Review
Biochemistry & Molecular Biology
Jitendra Kumar, Ayyagari Ramlal, Kamal Kumar, Anita Rani, Vachaspati Mishra
Summary: Phytopathogens, such as biotrophs, hemibiotrophs, and necrotrophs, pose serious stress on host plants, which need to develop immunity to counter these attacks. Plants utilize pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) to recognize and combat phytopathogens.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Ana R. Lopez-Perez, Piotr J. Balwierz, Boris Lenhard, Ferenc Muller, Fiona C. Wardle, Isabelle Manfroid, Marianne L. Voz, Bernard Peers
Summary: In this study, the gene regulatory network triggered by retinoic acid (RA) in the endoderm of zebrafish was investigated using RNA-seq, RAR ChIP-seq, and ATAC-seq assays. The findings identified a set of genes and regulatory regions regulated by RA signaling, defined direct RAR target genes in zebrafish, revealed conserved direct target genes between zebrafish and mice, and unveiled the role of the RAR-direct targets in chromatin accessibility upon RA treatment.
SCIENTIFIC REPORTS
(2021)
Review
Cell Biology
Wei Shen, Jiaxin Huang, Yan Wang
Summary: The article reviews the mechanisms of establishing different levels of NOTCH signaling strength, the developmental processes sensitive to perturbations in NOTCH signaling strength, and the transcriptional regulations affected by changes in NOTCH signaling strength. It is hoped that this will provide a new layer of diversity to explain the pleotropic functions of the NOTCH signaling pathway.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Developmental Biology
Jessica M. Kraus, Dion Giovannone, Renata Rydzik, Jeremy L. Balsbaugh, Isaac L. Moss, Jennifer L. Schwedler, Julien Y. Bertrand, David Traver, Kurt D. Hankenson, J. Gage Crump, Daniel W. Youngstrom
Summary: This study shows that Notch signaling is induced during the early stages of bone healing and its modulation can affect the size and quality of bone regeneration. The findings suggest that targeting Notch signaling may provide a new strategy to enhance bone healing in mammals.
Article
Biochemistry & Molecular Biology
Hung-Yu Shih, Chia-Wei Chang, Yi-Chieh Chen, Yi-Chuan Cheng
Summary: Bone morphogenetic protein (BMP) signaling plays a crucial role in the regulation of neural induction, neuronal specification, and neuronal differentiation. However, its role in neural progenitors is still not well understood. By manipulating BMP signaling in zebrafish embryos, researchers discovered that inhibiting BMP signaling during gastrulation can increase the proliferation of neural progenitors and decrease the number of neuronal precursors. This study also revealed that there is a fine balance between BMP and Notch signaling in regulating the proliferation of neural progenitor cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Developmental Biology
Yukino Wada, Hikaru Tsukatani, Chihiro Kuroda, Yurika Miyazaki, Miku Otoshi, Isao Kobayashi
Summary: This study identifies a previously unknown spatiotemporal regulatory mechanism of hematopoietic stem cell specification by somites in zebrafish, in which Jag2b-induced Notch signaling leads to the expression of wnt16 and HSC markers.
Article
Toxicology
Dou Yang, Juhua Xiao, Mengqi Wan, Jieping Liu, Ling Huang, Xue Li, Li Zhang, Fasheng Liu, Desheng Liang, Yongliang Zheng, Baogang Xie, Xinjun Liao, Guanghua Xiong, Huiqiang Lu, Zigang Cao, Shouhua Zhang
Summary: This study investigated the effects of roxadustat on early embryonic development using zebrafish. The results showed that roxadustat exposure caused abnormal embryonic development and liver metabolic imbalance in zebrafish embryos. Additionally, roxadustat down-regulated Notch signaling, which contributed to hepatotoxicity. This research provides valuable insights for the clinical use of roxadustat.
JOURNAL OF APPLIED TOXICOLOGY
(2023)
Article
Medicine, Research & Experimental
Ludovica Cotellessa, Federica Marelli, Paolo Duminuco, Michela Adamo, Georgios E. . Papadakis, Lucia Bartoloni, Naoko Sato, Mariarosaria Lang-Muritano, Amineh Troendle, Waljit S. . Dhillo, Annamaria Morelli, Giulia Guarnieri, Nelly Pitteloud, Luca Persani, Marco Bonomi, Paolo Giacobini, Valeria Vezzoli
Summary: Fertility in vertebrate species is controlled by GnRH neurons, which arise outside the central nervous system and migrate into the forebrain during development. Genetic disorders associated with infertility, such as CHH and Kallmann syndrome, are characterized by defects in GnRH neuron migration. The study found that Jag1/Notch signaling is involved in the development of GnRH neurons, and JAG1 insufficiency may contribute to the pathogenesis of CHH in humans.
Article
Genetics & Heredity
Ana Paula Azambuja, Marcos Simoes-Costa
Summary: The neural crest, a migratory stem cell population crucial in vertebrate embryo development, undergoes sequential gene expression changes during its formation, leading to progressive fate restriction. A gene circuit involving SP5 and AXUD1 downstream of the Wnt signaling pathway controls the temporal activation of neural crest genes, with inhibitory interactions preventing overlap between transcriptional states. This study highlights the importance of repressive interactions in the neural crest gene regulatory network and the temporal segregation of genes activated by the same upstream signal during fate restriction.
Article
Multidisciplinary Sciences
Hailun Zhu, Sihai Dave Zhao, Alokananda Ray, Yu Zhang, Xin Li
Summary: In this study, the authors used single-cell RNA sequencing to analyze the gene expression patterns in Drosophila neural progenitors and identified a gene regulatory network that controls the sequential generation of different neural types. They discovered previously unknown temporal transcription factors and characterized their roles in temporal patterning and neuronal specification. The study provides insights into the mechanisms involved in the temporal patterning of neural progenitors.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Markus Westphal, Paolo Panza, Edda Kastenhuber, Johanna Wehrle, Wolfgang Driever
Summary: Wnt/β-catenin signaling plays a crucial role in the development of dopaminergic neurons in zebrafish, specifically in the formation of the Otp-dependent dopaminergic neuron group. The activity of Wnt/β-catenin signaling promotes dopaminergic development during the proliferative stage of dopaminergic progenitor cells.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Yanjun Zong, Yuanyao Chen, Yongfeng Wang, Jingming Wang, Zhiquan Yu, Zixuan Ou, Jinyu Chen, Huiping Zhang, Chunyan Liu
Summary: This study reveals the cardiotoxicity of p,p'-DDE in zebrafish embryos and suggests its association with the JAK-STAT and Notch signaling pathways.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Developmental Biology
Sriivatsan G. Rajan, Lynne M. Nacke, Jagjot S. Dhingra, Ankur Saxena
Summary: This study in zebrafish identified the earliest time window of olfactory MCC differentiation, showing that OMCC cells derive from peridermal cells and are regulated by the Notch signaling pathway. The research also found regionally segregated Notch signaling regulates the number of OMCCs and the differentiation-associated genes during olfactory development.
CELLS & DEVELOPMENT
(2021)
Article
Oncology
Meimei Lin, Hengfen Dai, Lanlan Zheng, Peiqing Yu, Yan Chen, Ru Hong, Caiyun Zheng
Summary: This study found that Tryptanthrin can inhibit tumor growth by down-regulating Dll4 protein expression and up-regulating the expression of desma and Tnnt2c genes.
TRANSLATIONAL CANCER RESEARCH
(2023)
Article
Oncology
Giovanni Tossetta, Sonia Fantone, Rosaria Gesuita, Gaia Goteri, Martina Senzacqua, Fabio Marcheggiani, Luca Tiano, Daniela Marzioni, Roberta Mazzucchelli
Summary: Prostate cancer is a major cancer affecting men and can be treated with different therapies depending on the stage. IL-6 has been established as a key player in prostate cancer, while the role of CNTF in prostate cancer is less understood. This study found that CNTF is expressed in prostate cancer tissues and reduced the expression of MMP-2 and GLUT-1 through MAPK/ERK, AKT/PI3K, and Jak/STAT pathways in a castration-resistant prostate cancer model.
Letter
Hematology
Yoko Nishinaka-Arai, Akira Niwa, Shiori Matsuo, Yasuhiro Kazuki, Yuwna Yakura, Takehiko Hiroma, Tsutomu Toki, Tetsushi Sakuma, Takashi Yamamoto, Etsuro Ito, Mitsuo Oshimura, Tatsutoshi Nakahata, Megumu K. Saito
Article
Developmental Biology
Alice Pieplow, Meseret Dastaw, Tetsushi Sakuma, Naoaki Sakamoto, Takashi Yamamoto, Mamiko Yajima, Nathalie Oulhen, Gary M. Wessel
Summary: Researchers are exploring the manipulation of gene function through CRISPR-Cas9 editing of cis-regulatory sequences, aiming to minimize the side effects of typical mutations in coding regions. This approach allows for reducing gene activity without causing lethality from complete gene knockouts, and is also effective in rapidly identifying key regulatory sites essential for gene expression. The study further demonstrated this strategy by targeting established genomic cis-regulatory regions and utilizing a deadCas9-VP64 transcriptional activator to modulate gene transcription directly. Additionally, a traditional GFP reporter construct approach was paired with CRISPR-Cas9 to investigate the transcriptional regulation of a key gene in the sea urchin, providing insights into the potential post-transcriptional mechanisms behind its germ cell identity.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Anatomy & Morphology
Minami Ezawa, Fumika Kouno, Hideo Kubo, Tetsushi Sakuma, Takashi Yamamoto, Tsutomu Kinoshita
Summary: In Xenopus development, Pou5f3.3 plays a crucial role in establishing and maintaining hematopoietic progenitor cells, contributing to the regulation of peripheral blood cell homeostasis. Transplantation experiments demonstrate the migration of Pou5f3.3-positive cells from the hematopoietic dorsal-lateral plate to the liver and bone through the bloodstream, highlighting its significance in hematopoiesis.
Article
Engineering, Marine
Dipak Pandey, Takahiro Matsubara, Taiju Saito, Yukinori Kazeto, Koichiro Gen, Tetsushi Sakuma, Takashi Yamamoto, Miyuki Mekuchi, Rie Goto
Summary: The study utilized TALEN technology to achieve gene knockout in the kawakawa slc24a5 gene, investigating gene expression and functional differences, revealing association with melanin pigment formation. Experimental results showed that most TALEN-induced mutants exhibited mosaic patterns in retinal pigment epithelium cells.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2021)
Article
Cell Biology
Kaichi Watanabe, Yuhei Yasui, Yuta Kurose, Masashi Fujii, Takashi Yamamoto, Naoaki Sakamoto, Akinori Awazu
Summary: This study investigated the process of gastrulation in sea urchin embryos and found that omeprazole may induce partial exogastrulation by disrupting the apical-basal polarity of F-actin distribution.
Article
Biochemistry & Molecular Biology
Mohamed Nabil Bakr, Haruko Takahashi, Yutaka Kikuchi
Summary: By using gene expression signature classification and Cox regression analyses, a prognosis-related gene signature for melanoma was established and validated in multiple datasets, showing potential for predicting prognosis in melanoma patients.
Review
Oncology
Haruko Takahashi, Daisuke Kawahara, Yutaka Kikuchi
Summary: This review provides an overview of the tissue transparency techniques, optical observation methods, spatial transcriptomic analysis, and noninvasive medical imaging methods used for understanding malignant breast cancers. Understanding the structure and gene expression of breast cancer tissues, and their relationship to malignant transformation and metastasis, is essential. Recent technological advances in tissue-clearing methods combined with optical three-dimensional imaging have allowed for better analysis of breast cancer tissue structure. Noninvasive photoacoustic imaging methods have also provided valuable three-dimensional imaging features of breast cancer tissues.
Article
Medicine, General & Internal
Daisuke Kawahara, Ikuno Nishibuchi, Masashi Kawamura, Takahito Yoshida, Iemasa Koh, Katsuyuki Tomono, Masaki Sekine, Haruko Takahashi, Yutaka Kikuchi, Yoshiki Kudo, Yasushi Nagata
Summary: This study used radiomics features from T1- and T2-weighted MR images to predict the recurrence of cervical cancer patients treated with radiotherapy. The combination of T1- and T2-weighted MR images had the highest accuracy and sensitivity for predicting recurrence.
Article
Multidisciplinary Sciences
Masaki Shirai, Kazuya Takayama, Haruko Takahashi, Yudai Hirose, Masashi Fujii, Akinori Awazu, Nobuyoshi Shimoda, Yutaka Kikuchi
Summary: Genomic DNA methylation is an epigenetic marker regulated by DNA methyltransferases. A zebrafish model for DNA methylation research was created using the CRISPR/Cas9 genome-editing system. Whole-genome bisulfite sequencing revealed differentially methylated regions in the mutant compared to the wild-type fish.
Article
Gastroenterology & Hepatology
Tomoki Takashina, Akihiro Matsunaga, Yukiko Shimizu, Tetsushi Sakuma, Tadashi Okamura, Kunie Matsuoka, Takashi Yamamoto, Yukihito Ishizaka
Summary: A protein-based artificial transcription system was developed to engineer hepatocyte-like cells from human umbilical cord-derived mesenchymal stem cells. The engineered cells exhibited functional and molecular characteristics similar to hepatocytes, and significantly improved the survival rate in mice with hepatic failure. This transcription system could serve as a versatile tool for cell therapy for hepatic failures.
HEPATOLOGY COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Masaki Shirai, Nobuyoshi Shimoda, Haruko Takahashi, Kazuya Takayama, Yutaka Kikuchi
Summary: DNA methylation is a type of epigenetic regulation mediated by DNA methyltransferases (Dnmts), which control gene expression in vertebrates. The two types of de novo Dnmts, Dnmt3a and Dnmt3b, function in DNA methylation in different or overlapping genomic regions. In zebrafish, the homologs of Dnmt3a are Dnmt3aa and Dnmt3ab. Knock-out of dnmt3aa in zebrafish development alters gene expression, as revealed by microarray analysis. The generated transcriptome datasets from the dnmt3aa-deficient mutant may be useful for comparative analysis and studying human diseases caused by DNMT3A.
Article
Biochemistry & Molecular Biology
Mohamed Nabil Bakr, Haruko Takahashi, Yutaka Kikuchi
Summary: Through bioinformatics analysis, we found that CHRNA1 is highly expressed in metastatic melanoma samples compared to primary melanoma samples and is strongly associated with CHRNB1 and CHRNG. These muscle-type nicotinic acetylcholine receptors are correlated with ZEB1 and Rho/ROCK pathway-related genes in metastatic melanoma samples.
BIOCHEMISTRY AND BIOPHYSICS REPORTS
(2023)
Article
Materials Science, Biomaterials
Haruko Takahashi, Yutaka Kikuchi
Summary: This study introduced a novel 3D in vitro cancer-stroma co-culture system for analyzing interactions between cancer cells and surrounding cells within the tumor microenvironment. It demonstrated the phenotypic and morphological changes of fibroblasts into activated myofibroblasts, leading to cancer cell migration. The system also allows quantitative assessment of oncogenic or medicinal additives, providing insights into potential applications for analyzing crosstalk among cancer tissue-constructing cells and evaluating substances inducing tumorigenesis or inhibiting cancer progression.
BIOMATERIALS SCIENCE
(2021)
Meeting Abstract
Oncology
Yukihito Ishizaka, Yoichi Teratake, Tetsushi Sakuma, Takashi Yamamoto
Meeting Abstract
Oncology
Takuya Fukazawa, Etsuko Yokota, Tetsushi Sakuma, Yoshio Naomoto, Takashi Yamamoto, Tomoki Yamatsuji
