Article
Plant Sciences
Shuai Lu, Cong Gao, Yongzhou Wang, Yingying He, Junrong Du, Moxian Chen, Hua Zhao, Hui Fang, Baohua Wang, Yunying Cao
Summary: This study identified U2AF65A in plant species, conducted phylogenetic and bioinformatic analyses, and studied the localization and stress responses of OsU2AF65A in rice. Using Arabidopsis and rice mutants, the importance of U2AF65A in plant growth and stress responses was demonstrated. These findings provide an overview of the U2AF65 gene family and its role in plant development and stress tolerance.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Dina Marghani, Zhuo Ma, Anthony J. Centone, Weihua Huang, Meenakshi Malik, Chandra Shekhar Bakshi
Summary: This study elucidates the role of the osrR transcriptional regulator in the pathogenesis of tularemia caused by F. tularensis. The osrR regulator specifically regulates the oxidative and global stress response, virulence, metabolism, and other key pathways genes required by Francisella when exposed to oxidative stress. Understanding such regulatory mechanisms will help identify potential targets for developing effective therapies and vaccines to prevent tularemia.
JOURNAL OF BACTERIOLOGY
(2021)
Review
Microbiology
Daniel Cortes-Avalos, Noemy Martinez-Perez, Mario A. Ortiz-Moncada, Aylin Juarez-Gonzalez, Arturo A. Banos-Vargas, Paulina Estrada-de Los Santos, Ernesto Perez-Rueda, J. Antonio Ibarra
Summary: This review emphasizes the role of AraC/XylS family of transcriptional regulators in gene regulation, highlighting their abundance and diversity in bacterial genomes. By analyzing experimentally characterized members, the study proposes a grouping strategy and discusses the functional classification and regulatory schemes observed in these proteins. Additionally, a survey of proteins in bacterial genomes is presented, providing a panoramic view of this fascinating family of transcriptional regulators for future research.
FEMS MICROBIOLOGY REVIEWS
(2021)
Review
Microbiology
Daniel Cortes-Avalos, Noemy Martinez-Perez, Mario A. Ortiz-Moncada, Aylin Juarez-Gonzalez, Arturo A. Banos-Vargas, Paulina Estrada-de Los Santos, Ernesto Perez-Rueda, J. Antonio Ibarra
Summary: Transcriptional factors are vital in gene regulation across organisms, especially in Bacteria. The AraC/XylS family of transcriptional regulators is diverse and can be clustered based on functional classification. Experimental evidence and bioinformatics tools are used to update information and propose grouping for these proteins, aiming to stimulate future research in the field.
FEMS MICROBIOLOGY REVIEWS
(2021)
Review
Plant Sciences
June-Sik Kim, Keiichi Mochida, Kazuo Shinozaki
Summary: This review provides an overview of the current knowledge on ER stress sensing, activation, and downstream regulation of the unfolded protein response (UPR). Recent studies have shown that the UPR is also involved in plant growth and development, and it modulates both plant growth and stress tolerance by maintaining ER homeostasis.
Article
Plant Sciences
Yanyan Ma, Maofu Xue, Xiaofei Zhang, Songbi Chen
Summary: In this study, 10 MeMT genes in cassava were identified and their evolutionary relationship, conserved motifs, and tissue-specific expression were explored. The results suggest that MeMTs play an important role in plant growth and development, as well as in response to physiological stress through the regulation of ROS homeostasis.
Article
Biotechnology & Applied Microbiology
Danny Bergeron, Cedric Laforest, Stacey Carpentier, Annabelle Calve, Etienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Michelle S. Scott
Summary: The study reveals that snoRNA copy regulation affects family sizes, genomic location of the members, and controls both member and total family abundance to meet the needs of individual tissues. Additionally, the expression variability of individual snoRNA family members is preferred over the total variability of the family, pointing towards differential regulation mechanisms exist to ensure uniformity of the total family abundance across tissues.
Article
Biochemistry & Molecular Biology
Qi Liu, Xiangyu Sui, Ying Wang, Ming Zhu, Yijun Zhou, Fei Gao
Summary: Through a comprehensive analysis of the structure, evolution and expression of Thaumatin-like proteins (TLPs) in Ammopiptanthus nanus, 31 TLP genes were identified and classified into four groups. The majority of the AnTLPs contained conserved cysteine residues and had typical three-dimensional structure of plant TLPs. Gene expression analysis showed that several AnTLP genes were involved in cold-stress response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yisheng Fang, Dong Cao, Hongli Yang, Wei Guo, Wenqi Ouyang, Haifeng Chen, Zhihui Shan, Zhonglu Yang, Shuilian Chen, Xia Li, Limiao Chen, Xinan Zhou
Summary: The LOR gene family in soybean was investigated in this study, revealing that the genes are divided into eight subgroups located on 14 chromosomes. Most genes contain conserved motifs, with several pairs of tandem and segmental duplicated genes. Different expression patterns were observed among the 36 GmLOR genes in response to abiotic stress, with some showing significant upregulation after PEG and salt treatments, indicating their important roles in improving plant tolerance to abiotic stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Mei Zhang, Shuguang Jian, Zhengfeng Wang
Summary: This study identified and analyzed the CrHsp20 genes in Canavalia rosea, a halophyte that is well-adapted to high temperatures. The study found that these genes are greatly upregulated under heat stress, but show different expression patterns in response to salt, alkaline, or high osmotic stresses. Functional characterization of some CrHsp20 genes in yeast confirmed their role in abiotic stress tolerance. These findings contribute to understanding the adaptation mechanisms of C. rosea and may have implications for crop genetic improvement.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Fisheries
Huihui Xie, Jiabao Hu, Yajun Wang, Xubo Wang
Summary: This study conducted a comprehensive analysis of MMPs in Japanese flounder, including gene structures, evolutionary relationships, conserved domains, molecular evolution, and expression patterns. The analysis revealed that MMP genes could be grouped into 17 sub-families and were evolutionarily conserved and functionally-constrained. The expression profiling showed that MMPs had diverse functions in environmental stress, with different expression patterns observed under temperature stress and Edwardsiella tarda infection.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Zhixing Zhao, Guanghua Meng, Imran Zamin, Tao Wei, Dongdi Ma, Lizhe An, Xiule Yue
Summary: In this study, 18 TIFY family genes (FtTIFYs) in Tartary buckwheat were identified and their characteristics and roles were examined. The results showed that most FtTIFY genes responded to abiotic stresses and hormone treatments, suggesting their potential in enhancing stress resistance. Furthermore, the overexpression of two FtJAZ genes (FtJAZ10 and FtJAZ12) in tobacco improved its tolerance to heat stress. This study highlights the importance of FtTIFY family genes in responses to abiotic stress and provides candidate genes for developing stress-resistant crops.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Forestry
Jian Diao, Xin Hao, Wei Ma, Ling Ma
Summary: Genes homologous to members of the MRP gene family in pine wood nematode are identified and found to play important roles in drug resistance. Experimental results show that the expression of Bx-MRP family members increases after treatment with different drugs, indicating a positive role in the regulation of multidrug resistance.
JOURNAL OF FORESTRY RESEARCH
(2021)
Editorial Material
Endocrinology & Metabolism
Aoyuan Cui, Dong Ding, Yu Li
Summary: This article focuses on the roles of the ATF/CREB family in the regulation of glucose and lipid metabolism and cell growth in the liver, as well as its importance in liver physiology. Deregulated ATF/CREB family signaling is implicated in the progression of various diseases.
Article
Plant Sciences
Wei Hao, Weipeng Wang, Xiangfen Xiao, Jialiang Sun, Bingjie Wu, Yuping Zhao, Shuaishuai Pei, Wenjia Fan, Dongbei Xu, Tengfei Qin
Summary: YTH domain-containing proteins, involved in post-transcriptional regulation, play multiple roles in controlling the growth, development, and response to stress in plants. This study identified and analyzed YTH genes in four cotton species. Phylogenetic analysis categorized these genes into three subgroups, and various aspects of their characteristics were investigated. Expression patterns and the functional verification of GhYTH8 in drought tolerance provided important insights into the YTH gene family in cotton.
Article
Chemistry, Physical
S. M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. Germann, A. M. N. Niklasson
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2015)
Article
Biochemical Research Methods
Andrew H. Van Benschoten, Pavel V. Afonine, Thomas C. Terwilliger, Michael E. Wall, Colin J. Jackson, Nicholas K. Sauter, Paul D. Adams, Alexandre Urzhumtsev, James S. Fraser
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2015)
Article
Chemistry, Physical
Anders M. N. Niklasson, Susan M. Mniszewski, Christian F. A. Negre, Marc J. Cawkwell, Pieter J. Swart, Jamal Mohd-Yusof, Timothy C. Germann, Michael E. Wall, Nicolas Bock, Emanuel H. Rubensson, Hristo Djidjev
JOURNAL OF CHEMICAL PHYSICS
(2016)
Article
Chemistry, Physical
Christian F. A. Negre, Susan M. Mniszewski, Marc J. Cawkwell, Nicolas Bock, Michael E. Wall, Anders M. N. Niklasson
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2016)
Article
Multidisciplinary Sciences
Neda Vesselinova, Boian S. Alexandrov, Michael E. Wall
Article
Multidisciplinary Sciences
Andrew H. Van Benschoten, Lin Liu, Ana Gonzalez, Aaron S. Brewster, Nicholas K. Sauter, James S. Fraser, Michael E. Wall
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Chemistry, Multidisciplinary
Michael E. Wall
Article
Biochemistry & Molecular Biology
Michael E. Wall, Alexander M. Wolff, James S. Fraser
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2018)
Article
Chemistry, Multidisciplinary
Michael E. Wall
Editorial Material
Chemistry, Multidisciplinary
Michael E. Wall
Article
Chemistry, Multidisciplinary
Michael E. Wall, Gaetano Calabro, Christopher I. Bayly, David L. Mobley, Gregory L. Warren
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Chemistry, Multidisciplinary
Jaewoon Jung, Wataru Nishima, Marcus Daniels, Gavin Bascom, Chigusa Kobayashi, Adetokunbo Adedoyin, Michael Wall, Anna Lappala, Dominic Phillips, William Fischer, Chang-Shung Tung, Tamar Schlick, Yuji Sugita, Karissa Y. Sanbonmatsu
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2019)
Article
Multidisciplinary Sciences
Medhanjali Dasgupta, Dominik Budday, Saulo H. P. de Oliveira, Peter Madzelan, Darya Marchany-Rivera, Javier Seravalli, Brandon Hayes, Raymond G. Sierra, Sebastien Boutet, Mark S. Hunter, Roberto Alonso-Mori, Alexander Batyuk, Jennifer Wierman, Artem Lyubimov, Aaron S. Brewster, Nicholas K. Sauter, Gregory A. Applegate, Virendra K. Tiwari, David B. Berkowitz, Michael C. Thompson, Aina E. Cohen, James S. Fraser, Michael E. Wall, Henry van den Bedem, Mark A. Wilson
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Computer Science, Hardware & Architecture
Susan M. Mniszewski, James Belak, Jean-Luc Fattebert, Christian F. A. Negre, Stuart R. Slattery, Adetokunbo A. Adedoyin, Robert F. Bird, Choongseok Chang, Guangye Chen, Stephane Ethier, Shane Fogerty, Salman Habib, Christoph Junghans, Damien Lebrun-Grandie, Jamaludin Mohd-Yusof, Stan G. Moore, Daniel Osei-Kuffuor, Steven J. Plimpton, Adrian Pope, Samuel Temple Reeve, Lee Ricketson, Aaron Scheinberg, Amil Y. Sharma, Michael E. Wall
Summary: The ECP focuses on co-design to prepare key applications for exascale computing, with CoPA addressing challenges faced by particle-based applications through the development of proxy apps and libraries, aiming to improve performance and productivity.
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS
(2021)
Article
Chemistry, Physical
Zhen Su, Medhanjali Dasgupta, Frederic Poitevin, Irimpan I. Mathews, Henry van den Bedem, Michael E. Wall, Chun Hong Yoon, Mark A. Wilson
Summary: The reproducibility of diffuse scattering from different protein forms was high, indicating the potential for high-quality data. The liquid-like motions (LLM) model was effective in characterizing atomic mobility and distinguishing between alternative anisotropic atomic displacement parameter (ADP) models. Successful diffuse scattering experiments can benefit from understanding data reproducibility and utilizing LLM analysis.
STRUCTURAL DYNAMICS-US
(2021)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)