Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution.

Given the presence of highly repetitive genomic regions such as subtelomeric regions, understanding human genomic evolution remains challenging. Recently, long-read sequencing technology has facilitated the identification of complex genetic variants, including structural variants (SVs), at the single-nucleotide level. Here, we resolved SVs and their underlying DNA damage-repair mechanisms in subtelomeric regions, which are among the most uncharted genomic regions.

Boosting the Sodiation Kinetics of Sn Anode Using a Yolk-Shell Nanohybrid Structure for High-Rate and Ultrastable Sodium-Ion Batteries.

Metallic Sn (Tin) is a promising anode material for Na-ion batteries owing to its high theoretical capacity of 870 mAh g. However, its large volumetric changes, interfacial instability, and sluggish sodiation kinetics limit its practical applications. Herein, a hierarchical yolk-shell nanohybrid composed of an Sn yolk and a Carbon/Silicon oxycarbide (C/SiOC) bilayer shell is prepared via the simple pyrolysis of a silicone oil dispersion containing an Sn precursor.

Effects of high-fat diet on folic acid-induced kidney injury in mice.

Obesity is recognized as a significant contributor to the onset of kidney disease. However, the key processes involved in the development of kidney disease in obese individuals are not well understood. Here, we investigated the effects of high-fat diet (HFD)-induced obesity on folic acid (FA)-induced kidney injury in mice.

Discovery of -Aryl-'-[4-(aryloxy)cyclohexyl]squaramide-Based Inhibitors of LXR/SREBP-1c Signaling Pathway Ameliorating Steatotic Liver Disease: Navigating the Role of SIRT6 Activation.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is primarily attributed to the abnormal upregulation of hepatic lipogenesis, which is especially caused by the overactivation of the liver X receptor/sterol regulatory element-binding protein-1c (LXR/SREBP-1c) pathway in hepatocytes. In this study, we report the rational design and synthesis of a novel series of squaramides via bioisosteric replacement, which was evaluated for its inhibitory activity on the LXR/SREBP-1c pathway using dual cell-based assays. Compound was found to significantly downregulate LXR, SREBP-1c, and their target genes associated with lipogenesis.

KoNA: Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data.

During the last decade, the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges, including access to human data, as well as transfer, storage, and sharing of enormous amounts of data. To promote data-driven biological research, the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. Here, we introduce the Korean Nucleotide Archive (KoNA), a repository of nucleotide sequence data.

Comparison of structural variant callers for massive whole-genome sequence data.

Background: Detecting structural variations (SVs) at the population level using next-generation sequencing (NGS) requires substantial computational resources and processing time. Here, we compared the performances of 11 SV callers: Delly, Manta, GridSS, Wham, Sniffles, Lumpy, SvABA, Canvas, CNVnator, MELT, and INSurVeyor. These SV callers have been recently published and have been widely employed for processing massive whole-genome sequencing datasets.

FSP1 confers ferroptosis resistance in KEAP1 mutant non-small cell lung carcinoma in NRF2-dependent and -independent manner.

Ferroptosis, a type of cell death induced by lipid peroxidation, has emerged as a novel anti-cancer strategy. Cancer cells frequently acquire resistance to ferroptosis. However, the underlying mechanisms are poorly understood.

Deciphering the DNA methylation landscape of colorectal cancer in a Korean cohort.

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC.

Introduction of the Korea BioData Station (K-BDS) for sharing biological data.

A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates.

Regulating Na Electrodeposition by Sodiophilic Grafting onto Porosity-Gradient Gel Polymer Electrolytes for Dendrite-Free Sodium Metal Batteries.

Sodium metal batteries have been emerging as promising candidates for post-Li battery systems owing to the natural abundance, low costs, and high energy density of Na metal. However, exploiting an Na metal anode is accompanied by uncontrolled Na electrodeposition, particularly concerning dendrite growth, hampering practical Na metal battery applications. Herein, we propose sodiophilic gel polymer electrolytes with a porosity-gradient Janus structure to alleviate Na dendrite growth.

Ultrafast and Ultrastable Heteroarchitectured Porous Nanocube Anode Composed of CuS/FeS Embedded in Nitrogen-Doped Carbon for Use in Sodium-Ion Batteries.

The enhancement of the structural stability of conversion-based metal sulfides at high current densities remains a major challenge in realizing the practical application of sodium-ion batteries (SIBs). The instability of metal sulfides is caused by the large volume variation and sluggish reaction kinetics upon sodiation/desodiation. To overcome this, herein, a heterostructured nanocube anode composed of CuS/FeS embedded in nitrogen-doped carbon (CuS/FeS @NC) is synthesized.

Hierarchically Designed Nitrogen-Doped MoS/Silicon Oxycarbide Nanoscale Heterostructure as High-Performance Sodium-Ion Battery Anode.

Molybedenum disulfide (MoS) is regarded as a promising anode material for next-generation sodium-ion batteries (SIBs) owing to its high theoretical capacity. However, its low conductivity, large volume changes, and undesirable phase transformation hinder its practical applications. In this study, we synthesize a hierarchically designed core-shell heterostructure based on nitrogen-doped MoS/C and silicon oxycarbide (SiOC) (N-MoS/C@SiOC) via the facile pyrolysis of a suspension of an N-MoS/polyfurfural precursor in silicone oil.

Theoretical Design of Lithium Chloride Superionic Conductors for All-Solid-State High-Voltage Lithium-Ion Batteries.

The development of solid electrolytes (SEs) is a promising pathway to improve the energy density and safety of conventional Li-ion batteries. Several lithium chloride SEs, LiMCl (M = Y, Er, In, and Sc), have gained popularity due to their high ionic conductivity, wide electrochemical window, and good chemical stability. This study systematically investigated 17 LiMCl SEs to identify novel and promising lithium chloride SEs.

ChimerDB 4.0: an updated and expanded database of fusion genes.

Fusion genes represent an important class of biomarkers and therapeutic targets in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data (ChimerSeq) and text mining of publications (ChimerPub) with extensive manual annotations (ChimerKB). In this update, we present all three modules substantially enhanced by incorporating the recent flood of deep sequencing data and related publications.

Proteogenomic Characterization of Human Early-Onset Gastric Cancer.

We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival.

Conducting Polymer Coating on a High-Voltage Cathode Based on Soft Chemistry Approach toward Improving Battery Performance.

The surface of a 5 V class LiNiMnO particle is modified with poly(3,4-ethylenedioxythiophene) (PEDOT) conducting polymer by utilizing the hydrophobic characteristics of the 3,4-ethylenedioxythiophene (EDOT) monomer and the tail group of cetyl trimethyl ammonium bromide (CTAB) surfactants, in addition to the electrostatic attraction between cationic CTAB surfactant and cathode materials with a negative ζ potential in aqueous solution. With this novel concept, we design and prepare a uniform EDOT monomer layer on the cathode materials, and chemical polymerization of the EDOT coating layer is then carried out to achieve PEDOT-coated cathode materials via a simple one-pot preparation process. This uniform conducting polymer layer provides notable improvement in the power characteristics of electrodes, and stable electrochemical performance can be obtained especially at severe operating conditions such as the fully charged state and elevated temperatures owing to the successful suppression of the side reaction between the oxide particle and the electrolyte as well as the suppression of Mn dissolution from the oxide material.

An integrated clinical and genomic information system for cancer precision medicine.

Background: Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex nature of genomic information presents a huge challenge for clinicians in interpreting the patient's genomic alterations and selecting the optimum approved or investigational therapy. An elaborate and practical information system is urgently needed to support clinical decision as well as to test clinical hypotheses quickly.

Phosphorus-Rich CuP Embedded in Carbon Matrix as a High-Performance Anode for Lithium-Ion Batteries.

Phosphorus-rich CuP and its carbon composites have been investigated as an anode material for lithium-ion batteries. Through a facile, low-cost mechanochemical reaction, microsized composites composed of active CuP particles uniformly embedded in the carbon matrix have been successfully synthesized. Combined structural and electrochemical characterizations show that phosphorus-rich CuP undergoes irreversible reaction with lithium, giving metal-rich CuP and amorphous phosphorus at the end of the first cycle.

Controlling the defects and transition layer in SiO films grown on 4H-SiC via direct plasma-assisted oxidation.

The structural stability and electrical performance of SiO grown on SiC via direct plasma-assisted oxidation were investigated. To investigate the changes in the electronic structure and electrical characteristics caused by the interfacial reaction between the SiO film (thickness ~5 nm) and SiC, X-ray photoelectron spectroscopy (XPS), X-ray absorption spectroscopy (XAS), density functional theory (DFT) calculations, and electrical measurements were performed. The SiO films grown via direct plasma-assisted oxidation at room temperature for 300s exhibited significantly decreased concentrations of silicon oxycarbides (SiOC) in the transition layer compared to that of conventionally grown (i.

The facile synthesis and enhanced sodium-storage performance of a chemically bonded CuP2/C hybrid anode.

A chemically bonded CuP2/C hybrid synthesized using a one-step mechanochemical reaction has been evaluated as an anode in sodium-ion batteries. Due to the synergistic effects of the formation of a strong P-O-C bond and the stable nanoscale conducting framework, it exhibits a high capacity with superior cyclability and rate performance.

Frequent CTLA4-CD28 gene fusion in diverse types of T-cell lymphoma.

CTLA4 and CD28 are co-regulatory receptors with opposite roles in T-cell signaling. By RNA sequencing, we identified a fusion between the two genes from partial gene duplication in a case of angioimmunoblastic T-cell lymphoma. The fusion gene, which codes for the extracellular domain of CTLA4 and the cytoplasmic region of CD28, is likely capable of transforming inhibitory signals into stimulatory signals for T-cell activation.

High-Performance Zn-TiC-C Nanocomposite Alloy Anode with Exceptional Cycle Life for Lithium-Ion Batteries.

A Zn-based nanocomposite has been prepared through a facile, low-cost high-energy mechanochemical process and employed as an anode material for lithium-ion batteries. Structural characterization reveals that the micrometer-sized Zn-TiC-C nanocomposite is composed of Zn nanocrystals uniformly dispersed in a multifunctional TiC and conductive carbon matrix with a tap density of 1.3 g cm(-3).

Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses.

In proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample-specific variants--single nucleotide variants, insertions/deletions, and stop-codon mutations derived from Exome-seq and RNA-seq data.

A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma.

The molecular mechanisms underlying angioimmunoblastic T cell lymphoma (AITL), a common type of mature T cell lymphoma of poor prognosis, are largely unknown. Here we report a frequent somatic mutation in RHOA (encoding p.Gly17Val) using exome and transcriptome sequencing of samples from individuals with AITL.