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.     

NMR studies of conformations and molecular recognition of pyridinio-appended and nicotinamide-appended β-cyclodextrin

Abstract

The conformations of pyridinio-appended β-cyclodextrin (CDP⁺) and nicotinamide-appended β-cyclodextrin (CDNA⁺) were studied by NMR spectroscopy. The orientations of the pyridine residue of CDP⁺ and the nicotinamide residue of CDNA⁺ were determined by using a combination of NMR spectroscopic techniques. NMR spectra indicate that the shapes of the cavities of CDP⁺ and CDNA⁺ were changed after forming complexes. This change depended on the shape of the guest. CDNA⁺ could separate the ¹H resonances at the Cβ position of racemic tryptophan into two sets of resonances for each enantiomer.     

Autophagic failure promotes the exocytosis and intercellular transfer of α-synuclein

The accumulation of abnormal protein aggregates is a major characteristic of many neurodegenerative disorders, including Parkinson''s disease (PD). The intracytoplasmic deposition of α-synuclein aggregates and Lewy bodies, often found in PD and other α-synucleinopathies, is thought to be linked to inefficient cellular clearance mechanisms, such as the proteasome and autophagy/lysosome pathways. The accumulation of α-synuclein aggregates in neuronal cytoplasm causes numerous autonomous changes in neurons. However, it can also affect the neighboring cells through transcellular transmission of the aggregates. Indeed, a progressive spreading of Lewy pathology among brain regions has been hypothesized from autopsy studies. We tested whether inhibition of the autophagy/lysosome pathway in α-synuclein-expressing cells would increase the secretion of α-synuclein, subsequently affecting the α-synuclein deposition in and viability of neighboring cells. Our results demonstrated that autophagic inhibition, via both pharmacological and genetic methods, led to increased exocytosis of α-synuclein. In a mixed culture of α-synuclein-expressing donor cells with recipient cells, autophagic inhibition resulted in elevated transcellular α-synuclein transmission. This increase in protein transmission coincided with elevated apoptotic cell death in the recipient cells. These results suggest that the inefficient clearance of α-synuclein aggregates, which can be caused by reduced autophagic activity, leads to elevated α-synuclein exocytosis, thereby promoting α-synuclein deposition and cell death in neighboring neurons. This finding provides a potential link between autophagic dysfunction and the progressive spread of Lewy pathology.     

Separation of five oligostilbenes from Vitis amurensis by flow‐rate gradient high‐performance counter‐current chromatography

A rapid and efficient high‐performance counter‐current chromatography (HPCCC) method was developed to separate five oligostilbenes from the roots of Vitis amurensis. An n‐hexane/ethyl acetate/methanol/water system (4:8:4:10, v/v/v/v) was selected as an optimal two‐phase solvent system of which the upper phase was used as the stationary phase and the lower phase was used as the mobile one. Partition coefficient values for the target compounds under these optimized conditions were 0.28 ( 1 , ampleosin A), 7.12 ( 2 , (+)‐g‐viniferin), 2.26 ( 3 , vitisin A), 5.38 ( 4 , wilsonol C), and 11.23 ( 5 , vitisin B). Flow‐rate gradient HPCCC (4 mL/min in 0–70 min, 8 mL/min in 70–250 min) was applied to isolate the target compounds in as high purity as possible within the shortest possible run time. Under these conditions, ampelopsin A (12.1 mg), (+)‐g‐viniferin (10.4 mg), vitisin A (2.8 mg), wilsonol C (3.2 mg), and vitisin B (37 mg) were isolated with >95% purity from 150 mg of enriched oligostilbene extract. Although the K_D of the last eluted compound, vitisin B (K_D = 11.23), was relatively large, it was eluted in 115–145 min using the two‐phase solvent system. This study shows that HPCCC is an efficient tool for the isolation and purification of natural products.     

Synthesis and Biological Evaluation of Novel Isonucleosides with 1,2,4‐Triazole‐3‐Carboxamide

Novel 1,2,4‐triazole isonucleosides (1 and 2) were efficiently synthesized starting from D‐ribose and D‐xylose, respectively. The key steps were condensation of cyclic sulfate 8 with methyl‐1,2,4‐triazole‐3‐carboxylate and nucleophilic displacement of the tosylate 15 with methyl‐1,2,4‐triazole‐3‐carboxylate, respectively.     

Synthesis of 3-Alkylidenecepham-4-carboxylic Acid derivatives by Samarium(II) Iodide Reduction

Samarium(II) iodide promoted reductive deacetoxylation of 7-aminocephalosporanic acid derivatives to synthesize 3-alkylidenecepham-4-carboxylates, which could be valuable intermediates for the synthesis of new cephalosporin antibiotics, was investigated.     

Synthesis and Reactivity of the New Chiral Silylphosphite Esters {(+)-O,O-Dimethyl-L-tartrate}POSiR3 (R3 = Ph3, tBuMe2, Et3)

The new, chiral silylphosphite compounds (O,O-dimethyl-L-tartrato)POSiR₃, (R₃ = Ph₃, ^tBuMe₂, Et₃) have been synthesised and their activity as asymmetric phosphonylating reagents investigated.     

Effect of TaNx on electrical and optical properties of annealed TaNx/Ag/TaNx films

As‐deposited Ag(10 nm)/glass films exhibited agglomerated nanocrystals with seemingly thick boundaries. Introduction of a TaN_x layer below the Ag films resulted in dense and smooth structures, with a resistance at least three times lower than that of Ag/glass. For TaN_x(10 nm)/Ag(10 nm)/TaN_x(10 nm)/glass multilayer films, Auger electron spectroscopy results indicate that TaN_x acts as an effective barrier restraining the diffusion of Ag. After annealing (up to 573 K), no outward diffusion of Ag through either TaN_x layer was seen. However, partial oxidation of the outermost TaN_x layer to form Ta₂O₅ was observed. The films showed promising optical properties with 73% transmittance in the visible region and ~15% average transmittance in the near‐infrared region. The optical data obtained here was in good agreement with simulated predictions. Copyright © 2013 John Wiley & Sons, Ltd.