Novel multistranded, alternative, plasmid and helical transitional DNA and RNA microarrays: implications for therapeutics

Advances in Nanotechnology-Based Biosensing of Immunoregulatory Cytokines

Cytokines are a large group of small proteins secreted by immune and non-immune cells in response to external stimuli. Much attention has been given to the application of cytokines' detection in early disease diagnosis/monitoring and therapeutic response assessment. To date, a wide range of assays are available for cytokines detection. However, in specific applications, multiplexed or continuous measurements of cytokines with wearable biosensing devices are highly desirable. For such efforts, various nanomaterials have been extensively investigated due to their extraordinary properties, such as high surface area and controllable particle size and shape, which leads to their tunable optical emission, electrical, and magnetic properties. Different types of nanomaterials such as noble metal, metal oxide, and carbon nanoparticles have been explored for various biosensing applications. Advances in nanomaterial synthesis and device development have led to significant progress in pushing the limit of cytokine detection. This article reviews currently used methods for cytokines detection and new nanotechnology-based biosensors for ultrasensitive cytokine detection.

Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors

Carbonic anhydrases (CAs) are thought to be important for regulating pH in the tumor microenvironment. A few of the CA isoforms are upregulated in cancer cells, with only limited expression in normal cells. For these reasons, there is interest in developing inhibitors that target these tumor-associated CA isoforms, with increased efficacy but limited nonspecific cytotoxicity. Here we present some of the biophysical, biochemical, and cell based techniques and approaches that can be used to evaluate the potency of CA targeted inhibitors and decipher the role of CAs in tumorigenesis, cancer progression, and metastatic processes. These techniques include esterase activity assays, stop flow kinetics, and mass inlet mass spectroscopy (MIMS), all of which measure enzymatic activity of purified protein, in the presence or absence of inhibitors. Also discussed is the application of X-ray crystallography and Cryo-EM as well as other structure-based techniques and thermal shift assays to the studies of CA structure and function. Further, large-scale genomic and proteomic analytical methods, as well as cell based techniques like those that measure cell growth, apoptosis, clonogenicity, and cell migration and invasion, are discussed. We conclude by reviewing approaches that test the metastatic potential of CAs and how the aforementioned techniques have contributed to the field of CA cancer research.

Stretching of surface-tethered polymers in pressure-driven flow under confinement

We study the effect of pressure-driven flow on a single surface-tethered DNA molecule confined between parallel surfaces. The influence of flow and channel parameters as well as the length of the molecules on their extension and orientation is explored. In the experiments the chain conformations are imaged by laser scanning confocal microscopy. We find that the fractional extension of the tethered DNA molecules mainly depends on the wall shear stress, with effects of confinement being very weak. Experiments performed with molecules of different contour length show that the fractional extension is a universal function of the product of the wall shear stress and the contour length, a result that can be obtained from a simple scaling relation. The experimental results are in good agreement with results from coarse-grained molecular dynamics/Lattice-Boltzmann simulations.

Electric-field-induced stretching of surface-tethered polyelectrolytes in a microchannel

We study the stretching of a surface-tethered polyelectrolyte confined between parallel surfaces under the application of a dc electric field. We explore the influence of the electric-field strength, the length of the polyelectrolyte, and the degree of confinement on the conformation of the polyelectrolyte by single-molecule experiments and coarse-grained coupled lattice-Boltzmann molecular-dynamics simulations. The fractional extension of the polyelectrolyte is found to be a universal function of the product of the applied electric field and the molecular contour length, which is explained by simple scaling arguments. The degree of confinement does not have any significant influence on the stretching. We also confirm that an electrohydrodynamic equivalence principle relating the stretching in an electric field to that in a flow field is applicable.

Reverse engineering gene regulatory networks from measurement with missing values

Background

Gene expression time series data are usually in the form of high-dimensional arrays. Unfortunately, the data may sometimes contain missing values: for either the expression values of some genes at some time points or the entire expression values of a single time point or some sets of consecutive time points. This significantly affects the performance of many algorithms for gene expression analysis that take as an input, the complete matrix of gene expression measurement. For instance, previous works have shown that gene regulatory interactions can be estimated from the complete matrix of gene expression measurement. Yet, till date, few algorithms have been proposed for the inference of gene regulatory network from gene expression data with missing values.

Results

We describe a nonlinear dynamic stochastic model for the evolution of gene expression. The model captures the structural, dynamical, and the nonlinear natures of the underlying biomolecular systems. We present point-based Gaussian approximation (PBGA) filters for joint state and parameter estimation of the system with one-step or two-step missing measurements. The PBGA filters use Gaussian approximation and various quadrature rules, such as the unscented transform (UT), the third-degree cubature rule and the central difference rule for computing the related posteriors. The proposed algorithm is evaluated with satisfying results for synthetic networks, in silico networks released as a part of the DREAM project, and the real biological network, the in vivo reverse engineering and modeling assessment (IRMA) network of yeast Saccharomyces cerevisiae.

Conclusion

PBGA filters are proposed to elucidate the underlying gene regulatory network (GRN) from time series gene expression data that contain missing values. In our state-space model, we proposed a measurement model that incorporates the effect of the missing data points into the sequential algorithm. This approach produces a better inference of the model parameters and hence, more accurate prediction of the underlying GRN compared to when using the conventional Gaussian approximation (GA) filters ignoring the missing data points.

Electronic supplementary material

The online version of this article (doi:10.1186/s13637-016-0055-8) contains supplementary material, which is available to authorized users.

The role of RNA structure in posttranscriptional regulation of gene expression

As more information is gathered on the mechanisms of transcription and translation, it is becoming apparent that these processes are highly regulated. The formation of mRNA secondary and tertiary structures is one such regulatory process that until recently it has not been analysed in depth. Formation of these mRNA structures has the potential to enhance and inhibit alternative splicing of transcripts, and regulate rates and amount of translation. As this regulatory mechanism potentially impacts at both the transcriptional and translational level, while also potentially utilising the vast array of non-coding RNAs, it warrants further investigation. Currently, a variety of high-throughput sequencing techniques including parallel analysis of RNA structure (PARS), fragmentation sequencing (FragSeq) and selective 2-hydroxyl acylation analysed by primer extension (SHAPE) lead the way in the genome-wide identification and analysis of mRNA structure formation. These new sequencing techniques highlight the diversity and complexity of the transcriptome, and demonstrate another regulatory mechanism that could become a target for new therapeutic approaches.

Localization and quantification of intact, undamaged right-handed double-stranded B-DNA, and denatured single-stranded DNA in normal human epidermis and its effects on apoptosis and terminal differentiation (denucleation)

Quantification of two types of nucleic acids [double-stranded (ds-) and single-stranded (ss-) DNA] was performed to understand the distribution of DNA within the epidermal strata and to examine the effects of DNA structure on gene expression, viz., apoptosis and terminal differentiation. In addition, we examined the precise starting point of cell death within the epidermis (suprabasal layer); examined how DNA structure affects gene expression of melanocytes; and characterized the "transitional cells" located between the stratum granulosum and stratum corneum, viz., epidermal phase transition zone (EPTZ). Ultrasensitive anti-DNA antibody probes (ds-DNA, ss-DNA), the Feulgen reaction, histological stains (morphological characterization) and the terminal deoxyribonucleotidyl transferase (TUNEL) assay (apoptosis) were used to characterize cell death in normal human epidermis. This study characterized, for the first time, the deterioration of right-handed ds-B-DNA and the increase in denatured ss-DNA during epidermal maturation. For the first time, this approach also allowed for the quantitative and qualitative characterization of DNA content and structure in all epidermal strata, using anti-ds-B-DNA and anti-ss-DNA antibodies. In order to improve the retention and quality of DNA, a novel histotechnological processing procedure was used. The results indicate that the largest decline in DNA occurred within the stratum granulosum, followed by the EPTZ, and the stratum spinosum. Not all epidermal nuclei lost DNA, indicating two differentiating keratinocyte pathways, viz., apoptotic and non-apoptotic. Both pathways united in the stratum granulosum. These results suggest that keratinocyte terminal differentiation and apoptosis are distinct cellular events, cell death begins earlier than expected, and molecular epidermal events take place in a gradual and orderly manner within keratinocytes. During maturation, ds-B-DNA decreases as ss-DNA increases. Therefore, during differentiation of keratinocytes, both DNA content and DNA structure are altered.