RNA viruses are distributed throughout various environments, and most have recently been identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify novel RNA viruses from metatranscriptome data. To overcome this issue, we created a dataset of RNA-dependent RNA polymerase (RdRp) domains that are essential for all RNA viruses belonging to Orthornavirae. Genes with RdRp domains from various RNA viruses were clustered based on amino acid sequence similarities. A multiple sequence alignment was generated for each cluster, and a hidden Markov model (HMM) profile was created when the number of sequences was greater than three. We further refined 426 HMM profiles by detecting RefSeq RNA virus sequences and subsequently combined the hit sequences with the RdRp domains. As a result, 1,182 HMM profiles were generated from 12,502 RdRp domain sequences, and the dataset was named NeoRdRp. The majority of NeoRdRp HMM profiles successfully detected RdRp domains, specifically in the UniProt dataset. Furthermore, we compared the NeoRdRp dataset with two previously reported methods for RNA virus detection using metatranscriptome sequencing data. Our methods successfully identified the majority of RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. NeoRdRp may be repeatedly improved by the addition of new RdRp sequences and is applicable as a system for detecting various RNA viruses from diverse metatranscriptome data.

The present study examined the impact of age on medical student repeat-year experience and performance outcomes on the objective structured clinical examination (OSCE), Clinical Clerkship (CC), and other relevant examinations in the Japanese medical school system. This retrospective analysis examined the number of students with repeat-years and the years required to graduate, stratifying students by the age they entered medical school (Younger: within 4 years of high school graduation; Older: 5 or more years after high school graduation). Scores of the Pre-CC OSCE, Computer-based testing (CBT), CC performance, CC integrative test, and graduation exams were compared among those graduating from our medical school between 2018 and 2020, and examined correlations between student age and performance outcomes. From 2018 to 2020, 328 medical students graduated. Of these, 283 had entered within 4 years of high school graduation (Younger), while 45 did so 5 or more years after high school graduation (Older). The number of repeat-years did not differ significantly between groups. The average number of years required to graduate was slightly higher for the Older group and the Younger group scored significantly higher on the CC integrative test. No significant differences were found for the remaining tests. These results suggest that older medical students in general show no significant inferiority in their performance of most clinical skills and competencies relative to younger students in Japan.

The accuracy and correspondence between the measured concentrations from the survey and predicted concentrations on the basis of the three types of statistical antimicrobial use in Japan was evaluated. A monitoring survey of ten representative antimicrobials: ampicillin (APL), cefdinir (CDN), cefpodoxime proxetil (CPXP), ciprofloxacin (CFX), clarithromycin (CTM), doxycycline (DCL), levofloxacin (LFX), minocycline (MCL), tetracycline (TCL), and vancomycin (VMC), in the influent of sewage treatment plant (STP) located in urban areas of Japan, was conducted. Then, the measured values were verified in comparison with the predicted values estimated from the shipping volumes, sales volumes, and prescription volumes based on the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB). The results indicate that the correspondence ratios between the predicted concentrations calculated on the basis of shipping and NDB volumes and the measured concentrations (predicted concentration/measured concentration) generally agreed for the detected concentration of antimicrobials in the STP influent. The correspondence ratio on the basis of shipping volume was, for CFX, 0.1; CTM, 2.9; LFX, 0.5; MCL, 1.9; and VMC, 1.7, and on the basis of NDB volume the measured concentration was CFX, 0.1; CTM, 3.7; DCL, 0.4; LFX, 0.7; MCL, 1.9; TCL, 0.6; and VMC, 1.6. To our knowledge, this is the first report to evaluate the accuracy of predicted concentrations based on sales, shipping, NDB statistics and measured concentrations for antimicrobials in the STP influent.

Single cilia, 100 nm in diameter and 10 µm in length, were isolated from mouse tracheae with Triton X-100 (0.02%) treatment, and the effects of pH on ciliary beating were examined by measuring the ciliary beat frequency (CBF) and the ciliary bend distance (CBD—an index of amplitude) using a high-speed video microscope (250 fps). ATP (2.5 mM) plus 8Br-cAMP (10 µM) reactivated the CBF and CBD in the isolated cilia, similar to the cilia of in vivo tracheae. In the reactivated isolated cilia, an elevation in pH from 7.0 to 8.0 increased the CBF from 3 to 15 Hz and the CBD from 0.6 to 1.5 µm. The pH elevation also increased the velocity of the effective stroke; however, it did not increase the recovery stroke, and, moreover, it decreased the intervals between beats. This indicates that H⁺ (pH_i) directly acts on the axonemal machinery to regulate CBF and CBD. In isolated cilia priorly treated with 1 µM PKI-amide (a PKA inhibitor), 8Br-cAMP did not increase the CBF or CBD in the ATP-stimulated isolated cilia. pH modulates the PKA signal, which enhances the axonemal beating generated by the ATP-activated inner and outer dyneins.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel betacoronavirus, is the causative agent of COVID-19, which has caused economic and social disruption worldwide. To date, many drugs and vaccines have been developed for the treatment and prevention of COVID-19 and have effectively controlled the global epidemic of SARS-CoV-2. However, SARS-CoV-2 is highly mutable, leading to the emergence of new variants that may counteract current therapeutic measures. Electron microscopy (EM) is a valuable technique for obtaining ultrastructural information about the intracellular process of virus replication. In particular, EM allows us to visualize the morphological and subcellular changes during virion formation, which would provide a promising avenue for the development of antiviral agents effective against new SARS-CoV-2 variants. In this review, we present our recent findings using transmission electron microscopy (TEM) combined with electron tomography (ET) to reveal the morphologically distinct types of SARS-CoV-2 particles, demonstrating that TEM and ET are valuable tools for visually understanding the maturation status of SARS-CoV-2 in infected cells. This review also discusses the application of EM analysis to the evaluation of genetically engineered RNA viruses.