Linear amplification of marginally neutral baroclinic waves

Baroclinic wave development is investigated for unstable parallel shear flows in the limit of vanishing normal-mode growth rate. This development is described in terms of the propagation and interaction mechanisms of two coherent structures, called counter-propagating Rossby waves (CRWs). It is shown that, in this limit of vanishing normal-mode growth rate, arbitrary initial conditions produce sustained linear amplification of the marginally neutral normal mode (mNM). This linear excitation of the mNM is subsequently interpreted in terms of a resonance phenomenon. Moreover, while the mathematical character of the normal-mode problem changes abruptly as the bifurcation point in the dispersion diagram is encountered and crossed, it is shown that from an initial-value viewpoint, this transition is smooth. Consequently, the resonance interpretation remains relevant (albeit for a finite time) for wavenumbers slightly different from the ones defining cut-off points. The results are further applied to a two-layer version of the classic Eady model in which the upper rigid lid has been replaced by a simple stratosphere.

Comparison of amplification methods for transcriptomic analyses of low abundance prokaryotic RNA sources

Microarrays have established as instrumental for bacterial detection, identification, and genotyping as well as for transcriptomic studies. For gene expression analyses using limited numbers of bacteria (derived from in vivo or ex vivo origin, for example), RNA amplification is often required prior to labeling and hybridization onto microarrays. Evaluation of the fidelity of the amplification methods is crucial for the robustness and reproducibility of microarray results. We report here the first utilization of random primers and the highly processive Phi29 phage polymerase to amplify material for transcription profiling analyses. We compared two commercial amplification methods (GenomiPhi and MessageAmp kits) with direct reverse-transcription as the reference method, focusing on the robustness of mRNA quantification using either microarrays or quantitative RT-PCR. Both amplification methods using either poly-A tailing followed by in vitro transcription, or direct strand displacement polymerase, showed appreciable linearity. Strand displacement technique was particularly affordable compared to in vitro transcription-based (IVT) amplification methods and consisted in a single tube reaction leading to high amplification yields. Real-time measurements using low-, medium-, and highly expressed genes revealed that this simple method provided linear amplification with equivalent results in terms of relative messenger abundance as those obtained by conventional direct reverse-transcription.

Quantitative analysis of mRNA amplification by in vitro transcription

Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well as a description of inherent limitations is lacking. We show that published protocols produce a template-independent product in addition to amplifying real target mRNA thus reducing the specific activity of the final product. We describe a modified amplification protocol that minimizes the generation of template-independent product and can therefore generate the desired microgram quantities of message-derived material from 100 ng of total RNA. Application of a second, nested round of cDNA synthesis and in vitro transcription reduces the required starting material to 2 ng of total RNA. Quantitative analysis of these products on Caenorhabditis elegans Affymetrix GeneChips shows that this amplification does not reduce overall sensitivity and has only minor effects on fidelity.

A Novel Opto Electro Mechanical Interrogation System for Measuring Wavelength Shifts in Fiber Bragg Grating (FBG) Sensors

Here, we describe a novel FBG interrogation system in which FBGs are used as both sensing and reference elements. The reference FBGs is bonded to a mechanical flexure system having a linear amplification of 1:3.5, which is actuated using a piezo-actuator by applying a 0-150V ramp. The lengths of the reference gratings decide the maximum strain that can be applied to the reference grating, which in turn decides that strain range which can be interrogated. The main advantages of the present system are the on-line measurement of the wavelength shifts, small size, good sensitivity, multiplexing capability and low cost.

A new phototransistor with uni-travelling-carrier and optically gradual coupling properties

Based on appropriate combination of different band-gap InGaAsP, a new edge-coupled two-terminal double heterojunction phototransistor (ECTT-DHPT) was designed and fabricated, which is double heterojunction, free-aluminium, and works under uni-travelling-carrier mode and optically gradual coupling mode. This device is fully compatible with monolithic micro-wave integrated circuits (MMIC) and heterojunction bipolar transistor (HBT) in material and process. The DC characteristics reveal that the new ECTT-DHPT can perform good optoelectronic mix operation and linear amplification operation by optically biased at two appropriate value respectively. Responsivity of more than 52 A/W and dark current of 70 nA (when V-EC = 1 V) were obtained.

A New Edge-Coupled Two-Terminal Double Heterojunction Phototransistor (ECTT-DHPT) and Its DC Characteristics

A new ECTT-DHPT with InGaAsP(lambda=1.55 mu m) as base and InGaAsP(lambda=1.3 mu m) as collector as well as waveguide was designed and fabricated, the DC characteristics reveal that the ECTT-DRPT can perform good optoelectronic mix operation and linear amplification operation by optically biased at two appropriate value respectively. Responsivity of more than 52A/W and dark current of 70nA (when V-ce=1V) were obtained.

Power combining techniques into unbalanced loads for Class-E and inverse Class-E amplifiers

A power combining strategy for Class-E and inverse Class-E amplifiers operating at high frequencies such that they can operate into unbalanced loads is proposed. This power combining method is particularly important for the inverse Class-E amplifier configuration whose single-stage topology is naturally limited for small-to-medium power applications. Design examples for the power combining synthesis of classical Class-E and then inverse Class-E amplifiers with specification 3 V-1.5 W-2.5 GHz are given. For this specification, it is shown that a three-branch combiner has a natural 50 V output impedance. The resulting circuits are simulated within Agilent Advanced Design Systems environment with good agreement to theoretical prediction. Further the performance of the proposed circuits when operated in a Linear amplification using Nonlinear Components transmitter configuration whereby two-branch amplifiers are driven with constant amplitude conjugate input phase signals is investigated.

A filamentation instability for streaming cosmic rays

We demonstrate that cosmic rays form filamentary structures in the precursors of supernova remnant shocks due to their self-generated magnetic fields. The cosmic ray filamentation results in the growth of a long-wavelength instability, and naturally couples the rapid non-linear amplification on small scales to larger length-scales. Hybrid magnetohydrodynamics-particle simulations are performed to confirm the effect. The resulting large-scale magnetic field may facilitate the scattering of high-energy cosmic rays as required to accelerate protons beyond the knee in the cosmic ray spectrum at supernova remnant shocks. Filamentation far upstream of the shock may also assist in the escape of cosmic rays from the accelerator.

Evaluation of Quantitative RT-PCR Using Nonamplified and Amplified RNA

Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is a standard assay in molecular medicine for gene expression analysis. Samples from incisional/needle biopsies, laser-microdissected tumor cells and other biologic sources, normally available in clinical cancer studies, generate very small amounts of RNA that are restrictive for expression analysis. As a consequence, an RNA amplification procedure is required to assess the gene expression levels of such sample types. The reproducibility and accuracy of relative gene expression data produced by sensitive methodology as qRT-PCR when cDNA converted from amplified (A) RNA is used as template has not yet been properly addressed. In this study, to properly evaluate this issue, we performed 1 round of linear RNA amplification in 2 breast cell lines (C5.2 and HB4a) and assessed the relative expression of 34 genes using cDNA converted from both nonamplified (NA) and A RNA. Relative gene expression was obtained from beta actin or glyceraldehyde 3-phosphate dehydrogenase normalized data using different dilutions of cDNA, wherein the variability and fold-change differences in the expression of the 2 methods were compared. Our data showed that 1 round of linear RNA amplification, even with suboptimal-quality RNA, is appropriate to generate reproducible and high-fidelity qRT-PCR relative expression data that have similar confidence levels as those from NA samples. The use of cDNA that is converted from both A and NA RNA in a single qRT-PCR experiment clearly creates bias in relative gene expression data.

Relative expression of insulin like growth factor I (IGFI) and follicle stimulating hormone receptor (FSHR) in follicles and ovarian tissue from Bos primigenius indicus (Nelore)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Protein quantification from complex protein mixtures using a proteomics methodology with single-cell resolution

We have developed an extremely sensitive technique, termed immuno-detection amplified by T7 RNA polymerase (IDAT) that is capable of monitoring proteins, lipids, and metabolites and their modifications at the single-cell level. A double-stranded oligonucleotide containing the T7 promoter is conjugated to an antibody (Ab), and then T7 RNA polymerase is used to amplify RNA from the double-stranded oligonucleotides coupled to the Ab in the Ab-antigen complex. By using this technique, we are able to detect the p185her2/neu receptor from the crude lysate of T6–17 cells at 10−13 dilution, which is 109-fold more sensitive than the conventional ELISA method. Single-chain Fv fragments or complementarity determining region peptides of the Ab also can be substituted for the Ab in IDAT. In a modified protocol, the oligonucleotide has been coupled to an Ab against a common epitope to create a universal detector species. With the linear amplification ability of T7 RNA polymerase, IDAT represents a significant improvement over immuno-PCR in terms of sensitivity and has the potential to provide a robotic platform for proteomics.

Sequence variation can affect the performance of minor groove binder TaqMan probes in viral diagnostic assays

A minor groove binder (MGB) TaqMan real-time PCR assay was developed for the detection of respiratory syncytial virus (RSV) in clinical specimens. Upon evaluation of the assay, notable differences were observed in the overall fluorescent response obtained from RSV positive specimens, with some linear amplification curves deviating only slightly from baseline fluorescence. Sequencing of the probes targets in these RSV strains revealed single base mismatches with the MGB TaqMan probe. overall, these results highlight the usefulness of MGB TaqMan probes for the detection of mismatches, but suggest that MGB Taqman probes have limitations for routine screening for uncharacterised viral strains. (C) 2005 Elsevier B.V. All rights reserved.

Parabolic optical pulses under the action of the third-order dispersion

Recent developments in nonlinear optics reveal an interesting class of pulses with a parabolic intensity profile in the energy-containing core and a linear frequency chirp that can propagate in a fiber with normal group-velocity dispersion. Parabolic pulses propagate in a stable selfsimilar manner, holding certain relations (scaling) between pulse power, width, and chirp parameter. In the additional presence of linear amplification, they enjoy the remarkable property of representing a common asymptotic state (or attractor) for arbitrary initial conditions. Analytically, self-similar (SS) parabolic pulses can be found as asymptotic, approximate solutions of the nonlinear Schr¨odinger equation (NLSE) with gain in the semi-classical (largeamplitude/small-dispersion) limit. By analogy with the well-known stable dynamics of solitary waves - solitons, these SS parabolic pulses have come to be known as similaritons. In practical fiber systems, inherent third-order dispersion (TOD) in the fiber always introduces a certain degree of asymmetry in the structure of the propagating pulse, eventually leading to pulse break-up. To date, there is no analytic theory of parabolic pulses under the action of TOD. Here, we develop aWKB perturbation analysis that describes the effect of weak TOD on the parabolic pulse solution of the NLSE in a fiber gain medium. The induced perturbation in phase and amplitude can be found to any order. The theoretical model predicts with sufficient accuracy the pulse structural changes induced by TOD, which are observed through direct numerical NLSE simulations.

Parabolic optical pulses under the action of the third-order dispersion

Recent developments in nonlinear optics reveal an interesting class of pulses with a parabolic intensity profile in the energy-containing core and a linear frequency chirp that can propagate in a fiber with normal group-velocity dispersion. Parabolic pulses propagate in a stable selfsimilar manner, holding certain relations (scaling) between pulse power, width, and chirp parameter. In the additional presence of linear amplification, they enjoy the remarkable property of representing a common asymptotic state (or attractor) for arbitrary initial conditions. Analytically, self-similar (SS) parabolic pulses can be found as asymptotic, approximate solutions of the nonlinear Schr¨odinger equation (NLSE) with gain in the semi-classical (largeamplitude/small-dispersion) limit. By analogy with the well-known stable dynamics of solitary waves - solitons, these SS parabolic pulses have come to be known as similaritons. In practical fiber systems, inherent third-order dispersion (TOD) in the fiber always introduces a certain degree of asymmetry in the structure of the propagating pulse, eventually leading to pulse break-up. To date, there is no analytic theory of parabolic pulses under the action of TOD. Here, we develop aWKB perturbation analysis that describes the effect of weak TOD on the parabolic pulse solution of the NLSE in a fiber gain medium. The induced perturbation in phase and amplitude can be found to any order. The theoretical model predicts with sufficient accuracy the pulse structural changes induced by TOD, which are observed through direct numerical NLSE simulations.

Rapid multi sample DNA amplification using rotary-linear polymerase chain reaction device (PCRDisc)

Multiple sample DNA amplification was done by using a novel rotary-linear motion polymerase chain reaction (PCR) device. A simple compact disc was used to create the stationary sample chambers which are individually temperature controlled. The PCR was performed by shuttling the samples to different temperature zones by using a combined rotary-linear movement of the disc. The device was successfully used to amplify up to 12 samples in less than 30 min with a sample volume of 5 μl. A simple spring loaded heater mechanism was introduced to enable good thermal contact between the samples and the heaters. Each of the heater temperatures are controlled by using a simple proportional–integral–derivative pulse width modulation control system. The results show a good improvement in the amplification rate and duration of the samples. The reagent volume used was reduced to nearly 25% of that used in conventional method.