Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR

DNA amplification using Polymerase Chain Reaction (PCR) in a small volume is used in Lab-on-a-chip systems involving DNA manipulation. For few microliters of volume of liquid, it becomes difficult to measure and monitor the thermal profile accurately and reproducibly, which is an essential requirement for successful amplification. Conventional temperature sensors are either not biocompatible or too large and hence positioned away from the liquid leading to calibration errors. In this work we present a fluorescence based detection technique that is completely biocompatible and measures directly the liquid temperature. PCR is demonstrated in a 3 ILL silicon-glass microfabricated device using non-contact induction heating whose temperature is controlled using fluorescence feedback from SYBR green I dye molecules intercalated within sensor DNA. The performance is compared with temperature feedback using a thermocouple sensor. Melting curve followed by gel electrophoresis is used to confirm product specificity after the PCR cycles. (c) 2007 Elsevier B.V. All rights reserved.

Stimuli-responsive colorimetric and NIR fluorescence combination probe for selective reporting of cellular hydrogen peroxide

Hydrogen peroxide (H2O2) is a key reactive oxygen species and a messenger in cellular signal transduction apart from playing a vital role in many biological processes in living organisms. In this article, we present phenyl boronic acid-functionalized quinone-cyanine (QCy-BA) in combination with AT-rich DNA (exogenous or endogenous cellular DNA), i.e., QCy-BA subset of DNA as a stimuli-responsive NIR fluorescence probe for measuring in vitro levels of H2O2. In response to cellular H2O2 stimulus, QCy-BA converts into QCy-DT, a one-donor-two-acceptor (D2A) system that exhibits switch-on NIR fluorescence upon binding to the DNA minor groove. Fluorescence studies on the combination probe QCy-BA subset of DNA showed strong NIR fluorescence selectively in the presence of H2O2. Furthermore, glucose oxidase (GOx) assay confirmed the high efficiency of the combination probe QCy-BA subset of DNA for probing H2O2 generated in situ through GOx-mediated glucose oxidation. Quantitative analysis through fluorescence plate reader, flow cytometry and live imaging approaches showed that QCy-BA is a promising probe to detect the normal as well as elevated levels of H2O2 produced by EGF/Nox pathways and post-genotoxic stress in both primary and senescent cells. Overall, QCy-BA, in combination with exogenous or cellular DNA, is a versatile probe to quantify and image H2O2 in normal and disease-associated cells.

Structural studies of the hen's egg lipovitellins. NMR and fluorescence investigations

The pH dependent reversible association-dissociation reaction of α- and β-lipovitellins from egg yolk has been studied by 1H NMR and fluorescence probe methods. Increased mobility of the choline methyl groups has been demonstrated on dissociation. The lipid methylene resonance of β-lipovitellin shows clear doublet character suggesting that the fatty acid chains exist in distinct environments. The high field component increases with temperature but is suppressed on treatment with pronase, suggesting a significant role for proteins in maintaining the differences in lipid environments. 1-Anilino-8-naphthalene sulfonate has been shown to bind less effectively to the monomeric lipovitellins. This is in agreement with earlier results suggesting that dissociation may be accompanied by increased hydration and conformational changes.

Role of spacer chain length in dimeric micellar organization. Small angle neutron scattering and fluorescence studies

Micelles of different dimeric amphiphiles Br-, n-C(16)H(33)NMe(2)(+) -(CH)(m)-N(+)Me(2)-n-C16H33, Br- (where m = 3, 4, 5, 6, 8, 10, and 12) adapt different morphologies and internal packing arrangements in aqueous media depending on their spacer chain length (m). Detailed measurements of small angle neutron scattering (SANS) cross sections from different bis-cationic, dimeric surfactant micelles in aqueous media (D2O) are reported. The data have been analyzed using the Hayter and Penfold model for macro ion solution to compute the interparticle structure factor S(Q) taking into account the screened Coulomb interactions between the dimeric micelles. The SANS analysis clearly indicated that the extent of aggregate growth and the variations of shapes of the dimeric micelles depend primarily on the spacer chain length. With spacer chain length, m less than or equal to 4, the propensity of micellar growth was particularly pronounced. The effects of the variation of the concentration of dimeric surfactants with m = 5 and 10 on the SANS spectra and the effects of the temperature variation for the micellar system with m = 10 were also examined. The critical micelle concentrations (cmc) and their microenvironmental feature, namely, the microviscosities that the dimeric micellar aggregates offer to a solubilized, extrinsic fluorescence probe, 1,6-diphenyl-1,3,5-hexatriene, were also determined. The changes of cmcs and microviscosities as a function of spacer chain length have been explained in terms of conformational variations and progressive looping of the spacer in micellar core upon increasing m values.

Spatial filtering nearly eliminates the side-lobes in single- and multi-photon 4pi-type-C super-resolution fluorescence microscopy

Super-resolution microscopy has tremendously progressed our understanding of cellular biophysics and biochemistry. Specifically, 4pi fluorescence microscopy technique stands out because of its axial super-resolution capability. All types of 4pi-microscopy techniques work well in conjugation with deconvolution techniques to get rid of artifacts due to side-lobes. In this regard, we propose a technique based on spatial filter in a 4pi-type-C confocal setup to get rid of these artifacts. Using a special spatial filter, we have reduced the depth-of-focus. Interference of two similar depth-of-focus beams in a 4 pi geometry result in substantial reduction of side-lobes. Studies show a reduction of side-lobes by 46% and 76% for single and two photon variant compared to 4pi - type - C confocal system. This is incredible considering the resolving capability of the existing 4pi - type - C confocal microscopy. Moreover, the main lobe is found to be 150 nm for the proposed spatial filtering technique as compared to 690 nm of the state-of-art confocal system. Reconstruction of experimentally obtained 2PE - 4pi data of green fluorescent protein (GFP)-tagged mitocondrial network shows near elimination of artifacts arising out of side-lobes. Proposed technique may find interesting application in fluorescence microscopy, nano-lithography, and cell biology. (C) 2013 AIP Publishing LLC.

Plasma diagnostics of the high pressure oxygen-sputtering process

The characteristics of the high pressure oxygen-sputtering plasma in the pressure range 0.8–2.4 mbar have been studied using the Langmuir probe technique. The variation in plasma parameters such as positive ion density, electron density, mean electron energy and floating potential with pressure and temperature has been investigated. It has been observed that the positive ion density increases at high substrate temperatures whereas the negative ion density decreases. The study of the variation in mean electron energy and floating potential also indicated the possibility that the number of negative ions is less when the substrates are at elevated temperatures. Since the negative ions are supposed to cause re-sputtering and make the films off-stoichiometric, the reduction in the negative ion density as observed at elevated substrate temperatures is better suited for depositing stoichiometric YBa2Cu3O7−δ superconducting thin films.

Small-angle neutron scattering studies of different mixed micelles composed of dimeric and monomeric cationic surfactants

Measurements of small-angle neutron scattering (SANS) cross sections from different mixed micelles composed of CTAB and Br-, n-C16H33N+Me2-(CH2)(m)N+Me2-n-C16H33, Br- (16-m-16, 2Br(-), where m = 3, 5, and 10), in aqueous media (D2O) are reported. The data have been analyzed using the Hayter and Penfold model for macroion solution to compute the interparticle structure factor S(Q) taking into account the screened Coulomb interactions between the micelles. The aggregate composition matches with that predicted from an ideal mixing model. The SANS analysis further indicates that the extent of aggregate growth and the Variations of shapes of the mixed micelles could be modulated by the amount of dimeric surfactant present in these mixtures. With the spacer chain length m less than or equal to 4 in the dimeric surfactant, the propensity of micellar growth is particularly pronounced. The effect of the variation of the temperature for the mixed micellar system (23.1 mol % of 16-3-16, 2Br(-)) was also examined. The systemic microviscosities that the mixed micellar aggregates offer to a solubilized, extrinsic fluorescence probe, 1,6-diphenyl-1,3,5-hexatriene, were determined. The variation of the microviscosities of the mixed micelles as a function of percentages of the dimeric surfactants could be explained in terms of conformational variations and progressive looping of the spacer chain of dimeric surfactants in mixed micellar aggregates with increasing m values.

Studies on the structural and ionic transport properties at elevated temperatures of La1-xMnO3 +/-delta synthesized by a wet chemical method

Structural transformation and ionic transport properties are investigated on wet-chemically synthesized La1-xMnO3 (X=0.0-0.18) compositions. Powders annealed in oxygen/air at 1000-1080 K exhibit cubic symmetry and transform to rhombohedral on annealing at 1173-1573 K in air/oxygen. Annealing above 1773 K in air or in argon/helium at 1473 K stabilized distorted rhombohedral or orthorhombic symmetry. Structural transformations are confirmed from XRD and TEM studies. The total conductivity of sintered disks, measured by four-probe technique, ranges from 5 S cm(-1) at 298 K to 105 S cm(-1) at 1273 K. The ionic conductivity measured by blocking electrode technique ranges from 1.0X10(-6) S cm(-1) at 700 K to 2.0X10(-3) S cm(-1) at 1273 K. The ionic transference number of these compositions ranges from 3.0X10(-5) to 5.0X10(-5) at 1273 K. The activation energy deduced from experimental data for ionic conduction and ionic migration is 1.03-1.10 and 0.80-1.00 eV, respectively. The activation energy of formation, association and migration of vacancies ranges from 1.07 to 1.44 eV. (C) 2002 Elsevier Science B.V. All rights reserved.

Small-Angle Neutron-Scattering Studies of Mixed Micellar Structures Made of Dimeric Surfactants Having Imidazolium and Ammonium Headgroups

Planar imidazolium cation based gemini surfactants 16-Im-n-Im-16], 2Br(-) (where n = 2, 3, 4, 5, 6, 8, 10, and 12), exhibit different morphologies and internal packing arrangements by adopting different supramolecular assemblies in aqueous media depending on their number of spacer methylene units (CH2)(n). Detailed measurements of the small-angle neutron-scattering (SANS) cross sections from different imidazolium-based surfactant micelles in aqueous media (D2O) are reported. The SANS data, containing the information of aggregation behavior of such surfactants in the molecular level, have been analyzed on the basis of the Hayter and Penfold model for the macro ion solution to compute the interparticle structure factor S(Q) taking into account the screened Coulomb interactions between the dimeric surfactant micelles. The characteristic changes in the SANS spectra of the dimeric surfactant with n = 4 due to variation of temperature have also been investigated. These data are then compared with the SANS characterization data of the corresponding gemini micelles containing tetrahedral ammonium ion based polar headgroups. The critical micellar concentration of each surfactant micelle (cmc) has been determined using pyrene as an extrinsic fluorescence probe. The variation of cmc as a function of spacer chain length has been explained in terms of conformational variation and progressive looping of the spacer into the micellar interior upon increasing the n values. Small-angle neutron-scattering (SANS) cross sections from different mixed micelles composed of surfactants with ammonium headgroups, 16-A(0), 16-Am-n-Am-16], 2Br(-) (where n = 4), 16-I-0, and 16-Im-n-Im-16], 2Br(-) (where n = 4), in aqueous media (D2O) have also been analyzed. The aggregate composition matches with that predicted from the ideal mixing model.

Study of liquid fuel transport in a small carburetted engine in the context of cold-start HC emission control

In the present study, a detailed visualization of the transport of fuel film has been performed in a small carburetted engine with a transparent manifold at the exit of the carburettor. The presence of fuel film is observed significantly on the lower half of the manifold at idling, while at load conditions, the film is found to be distributed all throughout the manifold walls. Quantitative measurement of the fuel film in a specially-designed manifold of square cross section has also been performed using the planar laser-induced fluorescence (PLIF) technique. The measured fuel film thickness is observed to be of the order of 1 nun at idling, and in the range of 0.1 to 0.4 mm over the range of load and speed studied. These engine studies are complemented by experiments conducted in a carburettor rig to study the state of the fuel exiting the carburettor. Laser-based Particle/Droplet Image Analysis (PDIA) technique is used to identify fuel droplets and ligaments and estimate droplet diameters. At a throttle position corresponding to idling, the fuel exiting the carburettor is found to consist of very fine droplets of size less than 15 mu m and large fuel ligaments associated with length scales of the order of 500 mu m and higher. For a constant pressure difference across the carburettor, the fuel consists of droplets with an SMD of the order of 30 mu m. Also, the effect of liquid fuel film on the cold start HC emissions is studied. Based on the understanding obtained from these studies, strategies such as manifold heating and varying carburettor main jet nozzle diameter are implemented. These are observed to reduce emissions under both idling and varying load conditions.

Ionophore-mediated transmembrane movement of divalent cations in small unilamellar liposomes: An evaluation of the chlortetracycline fluorescence technique and correlations with black lipid membrane studies

Conceptual advances in the field of membrane transport have, in the main, utilized artificial membranes, both planar and vesicular. Systems of biological interest,viz., cells and organelles, resemble vesicles in size and geometry. Methods are, therefore, required to extend the results obtained with planar membranes to liposome systems. In this report we present an analysis of a fluorescence technique, using the divalent cation probe chlortetracycline, in small, unilamellar vesicles, for the study of divalent cation fluxes. An ion carrier (X537 A) and a pore former (alamethicin) have been studied. The rate of rise of fluorescence signal and the transmembrane ion gradient have been related to transmembrane current and potential, respectively. A second power dependence of ion conduction-including the electrically silent portion thereof — on X537 A concentration, has been observed. An exponential dependence of ldquocurrentrdquo on ldquotransmembrane potentialrdquo in the case of alamethicin is also confirmed. Possible errors in the technique are discussed.

Development of a probe-based blotting technique for the detection of Tobacco streak virus

Digoxigenin (DIG)-labeled DNA probe was developed for a sensitive and rapid detection of the Tobacco streak virus (TSV) isolates in India by dot-blot and tissue print hybridization techniques. DIG-labeled DNA probe complementary to the coat protein (CP) region of TSV sunflower isolate was designed and used to detect the TSV presence at field levels. Dot-blot hybridization was used to check a large number of TSV isolates with a single probe. In addition, a sensitivity of the technique was examined with the different sample extraction methods. Another technique, the tissue blot hybridization offered a simple, reliable procedure and did not require a sample processing. Thus, both non-radioactively labeled probe techniques could facilitate the sample screening during TSV outbreaks and offer an advantage in quarantine services.

Ellipsometry as a Sensitive Technique to Probe film -Substrate Interfaces: Al2O3 on Si(100)

An attempt has been made to study the film-substrate interface by using a sensitive, non- conventional tool. Because of the prospective use of gate oxide in MOSFET devices, we have chosen to study alumina films grown on silicon. Film-substrate interface of alumina grown by MOCVD on Si(100) was studied systematically using spectroscopic ellipsometry in the range 1.5-5.0 eV, supported by cross-sectional SEM, and SIMS. The (ε1,ε2) versus energy data obtained for films grown at 600°C, 700°C, and 750°C were modeled to fit a substrate/interface/film “sandwich”. The experimental results reveal (as may be expected) that the nature of the substrate -film interface depends strongly on the growth temperature. The simulated (ε1,ε2) patterns are in excellent agreement with observed ellipsometric data. The MOCVD precursors results the presence of carbon in the films. Theoretical simulation was able to account for the ellipsometry data by invoking the presence of “free” carbon in the alumina films.

Multispectral Bayesian reconstruction technique for real-time two color fluorescence microscopy

We have developed a real-time imaging method for two-color wide-field fluorescence microscopy using a combined approach that integrates multi-spectral imaging and Bayesian image reconstruction technique. To enable simultaneous observation of two dyes (primary and secondary), we exploit their spectral properties that allow parallel recording in both the channels. The key advantage of this technique is the use of a single wavelength of light to excite both the primary dye and the secondary dye. The primary and secondary dyes respectively give rise to fluorescence and bleed-through signal, which after normalization were merged to obtain two-color 3D images. To realize real-time imaging, we employed maximum likelihood (ML) and maximum a posteriori (MAP) techniques on a high-performance computing platform (GPU). The results show two-fold improvement in contrast while the signal-to-background ratio (SBR) is improved by a factor of 4. We report a speed boost of 52 and 350 for 2D and 3D images respectively. Using this system, we have studied the real-time protein aggregation in yeast cells and HeLa cells that exhibits dot-like protein distribution. The proposed technique has the ability to temporally resolve rapidly occurring biological events.

A low-power, low-cost soil-moisture sensor using dual-probe heat-pulse technique

This paper presents the development and testing of an integrated low-power and low-cost dual-probe heat-pulse (DPHP) soil-moisture sensor in view of the electrical power consumed and affordability in developing countries. A DPHP sensor has two probes: a heater and a temperature sensor probe spaced 3 mm apart from the heater probe. Supply voltage of 3.3V is given to the heater-coil having resistance of 33 Omega power consumption of 330 mW, which is among the lowest in this category of sensors. The heater probe is 40 mm long with 2 mm diameter and hence is stiff enough to be inserted into the soil. The parametric finite element simulation study was performed to ensure that the maximum temperature rise is between 1 degrees C and 5 degrees C for wet and dry soils, respectively. The discrepancy between the simulation and experiment is less than 3.2%. The sensor was validated with white clay and tested with red soil samples to detect volumetric water-content ranging from 0% to 30%. The sensor element is integrated with low-power electronics for amplifying the output from thermocouple sensor and TelosB mote for wireless communication. A 3.7V lithium ion battery with capacity of 1150 mAh is used to power the system. The battery is charged by a 6V and 300 mA solar cell array. Readings were taken in 30 min intervals. The life-time of DPHP sensor node is around 3.6 days. The sensor, encased in 30 mm x 20 mm x 10 mm sized box, and integrated with electronics was tested independently in two separate laboratories for validating as well as investigating the dependence of the measurement of soil-moisture on the density of the soil. The difference in the readings while repeating the experiments was found out to be less than 0.01%. Furthermore, the effect of ambient temperature on the measurement of soil-moisture is studied experimentally and computationally. (C) 2015 Elsevier B.V. All rights reserved.