Article
Multidisciplinary Sciences
Rie Seyama, Masashi Nishikawa, Yuri Uchiyama, Keisuke Hamada, Yuka Yamamoto, Masahiro Takeda, Takanori Ochi, Monami Kishi, Toshifumi Suzuki, Kohei Hamanaka, Atsushi Fujita, Naomi Tsuchida, Eriko Koshimizu, Kazuharu Misawa, Satoko Miyatake, Takeshi Mizuguchi, Shintaro Makino, Takashi Yao, Hidenori Ito, Atsuo Itakura, Kazuhiro Ogata, Koh-ichi Nagata, Naomichi Matsumoto
Summary: This study identified a rare RAC1 variant in a male patient, resulting in multiple anomalies and respiratory failure leading to death. The variant may deactivate downstream signals and affect normal cellular functions.
SCIENTIFIC REPORTS
(2023)
Article
Cell Biology
Luis Antonio Menezes Carreira, Dobromir Szadkowski, Franziska Muller, Lotte Sogaard-Andersen
Summary: Bacterial cells establish and invert the front-rear polarity of movement through the polarity module and the chemosensory system. The polarity module includes MglA, GEF, and GAP, which asymmetrically localize to the cell poles, while the chemosensory system interacts with the proteins of the polarity module, triggering their polar repositioning and causing irregular oscillation of the cells.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Cell Biology
Siarhei Hladyshau, Jorik P. Stoop, Kosei Kamada, Shuyi Nie, Denis Tsygankov
Summary: Rho-GTPases play a central role in regulating cytoskeletal organization and cell movement. Using a simulation model, we investigated the relationship between Rac1 and Cdc42 during membrane ruffling and observed GTPase behavior. Our model showed that membrane velocity is regulated by GTPase activation kinetics rather than concentration. We also demonstrated that cell-type specific delays between Rac1 and Cdc42 activation can be reproduced using a signaling motif involving feedback from Cdc42 to Rac1.
Article
Oncology
Qun Chen, Jing Jin, Xin Huang, Fan Wu, Hongguang Huang, Renya Zhan
Summary: The study found that EMP3 plays a critical role in immune modulation in GBM by affecting macrophage polarization and recruitment, leading to suppression of T cell infiltration into tumors and facilitating tumor progression. This suggests that EMP3 could be a potential therapeutic target for GBM treatment.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Ting Wang, Manivannan Yegambaram, Christine Gross, Xutong Sun, Qing Lu, Hui Wang, Xiaomin Wu, Archana Kangath, Haiyang Tang, Saurabh Aggarwal, Stephen M. Black
Summary: The study reveals that nitration of Rac1 plays a crucial role in its inhibition in acute lung injury, and the use of nitration shielding peptide NipR2 can alleviate the pathogenesis and prevent lung function loss.
Article
Oncology
Maria Kalli, Ruxuan Li, Gordon B. Mills, Triantafyllos Stylianopoulos, Ioannis K. Zervantonakis
Summary: Mechanical stress plays an important role in pancreatic cancer cell migration, and targeting aberrant signaling in cancer cells that have adapted to mechanical stress could be an effective approach to limit pancreatic cancer cell migration.
MOLECULAR CANCER RESEARCH
(2022)
Article
Multidisciplinary Sciences
Sean A. Murphy, Matthew Miyamoto, Anais Kervadec, Suraj Kannan, Emmanouil Tampakakis, Sandeep Kambhampati, Brian Leei Lin, Sam Paek, Peter Andersen, Dong-Ik Lee, Renjun Zhu, Steven S. An, David A. Kass, Hideki Uosaki, Alexandre R. Colas, Chulan Kwon
Summary: Cardiomyocyte maturation and the acquisition of phenotypes at the single cell level were analyzed in this study, revealing that peroxisome proliferator-activated receptor coactivator-1 mediates the phenotypic shift. The study provides a single-cell roadmap of heterogeneous transitions coupled to cellular features.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Cell Biology
Ivan de Curtis
Summary: Liquid-liquid phase separation plays a crucial role in the formation of biomolecular condensates and the spatial organization of cellular processes. Recent evidence suggests that components of plasma-membrane-associated platforms form biomolecular condensates near focal adhesions and indicate that phase separation regulates dynamic processes at the front of migrating cells.
TRENDS IN CELL BIOLOGY
(2021)
Article
Chemistry, Applied
Yishun Yao, Yanan Sun, Baozhong Cui, Hongfei Fu, Xiangwei Chen, Yunyang Wang
Summary: The study explored the impact of RF heating rate on POD enzyme activity, physiochemical properties, and cell structure of stem lettuce. RF heating led to increased POD enzyme inactivation efficiency, better physiochemical properties, and less cell damage compared to conventional HW blanching. Varying degrees of cell destruction with RF heating rates offer new possibilities for producing different types of fruit and vegetable products.
Article
Immunology
Samantha K. Lindberg, Graham G. Willsey, Nicholas J. Mantis
Summary: Secretory IgA (SIgA) protects the intestinal epithelium from enteric pathogens such as Salmonella enterica serovar Typhimurium (STm) through immune exclusion, but the underlying mechanism of how SIgA mediates the transition from motile and invasive state to an avirulent sessile state in STm is unknown. In this report, the snow globe assay was developed to visualize and quantify STm agglutination by the mouse monoclonal IgA Sal4. The results showed that agglutination was influenced by bacterial motility and cell-cell collisions.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Oncology
Wilfred Leung, Matt Teater, Ceyda Durmaz, Cem Meydan, Alexandra G. Chivu, Amy Chadburn, Edward J. Rice, Ashlesha Muley, Jeannie M. Camarillo, Jaison Arivalagan, Ziyi Li, Christopher R. Flowers, Neil L. Kelleher, Charles G. Danko, Marcin Imielinski, Sandeep S. Dave, Scott A. Armstrong, Christopher E. Mason, Ari M. Melnick
Summary: SETD2 is a histone methyltransferase responsible for H3K36me3 and its mutation can lead to DNA damage and tumor development. Heterozygous deficiency of Setd2 results in germinal center hyperplasia and increased competitive fitness, accelerating lymphomagenesis. SETD2 deficiency impairs DNA damage sensing and repair, leading to increased gene mutations and translocations.
Article
Chemistry, Physical
Ori Maller, Allison P. Drain, Alexander S. Barrett, Signe Borgquist, Brian Ruffell, Igor Zakharevich, Thanh T. Pham, Tina Gruosso, Hellen Kuasne, Johnathon N. Lakins, Irene Acerbi, J. Matthew Barnes, Travis Nemkov, Aastha Chauhan, Jessica Gruenberg, Aqsa Nasir, Olof Bjarnadottir, Zena Werb, Peter Kabos, Yunn-Yi Chen, E. Shelley Hwang, Morag Park, Lisa M. Coussens, Andrew C. Nelson, Kirk C. Hansen, Valerie M. Weaver
Summary: Stromal stiffening in malignant tumours is associated with poor treatment outcomes and increased tumour aggression. Identifying factors that regulate stromal stiffening could lead to biomarkers for patient stratification and interventions to improve outcomes. Experimental studies have shown that therapeutic targeting of tumour-associated macrophages and collagen crosslinking enzymes can reduce metastasis and stromal stiffening in aggressive breast cancer subtypes with stiff stroma. Additionally, the expression of lysyl hydroxylase 2 in the stroma has been linked to disease-specific mortality in breast cancer patients, indicating its potential as a stromal biomarker.
Article
Oncology
Merav E. Shaul, Asaf Zlotnik, Einat Tidhar, Asaf Schwartz, Ludovica Arpinati, Naomi Kaisar-Iluz, Sojod Mahroum, Inbal Mishalian, Zvi G. Fridlender
Summary: The study suggests that tumor-associated neutrophils play a crucial role in recruiting and modulating B cells into plasma cells in the tumor microenvironment, thereby opening new avenues in cancer immunotherapy targeting strategies.
CANCER IMMUNOLOGY RESEARCH
(2021)
Article
Oncology
Jiheng Xu, Rui Yang, Jingxia Li, Lidong Wang, Mitchell Cohen, Diane M. Simeone, Max Costa, Xue-Ru Wu
Summary: The stem-cell-like behavior of cancer cells in bladder cancer plays a crucial role and its molecular basis remains incompletely defined. This study demonstrates that SNHG1 induces the formation of stem-cell-like spheres and invasion of bladder cancer cells by upregulating Rho GTPase, Rac1. SNHG1 binds to DNMT3A and represses the transcription of miR-129-2-5p, resulting in increased Rac1 protein levels. High expression of Rac1 is associated with poor prognosis in bladder cancer patients.
Article
Microbiology
Aaron S. Dhanda, A. Wayne Vogl, Fern Ness, Metello Innocenti, Julian A. Guttman
Summary: Direct cell-to-cell spreading of Listeria monocytogenes requires the induction of actin-based membrane protrusions in donor cells, which are endocytosed by adjacent receiving cells. Formin mDia1 plays a vital role in the assembly of the F-actin shell during this process, leading to efficient cell-to-cell transfer of the bacteria.
Article
Multidisciplinary Sciences
Hideya Aragaki, Katsunori Ogoh, Yohei Kondo, Kazuhiro Aoki
Summary: Cell tracking is a critical tool for observing cell behavior and lineages over time, but current software lacks user-friendliness and features like manual correction and data analysis tools. This paper introduces LIM Tracker, a cell tracking software that integrates various tracking functions and offers interactive data visualization. It also includes deep learning recognition capabilities and can be used for a wide range of targets. The software is implemented as a plugin for ImageJ/Fiji.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Shuhao Lin, Daiki Hirayama, Gembu Maryu, Kimiya Matsuda, Naoya Hino, Eriko Deguchi, Kazuhiro Aoki, Ryo Iwamoto, Kenta Terai, Michiyuki Matsuda
Summary: EGFR ligands exhibit remarkable redundancy in the propagation of ERK activation waves during collective cell migration.
LIFE SCIENCE ALLIANCE
(2022)
Article
Multidisciplinary Sciences
Sae Tanaka, Kazuhiro Aoki, Kazuharu Arakawa
Summary: This study developed an in vivo expression system for tardigrades, enabling the introduction of GFP-fused proteins and genetically encoded indicators into tardigrade cells for fluorescence live imaging. The results showed tissue-specific expression of anhydrobiosis-related genes and suggested the regulation of gene expression changes in desiccation-induced species. This technology opens up possibilities for exploring anhydrobiosis mechanisms in tardigrade research.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Takashi Nakamura, Hirofumi Sakaguchi, Hiroaki Mohri, Yuzuru Ninoyu, Akihiro Goto, Taro Yamaguchi, Yoshitaka Hishikawa, Michiyuki Matsuda, Naoaki Saito, Takehiko Ueyama
Summary: This study found that Rac1 and Rac3 play important roles in the early development of sensory epithelia during embryonic development, but they are dispensable for the maturation of hair cells in the later stages after specification and for the maintenance of hearing after hearing maturation.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2023)
Article
Multidisciplinary Sciences
Keita Kamino, Nirag Kadakia, Fotios Avgidis, Zhe-Xuan Liu, Kazuhiro Aoki, Thomas S. Shimizu, Thierry Emonet
Summary: Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy is a major tool for studying cellular processes. However, inferring molecular interaction dynamics from the observables remains challenging, especially in the presence of measurement noise and photobleaching. This study introduces a probabilistic approach called B-FRET, which improves the signal-to-noise ratio (SNR) and reveals hidden signaling dynamics in noisy in vivo FRET time series.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Shigekazu Oda, Emi Sato-Ebine, Akinobu Nakamura, Koutarou D. Kimura, Kazuhiro Aoki
Summary: Optogenetic techniques responsive to red/near-infrared light were successfully implemented in C. elegans, allowing manipulation of cell signaling and induction of defecation motor program. These tools will greatly contribute to elucidating the molecular mechanisms underlying C. elegans behaviors.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Cell Biology
Katsuyuki Kunida, Nobuhiro Takagi, Kazuhiro Aoki, Kazushi Ikeda, Takeshi Nakamura, Yuichi Sakumura
Summary: Limitations in simultaneously observing the activity of multiple molecules in live cells hinder the understanding of how these molecules coordinate the dynamic regulation of cellular functions. This study proposes the motion-triggered average (MTA) algorithm to characterize pseudo-simultaneous dynamic changes in cell deformation and molecular activities. By using MTA, a pseudo-simultaneous time series is successfully extracted from individually observed activities of three Rho GTPases. The predictive mathematical regression model accurately predicts the edge velocity by using the activities of these molecules, providing numerical evidence for the regulation of edge movement by Rho GTPases. Data preprocessing using MTA combined with mathematical regression offers an effective strategy for reusing individual observations of molecular activities.
Article
Biology
A. Mencattini, M. D'Orazio, P. Casti, M. C. Comes, D. Di Giuseppe, G. Antonelli, J. Filippi, F. Corsi, L. Ghibelli, I. Veith, C. Di Natale, M. C. Parrini, E. Martinelli
Summary: One of the major problems in bioimaging is whether features extracted for a discrimination or regression task can remain valid in the presence of unpredictable perturbations during image acquisition process. This is especially important in the context of deep learning features due to the lack of known relationship between the black-box descriptors and the phenotypic properties of the biological entities. The use of pre-trained Convolutional Neural Networks (CNNs) is hindered by their lack of apparent physical meaning and sensitivity to unspecific biases.
COMMUNICATIONS BIOLOGY
(2023)
Article
Cell Biology
Tsuyoshi Hirashima, Naoya Hino, Kazuhiro Aoki, Michiyuki Matsuda
Summary: This article reviews the critical regulatory role of extracellular signal-regulated kinase (ERK) in various physiological and pathological processes and highlights the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent research has revealed the role of mechanical forces in activating the RTK-ERK signaling pathways, opening new avenues of research into mechanochemical interplay in multicellular tissues.
CURRENT OPINION IN CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Maho Yagi-Utsumi, Haruko Miura, Christian Ganser, Hiroki Watanabe, Methanee Hiranyakorn, Tadashi Satoh, Takayuki Uchihashi, Koichi Kato, Kei-ichi Okazaki, Kazuhiro Aoki
Summary: This study utilized the dynamic properties of multidomain proteins to develop a novel FRET-based biosensor by fusing b' and a' domains with fluorescent proteins. The biosensor demonstrated higher FRET efficiency in the oxidized form and has potential applications in studying cellular redox regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Kimiya Matsuda, Daiki Hirayama, Naoya Hino, Sota Kuno, Asako Sakaue-Sawano, Atsushi Miyawaki, Michiyuki Matsuda, Kenta Terai
Summary: The roles of each ErbB receptor in the proliferation, migration and survival of epithelial cells were investigated by systematically knocking out each ErbB gene or their combinations. ErbB1 was found to play a primary role in collective cell migration, followed by the ErbB2 and ErbB3 heterodimer. Either ErbB1 or the ErbB2 and ErbB3 complex was sufficient for promoting G1/S progression. Interestingly, ligand-independent ErbB2 activity was found to prevent apoptosis at high cell density.
JOURNAL OF CELL SCIENCE
(2023)
Meeting Abstract
Urology & Nephrology
Zhang Ning, Takeshi Sano, Ryosuke Ikeuchi, Hideaki Takada, Kenji Nakamura, Toru Sakatani, Akihiro Hamada, Yuki Kita, Michiyuki Matsuda, Takashi Kobayashi
JOURNAL OF UROLOGY
(2023)
Article
Cell Biology
Tetsuya Watabe, Shinya Yamahira, Michiyuki Matsuda, Kenta Terai
Summary: This study quantitatively demonstrates the impact of calcium transients on neighboring cells through PGE(2) using fluorescence microscopy and a simulation model.
CELL STRUCTURE AND FUNCTION
(2023)
Article
Biochemistry & Molecular Biology
Sachio Suzuki, Akinobu Nakamura, Yuka Hatano, Masaru Yoshikawa, Tatsuyuki Yoshii, Shunsuke Sawada, Kyoko Atsuta-Tsunoda, Kazuhiro Aoki, Shinya Tsukiji
Summary: This article reports a universal PM-targeting tag for protein translocation using loop-engineered eDHFR tag and m(D)cTMP pair. The method can be widely applied for conditional PM recruitment and activation of tag-fused signaling proteins with different fusion configurations, as well as reversibly and repeatedly controlling protein localization to generate synthetic signal oscillations.
CELL CHEMICAL BIOLOGY
(2022)