TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data by Guorui Zhang, Chao Song, Mingxue Yin, Liyuan Liu, Yuexin Zhang, Ye Li, Jianing Zhang, Maozu Guo, Chunquan Li

“…Herein, we propose Transcription Regulator Activity Prediction Tool (TRAPT), a multi-modality deep learning framework, which infers regulator activity by learning and integrating the regulatory potentials of target gene cis-regulatory elements and genome-wide binding sites. …”
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Communication between DNA polymerases and Replication Protein A within the archaeal replisome by Markel Martínez-Carranza, Léa Vialle, Clément Madru, Florence Cordier, Ayten Dizkirici Tekpinar, Ahmed Haouz, Pierre Legrand, Rémy A. Le Meur, Patrick England, Rémi Dulermo, J. Iñaki Guijarro, Ghislaine Henneke, Ludovic Sauguet

“…We demonstrate that archaeal RPA hosts a winged-helix domain (WH) that interacts with two key actors of the replisome: the DNA primase (PriSL) and the replicative DNA polymerase (PolD). Using an integrative structural biology approach, combining nuclear magnetic resonance, X-ray crystallography and cryo-electron microscopy, we unveil how RPA interacts with PriSL and PolD through two distinct surfaces of the WH domain: an evolutionarily conserved interface and a novel binding site. …”
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Metformin modulates FJX1 via upregulation of Hsa-miR-1306-3p to suppress colon adenocarcinoma viability by Jung-min Kim, Hae Jin Shin, Woo Ryung Kim, Eun Gyung Park, Du Hyeong Lee, Yun Ju Lee, Hyeon-su Jeong, Hyun-Young Roh, Ho Jeong Kwon, Yung Hyun Choi, Sun-Hee Leem, Heui-Soo Kim

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Divergent molecular pathways govern temperature-dependent wheat stem rust resistance genes by Tim C. Hewitt, Keshav Sharma, Jianping Zhang, Chunhong Chen, Prabin Bajgain, Dhara Bhatt, Smriti Singh, Pablo D. Olivera Firpo, Jun Yang, Qiaoli Wang, Narayana Upadhyaya, Curtis Pozniak, Robert McIntosh, Evans Lagudah, Peng Zhang, Matthew N. Rouse

“…Here, we clone Sr6 using mutagenesis and resistance gene enrichment and sequencing (MutRenSeq), identifying it to encode a nucleotide-binding leucine-rich repeat (NLR) protein with an integrated BED domain. …”
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Characterizing and engineering post-translational modifications with high-throughput cell-free expression by Derek A. Wong, Zachary M. Shaver, Maria D. Cabezas, Martin Daniel-Ivad, Katherine F. Warfel, Deepali V. Prasanna, Sarah E. Sobol, Regina Fernandez, Fernando Tobias, Szymon K. Filip, Sophia W. Hulbert, Peter Faull, Robert Nicol, Matthew P. DeLisa, Emily P. Balskus, Ashty S. Karim, Michael C. Jewett

“…First, we demonstrate how our workflow can be used to characterize the binding activity of RiPP recognition elements, an important first step in RiPP biosynthesis, and be integrated into a biodiscovery pipeline for computationally predicted RiPP products. …”
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<i>circSATB1</i> Modulates Cell Senescence in Age-Related Acute Myeloid Leukemia: A Mechanistic Proposal by Linxiang Han, Xi Wen, Ling Zhang, Xingcheng Yang, Ziyan Wei, Haodong Wu, Yichen Zhan, Huiting Wang, Yu Fang

“…Database analysis revealed that there may be two miRNA and nine RNA-binding proteins (RBPs) involved in regulating the cellular functions of <i>circSATB1</i>. …”
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Transcriptional regulatory networks underlying gene expression changes in Huntington's disease by Seth A Ament, Jocelynn R Pearl, Jeffrey P Cantle, Robert M Bragg, Peter J Skene, Sydney R Coffey, Dani E Bergey, Vanessa C Wheeler, Marcy E MacDonald, Nitin S Baliga, Jim Rosinski, Leroy E Hood, Jeffrey B Carroll, Nathan D Price

“…We reconstructed a genome‐scale model for the target genes of 718 transcription factors (TFs) in the mouse striatum by integrating a model of genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. …”
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Large-scale quantitative genomics analyzes the circRNA expression profile and identifies the key circRNA in regulating cell proliferation during the proliferation phase of rat LR by Xueqiang Guo, Wei Jin, Cuifang Chang, Yi Ding, Yahao Wang, Lifei Li, Yanhui Chen, Jingbo Zhang, Cunshuan Xu, Guangwen Chen, Jianlin Guo

“…Subsequently, 27 circRNAs were predicted to bind to 58 candidate miRNAs and compete for miRNA-binding sites with 2195 mRNAs. …”
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Comprehensive New Insights into Sweet Taste Transmission Mechanisms and Detection Methods by Yuanwei Sun, Shengmeng Zhang, Tianzheng Bao, Zilin Jiang, Weiwei Huang, Xiaoqi Xu, Yibin Qiu, Peng Lei, Rui Wang, Hong Xu, Sha Li, Qi Zhang

“…Furthermore, an intelligent detection framework integrating molecular recognition, multi-source data fusion, and artificial intelligence is proposed. …”
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Exploring the NANOG-TET2 interaction interface. Effects of a selected mutation and hypothesis on the clinical correlation with anemias by Claudia Testi, Roberta Piacentini, Roberta Piacentini, Alessandro Perrone, Chiara Bartoli, Daniele Leso, Domitilla Pavia, Elisa Pistolesi, Flavio Scipione, Irene Cotronea, Marco Adinolfi Falcone, Marco Ierani, Alberto Boffi, Lorenzo Di Rienzo

“…Notably, the mutation occurs in a protein region distant from the active site; moreover, the experimental structures of the interacting region of both proteins are unknown, making it difficult to validate the impact of TET2 mutation on its binding with NANOG. To address these challenges, we employed an integrated computational approach combining molecular docking, molecular dynamics simulations and protein-protein interaction prediction. …”
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Revealing the multi-target destruction induced by proanthocyanidins against Acetobacter sp. at the molecular level by Er-Fang Ren, Er-Fang Ren, Xiaoqin Feng, Yuanxin Feng, Kai Li, Xin-An Zeng, Qing-Hui Wen, Jin-Lin Cai, Zhong Han, Shan Chen, Debao Niu

“…Proanthocyanidins disrupted the cellular morphology and membrane integrity of Acetobacter sp., and affected the structure of cell membranes by interaction with membrane proteins. …”
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Affinity‐Based Isolation and One‐Pot Analysis of Extracellular Vesicles from Biofluids Using Phase Separated Zwitterionic Coacervates by Francesca Torrini, Roberto Frigerio, Jonathan Garlipp, Philippe Lenzen, Karl Normak, Carolina Paganini, Marina Cretich, Alessandro Gori, Paolo Arosio

“…They exhibit antifouling properties that minimize nonspecific binding, allowing for the selective isolation of EVs from biofluids upon functionalization of the polymer with a suitable affinity probe, as proved here with a membrane‐sensing peptide. …”
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Contribution of two-component response regulator OmpR to virulence, motility, exopolysaccharide production, and osmotic stress in Pseudomonas syringae pv. actinidiae by Lei Zhang, Xiaoxi Chang, Ke Zhang, Qian Wang, Min Fu, Lili Huang, Lixin Zhang

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In silico design of novel dihydropteridone derivatives with oxadiazoles as potent inhibitors of MCF-7 breast cancer cells by Mourad Aloui, Mohamed El fadili, Mohammed Er-rajy, Somdutt Mujwar, Hatem A. Abuelizz, Sara Er-rahmani, Elhalaoui Menana

“…These compounds exhibited favorable interactions with key breast cancer-related proteins, demonstrated enhanced dynamic stability within their binding sites, and adhered to established drug-likeness principles. …”
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Efficient synthesis of N-(ethylcarbamothioyl)-1-naphthamide: X-ray structure, Hirshfeld surface analysis, DFTs, and molecular modelling investigations as selective inhibitor of alk... by Pervaiz Ali Channar, Mohammad Y. Alshahrani, Aamer Saeed, Syeda Abida Ejaz, Hafiz Muhammad Attaullah, Sajid Ali Channar, Sher Qadir, Qamar Abbas, Ulrich Flörke, Tuncer Hökelek

“…Molecular docking studies demonstrated the compound (NA-MT) exhibit strong binding affinities to cIAP, which were further validated via Molecular Dynamics (MD) simulations. …”
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Cryo-TEM structure of β-glucocerebrosidase in complex with its transporter LIMP-2 by Jan Philipp Dobert, Jan-Hannes Schäfer, Thomas Dal Maso, Priyadarshini Ravindran, Dustin J. E. Huard, Eileen Socher, Lisa A. Schildmeyer, Raquel L. Lieberman, Wim Versées, Arne Moeller, Friederike Zunke, Philipp Arnold

“…One of the few known exceptions is the enzyme β-glucocerebrosidase (GCase) that requires the lysosomal integral membrane protein type-2 (LIMP-2) as a proprietary lysosomal transporter. …”
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Mitochondria‐associated membrane collapse is a common pathomechanism in SIGMAR1‐ and SOD1‐linked ALS by Seiji Watanabe, Hristelina Ilieva, Hiromi Tamada, Hanae Nomura, Okiru Komine, Fumito Endo, Shijie Jin, Pedro Mancias, Hiroshi Kiyama, Koji Yamanaka

“…ALS‐linked Sig1R variants were unstable and incapable of binding to inositol 1,4,5‐triphosphate receptor type 3 (IP3R3). …”
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Disruption of the blood–brain barrier contributes to neurobehavioral changes observed in rheumatic heart disease by Rukshan Ahamed Mohamed Rafeek, Riya Thapa, Samarjeet Saluja, Bipandeep Banga, David McMillan, Kadaba Sri Sriprakash, Nicholas M. Andronicos, Adam Hamlin, Natkunam Ketheesan

“…This highlights that impaired BBB integrity is essential for the development of neurobehavioral symptoms. …”
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An imaging-guided self-amplifying photo-immunotherapeutic nanoparticle for STING pathway activation and enhanced cancer therapy by Qiaoqi Chen, Huilin Yu, Lin Li, Hua Zhang, Mixiao Tan, Weiwei Liu, Min Zheng, Yaqin Hu, Long Cheng, Yushi Chen, Haitao Ran, Qiu Zeng, Yuan Guo

“…Collectively, this multifunctional nanoparticle offers a promising strategy that integrates imaging, targeting, and photothermal-enhanced immune activation for STING-mediated cancer immunotherapy. …”
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Nanoscale Curvature Regulates YAP/TAZ Nuclear Localization Through Nuclear Deformation and Rupture by Emmet A. Francis, Einollah Sarikhani, Vrund Patel, Dhivya Pushpa Meganathan, Leah Sadr, Anum Tahir, Zeinab Jahed, Padmini Rangamani

“…How do cells respond to local nanotopographical cues and integrate their responses across multiple length scales? …”
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