Development and Comparison of 4-Thiouridine to Cytidine Base Conversion Reaction.

To study transcriptome dynamics without harming cells, it is essential to convert chemical bases. 4-Thiouridine (4sU) is a biocompatible uridine analogue that can be converted into a cytidine analogue. Although several reactions can convert 4sU into a cytidine analogue, few studies have compared the features of these reactions. In this study, we performed three reported base conversion reactions, including osmium tetroxide, iodoacetamide, and sodium periodate treatment, as well as a new reaction using 2,4-dinitrofluorobenzene. We compared the reaction time, conversion efficacy, and effects on reverse transcription. These reactions successfully converted 4sU into a cytidine analogue quantitatively using trinucleotides. However, the conversion efficacy and effect on reverse transcription vary depending on the reaction with the RNA transcript. OsO4 treatment followed by NH4Cl treatment showed the best base-conversion efficiency. Nevertheless, each reaction has its own advantages and disadvantages as a tool for studying the transcriptome. Therefore, it is crucial to select the appropriate reaction for the target of interest.

The Effect of γ Phosphate Modified Deoxynucleotide Substrates on PCR Activity and Fidelity.

Controlling PCR fidelity is an important issue for molecular biology and high-fidelity PCR is essential for gene cloning. In general, fidelity control is achieved by protein engineering of polymerases. In contrast, only a few studies have reported controlling fidelity using chemically modified nucleotide substrates. In this report, we synthesized nucleotide substrates possessing a modification on Pγ and evaluated the effect of this modification on PCR fidelity. One of the substrates, nucleotide tetraphosphate, caused a modest decrease in Taq DNA polymerase activity and the effect on PCR fidelity was dependent on the type of mutation. The use of deoxyadenosine tetraphosphate enhanced the A : T→G : C mutation dramatically, which is common when using Taq polymerase. Conversely, deoxyguanosine tetraphosphate (dG4P) suppressed this mutation but increased the G : C→A : T mutation during PCR. Using an excess amount of dG4P suppressed both mutations successfully and total fidelity was improved.

Effect of Spinal Sagittal Alignment in Sitting Posture on Swallowing Function in Healthy Adult Women: A Cross-Sectional Study.

Swallowing function is both directly and indirectly related to postures, such as head and cervical angle and body position. However, the effects of different sitting postures on oropharyngeal swallowing have not been investigated. This study aimed to investigate whether the change in thoracolumbar alignment affected the oropharyngeal swallowing. A total of 58 healthy adult women (mean age 22.2 ± 1.67 years) without dysphagia were enrolled in this cross-sectional study. Participants were positioned in three sitting postures: comfortable sitting (CS), thoracic upright sitting (TUS), and slump sitting (SS). In each sitting posture, the kyphosis index (using a flexicurve), head and cervical angles (using a digital camera), swallowing speed (100-ml water swallowing test), and oral and articulatory function [by maximum tongue pressure (MTP) and oral diadochokinesis (ODK)] were evaluated. SS showed the largest kyphosis index and was associated with a greater anterior translation of the head. Swallowing speed was significantly decreased in SS compared with CS (p = 0.002) and TUS (p = 0.020) and ODK was significantly decreased in SS compared with other postures, for both /ta/ (p = 0.004) and /ka/ (p < 0.001) syllables. Further, MTP tended to decrease in SS compared with TUS (p = 0.064). Our results suggest that changes in sitting posture with different thoracolumbar alignments affect swallowing speed and oral and articulatory function. Consequently, adjustments to reduce sitting postural kyphosis may improve swallowing speed and oral and articulatory function.

Influence of Marker Number and Position on Accuracy of Breast Measurement With Three-Dimensional Camera.

BACKGROUND: The VECTRA H1 three-dimensional (3D) imaging system (Canfield Scientific, Parsippany, NJ) enables easy 3D image construction and measurement. Although the number and positions of markers on the skin for image synthesis might affect accuracy of measurements, few studies have mentioned the possibility. This study investigated the accuracy and reproducibility of distance measurements using VECTRA H1, focusing on the number and positions of markers. METHODS: A total of 3, 5, or 7 markers were attached to a female breast model including lateral markers 6 cm from the midline and photographed with VECTRA. Five markers were configured in more two ways, with the lateral markers either positioned 3 cm outside the midline (narrow interval) or 9 cm outside the midline (wide interval). 3D models were created three times under each condition, for a total of 15 models. Differences (measurement error) between measured values on 3D models and actual measured values were verified for six distances, such as distance between the nipples. RESULTS: The average difference was 11.1 mm with 3 markers (95% confidence interval (CI), 4.38-17.7 mm, p = 0.0028). In comparison, average difference was -0.395 mm (-0.866 to 0.0763 mm, p = 0.095) with 5 markers, and 0.139 mm (-0186 to 0.465 mm, p = 0.379) with 7 markers, all less than 1 mm. Average difference with narrow interval 5 markers was larger than one with wide interval. CONCLUSIONS: In 3D imaging of the breast using VECTRA H1, distance measurements offering clinically satisfactory accuracy can be made by setting appropriate marker conditions. LEVEL OF EVIDENCE V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics.

BACKGROUND: Computer-aided drug design is still a state-of-the-art process in medicinal chemistry, and the main topics in this field have been extensively studied and well reviewed. These topics include compound databases, ligand-binding pocket prediction, protein-compound docking, virtual screening, target/off-target prediction, physical property prediction, molecular simulation and pharmacokinetics/pharmacodynamics (PK/PD) prediction. Message and Conclusion: However, there are also a number of secondary or miscellaneous topics that have been less well covered. For example, methods for synthesizing and predicting the synthetic accessibility (SA) of designed compounds are important in practical drug development, and hardware/software resources for performing the computations in computer-aided drug design are crucial. Cloud computing and general purpose graphics processing unit (GPGPU) computing have been used in virtual screening and molecular dynamics simulations. Not surprisingly, there is a growing demand for computer systems which combine these resources. In the present review, we summarize and discuss these various topics of drug design.