Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

Coordinated development of island ecotourism: A comprehensive evaluation of Amami-Oshima Island

Island tourism has garnered growing attention especially with the rapid expansion of ecotourism in island destinations. While past research has explored the integrated development of island tourism, environment, and economy, there exists a demand for a more comprehensive exploration that incorporates social aspects. This study aimed to establish a comprehensive evaluation index system for island ecotourism using Amami-Oshima Island as an example. It uses four tourism subtypes, including environment, economic, social, and other-sector tourism, within the framework for island ecotourism. We employed a Coupling Coordination Degree Model and a Grey Verhulst model, utilizing data from Amami-Oshima Island from 2010 to 2021 as a basis for quantitative analysis of the current status of island ecotourism coupling coordination development and for making predictions. The research outcomes reveal the following: (1) Between 2010 and 2021, Amami-Oshima Island exhibited an overall upward trajectory in the comprehensive development of ecotourism. The environment-tourism subsystem demonstrated robust performance, the social-tourism subsystem displayed fluctuating growth, and the economic and the other-sector tourism dimensions generally progressed in tandem. (2) The coupling degree and coordination level of Amami-Oshima Island ecotourism showed an overall upward trend, with coordination evolving from a state of minimal coordination to an intermediate level. However, opportunities remain to enhance high-quality coordination through mutual influences and interdependencies. (3) Predictions indicate a slight increase in ecotourism coupling coordination on Amami-Oshima Island over the next nine years (2022–2030). Based on these findings, this paper presents several policy recommendations, serving as a guideline for ecotourism development on Amami-Oshima Island. The research results carry significant implications for understanding the present status and future trends of ecotourism on Amami-Oshima Island and offer valuable policy suggestions for the development of ecotourism on other islands

Human iPSC-derived hepatocyte system models cholestasis with tight junction protein 2 deficiency

BACKGROUND & AIMS: The truncating mutations in tight junction protein 2 (TJP2) cause progressive cholestasis, liver failure, and hepatocyte carcinogenesis. Due to the lack of effective model systems, there are no targeted medications for the liver pathology with TJP2 deficiency. We leveraged the technologies of patient-specific induced pluripotent stem cells (iPSC) and CRISPR genome-editing, and we aim to establish a disease model which recapitulates phenotypes of patients with TJP2 deficiency. METHODS: We differentiated iPSC to hepatocyte-like cells (iHep) on the Transwell membrane in a polarized monolayer. Immunofluorescent staining of polarity markers was detected by a confocal microscope. The epithelial barrier function and bile acid transport of bile canaliculi were quantified between the two chambers of Transwell. The morphology of bile canaliculi was measured in iHep cultured in the Matrigel sandwich system using a fluorescent probe and live-confocal imaging. RESULTS: The iHep differentiated from iPSC with TJP2 mutations exhibited intracellular inclusions of disrupted apical membrane structures, distorted canalicular networks, altered distribution of apical and basolateral markers/transporters. The directional bile acid transport of bile canaliculi was compromised in the mutant hepatocytes, resembling the disease phenotypes observed in the liver of patients. CONCLUSIONS: Our iPSC-derived in vitro hepatocyte system revealed canalicular membrane disruption in TJP2 deficient hepatocytes and demonstrated the ability to model cholestatic disease with TJP2 deficiency to serve as a platform for further pathophysiologic study and drug discovery. LAY SUMMARY: We investigated a genetic liver disease, progressive familial intrahepatic cholestasis (PFIC), which causes severe liver disease in newborns and infants due to a lack of gene called TJP2. By using cutting-edge stem cell technology and genome editing methods, we established a novel disease modeling system in cell culture experiments. Our experiments demonstrated that the lack of TJP2 induced abnormal cell polarity and disrupted bile acid transport. These findings will lead to the subsequent investigation to further understand disease mechanisms and develop an effective treatment