Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. by J'Zaria Simpson, Christine A Kozak, Guney Boso

“…ERVs thus represent molecular fossil records of ancient retroviruses and provide a unique opportunity to study viral-host interactions, including cross-species transmissions, in deep time. …”
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Differentially expressed genes in mycorrhized and nodulated roots of common bean are associated with defense, cell wall architecture, N metabolism, and P metabolism. by Kalpana Nanjareddy, Manoj-Kumar Arthikala, Brenda-Mariana Gómez, Lourdes Blanco, Miguel Lara

“…Here, we used ion torrent next-generation sequencing to perform comparative transcriptomics of common bean (Phaseolus vulgaris) roots colonized by AM or rhizobia. …”
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Nanoparticle-mediated targeting of PGC-1α reveals critical metabolic pathways in bladder cancer metastasis by Zhenghua Liu, Peng Xin, Weiwei Wu, Mingyue Jin, Yang Du, Yuanjun Jiang, Tao Liu, Hao Zhang

“…We employed comprehensive transcriptomic, proteomic, and metabolomic analyses to investigate the impact of PGC-1α silencing. …”
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Gibberellic acid-mediated transcriptional divergence underlies cold stress adaptation in two diploid cotton species by Dong Wang, Juyun Zheng, Ke Liu, Yanchao Xu, Dingsha Jin

“…Methods To explore the genetic basis of this difference, we conducted a comparative transcriptomic analysis under cold stress at 4 °C, identifying 697 and 311 species-specific differentially expressed genes (DEGs) in G. thurberi and G. trilobum, respectively. …”
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TRPV1 inhibition sensitizes tumors to PD-1 blockade by reversing resistance to CTL-mediated killing by Min Kyu Son, Hyo-Jung Lee, Eunho Cho, Se Jin Oh, Tae Woo Kim

“…Thus, our findings highlight TRPV1 as a promising therapeutic target for overcoming resistance to PD-1 blockade and provide a strong rationale for combining TRPV1 antagonists with anti-PD-1 therapy.…”
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Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray by Konstantinia Skreka, Marek Zywicki, Michael Karbiener, Alexander Hüttenhofer, Marcel Scheideler, Mathieu Rederstorff

“…Mammalian transcriptomes mainly consist of non protein coding RNAs. …”
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Nutritional sex-specificity on bacterial metabolites during mosquito (Aedes aegypti) development leads to adult sex-ratio distortion by Ottavia Romoli, Javier Serrato-Salas, Chloé Gapp, Yanouk Epelboin, Pol Figueras Ivern, Frédéric Barras, Mathilde Gendrin

“…When treating germ-free larvae with individual B vitamins, we detected a specific toxic effect related to biotin (vitamin B7) exposure at high concentrations. We then provided germ-free larvae with varying biotin doses and showed that males are sensitive to biotin toxicity at a lower concentration than females. …”
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Cutting-edge assessment techniques for B cell immune memory: an overview by Martina Bozhkova, Petya Gardzheva, Vanya Rangelova, Hristo Taskov, Marianna Murdjeva

“…Single-cell RNA Sequencing provides in-depth information about B-cell receptor diversity, functional states, transcriptomic changes associated with rare cell populations or dynamic cellular processes within the immune system. …”
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Suboptimal pre-anthesis water status mitigates wheat susceptibility to fusarium head blight and triggers specific metabolic responses by Larissa Adamik, Paul Samir Dou, Géraldine Philippe, Richard Blanc, Pedro Vásquez-Ocmín, Guillaume Marti, Thierry Langin, Ludovic Bonhomme

“…Considering the combined stress effects, a unique response signature emerged, highlighting that immune responses are strongly interwoven with physiological adjustments. Our findings provide new insights into the trade-offs that plants make under multiple challenges and identify original wheat metabolic determinants that may improve FHB resistance even in suboptimal physiological conditions.…”
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Pro-Fibrotic Macrophage Subtypes: SPP1+ Macrophages as a Key Player and Therapeutic Target in Cardiac Fibrosis? by Moritz Uhlig, Sebastian Billig, Jan Wienhold, David Schumacher

“…Advances in single-cell transcriptomics have revealed the pivotal role of SPP1+ macrophages in the pathogenesis of cardiac fibrosis, positioning them as critical mediators and promising therapeutic targets. …”
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Root growth and branching are enabled by brassinosteroid-regulated growth anisotropy and carbon allocation by Hitaishi Khandal, Guy Horev, Bas van den Herik, Yoram Soroka, Tamar Lahav, Tamar Avin-Wittenberg, Kirsten ten Tusscher, Sigal Savaldi-Goldstein

“…Our interdisciplinary approach, applied to two plant species and integrating shoot and root hormonal functions, provides a new understanding of how RSA is modulated at various scales.…”
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<i>ARID2</i> Deficiency Enhances Tumor Progression via ERBB3 Signaling in <i>TFE3</i>-Rearranged Renal Cell Carcinoma by Jinglong Tang, Shintaro Funasaki, Hidekazu Nishizawa, Shoichiro Kuroda, Takanobu Motoshima, Chang Wu, Amany Sayed Mawas, Yorifumi Satou, Yuichiro Arima, Hisashi Hasumi, Ryosuke Jikuya, Kazuhide Makiyama, Yuichi Oike, Yasuhito Tanaka, Masaya Baba, Tomomi Kamba

“…<i>ARID2</i> knockout (KO) enhanced TFE3-RCC cell migration, proliferation, and tumor growth. Transcriptomic analysis revealed ERBB3 as a key target gene regulated by both PRCC-TFE3 and <i>ARID2</i>. …”
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Development of a circadian-related prognostic signature highlights RBM17 as a stemness regulator in liver cancer by Jingsong Yan, Xiao Yang, Jiabin Lu, Shasha Wu, Yanchen Wang, Yuyang Du, Jingyi Zheng, Fenfen Wang, Han Gao, Hui Yang, Shaoyan Xi, Yan Li

“…Through the integration of single-cell, bulk, and spatial transcriptomics, we further elucidated the interconnections between LCGs dysregulation and the tumor microenvironment. …”
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Developing an efficient protocol for RNA extraction from Morelet's crocodile caudal scute biopsies by Asela Marisol Buenfil-Rojas, Mauricio González-Jáuregui, Mari Ochiai, Hisato Iwata

“…Further validation through quantitative PCR analyses confirmed the suitability of the extracted RNA for studies on gene expression levels and were sufficient for next-generation sequencing (NGS). This protocol may provide a basis for developing similar methodologies for other non-model species with hard tissues. • This study optimizes non-invasive RNA extraction from crocodile scutes, enabling conservation research and transcriptomic analysis.…”
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A TRIM Family-Based Strategy for TRIMCIV Target Prediction in a Pan-Cancer Context with Multi-Omics Data and Protein Docking Integration by Yisha Huang, Jiajia Xuan, Jiayan Liang, Xixi Liu, Yonglei Luo, Xuejuan Gao, Wanting Liu

“…TRIMCIVtargeter not only provides a cancer-related resource for studying TRIMCIV-mediated regulatory mechanisms but also offers a new perspective for family-specific PPI prediction, holding significant implications for biomarker discovery and therapeutic targeting in oncology. …”
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Integrative analysis of circulating tumor cells (CTCs) and exosomes from small‐cell lung cancer (SCLC) patients: a comprehensive approach by Dimitrios Papakonstantinou, Argyro Roumeliotou, Evangelia Pantazaka, Athanasios‐Nasir Shaukat, Athina Christopoulou, Angelos Koutras, Foteinos‐Ioannis Dimitrakopoulos, Vassilis Georgoulias, Anastasia Xagara, Evangelia Chantzara, Fillipos Koinis, Athanasios Kotsakis, Constantinos Stathopoulos, Galatea Kallergi

“…Conclusively, a comprehensive analysis of CTCs and exosomes provides useful prognostic and potential diagnostic tools for SCLC patients.…”
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Development and application of a stepwise-assembled modular biomimetic lung chip for analyzing formaldehyde-induced cellular ferroptosis by Siyu Chen, Zezhi Li, Quanping Yan, Chenfeng Hua, Pingping Shang, Kejian Liu, Junwei Zhao, Guangxiang Jin, Xiang Li, Fuwei Xie

“…Using this chip to investigate the formaldehyde-induced cellular ferroptosis, BEAS-2B cells were exposed to formaldehyde under a concentration gradient. Transcriptomic sequencing revealed the effects of different formaldehyde concentrations on the expression of ferroptosis-related genes in cells, identifying 12 ferroptosis-related genes (FRGS) and an enhancement of oxidative stress. …”
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Identification of stemness subtypes and prognostic modeling in thyroid cancer: the critical role of DPYSL3 in tumor progression and immune microenvironment by Jialong Yu, Wei Luo, Guangwei Xu, Mei Tao, Yuqi Wang, Qiman Dong, Linfei Hu, Xiukun Hou, Jingzhu Zhao, Dapeng Li, Songfeng Wei, Xianhui Ruan, Xiangqian Zheng

“…Conclusion This study provides a new strategy for thyroid cancer immunotherapy by integrating stemness-based classification and prognostic modeling.…”
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Candida albicans and Staphylococcus aureus reciprocally promote their virulence factor secretion and pro-inflammatory effects by Raymond Pasman, Bastiaan P. Krom, Martijs J. Jonker, Wim C. de Leeuw, Gertjan Kramer, Stanley Brul, Sebastian A. J. Zaat, Jianbo Zhang, Jianbo Zhang

“…Our findings support that C. albicans and S. aureus reciprocally promote their virulence potential and pro-inflammatory effects, which may provide mechanistic insights into the increased morbidity and mortality during their co-infection in vivo.…”
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Integrative Multi‐Omics Approaches Reveal Selectivity Profiles and Molecular Mechanisms of FIIN‐2, a Covalent FGFR Inhibitor by Ying Fu, Dandan Zhu, Xiaojuan Chen, Lingzhi Qu, Ming Guo, Shuhong Zhang, Guangyu Xu, Zhuchu Chen, Maoyu Li, Yongheng Chen

“…The integrative multi‐omics approach provides a valuable framework for the development and optimization of covalent kinase inhibitors.…”
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