Article
Developmental Biology
Sayuki Hirano, Yusuke Mii, Guillaume Charras, Tatsuo Michiue
Summary: This study reveals how mechanical signals regulate planar cell polarity (PCP) in the posterior neuroectoderm of Xenopus laevis. It shows that tension in the anterior-posterior direction plays a crucial role in maintaining PCP, and that cells sense tissue stretch indirectly through changes in their shape. Furthermore, the study suggests a cooperative relationship between tissue stretch direction and the diffusion of locally expressed Wnt ligands in establishing PCP.
Article
Cell Biology
Ilya Chuykin, Keiji Itoh, Kyeongmi Kim, Sergei Y. Sokol
Summary: This study demonstrates that the association of Vangl2 and Pk3 is inhibited by Fz3 through phosphorylation of Vangl2, affecting the establishment and orientation of PCP in the tissue. These findings provide new insights into the regulation of Vangl2-Pk3 complex formation by Frizzled receptor in the neural plate.
JOURNAL OF CELL SCIENCE
(2021)
Article
Neurosciences
Florian Regent, Zachary Batz, Ryan A. Kelley, Linn Gieser, Anand Swaroop, Holly Y. Chen, Tiansen Li
Summary: This study found that early nicotinamide treatment can significantly increase the yield of retinal organoids derived from different donors of human pluripotent stem cell lines. This treatment promotes neural differentiation of cells, increases the generation of eye field progenitors, and improves the efficiency of retinal organoid formation.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Review
Chemistry, Multidisciplinary
Hao-Ran Jia, Ya-Xuan Zhu, Qiu-Yi Duan, Fu-Gen Wu
Summary: Studying the molecular basis of cell surface and related biological activities is a cutting-edge field, where advanced cell imaging techniques allow us to understand how cell surface is structured and responds to signals. Researchers are now focusing on artificially manipulating the cell surface properties, developing more maneuverable labeling strategies for imaging, sensing, and biomedical applications. The future challenges and opportunities in visualizing cell surface structures and monitoring the microenvironment are discussed, highlighting the importance of cell surface-based studies.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Analytical
Lifeng Yin, Yingfeng Wang, Huayue Chen, Wu Deng
Summary: This paper improves the density peak clustering algorithm to achieve better clustering of multi-density data. It uses the K-nearest neighbor idea to select parameters and find the global bifurcation point to divide data with different densities. It also automatically determines the cluster center and the number of cluster centers by calculating the average value of the gamma height difference and finding the largest discontinuity point through two screenings. The clustering results are further improved and integrated using cluster fusion rules.
Article
Computer Science, Interdisciplinary Applications
Takashi Koretsune
Summary: In this study, two methods for constructing Maximally localized Wannier functions (MLWFs) using crystal symmetry are presented. The first method calculates input matrices for generating MLWFs based on wavefunctions in the irreducible Brillouin zone (IBZ), resulting in reduced computational costs and file sizes. The second method involves calculating symmetry-adapted Wannier functions compatible with the frozen window technique. Examples of Fe, Co3Sn2S2, Cu, and Nb are demonstrated. These methods are implemented in the PW2WANNIER90 code, which interfaces QUANTUM-ESPRESSO with WANNIER90, and the open-source python library, SYMWANNIER.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Cell & Tissue Engineering
Kim M. A. De Kleijn, Wieteke A. Zuure, Kirsten R. Straasheijm, Marijn B. Martens, M. Cristina Avramut, Roman I. Koning, Gerard J. M. Martens
Summary: Three-dimensional human brain spheroids are important tools for studying CNS development and (dys)function. Current models lack cell-type variety, limiting the exploration of CNS (disease) mechanisms. In this study, a 5-month culture protocol was developed to generate human cortical spheroids with a wide variety of cell types. The spheroids contained neuroectoderm-derived neural progenitors, mature neurons, astrocytes, oligodendrocytes, microglia, and endothelial cells. Transcriptomic analysis revealed similarity to the dorsal frontal region of human fetal brains. Inflammatory stimulation of the spheroids induced neuroinflammation, demonstrating their applicability.
STEM CELL RESEARCH & THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Clementine Vincent, Javier Gilabert-Juan, Rachel Gibel-Russo, Daniel Alvarez-Fischer, Marie-Odile Krebs, Gwenaelle Le Pen, Alain Prochiantz, Ariel A. Di Nardo
Summary: The study indicated that OTX2 plays a crucial role in regulating anxiety-related phenotypes in mice by synthesizing in choroid plexus and being secreted into the cerebrospinal fluid, affecting the parvalbumin interneurons.
MOLECULAR PSYCHIATRY
(2021)
Article
Multidisciplinary Sciences
Richa Karmakar, Timothy Tyree, Richard H. Gomer, Wouter-Jan Rappel
Summary: Chemotaxis plays a crucial role in biological processes where cells are guided by chemical gradients. In Dictyostelium discoideum, cell aggregates are formed through periodic pulses of cAMP and secretion of PDE, allowing for cell motion and dispersion. The competition between cAMP and PDE results in the formation of a gradient directed away from the aggregate, leading to outward cell motion.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Veterinary Sciences
Alice Ferreira, Daniela Silva, Carina Almeida, Maria Elisa Rodrigues, Sonia Silva, Joana Castro, Dalila Mil-Homens, Isidro Garcia-Menino, Azucena Mora, Mariana Henriques, Ana Oliveira
Summary: This study evaluated the efficacy of phage vB_EcoM_FJ1 (FJ1) in reducing the load of pathogenic Escherichia coli (ETEC) and found that encapsulated FJ1 in microparticles significantly reduced the quantity of ETEC. Bacteriophage-insensitive mutants (BIMs) displayed weaker adaptability in the pig model.
VETERINARY RESEARCH
(2023)
Article
Materials Science, Multidisciplinary
Bowei Zhang, Hezu Wang, Yan Su, Wenguang Yang, Xuelong Hao, Zequn Zhang, Fengqin Wang, Wei Xue, Junsheng Wu
Summary: Understanding the influence of purities on the electrochemical performance of pure aluminum in alkaline media is significant. The study comprehensively investigates secondary phase precipitate-induced localized corrosion of pure aluminum in NaOH solution through quasi-in-situ and cross-section observations, coupled with finite element simulation. The results show that Al-Fe secondary phase precipitates appear as clusters and aggravate localized galvanic corrosion as cathodic phases due to their higher potentials than the substrate. Finite element simulation reveals non-uniform current density distribution inside the precipitate cluster and a gradual decrease in current density on the aluminum substrate with distance.
INTERNATIONAL JOURNAL OF MINERALS METALLURGY AND MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Barnali Das, Pralay Mitra
Summary: The study develops ProMoCell and ProModb, which are used for clustering and storing cellular-level functional modules respectively, utilizing real-time web scraping and data from multiple online sources. These web services are synchronized with the KEGG pathway database and provide users with a comprehensive and efficient tool for browsing and extracting functional modules and interaction network data of cells. These services are of significant importance in pharmacological research.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Computer Science, Artificial Intelligence
Frederic Ros, Serge Guillaume, Rabia Riad, Mohamed El Hajji
Summary: In this paper, a new density-based clustering algorithm called S-DBSCAN is proposed. It combines the concepts of distance, k-nearest neighbors, and density peaks in a hierarchical process to partition data into clusters. The algorithm is self-tuning and does not rely on a global density threshold. Experimental results demonstrate its effectiveness.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Cell Biology
Joan Domingo-Reines, Gonzalo Martinez-Navajas, Rosa Montes, Mar Lamolda, Iris Simon, Julio Castano, Rosa Rios-Pelegrina, Javier Luis Lopez-Hidalgo, Raimundo Garcia del Moral, Juan A. Marchal, Pedro J. Real, Veronica Ramos-Mejia
Summary: Pediatric acute myeloid leukemia (AML) is a rare and heterogeneous disease that is the major cause of mortality in children with leukemia. Researchers report the generation and characterization of human embryonic stem cell clonal lines with inducible expression of NK5A, aiming to gain knowledge on its participation during the leukemogenic process.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Frederic Ros, Serge Guillaume, Rabia Riad
Summary: Path-scan is a clustering algorithm aimed at discovering natural partitions by utilizing a density differential approach to connect core points and extract partitions at different levels of granularity.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Chao Liu, Dijuan Zhang, Yuxian Shen, Xiaofang Tao, Lihua Liu, Yongwang Zhong, Shengyun Fang
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2015)
Article
Anatomy & Morphology
Chao Liu, Ruyu Sun, Jian Huang, Dijuan Zhang, Dake Huang, Weiqin Qi, Shenghua Wang, Fenfen Xie, Yuxian Shen, Cailiang Shen
FRONTIERS IN NEUROANATOMY
(2017)
Article
Biochemistry & Molecular Biology
Chao Liu, Yongwang Zhong, Andria Apostolou, Shengyun Fang
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2013)
Article
Biochemistry & Molecular Biology
Chao Liu, Yaping Sun, Joshua Arnold, Bingwei Lu, Su Guo
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2014)
Article
Neurosciences
Zhenzhen Wang, Jian Huang, Chang Liu, Lihua Liu, Yuxian Shen, Cailiang Shen, Chao Liu
FRONTIERS IN NEUROSCIENCE
(2019)
Article
Biochemistry & Molecular Biology
Zengyi Liu, Lihua Liu, Ruyu Sun, Chao Liu
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY
(2020)
Article
Neurosciences
Jing Jiang, Xiujuan Hu, Lihua Liu, Zhicheng He, Qingjie Wu, Qunchao Li, Xianwei Hu, Nan Jiang, Chao Liu
Summary: The expression of K48 and K63 ubiquitin lysine linkages in midbrain dopamine neurons is age-related and may be involved in the loss of dopamine neurons. Aging promotes the formation of protein aggregates positive for both K48 and K63 ubiquitin linkages in the substantia nigra pars compacta.
Article
Reproductive Biology
Xiujuan Hu, Zhijun Dai, Ruolang Pan, Yi Zhang, Lihua Liu, Yafei Wang, Xueying Chen, Dengpan Yao, Mingyun Hong, Chao Liu
Summary: In this study, human menstrual blood mesenchymal stem cells loaded on a collagen scaffold were transplanted to a long-term rat model of intrauterine adhesion (IUA). The results showed that the transplantation of MBMSCs promoted endometrial regeneration, decreased fibrosis, and regulated the expression of specific proteins.
REPRODUCTIVE TOXICOLOGY
(2022)
Article
Neurosciences
Xueying Chen, Tianyi Zhao, Naiyu Ke, Yutong Qian, Wanrong Wang, Lihua Liu, Chao Liu
Summary: This study establishes methods for the in-vitro induction and long-term maintenance of human spinal cord neural stem cells (NSCs). The generated NSCs express specific markers and can be maintained for more than 40 days under an in vitro culture system.
Article
Geriatrics & Gerontology
Tianyi Zhao, Chang Liu, Lihua Liu, Xinmeng Wang, Chao Liu
Summary: The aging process affects cellular compositions in the spinal cord, leading to the accumulation of abnormal protein aggregates. Dysregulation of proteostasis and dysfunction of the ubiquitin-proteasome system (UPS) and autophagy are key factors in this process. Understanding the molecular mechanisms of spinal cord aging is crucial for the development of rejuvenation therapies. Our study identified an increase in STAT3 expression and a decrease in Tuj1 expression in aging mouse spinal cords, along with an increase in coaggregation of lysine-48 and lysine-63 ubiquitin with STAT3. These findings highlight the importance of STAT3 and its region-specific aggregation and ubiquitin-conjugation in spinal cord aging.
Review
Cell & Tissue Engineering
Nai-Yu Ke, Tian-Yi Zhao, Wan-Rong Wang, Yu-Tong Qian, Chao Liu
Summary: The gene regulatory network, including the chromatin-remodeling complex BAF, plays a crucial role in determining the fate of neural stem/progenitor cells (NSPCs) and their progeny. Abnormalities in the BAF complex can lead to abnormal neural differentiation and neurodevelopmental disorders. Understanding the mechanism of BAF complex regulation in NSPCs can provide insights into neurodevelopment and have clinical applications.
WORLD JOURNAL OF STEM CELLS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Xueying Chen, Xiujuan Hu, Jing Jiang, Jie Tao, Lihua Liu, Shengyun Fang, Yuxian Shen, Qingsong Hu, Chao Liu
Article
Chemistry, Multidisciplinary
Dong Chen, Yi-pei Li, Yan-xia Yu, Tian Zhou, Chao Liu, Er-kang Fei, Feng Gao, Chen-chen Mu, Hai-gang Ren, Guang-hui Wang
ACTA PHARMACOLOGICA SINICA
(2018)
Article
Multidisciplinary Sciences
Chao Liu, Dijuan Zhang, Yuxian Shen, Xiaofang Tao, Lihua Liu, Yongwang Zhong, Shengyun Fang