Article
Biotechnology & Applied Microbiology
Mengjia Zhang, Nansheng Chen
Summary: This study constructed the complete chloroplast genomes of seven Thalassionema strains, revealing genetic differences within and between species. Additionally, the study identified genomic differences between Thalassionema species and other diatoms. The study also provided insights into the phylogenetic position and emergence time of Thalassionema species.
Article
Plant Sciences
Yichao Wang, Shuya Liu, Jing Wang, Yanxin Yao, Yang Chen, Qing Xu, Zengxia Zhao, Nansheng Chen
Summary: Mitochondrial genomes can be used as super barcodes to distinguish diatom species with higher resolution compared to common molecular markers. Comparative analysis of mitochondrial genomes revealed extensive genome rearrangement events and showed their value in evolutionary studies.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Munehisa Shimamura, Koichi Kaikita, Hironori Nakagami, Tomohiro Kawano, Nan Ju, Hiroki Hayashi, Ryo Nakamaru, Shota Yoshida, Tsutomu Sasaki, Hideki Mochizuki, Kenichi Tsujita, Ryuichi Morishita
Summary: Researchers redesigned an S100A9 vaccine that successfully produced antibodies and showed anti-thrombotic effects in cynomolgus monkeys. The vaccine was able to neutralize the anti-thrombotic effects of the produced antibodies and did not prolong bleeding time in vaccinated monkeys. Further studies are needed to enhance the vaccine's effectiveness and safety, but it may offer a promising approach to improving adherence to antiplatelet drugs in clinical settings.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Jinghui Zheng, Xiaobo Wang, Tong Feng, Saif ur Rehman, Xiuying Yan, Huiquan Shan, Xiaocong Ma, Weiguan Zhou, Wenhua Xu, Liying Lu, Jiasheng Liu, Xier Luo, Kuiqing Cui, Chaobin Qin, Weihua Chen, Jun Yu, Zhipeng Li, Jue Ruan, Qingyou Liu
Summary: The genomes of three leech species were sequenced and assembled, and it was found that bloodsucking leeches have enhanced auditory sense and genes related to anticoagulation, analgesia, and anti-inflammation. The expanded gene families in bloodsucking leeches may aid in body swelling and storing prey blood. The findings are important for leech culture and strain optimization.
Article
Multidisciplinary Sciences
Jason Pugh, Lisbeth Guethlein, Peter Parham
Summary: KIR3DL2 is an inhibitory NK cell receptor that recognizes a common epitope of human and pathogen DNA, allowing NK cells to differentiate between self and pathogen DNA and respond accordingly to activate immune responses.
Article
Biochemical Research Methods
Le Zhang, Zichun Dai, Jun Yu, Ming Xiao
Summary: By reviewing previous studies on CpG-related genes, it is suggested that approximately half of human genes, particularly housekeeping genes, are regulated by CpG islands (CGIs). However, the specific definition of CGIs, their positioning in gene structures, and the regulatory mechanisms associated with CGIs require further explanation. Combining different analysis methods, it has been found that genes associated with high CpG density are more likely to be housekeeping genes, while the characteristics of genes with intermediate CpG density are less distinct.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Xiaoyu Zhuo, Alan Y. Du, Erica C. Pehrsson, Daofeng Li, Ting Wang
Summary: This study investigated the association between epigenomic differences between human and chimpanzee and lineage-specific indels, revealing that different types of indels are associated with specific epigenomic diversity between the two species.
Article
Biology
Remi Allio, Marie-Ka Tilak, Celine Scornavacca, Nico L. Avenant, Andrew C. Kitchener, Erwan Corre, Benoit Nabholz, Frederic Delsuc
Summary: In the context of ongoing biodiversity erosion, genomic resources from wildlife are crucial for conservation efforts. This study utilized roadkill samples to investigate the genetic diversity of the bat-eared fox and aardwolf, revealing potential new species within the aardwolf taxon through a novel Genetic Differentiation index. The research also generated a genome-wide Carnivora phylogeny that includes the newly identified aardwolf species.
Article
Genetics & Heredity
Sawsan Sami Wehbi, Heinrich Zu Dohna
Summary: The study used comparative methods to estimate parameters for the evolution of retrotransposition rates and inferred L1 dynamics. The results showed a positive correlation between new L1 emergence rates in the human population and cell-culture based retrotransposition activities, along with an evolutionary trend towards lower retrotransposition activity. However, this trend is insufficient to counterbalance the increase in active L1s resulting from continuing retrotransposition.
Article
Environmental Sciences
Ziyan He, Yang Chen, Yichao Wang, Kuiyan Liu, Qing Xu, Yang Li, Nansheng Chen
Summary: This study reports the full-length chloroplast genomes of nine Pseudo-nitzschia species and investigates their genomic structures and features. The findings provide critical genomic resources for future research on the biodiversity and speciation of Pseudo-nitzschia species.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Qing Xu, Zongmei Cui, Nansheng Chen
Summary: This study constructed full-length chloroplast genomes for seven Chaetoceros species, revealing their conserved genome arrangement and specific divergence. The availability of these cpDNAs provides valuable reference sequences for studying the evolutionary relationships among Chaetoceros species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Horticulture
Maria Gladysheva-Azgari, Fedor Sharko, Natalia Slobodova, Kristina Petrova, Eugenia Boulygina, Svetlana Tsygankova, Irina Mitrofanova
Summary: The study aimed to investigate the plastid genomes of Actinidia species and found that the gene composition and sequences are conserved. However, some species showed significant structural rearrangements in their chloroplast chromosomes, resulting in the presence of two main forms.
Article
Biochemistry & Molecular Biology
Xavier Farre, Ruben Molina, Fabio Barteri, Paul R. H. J. Timmers, Peter K. Joshi, Baldomero Oliva, Sandra Acosta, Borja Esteve-Altava, Arcadi Navarro, Gerard Muntane
Summary: The study identified amino acid changes and genes related to longevity in mammals, with pathways involved in regulating lifespan. It also found that certain genes explain a larger fraction of human lifespan heritability than expected, with longevity-associated proteins being significantly more stable. Overall, the research demonstrates the potential of comparative genomics in enhancing understanding of human genome-wide association studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Ignacio Vasquez, Ahmed Hossain, Hajarooba Gnanagobal, Katherinne Valderrama, Briony Campbell, Michael Ness, Steve J. Charette, Anthony K. Gamperl, Rocco Cipriano, Cristopher Segovia, Javier Santander
Summary: In this study, the complete closed genomes of four Aeromonas salmonicida strains were sequenced and compared to elucidate their molecular diversity and pathogenic evolution. The genomic differences between typical and atypical strains were found to be mainly related to insertion sequences (ISs) activity. The relationship between phenotype and A. salmonicida subspecies' taxonomy was not evident.
Article
Chemistry, Multidisciplinary
Li-Juan Wang, Qian Han, Jian-Ge Qiu, Chun-Yang Zhang
Summary: A nanodevice for one-step detection of CpG methylation with high specificity and sensitivity was demonstrated, capable of detecting very low methylation levels in vitro and distinguishing methylation levels in different tumor cells in vivo.
Article
Plant Sciences
Shiori S. Aki, Kei Yura, Takashi Aoyama, Tomohiko Tsuge
Summary: The COP9 signalosome (CSN) complex in Arabidopsis thaliana governs various developmental processes, with a specific CSN1 subunit transgenic plant showing defects in pollen development related to SAP130. Analysis of their interaction revealed that approximately 100 amino-acid residues at the N-terminal end of CSN1 are essential for the interaction, supporting a model where CSN1 embeds itself in the complex and reaches out to targets through its N-terminal portion. This study is the first to document the identical loss-of-function phenotypes of CSN1 and SAP130 during male gametogenesis, suggesting coordinated regulation of male reproductive organ development by SAP130 and CSN1.
JOURNAL OF PLANT RESEARCH
(2021)
Article
Biology
Keiichi Inoue, Masayuki Karasuyama, Ryoko Nakamura, Masae Konno, Daichi Yamada, Kentaro Mannen, Takashi Nagata, Yu Inatsu, Hiromu Yawo, Kei Yura, Oded Beja, Hideki Kandori, Ichiro Takeuchi
Summary: Inoue, Takeuchi and colleagues propose a machine learning-based protocol to screen rhodopsins for their likelihood to be red-shifted. After experimental verification, their tool shows remarkable success at identifying rhodopsins that showed red-shift gains.
COMMUNICATIONS BIOLOGY
(2021)
Correction
Biology
Keiichi Inoue, Masayuki Karasuyama, Ryoko Nakamura, Masae Konno, Daichi Yamada, Kentaro Mannen, Takashi Nagata, Yu Inatsu, Hiromu Yawo, Kei Yura, Oded Beja, Hideki Kandori, Ichiro Takeuchi
COMMUNICATIONS BIOLOGY
(2021)
Article
Plant Sciences
Xiaojuan Zhang, Mika Nomoto, Marta Garcia-Leon, Naoki Takahashi, Mariko Kato, Kei Yura, Masaaki Umeda, Vicente Rubio, Yasuomi Tada, Tsuyoshi Furumoto, Takashi Aoyama, Tomohiko Tsuge
Summary: This study found that the plant CFI 25 subunit plays an important role in maintaining the diversity of mRNA 3' ends. Multiple forms of CFI exist in plants, and AtCFI 25a is essential for maintaining the proper diversity of 3' end lengths of transcripts coding for CFI subunits and plays important roles in Arabidopsis development.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu
Summary: Protein Data Bank Japan (PDBj), a founding member of the worldwide Protein Data Bank (wwPDB), has continuously improved and expanded its query search interface and services over the past 20 years, making significant contributions to the acceptance, processing, and distribution of experimentally determined biological macromolecular structures. During the COVID-19 pandemic, PDBj has also provided feature pages for COVID-19 related entries and outreach content for high school students and teachers.
Article
Multidisciplinary Sciences
Saki Aoto, Mayumi Hangai, Hitomi Ueno-Yokohata, Aki Ueda, Maki Igarashi, Yoshikazu Ito, Motoko Tsukamoto, Tomoko Jinno, Mika Sakamoto, Yuka Okazaki, Fuyuki Hasegawa, Hiroko Ogata-Kawata, Saki Namura, Kazuaki Kojima, Masao Kikuya, Keiko Matsubara, Kosuke Taniguchi, Kohji Okamura
Summary: Deep learning has permeated many aspects of human life, particularly image recognition using convolutional neural networks. However, the need for big data and laborious manual annotation often hinders the application of deep learning. To address this issue, we collected 2429 constrained headshot images of 277 volunteers and established an online procedure to obtain informed consent and image data.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Keigo Ide, Yohei Nishikawa, Toru Maruyama, Yuko Tsukada, Masato Kogawa, Hiroki Takeda, Haruka Ito, Ryota Wagatsuma, Rimi Miyaoka, Yoshikatsu Nakano, Koji Kinjo, Michihiro Ito, Masahito Hosokawa, Kei Yura, Shoichiro Suda, Haruko Takeyama
Summary: This study utilized a novel single-cell genomics technique to obtain the genomes of uncultured coral-associated Endozoicomonas spp. and discovered that different Endozoicomonas species may have varying host adaptation strategies and functional potentials.
Article
Genetics & Heredity
Hidetaka Uryu, Ohsuke Migita, Minami Ozawa, Chikako Kamijo, Saki Aoto, Kohji Okamura, Fuyuki Hasegawa, Torayuki Okuyama, Motomichi Kosuga, Kenichiro Hata
Summary: Fabry disease is a rare congenital lysosomal storage disease that is difficult to diagnose early. In this study, a deep neural network model was built using artificial intelligence and a novel image amplification method to detect Fabry disease from urine samples, achieving high sensitivity and specificity.
MOLECULAR GENETICS AND METABOLISM REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Masatada Tamakoshi, Atsushi Hijikata, Kei Yura, Kenshiro Oshima, Hidehiro Toh, Kaoru Mitsuoka, Tairo Oshima, Yoshitaka Bessho
Summary: A Thermus thermophilus lytic phage OMN1 was isolated from a Japanese hot spring. OMN1 has a unique morphology, with an icosahedral head and a contractile tail, and belongs to Myoviridae family. The receptor molecules for the phage were uniformly distributed on the outer surface of the host cells. Analysis of the OMN1 genome revealed the presence of DNA fragments from different origins, suggesting a gradual evolution through gene recombination for host cell adaptation. This newly isolated phage provides important insights into the evolution of thermophilic phages.
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Atsushi Hijikata, Tairo Oshima, Kei Yura, Yoshitaka Bessho
Summary: ThermusQ is a website that aims to gather and provide molecular information on Thermus thermophilus bacterium. It includes genome sequences of various strains and phages, and offers tools for retrieving sequence data. The website enables researchers to identify strain-specific characteristics and missing important data.
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Koyu Hon-nami, Atsushi Hijikata, Kei Yura, Yoshitaka Bessho
Summary: In this study, the confirmation of 19 c-type cytochromes among 27 selected genes in thermophilic microorganisms was described. The analysis of these genes using a bioinformatics approach revealed the presence of unique beta-strands in the c-type cytochrome domains of Thermus, leading to the proposal of new names for these genes.
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Ryo Yokomizo, Tiago J. S. Lopes, Nagisa Takashima, Sou Hirose, Ayako Kawabata, Masataka Takenaka, Yasushi Iida, Nozomu Yanaihara, Kei Yura, Haruhiko Sago, Aikou Okamoto, Akihiro Umezawa
Summary: The study analyzed pathological images of OCCC and used machine learning to establish a classifier that accurately predicted recurrence, progression-free survival, and overall survival of patients, providing valuable prognosis information and assisting in personalized treatment strategies.
BIOINFORMATICS AND BIOLOGY INSIGHTS
(2022)
Article
Ecology
Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Ryota Wagatsuma, Katsuhiko Mineta, Kai Takahashi, Keigo Ide, Kei Yura, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama
Summary: An improved single-cell genomics platform, SAG-gel, was developed to overcome the limitations of current metagenomics. By using gel beads, SAG-gel achieved efficient single-cell isolation, lysis, and whole genome amplification. The versatility of SAG-gel was validated through single-cell genome sequencing of model bacteria and environmental samples. The results showed improved genome coverage and revealed virus-host linkages.
ISME COMMUNICATIONS
(2022)
Article
Biophysics
Ha T. T. Duong, Hirofumi Suzuki, Saki Katagiri, Mayu Shibata, Misae Arai, Kei Yura
Summary: Sequencing individual human genomes allows for studying the relationship between nucleotide variations, amino acid substitutions, their effects on protein structures and diseases. This study focuses on actin, a highly conserved protein, and finds that variations on the surface of the protein tend to be pathogenic, while variations buried inside the protein are more benign.
BIOPHYSICS AND PHYSICOBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Masato Kogawa, Rimi Miyaoka, Franziska Hemmerling, Masahiro Ando, Kei Yura, Keigo Ide, Yohei Nishikawa, Masahito Hosokawa, Yuji Ise, Jackson K. B. Cahn, Kentaro Takada, Shigeki Matsunaga, Tetsushi Mori, Joern Piel, Haruko Takeyama
Summary: This study presents an analysis pipeline for the efficient identification of uncultivated producers in the microbiomes, highlighting the importance of complementary technologies. It reveals a new bacterium as the producer of previously unassigned antifungal compounds in a chemically rich bacteriosponge, suggesting an even higher chemical richness than previously appreciated. The research also shows remarkable parallels between distantly related symbionts of the same host and adds functional support for diverse chemically prolific lineages in microbial dark matter.