Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement by Jingye Cheng, Yong Jia, Camilla Hill, Tianhua He, Ke Wang, Ganggang Guo, Sergey Shabala, Meixue Zhou, Yong Han, Chengdao Li

“…Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. …”
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Adaptive mechanisms to hypoxia and hyperoxia in juvenile turbot, Scophthalmus maximus by Yi Chen, Yuntian Zhang, Rongwei Zhang, Hongsheng Deng, Xiangyu Meng, Kotoya Inaba, Tatsu Osato, Xiaoran Zhao, Xiaoran Zhao, Yuzhe Han, Yuzhe Han, Tongjun Ren, Tongjun Ren

“…The results suggest that hyperoxia significantly enhances turbot growth without compromising the composition of intestinal microbiome, whereas hypoxia markedly impairs growth and induces alterations in intestinal microbiome. Transcriptomic analysis revealed various pathways implicated in adaptation to both hypoxic and hyperoxic conditions, encompassing amino acid metabolism, protein metabolism, lipid metabolism, carbohydrate metabolism, the PPAR signaling pathway, etc. …”
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Therapeutic Potential of Emricasan, a Pan-Caspase Inhibitor, in Reducing Cell Death and Extracellular Matrix Accumulation in Fuchs Endothelial Corneal Dystrophy by Sohya Fujimoto, Mako Endo, Shigehito Tonomura, Fuuga Tsuji, Hirotaka Haraguchi, Kanna Hasegawa, Taisuke Numao, Ayaka Izumi, Theofilos Tourtas, Ursula Schlötzer-Schrehardt, Friedrich Kruse, Yuki Oyama, Masahito Ikawa, Albert S. Jun, Noriko Koizumi, Naoki Okumura

“…Endothelial cell density, hexagonality, cell size variation, and guttae area were evaluated by contact specular microscopy, while transcriptomic changes were analyzed via RNA sequencing. …”
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Platelet-derived extracellular vesicles induced through different activation pathways drive melanoma progression by functional and transcriptional changes by Zeynep Tavukcuoglu, Umar Butt, Alessandra V. S. Faria, Johannes Oesterreicher, Wolfgang Holnthoner, Saara Laitinen, Mari Palviainen, Pia R-M Siljander

“…Conclusions Our study revealed both shared and distinct, cancer-promoting functions of PEVs, which contributed to the transcriptome and metastatic capabilities of the melanoma spheroids. …”
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Low light reduces saffron corm yield by inhibiting starch synthesis by Weijing Yang, Weijing Yang, Xin Li, Xin Li, Fei Chang, Fei Chang, Xue Qiu, Xulong Huang, Xulong Huang, Zhan Feng, Zhan Feng, Jie Yan, Jie Yan, Qinghua Wu, Qinghua Wu, Feiyan Wen, Feiyan Wen, Jin Pei, Jin Pei, Tao Zhou, Tao Zhou

“…Despite the marked inhibition of photosynthetic capacity, initial DW, sucrose and glucose concentrations in leaves were comparable to those under NL. Carbohydrate analysis revealed that starch concentration in the mother corms under LL decreased by 18.00% relative to NL, while sucrose and glucose concentrations increased by 28.44% and 68.44%, respectively. …”
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Adventitial fibroblasts direct smooth muscle cell-state transition in pulmonary vascular disease by Slaven Crnkovic, Helene Thekkekara Puthenparampil, Shirin Mulch, Valentina Biasin, Nemanja Radic, Jochen Wilhelm, Marek Bartkuhn, Ehsan Bonyadi Rad, Alicja Wawrzen, Ingrid Matzer, Ankita Mitra, Ryan D Leib, Bence Miklos Nagy, Anita Sahu-Osen, Francesco Valzano, Natalie Bordag, Matthias Evermann, Konrad Hoetzenecker, Andrea Olschewski, Senka Ljubojevic-Holzer, Malgorzata Wygrecka, Kurt Stenmark, Leigh M Marsh, Vinicio de Jesus Perez, Grazyna Kwapiszewska

“…Bidirectional cellular crosstalk was examined using direct and indirect co-culture models, and phenotypic responses were assessed via transcriptome analysis. Results: PASMC and PAAF undergo distinct phenotypic shifts during pulmonary vascular remodeling, with limited shared features, such as reduced mitochondrial content and hyperpolarization. …”
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Local Inflammation Precedes Diaphragm Wasting and Fibrotic Remodelling in a Mouse Model of Pancreatic Cancer by Daria Neyroud, Andrew C. D'Lugos, Enrique J. Trevino, Chandler S. Callaway, Jacqueline Lamm, Orlando Laitano, Brittney Poole, Michael R. Deyhle, Justina Brantley, Lam Le, Andrew R. Judge, Sarah M. Judge

“…These biological processes were supported by changes in the diaphragm transcriptome. Ingenuity pathway analysis predicted factors involved in inflammatory responses to tissue injury, including TGF‐β1, angiotensin and PDGF BB, as top upstream regulators activated in diaphragms prior to and throughout cachexia progression, while PGC‐1α and the insulin receptor were among the top upstream regulators predicted to be suppressed. …”
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snRNA-seq reveals subcutaneous white adipose tissue remodeling upon return to thermoneutrality after cold stimulation by Yusha Yang, Yusha Yang, Guanyu Zhang, Ting Yi, Ting Yi, Shuran Yang, Shuran Yang, Shuai Wu, Yongqiang Zhang, Li Zhang, Xi Li, Xiuxuan Wu, Xiuxuan Wu, Jun Li, Danfeng Yang

“…Subsequently, we employed single-nucleus RNA sequencing (snRNA-seq) to comprehensively characterize iWAT cellular dynamics during cold stimulation and the subsequent two-week period after the return to thermoneutrality.ResultsOur findings revealed that while iWAT phenotypically reverts to a white state after 2 weeks of rewarming, as evidenced by structural, functional, and bulk transcriptomic characteristics, significant cold-induced molecular and cellular signatures persist. …”
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Molecular characterization and expression profiles of cytochrome P450 reductase gene in Sogatella furcifera (Hemiptera: Delphacidae) by YU Hang, LIU Su, ZHU Qingzi, ZHOU Wenwu, LIANG Qingmei, SHI Xiaoxiao, ZHU Zijie, ZHU Zengrong

“…The expression of SfCPR was activated soon (6 h) after treatment with buprofezin and imidacloprid, while the response of SfCPR expression to deltamethrin was relatively slow (12 h).In conclusion, this work is the first report about the cDNA sequence information, secondary structure and transcription profiles of CPR gene in the S. furcifera. …”
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OTUD1 regulates cytokine expression and related pathways in goose fatty liver by promoting deubiquitination of its target proteins by Xiaoyi Zhou, Ya Xing, Yuqing Wang, Mengqing Lv, Pei Zhang, Suyan Zhu, Jing Ge, Long Liu, Minmeng Zhao, Haizhou Gong, Daoqing Gong, Tuoyu Geng

“…OTUD1 gene overexpression and subsequent transcriptome sequencing analysis were performed to identify the differentially expressed genes (DEG) and the pathways where the DEGs are enriched. …”
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TLR3-overexpressing umbilical cord mesenchymal stromal cells suppress immune responses to attenuate high-risk corneal transplantation rejection by Yaqi Cheng, Huaxin Chen, Simin Gu, Weihua Li, Huan Yu, Jianqiang Zhang, Huini Zhang, Jiayi Lin, Haocheng Zhu, Youyu Liu, Wenqiong Li, Ting Fu, Haoyu Zeng, Tao Wang, Shiqi Ling

“…Methods New Zealand rabbits that underwent high-risk corneal transplantation were treated with UC-MSC-coated contact lenses (MSCohi-O), while blank lenses and untreated grafts served as controls. …”
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α-Mangostin prevents diabetic cardiomyopathy by inhibiting oxidative damage and lipotoxicity through the AKT–FOXO1–CD36 pathway by Xue Bai, Ziqian Zhang, Miao Zhang, Jiaojiao Xu, Keting Dong, Qian Du, Lei Chen, Ping Ma, Jianhong Yang

“…Molecular mechanisms were investigated through transcriptome analysis, quantitative PCR (RT-qPCR), and Western blotting. …”
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The Chinese Herbal TiaoGanXiaoZhi Formula Alleviates the Progression of Metabolic‐Associated Fatty Liver Disease by Regulating the Gut Microbiota by Wenying Qi, Xu Cao, Yue Chen, Hening Chen, Xiaoke Li, Ningyi Zhang, Ruijia Liu, Wei Wang, Shihao Zheng, Size Li, Qiyao Liu, Xiaobin Zao, Yong‐An Ye

“…Results Compared to the MAFLD mouse model group, TGXZ treatment significantly downregulated the weight of white adipose tissue (1.61 ± 0.66 vs. 3.06 ± 0.34 g, p < 0.0010), liver weight (1.22 ± 0.16 vs. 1.98 ± 0.39 g, p = 0.0031), and the levels of alanine aminotransferase (20.6 ± 3.4 vs. 46.1 ± 12.3 U/L, p < 0.0010), aspartate aminotransferase (99.9 ± 19.1 vs. 168.4 ± 34.3 U/L, p = 0.0014), cholesterol (2.95 ± 0.56 vs. 4.38 ± 0.34 mmol/L, p = 0.0053), triglycerides (2.25 ± 0.41 vs. 4.18 ± 0.67 mmol/L, p < 0.0010), low‐density lipoprotein (0.66 ± 0.11 vs. 1.41 ± 0.52 mmol/L, p = 0.0073), and total bile acid (0.71 ± 0.41 vs. 2.18 ± 0.61 mmol/L, p = 0.0017), except for high‐density lipoprotein (2.41 ± 0.81 vs. 2.55 ± 0.31 mmol/L, p = 0.5655). The liver transcriptome, fecal microbiota sequencing, and fecal lipidomics analysis demonstrated that TGXZ treatment improved the expression of genes related to lipid metabolism, alleviated intestinal microbiota disorders, and mitigated lipid disturbances caused by MAFLD. …”
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An Integrated Approach Utilizing Single-Cell and Bulk RNA-Sequencing for the Identification of a Mitophagy-Associated Genes Signature: Implications for Prognostication and Therapeu... by Yuke Zhang, Li Ding, Zhijin Zhang, Liliang Shen, Yadong Guo, Wentao Zhang, Yang Yu, Zhuoran Gu, Ji Liu, Aimaitiaji Kadier, Jiang Geng, Shiyu Mao, Xudong Yao

“…Target genes were narrowed down at the bulk transcriptome level to construct a PARD prognosis prediction nomogram. …”
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Antibacterial and antibiofilm activities and mechanisms of Toona sinensis extracts against Bacillus cereus and its application in milk by Yuru Wei, Lei Lei, Honglin Jiang, Qingquan Du, Decheng Liu, Lu Chen, Xiaoshan Shi, Yanxiang Wang, Jingjing Li, Yuanliang Hu, Xian Xia, Junming Tu

“…Moreover, the extracts demonstrated remarkable antibiofilm activity against B. cereus, reducing biofilm biomass to less than 40 % (P < 0.05). Transcriptome analysis revealed its antibacterial and antibiofilm mechanisms. …”
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Glucosylceramides containing very long-acyl-chain fatty acid are critical for cotton fiber elongation by influencing brassinosteroid synthesis and signaling by Qiaoling Wang, Xingying Yan, Qi Niu, Hongju Zhang, Huidan Tian, Zheng Chen, Fan Xu, Yu You, Yinghui Gao, Zhiqing Qiao, Ming Luo

“…Contrarily, suppressing GhGCS1 expression inhibited GluCer synthesis and fiber elongation, which was similar as the exogenous application of GluCer synthesis inhibitor, PDMP. Transcriptome analysis revealed that the fiber elongation regulated by GhGCS1 was associated with brassinosteroid (BR) synthesis and signaling related gene expression. …”
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DNA methylation changes during acute COVID-19 are associated with long-term transcriptional dysregulation in patients’ airway epithelial cells by Marey Messingschlager, Sebastian D Mackowiak, Maria Theresa Voelker, Matthias Bieg, Jennifer Loske, Robert Lorenz Chua, Johannes Liebig, Sören Lukassen, Loreen Thürmann, Anke Seegebarth, Sven Twardziok, Daria Doncevic, Carl Herrmann, Stephan Lorenz, Sven Klages, Fridolin Steinbeis, Martin Witzenrath, Florian Kurth, Christian Conrad, Leif E Sander, Naveed Ishaque, Roland Eils, Irina Lehmann, Sven Laudi, Saskia Trump

“…Hypomethylated regions affected immune regulatory genes, while hypermethylated regions were associated with genes governing ciliary function. …”
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Liver transplant-facilitated CD161+Vα7.2+ MAIT cell recovery demonstrates clinical benefits in hepatic failure patients by Wei Wang, Chen Dai, Peng Zhu, Mi Wu, Haoquan Zhang, Qing Wei, Ting Zhou, Xiaosheng Tan, Ying Jiang, Xue Cheng, Zhihui Liang, Xiongwen Wu, Zhishui Chen, Xiufang Weng

“…Liver transplantation facilitates a gradual recovery of recipient-originated MAIT cells. Transcriptome analysis reveals enhanced MAIT cell activation, while TCR mining demonstrates clonotype overlap between circulating and hepatic MAIT cells during significant liver injury. …”
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Cow Placenta Peptides Ameliorate D-Galactose-Induced Intestinal Barrier Damage by Regulating TLR/NF-κB Pathway by Yuquan Zhao, Zhi Zeng, Weijian Zheng, Zeru Zhang, Hanwen Zhang, Yuxin Luo, Kunshan Zhao, Yuyan Ding, Wei Lu, Fuxing Hao, Yixin Huang, Liuhong Shen

“…CPP notably alleviated intestinal oxidative stress and inflammation, restored tight junction expression, and enhanced intestinal barrier integrity. Transcriptome sequencing identified 1396 DEGs associated with CPP’s effects, highlighting <i>TLR4</i>, <i>IL-1β</i>, and <i>Mmp9</i> as core regulatory genes through protein–protein interaction network analysis. …”
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The extracellular matrix protein type I collagen and fibronectin are regulated by β-arrestin-1/endothelin axis in human ovarian fibroblasts by Ilenia Masi, Flavia Ottavi, Valentina Caprara, Danila Del Rio, Martina Kunkl, Francesca Spadaro, Valerio Licursi, Loretta Tuosto, Anna Bagnato, Laura Rosano’

“…At the molecular level, ET-1 triggers the activation of COL1A1 promoter activity and its enhanced expression via β-arr1 nuclear function. Transcriptome analysis of β-arr1-silenced HOFs confirms the nuclear role of β-arr1 in collagen and ECM remodeling-related protein transcriptional regulation. …”
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