Genetic analyzer-dependent DNA methylation detection and its application to existing age prediction models

DNA methylation is the most promising biomarker for estimating human age. There are various methods used for analyzing DNA methylation. Among those, the SNaPshot assay-based method provides a semi-quantitative measurement of DNA methylation using capillary electrophoresis on genetic analyzers. However, DNA methylation measures produced using different types of genetic analyzers have never been compared, although differences in methylation values can directly affect age estimates. To evaluate the differences between the results generated by different genetic analyzers, we analyzed the same blood, saliva, and control methylated DNA using three genetic analyzers—the Applied Biosystems 3130, 3500, and SeqStudio—and compared the methylation values at five CpG sites: ELOVL2, FHL2, KLF14, MIR29B2C, and TRIM59. The methylation value at each of the five CpG sites decreased in the order 3130, 3500, and SeqStudio. The differences in the results produced by the different genetic analyzers resulted in significant errors when applying the 3500 and SeqStudio data to a previous age estimation model constructed using the 3130 Genetic Analyzer data. Therefore, DNA methylation measurements from 3500 and SeqStudio were corrected using the regression functions obtained by plotting the DNA methylation data of one instrument versus the other to facilitate the application of DNA methylation data from one instrument to the age prediction model based on other instruments. The age prediction accuracy obtained by applying corrected 3500 and SeqStudio data to the existing age estimation model was as high as observed in the 3130 data.     

Site‐specific reversible immobilization and purification of His‐tagged protein on poly(2‐acetamidoacrylic acid) hydrogel beads

Ni²⁺‐complexed poly(2‐acetamidoacrylic acid) (PAAA) hydrogel beads were developed for the site‐specific reversible immobilization and purification of the histidine‐tagged green fluorescent protein (His‐tagged GFP). PAAA hydrogel beads were prepared by photopolymerization, and significantly improved mechanical properties of PAAA hydrogel beads were observed in comparison with PAAA hydrogel from our previous study. Confocal laser scanning microscopy was used to determine the binding of His‐tagged GFP to the hydrogel beads in three‐dimensional space. Photoluminescence spectroscopy revealed 89% of binding efficiency of His‐tagged GFP to the Ni²⁺‐PAAA hydrogel beads, 51% of yielding recovery. The maximum binding capacity of His‐tagged GFP was estimated to be 0.45 µg/mg of Ni²⁺‐PAAA hydrogel beads. The recombinant His‐tagged GFP from the soluble fraction of E. coli BL21(DE3) cell lysates was purified with Ni²⁺‐PAAA hydrogel beads. The major advantage of the Ni²⁺‐PAAA hydrogel beads system was simple preparation procedures of producing the matrix, because PAAA hydrogel beads had relatively enhanced mechanical strength than soft hydrogels. Copyright © 2012 John Wiley & Sons, Ltd.     

Characterization of Nitro-Substituted Polybenzimidazole Synthesized by the Reaction with Nitric Acid

Abstract

Nitro-substituted poly[2,2′-(m-phenylene)-5,5′-bibenzimidazole]s (PBIs) were synthesized by the reaction of PBI with nitric acid in sulfuric acid under various conditions. The number of nitro groups substituted on the aromatic ring of PBI per polymeric unit varied from 1.44 to 3.55 according to the reaction conditions. An increase in reaction temperature and concentration of the nitric acid increased the degree of substitution. The inherent viscosity of the substituted polymer increased as the reaction temperature decreased. When the reaction temperature was 30°C, the inherent viscosity of the polymer increased as the concentration of nitric acid increased. The nitro-substituted PBI exhibited polyelectrolyte behavior in formic acid. The nitro groups substituted on PBI were dissociated when the polymer was heated to 450°C, displaying exothermic behavior, and the decomposition of polymer was proportional to its nitro group content. All nitro-substituted PBIs showed better solubilities in polar aprotic and acidic solvents, such as dimethylacetamide, dimethylsulfoxide, dimethylformamide, N-methylpyrrolidone, formic acid, sulfuric acid, and trifluoromethanesulfonic acid.     

Contralaterally transplanted human embryonic stem cell-derived neural precursor cells (ENStem-A) migrate and improve brain functions in stroke-damaged rats

The transplantation of neural precursor cells (NPCs) is known to be a promising approach to ameliorating behavioral deficits after stroke in a rodent model of middle cerebral artery occlusion (MCAo). Previous studies have shown that transplanted NPCs migrate toward the infarct region, survive and differentiate into mature neurons to some extent. However, the spatiotemporal dynamics of NPC migration following transplantation into stroke animals have yet to be elucidated. In this study, we investigated the fates of human embryonic stem cell (hESC)-derived NPCs (ENStem-A) for 8 weeks following transplantation into the side contralateral to the infarct region using 7.0T animal magnetic resonance imaging (MRI). T2- and T2*-weighted MRI analyses indicated that the migrating cells were clearly detectable at the infarct boundary zone by 1 week, and the intensity of the MRI signals robustly increased within 4 weeks after transplantation. Afterwards, the signals were slightly increased or unchanged. At 8 weeks, we performed Prussian blue staining and immunohistochemical staining using human-specific markers, and found that high percentages of transplanted cells migrated to the infarct boundary. Most of these cells were CXCR4-positive. We also observed that the migrating cells expressed markers for various stages of neural differentiation, including Nestin, Tuj1, NeuN, TH, DARPP-32 and SV38, indicating that the transplanted cells may partially contribute to the reconstruction of the damaged neural tissues after stroke. Interestingly, we found that the extent of gliosis (glial fibrillary acidic protein-positive cells) and apoptosis (TUNEL-positive cells) were significantly decreased in the cell-transplanted group, suggesting that hESC-NPCs have a positive role in reducing glia scar formation and cell death after stroke. No tumors formed in our study. We also performed various behavioral tests, including rotarod, stepping and modified neurological severity score tests, and found that the transplanted animals exhibited significant improvements in sensorimotor functions during the 8 weeks after transplantation. Taken together, these results strongly suggest that hESC-NPCs have the capacity to migrate to the infarct region, form neural tissues efficiently and contribute to behavioral recovery in a rodent model of ischemic stroke.     

Negative-pressure wound therapy induces endothelial progenitor cell mobilization in diabetic patients with foot infection or skin defects

Non healing chronic wounds are difficult to treat in patients with diabetes and can result in severe medical problems for these patients and for society. Negative-pressure wound therapy (NPWT) has been adopted to treat intractable chronic wounds and has been reported to be effective. However, the mechanisms underlying the effects of this treatment have not been elucidated. To assess the vasculogenic effect of NPWT, we evaluated the systemic mobilization of endothelial progenitor cells (EPCs) during NPWT. Twenty-two of 29 consecutive patients who presented at the clinic of Seoul National Universty Hospital between December 2009 and November 2010 who underwent NPWT for diabetic foot infections or skin ulcers were included in this study. Peripheral blood samples were taken before NPWT (pre-NPWT) and 7–14 days after the initiation of NPWT (during-NPWT). Fluorescence-activated cell sorting (FACS) analysis showed that the number of cells in EPC-enriched fractions increased after NPWT, and the numbers of EPC colony forming units (CFUs) significantly increased during NPWT. We believe that NPWT is useful for treating patients with diabetic foot infections and skin ulcers, especially when these conditions are accompanied by peripheral arterial insufficiency. The systemic mobilization of EPCs during NPWT may be a mechanism for healing intractable wounds in diabetic patients with foot infections or skin defects via the formation of increased granulation tissue with numerous small blood vessels.     

Agar-based heat-sensitive gel with linear thermal response over 65–80 °C

A nontoxic heat-sensitive gel containing 1.5 % (w/v) agar and 25 % (w/v) bovine serum albumin (BSA) was fabricated in this study. Optical density measurements with 808 nm near-infrared (NIR) laser indicated that, in spite of its BSA content, the current agar + BSA gel remained similar to agar only gel in terms of its optical response to NIR laser. The thermal response of the current agar + BSA gel to high temperatures was quantified using magnetic resonance imaging (MRI). According to the MRI measurements of T2 relaxation rate as a function of heating temperature, the current agar + BSA gel showed a linear response to heating temperatures between 65 and 80 °C, while it remained thermally stable at temperatures up to 80 °C. Therefore, the current agar + BSA gel can be used as thermal dosimeters or volumetric heat-sensitive gel phantoms in typical thermal therapy regime.     

Effects of Zn, Al and Ti substitution on the electrochemical properties of LiNiO2 synthesized by the combustion method

LiNi_{1 ? y} Ti _y O₂ (0.000 ≤ y ≤ 0.100) and LiNi_0.990M_0.010O2 (M = Zn, Al, and Ti) were synthesized by the combustion method. The effects of Zn, Al and Ti substitution for Ni of LiNiO₂ on the electrochemical properties of LiNiO₂ were investigated. LiNi_0.995Ti_0.005O₂ has the largest first discharge capacity (188.1 mA h/g) among the Ti-substituted samples. LiNi_0.990Ti_0.010O₂ has a relatively large first discharge capacity (185.5 mA h/g) and a relatively good cycling performance. Among LiNi_0.990M_0.010O₂ (M = Ni, Zn, Al, and Ti), LiNiO₂ has the largest discharge capacities at a rate of 0.1 C from n = 1(189.3 mA h/g) to n = 10. LiNi_0.990Al_0.010O₂ has the lowest discharge capacities from n = 1 to n = 10, but it has the best cycling performance. LiNi_0.990Zn_0.010O₂ showed poor crystallinity, LiNi_0.990Ti_0.010O₂ showed high cation mixing, and LiNi_0.990Al_0.010O₂ had good crystallinity and showed low cation mixing. Fewer occurrence of phase transitions and the least change of the ?dx/|dV| vs. voltage curve at the second cycle from the curve at the first cycle of LiNi_0.990Al_0.010O₂ suggest that Al substitution stabilizes the structure and leads to a good cycling performance.     

Liquid chromatographic resolution of racemic rasagiline and its analogues on a chiral stationary phase based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid

A liquid chromatographic chiral stationary phase based on (+)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid was applied to the resolution of 15 analytes, including racemic rasagiline, a chiral drug for the treatment of Parkinson's disease, and its analogues. The composition of mobile phase was optimized to be ethanol/acetonitrile/acetic acid/triethylamine (80:20:0.2:0.3, v/v/v/v) by evaluating the chromatographic results for the resolution of five selected analytes under various mobile phase conditions. Under the optimized mobile phase conditions, racemic rasagiline was resolved quite well with a separation factor of 1.48 and resolution of 2.71 and its 14 analogues were also resolved reasonably well with separation factors of 1.06–1.54 and resolutions of 0.54–2.11. Among 15 analytes, racemic rasagiline was resolved best except for just one analyte. The analyte structure–enantioselectivity relationship indicated that racemic rasagiline has the most appropriate structural characteristics for resolution on the chiral stationary phase.