Physiological Roles of Class I HDAC Complex and Histone Demethylase

Epigenetic gene silencing is one of the fundamental mechanisms for ensuring proper gene expression patterns during cellular differentiation and development. Histone deacetylases (HDACs) are evolutionally conserved enzymes that remove acetyl modifications from histones and play a central role in epigenetic gene silencing. In cells, HDAC forms a multiprotein complex (HDAC complex) in which the associated proteins are believed to help HDAC carry out its cellular functions. Though each HDAC complex contains distinct components, the presence of isoforms for some of the components expands the variety of complexes and the diversity of their cellular roles. Recent studies have also revealed a functional link between HDAC complexes and specific histone demethylases. In this paper, we summarize the distinct and cooperative roles of four class I HDAC complexes, Sin3, NuRD, CoREST, and NCoR/SMRT, with respect to their component diversity and their relationship with specific histone demethylases

Researchers support preprints and open access publishing, but with reservations: A questionnaire survey of MBSJ members

This is the peer reviewed version of the following article: Ide K., Nakayama J.i.. Researchers support preprints and open access publishing, but with reservations: A questionnaire survey of MBSJ members. Genes to Cells 28, 333 (2023), which has been published in final form at https://doi.org/10.1111/gtc.13015. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.Since the 1990s, journals have become increasingly online and open access. In fact, about 50% of articles published in 2021 were open access. The use of preprints (i.e., non-peer-reviewed articles) has also increased. However, there is limited awareness of these concepts among academics. Therefore, we conducted a questionnaire-based survey among members of the Molecular Biology Society of Japan. The survey was conducted between September 2022 and October 2022, with 633 respondents, 500 of whom (79.0%) were faculty members. In total, 478 (76.6%) respondents had published articles as open access, and 571 (91.5%) wanted to publish their articles in open access. Although 540 (86.5%) respondents knew about preprints, only 183 (33.9%) had posted preprints before. In the open-ended section of the questionnaire survey, several comments were made about the cost burdens associated with open access and the difficulty of how academic preprints are handled. Although open access is widespread, and recognition of preprints is increasing, some issues remain that need to be addressed. Academic and institutional support, and transformative agreement may help reduce the cost burden. Guidelines for handling preprints in academia are also important for responding to changes in the research environment

An Analytical Model of Traffic Equilibrium with Stochastic Demands

金沢大学理工研究域　環境デザイン学

Contribution of RING domain to retrovirus restriction by TRIM5α depends on combination of host and virus

AbstractThe anti-retroviral restriction factor TRIM5α contains the RING domain, which is frequently observed in E3 ubiquitin ligases. It was previously proposed that TRIM5α restricts human immunodeficiency virus type 1 (HIV-1) via proteasome-dependent and -independent pathways. Here we examined the effects of RING domain mutations on retrovirus restriction by TRIM5α in various combinations of virus and host species. Simian immunodeficiency virus isolated from macaque (SIVmac) successfully avoided attacks by RING mutants of African green monkey (AGM)-TRIM5α that could still restrict HIV-1. Addition of proteasome inhibitor did not affect the anti-HIV-1 activity of AGM-TRIM5α, whereas it disrupted at least partly its anti-SIVmac activity. In the case of mutant human TRIM5α carrying proline at the position 332, however, both HIV-1 and SIVmac restrictions were eliminated as a result of RING domain mutations. These results suggested that the mechanisms of retrovirus restriction by TRIM5α vary depending on the combination of host and virus

Semi-dynamic traffic assignment model with mode and route choices under stochastic travel times

Transportation network conditions vary significantly during the course of a day. In many urban areas, public transit and (private) automobiles constitute the actual forms of transportation that use such networks. Public transportation by rail is more reliable than by automobiles or buses; therefore, ordinary static and deterministic traffic assignment models with combined mode and route choices may not be suitable to assess a transportation network that includes public railways. Moreover, within-day dynamics and reliability need to be incorporated in such a model. In this paper, we use a semi-dynamic traffic assignment model that considers within-day dynamics by improving the static traffic assignment model. In addition, stochastic travel times are incorporated into the model. Thus, we propose a semi-dynamic traffic assignment model with mode choice between public transit and automobiles, route choice with stochastic travel times, and an accompanying computing algorithm. This model enables us to assess within-day dynamics of transportation networks and travel time reliability of public railways. Copyright © 2012 John Wiley & Sons, Ltd

An Application of the Simulated Annealing to the Calculation of a Combined Mode Choice and Route Choice Network Equilibrium Model with Road Travel Time Uncertainty

金沢大学理工研究域　環境デザイン学系Travel time of public transport such as railway and Light Rail Transit (LRT) is more reliable than road traffic. When assessing the effect of railway transits, the reliability should be considered. Otherwise, the effect may be underestimated. Then, we should not only treat both transit and road users simultaneously and consistently, but also travel time uncertainty of cars and the reliability (or punctuality) of railway for exact evaluation. A network equilibrium model with combined mode and route choice considering road travel time uncertainty does not necessarily have a unique solution, but may have many local solutions, because of the interaction between modes. The simulated annealing is one of the useful techniques to such a problem, to the calculation of the network equilibrium model with combined mode and route choice. In this paper, we apply the network equilibrium model proposed to the Kanazawa urban area using the simulated annealing technique

Population genomics of the fission yeast Schizosaccharomyces pombe.

The fission yeast Schizosaccharomyces pombe has been widely used as a model eukaryote to study a diverse range of biological processes. However, population genetic studies of this species have been limited to date, and we know very little about the evolutionary processes and selective pressures that are shaping its genome. Here, we sequenced the genomes of 32 worldwide S. pombe strains and examined the pattern of polymorphisms across their genomes. In addition to introns and untranslated regions (UTRs), intergenic regions also exhibited lower levels of nucleotide diversity than synonymous sites, suggesting that a considerable amount of noncoding DNA is under selective constraint and thus likely to be functional. A number of genomic regions showed a reduction of nucleotide diversity probably caused by selective sweeps. We also identified a region close to the end of chromosome 3 where an extremely high level of divergence was observed between 5 of the 32 strains and the remain 27, possibly due to introgression, strong positive selection, or that region being responsible for reproductive isolation. Our study should serve as an important starting point in using a population genomics approach to further elucidate the biology of this important model organism

A Case of Pulmonary Sarcoma with Significant Extension into the Right Lung

A female patient in her 30s was referred to us with a mass approximately 8 centimeters in diameter in right lung segment 6. Bronchoscopy was done, and a tumorous lesion obstructing right B6 was found. Biopsy of this lesion supported suspicions of sarcoma or spindle cell carcinoma. Contrast-enhanced CT showed that the mass extended to and obstructed the right main pulmonary artery. A skip lesion was also suspected in the periphery of pulmonary artery trunk. The tumor was removed by right pneumonectomy accompanied by resection of the main and left pulmonary arteries under cardiopulmonary bypass. The pulmonary artery trunk and the left pulmonary artery were reconstructed with a vascular graft. Collectively, intimal sarcoma originating from the right main pulmonary artery with extension into the right lung was diagnosed. Significant extension of pulmonary artery sarcoma into the lung, as was observed in the present case, is considered to be rare, and to our knowledge this is the first report in which the primary lesion was biopsied by bronchoscopy

Posttraumatic Cranial Cystic Fibrous Dysplasia

A 14-year-old was girl admitted to our hospital with a subcutaneous mass of the occipital head. The mass had grown for 6 years, after she had sustained a head injury at the age of 6, and was located directly under a previous wound. Skull X-ray Photograph (xp), computed tomography (CT), and magnetic resonance imaging (MRI) showed a bony defect and cystic changes in the skull corresponding to a subcutaneous mass. Bone scintigraphy revealed partial accumulation. The patient underwent total removal of the skull mass, and the diagnosis from the pathological findings of the cyst wall was fibrous dysplasia (FD). The radiographic findings for cystic cranial FD can be various. Progressive skull disease has been reported to be associated with head trauma, but the relationship between cranial FD and head trauma has not been previously reported. Previous studies have suggested that c-fos gene expression is a key mechanism in injury-induced FD