Investigation of Splicing Quantitative Trait Loci in

The alteration of alternative splicing patterns has an effect on the quantification of functional proteins, leading to phenotype variation. The splicing quantitative trait locus (sQTL) is one of the main genetic elements affecting splicing patterns. Here, we report the results of genome-wide sQTLs across 141 strains of Arabidopsis thaliana with publicly available next generation sequencing datasets. As a result, we found 1,694 candidate sQTLs in Arabidopsis thaliana at a false discovery rate of 0.01. Furthermore, among the candidate sQTLs, we found 25 sQTLs that overlapped with the list of previously examined trait-associated single nucleotide polymorphisms (SNPs). In summary, this sQTL analysis provides new insight into genetic elements affecting alternative splicing patterns in Arabidopsis thaliana and the mechanism of previously reported trait-associated SNPs

A case of life-threatening valvulitis mimicking infective endocarditis in systemic juvenile idiopathic arthritis

Differential diagnosis of an intracardiac mass is difficult when detected only by echocardiography before a biopsy is completed. However, treatment cannot be postponed until the biopsy results are obtained. We report the case of a 12-year-old girl who presented with an intracardiac mass in the mitral valve mimicking infective endocarditis and severe mitral regurgitation. The mass was finally diagnosed as valvulitis associated with systemic juvenile idiopathic arthritis, which was complicated with macrophage activation syndrome. After careful exclusion of acute infectious disease, we started steroid pulse therapy and administered tocilizumab to treat the cytokine storm before performing the surgery. Finally, we performed mass excision and mitral valve replacement after immunosuppressant therapy.N

In Situ Observation of Resistive Switching in an Asymmetric Graphene Oxide Bilayer Structure

Graphene oxide decorated with oxygen functional groups is a promising candidate as an active layer in resistive switching devices due to its controllable physical-chemical properties, high flexibility, and transparency. However, the origin of conductive channels and their growth dynamics remain a major challenge. We use in situ transmission electron microscopy techniques to demonstrate that nanoscale graphene oxide sheets bonded with oxygen dynamically change their physical and chemical structures upon an applied electric field. Artificially engineered bilayer reduced graphene oxide films with asymmetric oxygen content exhibit nonvolatile write-once-read-many memory behaviors without experiencing the bubble destruction due to the efficient migration of oxygen ions. We clearly observe that a conductive graphitic channel with a conical shape evolves from the upper oxygen-rich region to the lower oxygen-poor region. These findings provide fundamental guidance for understanding the oxygen motions of oxygen-containing carbon materials for future carbon-based nanoelectronics

Performance evaluation of commercial library construction kits for PCR-based targeted sequencing using a unique molecular identifier

Abstract Background Target enrichment is a critical component of targeted deep next-generation sequencing for the cost-effective and sensitive detection of mutations, which is predominantly performed by either hybrid selection or PCR. Despite the advantages of efficient enrichment, PCR-based methods preclude the identification of PCR duplicates and their subsequent removal. Recently, this limitation was overcome by assigning a unique molecular identifier(UMI) to each template molecule. Currently, several commercial library construction kits based on PCR enrichment are available for UMIs, but there have been no systematic studies to compare their performances. In this study, we evaluated and compared the performances of five commercial library kits from four vendors: the Archer® Reveal ctDNA™ 28 Kit, NEBNext Direct® Cancer HotSpot Panel, Nugen Ovation® Custom Target Enrichment System, Qiagen Human Comprehensive Cancer Panel(HCCP), and Qiagen Human Actionable Solid Tumor Panel(HASTP). Results We evaluated and compared the performances of the five kits using 50 ng of genomic DNA for the library construction in terms of the library complexity, coverage uniformity, and errors in the UMIs. While the duplicate rates for all kits were dramatically decreased by identifying unique molecules with UMIs, the Qiagen HASTP achieved the highest library complexity based on the depth of unique coverage indicating superb library construction efficiency. Regarding the coverage uniformity, the kits from Nugen and NEB performed the best followed by the kits from Qiagen. We also analyzed the UMIs, including errors, which allowed us to adjust the depth of unique coverage and the length required for sufficient complexity. Based on these comparisons, we selected the Qiagen HASTP for further performance evaluations. The targeted deep sequencing method based on PCR target enrichment combined with UMI tagging sensitively detected mutations present at a frequency as low as 1% using 6.25 ng of human genomic DNA as the starting material. Conclusion This study is the first systematic evaluation of commercial library construction kits for PCR-based targeted deep sequencing utilizing UMIs. Because the kits displayed significant variability in different quality metrics, our study offers a practical guideline for researchers to choose appropriate options for PCR-based targeted sequencing and useful benchmark data for evaluating new kits

<i>In Situ</i> Observation of Resistive Switching in an Asymmetric Graphene Oxide Bilayer Structure

Graphene oxide decorated with oxygen functional groups is a promising candidate as an active layer in resistive switching devices due to its controllable physical-chemical properties, high flexibility, and transparency. However, the origin of conductive channels and their growth dynamics remain a major challenge. We use <i>in situ</i> transmission electron microscopy techniques to demonstrate that nanoscale graphene oxide sheets bonded with oxygen dynamically change their physical and chemical structures upon an applied electric field. Artificially engineered bilayer reduced graphene oxide films with asymmetric oxygen content exhibit nonvolatile write-once-read-many memory behaviors without experiencing the bubble destruction due to the efficient migration of oxygen ions. We clearly observe that a conductive graphitic channel with a conical shape evolves from the upper oxygen-rich region to the lower oxygen-poor region. These findings provide fundamental guidance for understanding the oxygen motions of oxygen-containing carbon materials for future carbon-based nanoelectronics

<i>In Situ</i> Observation of Resistive Switching in an Asymmetric Graphene Oxide Bilayer Structure

Graphene oxide decorated with oxygen functional groups is a promising candidate as an active layer in resistive switching devices due to its controllable physical-chemical properties, high flexibility, and transparency. However, the origin of conductive channels and their growth dynamics remain a major challenge. We use <i>in situ</i> transmission electron microscopy techniques to demonstrate that nanoscale graphene oxide sheets bonded with oxygen dynamically change their physical and chemical structures upon an applied electric field. Artificially engineered bilayer reduced graphene oxide films with asymmetric oxygen content exhibit nonvolatile write-once-read-many memory behaviors without experiencing the bubble destruction due to the efficient migration of oxygen ions. We clearly observe that a conductive graphitic channel with a conical shape evolves from the upper oxygen-rich region to the lower oxygen-poor region. These findings provide fundamental guidance for understanding the oxygen motions of oxygen-containing carbon materials for future carbon-based nanoelectronics

<i>In Situ</i> Observation of Resistive Switching in an Asymmetric Graphene Oxide Bilayer Structure

Graphene oxide decorated with oxygen functional groups is a promising candidate as an active layer in resistive switching devices due to its controllable physical-chemical properties, high flexibility, and transparency. However, the origin of conductive channels and their growth dynamics remain a major challenge. We use <i>in situ</i> transmission electron microscopy techniques to demonstrate that nanoscale graphene oxide sheets bonded with oxygen dynamically change their physical and chemical structures upon an applied electric field. Artificially engineered bilayer reduced graphene oxide films with asymmetric oxygen content exhibit nonvolatile write-once-read-many memory behaviors without experiencing the bubble destruction due to the efficient migration of oxygen ions. We clearly observe that a conductive graphitic channel with a conical shape evolves from the upper oxygen-rich region to the lower oxygen-poor region. These findings provide fundamental guidance for understanding the oxygen motions of oxygen-containing carbon materials for future carbon-based nanoelectronics