Trends in microRNA detection

MicroRNAs (miRNAs) are short, ~22 nucleotide length RNAs that perform gene regulation. Recently, miRNA has been shown to be linked with the onset of cancer and other diseases based on miRNA expression levels. It is important, therefore, to understand miRNA function as it pertains to disease onset; however, in order to fully understand miRNA’s role in a disease, it is necessary to detect the expression levels of these small molecules. The most widely used miRNA detection method is Northern blotting, which is considered as the standard of miRNA detection methods. This method, however, is time-consuming and has low sensitivity. This has led to an increase in the amount of detection methods available. These detection methods are either solid phase, occurring on a solid support, or solution phase, occurring in solution. While the solid-phase methods are adaptable to high-throughput screening and possess higher sensitivity than Northern blotting, they lack the ability for in vivo use and are often time-consuming. The solution-phase methods are advantageous in that they can be performed in vivo, are very sensitive, and are rapid; however, they cannot be applied in high-throughput settings. Although there are multiple detection methods available, including microarray technology, luminescence-based assays, electrochemical assays, etc., there is still much work to be done regarding miRNA detection. The current gaps of miRNA detection include the ability to perform multiplex, sensitive detection of miRNA with single-nucleotide specificity along with the standardization of these new methods. Current miRNA detection methods, gaps in these methods, miRNA therapeutic options, and the future outlook of miRNA detection are presented here.     

An extensive study on isosorbide-5-mononitrate acid adducts for quantification in human plasma using liquid chromatography/electrospray ionization tandem mass spectrometry and its application to bioequivalence sample analysis

A rapid and sensitive liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method for the determination of isosorbide-5-mononitrate (5-ISMN), used in the treatment of angina pectoris, in human plasma is described. The quantification of 5-ISMN was performed via stable acetate adduct formation with a high relative abundance. The plasma filtrate obtained after solid-phase extraction (SPE), using a polymer based, hydrophilic-lipophilic balanced (HLB) cartridge, was submitted directly to reversed-phase high-performance liquid chromatography separation followed by ESI and detection of the resulting ions using triple-quadrupole mass spectrometry in selected reaction monitoring (SRM) mode. There was no significant matrix effect on the analysis. For validation of the method, the recovery of the free analyte response was compared to that obtained from an optimized extraction method. The analyte stability was examined under conditions mimicking the sample storage, handling, and analytical procedures. The extraction procedure yielded extremely clean extracts with a recovery of 95.51% and 93.98% for iossorbide-5-mononitrate and topiramate (internal standard (IS)), respectively. The calibration curves were linear for the dynamic range of 10.0 to 1000.0 ng/mL with a correlation coefficient r > or = 0.9985. The intra-assay and inter-assay precision for the samples at the lower limit of quantification (LLOQ) were 9.02 and 13.30%, respectively. The intra-assay accuracies at LLOQ, LQC, MQC and HQC levels varied from 98.13 to 118.15, 102.34 to 105.21, 100.69 to 109.68, and 95.76 to 102.92%, respectively, while the inter-assay accuracies ranged from 93.10 to 118.15, 93.03 to 107.04, 86.97 to 109.68 and 86.18 to 105.85%, respectively, at these levels. The method is rugged and fast with a total run time of 2 min. The method was successfully applied for a bioequivalence study in 24 human subject samples after oral administration of 60 mg extended release (ER) formulations.     

Analyses of Lattice Traffic Flow Model on a Gradient Highway

The optimal current difference lattice hydrodynamic model is extended to investigate the traffic flow dynamics on a unidirectional single lane gradient highway. The effect of slope on uphill/downhill highway is examined through linear stability analysis and shown that the slope significantly affects the stability region on the phase diagram.Using nonlinear stability analysis, the Burgers, Korteweg-deVries(KdV) and modified Korteweg-deVries(mKdV) equations are derived in stable, metastable and unstable region, respectively. The effect of reaction coefficient is examined and concluded that it plays an important role in suppressing the traffic jams on a gradient highway. The theoretical findings have been verified through numerical simulation which confirm that the slope on a gradient highway significantly influence the traffic dynamics and traffic jam can be suppressed efficiently by considering the optimal current difference effect in the new lattice model.     

Solution-phase detection of dual microRNA biomarkers in serum

A strategy for the simultaneous detection of multiple microRNA (miRNA) targets was developed utilizing fluorophore/quencher-labeled oligonucleotide probe sets. Two miRNA targets (miR-155 and miR-103), whose misregulation has afforded them status as putative biomarkers in certain types of cancer, were detected using our assay design. In the absence of target, the complementary fluorophore-probe and quencher-probe hybridize, resulting in a fluorescence resonance energy transfer-based quenching of the fluorescence signal. In the presence of unlabeled target, however, the antisense quencher-probe can hybridize with the target, resulting in increased fluorescence intensity as the quencher-probe is sequestered beyond the Förster radius of the fluorescent-probe. The assay design was tested in multiple matrices of buffer, cellular extract, and serum; and detection limits were found to be matrix-dependent, ranging from 0.34 to 8.89 pmol (3.4–59.3 nM) for miR-155 and 2.90–11.8 pmol (19.3–79.0 nM) for miR-103. Single, double, and triple nucleotide selectivity was also tested. Additionally, miR-155 concentrations were assessed in serum samples obtained directly from breast cancer patients without the need for RNA extraction. This assay is quantitative, possesses a low detection limit, can be applied in multiple complex matrices, and can obtain single-nucleotide selectivity. This method can be employed for the multiplex detection of solution-phase DNA or RNA targets and, more specifically, for the direct detection of serum miRNA biomarkers.     

Nonlinear analysis of traffic continuum jams in an anisotropic model

This paper presents our study of the nonlinear stability of a new anisotropic continuum traffic flow model in which the dimensionless parameter or anisotropic factor controls the non-isotropic character and diffusive influence. In order to establish traff~c flow stability criterion or to know the critical parameters that lead, on one hand, to a stable response to perturbations or disturbances or, on the other hand, to an unstable response and therefore to a possible congestion, a nonlinear stability criterion is derived by using a wavefront expansion technique. The stability criterion is illustrated by numerical results using the finite difference method for two different values of anisotropic parameter. It is also been observed that the newly derived stability results are consistent with previously reported results obtained using approximate linearisation methods. Moreover, the stability criterion derived in this paper can provide more refined information from the perspective of the capability to reproduce nonlinear traffic flow behaviors observed in real traffic than previously established methodologies.     

Analyses of a heterogeneous lattice hydrodynamic model with low and high-sensitivity vehicles

Basic lattice model is extended to study the heterogeneous traffic by considering the optimal current difference effect on a unidirectional single lane highway. Heterogeneous traffic consisting of low- and high-sensitivity vehicles is modeled and their impact on stability of mixed traffic flow has been examined through linear stability analysis. The stability of flow is investigated in five distinct regions of the neutral stability diagram corresponding to the amount of higher sensitivity vehicles present on road. In order to investigate the propagating behavior of density waves non linear analysis is performed and near the critical point, the kink antikink soliton is obtained by driving mKdV equation. The effect of fraction parameter corresponding to high sensitivity vehicles is investigated and the results indicates that the stability rise up due to the fraction parameter. The theoretical findings are verified via direct numerical simulation.     

A time-delay model for the effect of toxicant in a single species growth with stage-structure

In this paper, we investigate a single-species growth model with stage-structure consisting of immature and mature stages for the effects of toxicants with constant maturation time-delay. We study the dynamics of our model in three cases: an instantaneous emission of toxicant, a constant emission of toxicant, and a periodic emission of toxicant into the environment. We present results on positivity and boundedness of all solutions under appropriate conditions. The model equations are analyzed mathematically with regard to the nature of equilibria and their stabilities using the theory of nonlinear differential equations and computer simulations. It is shown that under suitable conditions, there exists a globally asymptotically stable positive equilibrium. It is concluded from the analysis that as the concentration of toxicant in the environment increases, equilibrium densities of both immature and mature populations decrease. It is also noted that the effects of toxicants are more on the equilibrium level of immature population in comparison to the mature population.