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.     

The role of DNA diffusion in solid phase polymerase chain reaction with gel-immobilized primers in planar and capillary microarray format

The solid phase polymerase chain reaction (PCR) on a gel-based microarray system was studied under various durations of individual stages of the PCR cycle and spatial restriction of the reaction volume. Combining the experimental study with numerical modeling, we demonstrated that the diffusion of the PCR product in and out of a microarray element during the annealing and melting stages, respectively, is the main factor responsible for distinctive features of the studied type of PCR. The restriction of reaction volume leads to faster PCR signal growth. Particularly, the capillary array, whereby gel-based microarray elements are located on a glass bar inserted into capillary chamber, was found to be a suitable format for the development of the platform.     

DNA capture-probe based separation of double-stranded polymerase chain reaction amplification products in poly(dimethylsiloxane) microfluidic channels

Herein, we describe the development of a novel primer system that allows for the capture of double-stranded polymerase chain reaction (PCR) amplification products onto a microfluidic channel without any preliminary purification stages. We show that specially designed PCR primers consisting of the main primer sequence and an additional “tag sequence” linked through a poly(ethylene glycol) molecule can be used to generate ds-PCR amplification products tailed with ss-oligonucleotides of two forensically relevant genes (amelogenin and human c-fms (macrophage colony-stimulating factor) proto-oncogene for the CSF-1 receptor (CSF1PO). Furthermore, with a view to enriching and eluting the ds-PCR products of amplification on a capillary electrophoretic-based microfluidic device we describe the capture of the target ds-PCR products onto poly(dimethylsiloxane) microchannels modified with ss-oligonucleotide capture probes.     

Detection of hemoglobin E in Endhra Pradesh: Mutational analysis using polymerase chain reaction and restriction enzyme Mnl 1

Hemoglobin E (beta-26^{Glutamic acid→Lysine}) is the second most prevalent hemoglobin variant in the world. 293 blood samples from cases referred from several hospitals in the region of Andhra Pradesh were screened for the detection of hemoglobinopathies. Four samples were found to be in heterozygous state for Hb E condition. Mutation in two of these heterozygotes was analysed using a 722 base pair (bp) amplified DNA fragment from beta-globin gene and restriction enzyme Mnl 1. A 232bp DNA fragment was found to be associated with the Hb E mutation.     

A microfluidic device for simultaneous measurement of viscosity and flow rate of blood in a complex fluidic network

Blood viscosity has been considered as one of important biophysical parameters for effectively monitoring variations in physiological and pathological conditions of circulatory disorders. Standard previous methods make it difficult to evaluate variations of blood viscosity under cardiopulmonary bypass procedures or hemodialysis. In this study, we proposed a unique microfluidic device for simultaneously measuring viscosity and flow rate of whole blood circulating in a complex fluidic network including a rat, a reservoir, a pinch valve, and a peristaltic pump. To demonstrate the proposed method, a twin-shaped microfluidic device, which is composed of two half-circular chambers, two side channels with multiple indicating channels, and one bridge channel, was carefully designed. Based on the microfluidic device, three sequential flow controls were applied to identify viscosity and flow rate of blood, with label-free and sensorless detection. The half-circular chamber was employed to achieve mechanical membrane compliance for flow stabilization in the microfluidic device. To quantify the effect of flow stabilization on flow fluctuations, a formula of pulsation index (PI) was analytically derived using a discrete fluidic circuit model. Using the PI formula, the time constant contributed by the half-circular chamber is estimated to be 8 s. Furthermore, flow fluctuations resulting from the peristaltic pumps are completely removed, especially under periodic flow conditions within short periods (T < 10 s). For performance demonstrations, the proposed method was applied to evaluate blood viscosity with respect to varying flow rate conditions [(a) known blood flow rate via a syringe pump, (b) unknown blood flow rate via a peristaltic pump]. As a result, the flow rate and viscosity of blood can be simultaneously measured with satisfactory accuracy. In addition, the proposed method was successfully applied to identify the viscosity of rat blood, which circulates in a complex fluidic network. These observations confirm that the proposed method can be used for simultaneous measurement of viscosity and flow rate of whole blood circulating in the complex fluid network, with sensorless and label-free detection. Furthermore, the proposed method will be used in evaluating variations in the viscosity of human blood during cardiopulmonary bypass procedures or hemodialysis.     

Simulation of single DNA molecule stretching and immobilization in a de-wetting two-phase flow over micropillar-patterned surface

We investigate single DNA stretching dynamics in a de-wetting flow over micropillars using Brownian dynamics simulation. The Brownian dynamics simulation is coupled with transient flow field computation through a numerical particle tracking algorithm. The droplet formation on the top of the micropillar during the de-wetting process creates a flow pattern that allows DNA to stretch across the micropillars. It is found that DNA nanowire forms if DNA molecules could extend across the stagnation point inside the connecting water filament before its breakup. It also shows that DNA locates closer to the top wall of the micropillar has higher chance to enter the flow pattern of droplet formation and thus has higher chance to be stretched across the micropillars. Our simulation tool has the potential to become a design tool for DNA manipulation in complex biomicrofluidic devices.     

Release monitoring of single cells on a microfluidic device coupled with fluorescence microscopy and electrochemistry

A method for monitoring the biological exocytotic phenomena on a microfluidic system was proposed. A microfluidic device coupled with functionalities of fluorescence imaging and amperometric detection has been developed to enable the real-time monitoring of the exocytotic events. Exocytotic release of single SH-SY5Y neuroblastoma cells was studied. By staining the cells located on integrated microelectrodes with naphthalene-2,3-dicarboxaldehyde, punctuate fluorescence consistent with localization of neurotransmitters stored in vesicles was obtained. The stimulated exocytotic release was successfully observed at the surface of SH-SY5Y cells without refitting the commercial inverted fluorescence microscope. Spatially and temporally resolved exocytotic events from single cells on a microfluidic device were visualized in real time using fluorescence microscopy and were amperometrically recorded by the electrochemical system simultaneously. This coupled technique is simple and is hoped to provide new insights into the mechanisms responsible for the kinetics of exocytosis.     

Thermal diffusion and diffusion thermo effects on unsteady MHD free convection flow over a stretching surface considering Joule heating and viscous dissipation with thermal stratification,chemical reaction and Hall current

The present investigation is concerned with the effects of thermal-diffusion and diffusion-thermo on an unsteady MHD free convection boundary layer flow with heat and mass transfer of an electrically conducting fluid over a stretching sheet in the presence of strong magnetic field with Hall current, thermal stratification, chemical reaction, heat generation, thermal radiation, Joule heating and viscous dissipation. The transformed nonlinear boundary layer equations are numerically solved by applying Keller-box method. The influence of various embedded flow parameters on the local skin friction, the local Nusselt number and the local Sherwood number has been carefully analyzed through graphs. It is found that the shear stress and the rate of mass transfer increase with an increasing of current density _Jh$J_h$ while the reverse trend is observed on the rate of heat transfer. It is also found that the shear stress and the rate of heat transfer increase with an increasing of Sr  , whereas the reverse trend is observed on the rate of mass transfer. Further, the shear stress and the rate of mass transfer increase with an increasing of Du$Du$ while the reverse trend is seen on the rate of heat transfer. The numerical results are compared and found to be in good agreement with previously published results under special cases.     

Adiabatic flow of hydrogen gas through a rocket nozzle with and without composition change

A procedure is described for determining the characteristics of adiabatic flow through a rocket nozzle with and without composition change. The method of calculation is illustrated for the expansion of pure hydrogen gas from a chamber temperature of 306° K. and a pressure of 20.42 atm. to atmospheric pressure.The study indicates that the exhaust velocity and temperature are highest for flow where complete equilibrium is reached at each temperature with respect to the reaction

$\text{H}{}_2\text{?2H}$

Flow with composition change requires a nozzle exit to nozzle throat area ratio somewhat greater than that determined for adiabatic flow without composition change for the same ratio of chamber pressure to exit pressure.The residence time in a given temperature range is computed as a function of gas temperature for the two types of flow. The results of this calculation may be used to determine the minimum required reaction rates which allow composition changes during flow through the nozzle.     

Electrokinetic trapping and surface enhanced Raman scattering detection of biomolecules using optofluidic device integrated with a microneedles array

In this study, microneedles which possess sharp tips were utilized to trap and detect the biomolecules. Owing to the large curvature, the tips of the microneedles created a substantially high gradient of electric field under the non-uniform electric field which served as not only the trapping sites but also the substrate for surface enhanced Raman scattering (SERS). Separation of polystyrene microparticles with different sizes and two kinds of biomolecules (Staphylococcus aureus (S. aureus) and the red blood cells (RBCs)) were demonstrated. Moreover, in situ detection of S. aureus was performed immediately after separation was completed. The results showed that, after 15 s of sample collection, the Raman signals of S. aureus were detected and greatly enhanced through SERS effect.     

Microprocessor-based simulation of sampled data systems with/without a hold device using a set of sample-and-hold functions and Dirac delta functions

In the present work, Dirac delta function (DF) set and sample-and-hold functions (SHF) set are used for microprocessor-based simulation of discrete time as well as sample-and-hold systems. Such simulations are useful for identification of control systems with known input and output sequence. The presented method utilizes operational matrices of different orders in the DF and SHF domain to develop different operational transfer functions. A few open-loop as well as closed-loop systems have been studied and the simulation results obtained are compared with exact solutions derived with the help of z-transform analysis. Experiments have also been carried out to establish the validity of the proposal.     

Highly sensitive FET sensors for cadmium detection in one drop of human serum with a hand-held device and investigation of the sensing mechanism

As the heavy metal contamination is becoming worse, monitoring the heavy metal content in water or human body gets more and more important. In this research, a cadmium ion-selective field effect transistor (Cd-ISFET) for rapidly detecting cadmium ions has been developed and the mechanism of the sensor is also investigated in depth. Our Cd-ISFET sensor exhibits high sensitivity beyond the ideal Nernst sensitivity, wide dynamic range, low detection limit (∼10⁻¹¹M), which is comparable with inductively coupled plasma mass spectrometry, and easy operation enabling people to detect cadmium ion by themselves. From the analysis of electrical measurement results, this Cd-ISFET is preferred to operate at the bias with the maximum transconductance of the FET to enhance the sensor signal. The AC impedance measurement is carried out to directly investigate the mechanism of an ion-selective membrane (ISM). From impedance results, the real part of the total impedance, which is the resistance, was shown to dominate the sensor signal. The potential drop across the ISM is caused by the heavy metal ion in the membrane, which is employed to the gate of the FET via an extended gate electrode. Cadmium ion detection in one drop of human serum with this sensor was demonstrated. This cost-effective and highly sensitive sensor is promising and can be used by anyone and anywhere to prevent people from cadmium poisoning.