Article
Multidisciplinary Sciences
Yanxing Ma, Hainan Tian, Rao Lin, Wei Wang, Na Zhang, Saddam Hussain, Wenting Yang, Chen Zhang, Ganghua Zhou, Tianya Wang, Shucai Wang
Summary: The expression of stress response genes is regulated by ABA dependent and ABA independent pathways. A novel transcription factor, DRG, has been identified as a regulator of ABA response in Arabidopsis, with its homologs, AITRL, functioning as transcription repressors and affecting the ABA response of some ABA signaling component genes. The AITRLs are evolutionally conserved in embryophytes and play a role in modulating ABA responses in plants.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
Jiyoen Kim, Maria de Haro, Ismael Al-Ramahi, Lorena Laura Garaicoechea, Hyun-Hwan Jeong, Jun Young Sonn, Bakhos Tadros, Zhandong Liu, Juan Botas, Huda Yahya Zoghbi
Summary: Tauopathies are neurodegenerative diseases characterized by the accumulation of tau proteins. A genetic screening of potentially druggable genes identified three genes (USP7, RNF130, and RNF149) that regulate tau levels by targeting the C terminus of CHIP. Knockdown of these genes reduced tau levels and rescued disease phenotypes, suggesting a potential therapeutic strategy for Alzheimer disease and other tauopathies.
Article
Biochemistry & Molecular Biology
Shuai Fu, Kun Wang, Tingting Ma, Yan Liang, Zhonghua Ma, Jianxiang Wu, Yi Xu, Xueping Zhou
Summary: This study identifies a microtubule-associated E3 ligase (MEL) that promotes the degradation of a serine hydroxymethyltrasferase (SHMT1), resulting in broad-spectrum resistance to pathogens. The findings suggest the potential utility of the MEL-SHMT1 module in generating broad-spectrum resistant rice to global destructive pathogens.
Article
Multidisciplinary Sciences
Kaitlyn McGrath, Shivani Agarwal, Marco Tonelli, Mykola Dergai, Anthony L. Gaeta, Andrew K. Shum, Jessica Lacoste, Yongbo Zhang, Wenyu Wen, Daayun Chung, Grant Wiersum, Aishwarya Shevade, Sofia Zaichick, Damian B. van Rossum, Ludmilla Shuvalova, Jeffrey N. Savas, Sergei Kuchin, Mikko Taipale, Kim A. Caldwell, Guy A. Caldwell, Dirk Fasshauer, Gabriela Caraveo
Summary: Ykt6, a soluble SNARE protein, plays a critical role in vesicular fusion pathways. Phosphorylation at a conserved site triggers a conformational change, leading to altered protein interactions and enhanced toxicity in PD models. This study reveals a mechanism regulating Ykt6 conformation and activity with potential implications for Parkinson's disease.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Olanrewaju B. Morenikeji, Kahleel Bernard, Ellis Strutton, Madeleine Wallace, Bolaji N. Thomas
Summary: Coronaviruses are a family of viruses, with only alpha- and betacoronaviruses observed to infect humans. The recent emergence of SARS-CoV-2, causing COVID-19, has led to severe cases with acute respiratory distress syndrome (ARDS) from cytokine storm. Long non-coding RNAs (lncRNAs) identified to regulate gene expression during the COVID-19 cytokine storm may serve as promising disease markers or drug targets for further analysis.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Sophie Tissot, Lena Guimard, Jordan Meliani, Justine Boutry, Antoine M. Dujon, Jean-Pascal Capp, Jacint Tokolyi, Peter A. Biro, Christa Beckmann, Laura Fontenille, Nam Do Khoa, Rodrigo Hamede, Benjamin Roche, Beata Ujvari, Aurora M. Nedelcu, Frederic Thomas
Summary: Changes in food availability may be an important factor affecting tumor occurrence and progression. Frequent overfeeding promotes tumor emergence, while lean diets may have a protective effect.
SCIENTIFIC REPORTS
(2023)
Article
Biology
Naokazu Inoue, Yoshihisa Hagihara, Ikuo Wada
Summary: The study demonstrates the essential role of evolutionarily conserved factors DCST1 and DCST2 in sperm-egg fusion in mice, and how the protein stability of SPACA6 is regulated differently by DCST1/2 and IZUMO1. This suggests that spermatozoa ensure proper fertilization in mammals by integrating various molecular pathways, including an evolutionarily conserved system developed over nearly one billion years of evolution.
Article
Multidisciplinary Sciences
Milan Kumar Samanta, Srimonta Gayen, Clair Harris, Emily Maclary, Yumie Murata-Nakamura, Rebecca M. Malcore, Robert S. Porter, Patricia M. Garay, Christina N. Vallianatos, Paul B. Samollow, Shigeki Iwase, Sundeep Kalantry
Summary: In this study, the researchers discovered an essential role of the X-linked homolog of an ancestral X-Y gene pair, Kdm5c-Kdm5d, in the expression of Xist lncRNA. They found that Kdm5c encodes a demethylase that enhances Xist expression, and this function is strongly conserved in mammals.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Daniel A. Nissley, Anna Carbery, Mark Chonofsky, Charlotte M. Deane
Summary: This study found that in yeast, the ribosome occupancy profiles of paralogous domains tend to be significantly more similar to one another than to profiles of non-paralogous domains. This indicates that entire ribosome occupancy profiles are conserved between even distantly related domains, supporting the hypothesis that translation schedule is conserved between structurally related domains to retain folding pathways and facilitate efficient folding.
Article
Chemistry, Medicinal
Namita Dube, Sabab Hasan Khan, Riley Sasse, C. Denise Okafor
Summary: Allosteric pathways in proteins allow for the transmission of signals between distant sites through inter-residue interactions. This study utilizes molecular dynamics simulations and suboptimal path analysis to identify new allosteric networks in steroid receptors, focusing on evolutionarily conserved pathways. The investigation reveals a conserved network connecting a predicted allosteric site located between helices 9 and 10 of the ligand-binding domain to the activation function surface 2 (AF-2). The importance of this site is highlighted by its presence in a region characterized by conserved inter-residue contacts.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Namita Dube, Sabab Hasan Khan, Riley Sasse, C. Denise Okafor
Summary: Allosteric pathways in proteins involve networks of amino acid residues that transmit signals between distant sites. This study uses molecular dynamics simulations and suboptimal path analysis to discover new allosteric networks in steroid receptors, focusing on evolutionarily conserved pathways. The researchers identify a conserved network connecting a predicted allosteric site between helices 9 and 10 of the ligand-binding domain to the activation function surface 2 (AF-2). The study suggests the evolutionary importance of this site in steroid receptors and provides an approach to discover previously unknown allosteric sites in proteins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Lian Xu, Zhifeng Chen, Xiaodi Li, Hui Xu, Yu Zhang, Weiwei Yang, Jing Chen, Shuqiang Zhang, Lingchi Xu, Songlin Zhou, Guicai Li, Bin Yu, Xiaosong Gu, Jian Yang
Summary: This study re-analyzed 21 RNA-seq datasets and identified 53 evolutionarily conserved injury response genes, including species-preference injury response candidates and genes related to pre-regenerative and regenerating states. Furthermore, a large sex difference in response to sciatic nerve injury was found.
Article
Biochemistry & Molecular Biology
Marion Lebouvier, Paula Miramon-Puertolas, Patrick R. H. Steinmetz
Summary: This study investigates the absorption and transport of nutrients, especially lipids, in the oocytes of the cnidarian Nematostella vectensis. The researchers found that an extracellular matrix-based lipid transport system plays a crucial role in this process, suggesting its existence before the divergence of cnidarians and bilaterians and providing a foundation for the evolution of bilaterian circulatory systems.
Article
Biochemistry & Molecular Biology
David Stuart, Malin Sandstrom, Helmy M. Youssef, Shakhira Zakhrabekova, Poul Erik Jensen, David Bollivar, Mats Hansson
Summary: Ferredoxins are important single-electron carrier proteins in various cellular reactions. In chloroplasts, a specific isoform named VirK plays an essential role in the aerobic cyclase reaction of chlorophyll biosynthesis, which cannot be complemented by other ferredoxins, highlighting the specific function of this isoform.
Article
Biochemistry & Molecular Biology
Kheerthana Duraivelan, Sagarika Dash, Dibyendu Samanta
Summary: Nectins, a family of cell surface glycoproteins, mediate cell-cell adhesion and signaling pathways, with specific heterophilic interactions dictating their physiological relevance.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Cell Biology
Kaori Watanabe, Yuki Furumizo, Tadao Usui, Yukako Hattori, Tadashi Uemura
Article
Cell Biology
Taiichi Tsuyama, Asako Tsubouchi, Tadao Usui, Hiromi Imamura, Tadashi Uemura
JOURNAL OF CELL BIOLOGY
(2017)
Article
Biology
Koun Onodera, Shumpei Baba, Akira Murakami, Tadashi Uemura, Tadao Usui
Article
Cell Biology
Yasutetsu Kanaoka, Henrik Skibbe, Yusaku Hayashi, Tadashi Uemura, Yukako Hattori
Article
Cell Biology
Kaori Watanabe, Yasutetsu Kanaoka, Shoko Mizutani, Hironobu Uchiyama, Shunsuke Yajima, Masayoshi Watada, Tadashi Uemura, Yukako Hattori
Article
Cell Biology
Masayoshi Watada, Yusaku Hayashi, Kaori Watanabe, Shoko Mizutani, Ayumi Mure, Yukako Hattori, Tadashi Uemura
Article
Biochemical Research Methods
Goshi M. Ogita, Takefumi M. Kondo, Keisuke M. Ikawa, Tadashi M. Uemura, Shuji M. Ishihara, Kaoru M. Sugimura
Summary: Thanks to recent advances in imaging techniques, researchers have developed an efficient and rapid method to extract mechanical parameters from image data, which can provide valuable insights into the mechanical control of morphogenesis. By applying this method to Drosophila epithelial tissues, they discovered that junction remodeling and resistance to extrinsic pulling are controlled through different tension parameters. This method also proved effective in detecting changes in anisotropic tension parameters in genetically or surgically manipulated tissues. The proposed method is expected to be a powerful tool in dissecting the mechanical control of morphogenesis.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biology
Maiko Abe, Takumi Kamiyama, Yasushi Izumi, Qingyin Qian, Yuma Yoshihashi, Yousuke Degawa, Kaori Watanabe, Yukako Hattori, Tadashi Uemura, Ryusuke Niwa
Summary: This study investigated how specialist fruit flies adapt to limited nutritional conditions. The findings showed that a high-glucose diet impaired gut immune function in the specialist fruit flies and shortened their lifespan.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Cell Biology
Shuangyu Luo, Kanji Furuya, Kimiya Matsuda, Yuma Tsukasa, Tadao Usui, Tadashi Uemura
Summary: In vivo, cells collectively migrate in various contexts, and coordinated epithelial rotation is a unique form of collective cell migration that has been studied in vitro. This study investigated the role of E-cadherin in collective cell migration on spatially confined surfaces. The results showed that MDCK cells lacking E-cadherin exhibited less coordinated migration without large-scale rotation compared to wild-type cells. The loss of E-cadherin also led to a decrease in global migration speed, a decrease in coordination, and an increase in topological defects. These findings demonstrate the importance of E-cadherin in initiating collective epithelial rotations under two-dimensional confinement.
Article
Developmental Biology
Taiichi Tsuyama, Yusaku Hayashi, Hanae Komai, Kohei Shimono, Tadashi Uemura
Summary: This study investigated the developmental processes of the adult-type fat body (AFB) in Drosophila. It identified precursor cells that give rise to the AFB and described the dynamic cellular behaviors underlying AFB formation. The study also examined the roles of ecdysone signaling and the transcription factor Serpent in adult fat body organogenesis.
Article
Biology
Kai Li, Yuma Tsukasa, Misato Kurio, Kaho Maeta, Akimitsu Tsumadori, Shumpei Baba, Risa Nishimura, Akira Murakami, Koun Onodera, Takako Morimoto, Tadashi Uemura, Tadao Usui
Summary: We identified a protein called Bero that negatively regulates escape behavior in fruit flies. It is expressed in neurons that produce abdominal leucokinin and modulates escape behavior by regulating their activity.
Article
Cell Biology
Masaki Arata, Kaoru Sugimura, Tadashi Uemura
DEVELOPMENTAL CELL
(2017)