Stalled ribosome rescue factors exert different roles depending on types of antibiotics in Escherichia coli.

Escherichia coli possesses three stalled-ribosome rescue factors, tmRNA·SmpB (primary factor), ArfA (alternative factor to tmRNA·SmpB), and ArfB. Here, we examined the susceptibility of rescue factor-deficient strains from E. coli SE15 to various ribosome-targeting antibiotics.

Distinct genomic features of Transeurasian strains of Epstein-Barr virus in East Asia.

More than 95% of adult humans worldwide are latently infected with Epstein-Barr virus (EBV). Recent studies indicated that different EBV strains colonize different regions of Asia, where nasopharyngeal carcinoma (NPC) is endemic (southern China) or non-endemic (Japan/Korea). We searched for viral single nucleotide variant markers throughout the EBV genome by comparing the coding sequences of Japanese/Korean and NPC-endemic Chinese strains.

Human Cytomegalovirus Replication Enhanced By Placental MicroRNAs.

Placental trophoblasts constitute the interface between the fetal and maternal environments and physically prevent maternal-fetal viral transmission. However, congenital human cytomegalovirus (HCMV) infection in the early stages of pregnancy results in severe symptoms in the fetus. HCMV is the most common causative agent of intrauterine infection.

The evolutionary modifications of a GoLoco motif in the AGS protein facilitate micromere formation in the sea urchin embryo.

The evolutionary introduction of asymmetric cell division (ACD) into the developmental program facilitates the formation of a new cell type, contributing to developmental diversity and, eventually, species diversification. The micromere of the sea urchin embryo may serve as one of those examples: an ACD at the 16-cell stage forms micromeres unique to echinoids among echinoderms. We previously reported that a polarity factor, activator of G-protein signaling (AGS), plays a crucial role in micromere formation.

Human iPSC-liver organoid transplantation reduces fibrosis through immunomodulation.

Donor organ shortages for transplantation remain a serious global concern, and alternative treatment is in high demand. Fetal cells and tissues have considerable therapeutic potential as, for example, organoid technology that uses human induced pluripotent stem cells (hiPSCs) to generate unlimited human fetal-like cells and tissues. We previously reported the in vivo vascularization of early fetal liver-like hiPSC-derived liver buds (LBs) and subsquent improved survival of recipient mice with subacute liver failure.

The evolutionary modifications of a GoLoco motif in the AGS protein facilitate micromere formation in the sea urchin embryo.

The evolutionary introduction of asymmetric cell division (ACD) into the developmental program facilitates the formation of a new cell type, contributing to developmental diversity and, eventually, to species diversification. The micromere of the sea urchin embryo may serve as one of those examples: An ACD at the 16-cell stage forms micromeres unique to echinoids among echinoderms. We previously reported that a polarity factor, Activator of G-protein Signaling (AGS), plays a crucial role in micromere formation.

Discovery of Novel Bicyclic Pyrazoles as Potent PIP5K1C Inhibitors.

Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) is generated by phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) from phosphatidylinositol 4-phosphate (PI4P). Structurally diverse and selective inhibitors against PIP5Ks are required to further elucidate the therapeutic potential for PIP5K inhibition, although the effects of PIP5K inhibition on various diseases and their symptoms, such as cancer and chronic pain, have been reported. Our medicinal chemistry efforts led to novel and potent PIP5K1C inhibitors.

A Case of Anterior Arytenoid Cartilage Dislocation During Nasal Tracheal Intubation Using an Indirect Video Laryngoscope.

Arytenoid cartilage dislocation can occur as a complication of tracheal intubation and laryngeal trauma, but its occurrence with indirect video laryngoscopy has not been reported. This paper reports anterior arytenoid dislocation occurring after nasotracheal intubation performed under indirect laryngoscopy using a video laryngoscope (McGRATH MAC; Medtronic). The dislocation is presumed to have resulted from the laryngoscope blade being initially inserted too deeply and applying pressure to the posterior aspect of the left cricoarytenoid joint.

Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.

Assays such as CITE-seq can measure the abundance of cell surface proteins on individual cells using antibody derived tags (ADTs). However, many ADTs have high levels of background noise that can obfuscate down-stream analyses. In an exploratory analysis of PBMC datasets, we find that some droplets that were originally called 'empty' due to low levels of RNA contained high levels of ADTs and likely corresponded to neutrophils.

Characterization of highly active mutational signatures in tumors from a large Chinese population.

The majority of mutational signatures have been characterized in tumors from Western countries and the degree to which mutational signatures are similar or different in Eastern populations has not been fully explored. We leveraged a large-scale clinical sequencing cohort of tumors from a Chinese population containing 25 tumor types and found that the highly active mutational signatures were similar to those previously characterized. The aristolochic acid signature SBS22 was observed in four soft tissue sarcomas and the POLE-associated signature SBS10 was observed in a gallbladder carcinoma.

Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM.

Background: Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from single-cell RNA-sequencing (scRNA-seq) data to make these calculations. Single-nuclei RNA-sequencing (snRNA-seq) reference data can be used instead of scRNA-seq data for tissues such as human brain where single-cell data are difficult to obtain, but accuracy suffers due to sequencing differences between the technologies.

Socioeconomic disparities in treatment and survival in patients with hypopharyngeal malignancy.

Background: This retrospective study utilizes The Surveillance, Epidemiology, and End Results database to investigate socioeconomic factors leading to treatment disparities in hypopharyngeal malignancy.

Methods: Treatment was compared to National Cancer Care Network guidelines. Novel analyses, including logistic modeling, allowed survival analysis and identification of socioeconomic variables not previously considered in staging and management guidelines.

Interactive analysis of single-cell data using flexible workflows with SCTK2.

Analysis of single-cell RNA sequencing (scRNA-seq) data can reveal novel insights into the heterogeneity of complex biological systems. Many tools and workflows have been developed to perform different types of analyses. However, these tools are spread across different packages or programming environments, rely on different underlying data structures, and can only be utilized by people with knowledge of programming languages.

A systematic review and meta-analysis of neuromodulators to treat chronic airway hypersensitivity.

Objectives: Chronic laryngitis can present with numerous symptoms, including chronic cough. Patients who do not respond to standard treatment are sometimes diagnosed with chronic airway hypersensitivity (CAH). In many centers, neuromodulators are prescribed off-label despite limited evidence of efficacy.

Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.

Assays such as CITE-seq can measure the abundance of cell surface proteins on individual cells using antibody derived tags (ADTs). However, many ADTs have high levels of background noise that can obfuscate down-stream analyses. Using an exploratory analysis of PBMC datasets, we find that some droplets that were originally called "empty" due to low levels of RNA contained high levels of ADTs and likely corresponded to neutrophils.

Vasa, a regulator of localized mRNA translation on the spindle.

Localized mRNA translation is a biological process that allows mRNA to be translated on-site, which is proposed to provide fine control in protein regulation, both spatially and temporally within a cell. We recently reported that Vasa, an RNA-helicase, is a promising factor that appears to regulate this process on the spindle during the embryonic development of the sea urchin, yet the detailed roles and functional mechanisms of Vasa in this process are still largely unknown. In this review article, to elucidate these remaining questions, we first summarize the prior knowledge and our recent findings in the area of Vasa research and further discuss how Vasa may function in localized mRNA translation, contributing to efficient protein regulation during rapid embryogenesis and cancer cell regulation.

Polymethylmethacrylate Membrane Dialyzer: Historic but Modern.

Polymethylmethacrylate (PMMA) hollow fiber membranes are one of the synthetic polymer hollow fiber membranes used to the hollow fiber artificial kidney. A PMMA hollow fiber membrane (PMMA membrane) has unique properties including the uniform structure and the adsorption property. Hemodialyzers using PMMA membranes, Filtryzer®, were approved in Japan in 1977 and have been used worldwide for over 40 years and so is a historical hemodialyzer.

Complete Genome Sequence of sp. Strain L3-i23 Isolated from Soil in Japan.

This study describes the complete genome sequence of sp. strain L3-i23, acquired from an assembly of long reads and subsequently polished using short reads. The complete genome comprises a 3,139,863-bp chromosome with a GC content of 69.

MPS1 inhibition primes immunogenicity of KRAS-LKB1 mutant lung cancer.

KRAS-LKB1 (KL) mutant lung cancers silence STING owing to intrinsic mitochondrial dysfunction, resulting in T cell exclusion and resistance to programmed cell death (ligand) 1 (PD-[L]1) blockade. Here we discover that KL cells also minimize intracellular accumulation of 2'3'-cyclic GMP-AMP (2'3'-cGAMP) to further avoid downstream STING and STAT1 activation. An unbiased screen to co-opt this vulnerability reveals that transient MPS1 inhibition (MPS1i) potently re-engages this pathway in KL cells via micronuclei generation.

Celda: a Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data.

Single-cell RNA-seq (scRNA-seq) has emerged as a powerful technique to quantify gene expression in individual cells and to elucidate the molecular and cellular building blocks of complex tissues. We developed a novel Bayesian hierarchical model called Cellular Latent Dirichlet Allocation (Celda) to perform co-clustering of genes into transcriptional modules and cells into subpopulations. Celda can quantify the probabilistic contribution of each gene to each module, each module to each cell population and each cell population to each sample.

Vasa nucleates asymmetric translation along the mitotic spindle during unequal cell divisions.

mRNA translation on the spindle is hypothesized to be an essential strategy for the localized production of cell regulators. This mechanism may be important particularly in early embryonic cells, which have a large diffusion volume and that undergo rapid cell divisions. Evidence to test such a hypothesis has been, however, limited.