An efficient algorithm for minimum degeneracy primer selection

Selecting degenerate primers for multiplex polymerase chain reaction (MP-PCR) experiments, called the degenerate primer design problem (DPDP), is an important problem in computational molecular biology and has drawn the attention of numerous researchers in the recent past. Several variants of DPDP were formulated by Linhart and Shamir and proven to be NP-complete. A number of algorithms have been proposed for one such variant, namely, the maximum coverage degenerate primer design problem (MC-DPDP). In this paper, we consider another important variant called the minimum degeneracy degenerate primer design with errors problem (MD-DPDEP), propose an algorithm to design a degenerate primer of minimum degeneracy for a given set of DNA sequences and show experimental results of its performance on random and real biological datasets. Our algorithm combines methodologies in motif discovery and an iterative technique to design the primer     

Nanofibrous scaffold engineering using electrospinning

Scaffold plays a critical role in tissue engineering where it provides necessary structural support for the cells to accommodate and to guide their growth in the three dimensional space into a specific tissue. Therefore, engineering scaffolds favorable for cell/tissue growth is of great importance and a pre-requisite for scaffold-based tissue engineering. Electrospinning is a versatile method that has been recently adapted in engineering nano-fibrous scaffolds that mimic the structural features of biological extracellular matrix (ECM). It offers many advantages over conventional scaffold methodologies, for example, capable of producing ultra-fine fibers with high porosity, high spatial orientation, high aspect ratio, and high surface area, which are highly required for the initial cell attachment, tissue formation, and continued function. Considering these astonishing merits, this article emphasis on nano-fibrous scaffold engineering by electrospinning.     

Human Papillomavirus E6/E7-Specific siRNA Potentiates the Effect of Radiotherapy for Cervical Cancer in Vitro and in Vivo

The functional inactivation of TP53 and Rb tumor suppressor proteins by the HPV-derived E6 and E7 oncoproteins is likely an important step in cervical carcinogenesis. We have previously shown siRNA technology to selectively silence both E6/E7 oncogenes and demonstrated that the synthetic siRNAs could specifically block its expression in HPV-positive cervical cancer cells. Herein, we investigated the potentiality of E6/E7 siRNA candidates as radiosensitizers of radiotherapy for the human cervical carcinomas. HeLa and SiHa cells were transfected with HPV E6/E7 siRNA; the combined cytotoxic effect of E6/E7 siRNA and radiation was assessed by using the cell viability assay, flow cytometric analysis and the senescence-associated β-galactosidase (SA-β-Gal) assay. In addition, we also investigated the effect of combined therapy with irradiation and E6/E7 siRNA intravenous injection in an in vivo xenograft model. Combination therapy with siRNA and irradiation efficiently retarded tumor growth in established tumors of human cervical cancer cell xenografted mice. In addition, the chemically-modified HPV16 and 18 E6/E7 pooled siRNA in combination with irradiation strongly inhibited the growth of cervical cancer cells. Our results indicated that simultaneous inhibition of HPV E6/E7 oncogene expression with radiotherapy can promote potent antitumor activity and radiosensitizing activity in human cervical carcinomas.     

Preparation and characterization of 3,3′‐bis (maleimidophenyl)phenylphosphine oxide (BMI)/polysulfone modified epoxy intercrosslinked matrices

An intercrosslinked network of polysulfone (PSF)—bismaleimide (BMI) modified epoxy matrix system was made by using diglycidyl ether of bisphenol A (DGEBA) epoxy resin, hydroxyl terminated polysulfone and bismaleimide (3,3′‐bis(maleimidophenyl) phenylphosphine oxide) with diaminodiphenylmethane (DDM) as curing agent. BMI–PSF–epoxy matrices were characterized using differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and heat deflection temperature (HDT) analysis. The matrices, in the form of castings, were characterized for their mechanical properties such as tensile strength, flexural strength, and unnotched Izod impact test as per ASTM methods. Mechanical studies indicated that the introduction of polysulfone into epoxy resin improves the toughness to an appreciable extent with insignificant increase in stress–strain properties. DSC studies indicated that the introduction of polysulfone decreases the glass transition temperature, whereas the incorporation of bismaleimide into epoxy resin influences the mechanical and thermal properties according to its percentage content. DSC thermograms of polysulfone as well as BMI modified epoxy resin show a unimodal reaction exotherm. The thermal stability and flame retardant properties of cured epoxy resins were improved with the introduction of bismaleimide and polysulfone. Water absorption characteristics were studied as per ASTM method and the morphology of the BMI modified epoxy and PSF‐epoxy systems were studied by scanning electron microscope. POLYM. COMPOS., 2008. © 2008 Society of Plastics Engineers     

An optimization study for preventing silica gelation and improving filtration effectiveness during pH reduction of high concentration silica solutions

The steam generation processes at the steam-assisted gravity drainage facilities result in huge quantities of wastewater streams, which are characterized by high pH and high silica levels. These concentrated streams need to be neutralized before their disposal via down-hole injection. The neutralization of these high-pH brines results in the formation of a gel-like substance, which makes it difficult to filter the amorphous silica gel. The wastewater used in this study was synthetically prepared using sodium metasilicate to mimic high-concentration silica solutions. Our experiments did not show any advantage of a two-step pH-neutralization process over the single-step process for suppressing silica gelation. A systematic experimental campaign was undertaken to investigate the effects of SiO₂ concentration, NaCl:SiO₂ ratio, and pH on the residual silica concentration, percent silica removal, filtration rate, and filtration effectiveness. For NaCl:SiO₂ ratios higher than 4.5, silica precipitation during pH reduction did not lead to the formation of gel or sol. The response surface methodology (RSM), based on the Doehlert design of experiments, was implemented to optimize the responses and provide high efficacy with fewer experiments. The results from the analysis of variance (ANOVA) analyses of the experimental data were used to evaluate the significance of each term in the quadratic model. 3D response surfaces and 2D contour plots were generated for determining the optimal ranges of independent factors for achieving the maximum silica removal, the highest filtration rate, the best filtration effectiveness, and the minimum residual silica concentration. An optimum operating region was established from the RSM analysis and overlay plot.     

Analysis of Mechanical and Tribological Properties of Silicon Incorporated Diamond like Carbon Nanocomposite Coating

Silicon - The Silicon (Si) contained diamond like carbon (DLC) nanocomposite were prepared by using thermal chemical vapour deposition (CVD) technique by varying the acetylene (C2H2) flowrates. The...