Article
Biochemistry & Molecular Biology
K. Nagaraju Shivaprakash, Sandeep Sen, Seema Paul, Joseph M. Kiesecker, Kamaljit S. Bawa
Summary: Most new infectious diseases emerge when pathogens transfer from animals to humans. The risk of carrying zoonotic diseases is not equal for all mammal species in wildlife trade, and mitigation measures should prioritize species with the highest risk of carrying zoonotic viruses. Curbing the sales of wildlife products and developing principles that support sustainable and healthy wildlife trade could help prevent future zoonotic outbreaks.
Article
Biochemistry & Molecular Biology
Masaki Takasugi, Yuya Yoshida, Yoshiki Nonaka, Naoko Ohtani
Summary: Despite comprehensive transcriptome analyses, the actual impact of transcriptome on aging and species maximum lifespan (MLS) has remained elusive. However, our study found significant similarities between transcriptomic signatures associated with mammalian MLS and aging, suggesting that gene expression patterns associated with MLS contribute to extended lifespan within and across species. Furthermore, we identified evidence of co-evolution between MLS and promoter sequences of MLS-associated genes, highlighting the evolutionary contribution of specific transcription factor binding motifs in shaping MLS-associated gene expression signature. This study emphasizes the importance of considering the adaptive aspects of aging transcriptome and demonstrates the power of cross-species genomics in understanding adaptive aging transcriptome.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Chun-Chieh Liao, Po-Ying Fu, Chih-Wei Huang, Chia-Hsien Chuang, Yun Yen, Chung-Yen Lin, Shu-Hwa Chen
Summary: Motivation: Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. In this study, we merged widely used 16S rRNA sequence databases and a collection of novel sequences into an integrated resource named MetaSquare version 1.0. The database contains over 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods.
Article
Biochemistry & Molecular Biology
Ahyoung Choi, Insu Jang, Heewon Han, Min-Seo Kim, Jinhyuk Choi, Jieun Lee, Sung-Yup Cho, Yukyung Jun, Charles Lee, Jaesang Kim, Byungwook Lee, Sanghyuk Lee
Summary: iCSDB is an integrated database of CRISPR screening experiments using human cell lines, compiling data from DepMap and BioGRID ORCS, covering numerous human cell lines and cancer types. The database also integrates clinical and molecular information, and provides interactive tools and viewers to help users choose and compare screening results.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Aurelio Patelli, Luciano Pietronero, Andrea Zaccaria
Summary: This paper presents an integrated database suitable for investigating the economic development of countries. The database combines the export flow of services and physical goods, creating a comprehensive view of the international market. The quality of the database is supported by computing the main metrics of the Economic Fitness and Complexity framework, such as building a network of economic activities and evaluating the competitiveness of countries.
Article
Environmental Sciences
Janani Ravichandran, Bagavathy Shanmugam Karthikeyan, Palak Singla, S. R. Aparna, Areejit Samal
Summary: This study established the first dedicated knowledgebase, NeurotoxKb 1.0, focusing on environmental neurotoxicants specific to mammals, compiling detailed information on 475 potential neurotoxicants. Through analyzing global chemical regulations and human biospecimens, potential neurotoxicants were identified in external exposomes and detected in human samples, providing insights into human exposure risks associated with these neurotoxicants. The construction of a chemical similarity network revealed the diversity of toxicological space among the 475 potential neurotoxicants.
Article
Plant Sciences
Atsushi Fukushima, Mikiko Takahashi, Hideki Nagasaki, Yusuke Aono, Makoto Kobayashi, Miyako Kusano, Kazuki Saito, Norio Kobayashi, Masanori Arita
Summary: The advancement of metabolomics has enabled rapid detection and quantification of cellular metabolites. However, shortcomings in data sharing still exist. To address these issues, RIKEN developed the RIKEN PMM, a database that stores plant metabolomic data and experimental metadata.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Arif Canakoglu, Pietro Pinoli, Anna Bernasconi, Tommaso Alfonsi, Damianos P. Melidis, Stefano Ceri
Summary: ViruSurf is a large public database containing viral sequences and curated metadata from various sources, offering complex search functionalities. It includes harmful virus species to humans and enables faster responses to potential threats from new viruses in the future.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Apoorv Gupta, Sandhya Pathak, Rajeev Varshney, Yasmin Ahmad, Pankaj Khurana
Summary: HighAltitudeOmicsDB is a unique resource that provides detailed information on genes/proteins, protein-protein interactions, and gene ontology semantic similarities related to high altitude conditions, aiming to facilitate research and analysis on the complex mechanisms of high altitude acclimatization.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Medicinal
Bailu Yan, Xinchun Ran, Anvita Gollu, Zihao Cheng, Xiang Zhou, Yiwen Chen, Zhongyue J. Yang
Summary: Data-driven modeling is crucial for biocatalyst design and discovery, and a biocatalytic database integrating enzyme structure and function data is urgently needed. In this study, we introduce IntEnzyDB as an integrated structure-kinetics database, which allows easy statistical modeling and machine learning. Using this database, we investigated the effects of mutations on enzyme efficiency, and found that efficiency-enhancing mutations are globally encoded. Furthermore, we provide a web interface for public access to enzymology data stored in IntEnzyDB.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Ruofan Ding, Qixuan Wang, Lihai Gong, Ting Zhang, Xudong Zou, Kewei Xiong, Qi Liao, Mireya Plass, Lei Li
Summary: Researchers have developed a comprehensive database called scQTLbase for searching, analyzing, and visualizing single-cell expression quantitative trait loci (sc-eQTLs). The database includes 304 datasets spanning 57 cell types and 95 cell states. It offers various functionalities such as gene expression visualization, a genome browser, and colocalization visualization based on GWAS datasets.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Long-Fei Zhao, Jin-Ge Zhang, Feng-Yu Qi, Wei-Yan Hou, Yin-Rui Li, Dan-Dan Shen, Li-Juan Zhao, Lin Qi, Hong-Min Liu, Yi-Chao Zheng
Summary: This study developed the first web-based public database called Sex Differences in Cancer (SDC) to analyze the impact of sex differences in cancer by integrating resources from multiple databases. SDC contains various types of cancer, molecular data, donors, and cancer cell lines, providing different modules for users to study the effects of sex differences.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Clare Pacini, Joshua M. Dempster, Isabella Boyle, Emanuel Goncalves, Hanna Najgebauer, Emre Karakoc, Dieudonne van der Meer, Andrew Barthorpe, Howard Lightfoot, Patricia Jaaks, James M. McFarland, Mathew J. Garnett, Aviad Tsherniak, Francesco Iorio
Summary: This study integrates two large CRISPR-Cas9 screens to correct biases, provide greater statistical power, identify additional biomarkers, and improve the detection of common essential genes, enhancing cancer-specific analyses.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Koichi Arakawa, Tamiko Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto
Summary: The study constructed a foundation for discovering glycan and virus interaction data using Semantic Web technologies. An ontology was created to encapsulate the semantics of virus-glycan interactions, and RDF was used to represent the data obtained from non-RDF related databases and literature. The data has been made publicly available as open data and a service for free searches using SPARQL is provided.
Article
Biochemistry & Molecular Biology
George Minadakis, Kyproula Christodoulou, George Tsouloupas, George M. Spyrou
Summary: PathIN is a web-service that enables the rapid creation of pathway-based networks at multiple biological levels and is supported by a database repository of reference pathway networks. It offers five different methodologies for generating networks and is expected to be a valuable tool for understanding molecular mechanism networks related to specific diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Hsian-Jean Chin, Michael S. Dobbie, Xiang Gao, James E. Hennessy, Ki-Hoan Nam, Je Kyung Seong, Toshihiko Shiroishi, Toru Takeo, Atsushi Yoshiki, Jing Zao, Chi-Kuang Leo Wang
Summary: The Asian Mouse Mutagenesis Resource Association (AMMRA) is a non-profit organization dedicated to supporting biomedical research and fostering international collaboration. By working closely with consortiums like the International Mouse Phenotyping Consortium and the International Mouse Strain Resource, AMMRA aims to strengthen global connections and enhance the quality of life science research worldwide.
Article
Biochemistry & Molecular Biology
Saori Mizuno-Iijima, Toshiaki Nakashiba, Shinya Ayabe, Hatsumi Nakata, Fumio Ike, Noriko Hiraiwa, Keiji Mochida, Atsuo Ogura, Hiroshi Masuya, Shoko Kawamoto, Masaru Tamura, Yuichi Obata, Toshihiko Shiroishi, Atsushi Yoshiki
Summary: The RIKEN BioResource Research Center is a comprehensive biological resource center in Japan, responsible for the collection, preservation, quality control, and distribution of mouse resources. The center has collected over 9000 strains created by Japanese scientists, including Nobel laureates, and distributed them to researchers worldwide, resulting in numerous publications and patents. Their efforts in maintaining high-quality mouse resources have contributed to reproducible life science studies and innovation globally.
Article
Biochemistry & Molecular Biology
Ryuichi Nakagawa, Kei Takasawa, Maki Gau, Atsumi Tsuji-Hosokawa, Hideya Kawaji, Yasuhiro Murakawa, Shuji Takada, Masashi Mikami, Satoshi Narumi, Maki Fukami, Rajini Sreenivasan, Tetsuo Maruyama, Elena J. Tucker, Liang Zhao, Josephine Bowles, Andrew Sinclair, Peter Koopman, Yoshihide Hayashizaki, Tomohiro Morio, Kenichi Kashimada
Summary: This study identified enhancers of five ovarian genes involved in early ovarian development using the expression of enhancer derived transcripts (eRNAs) as a characterization of active enhancers. Two candidate sequences for enhancers of Wnt4 and Rspo1 were identified and their enhancer activities were confirmed. Rare sequence variants were also found in these enhancer sequences in patients with impaired ovarian development. This research advances an important unmet need in forward human genetics.
HUMAN MOLECULAR GENETICS
(2022)
Article
Medicine, General & Internal
Keiichiro Yoshioka, Hironori Sato, Takeshi Kawasaki, Daisuke Ishii, Takuro Imamoto, Mitsuhiro Abe, Yoshinori Hasegawa, Osamu Ohara, Koichiro Tatsumi, Takuji Suzuki
Summary: RNA sequencing analysis revealed differential gene expression patterns in peripheral blood mononuclear cells (PBMCs) between patients with pulmonary sarcoidosis and healthy controls, with 270 differentially expressed genes involved in various biological processes related to the pathobiology of sarcoidosis. Enrichment analysis of gene ontology and KEGG pathways indicated the potential involvement of specific signaling pathways in sarcoidosis pathogenesis, providing insight into potential therapeutic targets for the disease.
FRONTIERS IN MEDICINE
(2022)
Article
Biology
Yuki Sakamoto, Anna Ishimoto, Yuuki Sakai, Moeko Sato, Ryuichi Nishihama, Konami Abe, Yoshitake Sano, Teiichi Furuichi, Hiroyuki Tsuji, Takayuki Kohchi, Sachihiro Matsunaga
Summary: Researchers developed an improved tissue clearing method, iTOMEI, for fluorescence microscopy of both plant and animal tissues. This method efficiently removes chlorophyll and autofluorescence signals while preserving the desired fluorescence protein signals.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemical Research Methods
Hironori Sato, Daisuke Nakajima, Masaki Ishikawa, Ryo Konno, Ren Nakamura, Osamu Ohara, Yusuke Kawashima
Summary: This study analyzed proteins in dried saliva spots to improve the diagnosis of genetic diseases in newborns. Results showed that dried saliva spots could be used as an alternative tool for detecting causative proteins.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Yusuke Kawashima, Hirotaka Nagai, Ryo Konno, Masaki Ishikawa, Daisuke Nakajima, Hironori Sato, Ren Nakamura, Tomoyuki Furuyashiki, Osamu Ohara
Summary: This paper discusses the demand for high proteome coverage in single-shot measurements and focuses on data-independent acquisition (DIA)-MS and ion mobility spectrometry as techniques for deep proteome analysis. The researchers aimed to expand the proteome coverage by optimizing high-field asymmetric waveform ion mobility spectrometry parameters in DIA-MS. The approach was applied to the analysis of host proteins in mouse feces and proved to be useful in understanding mental illness pathologies.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Neurosciences
Hiroki Sasaguri, Shoko Hashimoto, Naoto Watamura, Kaori Sato, Risa Takamura, Kenichi Nagata, Satoshi Tsubuki, Toshio Ohshima, Atsushi Yoshiki, Kenya Sato, Wakako Kumita, Erika Sasaki, Shinobu Kitazume, Per Nilsson, Bengt Winblad, Takashi Saito, Nobuhisa Iwata, Takaomi C. Saido
Summary: This article introduces transgenic mouse models of Alzheimer's disease (AD) and discusses their limitations and applications. The first generation models have artificial phenotypes, while the second generation models have specific strengths and weaknesses. The third generation models exhibit more pathology and are suitable for preclinical studies. The article also provides a technical guide for using App knock-in mice in AD research and discusses the latest advances in using human tau knock-in mice and non-human primate models of AD.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Sanna Vuoristo, Shruti Bhagat, Christel Hyden-Granskog, Masahito Yoshihara, Lisa Gawriyski, Eeva-Mari Jouhilahti, Vipin Ranga, Mahlet Tamirat, Mikko Huhtala, Ida Kirjanov, Sonja Nykanen, Kaarel Krjutskov, Anastassius Damdimopoulos, Jere Weltner, Kosuke Hashimoto, Gaelle Recher, Sini Ezer, Priit Paluoja, Pauliina Paloviita, Yujiro Takegami, Ai Kanemaru, Karolina Lundin, Tomi T. Airenne, Timo Otonkoski, Juha S. Tapanainen, Hideya Kawaji, Yasuhiro Murakawa, Thomas R. Burglin, Markku Varjosalo, Mark S. Johnson, Timo Tuuri, Shintaro Katayama, Juha Kere
Summary: Double homeobox 4 (DUX4) is expressed at the early pre-implantation stage in human embryos and significantly affects the chromatin accessibility of non-coding DNA. It activates newly identified transcribed enhance-like regions and is associated with increased expression of target embryonic genome activation genes.
Article
Biochemical Research Methods
Masaki Ishikawa, Ryo Konno, Daisuke Nakajima, Mari Gotoh, Keiko Fukasawa, Hironori Sato, Ren Nakamura, Osamu Ohara, Yusuke Kawashima
Summary: In this study, an ultrafast proteomic method was established using a 5-min gradient LC and quadrupole-Orbitrap MS. By optimizing parameters, the method achieved a high throughput and sensitivity for measuring a large number of samples. The method was demonstrated to be applicable for chemical responsivity screening.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Engineering, Biomedical
Masaru Koido, Chung-Chau Hon, Satoshi Koyama, Hideya Kawaji, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Kaoru Ito, Jun Sese, Nicholas F. Parrish, Yoichiro Kamatani, Piero Carninci, Chikashi Terao
Summary: A machine-learning model called MENTR has been developed to link genome sequence and non-coding RNA expression at the cell type level. This model can predict the effects of RNA transcription and identify genetic variants associated with complex traits.
NATURE BIOMEDICAL ENGINEERING
(2023)
Article
Biochemical Research Methods
Yusuke Kawashima, Masaki Ishikawa, Ryo Konno, Daisuke Nakajima, Osamu Ohara
Summary: In this study, a new insertion spray ionization (InSpIon) system was developed, which improved the reproducibility of proteome analysis by stabilizing the spray with a spray tip inserted into the InSpIon tube.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Rheumatology
Hironori Sato, Yuzaburo Inoue, Yusuke Kawashima, Ryo Konno, Osamu Ohara, Masataka Kuwana, Norimoto Kobayashi, Shunichiro Takezaki, Shinji Akioka
Summary: By comprehensively analyzing the proteins in the serum of JDM patients, we identified specific protein expression profiles for muscle-specific autoantibodies (MSAs) associated with different clinical features. We detected numerous proteins related to muscle development and IFN regulation in JDM sera. Pathway analysis revealed a significant upregulation of the type I IFN and proteasome pathways specifically in the anti-MDA5 antibody group. These findings indicate that the pathways associated with clinical features of MSAs vary depending on protein accumulation.
Article
Oncology
Koichiro Kanamori, Kentaro Suina, Takehito Shukuya, Fumiyuki Takahashi, Takuo Hayashi, Kieko Hara, Tsuyoshi Saito, Yoichiro Mitsuishi, Shoko Sonobe Shimamura, Wira Winardi, Ken Tajima, Ryo Ko, Tomoyasu Mimori, Tetsuhiko Asao, Masayoshi Itoh, Hideya Kawaji, Yoshiyuki Suehara, Kazuya Takamochi, Kenji Suzuki, Kazuhisa Takahashi
Summary: This study found that CALML5 gene is significantly upregulated in thymic squamous cell carcinoma compared to type B3 thymoma. Immunohistochemical validation showed that CALML5 has a high sensitivity (73.1%) and specificity (94.7%) as a marker for diagnosing thymic carcinoma.
Letter
Hematology
Yukiko Komeno, Toru Uchiyama, Fuyuko Kawano, Yuya Kurihara, Mineo Kurokawa, Osamu Ohara, Shinji Kunishima, Akira Ishiguro
ANNALS OF HEMATOLOGY
(2023)
