Review
Plant Sciences
Huiying Xu, Peirui Chen, Yi Tao
Summary: The article discusses how plants respond to shade, classifying them into shade avoiding and shade tolerance plants. Shade avoiding plants induce shade avoidance responses (SARs) to outgrow competitors, while shade tolerance plants induce shade tolerance responses (STRs) to enhance survival rates.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Yanzhao Sun, Yanyan Zheng, Heng Yao, Zhaodong Ma, Mengwei Xiao, Haiyang Wang, Yang Liu
Summary: In the natural ecosystem, plants grow densely to maximize yield. This high-density planting triggers shade avoidance responses and competition for light and nutrition. The molecular mechanisms underlying shade avoidance and nutrition have been extensively studied, but their intersection remains poorly understood. In this study, we demonstrate that simulated shade undermines phosphate starvation response and involves the phytohormone JA. Our findings reveal a previously unrecognized molecular framework where plants integrate light and hormone signaling to modulate phosphate responses under plant competition.
Article
Multidisciplinary Sciences
Sebastian Zeltzer, Pierce Longmire, Marek Svoboda, Giovanni Bosco, Felicia Goodrum
Summary: Human cells have multiple specialized DNA polymerases for chromosomal DNA synthesis and repair, while complex DNA viruses may rely on host polymerases for synthesis. This study shows that error-prone Y-family polymerases can restrict human cytomegalovirus genome synthesis, while other TLS polymerases are required for optimal replication. Host polymerases also suppress viral genome rearrangements, indicating their role in ensuring viral genome stability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Chrysoula K. Pantazopoulou, Franca J. Bongers, Ronald Pierik
Summary: Suppressing shade avoidance responses can enhance the performance of a monoculture community against invading competitors, leading to better suppression of invaders and larger community growth. Insights from this study may help in weed suppression in crop stands.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Plant Sciences
Maria Jimena Ruiz-Diaz, Daniel Matsusaka, Jimena Cascales, Diego H. Sanchez, Maximiliano Sanchez-Lamas, Pablo D. Cerdan, Javier F. Botto
Summary: This study explores the genetic basis of shade avoidance response (SAR) in Arabidopsis thaliana and identifies the role of polymorphisms in the PHYB gene in seed germination, seedling development, and shade avoidance response.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mara Cucinotta, Alex Cavalleri, Andrea Guazzotti, Chiara Astori, Silvia Manrique, Aureliano Bombarely, Stefania Oliveto, Stefano Biffo, Dolf Weijers, Martin M. Kater, Lucia Colombo
Summary: The plant hormone auxin regulates gene expression through the canonical AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) combinatorial system. ARF5/MONOPTEROS (MP) can activate gene transcription in cells with elevated auxin levels and in ovules with low auxin levels, expressing a splice variant that lacks the Aux/IAA interaction domain and can function as a transcriptional activator in subthreshold auxin concentration regions.
Review
Biochemistry & Molecular Biology
Daniela Muoio, Natalie Laspata, Elise Fouquerel
Summary: The ADP-ribose transferase (ART) family consists of 17 enzymes that play important roles in various biological processes, such as DNA repair, replication, and transcription regulation. Five members of this family are crucial for maintaining genome stability and protecting telomere integrity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Plant Sciences
Ashutosh Sharma, Ashley J. Pridgeon, Wei Liu, Francisca Segers, Bhavana Sharma, Gareth I. Jenkins, Keara A. Franklin
Summary: Plants monitor reductions in red to far-red ratio (R:FR) to determine the proximity and density of encroaching vegetation and initiate shade avoidance adaptations. UV-B perceived by UVR8 photoreceptor rapidly inhibits shade avoidance, while long-term inhibition is sustained by HY5 and HYH genes, which regulate transcriptional reprogramming of genes involved in hormone signaling and cell wall modification.
Article
Plant Sciences
Xiaoxiao Yan, Lipeng Cui, Xiangyang Liu, Yuchao Cui, Zhaojun Wang, Hongying Zhang, Liang Chen, Hong Cui
Summary: Through bioinformatics analysis and transgenic experiments, it was found that the NbJAZ3 protein regulates glandular trichome density development in tobacco by inhibiting the expression of the NbWo gene.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Biochemistry & Molecular Biology
Jesse J. Kupers, Basten L. Snoek, Lisa Oskam, Chrysoula K. Pantazopoulou, Sanne E. A. Matton, Emilie Reinen, Che-Yang Liao, Eline D. C. Eggermont, Harold Weekamp, Muthanna Biddanda-Devaiah, Wouter Kohlen, Dolf Weijers, Ronald Pierik
Summary: Although plants are immobile, they can respond to environmental cues by flexibly moving their organs. In dense vegetation, plants use far-red light perception to detect neighboring plants. They respond by growing asymmetrically on the leafstalk, resulting in upward movement of the leaves. The plant hormone auxin is required for this response, but its remote regulation of movement is not well understood.
Article
Plant Sciences
Sofia Romero-Montepaone, Romina Sellaro, Carlos Esteban Hernando, Cecilia Costigliolo-Rojas, Luciana Bianchimano, Edmundo L. Ploschuk, Marcelo J. Yanovsky, Jorge J. Casal
Summary: The study found a close genetic link between the growth responses of Arabidopsis thaliana stems to warmth and shade, which is also closely related to PIF4 levels; both cues enhanced the expression of growth-related genes, but only warmth promoted the expression of heat-related genes; an increase in temperature significantly increased the amount of light needed for carbon balance.
Article
Developmental Biology
Collin Knudsen, Woo Seuk Koh, Tomomi Izumikawa, Eriko Nakato, Takuya Akiyama, Akiko Kinoshita-Toyoda, Greg Haugstad, Guichuan Yu, Hidenao Toyoda, Hiroshi Nakato
Summary: Heparan sulfate (HS) and chondroitin sulfate (CS) are glycosaminoglycans that are found in most animal species. This study focused on the role of CS in development by generating mutants for Chondroitin sulfate synthase (Chsy) in Drosophila. The mutants showed altered stiffness of the basement membrane and muscle dysfunction in the ovary, leading to degradation of the organ structure.
Article
Multidisciplinary Sciences
Chrysoula K. Pantazopoulou, Sara Buti, Chi Tam Nguyen, Lisa Oskam, Daan A. Weits, Edward E. Farmer, Kaisa Kajala, Ronald Pierik
Summary: Plants detect their neighbors through touch, which triggers a calcium response and drives leaf movement. This touch-induced hyponasty mechanism is adaptive and involves an increase in cytosolic calcium concentration in leaf tip trichomes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Alexander A. Morano, Rachel M. Rudlaff, Jeffrey D. Dvorin
Summary: The study identifies a Plasmodium basal complex protein essential for its maintenance and expansion. Through microscopy techniques, the researchers demonstrate that PfPPP8 is required for uniform expansion and integrity of the basal complex. They also discover a new pseudophosphatase family and identify two additional basal complex proteins. This work uncovers the role of PfPPP8 in segmentation, establishes the dynamic structure of the P. falciparum basal complex, and highlights the importance of the pseudophosphatase in cell division of the malaria parasite.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Abhishesh Bajracharya, Jing Xi, Karlie F. Grace, Eden E. Bayer, Chloe A. Grant, Caroline H. Clutton, Scott R. Baerson, Ameeta K. Agarwal, Yongjian Qiu
Summary: Moderately elevated ambient temperatures stimulate the growth of specific plant organs through the activation of PIF4 and HMR, which in turn activate auxin-related genes. The Mediator subunit MED14 is essential for this process.
Article
Biochemistry & Molecular Biology
Li Zheng, Yuan Meng, Judith L. Campbell, Binghui Shen
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Shafat Ali, Yilan Zhang, Mian Zhou, Hongzhi Li, Weiwei Jin, Li Zheng, Xiaochun Yu, Jeremy M. Stark, Jeffrey N. Weitzel, Binghui Shen
Article
Multidisciplinary Sciences
Tanay Thakar, Wendy Leung, Claudia M. Nicolae, Kristen E. Clements, Binghui Shen, Anja-Katrin Bielinsky, George-Lucian Moldovan
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Yilan Zhang, Qi Zhang, LuLu Li, Dan Mu, Ke Hua, Shusheng Ci, Lei Shen, Li Zheng, Binghui Shen, Zhigang Guo
FREE RADICAL BIOLOGY AND MEDICINE
(2020)
Article
Microbiology
Fong-Fong Chu, R. Steven Esworthy, Binghui Shen, James H. Doroshow
Article
Cell Biology
Jacob Paiano, Nicholas Zolnerowich, Wei Wu, Raphael Pavani, Chen Wang, Hongzhi Li, Li Zheng, Binghui Shen, Barry P. Sleckman, Bo-Ruei Chen, Andre Nussenzweig
Summary: The study reveals that Pol alpha reduces resection at DSBs in the presence of 53BP1, but is unable to counteract excessive resection in the absence of 53BP1. This suggests that 53BP1 likely protects DNA ends by inhibiting resection.
GENES & DEVELOPMENT
(2021)
Editorial Material
Cell Biology
Bing Liu, Daniela Duenas, Li Zheng, Karen Reckamp, Binghui Shen
Article
Multidisciplinary Sciences
Haitao Sun, Zhaoning Lu, Amanpreet Singh, Yajing Zhou, Eric Zheng, Mian Zhou, Jinhui Wang, Xiwei Wu, Zunsong Hu, Zhaohui Gu, Judith L. Campbell, Li Zheng, Binghui Shen
Summary: Under restrictive temperature stress, an error-prone Okazaki fragment maturation (OFM) pathway is activated in rad27 Delta cells, leading to the generation of mutations that enable cells to adapt to environmental stress.
Article
Biotechnology & Applied Microbiology
Lei-Si Zhang, Jun Wang, Ming-Zhu Xu, Tian-Mei Wu, Si-Man Huang, Han-Yu Cao, Ai-Ning Sun, Song-Bai Liu, Sheng-Li Xue
Summary: The presence of FLT3-ITD mutation is associated with poor outcomes in AML patients. Venetoclax combined with hypomethylating agents has shown promising efficacy in FLT3-mutated AML, but there are cases where patients do not respond to this treatment. This study investigates the safety and response to gilteritinib and venetoclax-based therapy in FLT3-ITD mutated AML patients who are unresponsive to Venetoclax plus azacitidine, providing potential new hope for these patients.
ONCOTARGETS AND THERAPY
(2022)
Editorial Material
Genetics & Heredity
Lingzi Ma, Haitao Sun, Tharindumala Abeywardana, Li Zheng, Binghui Shen
Summary: Proper function of structure-specific nucleases is crucial for the completion of Okazaki fragment maturation process. Dysregulation of these nucleases leads to abnormal OFM and a range of mutations, some of which may confer survival advantages under specific stresses and can be targeted for therapeutic intervention in human cancers.
TRENDS IN GENETICS
(2022)
Review
Cell Biology
Haitao Sun, Lingzi Ma, Ya-Fang Tsai, Tharindu Abeywardana, Binghui Shen, Li Zheng
Summary: Unsuccessful processing of Okazaki fragments leads to DNA breaks accumulation, which is associated with various human diseases. The study focuses on the detection and repair of unprocessed Okazaki fragments and the consequences of improper Okazaki fragment maturation (OFM) on genome stability and cell viability, especially in cancer cells. The canonical OFM pathways and their regulation of genomic integrity and cell survival are examined, as well as the alternative error-prone OFM processes induced by environmental stresses, which may drive mutagenesis, cellular evolution, and resistance to cancer therapies.
TRENDS IN CELL BIOLOGY
(2023)
Meeting Abstract
Hematology
Haojie Dong, Xin He, Lei Zhang, Wei Chen, Yichun Lin, Songbai Liu, Huafeng Wang, Wenfeng Huang, Sierra Min Li, Yinghui Zhu, Dandan Zhao, Lucy Ghoda, Rui Su, Jianjun Chen, Ritin Sharma, Patrick Pirrotte, Xiwei Wu, Weidong Hu, Weidong Han, Binghui Shen, Ya-Huei Kuo, Jie Jin, Amandeep Salhotra, Jeffrey Wang, Guido Marcucci, Yun Luo, Ling Li
Article
Biochemistry & Molecular Biology
Wenpeng Liu, Piotr Polaczek, Ivan Roubal, Yuan Meng, Won-chae Choe, Marie-Christine Caron, Carl A. Sedgeman, Yu Xi, Changwei Liu, Qiong Wu, Li Zheng, Jean-Yves Masson, Binghui Shen, Judith L. Campbell
Summary: The FANCD2 protein and RAD51 protein protect stalled forks through different mechanisms. FANCD2 inhibits DNA2 nuclease activity and stabilizes RAD51, while RAD51 stimulates the strand exchange activity. A model is proposed to explain the genetic interactions between FANCD2 and BRCA2 in the FA/BRCA fork protection pathway.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Xiebing Bao, Yao Chen, Xiao Lou, Jiahui Du, Huijun Li, Nian Liu, Zaixiang Tang, Jingsheng Hua, Weiqiang Guo, Song-Bai Liu
Summary: This study revealed that ERCC3 is overexpressed in AML and high ERCC3 expression can be considered as a biomarker conducive to allo-HSCT in AML patients. ERCC3 and its co-expressed genes are mainly involved in chemical carcinogenesis/reactive oxygen species, ubiquitin-mediated protein degradation, and oxidative phosphorylation pathways. Additionally, almost all m(6)A-related coding genes (except GF2BP1) are positively associated with ERCC3 expression. A ceRNA regulatory network containing ERCC3 in AML was also constructed, identifying 6 pairs of ceRNA networks that regulate ERCC3 expression through noncoding RNA.
CLINICAL & TRANSLATIONAL ONCOLOGY
(2023)
Article
Medicine, Research & Experimental
Brandon Tan, Keren Zhou, Wei Liu, Emily Prince, Ying Qing, Yangchan Li, Li Han, Xi Qin, Rui Su, Sheela Pangeni Pokharel, Lu Yang, Zhicong Zhao, Chao Shen, Wei Li, Zhenhua Chen, Zheng Zhang, Xiaolan Deng, Andrew Small, Kitty Wang, Keith Leung, Chun-Wei Chen, Binghui Shen, Jianjun Chen
Summary: This study reveals the essential role of the m(6)A reader YTHDC1 in promoting triple negative breast cancer (TNBC) metastasis. YTHDC1 enhances the nuclear export and expression of SMAD3 to augment the TGF-beta signaling cascade, leading to the formation of lung metastasis in TNBC.
