Article
Biotechnology & Applied Microbiology
Rosa E. Cardoza, Susan P. McCormick, Inmaculada Izquierdo-Bueno, Natalia Martinez-Reyes, Laura Lindo, Daren W. Brown, Isidro G. Collado, Robert H. Proctor, Santiago Gutierrez
Summary: The current study identified aspinolide biosynthetic genes (asp1 and asp2) in Trichoderma arundinaceum and found that they are part of a gene cluster shared with Aspergillus ochraceus. Deletion of these genes confirmed their essential role in aspinolide production. Furthermore, a mutation in asp2 led to increased inhibition of fungal growth and coincided with increased HA production, suggesting a trade-off between the two metabolites.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Qizhong Cai, Changzheng Liu, Lu Liu, Yuewei Ge, Xuanxuan Cheng, Bi Luo, Liangyun Zhou, Quan Yang
Summary: In this study, two Uridine-diphosphate-dependent glycosyltransferases (UGTs) were cloned from the transcriptome data of Fallopia multiflora and shown to catalyze the glycosylation of various compounds, leading to the biosynthesis of tranquil glycosides and anthraquinones in the plant.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Xiaomei He, Wenwu Zhang, Irfan Ali Sabir, Chunyan Jiao, Guohui Li, Yan Wang, Fucheng Zhu, Jun Dai, Longyun Liu, Cunwu Chen, Yingyu Zhang, Cheng Song
Summary: In this study, differentially expressed genes involved in the JA signaling pathway were identified and the critical roles of the bHLH family, particularly the MYC2 subfamily, were revealed. Evolutionary analysis showed that whole genome duplication and segmental duplication events drove the expansion and functional divergence of bHLH genes. Multiple sequence alignments demonstrated the presence of conserved domains in all bHLH proteins. Expression profiling and qRT-PCR results suggested that bHLH subgroups IIIe and IIId may have an antagonistic role in the JA-mediated expression of stress-related genes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Meijie Zhang, Wenqi Xu, Huan Mei, Ge Song, Naicen Ge, Ye Tao, Weida Liu, Guanzhao Liang
Summary: This study analyzed the whole genome sequences of 25 species of Mucorales genera and 22 important non-Mucorales pathogenic species to identify target genes for monitoring Mucorales species and potential genomic imprints of virulence. The study found that the virulence-related proteins in Mucorales species varied significantly in copy numbers. This research is important for understanding the mechanisms of mucormycosis and developing prevention and treatment strategies.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yizhou Huang, Jie Luo, Yue Zhang, Tao Zhang, Xiangwei Fei, Liqing Chen, Yingfan Zhu, Songyue Li, Caiyun Zhou, Kaihong Xu, Yunlong Ma, Jun Lin, Jianhong Zhou
Summary: Using integrative analysis of large-scale genome-wide association studies and blood-based eQTL dataset, we identified 14 genes associated with the risk of endometriosis. Functional enrichment analysis revealed their involvement in metabolic and immune-related pathways. Differential gene expression analysis confirmed abnormal expression levels of several genes in peripheral blood samples and ectopic endometrium. Functional experiments further validated MKNK1 and TOP3A as novel risk-related genes for endometriosis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Jennifer Jessica Bruscadin, Taina Figueiredo Cardoso, Wellison Jarles da Silva Diniz, Juliana Afonso, Marcela Maria de Souza, Juliana Petrini, Bruno Gabriel Nascimento Andrade, Vinicius Henrique da Silva, Jose Bento Sterman Ferraz, Adhemar Zerlotini, Gerson Barreto Moura, Luiz Lehmann Coutinho, Luciana Correia de Almeida Regitano
Summary: This study utilized a large dataset of imputed SNP genotypes and RNA-Seq data from Nelore steers to identify ASE SNPs and aseQTLs in muscle, demonstrating the cis-regulatory effect of these variants and discovering numerous novel ASE regions. These findings highlight the potential of using ASE to uncover cis-regulatory SNPs affecting muscle-related traits.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Immunology
Hyun-Sup Song, Soeun Park, Ji-Won Huh, Yu-Ran Lee, Da-Jung Jung, Chorong Yang, So Hyun Kim, Ho Min Kim, You-Me Kim
Summary: Toll-like receptors (TLRs) play critical roles in host defense against pathogens, and UNC93B1 is a protein that affects the proper signaling of TLRs. This study found that glycosylation of a specific asparagine residue in UNC93B1 is required for TLR9 signaling, while it does not affect TLR7 signaling.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Jim Clauwaert, Gerben Menschaert, Willem Waegeman
Summary: The paper introduces a new approach to gather insights on the transcription process in Escherichia coli, utilizing a transformer-based neural network framework to identify transcription factors and characterize their binding sites and consensus sequences.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Cell Biology
Jacob A. Herman, Sonali Arora, Lucas Carter, Jun Zhu, Sue Biggins, Patrick J. Paddison
Summary: In this study, researchers developed a method using CRISPR-Cas9-induced mutations to identify functional regions in protein-coding genes. They applied this method to human mitotic genes and discovered numerous regions required for cell proliferation, including experimentally characterized, homology-predicted, and novel domains.
GENES & DEVELOPMENT
(2022)
Article
Food Science & Technology
Eiseul Kim, Hyeon-Be Kim, Seung-Min Yang, Dayoung Kim, Hae-Yeong Kim
Summary: Identification of specific genes for the Lactobacillus plantarum group through comparative genomics led to the development of an accurate real-time PCR assay for detection. The specificity of primers was confirmed through evaluation on lactic acid bacteria, and the developed assay successfully distinguished and quantified L. plantarum group species or subspecies in probiotic products and fermented food samples.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Chemistry, Analytical
Abigail A. Enders, Nicole M. North, Chase M. Fensore, Juan Velez-Alvarez, Heather C. Allen
Summary: This study develops a generalizable model using machine learning algorithm with convolutional neural networks to identify functional groups in gas-phase FTIR spectra, reducing analysis time and facilitating interpretation. The model successfully trains for 15 common organic functional groups, expanding the application of FTIR measurements for easy analysis of organic samples. The approach utilizes image-based CNNs for predicting functional groups, marking the first implementation of ML in this area.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Dario Kringel, Sebastian Malkusch, Eija Kalso, Jorn Lotsch
Summary: The genetic background of pain is being increasingly well understood, leading to the development of a cost-effective next generation sequencing-based pain-genotyping assay that identifies the most representative genes associated with pain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Yaxing Su, Yanan Xu, Hailing Liang, Gaoqing Yuan, Xiaogang Wu, Dehong Zheng
Summary: This study identified key genes required for R. solanacearum survival in tomato plants using transposon insertion sequencing technology, highlighting the importance of genes related to cell wall/membrane/envelope biogenesis, amino acid transport and metabolism, energy production and conversion, posttranslational modification, protein turnover, and chaperones in the pathogenic mechanism of this bacterium.
Article
Microbiology
Lucas Moriniere, Laurene Mirabel, Erwan Gueguen, Franck Bertolla
Summary: Understanding the molecular interaction between the phytopathogenic bacterium Xanthomonas hortorum pv. vitians and its host lettuce is crucial for disease control efforts. Through transposon insertion sequencing and comparative genomics, this study identified critical genes for the pathogen's fitness during infection. The findings highlight important metabolic pathways and cellular functions for Xanthomonas host adaptation and pathogenesis.
Article
Microbiology
Robert F. Potter, Kailun Zhang, Ben Reimler, Jamie Marino, Carol E. Muenks, Kelly Alvarado, Meghan A. Wallace, Lars F. Westblade, Erin McElvania, Melanie L. Yarbrough, David A. Hunstad, Gautam Dantas, Carey-Ann D. Burnham
Summary: A comparative genomic analysis of 2,060 Proteus genomes revealed significant genetic variation among different subspecies of Proteus mirabilis. These findings are important for a better understanding of the biology and infection mechanisms of Proteus mirabilis.
Review
Clinical Neurology
Daisuke Ito, Satoru Morimoto, Shinichi Takahashi, Kensuke Okada, Jin Nakahara, Hideyuki Okano
Summary: Significant progress has been made in drug screening for amyotrophic lateral sclerosis using patient-derived induced pluripotent stem cells, leading to the identification of candidate drugs and the advancement of clinical trials. This stem cell-based approach shows safety and positive effects, reducing costs and time compared to animal testing.
Article
Biotechnology & Applied Microbiology
Ryota Tamura, Hiroyuki Miyoshi, Kent Imaizumi, Masahiro Yo, Yoshitaka Kase, Tsukika Sato, Mizuto Sato, Yukina Morimoto, Oltea Sampetrean, Jun Kohyama, Munehisa Shinozaki, Atsushi Miyawaki, Kazunari Yoshida, Hideyuki Saya, Hideyuki Okano, Masahiro Toda
Summary: This study demonstrates the potential benefit of gene-edited induced pluripotent stem cells (iPSCs) for the treatment of invasive glioma stem cells (GSCs). Neural stem cells (NSCs) derived from CRISPR/Cas9-edited iPSCs expressing a suicide gene showed enhanced tumor-trophic migratory capacity and significant in vivo antitumor effects. The study also identified key signaling pathways and gene expressions associated with the efficacy of therapeutic iPSC-NSCs.
BIOENGINEERING & TRANSLATIONAL MEDICINE
(2023)
Article
Cell Biology
Satoru Morimoto, Koichi Saeki, Masaru Takeshita, Kunio Hirano, Mariko Shirakawa, Yumiko Yamada, Shiho Nakamura, Fumiko Ozawa, Hideyuki Okano
Summary: The study developed an intranasal vaccine for COVID-19 by using a Sendai virus vector loaded with the receptor binding domain of SARS-CoV-2 as an antigen. The vaccine induced a strong immune response, with increased levels of S-RBD-specific antibodies in serum and bronchoalveolar lavage fluid. The booster dose further enhanced the production of neutralizing antibodies, indicating the effectiveness of the vaccine.
Article
Cell Biology
Sho Yoshimatsu, Mayutaka Nakajima, Iki Sonn, Rie Natsume, Kenji Sakimura, Ena Nakatsukasa, Toshikuni Sasaoka, Mari Nakamura, Takashi Serizawa, Tsukika Sato, Erika Sasaki, Hongkui Deng, Hideyuki Okano
Summary: This study compared the gene expression profiles of mouse, human, and common marmoset EPSCs using transcriptomic approaches. The marmoset EPSC-like cells displayed a distinct morphology but exhibited a pluripotent state similar to embryonic stem cells. They also showed interspecies chimeric contribution to mouse embryos. Furthermore, the gene expression of the marmoset EPSC-like cells resembled that of human EPSCs. Overall, this study evaluated the efficacy of the method for deriving marmoset EPSCs.
Article
Biochemistry & Molecular Biology
Tosho Kondo, Ihori Ebinuma, Hirotaka Tanaka, Yukitoshi Nishikawa, Takaki Komiya, Mitsuru Ishikawa, Hideyuki Okano
Summary: In this study, an effective high-throughput screening system was established using induced pluripotent stem cells (iPSCs) to generate motor neurons. The generated motor neurons exhibited characteristics similar to ALS neurons and showed abnormal protein accumulation and hyperexcitability. Treatment with rapamycin and retigabine normalized activity and improved neuronal survival. This study provides a valuable platform for discovering novel ALS therapeutics and personalized medicine approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yoshimi Kanie, Yuya Maegawa, Yi Wei, Osamu Kanie
Summary: O-Linked alpha-N-acetylgalactosamine (alpha-GalNAc) in Gc protein is crucial for macrophage activation, and the GalNAc-attached form is known as Gc macrophage activating factor (GcMAF). The glycans on Gc protein are hydrolyzed by alpha-Sia-ase and beta-Gal-ase, resulting in the production of GcMAF. In this study, we investigated the protective effects of an iminocyclitol inhibitor against GcMAF by inhibiting alpha-GalNAc-ase activity. Detailed mass spectrometric analyses and tandem mass spectrometric (MS/MS) analysis were performed to study the glycosylation site and glycan structure.
Article
Cell & Tissue Engineering
Shota Okura, Honoka Ishii, Ayano Suzuki, Chika Saegusa, Ko Fujiki, Kenshi Sugano, Noriomi Suzuki, Tsubasa Saeki, Saeko Matsuzaki, Hiroyuki Ozawa, Masato Fujioka, Makoto Hosoya, Hideyuki Okano
Summary: We have established two human-induced pluripotent stem cell (iPSC) lines from individuals without auditory disorders and confirmed normal hearing through extensive audiometry tests. These iPSC lines express pluripotency genes and are capable of differentiating into the three germ layers. They will be used as controls for pathological analysis and drug screening for ear disorders.
STEM CELL RESEARCH
(2023)
Article
Cell & Tissue Engineering
Ryotaro Imai, Ryota Tamura, Masahiro Yo, Mizuto Sato, Mariko Fukumura, Kento Takahara, Yoshitaka Kase, Hideyuki Okano, Masahiro Toda
Summary: Despite limited treatment options for traumatic brain injury (TBI), neural stem/progenitor cells (NS/PCs) derived from induced pluripotent stem cells (iPSCs) expressing yCD-UPRT showed promising results in functional recovery. The transplanted iPSC-derived NS/PCs displayed stable expression of the therapeutic gene and concentrated around the damaged cortex, leading to improved behavioral performance and prevention of secondary brain injury in a TBI mouse model. In addition, selective elimination of undifferentiated NS/PCs using 5-fluorocytosine (5-FC) demonstrated the safety of this regenerative medicine approach.
Article
Biology
Miho Isoda, Tsukasa Sanosaka, Ryo Tomooka, Yo Mabuchi, Munehisa Shinozaki, Tomoko Andoh-Noda, Satoe Banno, Noriko Mizota, Ryo Yamaguchi, Hideyuki Okano, Jun Kohyama
Summary: A single-cell approach identified cellular properties of neural and mesenchymal origins in human induced pluripotent stem cells, shedding light on the causes of undesired grafts after transplantation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Immunology
Emi Qian, Masahiro Uemura, Hiroya Kobayashi, Shiho Nakamura, Fumiko Ozawa, Sho Yoshimatsu, Mitsuru Ishikawa, Osamu Onodera, Satoru Morimoto, Hideyuki Okano
Summary: CARASIL is a inherited small vessel disease caused by mutations in the HTRA1 gene. Heterozygous mutations in HTRA1 have been found to cause clinical features of the disease. Researchers have successfully established a hiPSC line from a patient with heterozygous HTRA1-related CSVD, which has normal morphology and karyotype. The hiPSCs expressed pluripotency-related markers and had the ability to differentiate into all three germ layers in vitro, providing a valuable tool for studying the cellular mechanisms of HTRA1 mutation.
INFLAMMATION AND REGENERATION
(2023)
Article
Biochemistry & Molecular Biology
Hitomi Ono-Minagi, Tsutomu Nohno, Takashi Serizawa, Yu Usami, Takayoshi Sakai, Hideyuki Okano, Hideyo Ohuchi
Summary: This study investigates the embryonic origin of salivary and lacrimal glands using transgenic mice and demonstrates that these glands contain cells derived from all three germ layers. Specifically, a subset of cells derived from neural crest differentiate into epithelial cells and express high levels of stem cell markers. These cells play an important role in the regenerative response following tissue damage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Clinical Neurology
Hiroya Kobayashi, Koji Ueda, Satoru Morimoto, Mitsuru Ishikawa, Nicolas Leventoux, Ryogen Sasaki, Yoshifumi Hirokawa, Yasumasa Kokubo, Hideyuki Okano
Summary: The proteins in extracellular vesicles derived from astrocytes in patients with Kii ALS/PDC exhibit distinctive patterns compared to healthy individuals, with increased proteins related to proteostasis and decreased proteins related to anti-inflammation.
NEUROLOGICAL SCIENCES
(2023)
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
Tiejun Cheng, Tamiko Ono, Masaaki Shiota, Issaku Yamada, Kiyoko F. Aoki-Kinoshita, Evan E. Bolton
Summary: The GlyCosmos Glycoscience Portal and PubChem are two major portals for glycoscience and chemistry, respectively. They have made efforts to integrate their complementary data, allowing users to easily access and utilize glycan-related information. This integration provides improved awareness and enhanced access to glycan-related information for life science researchers.
Review
Biochemistry & Molecular Biology
Hideyuki Okano, Satoru Morimoto, Chris Kato, Jin Nakahara, Shinichi Takahashi
Summary: In recent years, clinical trials using iPSC technology for disease modeling and drug discovery have shown promising results, particularly for the treatment of ALS. ROPi has been identified as a potential ALS treatment and has undergone clinical trials and reverse translational research, demonstrating its ability to delay disease progression and prolong survival in ALS patients.
JOURNAL OF NEUROCHEMISTRY
(2023)