Front Cell Dev Biol
June 2024
iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan.
Juvenile nephronophthisis is an inherited renal ciliopathy with cystic kidney disease, renal fibrosis, and end-stage renal failure in children and young adults. Mutations in the gene encoding nephrocystin-1 protein have been identified as the most frequently responsible gene and cause the formation of cysts in the renal medulla. The molecular pathogenesis of juvenile nephronophthisis remains elusive, and no effective medicines to prevent end-stage renal failure exist even today.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
July 2024
Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1, was isolated as a pure co-culture with sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes.
View Article and Find Full Text PDFNat Commun
July 2024
PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Grafenstaden, 67404, Strasbourg, France.
The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework.
View Article and Find Full Text PDFGenomics Inform
June 2024
Fuku Inc, Tokyo, 113-0033, Japan.
This study evaluated large language models (LLMs), particularly the GPT-4 with vision (GPT-4 V) and GPT-4 Turbo, for annotating biomedical figures, focusing on cellular senescence. We assessed the ability of LLMs to categorize and annotate complex biomedical images to enhance their accuracy and efficiency. Our experiments employed prompt engineering with figures from review articles, achieving more than 70% accuracy for label extraction and approximately 80% accuracy for node-type classification.
View Article and Find Full Text PDFFront Bioeng Biotechnol
June 2024
Department of Biomedical Engineering, Izmir Kâtip Çelebi University, İzmir, Türkiye.
Curr Microbiol
June 2024
Department of Medical Biotechnology, College of Medicine and Public Health, Flinders University, Adelaide, Australia.
Two endophytic actinobacteria, strains MK5 and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic actinobacteria with a well-developed substrate and aerial mycelia that formed spiral spore chains. The type strains that shared the high 16S rRNA gene sequence similarity with both strains were Streptomyces naganishii NBRC 12892 (99.
View Article and Find Full Text PDFTransl Lung Cancer Res
May 2024
Department of Human Pathology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan.
The 36th International Mammalian Genome Conference (IMGC) was held in a hybrid format at the Tsukuba International Congress Center in Tsukuba, Ibaraki, Japan, for 4 days from March 28 to 31, 2023. This international conference on functional genomics of mouse, human, and other mammalian species attracted 246 participants in total, of which 129 were from outside Japan, including Europe, the United States and Asia, and 117 participants were from Japan. The conference included three technical workshops, keynote lectures by domestic researchers, commemorative lectures for the conference awards, 57 oral presentations, and 97 poster presentations.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
June 2024
Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
During a study on the diversity of culturable actinobacteria from coastal halophytes in Thailand, strain LSe6-5 was isolated from leaves of sea purslane ( L.), and a polyphasic approach was employed to determine its taxonomic position. The 16S rRNA gene sequences analysis indicated that the strain was most closely related to Tu 6233 (99.
View Article and Find Full Text PDFMicroorganisms
April 2024
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
A novel acidophilic, aerobic bacterium strain, MYW30-H2, was isolated from a heap of polymetallic mine. Cells of strain MYW30-H2 were Gram-stain-positive, endospore-forming, motile, and rod-shaped. Strain MYW30-H2 grew at a temperature range of 30-45 °C (optimum 40 °C) and a pH range of 3.
View Article and Find Full Text PDFBMC Med Inform Decis Mak
May 2024
Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Background: One significant challenge in addressing the coronavirus disease 2019 (COVID-19) pandemic is to grasp a comprehensive picture of its infectious mechanisms. We urgently need a consistent framework to capture the intricacies of its complicated viral infectious processes and diverse symptoms.
Results: We systematized COVID-19 infectious processes through an ontological approach and provided a unified description framework of causal relationships from the early infectious stage to severe clinical manifestations based on the homeostasis imbalance process ontology (HoIP).
Data Brief
June 2024
Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
A ubiquitous and pink-pigmented facultatively methylotrophic bacterium, designated LRY1-08 (=JCM 33120), was isolated from a lichen in Thailand. Strain LRY1-08 and NBRC 112876 shared 99.92 % similarity based on the 16S rRNA gene sequence.
View Article and Find Full Text PDFHum Genome Var
May 2024
Department of Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Neurofibromatosis type 1 (NF1) is an autosomal dominant nevus disease characterized by multiple manifestations, primarily café-au-lait macules and neurofibromas. Here, we present the case of an NF1 patient with 47,XYY mosaicism whose diagnosis was prompted by café-au-lait macules on the skin and mandibular neurofibromas. Targeted next-generation sequencing of the patient's blood sample revealed a novel frameshift mutation in NF1 (NM_000267.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
May 2024
Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand.
Two novel Gram-negative, aerobic, rod-shaped, non-motile bacteria, strains TBRC 10068 and TBRC 16381, were isolated from a fluid sample from a close-pitcher cup () and an insect sample (), respectively. Comparing the 16S rRNA gene sequences with those found in EzBioCloud's publicly available databases revealed that the two strains exhibited a close genetic relationship with A911; the calculated sequence similarities were 98.56 and 97.
View Article and Find Full Text PDFEur Heart J
July 2024
Department of Cardiology, Sapporo Teishinkai Hospital, N33, E1, Sapporo 065-0033, Japan.
Background And Aims: Brugada syndrome (BrS) is an inherited arrhythmia with a higher disease prevalence and more lethal arrhythmic events in Asians than in Europeans. Genome-wide association studies (GWAS) have revealed its polygenic architecture mainly in European populations. The aim of this study was to identify novel BrS-associated loci and to compare allelic effects across ancestries.
View Article and Find Full Text PDFSci Rep
May 2024
Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand.
Pradimicin U is a new dihydrobenzo[a]naphthacenequinone compound found to be active on a screen designed to investigate compounds with antimicrobial activity, produced by the actinomycete designated strain FMUSA5-5. The strain was isolated from a bio-fertilizer of Musa spp. collected from Suphanburi province, Thailand.
View Article and Find Full Text PDFSci Data
May 2024
Life Science Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Although cellular senescence is a key factor in organismal aging, with both positive and negative effects on individuals, its mechanisms remain largely unknown. Thus, integrating knowledge is essential to explain how cellular senescence manifests in tissue damage and age-related diseases. Here, we propose an ontological model that organizes knowledge of cellular senescence in a computer-readable form.
View Article and Find Full Text PDFStem Cell Reports
June 2024
Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; The Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan; Bioresource Engineering Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan. Electronic address:
Removal of somatic histone H3 lysine 9 trimethylation (H3K9me3) from the embryonic genome can improve the efficiency of mammalian cloning using somatic cell nuclear transfer (SCNT). However, this strategy involves the injection of histone demethylase mRNA into embryos, which is limiting because of its invasive and labor-consuming nature. Here, we report that treatment with an inhibitor of G9a (G9ai), the major histone methyltransferase that introduces H3K9me1/2 in mammals, greatly improved the development of mouse SCNT embryos.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
May 2024
Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan.
Obligately anaerobic, Gram-stain-negative, wavy rods, strains 17YCFAHCo10, 18YCFAH0.3Co2 and 19YCFAH0.3Co2, were isolated from faecal samples of healthy Japanese people.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
May 2024
Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
Sci Rep
May 2024
Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy.
The identification of regulatory networks contributing to fetal/adult gene expression switches is a major challenge in developmental biology and key to understand the aberrant proliferation of cancer cells, which often reactivate fetal oncogenes. One key example is represented by the developmental gene LIN28B, whose aberrant reactivation in adult tissues promotes tumor initiation and progression. Despite the prominent role of LIN28B in development and cancer, the mechanisms of its transcriptional regulation are largely unknown.
View Article and Find Full Text PDFStem Cell Res
June 2024
iPS Cell Advanced Characterization and Development Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan. Electronic address:
Rett syndrome is characterized by severe global developmental impairments with autistic features and loss of purposeful hand skills. Here we show that human induced pluripotent stem cell (hiPSC) lines derived from four Japanese female patients with Rett syndrome are generated from peripheral blood mononuclear cells using Sendai virus vectors. The generated hiPSC lines showed self-renewal and pluripotency and carried heterozygous frameshift, missense, or nonsense mutations in the MECP2 gene.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
May 2024
Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
Four newly discovered Gram-stain-negative bacteria, designated as BL00010, BL00058, D8-11 and BL00200, were isolated from water samples collected at three hydrological monitoring stations (namely Chiang Saen, Chiang Khan and Nong Khai) located along the Mekong River in Thailand. An investigation encompassing phenotypic, chemotaxonomic and genomic traits was conducted. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that all four isolates represented members of the genus .
View Article and Find Full Text PDFFront Microbiol
April 2024
Department of Medical Biotechnology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia.
Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of as a novel species and study its antibiotics production.
View Article and Find Full Text PDFSci Rep
April 2024
RIKEN Cell Bank, Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan.
K-562 is a well-known in vitro cellular model that represents human leukemia cell lines. Although the K-562 cells have been extensively characterized, there are inconsistencies in the data across publications, showing the presence of multiple K-562 cell lines. This suggests that analyzing a single K-562 cell line is insufficient to provide reliable reference data.
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