Apurinic/apyrimidinic (AP) sites are DNA lesions created under normal growth conditions that result in cytotoxicity, replication-blocks, and mutations. AP sites are susceptible to β-elimination and are liable to be converted to DNA strand breaks. HMCES (5-hydroxymethylcytosine binding, ES cell specific) protein interacts with AP sites in single stranded (ss) DNA exposed at DNA replication forks to generate a stable thiazolidine protein-DNA crosslink and protect cells against AP site toxicity. The crosslinked HMCES is resolved by proteasome-mediated degradation; however, it is unclear how HMCES-crosslinked ssDNA and the resulting proteasome-degraded HMCES adducts are processed and repaired. Here, we describe methods for the preparation of thiazolidine adduct-containing oligonucleotides and determination of their structure. We demonstrate that the HMCES-crosslink is a strong replication blocking adduct and that protease-digested HMCES adducts block DNA replication to a similar extent as AP sites. Moreover, we show that the human AP endonuclease APE1 incises DNA 5′ to the protease-digested HMCES adduct. Interestingly, while HMCES-ssDNA crosslinks are stable, the crosslink is reversed upon the formation of dsDNA, possibly due to a catalytic reverse reaction. Our results shed new light on damage tolerance and repair pathways for HMCES-DNA crosslinks in human cells.
Proton-transfer-reaction (PTR) mass spectrometry (MS) is capable of detecting trace-level volatile organic compounds (VOCs) in gaseous samples in real time. Therefore, PTR-MS has become a popular method in many different study areas. Most of the currently reported PTR-MS applications are designed to determine volatile compounds. However, the method might be applicable for nonvolatile organic compound detection. Supercritical fluid chromatography (SFC) has been studied in the last 5 decades. This approach has high separation efficiency and predictable retention behavior, making separation optimization easy. Atmospheric ionization techniques, such as atmospheric chemical ionization (APCI) and electrospray ionization (ESI), are the most studied SFC-MS interfaces. These processes require the addition of makeup solvents to prevent precipitation or crystallization of the solute while depressurizing the mobile phase. In contrast, the PTR process is carried out in a vacuum; supercritical carbon dioxide may release solute into the PTR flow tube without a phase transition as long as it is maintained above a critical temperature. Therefore, this might constitute yet another use for the SFC-MS interface. Caffeine and a few other nonpolar compounds in supercritical carbon dioxide were successfully detected with time-of-flight MS without adding solvent by using preliminarily assembled supercritical flow injection and supercritical fluid extraction (SFE)-PTR interfaces.
Simultaneous ion counting and waveform averaging implemented on a field-programmable gate array compiled with a high-speed digitizer was applied to ultraperformance liquid chromatography-time-of-flight mass spectrometric analysis of sulfa drugs. Ion counting was carried out by a “Peak Detection” (PKD) function that works together with signal averaging (AVG). Sulfadimidine (SDD) and sulfadimethoxine (SDMX) were measured in human serum (HS) model sample matrix. By using simultaneous PKD and AVG acquisition, we observed a unified calibration curve for more than 3 orders of magnitude of sample amounts (0.010–100.0 pmol). The ion count rate for the “practical” sample amounts, such as less than 1 pmol, was below 30%, which is suitable for PKD-based ion counting for quantitative accuracy and excellent peak identification performance. Samples containing 200 fmol or less could not be identified from the AVG waveform. Adding HS treated with acetonitrile severely suppressed the SDMX ion to less than one-half (58.1%). However, a linear response was observed for chromatographic peak area for analytes calculated from PKD waveforms. Also, the mass-resolving power calculated from the peak on the PKD waveform was 24% better than the corresponding AVG waveform, which also improves performance for analyte identification.
To demonstrate the psychophysical effect of edge-grain patterns on visual impressions received by human observers, printed images of the edge-grain patterns of 16 species were prepared as wellregulated visual stimuli, and impressions of the patterns on 32 subjects were evaluated using six categories. Image characteristics of the patterns were expressed numerically using contrast values that were derived by multi-resolution contrast analysis (MRCA) proposed by the authors, and relationships between the image characteristics and the visual impressions were examined. The difference in lightness between local areas with a certain size in the image was used as the contrast value, which could be used to detect the change in lightness due to the particular feature in the edge-grain pattern. While some impressions were almost independent of the contrast values, other impressions showed highly positive or negative linear relationships to the contrast values, derived at the optimal filter size in MRCA. Moreover, these optimal sizes were rarely affected by color information. The contrast value proposed in this paper would be a good numerical index that could be used not only to describe image characteristics of the edge-grain patterns but also to estimate some of their visual impressions.
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