes pretreated with minicircle ACE2, ACE2 protein in plasma increased markedly and this was associated with a more than 100-fold increase in serum ACE2 activity. However, minicircle ACE2 did not result in changes in urinary ACE2 activity as compared to untreated diabetic mice. In both diabetic groups, glomerular filtration rate increased significantly and to the same extent as compared to non-diabetic controls. Albuminuria, glomerular mesangial expansion, glomerular cellularity, and glomerular size were all increased to a similar extent in minicircle ACE2-treated and untreated diabetic mice, as compared to non-diabetic controls. Recombinant mouse ACE2 given for 4 weeks by intraperitoneal daily injections in mice with streptozotocin-induced diabetic nephropathy also failed to improve albuminuria or kidney pathology. Thus, a profound augmentation of ACE2 confined to the circulation failed to ameliorate the glomerular lesions and hyperfiltration characteristic of early diabetic nephropathy. These findings emphasize the importance of targeting the kidney rather than the circulatory renin angiotensin system to combat diabetic nephropathy. Copyright © 2016 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

HER-2 amplification in tubular carcinoma of the breast.

PubMed

Oakley, Gerard J; Tubbs, Raymond R; Crowe, Joseph; Sebek, Bruce; Budd, G Thomas; Patrick, Rebecca J; Procop, Gary W

2006-07-01

The prognostic and therapeutic implications of HER-2 gene amplification and estrogen and progesterone receptor status in breast cancer are well described. To address the relative paucity of information concerning HER-2 amplification for tubular carcinomas, we assessed the frequency of gene amplification in 55 tubular carcinomas of the breast from 54 patients, 5 of which had axillary node metastases. The HER-2 gene copy number was assessed by fluorescence in situ hybridization for the majority of tumors analyzed, whereas estrogen and progesterone receptor status was achieved by immunohistochemical analysis. HER-2 gene amplification was not observed in any of the tumors examined, and most were estrogen receptor-positive. This HER-2 gene amplification frequency was significantly lower than the frequency of gene amplification previously reported for all invasive ductal carcinoma of no special type (P < .01). HER-2 gene amplification likely occurs infrequently, or not at all, in tubular carcinomas of the breast, whereas most express estrogen receptors.

Gene amplification during myogenic differentiation

PubMed Central

Fischer, Ulrike; Ludwig, Nicole; Raslan, Abdulrahman; Meier, Carola; Meese, Eckart

2016-01-01

Gene amplifications are mostly an attribute of tumor cells and drug resistant cells. Recently, we provided evidence for gene amplifications during differentiation of human and mouse neural progenitor cells. Here, we report gene amplifications in differentiating mouse myoblasts (C2C12 cells) covering a period of 7 days including pre-fusion, fusion and post-fusion stages. After differentiation induction we found an increase in copy numbers of CDK4 gene at day 3, of NUP133 at days 4 and 7, and of MYO18B at day 4. The amplification process was accompanied by gamma-H2AX foci that are indicative of double stand breaks. Amplifications during the differentiating process were also found in primary human myoblasts with the gene CDK4 and NUP133 amplified both in human and mouse myoblasts. Amplifications of NUP133 and CDK4 were also identified in vivo on mouse transversal cryosections at stage E11.5. In the course of myoblast differentiation, we found amplifications in cytoplasm indicative of removal of amplified sequences from the nucleus. The data provide further evidence that amplification is a fundamental mechanism contributing to the differentiation process in mammalians. PMID:26760505

An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples

USGS Publications Warehouse

Murphy, M.A.; Waits, L.P.; Kendall, K.C.; Wasser, S.K.; Higbee, J.A.; Bogden, R.

2002-01-01

Relatively few large-scale faecal DNA studies have been initiated due to difficulties in amplifying low quality and quantity DNA template. To improve brown bear faecal DNA PCR amplification success rates and to determine post collection sample longevity, five preservation methods were evaluated: 90% ethanol, DETs buffer, silica-dried, oven-dried stored at room temperature, and oven-dried stored at -20??C. Preservation effectiveness was evaluated for 50 faecal samples by PCR amplification of a mitochondrial DNA (mtDNA) locus (???146 bp) and a nuclear DNA (nDNA) locus (???200 bp) at time points of one week, one month, three months and six months. Preservation method and storage time significantly impacted mtDNA and nDNA amplification success rates. For mtDNA, all preservation methods had ??? 75% success at one week, but storage time had a significant impact on the effectiveness of the silica preservation method. Ethanol preserved samples had the highest success rates for both mtDNA (86.5%) and nDNA (84%). Nuclear DNA amplification success rates ranged from 26-88%, and storage time had a significant impact on all methods but ethanol. Preservation method and storage time should be important considerations for researchers planning projects utilizing faecal DNA. We recommend preservation of faecal samples in 90% ethanol when feasible, although when collecting in remote field conditions or for both DNA and hormone assays a dry collection method may be advantageous.

An exact solution for effects of topography on free Rayleigh waves

USGS Publications Warehouse

Savage, W.Z.

2004-01-01

An exact solution for the effects of topography on Rayleigh wave amplification is presented. The solution is obtained by incorporating conformal mapping into complex-variable stress functions developed for free Rayleigh wave propagation in an elastic half-space with a flat upper surface. Results are presented for free Rayleigh wave propagation across isolated symmetric ridges and valleys. It is found for wavelengths that are comparable to ridge widths that horizontal Rayleigh wave amplitudes are amplified at ridge crests and that vertical amplitudes are strongly reduced near ridge crests relative to horizontal and vertical amplitudes of free Rayleigh waves in the flat case. Horizontal amplitudes are strongly deamplified at valley bottoms relative to those for the flat case for Rayleigh wavelengths comparable to valley widths. Wave amplitudes in the symmetric ridges and valleys asymptotically approach those for the flat case with increased wavelengths, increased ridge and valley widths, and with horizontal distance from and depth below the isolated ridges and valleys. Also, prograde particle motion is predicted near crests of narrow ridges and near the bottoms of narrow valleys. Finally, application of the theory at two sites known for topographic wave amplification gives a predicted surface wave amplification ratio of 3.80 at the ridge center for a frequency of 1.0 Hz at Robinwood Ridge in northern California and a predicted surface wave amplification ratio of 1.67 at the ridge center for the same frequency at the Cedar Hill Nursery site at Tarzana in southern California.

Signal Amplification in Field Effect-Based Sandwich Enzyme-Linked Immunosensing by Tuned Buffer Concentration with Ionic Strength Adjuster.

PubMed

Kumar, Satyendra; Kumar, Narendra; Panda, Siddhartha

2016-04-01

Miniaturization of the sandwich enzyme-based immunosensor has several advantages but could result in lower signal strength due to lower enzyme loading. Hence, technologies for amplification of the signal are needed. Signal amplification in a field effect-based electrochemical immunosensor utilizing chip-based ELISA is presented in this work. First, the molarities of phosphate buffer saline (PBS) and concentrations of KCl as ionic strength adjuster were optimized to maximize the GOx glucose-based enzymatic reactions in a beaker for signal amplification measured by change in the voltage shift with an EIS device (using 20 μl of solution) and validated with a commercial pH meter (using 3 ml of solution). The PBS molarity of 100 μM with 25 mM KCl provided the maximum voltage shift. These optimized buffer conditions were further verified for GOx immobilized on silicon chips, and similar trends with decreased PBS molarity were obtained; however, the voltage shift values obtained on chip reaction were lower as compared to the reactions occurring in the beaker. The decreased voltage shift with immobilized enzyme on chip could be attributed to the increased Km (Michaelis-Menten constant) values in the immobilized GOx. Finally, a more than sixfold signal enhancement (from 8 to 47 mV) for the chip-based sandwich immunoassay was obtained by altering the PBS molarity from 10 to 100 μM with 25 mM KCl.

Exploration of S-wave velocity profiles at strong motion stations in Eskisehir, Turkey, using microtremor phase velocity and S-wave amplification

NASA Astrophysics Data System (ADS)

Yamanaka, Hiroaki; Özmen, Ögur Tuna; Chimoto, Kosuke; Alkan, Mehmet Akif; Tün, Muammer; Pekkan, Emrah; Özel, Oguz; Polat, Derya; Nurlu, Murat

2018-05-01

We have explored 1D S-wave velocity profiles of shallow and deep soil layers over a basement at strong motion stations in Eskisehir Province, Turkey. Microtremor array explorations were conducted at eight strong motion stations in the area to know shallow 1D S-wave velocity models. Rayleigh wave phase velocity at a frequency range from 3 to 30 Hz was estimated with the spatial autocorrelation analysis of array records of vertical microtremors at each station. Individual phase velocity was inverted to a shallow S-wave velocity profile. Low-velocity layers were identified at the stations in the basin. Site amplification factors from S-wave parts of earthquake records that had been estimated at the strong motion stations by Yamanaka et al. (2017) were inverted to the S-wave velocities and Q-values of the sedimentary layers. The depths to the basement with an S-wave velocity of 2.2 km/s are about 1 km in the central part of the basin, while the basement becomes shallow as 0.3 km in the marginal part of the basin. We finally discussed the effects of the shallow and deep sedimentary layers on the 1D S-wave amplification characteristics using the revealed profiles. It is found that the shallow soil layers have no significant effects in the amplification at a frequency range lower than 3 Hz in the area.

Rapid detection of Cronobacter sakazakii by real-time PCR based on the cgcA gene and TaqMan probe with internal amplification control.

PubMed

Hu, Shuangfang; Yu, Yigang; Li, Rong; Wu, Xinwei; Xiao, Xinglong; Wu, Hui

2016-03-01

Cronobacter sakazakii is a severe virulent strain that is frequently detected in powdered infant formula (PIF). Therefore, it is necessary to develop a fast and specific detection method. The specificity of our newly developed quantitative real-time PCR (qRT-PCR) was validated with DNA from 46 strains. Among them, 12 C. sakazakii strains were correctly amplified, whereas no positive florescent signal was observed from 34 nontarget controls. The detection limit of C. sakazakii was about 110 CFU/mL in broth and 1100 CFU/g in PIF. After enrichment in buffered peptone water for 6 h, our developed qRT-PCR assay could reliably detect C. sakazakii when the inoculation level was as low as 2 CFU/25 g (0.08 CFU/g) in PIF. The growth of C. sakazakii could be inhibited by the presence of Lactobacillus pentosus and Bacillus cereus, which used a longer enrichment period before the isolation was accomplished. However, at 5 and 50 CFU/25 g inoculation levels of C. sakazakii in the presence of 4 × 10(6) CFU L. pentosus/25 g or of 2 × 10(4) CFU B. cereus/25 g, the qRT-PCR assay could detect the presence of Cronobacter even though these artificially spiked samples were negative in culture. Therefore, our results indicated that the qRT-PCR assay could detect samples containing inhibitors and could avoid false negatives by using an internal amplification control.

Development of a 5'-nuclease real-time PCR assay targeting fliP for the rapid identification of Burkholderia mallei in clinical samples.

PubMed

Tomaso, Herbert; Scholz, Holger C; Al Dahouk, Sascha; Eickhoff, Meike; Treu, Thomas M; Wernery, Renate; Wernery, Ulrich; Neubauer, Heinrich

2006-02-01

Burkholderia mallei is a potential biological agent that causes glanders or farcy in solipeds, a disease notifiable to the Office International des Epizooties (OIE). The number of reported outbreaks has increased steadily during the last decade, but diagnosis is hampered by the low bacterial load in infected tissues and excretions. We developed a B. mallei-specific 5'-nuclease real-time PCR assay that targets the fliP gene of B. mallei and includes an internal amplification control. Specificity was assessed with 19 B. mallei strains, 27 Burkholderia pseudomallei strains, other Burkholderia strains of 29 species, and clinically relevant non-Burkholderia organisms. Amplification products were observed in all B. mallei strains but in no other bacteria. The linear range of the B. mallei real-time PCR covered concentrations from 240 pg to 70 fg of bacterial DNA/reaction. The detection limit was 60 fg of B. mallei DNA. The clinical applicability of the assay was demonstrated by use of organ samples from diseased horses of a recent outbreak that was reported to the OIE by the United Arab Emirates in 2004. Compared with conventional PCR, our rapid 5'-nuclease real-time PCR assay for the specific identification of B. mallei has a lower risk of carryover contamination and eliminates the need for post-PCR manipulations. This real-time PCR assay also shortens the turnaround time for results and has the potential for automation.

Basin-edge generated Rayleigh waves in the Almaty basin and corresponding consequences for ground motion amplification

NASA Astrophysics Data System (ADS)

Pilz, Marco; Parolai, Stefano; Petrovic, Bojana; Silacheva, Natalya; Abakanov, Tanatkan; Orunbaev, Sagynbek; Moldobekov, Bolot

2018-04-01

During the past two centuries, several large earthquakes have caused extensive damages in the city of Almaty in Kazakhstan. Increasing the preparedness for future events, the definition of the optimal engineering designs for civil structures and the corresponding mitigation of earthquake risks involves the accomplishment of site response studies. To this regard, a temporary seismological network of 15 stations was installed in the city aiming at the accurate identification of local variations of site response at different locations. As the city is settled on a deep sediment-filled plain with laterally strongly varying thicknesses, bound to the south by the Tien-Shan mountain range, the city might face important site effects: large amplification and significant increase of shaking duration. In addition, surface waves in the low-frequency range around and slightly higher than the fundamental resonance frequency, which could be generated at the boundaries of the basin, can carry a large amount of energy. In turn, this will influence both the spatial distribution of the level of amplification and the temporal lengthening of ground motion significantly. For quantifying these effects, we apply complex trace analysis, which uses the instantaneous polarization characteristics of the seismic signal for separating waves arriving at a single site from different directions. In this way, secondary surface waves originating at various sites along the edge of the Almaty basin can be identified as well as their generation regions. After having assessed 1-D amplification effects with well-established techniques like the standard spectral ratio and the horizontal-to-vertical spectral ratio techniques, the results further indicate that thick layers of soft clay deposits and the 3-D structure of the basin give rise to lengthening of ground motion and high amplification values at low frequencies around 0.2 Hz. The steep structure of the sediment-bedrock interface at the southern edge of the Almaty basin can generate surface waves with distinct azimuths, meaning that the spatial variability of ground motion is not only related to a simple 1-D response but it can be strongly modified by secondary waves generated at the margin of the basin.

A HER2-specific Modified Fc Fragment (Fcab) Induces Antitumor Effects Through Degradation of HER2 and Apoptosis

PubMed Central

Leung, Kin-Mei; Batey, Sarah; Rowlands, Robert; Isaac, Samine J; Jones, Phil; Drewett, Victoria; Carvalho, Joana; Gaspar, Miguel; Weller, Sarah; Medcalf, Melanie; Wydro, Mateusz M; Pegram, Robert; Mudde, Geert C; Bauer, Anton; Moulder, Kevin; Woisetschläger, Max; Tuna, Mihriban; Haurum, John S; Sun, Haijun

2015-01-01

FS102 is a HER2-specific Fcab (Fc fragment with antigen binding), which binds HER2 with high affinity and recognizes an epitope that does not overlap with those of trastuzumab or pertuzumab. In tumor cells that express high levels of HER2, FS102 caused profound HER2 internalization and degradation leading to tumor cell apoptosis. The antitumor effect of FS102 in patient-derived xenografts (PDXs) correlated strongly with the HER2 amplification status of the tumors. Superior activity of FS102 over trastuzumab or the combination of trastuzumab and pertuzumab was observed in vitro and in vivo when the gene copy number of HER2 was equal to or exceeded 10 per cell based on quantitative polymerase chain reaction (qPCR). Thus, FS102 induced complete and sustained tumor regression in a significant proportion of HER2-high PDX tumor models. We hypothesize that the unique structure and/or epitope of FS102 enables the Fcab to internalize and degrade cell surface HER2 more efficiently than standard of care antibodies. In turn, increased depletion of HER2 commits the cells to apoptosis as a result of oncogene shock. FS102 has the potential of a biomarker-driven therapeutic that derives superior antitumor effects from a unique mechanism-of-action in tumor cells which are oncogenically addicted to the HER2 pathway due to overexpression. PMID:26234505

RUNX1 Amplification Increases the Risk for Thrombosis in Children With B-cell Acute Lymphoblastic Leukemia.

PubMed

Boucher, Maria O; Smitherman, Andrew B; Pahl, Kristy S; Rao, Kathleen W; Deal, Allison M; Blatt, Julie

2016-04-01

RUNX1 (AML1) amplification in patients with B-cell acute lymphoblastic leukemia (B-ALL) has been associated with poor survival for unclear reasons. Our anecdotal experience suggests that children with B-ALL and RUNX1 amplification might be predisposed to thrombosis. We performed a retrospective cohort study of children with B-ALL treated from 2008 to 2014 at the North Carolina Children's Hospital. Patient demographics, cytogenetics, and diagnosis of thrombosis were extracted by blinded chart review. Analysis was performed examining the relationship between RUNX1 amplification and thrombosis. We identified 119 patients with B-ALL and a median age of 4.9 years (interquartile range, 2.9 to 8.6 y) at diagnosis. Four patients (3%) had RUNX1 amplification. The average number of RUNX1 copies among those with amplification was 5 (SD 0.81 [range, 4 to 6]). Eighteen thromboses were diagnosed within 6 months of starting treatment. These events were more likely among patients with RUNX1 amplification than in patients without amplification (75% vs. 13%; RR 5.75, 95% confidence interval, 2.75-12.01). RUNX1 amplification may predispose to early thrombotic events in children with B-ALL which could, in part, contribute to their poorer outcomes. Treatment implications, including possible prophylactic anticoagulation of patients with of RUNX1 amplification, justify larger studies to confirm these findings.

An evaluation of direct PCR amplification

PubMed Central

Hall, Daniel E.; Roy, Reena

2014-01-01

Aim To generate complete DNA profiles from blood and saliva samples deposited on FTA® and non-FTA® paper substrates following a direct amplification protocol. Methods Saliva samples from living donors and blood samples from deceased individuals were deposited on ten different FTA® and non-FTA® substrates. These ten paper substrates containing body fluids were kept at room temperature for varying lengths of time ranging from one day to approximately one year. For all assays in this research, 1.2 mm punches were collected from each substrate containing one type of body fluid and amplified with reagents provided in the nine commercial polymerase chain reaction (PCR) amplification kits. The substrates were not subjected to purification reagent or extraction buffer prior to amplification. Results Success rates were calculated for all nine amplification kits and all ten substrates based on their ability to yield complete DNA profiles following a direct amplification protocol. Six out of the nine amplification kits, and four out of the ten paper substrates had the highest success rates overall. Conclusion The data show that it is possible to generate complete DNA profiles following a direct amplification protocol using both standard (non-direct) and direct PCR amplification kits. The generation of complete DNA profiles appears to depend more on the success of the amplification kit rather than the than the FTA®- or non-FTA®-based substrates. PMID:25559837

CDK4 Amplification Predicts Recurrence of Well-Differentiated Liposarcoma of the Abdomen

PubMed Central

Ha, Sang Yun; Paik, Kwang Yeol; Lee, Seung Eun; Kim, Jong Man; Park, Jae Berm; Kwon, Choon Hyuck David; Joh, Jae-Won; Choi, Yoon-La; Kim, Sung Joo

2014-01-01

Background The absence of CDK4 amplification in liposarcomas is associated with favorable prognosis. We aimed to identify the factors associated with tumor recurrence in patients with well-differentiated (WD) and dedifferentiated (DD) liposarcomas. Methods From 2000 to 2010, surgical resections for 101 WD and DD liposarcomas were performed. Cases in which complete surgical resections with curative intent were carried out were selected. MDM2 and CDK4 gene amplification were analyzed by quantitative real-time polymerase chain reaction (Q-PCR). Results There were 31 WD and 17 DD liposarcomas. Locoregional recurrence was observed in 11 WD and 3 DD liposarcomas. WD liposarcomas showed better patient survival compared to DD liposarcomas (P<0.05). Q-PCR analysis of the liposarcomas revealed the presence of CDK4 amplification in 44 cases (91.7%) and MDM2 amplification in 46 cases (95.8%). WD liposarcomas with recurrence after surgical resection had significantly higher levels of CDK4 amplification compared to those without recurrence (P = 0.041). High level of CDK4 amplification (cases with CDK4 amplification higher than the median 7.54) was associated with poor recurrence-free survival compared to low CDK4 amplification in both univariate (P = 0.012) and multivariate analyses (P = 0.020). Conclusions Level of CDK4 amplification determined by Q-PCR was associated with the recurrence of WD liposarcomas after surgical resection. PMID:25121597

Terrain Classification of Aster gDEM for Seismic Microzonation of Port-Au Haiti, Using - and - Based Analytic Methods

NASA Astrophysics Data System (ADS)

Yong, A.; Hough, S. E.; Cox, B. R.; Rathje, E. M.; Bachhuber, J.; Hulslander, D.; Christiansen, L.; Abrams, M.

2010-12-01

The aftermath of the M7.0 Haiti earthquake of 12 January 2010 witnessed an impressive scientific response from the international community. In addition to conventional post-earthquake investigations, there was also an unprecedented reliance on remote-sensing technologies for scientific investigation and damage assessment. These technologies include sensors from both aerial and space-borne observational platforms. As part of the Haiti earthquake response and recovery effort, we develop a seismic zonation map of Port-au-Prince based on high-resolution satellite imagery as well as data from traditional seismographic monitoring stations and geotechnical site characterizations. Our imagery consists of a global digital elevation model (gDEM) of Hispaniola derived from data recorded by NASA-JPL's Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) instrument onboard the multi-platform satellite Terra. To develop our model we also consider recorded waveforms from portable seismographic stations (Hough et al., in review) and 36 geotechnical shear-wave velocity surveys (Cox et al., in review). Following a similar approach developed by Yong et al. (2008; Bull. Seism Soc. Am.), we use both pixel- and object- based imaging analytic methods to systematically identify and extract local terrain features that are expected to amplify seismic ground motion. Using histogram-stretching techniques applied to the rDEM values, followed by multi-resolution, segmentations of the imagery into terrain types, we systematically classify the terrains of Hispaniola. By associating available Vs30 (average shear-wave velocity in the upper 30 meter depth) calculated from the MASW (Multi-channel Analysis of Surface Wave) survey method, we develop a first-order site characterization map. Our results indicate that the terrain-based Vs30 estimates are significantly associated with amplitudes recorded at station sites. We also find that the damage distribution inferred from UNOSAT (UNITAR Operational Satellite Applications Program) data matches our estimates. However, the strongest amplifications are observed at two stations on a foothill ridge, where Vs30 values indicate that amplification should be relatively lower. Hough et al. (2010, this session) conclude that the observations can be explained by topographic amplification along a steep, narrow ridge. On the basis of these preliminary results, we conclude that the terrain-based framework, which characterizes topographic amplification as well as sediment-induced amplification, is needed to develop a microzonation map for Port-au-Prince.

Afatinib demonstrates remarkable activity against HER2-amplified uterine serous endometrial cancer in vitro and in vivo.

PubMed

Schwab, C L; Bellone, S; English, D P; Roque, D M; Lopez, S; Cocco, E; Nicoletti, R; Bortolomai, I; Bonazzoli, E; Ratner, E; Silasi, D-A; Azodi, M; Schwartz, P E; Rutherford, T J; Santin, A D

2014-10-28

Uterine serous carcinomas (USCs) are an aggressive form of uterine cancer that may rely on HER2/neu amplification as a driver of proliferation. The objective of this paper is to assess the sensitivity of USC cell lines with and without HER2/neu gene amplification to afatinib, an irreversible ErbB tyrosine kinase inhibitor, and to test the efficacy of afatinib in the treatment of HER2-amplified USC xenografts. Eight of fifteen primary USC cell lines (four with HER2 amplification and four without) demonstrating similar in vitro growth rates were treated with scalar concentrations of afatinib. Effects on cell growth, signalling and cell cycle distribution were determined by flow cytometry assays. Mice harbouring xenografts of HER2/neu-amplified USC were treated with afatinib by gavage to determine the effect on tumour growth and overall survival. Primary chemotherapy-resistant USC cell lines harbouring HER2/neu gene amplification were exquisitely sensitive to afatinib exposure (mean ± s.e.m. IC50=0.0056 ± 0.0006 μM) and significantly more sensitive than HER2/neu-non-amplified USC cell lines (mean ± s.e.m. IC50=0.563 ± 0.092 μM, P<0.0001). Afatinib exposure resulted in abrogation of cell survival, inhibition of HER2/neu autophosphorylation and S6 transcription factor phosphorylation in HER2/neu overexpressing USC and inhibited the growth of HER2-amplified tumour xenografts improving overall survival (P=0.0017). Afatinib may be highly effective against HER2/neu-amplified chemotherapy-resistant USC. The investigation of afatinib in patients harbouring HER2/neu-amplified USC is warranted.

Strong Effects of Vs30 Heterogeneity on Physics-Based Scenario Ground-Shaking Computations

NASA Astrophysics Data System (ADS)

Louie, J. N.; Pullammanappallil, S. K.

2014-12-01

Hazard mapping and building codes worldwide use the vertically time-averaged shear-wave velocity between the surface and 30 meters depth, Vs30, as one predictor of earthquake ground shaking. Intensive field campaigns a decade ago in Reno, Los Angeles, and Las Vegas measured urban Vs30 transects with 0.3-km spacing. The Clark County, Nevada, Parcel Map includes urban Las Vegas and comprises over 10,000 site measurements over 1500 km2, completed in 2010. All of these data demonstrate fractal spatial statistics, with a fractal dimension of 1.5-1.8 at scale lengths from 0.5 km to 50 km. Vs measurements in boreholes up to 400 m deep show very similar statistics at 1 m to 200 m lengths. When included in physics-based earthquake-scenario ground-shaking computations, the highly heterogeneous Vs30 maps exhibit unexpectedly strong influence. In sensitivity tests (image below), low-frequency computations at 0.1 Hz display amplifications (as well as de-amplifications) of 20% due solely to Vs30. In 0.5-1.0 Hz computations, the amplifications are a factor of two or more. At 0.5 Hz and higher frequencies the amplifications can be larger than what the 1-d Building Code equations would predict from the Vs30 variations. Vs30 heterogeneities at one location have strong influence on amplifications at other locations, stretching out in the predominant direction of wave propagation for that scenario. The sensitivity tests show that shaking and amplifications are highly scenario-dependent. Animations of computed ground motions and how they evolve with time suggest that the fractal Vs30 variance acts to trap wave energy and increases the duration of shaking. Validations of the computations against recorded ground motions, possible in Las Vegas Valley due to the measurements of the Clark County Parcel Map, show that ground motion levels and amplifications match, while recorded shaking has longer duration than computed shaking. Several mechanisms may explain the amplification and increased duration of shaking in the presence of heterogeneous spatial distributions of Vs: conservation of wave energy across velocity changes; geometric focusing of waves by low-velocity lenses; vertical resonance and trapping; horizontal resonance and trapping; and multiple conversion of P- to S-wave energy.

Beam cleaning of an incoherent laser via plasma Raman amplification

DOE PAGES

Edwards, Matthew R.; Qu, Kenan; Mikhailova, Julia M.; ...

2017-09-25

We show that backward Raman amplification in plasma can efficiently compress a temporally incoherent pump laser into an intense coherent amplified seed pulse, provided that the correlation time of the pump is longer than the inverse plasma frequency. One analytical theory for Raman amplification using pump beams with different correlation functions is developed and compared to numerical calculations and particle-in-cell simulations. Since incoherence on scales shorter than the instability growth time suppresses spontaneous noise amplification, we point out a broad regime where quasi-coherent sources may be used as efficient low-noise Raman amplification pumps. As the amplified seed is coherent, Ramanmore » amplification provides an additional a beam-cleaning mechanism for removing incoherence. At near-infrared wavelengths, finite coherence times as short as 50 fs allow amplification with only minor losses in efficiency.« less

Beam cleaning of an incoherent laser via plasma Raman amplification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edwards, Matthew R.; Qu, Kenan; Mikhailova, Julia M.

We show that backward Raman amplification in plasma can efficiently compress a temporally incoherent pump laser into an intense coherent amplified seed pulse, provided that the correlation time of the pump is longer than the inverse plasma frequency. One analytical theory for Raman amplification using pump beams with different correlation functions is developed and compared to numerical calculations and particle-in-cell simulations. Since incoherence on scales shorter than the instability growth time suppresses spontaneous noise amplification, we point out a broad regime where quasi-coherent sources may be used as efficient low-noise Raman amplification pumps. As the amplified seed is coherent, Ramanmore » amplification provides an additional a beam-cleaning mechanism for removing incoherence. At near-infrared wavelengths, finite coherence times as short as 50 fs allow amplification with only minor losses in efficiency.« less

Gene amplification-associated overexpression of the RNA editing enzyme ADAR1 enhances human lung tumorigenesis.

PubMed

Anadón, C; Guil, S; Simó-Riudalbas, L; Moutinho, C; Setien, F; Martínez-Cardús, A; Moran, S; Villanueva, A; Calaf, M; Vidal, A; Lazo, P A; Zondervan, I; Savola, S; Kohno, T; Yokota, J; Ribas de Pouplana, L; Esteller, M

2016-08-18

The introduction of new therapies against particular genetic mutations in non-small-cell lung cancer is a promising avenue for improving patient survival, but the target population is small. There is a need to discover new potential actionable genetic lesions, to which end, non-conventional cancer pathways, such as RNA editing, are worth exploring. Herein we show that the adenosine-to-inosine editing enzyme ADAR1 undergoes gene amplification in non-small cancer cell lines and primary tumors in association with higher levels of the corresponding mRNA and protein. From a growth and invasion standpoint, the depletion of ADAR1 expression in amplified cells reduces their tumorigenic potential in cell culture and mouse models, whereas its overexpression has the opposite effects. From a functional perspective, ADAR1 overexpression enhances the editing frequencies of target transcripts such as NEIL1 and miR-381. In the clinical setting, patients with early-stage lung cancer, but harboring ADAR1 gene amplification, have poor outcomes. Overall, our results indicate a role for ADAR1 as a lung cancer oncogene undergoing gene amplification-associated activation that affects downstream RNA editing patterns and patient prognosis.

A Digital Microfluidics Platform for Loop-Mediated Isothermal Amplification Detection

PubMed Central

Veigas, Bruno; Águas, Hugo; Fortunato, Elvira; Martins, Rodrigo; Baptista, Pedro Viana; Igreja, Rui

2017-01-01

Digital microfluidics (DMF) arises as the next step in the fast-evolving field of operation platforms for molecular diagnostics. Moreover, isothermal schemes, such as loop-mediated isothermal amplification (LAMP), allow for further simplification of amplification protocols. Integrating DMF with LAMP will be at the core of a new generation of detection devices for effective molecular diagnostics at point-of-care (POC), providing simple, fast, and automated nucleic acid amplification with exceptional integration capabilities. Here, we demonstrate for the first time the role of coupling DMF and LAMP, in a dedicated device that allows straightforward mixing of LAMP reagents and target DNA, as well as optimum temperature control (reaction droplets undergo a temperature variation of just 0.3 °C, for 65 °C at the bottom plate). This device is produced using low-temperature and low-cost production processes, adaptable to disposable and flexible substrates. DMF-LAMP is performed with enhanced sensitivity without compromising reaction efficacy or losing reliability and efficiency, by LAMP-amplifying 0.5 ng/µL of target DNA in just 45 min. Moreover, on-chip LAMP was performed in 1.5 µL, a considerably lower volume than standard bench-top reactions. PMID:29144379

Real-Time Sequence-Validated Loop-Mediated Isothermal Amplification Assays for Detection of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

PubMed Central

Bhadra, Sanchita; Jiang, Yu Sherry; Kumar, Mia R.; Johnson, Reed F.; Hensley, Lisa E.; Ellington, Andrew D.

2015-01-01

The Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF)1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD) for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU) (5 to 50 PFU/ml) of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens. PMID:25856093

A Graphene-enhanced imaging of microRNA with enzyme-free signal amplification of catalyzed hairpin assembly in living cells.

PubMed

Liu, Haiyun; Tian, Tian; Ji, Dandan; Ren, Na; Ge, Shenguang; Yan, Mei; Yu, Jinghua

2016-11-15

In situ imaging of miRNA in living cells could help us to monitor the miRNA expression in real time and obtain accurate information for studying miRNA related bioprocesses and disease. Given the low-level expression of miRNA, amplification strategies for intracellular miRNA are imperative. Here, we propose an amplification strategy with a non-destructive enzyme-free manner in living cells using catalyzed hairpin assembly (CHA) based on graphene oxide (GO) for cellular miRNA imaging. The enzyme-free CHA exhibits stringent recognition and excellent signal amplification of miRNA in the living cells. GO is a good candidate as a fluorescence quencher and cellular carrier. Taking the advantages of the CHA and GO, we can monitor the miRNA at low level in living cells with a simple, sensitive and real-time manner. Finally, imaging of miRNAs in the different expression cells is realized. The novel method could supply an effective tool to visualize intracellular low-level miRNAs and help us to further understand the role of miRNAs in cellular processes. Copyright © 2016 Elsevier B.V. All rights reserved.

Recombinase polymerase and enzyme-linked immunosorbent assay as a DNA amplification-detection strategy for food analysis.

PubMed

Santiago-Felipe, S; Tortajada-Genaro, L A; Puchades, R; Maquieira, A

2014-02-06

Polymerase chain reaction in conjunction with enzyme-linked immunosorbent assay (PCR-ELISA) is a well-established technique that provides a suitable rapid, sensitive, and selective method for a broad range of applications. However, the need for precise rapid temperature cycling of PCR is an important drawback that can be overcome by employing isothermal amplification reactions such as recombinase polymerase amplification (RPA). The RPA-ELISA combination is proposed for amplification at a low, constant temperature (40°C) in a short time (40 min), for the hybridisation of labelled products to specific 5'-biotinylated probes/streptavidin in coated microtiter plates at room temperature, and for detection by colorimetric immunoassay. RPA-ELISA was applied to screen common safety threats in foodstuffs, such as allergens (hazelnut, peanut, soybean, tomato, and maize), genetically modified organisms (P35S and TNOS), pathogenic bacteria (Salmonella sp. and Cronobacter sp.), and fungi (Fusarium sp.). Satisfactory sensitivity and reproducibility results were achieved for all the targets. The RPA-ELISA technique does away with thermocycling and provides a suitable sensitive, specific, and cost-effective method for routine applications, and proves particularly useful for resource-limited settings. Copyright © 2013 Elsevier B.V. All rights reserved.

Semi-automated repetitive sequence-based PCR amplification for species of the Scedosporium apiospermum complex.

PubMed

Matray, Olivier; Mouhajir, Abdelmounaim; Giraud, Sandrine; Godon, Charlotte; Gargala, Gilles; Labbé, Franck; Rougeron, Amandine; Ballet, Jean-Jacques; Zouhair, Rachid; Bouchara, Jean-Philippe; Favennec, Loïc

2016-05-01

The Scedosporium apiospermum species complex usually ranks second among the filamentous fungi colonizing the airways of patients with cystic fibrosis (CF), but little is known about the molecular epidemiology of the airway colonization. Polymerase chain reaction (PCR) amplification of repetitive sequences (rep-PCR) was applied to the retrospective analysis of a panel of isolates already studied by random amplification of polymorphic DNA (RAPD) and comprising 63 isolates recovered from sputa from 9 CF patients. Results were compared to those obtained previously by RAPD, and herein by beta-tubulin (TUB) gene sequencing and Multilocus Sequence Typing (MLST). Within the panel of isolates studied,S. apiospermum sensu stricto and Scedosporium boydii, as expected, were the predominant species with 21 and 36 isolates, respectively. Four isolates from one patient were identified as Scedosporium aurantiacum, whereas two isolates belonged to the Pseudallescheria ellipsoidea subgroup of S. boydii rep-PCR analysis of these isolates clearly differentiated the three species and P. ellipsoidea isolates, whatever the rep-PCR kit used, and also permitted strain differentiation. When using the mold primer kit, results from rep-PCR were in close agreement with those obtained by MLST. For both S. apiospermum and S. boydii, 8 genotypes were differentiated by rep-PCR and MLST compared to 10 by RAPD. All S. aurantiacum isolates shared the same RAPD genotype and exhibited the same rep-PCR profile and sequence type. These results illustrate the efficacy of rep-PCR for both species identification within the S. apiospermum complex and genotyping for the two major species of this complex.Abstract presentation: Part of this work was presented during the 18th Congress of the International Society for Human and Animal Mycology, Berlin (Germany), June 2012.S. Giraud, C. Godon, A. Rougeron, J.P. Bouchara and L. Favennec are members of the ECMM/ISHAM working group on Fungal respiratory infections in Cystic Fibrosis(Fri-CF). © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The role of local soil-induced amplification in the 27 July 1980 northeastern Kentucky earthquake

USGS Publications Warehouse

Woolery, E.W.; Lin, T.-L.; Wang, Z.; Shi, B.

2008-01-01

Amplification of earthquake ground motions by near-surface soil deposits was believed to have occurred in Maysville, Kentucky, U.S.A. during the northeast Kentucky (Sharpsburg) earthquake (mb,Lg 5.3) of July 27, 1980. The city of Maysville, founded on approximately 30 m of Late Quaternary Ohio River flood plain alluvium, was 52 km from the epicenter, but experienced equivalent or higher Modified Mercalli Intensity (MMI) VII, compared with the epicentral area of the earthquake (i.e., MMI VI-VII). In this study, dynamic soil properties were obtained at 10 sites in Maysville using seismic P-wave and S-wave (SH-mode) refraction and reflection methods. Synthetically generated composite time histories and limited geotechnical information, along with the measured dynamic properties, were used to perform one-dimensional linear-equivalent amplification analyses. The results indicated the soils generated ground-motion amplification factors between 3.0 and 6.0 and at a frequency range between 2.0 and 5.0 Hz (0.2 to 0.5 s). The building damage in Maysville from the Sharpsburg earthquake was predominantly found in one- to three-story masonry structures. The estimated fundamental period for one- to three-story masonry buildings is approximately 0.11 to 0.26 s (3.8 to 9 Hz). These correlations suggest the elevated ground motion intensity in Maysville can be accounted for by near-surface soil-amplification effects and resonance of the ground motion by the buildings (i.e., double resonance).

Efficient Sub-Bandgap Light Absorption and Signal Amplification in Silicon Photodetectors

NASA Astrophysics Data System (ADS)

Liu, Yu-Hsin

This thesis focuses on two areas in silicon photodetectors, the first being enhancing the sub-bandgap light absorption of IR wavelenghts in silicon, and the second being intrinsic signal amplification in silicon photodetectors. Both of these are achieved using heavily doped p-n junction devices which create localized states that relax the k-selection rule of indirect bandgap material. The probability of transitions between impurity band and the conduction/valence band would be much more efficient than the one between band-to-band transition. The waveguide-coupled epitaxial p-n photodetector was demonstrated for 1310 nm wavelength detection. Incorporated with the Franz-Keldysh effect and the quasi-confined epitaxial layer design, an absorption coefficient around 10 cm-1 has been measured and internal quantum efficiency nearly 100% at -2.5V. The absorption coefficient is calculated from the wave function of the electron and hole in p-n diode. The heavily doped impurity wave function can be formulated as a delta function, and the quasi-confined conduction band energy states, and the wave function on each level can be obtained from the Silvaco software. The calculated theoretical absorption coefficient increases with the increasing applied bias and the doping concentration, which matches the experimental results. To solve the issues of large excess noise and high operation bias for avalanche photodiodes based on impact ionization, I presented a detector using the Cycling Excitation Process (CEP) for signal amplification. This can be realized in a heavily doped and highly compensated Si p-n junction, showing ultra high gain about 3000 at very low bias (<4 V), and possessing an intrinsic, phonon-mediated regulation process to keep the device stable without any quenching device required in today's Geiger-mode avalanche detectors. The CEP can be formulated with the rate equations in conduction bands and impurity states. The gain expression, which is a function of the primary photocurrent and related to the phonon absorption time, predicts the same trend of the gain increasing with temperature and decreasing with increasing primary photocurrent.

Methods and devices based on brillouin selective sideband amplification

NASA Technical Reports Server (NTRS)

Yao, X. Steve (Inventor)

2003-01-01

Opto-electronic devices and techniques using Brillouin scattering to select a sideband in a modulated optical carrier signal for amplification. Two lasers respectively provide a carrier signal beam and a Brillouin pump beam which are fed into an Brillouin optical medium in opposite directions. The relative frequency separation between the lasers is adjusted to align the frequency of the backscattered Brillouin signal with a desired sideband in the carrier signal to effect a Brillouin gain on the sideband. This effect can be used to implement photonic RF signal mixing and conversion with gain, conversion from phase modulation to amplitude modulation, photonic RF frequency multiplication, optical and RF pulse generation and manipulation, and frequency-locking of lasers.

A nanoscale piezoelectric transformer for low-voltage transistors.

PubMed

Agarwal, Sapan; Yablonovitch, Eli

2014-11-12

A novel piezoelectric voltage transformer for low-voltage transistors is proposed. Placing a piezoelectric transformer on the gate of a field-effect transistor results in the piezoelectric transformer field-effect transistor that can switch at significantly lower voltages than a conventional transistor. The piezoelectric transformer operates by using one piezoelectric to squeeze another piezoelectric to generate a higher output voltage than the input voltage. Multiple piezoelectrics can be used to squeeze a single piezoelectric layer to generate an even higher voltage amplification. Coupled electrical and mechanical modeling in COMSOL predicts a 12.5× voltage amplification for a six-layer piezoelectric transformer. This would lead to more than a 150× reduction in the power needed for communications.

Impact of pumping configuration on all-fibered femtosecond chirped pulse amplification

NASA Astrophysics Data System (ADS)

Lecourt, Jean-Bernard; Duterte, Charles; Bertrand, Anthony; Liégeois, Flavien; Hernandez, Yves; Giannone, Domenico

2008-04-01

We experimentally compared the co- and counter-propagative pumping scheme for the amplification of ultra-short optical pulses. According to pumping direction we show that optical pulses with a duration of 75 fs and 100mW of average output power can be obtained for co-propagative pumping, while pulse duration is never shorter than 400 fs for the counter-propagative case. We show that the impact of non-linear effects on pulse propagation is different for the two pumping configurations. We assume that Self Phase Modulation (SPM) is the main effect in the copropagative case, whereas the impact of Stimulated Raman Scattering is bigger for the counter-propagative case.

The effect of working memory capacity limitations on the intuitive assessment of correlation: amplification, attenuation, or both?

PubMed

Cahan, Sorel; Mor, Yaniv

2007-03-01

This article challenges Yaakov Kareev's (1995a, 2000) argument regarding the positive bias of intuitive correlation estimates due to working memory capacity limitations and its adaptive value. The authors show that, under narrow window theory's primacy effect assumption, there is a considerable between-individual variability of the effects of capacity limitations on the intuitive assessment of correlation, in terms of both sign and magnitude: Limited capacity acts as an amplifier for some individuals and as a silencer for others. Furthermore, the average amount of attenuation exceeds the average amount of amplification, and the more so, the smaller the capacity. Implications regarding the applicability and contribution of the bias notion in this context and the evaluation of the adaptive value of capacity limitations are discussed.

Gravitational lensing in observational cosmology

NASA Astrophysics Data System (ADS)

Nottale, L.

This paper reviews some previous theoretical and observational results concerning the various effects of gravitational lensing, and also presents still unpublished results in this field. The theoretical section deals with the Optical Scalar Equation (OSE) approach. We recall the form of these equations, which relate the deformations of the cross sectional area of a light beam to the material and energetic distribution it encounters, via the two basic contributions to lensing, the matter or Ricci term and the shear term. The introduction of a new distance, the optical distance, allows to write the OSE in a simplified way from which new solutions are easily derived. We demonstrate here that a general form may be obtained for the amplification formula in the exact relativistic treatment, provided the Universe is assumed to be Friedmannian in the mean. New results are also presented concerning the probability distribution of amplifications, the relation from matter term to shear terms (the first ones give the mean of the second ones) and the problem of energy conservation. We recall how our method let to an analytical formula yielding the amplification by any number of lenses placed anywhere along the line of sight and present new general solutions for lensing by large scale density inhomogeneities. The gravitational redshift effects are also considered, either due to the crossing by photons of inhomogeneities, or intrinsic to them ; generalized solutions to the last problem are given. Some observational evidence concerning various lensing effects, either statistical or applying to individual sources, are considered. We first recall how the dependence of the amplification formula on the various physical parameters points towards the optimisation of lensing by very rich clusters of galaxies lying at redshifts around 0.7, which may give rise to very large amplifications for reasonable values of the density parameter. Recent results concerning a statistical effect of amplification of Brightest Cluster Galaxies by foreground clusters are analysed, including the discussion of a selection effect precisely due to gravitational luminosity amplification. It results in an artificial increase of the deceleration parameter of the Universe measured from the Hubble diagram of these objects. We recall our proposal that the sample of distant 3C radiogalaxies of redshift > 1 is strongly perturbed by lensing effects, mostly by foreground clusters of galaxies (i.e. only the luminosity is changed without image multiplication), but also for some objects by galaxies, producing gravitational mirages. The case of 3C324, for which definite evidence for multiple imaging has been recently obtained, is described, including detailed modelling of the lensing configuration. We present a highly significant statistical effect of lensing on absorption line QSOs due to matter lying at the absorption redshifts. Microlensing is also considered, and we recall our recent proposal that the variability of some among the OVV QSOs turning to BL Lac at maximum brightness, like the eruptive object 0846 +51W1, is a consequence of microlensing by stars or compact objects constituting foreground galaxy halos. Finally, discrepant redshift associations are considered. We recall how the case of anomalous quintets of galaxies have been explained by the gravitational lensing effects of quartets halos on background galaxies. Then we present evidence that the Arp QSO-galaxy associations may be the result of the combined lensing effects of several superposed galaxies, groups and clusters. Cet article présente une revue de certains résultats théoriques et observationnels concernant les divers effets de lentille gravitationnelle, complétée par des résultats nouveaux non encore publiés. Dans la partie théorique, nous considérons essentiellement l'approche relativiste employant les équations scalaires optiques. La forme de ces équations est rappelée : elles relient les diverses déformations subies par la section d'un faisceau lumineux au cours de sa propagation, à la distribution matérielle et énergétique qu'il rencontre sur son trajet entre la source et l'observateur. Les deux contributions aux effets d'optique apparaissant dans ces équations (et leurs solutions) sont les termes de matière et les termes de cisaillement. Nous montrons comment une nouvelle distance peut être introduite, la distance optique, en fonction de laquelle les équations se simplifient et de nouvelles solutions analytiques peuvent être établies. En particulier, nous démontrons que la formule d'amplification gravitationnelle peut s'écrire sous une forme très générale sous la simple hypothèse que l'Univers est en moyenne de type Friedmann-Robertson-Walker. De nouveaux résultats sont aussi présentés concernant la distribution de probabilité des amplifications, les rapports entre termes de matière et termes de cisaillement (les premiers donnant la moyenne des seconds), et le problème de la conservation de l'énergie. Nous rappelons comment une formule analytique peut être obtenue pour des amplifications multiples et présentons des solutions nouvelles au problème de l'amplification par des hétérogénéités à très grande échelle. Enfin, les effets de décalages spectraux gravitationnels sont aussi considérés, qu'ils soient dus à des effets de traversée d'excès de densité, ou intrinsèques à ceux-ci ; dans ce dernier cas, une généralisation de solutions déjà connues est proposée. On considère ensuite le problème de la mise en évidence observationnelle des divers effets d'optique gravitationnelle, qu'ils soient de nature statistique ou qu'ils concernent des objets individuels. A la suite d'une analyse décrivant la dépendance de la formule d'amplification en fonction des différents paramètres y intervenant, nous insistons tout particulièrement sur le rôle cosmologique que jouent probablement les amas de galaxies très riches de décalages spectraux autour de 0,7 qui peuvent donner lieu à des amplifications quasi-infinies. La mise en évidence récente d'un effet statistique d'amplification par des amas d'avant-plan sur les galaxies les plus brillantes des amas est rappelée, ainsi que celle d'un important effet de sélection observationnel, précisément dû aux amplifications, qui augmente artificiellement la valeur de q0 mesurée à partir du diagramme de Hubble. L'extrapolation de cet effet à des objets plus lointains nous a conduit à proposer que les radiogalaxies lointaines du catalogue 3C de z < 1 étaient fortement affectées par les effets de lentille gravitationnelle, essentiellement par les amas (qui les amplifient la plupart du temps sans multiplication d'image), mais aussi dans certains cas par des galaxies qui peuvent alors provoquer des effets de mirage. Le cas de 3C324, pour lequel des preuves observationelles de multiplication d'image ont été récemment obtenues, est analysé en particulier ; un modèle détaillé en est présenté. Un autre effet statistique récemment démontré concerne les quasars à raies d'absorption, dont la luminosité est fortement corrélée à l'amplification prédite par de la matière située aux décalages spectraux d'absorption. On considère également les effets de microlentille : nous rappelons notre proposition récente que la variabilité de certains OVVs tels que le BL Lac éruptif 0846 + 51W1 est une conséquence du passage d'étoiles ou d'objets compacts du halo de galaxies intervenantes devant les régions centrales d'un quasar. Le lien entre effets d'optique gravitationnelle et associations de décalages spectraux discordants est évoqué. Le cas des quintets de galaxies discordant a été récemment expliqué par les effets (amplification, agrandissement, changement de densité superficielle d'objets lointains) des halos de groupes compacts de galaxies. Nous démontrons pour finir que les associations QSOsgalaxies de Arp peuvent s'expliquer par les effets de lentille gravitationnelle combinés de plusieurs galaxies, groupes et amas vus en superposition.

Site Effect and Expected Seismic Performance of Buildings in Palestine- Case Study: Nablus City

DOE Office of Scientific and Technical Information (OSTI.GOV)

Al-Dabbeek, Jalal N.; El-Kelani, Radwan J.

2008-07-08

The effects of local geology on ground-motion amplification and building damage were studied in Palestine-West Bank. Nakamura's method of microtremor analysis was applied in this study. The measurements showed significantly higher amplification in the frequency range of building vulnerability in different parts of Nablus city. This finding is consistent with the distribution of the earthquake damage grades in the urban areas struck by the 11 February 2004 earthquake (ML = 5.2) with a focal depth of 17 km beneath the northeastern part of the Dead Sea Basin. Quite large differences in amplification between around 1 and 9 were computed betweenmore » the eastern and western rims of the city. The downtown built in the central part of the city on soft clay, marl and valley deposits, whereas the northern and southern parts of urban areas in Nablus city lying on mountains consist of consolidated carbonates bedrock. In the central part of the city and at the rims, where the thickness of fluvial deposits and soft formations is about 15 m, amplifications between 6.74 and 8.67 for dominant natural period range of 0.8-1.1 sec were obtained. On the southern and northern mountains, which are located on limestone rocks covered with a thin layer of soil, the amplification in the same frequency range was low. Calculating the natural period of the existing common buildings (T{sub b}) in the studied area (buildings with 10-12 stories), by using the dynamic analysis method. The values of T{sub b} obtained were much closed to the site dominant natural period (Ts). The findings of this study indicate that the expected differences in damage grades for urban areas in Nablus city could be attributed to variations in the thickness and physical properties of Tertiary-Quaternary sediments, which appear to be rather heterogeneous.« less

Site Effect and Expected Seismic Performance of Buildings in Palestine- Case Study: Nablus City

NASA Astrophysics Data System (ADS)

Al-Dabbeek, Jalal N.; El-Kelani, Radwan J.

2008-07-01

The effects of local geology on ground-motion amplification and building damage were studied in Palestine-West Bank. Nakamura's method of microtremor analysis was applied in this study. The measurements showed significantly higher amplification in the frequency range of building vulnerability in different parts of Nablus city. This finding is consistent with the distribution of the earthquake damage grades in the urban areas struck by the 11 February 2004 earthquake (ML = 5.2) with a focal depth of 17 km beneath the northeastern part of the Dead Sea Basin. Quite large differences in amplification between around 1 and 9 were computed between the eastern and western rims of the city. The downtown built in the central part of the city on soft clay, marl and valley deposits, whereas the northern and southern parts of urban areas in Nablus city lying on mountains consist of consolidated carbonates bedrock. In the central part of the city and at the rims, where the thickness of fluvial deposits and soft formations is about 15 m, amplifications between 6.74 and 8.67 for dominant natural period range of 0.8-1.1 sec were obtained. On the southern and northern mountains, which are located on limestone rocks covered with a thin layer of soil, the amplification in the same frequency range was low. Calculating the natural period of the existing common buildings (Tb) in the studied area (buildings with 10-12 stories), by using the dynamic analysis method. The values of Tb obtained were much closed to the site dominant natural period (Ts). The findings of this study indicate that the expected differences in damage grades for urban areas in Nablus city could be attributed to variations in the thickness and physical properties of Tertiary-Quaternary sediments, which appear to be rather heterogeneous.

Directional Site Amplification Effect on Tarzana Hill, California

NASA Astrophysics Data System (ADS)

Graizer, V.; Shakal, A.

2003-12-01

Significantly amplified ground accelerations at the Tarzana Hill station were recorded during the 1987 Mw 5.9 Whittier Narrows and the 1994 Mw 6.7 Northridge earthquakes. Peak horizontal ground acceleration at the Tarzana station during the 1999 Mw 7.1 Hector Mine earthquake was almost twice as large as the accelerations recorded at nearby stations. The Tarzana site was drilled to a depth of 100 m. A low shear-wave velocity near the surface of 100 m/sec increasing to near 750 m/sec at 100 m depth was measured. The 20 m high hill was found to be well drained with a water table near 17 m. Modelo formation (extremely weathered at the surface to fresh at depth) underlies the hill. The subsurface geology and velocities obtained allow classification of this location as a soft-rock site. After the Northridge earthquake the California Strong Motion Instrumentation Program significantly increased instrumentation at Tarzana to study the unusual site amplification effect. Current instrumentation at Tarzana consists of an accelerograph at the top of Tarzana hill (Tarzana - Cedar Hill B), a downhole instrument at 60 m depth, and an accelerograph at the foot of the hill (Tarzana - Clubhouse), 180 m from the Cedar Hill B station. The original station, Tarzana - Cedar Hill Nursery A, was lost in 1999 due to construction. More than twenty events, including the Hector Mine earthquake, were recorded by all these instruments at Tarzana. Comparison of recordings and response spectra demonstrates strong directional resonance on the top of the hill in a direction perpendicular to the strike of the hill in the period range from 0.04 to 0.8 sec (1.2 to 25 Hz). There is practically no amplification from the bottom to the top of the hill for the component parallel to the strike of the hill. In contrast to accelerations recorded during the Hector Mine earthquake (high frequency part of seismic signal), displacements (relatively low frequency part of seismic signal) demonstrate almost no site amplification from the bottom of the hole to the surface at periods greater than 1.5 sec, in either direction. The directional effect at Tarzana hill seems to be azimuth dependent. Relatively higher amplification at the perpendicular component is produced for the earthquake sources located north of the station. We were not able to see any differences in hill response before and after development (a relatively small part of the hill was developed). The source of the site amplification that produces large motions at Tarzana is still under investigation with "the usual suspects" like topography and shear wave velocity profile not providing the explanation. New data recorded at Tarzana in recent years clearly show that the Tarzana effect is a very localized high-frequency effect observed only at the top of the hill. Drilling at Tarzana was co-funded by CSMIP and by the National Science Foundation through the Resolution of Site Response Issues from the Northridge Earthquake Project (ROSRINE).

Self-optimizing Pitch Control for Large Scale Wind Turbine Based on ADRC

NASA Astrophysics Data System (ADS)

Xia, Anjun; Hu, Guoqing; Li, Zheng; Huang, Dongxiao; Wang, Fengxiang

2018-01-01

Since wind turbine is a complex nonlinear and strong coupling system, traditional PI control method can hardly achieve good control performance. A self-optimizing pitch control method based on the active-disturbance-rejection control theory is proposed in this paper. A linear model of the wind turbine is derived by linearizing the aerodynamic torque equation and the dynamic response of wind turbine is transformed into a first-order linear system. An expert system is designed to optimize the amplification coefficient according to the pitch rate and the speed deviation. The purpose of the proposed control method is to regulate the amplification coefficient automatically and keep the variations of pitch rate and rotor speed in proper ranges. Simulation results show that the proposed pitch control method has the ability to modify the amplification coefficient effectively, when it is not suitable, and keep the variations of pitch rate and rotor speed in proper ranges

Soliton-induced relativistic-scattering and amplification.

PubMed

Rubino, E; Lotti, A; Belgiorno, F; Cacciatori, S L; Couairon, A; Leonhardt, U; Faccio, D

2012-01-01

Solitons are of fundamental importance in photonics due to applications in optical data transmission and also as a tool for investigating novel phenomena ranging from light generation at new frequencies and wave-trapping to rogue waves. Solitons are also moving scatterers: they generate refractive index perturbations moving at the speed of light. Here we found that such perturbations scatter light in an unusual way: they amplify light by the mixing of positive and negative frequencies, as we describe using a first Born approximation and numerical simulations. The simplest scenario in which these effects may be observed is within the initial stages of optical soliton propagation: a steep shock front develops that may efficiently scatter a second, weaker probe pulse into relatively intense positive and negative frequency modes with amplification at the expense of the soliton. Our results show a novel all-optical amplification scheme that relies on soliton induced scattering.

Enzymatic amplification of a flow-injected thermometric enzyme-linked immunoassay for human insulin.

PubMed

Mecklenburg, M; Lindbladh, C; Li, H; Mosbach, K; Danielsson, B

1993-08-01

A flow-injected thermometric enzyme linked immunoassay for human insulin which employs the lactate dehydrogenase/lactate oxidase (LDH/LOD) substrate recycling system for signal amplification is described. The system is composed of two columns, an immunosorbent column containing immobilized anti-insulin antibodies for sensing and a recycling column containing immobilized LDH/LOD/Catalase for detection. The effect of flow rates, conjugate concentrations, and chromatographic support material upon the sensitivity of the assay are investigated. The assay has a detection limit of 0.025 microgram/ml and a linear range from 0.05 to 2 micrograms/ml. This corresponds to a 10-fold increase in sensitivity over the unamplified system. A recombinant human insulin-proinsulin conjugate was also tested. The results show that enzymatic amplification can be employed to increase the sensitivity and reproducibility of flow injection assay-based biosensors. The implications of these results upon on-line analysis are discussed.

Raman-noise-induced quantum limits for χ(3) nondegenerate phase-sensitive amplification and quadrature squeezing

NASA Astrophysics Data System (ADS)

Voss, Paul L.; Köprülü, Kahraman G.; Kumar, Prem

2006-04-01

We present a quantum theory of nondegenerate phase-sensitive parametric amplification in a χ(3) nonlinear medium. The nonzero response time of the Kerr (χ(3)) nonlinearity determines the quantum-limited noise figure of χ(3) parametric amplification, as well as the limit on quadrature squeezing. This nonzero response time of the nonlinearity requires coupling of the parametric process to a molecular vibration phonon bath, causing the addition of excess noise through spontaneous Raman scattering. We present analytical expressions for the quantum-limited noise figure of frequency nondegenerate and frequency degenerate χ(3) parametric amplifiers operated as phase-sensitive amplifiers. We also present results for frequency nondegenerate quadrature squeezing. We show that our nondegenerate squeezing theory agrees with the degenerate squeezing theory of Boivin and Shapiro as degeneracy is approached. We have also included the effect of linear loss on the phase-sensitive process.

[Development and validation of event-specific quantitative PCR method for genetically modified maize LY038].

PubMed

Mano, Junichi; Masubuchi, Tomoko; Hatano, Shuko; Futo, Satoshi; Koiwa, Tomohiro; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Akiyama, Hiroshi; Teshima, Reiko; Kurashima, Takeyo; Takabatake, Reona; Kitta, Kazumi

2013-01-01

In this article, we report a novel real-time PCR-based analytical method for quantitation of the GM maize event LY038. We designed LY038-specific and maize endogenous reference DNA-specific PCR amplifications. After confirming the specificity and linearity of the LY038-specific PCR amplification, we determined the conversion factor required to calculate the weight-based content of GM organism (GMO) in a multilaboratory evaluation. Finally, in order to validate the developed method, an interlaboratory collaborative trial according to the internationally harmonized guidelines was performed with blind DNA samples containing LY038 at the mixing levels of 0, 0.5, 1.0, 5.0 and 10.0%. The precision of the method was evaluated as the RSD of reproducibility (RSDR), and the values obtained were all less than 25%. The limit of quantitation of the method was judged to be 0.5% based on the definition of ISO 24276 guideline. The results from the collaborative trial suggested that the developed quantitative method would be suitable for practical testing of LY038 maize.

On the Causes of and Long Term Changes in Eurasian Heat Waves

NASA Technical Reports Server (NTRS)

Schubert, Siegfried; Wang, Hailan; Koster, Randal; Suarez, Max

2012-01-01

The MERRA reanalysis, other observations, and the GEOS-S model have been used to diagnose the causes of Eurasian heat waves including the recent extreme events that occurred in Europe during 2003 and in Russia during 2010. The results show that such extreme events are an amplification of natural patterns of atmospheric variability (in this case a particular large-scale atmospheric planetary wave) that develop over the Eurasian continent as a result of internal atmospheric forcing. The amplification occurs when the wave occasionally becomes locked in place for several weeks to months resulting in extreme heat and drying with the location depending on the phase of the upper atmospheric wave. Model experiments suggest that forcing from both the ocean (SST) and land playa role phase-locking the waves. An ensemble of very long GEOS-S model simulations (spanning the 20th century) forced with observed SST and greenhouse gases show that the model is capable of generating very similar heat waves, and that they have become more extreme in the last thirty years as a result of the overall warming of the Asian continent.

TRASER - Total Reflection Amplification of Spontaneous Emission of Radiation

PubMed Central

Zachary, Christopher B.; Gustavsson, Morgan

2012-01-01

Background and Objective Light and lasers in medical therapy have made dramatic strides since their invention five decades ago. However, the manufacture of lasers can be complex and expensive which often makes treatments limited and costly. Further, no single laser will provide the correct parameters to treat all things. Hence, laser specialists often need multiple devices to practice their specialty. A new concept is described herein that has the potential to replace many lasers and light sources with a single ‘tunable’ device. Study Design/Material and Methods This device amplifies spontaneous emission of radiation by capturing and retaining photons through total internal reflection, hence the acronym Total Reflection Amplification of Spontaneous Emission of Radiation, or TRASER. Results Specific peaks of light can be produced in a reproducible manner with high peak powers of variable pulse durations, a large spot size, and high repetition rate. Conclusion Considering the characteristics and parameters of Traser technology, it is possible that this one device would likely be able to replace the pulsed dye laser and many other light based systems. PMID:22558261

Approaches to Selection and Fitting of Amplification for Infants and Toddlers.

ERIC Educational Resources Information Center

Beauchaine, Kathryn L.

This paper addresses three areas related to amplification for infants and toddlers with hearing impairments: (1) identification issues as they relate to early amplification; (2) selection of amplification; and (3) assessment of aided function. Identification issues discussed include the goal of early identification of hearing loss and the impact…

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

PubMed

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.

Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices

PubMed Central

Zanoli, Laura Maria; Spoto, Giuseppe

2012-01-01

Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed. PMID:25587397

Amplification of seismic waves by the Seattle basin, Washington State

USGS Publications Warehouse

Pratt, T.L.; Brocher, T.M.; Weaver, C.S.; Creager, K.C.; Snelson, C.M.; Crosson, R.S.; Miller, K.C.; Trehu, A.M.

2003-01-01

Recordings of the 1999 Mw 7.6 Chi-Chi (Taiwan) earthquake, two local earthquakes, and five blasts show seismic-wave amplification over a large sedimentary basin in the U.S. Pacific Northwest. For weak ground motions from the Chi-Chi earthquake, the Seattle basin amplified 0.2- to 0.8-Hz waves by factors of 8 to 16 relative to bedrock sites west of the basin. The amplification and peak frequency change during the Chi-Chi coda: the initial S-wave arrivals (0-30 sec) had maximum amplifications of 12 at 0.5-0.8 Hz, whereas later arrivals (35-65 sec) reached amplifications of 16 at 0.3-0.5 Hz. Analysis of local events in the 1.0- to 10.0-Hz frequency range show fourfold amplifications for 1.0-Hz weak ground motion over the Seattle basin. Amplifications decrease as frequencies increase above 1.0 Hz, with frequencies above 7 Hz showing lower amplitudes over the basin than at bedrock sites. Modeling shows that resonance in low-impedance deposits forming the upper 550 m of the basin beneath our profile could cause most of the observed amplification, and the larger amplification at later arrival times suggests surface waves also play a substantial role. These results emphasize the importance of shallow deposits in determining ground motions over large basins.

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

PubMed

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.

Improved amplification results following episodes of failure to amplify at the Amelogenin Locus using PowerPlex® ESI 16 Fast System.

PubMed

Berlyne, Sigal; Oz, Carla; Einot, Naftaly; Avraham, Shlomit; Ram, Tanya; Goldberg, Miri D; Gafny, Ron

2017-07-01

In 2012 the Israel Police DNA Casework laboratory adopted the 16 STR PowerPlex ® ESI kit for routine use. The Promega Company updated this kit and developed the PowerPlex ® ESI 16 Fast System in which all autosomal primer pairs remained identical to the original set, except at the amelogenin site. The master mix was improved and optimized which allowed for direct, faster and more robust amplification. Prior to implementing the PowerPlex ® ESI 16 Fast System in our lab, we conducted a preliminary assay where 213 casework samples were amplified using the new kit. These samples had previously been extracted by one of two extraction kits employed by our lab. (the PrepFiler ExpressTM and PrepFiler BTATM Forensic DNA Extraction Kits). The amplification results from these samples were compared to samples amplified using the original PowerPlex ® ESI 16 kit. Multiple incidents of failure to amplify at the amelogenin locus were noted using the new system with the recommended protocol at a rate of 13% (28 of 213 samples). Experiments were performed to understand whether these amplification failures could be a result of primer binding site mutations, extraction method reagents and/or inhibitors. The conclusions reached following these experiments, in conjunction with consultation with the manufacturer, led to the trial of a modified amplification protocol where the suggested annealing temperature was reduced by 2 degrees. To evaluate the efficiency of this altered protocol, a comparison study was undertaken where 88 additional casework samples were chosen and amplified using both the modified 58°C and the recommended 60°C annealing temperatures. We concluded that the most effective method in our laboratory for achieving a consistent and balanced amplification at the amelogenin locus was to reduce the annealing temperature from the manufacturer's recommended 60°C to 58°C. This modification resulted in a reduction of the failure to amplify at the amelogenin locus from 13% (28/213) to 1.1% (1/88) without any observed changes to the autosomal STR amplification results. Copyright © 2017 Elsevier B.V. All rights reserved.

Precision chemical heating for diagnostic devices.

PubMed

Buser, J R; Diesburg, S; Singleton, J; Guelig, D; Bishop, J D; Zentner, C; Burton, R; LaBarre, P; Yager, P; Weigl, B H

2015-12-07

Decoupling nucleic acid amplification assays from infrastructure requirements such as grid electricity is critical for providing effective diagnosis and treatment at the point of care in low-resource settings. Here, we outline a complete strategy for the design of electricity-free precision heaters compatible with medical diagnostic applications requiring isothermal conditions, including nucleic acid amplification and lysis. Low-cost, highly energy dense components with better end-of-life disposal options than conventional batteries are proposed as an alternative to conventional heating methods to satisfy the unique needs of point of care use.

Quantitative control of CaCO3 growth on quartz crystal microbalance sensors as a signal amplification method.

PubMed

Wu, Congcong; Sun, Zhaomei; Liu, Li-Shang

2017-07-10

The surface crystallization of CaCO 3 on gold was monitored by a quartz crystal microbalance (QCM). Quantitative control of the grown crystals was realized by adjusting the ratio of two functional groups, -N(CH 3 ) 3 and -COOH, on SAMs. Crystals with uniform size, morphology and polymorphism were obtained. The amount of crystals formed was found to increase with an increase in the -COOH group. The proposed quantitative control of crystallization can be an effective mass amplification strategy for QCM to enhance its assay sensitivity.

Photon number amplification/duplication through parametric conversion

NASA Technical Reports Server (NTRS)

Dariano, G. M.; Macchiavello, C.; Paris, M.

1993-01-01

The performance of parametric conversion in achieving number amplification and duplication is analyzed. It is shown that the effective maximum gains G(sub *) remain well below their integer ideal values, even for large signals. Correspondingly, one has output Fano factors F(sub *) which are increasing functions of the input photon number. On the other hand, in the inverse (deamplifier/recombiner) operating mode quasi-ideal gains G(sub *) and small factors F(sub *) approximately equal to 10 percent are obtained. Output noise and non-ideal gains are ascribed to spontaneous parametric emission.

Of Mice and Men: Empirical Support for the Population-Based Social Epistasis Amplification Model (a Comment on ).

PubMed

Sarraf, Matthew Alexandar; Woodley Of Menie, Michael Anthony

2017-01-01

This commentary article offers new perspective on recent research investigating the behavioral and social ecological effects of a mutation related to autism spectrum disorders in mice. The authors explain the consistency of this research on mice with predictions advanced by a theory of the role of mutations in altering interorganismal gene-gene interactions (social epistasis) in social species including humans, known as the social epistasis amplification model. The potential significance of the mouse research for understanding contemporary human behavioral trends is explored.

Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants.

PubMed

Liu, Weipeng; Zhu, Minjun; Liu, Hongxing; Wei, Jitao; Zhou, Xiaoming; Xing, Da

2016-07-15

Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays. Copyright © 2016 Elsevier B.V. All rights reserved.

A Methodology to Objectively Assess the Performance of Sound Field Amplification Systems Demonstrated Using 50 Physical Simulations of Classroom Conditions

PubMed Central

Dance, Stephen; Backus, Bradford; Morales, Lorenzo

2018-01-01

Introduction: The effect of a sound reinforcement system, in terms of speech intelligibility, has been systematically determined under realistic conditions. Different combinations of ambient and reverberant conditions representative of a classroom environment have been investigated. Materials and Methods: By comparing the measured speech transmission index metric with and without the system in the same space under different room acoustics conditions, it was possible to determine when the system was most effective. A new simple criterion, equivalent noise reduction (ENR), was introduced to determine the effectiveness of the sound reinforcement system which can be used to predict the speech transmission index based on the ambient sound pressure and reverberation time with and without amplification. Results: This criterion had a correlation, R2 > 0.97. It was found that sound reinforcement provided no benefit if the competing noise level was less than 40 dBA. However, the maximum benefit of such a system was equivalent to a 7.7 dBA noise reduction. Conclusion: Using the ENR model, it would be possible to determine the suitability of implementing sound reinforcement systems in any room, thus providing a tool to determine if natural acoustic treatment or sound field amplification would be of most benefit to the occupants of any particular room. PMID:29785972

A methodology to objectively assess the performance of sound field amplification systems demonstrated using 50 physical simulations of classroom conditions.

PubMed

Dance, Stephen; Backus, Bradford; Morales, Lorenzo

2018-01-01

The effect of a sound reinforcement system, in terms of speech intelligibility, has been systematically determined under realistic conditions. Different combinations of ambient and reverberant conditions representative of a classroom environment have been investigated. By comparing the measured speech transmission index metric with and without the system in the same space under different room acoustics conditions, it was possible to determine when the system was most effective. A new simple criterion, equivalent noise reduction (ENR), was introduced to determine the effectiveness of the sound reinforcement system which can be used to predict the speech transmission index based on the ambient sound pressure and reverberation time with and without amplification. This criterion had a correlation, R 2 > 0.97. It was found that sound reinforcement provided no benefit if the competing noise level was less than 40 dBA. However, the maximum benefit of such a system was equivalent to a 7.7 dBA noise reduction. Using the ENR model, it would be possible to determine the suitability of implementing sound reinforcement systems in any room, thus providing a tool to determine if natural acoustic treatment or sound field amplification would be of most benefit to the occupants of any particular room.

DNase I enzyme-aided fluorescence signal amplification based on graphene oxide-DNA aptamer interactions for colorectal cancer exosome detection.

PubMed

Wang, Hui; Chen, Hui; Huang, Zhipeng; Li, Tengda; Deng, Anmei; Kong, Jilie

2018-07-01

Exosomes have proved to be an effective cancer biomarker with significant potential, and several cell-specific molecules have been found in colorectal cancer (CRC) exosomes. Nevertheless, it is challenging to use exosomes in clinical lab diagnostics due to their nanoscale and the lack of a convenient and effective detection platform. Here, we developed a DNase I enzyme-aided fluorescence amplification method for CRC exosome detection, based on graphene oxide (GO)-DNA aptamer (CD63 and EpCAM aptamers) interactions. The fluorescence of fluorophore-labeled aptamers quenched by GO, recovered after incubation with samples containing CRC exosomes. The DNase I enzyme digested the single-stranded DNA aptamers on the exosome surface and the exosomes were able to interact with more fluorescent aptamer probes, resulting in an increase of signal amplification. The limit of detection for CRC exosomes is 2.1 × 10 4 particles/μl. Consequently, a rapid and effective method with high sensitivity was established. The method was verified in 19 clinical blood serum samples to distinguish healthy and CRC patients, showing significant diagnostic power. Moreover, it can be expanded to other kinds of cancer exosomes, in addition to CRC. Copyright © 2018 Elsevier B.V. All rights reserved.

The effects of variable sample biomass on comparative metagenomics.

PubMed

Chafee, Meghan; Maignien, Loïs; Simmons, Sheri L

2015-07-01

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Assessment of ERBB2 and EGFR gene amplification and protein expression in gastric carcinoma by immunohistochemistry and fluorescence in situ hybridization

PubMed Central

2011-01-01

Background The goal of this study was to investigate ERBB2(HER2) and EGFR gene amplification and protein expression in gastric cancer. Fluorescence in situ hybridization (FISH) and immunohistochemistry were used to analyze ERBB2 and EGFR gene amplification and protein expression in 69 cases of gastric cancer. Results FISH analysis revealed that 20.3% of the cases exhibited ERBB2 gene amplification. Increases in ERBB2 copy number and gene amplification were present in 52.2% of the samples. Expression of the ERBB2 protein was observed in 42.0% of cases. FISH analysis detected EGFR gene amplification in 29.0% of samples. Increases in EGFR copy number and gene amplification occurred in 57.9% of samples, and EGFR protein expression was present in 52.2% of samples. Both ERBB2 and EGFR gene amplification were 3 cases (4.3%), but abnormalities in both ERBB2 and EGFR gene copy number were present 36.2% of samples. ERBB2 and EGFR gene amplification were significantly associated with the depth of tumor invasion (P < 0.05) and lymph node metastasis (P < 0.05), but not with sex, age, or histological type (P > 0.05). Conclusions Our data indicated that ERBB2 and EGFR genetic abnormalities were associated with the prognosis of gastric cancer. Clinical assessment of ERBB2 and EGFR amplification may represent an important factor for the development of personalized treatment programs for gastic cancer. PMID:21689422

Fibroblast growth factor receptor 1 gene amplification is associated with poor survival in patients with resected esophageal squamous cell carcinoma

PubMed Central

Kim, Dae Joon; Lee, Chang-Geol; Hur, Jin; Chung, Hyunsoo; Park, Jun Chul; Jung, Da Hyun; Shin, Sung Kwan; Lee, Sang Kil; Lee, Yong Chan; Kim, Hye Ryun; Moon, Yong Wha; Kim, Joo Hang; Shim, Young Mog; Jewell, Susan S.; Kim, Hyunki; Choi, Yoon-La; Cho, Byoung Chul

2015-01-01

To investigate the frequency and the prognostic impact of fibroblast growth factor receptor 1 (FGFR1) gene amplification in 526 curatively resected esophageal squamous cell carcinoma (ESCC). Using fluorescent in situ hybridization, high amplification was defined by an FGFR1/centromer 8 ratio is ≥ 2.0, or average number of FGFR1 signals/tumor cell nucleus ≥ 6.0, or percentage of tumor cells containing ≥ 15 FGFR1 signals or large cluster in ≥ 10%. Low amplification was defined by ≥ 5 FGFR1 signals in ≥ 50%. FGFR2 and FGFR3 mutations were assessed by direct sequencing in 388 cases and no mutation was detected. High and low amplification were detected in 8.6% and 1.1%, respectively. High FGFR1 amplification had significantly shorter disease-free survival (34.0 vs 158.5 months P=0.019) and overall survival (52.2 vs not reached P=0.022) than low/no amplification group. After adjusting for sex, smoking, stage, histology, and adjuvant treatment, high FGFR1 amplification had a greater risk of recurrence (adjusted hazard ratio [AHR], 1.6; P=0.029) and death (AHR, 1.53; P=0.050). High amplification was significantly higher in current smokers than former and never-smokers (Ptrend<0.001) and increased proportional to smoking dosage. High FGFR1 amplification is a frequent oncogenic alteration and an independent poor prognostic factor in resected ESCC. PMID:25537505

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strizhkov, B. N.; Drobyshev, A. L.; Mikhailovich, V. M.

PCR amplification on a microarray of gel-immobilized primers (microchip) has been developed. One of a pair of PCR primers was immobilized inside a separate microchip polyacrylamide porous gel pad of 0.1 x 0.1 x 0.02 (or 0.04) micron in size and 0.2 (or 0.4) nL in volume. The amplification was carried out simultaneously both in solution covering the microchip array and inside gel pads. Each gel pad contained the immobilized forward primers, while the fluorescently labeled reverse primers, as well as all components of the amplification reaction, diffused into the gel pads from the solution. To increase the amplification efficiency,more » the forward primers were also added into the solution. The kinetics of amplification was measured in real time in parallel for all gel pads with a fluorescent microscope equipped with a charge-coupled device (CCD) camera. The accuracy of the amplification was assessed by using the melting curves obtained for the duplexes formed by the labeled amplification product and the gel-immobilized primers during the amplification process; alternatively, the duplexes were produced by hybridization of the extended immobilized primers with labeled oligonucleotide probes. The on-chip amplification was applied to detect the anthrax toxin genes and the plasmid-borne beta-lactamase gene responsible for bacterial ampicillin resistance. The allele-specific type of PCR amplification was used to identify the Shiga toxin gene and discriminate it from the Shiga-like one. The genomic mutations responsible for rifampicin resistance of the Mycobacterium tuberculosis strains were detected by the same type of PCR amplification of the rpoB gene fragment isolated from sputum of tuberculosis patients. The on-chip PCR amplification has been shown to be a rapid, inexpensive and powerful tool to test genes responsible for bacterial toxin production and drug resistance, as well as to reveal point nucleotide mutations.« less

Pre-amplification in the context of high-throughput qPCR gene expression experiment.

PubMed

Korenková, Vlasta; Scott, Justin; Novosadová, Vendula; Jindřichová, Marie; Langerová, Lucie; Švec, David; Šídová, Monika; Sjöback, Robert

2015-03-11

With the introduction of the first high-throughput qPCR instrument on the market it became possible to perform thousands of reactions in a single run compared to the previous hundreds. In the high-throughput reaction, only limited volumes of highly concentrated cDNA or DNA samples can be added. This necessity can be solved by pre-amplification, which became a part of the high-throughput experimental workflow. Here, we focused our attention on the limits of the specific target pre-amplification reaction and propose the optimal, general setup for gene expression experiment using BioMark instrument (Fluidigm). For evaluating different pre-amplification factors following conditions were combined: four human blood samples from healthy donors and five transcripts having high to low expression levels; each cDNA sample was pre-amplified at four cycles (15, 18, 21, and 24) and five concentrations (equivalent to 0.078 ng, 0.32 ng, 1.25 ng, 5 ng, and 20 ng of total RNA). Factors identified as critical for a success of cDNA pre-amplification were cycle of pre-amplification, total RNA concentration, and type of gene. The selected pre-amplification reactions were further tested for optimal Cq distribution in a BioMark Array. The following concentrations combined with pre-amplification cycles were optimal for good quality samples: 20 ng of total RNA with 15 cycles of pre-amplification, 20x and 40x diluted; and 5 ng and 20 ng of total RNA with 18 cycles of pre-amplification, both 20x and 40x diluted. We set up upper limits for the bulk gene expression experiment using gene expression Dynamic Array and provided an easy-to-obtain tool for measuring of pre-amplification success. We also showed that variability of the pre-amplification, introduced into the experimental workflow of reverse transcription-qPCR, is lower than variability caused by the reverse transcription step.

Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality.

PubMed

Bækvad-Hansen, Marie; Bybjerg-Grauholm, Jonas; Poulsen, Jesper B; Hansen, Christine S; Hougaard, David M; Hollegaard, Mads V

2017-06-01

The overall aim of this study is to evaluate whole genome amplification of DNA extracted from dried blood spot samples. We wish to explore ways of optimizing the amplification process, while decreasing the amount of input material and inherently the cost. Our primary focus of optimization is on the amount of input material, the amplification reaction volume, the number of replicates and amplification time and temperature. Increasing the quality of the amplified DNA and the subsequent results of array genotyping is a secondary aim of this project. This study is based on DNA extracted from dried blood spot samples. The extracted DNA was subsequently whole genome amplified using the REPLIg kit and genotyped on the PsychArray BeadChip (assessing > 570,000 SNPs genome wide). We used Genome Studio to evaluate the quality of the genotype data by call rates and log R ratios. The whole genome amplification process is robust and does not vary between replicates. Altering amplification time, temperature or number of replicates did not affect our results. We found that spot size i.e. amount of input material could be reduced without compromising the quality of the array genotyping data. We also showed that whole genome amplification reaction volumes can be reduced by a factor of 4, without compromising the DNA quality. Whole genome amplified DNA samples from dried blood spots is well suited for array genotyping and produces robust and reliable genotype data. However, the amplification process introduces additional noise to the data, making detection of structural variants such as copy number variants difficult. With this study, we explore ways of optimizing the amplification protocol in order to reduce noise and increase data quality. We found, that the amplification process was very robust, and that changes in amplification time or temperature did not alter the genotyping calls or quality of the array data. Adding additional replicates of each sample also lead to insignificant changes in the array data. Thus, the amount of noise introduced by the amplification process was consistent regardless of changes made to the amplification protocol. We also explored ways of decreasing material expenditure by reducing the spot size or the amplification reaction volume. The reduction did not affect the quality of the genotyping data.

Molecular Identification of an Invasive Wood-Boring Insect Lyctus brunneus (Coleoptera: Bostrichidae: Lyctinae) Using Frass by Loop-Mediated Isothermal Amplification and Nested PCR Assays.

PubMed

Ide, Tatsuya; Kanzaki, Natsumi; Ohmura, Wakako; Okabe, Kimiko

2016-03-27

Lyctus brunneus(Stephens) is one of the most destructive and worldwide invasive pests of seasoned woods for wooden products. This and other pestLyctusspecies have had their distribution expanded by international and domestic human transportation of infested wood and wood products. Rapid detection and accurate identification ofLyctusspecies are effective tools for helping to eradicate them in new introduction sites. The accurate species-level identification of adults requires expert knowledge about their morphology. However, it takes much time and effort to recover suitable adult specimens because they are borers inside wood. Frass ofLyctusspecies can easily be detected and recovered in and around infested wood. Thus, frass was tested to see if it was a suitable sample to allow development of a rapid and technically easy molecular detection and identification method forL.brunneus.Species-specific primers were designed from the cytochrome c oxidase subunit I region ofL.brunneusand used in development and testing of methods for successfully identifying them from their frass using the loop-mediated isothermal amplification (LAMP) or species-specific nested polymerase chain reaction (PCR) assays. The LAMP assay was faster and more sensitive for detecting the presence of DNA derived fromL.brunneusin their frass than the nested PCR assay. These methodologies will be applicable for the rapid detection and identification of other wood-boring invasive pests in regulatory applications. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Development of a real-time fluorescence loop-mediated isothermal amplification assay for rapid and quantitative detection of Fusarium oxysporum f. sp. cubense tropical race 4 in soil.

PubMed

Zhang, Xin; Zhang, He; Pu, Jinji; Qi, Yanxiang; Yu, Qunfang; Xie, Yixian; Peng, Jun

2013-01-01

Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt (Panama disease), is one of the most devastating diseases of banana (Musa spp.). The Foc tropical race 4 (TR4) is currently known as a major concern in global banana production. No effective resistance is known in Musa to Foc, and no effective measures for controlling Foc once banana plants have been infected in place. Early and accurate detection of Foc TR4 is essential to protect banana industry and guide banana planting. A real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) was developed for the rapid and quantitative detection of Foc TR4 in soil. The detection limit of the RealAmp assay was approximately 0.4 pg/µl plasmid DNA when mixed with extracted soil DNA or 10(3) spores/g of artificial infested soil, and no cross-reaction with other relative pathogens were observed. The RealAmp assay for quantifying genomic DNA of TR4 was confirmed by testing both artificially and naturally infested samples. Quantification of the soil-borne pathogen DNA of Foc TR4 in naturally infested samples was no significant difference compared to classic real-time PCR (P>0.05). Additionally, RealAmp assay was visual with an improved closed-tube visual detection system by adding SYBR Green I fluorescent dye to the inside of the lid prior to amplification, which avoided the inhibitory effects of the stain on DNA amplification and makes the assay more convenient in the field and could thus become a simple, rapid and effective technique that has potential as an alternative tool for the detection and monitoring of Foc TR4 in field, which would be a routine DNA-based testing service for the soil-borne pathogen in South China.

Perceptual sensitivity to spectral properties of earlier sounds during speech categorization.

PubMed

Stilp, Christian E; Assgari, Ashley A

2018-02-28

Speech perception is heavily influenced by surrounding sounds. When spectral properties differ between earlier (context) and later (target) sounds, this can produce spectral contrast effects (SCEs) that bias perception of later sounds. For example, when context sounds have more energy in low-F 1 frequency regions, listeners report more high-F 1 responses to a target vowel, and vice versa. SCEs have been reported using various approaches for a wide range of stimuli, but most often, large spectral peaks were added to the context to bias speech categorization. This obscures the lower limit of perceptual sensitivity to spectral properties of earlier sounds, i.e., when SCEs begin to bias speech categorization. Listeners categorized vowels (/ɪ/-/ɛ/, Experiment 1) or consonants (/d/-/g/, Experiment 2) following a context sentence with little spectral amplification (+1 to +4 dB) in frequency regions known to produce SCEs. In both experiments, +3 and +4 dB amplification in key frequency regions of the context produced SCEs, but lesser amplification was insufficient to bias performance. This establishes a lower limit of perceptual sensitivity where spectral differences across sounds can bias subsequent speech categorization. These results are consistent with proposed adaptation-based mechanisms that potentially underlie SCEs in auditory perception. Recent sounds can change what speech sounds we hear later. This can occur when the average frequency composition of earlier sounds differs from that of later sounds, biasing how they are perceived. These "spectral contrast effects" are widely observed when sounds' frequency compositions differ substantially. We reveal the lower limit of these effects, as +3 dB amplification of key frequency regions in earlier sounds was enough to bias categorization of the following vowel or consonant sound. Speech categorization being biased by very small spectral differences across sounds suggests that spectral contrast effects occur frequently in everyday speech perception.

Overview of topographic effects based on experimental observations: meaning, causes and possible interpretations

NASA Astrophysics Data System (ADS)

Massa, Marco; Barani, Simone; Lovati, Sara

2014-06-01

The paper presents an extensive review of topographic effects in seismology taking into account the knowledge of 40 yr of scientific literature. An overview of topographic effects based on experimental observations and numerical modelling is presented with the aim of highlighting meaning and causes of these phenomena as well as possible correlations between site response (fundamental frequency, amplification level) and geometrical (width and shape ratio of a relief) parameters. After a thorough summary of topographic effects, the paper focuses on five Italian sites whose seismic response is potentially affected by local morphology, as already evidenced by previous studies. In this study, seismic data recorded at these sites are analysed computing directional spectral ratios both in terms of horizontal to vertical spectral ratios (HVSRs) and, wherever possible, in terms of standard spectral ratios (SSRs). The analysis lead to the conclusion that wavefield tends to be polarized along a direction perpendicular to the main axis of a topographic irregularity, direction along which ground motion amplification is maximum. The final section of the article compares and contrasts different spectral ratio techniques in order to examine their effectiveness and reliability in detecting topographic effects. The examples discussed in the paper show that site responses based on HVSRs rather than SSR measurements could lead to misinterpretation of ground response results, both as concerns the definition of the site fundamental frequency and amplification level. Results and findings of this work will be used as starting point to discuss the influence of topographic effects on ground motion prediction equations and regulations for design. These topics will be discussed in the companion article.

Amplification of effects of photons on wound healing

NASA Astrophysics Data System (ADS)

Dyson, Mary

2009-02-01

Following the absorption of photons by cells either resident in or in transit through the skin at and around a wound site, healing can be modulated. This is due to the primary, secondary and tertiary cellular effects of the photons. The main primary effect of phototherapy is photon absorption. This initiates secondary effects within the cells that have absorbed the photons. Secondary effects are restricted to cells that have absorbed a suprathreshold quantity of photonic energy. Photon absorption can lead to an increase in ATP synthesis and the release of reactive oxygen species that can activate specific transcription factors resulting in changes in synthesis of the enzymes needed for cellular proliferation, migration, phagocytosis and protein synthesis, all essential for wound healing. The amount of ATP production is limited in each cell by the availability of ADP and phosphate. Spatial and temporal amplification of the effects of photon absorption increases the range and duration of phototherapy. It may be caused in part by tertiary effects initiated in cells that have not absorbed photons by regulatory proteins such as cytokines secreted by cells that have absorbed photons. Amplification may also be due to changes induced by photons in immune cells, stem cells and soluble protein mediators while in transit through the dermal capillaries. The peripheral location of these capillaries makes their contents readily accessible to photons. The longer the duration of treatment, the greater will be the number of cells in transit that can be affected by photons. Depth of effect may be increased by transduction of electromagnetic energy into mechanical energy. For a treatment to be clinically effective on wound healing, its duration and power may each be important. Components of the immune system, endocrine system and nervous system may also amplify the effects of photons on wound healing.

Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications.

PubMed

Sho, Shonan; Court, Colin M; Winograd, Paul; Lee, Sangjun; Hou, Shuang; Graeber, Thomas G; Tseng, Hsian-Rong; Tomlinson, James S

2017-07-01

Sequencing analysis of circulating tumor cells (CTCs) enables "liquid biopsy" to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies. Single pancreatic cancer cells (HPAF-II) were isolated using laser microdissection. WGA was performed using multiple displacement amplification (MDA), multiple annealing and looping based amplification (MALBAC) and PicoPLEX. Quality of amplified DNA products were assessed using a multiplex/RT-qPCR based method that evaluates for 8-cancer related genes and QC-scores were assigned. We utilized this scoring system to assess the impact of de novo modifications to the WGA protocol. WGA products were subjected to Sanger sequencing, array comparative genomic hybridization (aCGH) and next generation sequencing (NGS) to evaluate their performances in respective downstream analyses providing validation of the QC-score. Single-cell WGA products exhibited a significant sample-to-sample variability in amplified DNA quality as assessed by our 8-gene QC assay. Single-cell WGA products that passed the pre-analysis QC had lower amplification bias and improved aCGH/NGS performance metrics when compared to single-cell WGA products that failed the QC. Increasing the number of cellular input resulted in improved QC-scores overall, but a resultant WGA product that consistently passed the QC step required a starting cellular input of at least 20-cells. Our modified-WGA protocol effectively reduced this number, achieving reproducible high-quality WGA products from ≥5-cells as a starting template. A starting cellular input of 5 to 10-cells amplified using the modified-WGA achieved aCGH and NGS results that closely matched that of unamplified, batch genomic DNA. The modified-WGA protocol coupled with the 8-gene QC serve as an effective strategy to enhance the quality of low-template WGA reactions. Furthermore, a threshold number of 5-10 cells are likely needed for a reliable WGA reaction and product with high fidelity to the original starting template.

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

PubMed Central

2009-01-01

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-type KRAS resulted in the inhibition of cell growth and suppression of p44/42 MAP kinase and AKT activity. Conclusion Our study highlights the utility of DGS for identification of copy-number alterations. Using DGS, we identified KRAS as a gene that is amplified in human gastric cancer. We demonstrated that gene amplification likely forms the molecular basis of overactivation of KRAS in gastric cancer. Additional studies using a larger cohort of gastric cancer specimens are required to determine the diagnostic and therapeutic implications of KRAS amplification and overexpression. PMID:19545448

Determination of genotoxic effects of boron and zinc on Zea mays using protein and random amplification of polymorphic DNA analyses.

PubMed

Erturk, Filiz Aygun; Nardemir, Gokce; Hilal, A Y; Arslan, Esra; Agar, Guleray

2015-11-01

In this research, we aimed to determine genotoxic effects of boron (B) and zinc (Zn) on Zea mays by using total soluble protein content and random amplification of polymorphic DNA (RAPD) analyses. For the RAPD analysis, 16 RAPD primers were found to produce unique polymorphic band profiles on treated maize seedlings. With increased Zn and B concentrations, increased polymorphism rate was observed, while genomic template stability and total soluble protein content decreased. The treatment with Zn was more effective than that of B groups on the levels of total proteins. The obtained results from this study revealed that the total soluble protein levels and RAPD profiles were performed as endpoints of genotoxicity and these analyses can offer useful biomarker assays for the evaluation of genotoxic effects on Zn and B polluted plants. © The Author(s) 2013.

c-MYC amplification and c-myc protein expression in pancreatic acinar cell carcinomas. New insights into the molecular signature of these rare cancers.

PubMed

La Rosa, Stefano; Bernasconi, Barbara; Vanoli, Alessandro; Sciarra, Amedeo; Notohara, Kenji; Albarello, Luca; Casnedi, Selenia; Billo, Paola; Zhang, Lizhi; Tibiletti, Maria Grazia; Sessa, Fausto

2018-05-02

The molecular alterations of pancreatic acinar cell carcinomas (ACCs) and mixed acinar-neuroendocrine carcinomas (MANECs) are not completely understood, and the possible role of c-MYC amplification in tumor development, progression, and prognosis is not known. We have investigated c-MYC gene amplification in a series of 35 ACCs and 4 MANECs to evaluate its frequency and a possible prognostic role. Gene amplification was investigated using interphasic fluorescence in situ hybridization analysis simultaneously hybridizing c-MYC and the centromere of chromosome 8 probes. Protein expression was immunohistochemically investigated using a specific monoclonal anti-c-myc antibody. Twenty cases had clones with different polysomies of chromosome 8 in absence of c-MYC amplification, and 5 cases had one amplified clone and other clones with chromosome 8 polysomy, while the remaining 14 cases were diploid for chromosome 8 and lacked c-MYC amplification. All MANECs showed c-MYC amplification and/or polysomy which were observed in 54% pure ACCs. Six cases (15.3%) showed nuclear immunoreactivity for c-myc, but only 4/39 cases showed simultaneous c-MYC amplification/polysomy and nuclear protein expression. c-myc immunoreactivity as well as c-MYC amplification and/or chromosome 8 polysomy was not statistically associated with prognosis. Our study demonstrates that a subset of ACCs shows c-MYC alterations including gene amplification and chromosome 8 polysomy. Although they are not associated with a different prognostic signature, the fact that these alterations are present in all MANECs suggests a role in the acinar-neuroendocrine differentiation possibly involved in the pathogenesis of MANECs.

Development of homologous viral internal controls for use in RT-PCR assays of waterborne enteric viruses.

PubMed

Parshionikar, Sandhya U; Cashdollar, Jennifer; Fout, G Shay

2004-10-01

Enteric viruses often contaminate water sources causing frequent outbreaks of gastroenteritis. Reverse transcription-polymerase chain reaction (RT-PCR) assays are commonly used for detection of human enteric viruses in environmental and drinking water samples. RT-PCR provides a means to rapidly detect low levels of these viruses, but it is sensitive to inhibitors that are present in water samples. Inhibitors of RT-PCR are concentrated along with viruses during sample processing. While procedures have been developed to remove inhibitors, none of them completely remove all inhibitors from all types of water matrices. This problem requires that adequate controls be used to distinguish true from potentially false-negative results. To address this problem, we have developed homologous viral internal controls for hepatitis A virus (HAV), poliovirus, Norwalk virus and rotavirus. These internal controls can be used in RT-PCR assays for the detection of the above viruses by competitive amplification, thereby allowing the detection of false negatives in processed water samples. The internal controls developed in this study were successfully tested with virus-seeded environmental water sample concentrates.

Signal amplification of microRNAs with modified strand displacement-based cycling probe technology.

PubMed

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.

PDGFRA amplification is common in pediatric and adult high-grade astrocytomas and identifies a poor prognostic group in IDH1 mutant glioblastoma

PubMed Central

Phillips, Joanna J.; Aranda, Derick; Ellison, David W.; Judkins, Alexander R.; Croul, Sidney E.; Brat, Daniel J.; Ligon, Keith L.; Horbinski, Craig; Venneti, Sriram; Zadeh, Gelareh; Santi, Mariarita; Zhou, Shengmei; Appin, Christina L.; Sioletic, Stefano; Sullivan, Lisa M.; Martinez-Lage, Maria; Robinson, Aaron E.; Yong, William H.; Cloughesy, Timothy; Lai, Albert; Phillips, Heidi S.; Marshall, Roxanne; Mueller, Sabine; Haas-Kogan, Daphne A.; Molinaro, Annette M.; Perry, Arie

2013-01-01

High-grade astrocytomas (HGAs), corresponding to WHO grades III (AA) and IV (GBM), are biologically aggressive and their molecular classification is increasingly relevant to clinical management. PDGFRA amplification is common in HGAs, although its prognostic significance remains unclear. Using fluorescence in situ hybridization (FISH), the most sensitive technique for detecting PDGFRA copy number gains, we determined PDGFRA amplification status in 123 pediatric and 263 adult HGAs. A range of PDGFRA FISH patterns were identified and cases were scored as non-amplified (normal and polysomy) or amplified (low-level and high-level). PDGFRA amplification was frequent in pediatric (29.3%) and adult (20.9%) tumors. Amplification was not prognostic in pediatric HGAs. In adult tumors diagnosed initially as GBM, the presence of combined PDGFRA amplification and IDH1R132H mutation was a significant independent prognostic factor (p=0.01). In HGAs, PDGFRA amplification is common and can manifest as high-level and focal or low-level amplifications. Our data indicate that the latter is more prevalent than previously reported with copy number averaging techniques. To our knowledge, this is the largest survey of PDGFRA status in adult and pediatric HGAs and suggests PDGFRA amplification increases with grade and is associated with a less favorable prognosis in IDH1 mutant de novo GBMs. PMID:23438035

Non-biased and efficient global amplification of a single-cell cDNA library

PubMed Central

Huang, Huan; Goto, Mari; Tsunoda, Hiroyuki; Sun, Lizhou; Taniguchi, Kiyomi; Matsunaga, Hiroko; Kambara, Hideki

2014-01-01

Analysis of single-cell gene expression promises a more precise understanding of molecular mechanisms of a living system. Most techniques only allow studies of the expressions for limited numbers of gene species. When amplification of cDNA was carried out for analysing more genes, amplification biases were frequently reported. A non-biased and efficient global-amplification method, which uses a single-cell cDNA library immobilized on beads, was developed for analysing entire gene expressions for single cells. Every step in this analysis from reverse transcription to cDNA amplification was optimized. By removing degrading excess primers, the bias due to the digestion of cDNA was prevented. Since the residual reagents, which affect the efficiency of each subsequent reaction, could be removed by washing beads, the conditions for uniform and maximized amplification of cDNAs were achieved. The differences in the amplification rates for randomly selected eight genes were within 1.5-folds, which could be negligible for most of the applications of single-cell analysis. The global amplification gives a large amount of amplified cDNA (>100 μg) from a single cell (2-pg mRNA), and that amount is enough for downstream analysis. The proposed global-amplification method was used to analyse transcript ratios of multiple cDNA targets (from several copies to several thousand copies) quantitatively. PMID:24141095

A systematic analysis of directional site effects at stations of the Italian Seismic Network to test the role of local topography

NASA Astrophysics Data System (ADS)

Pischiutta, Marta; Cianfarra, Paola; Salvini, Francesco; Cara, Fabrizio; Vannoli, Paola

2018-03-01

Directional site effects observed at seismological stations on pronounced relief are analyzed. We investigate the ground motion properties calculating horizontal-to-vertical spectral ratios and horizontal polarization of both ambient vibrations and earthquake records using broadband seismograms of the Italian Seismic Network. We find that a subset of 47 stations with pronounced relief, results in a significant (>2) directional amplification of the horizontal component, with a well defined, site-specific direction of motion. However, the horizontal spectral response of sites is not uniform, varying from an isolated (resonant) frequency peak to a broadband amplification, interesting frequency bands as large as 1-10 Hz in many cases. Using the 47 selected stations, we have tried to establish a relation between directional amplification and topography geometry in a 2D-vision, when applicable, through a morphological analysis of the Digital Elevation Model using Geographic Information Systems. The procedure computes the parameters that characterize the geometry of topographic irregularities (size and slope), in combination with a principal component analysis that automatically yields the orientation of the elongated ridges. In seeking a relation between directional amplification and the surface morphology, we have found that it is impossible to fit the variety of observations with a resonant topography model as well as to identify common features in the ground motion behavior for stations with similar topography typologies. We conclude that, rather than the shape of the topography, local structural complexities and details of the near-surface structure must play a predominant role in controlling ground motion properties at sites with pronounced relief.

The stability of H/V spectral ratios from noise measurements in Armutlu Peninsula (Turkey)

NASA Astrophysics Data System (ADS)

Livaoǧlu, Hamdullah; Irmak, T. Serkan; Caka, Deniz; Yavuz, Evrim; Lühr, B. G.; Woith, H.; Tunç, B.; Baris, S.

2016-04-01

The horizontal to vertical spectral ratio (H/V) method has been successfully using in order to estimate the fundamental resonance frequency of the sedimentary cover, its thickness and amplification factor since at least 3 decades. There are numerous studies have been carried out on the stability of the H/V spectral ratios. Almost all studies showed that fundamental frequency is stable even measurements are repeated at different times. From this point of view, the results will show us an approach whether the stations are suitable for accurate estimate of earthquake studies and engineering purposes or not. Also we want to see if any effects of the amplification factor changing on the seismograms for Armutlu Seismic Network (ARNET) even though seismic stations are established far away from cultural noise and located on hard rock sites. It has been selected one hour recorded data of all stations during the most stationary times. The amplification and resonant frequency variations of H/V ratio were calculated to investigate temporal stability in time. There is a total harmony in fundamental frequencies values and H/V spectral ratio values in time-lagged periods. Some stations shows secondary minor peaks in high frequency band due to a shallow formation effect or cultural noises around. In the east side of the area ILYS station shows amplitude peak in lower fundamental frequency band from expected. This could compose a high amplification in lower frequencies and so that yield less reliable results in local earthquakes studies. By the experimental results from ambient noise analysis, it could be worked up for relocation of one station.

A systematic analysis of directional site effects at stations of the Italian seismic network to test the role of local topography

NASA Astrophysics Data System (ADS)

Pischiutta, Marta; Cianfarra, Paola; Salvini, Francesco; Cara, Fabrizio; Vannoli, Paola

2018-07-01

Directional site effects observed at seismological stations on pronounced relief are analysed. We investigate the ground motion properties calculating horizontal-to-vertical spectral ratios and horizontal polarization of both ambient vibrations and earthquake records using broad-band seismograms of the Italian seismic network. We find that a subset of 47 stations with pronounced relief results in a significant (>2) directional amplification of the horizontal component, with a well-defined, site-specific direction of motion. However, the horizontal spectral response of sites is not uniform, varying from an isolated (resonant) frequency peak to a broad-band amplification, interesting frequency bands as large as 1-10 Hz in many cases. Using 47 selected stations, we have tried to establish a relation between directional amplification and topography geometry in a 2-D vision, when applicable, through a morphological analysis of the digital elevation model using geographic information systems. The procedure computes the parameters that characterize the geometry of topographic irregularities (size and slope), in combination with a principal component analysis that automatically yields the orientation of the elongated ridges. In seeking a relation between directional amplification and the surface morphology, we have found that it is impossible to fit the variety of observations with a resonant topography model as well as to identify common features in the ground motion behaviour for stations with similar topography typologies. We conclude that, rather than the shape of the topography, local structural complexities and details of the near-surface structure must play a predominant role in controlling ground motion properties at sites with pronounced relief.