Type I-E* CRISPR-Cas of Klebsiella pneumoniae upregulates bacterial virulence by targeting endogenous histidine utilization system by Jieying Li, Yuxiao Liu, Jingsi Jiang, Fang Chen, Nan Zhang, Xun Kang, Lin Liu, Yingjuan Wang, Qianfeng Xia, Chuanlong Zhu, Dai Kuang

“…Furthermore, the overexpression of hutT mitigated CRISPR-Cas-mediated repression of the Hut operon, as observed in virulence assays, while simultaneous deletion of hutH and casABECD restored the reduced virulence in the ΔcasABECD strain. …”
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Next-Generation Sequencing–Based Molecular Profiling of Conjunctival Squamous Cell Carcinoma and Its Potential Application for Therapy by Hakan Demirci, MD, Josh N. Vo, PhD, Yi-Mi Wu, PhD, Victor Elner, MD, Arul M. Chinnaiyan, MD, PhD, Dan Robinson, PhD, F. Yesim Demirci, MD

“…Methods: Integrative exome and transcriptome analysis of fresh-frozen tumor and matching normal samples. …”
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MicroRNA-27b alleviates septic cardiomyopathy by targeting the Mff/MAVS axis by Xincai Wang, Long Huang, Jingqing Xu, Min Li, Hongxuan Zhang, Yuqing Yao, Yaqing Liu, Xingsheng Lin, Xiuling Shang

“…ObjectiveTo investigate the protective role of microRNA-27b (miR-27b) in septic cardiomyopathy (SCM) and its regulatory mechanism on the mitochondrial fission factor (Mff)/mitochondrial antiviral signaling protein (MAVS) axis.MethodsTranscriptome data from septic patients’ cardiac tissues (GSE79962) were analyzed. …”
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Unveiling the Mechanisms of a Remission in Major Depressive Disorder (MDD)-like Syndrome: The Role of Hippocampal Palmitoyltransferase Expression and Stress Susceptibility by Careen A. Schroeter, Anna Gorlova, Michael Sicker, Aleksei Umriukhin, Alisa Burova, Boris Shulgin, Sergey Morozov, Joao P. Costa-Nunes, Tatyana Strekalova

“…At the 1st after-stress week, sucrose preference, forced swim, novel cage, and fear-conditioning tests were carried out; the sucrose test and 5-day Morris water maze test followed by a sacrifice of mice on post-stress day 31 for all mice were performed. Transcriptome Illumina analysis of hippocampi was carried out. …”
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Identification of <i>Peroxiredoxin</i> (<i>PRX</i>) Genes from Pepper Fruits: Involvement in Ripening and Modulation by Nitric Oxide (NO) by Fátima Ramírez-Mellado, Salvador González-Gordo, José M. Palma, Francisco J. Corpas

“…Among these, only CaPRX1-Cys was not detected in the transcriptome (RNA-Seq) of sweet pepper fruits reported previously. …”
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Preclinical and clinical evaluation of intratumoral injection of an IL-12 expressing SKV-012 oncolytic virus for advanced solid tumors by Jing Jin, Zheng Jiang, Jun Liu, Hui Yang, Long Xu, Weiwei Zhang, Xingchen Peng, Nian Yang, Zongliang Zhang, Liangxue Zhou, Aiping Tong, Huaqing Lu, Yongdong Chen, Liyuan Jin

“…Primary endpoints were safety and tolerability, while secondary endpoints were antitumor response and changes in the tumor microenvironment (TME), assessed by RECIST v1.1 criteria and multiplex immunohistochemistry and single-cell transcriptome analysis.Results SKV-012-infected tumor cells secreted high levels of IL-12 and exhibited increased ICP34.5 expression. …”
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Dissecting the genetic architecture of yield-related traits by QTL mapping in maize by Hao Zhang, Hao Zhang, Ting Li, Zhenyu Zhang, Jie Wang, Haoxiang Yang, Jiachen Liu, Wanchao Zhu, Wanchao Zhu, Jiquan Xue, Jiquan Xue, Shutu Xu, Shutu Xu

“…Key candidate genes were identified through the integration of RNA-seq data, gene-based association analysis and classic yield-related genes network dataset.ResultsGreater phenotypic variation was observed in RIL population than that in the IB1 and IB2 populations, while similar phenotype variations between IB1 and IB2 populations. …”
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Dendritic cell vaccination and CD40-agonist combination therapy licenses T cell-dependent antitumor immunity in a pancreatic carcinoma murine model by Sjoerd H van der Burg, Thorbald van Hall, Heleen Vroman, Menno van Nimwegen, Christianne Groeneveldt, Priscilla Kinderman, Dana A M Mustafa, Nadine van Montfoort, Joachim Aerts, Melanie Lukkes, Sai Ping Lau, Casper H J van Eijck, Larissa Klaase, Mandy van Gulijk, Jasper Dumas, Sanne L A Lievense, Ralph Stadhouders, Yunlei Li, Andrew Stubbs, Koen A Marijt, Floris Dammeijer

“…In established disease, combination with stimulating CD40 antibody was necessary to improve survival, while anti-CD40 alone was ineffective. Extensive analysis of the TME showed that anti-CD40 monotherapy did improve CD8 +T cell infiltration, but these essential effector cells displayed hallmarks of exhaustion, including PD-1, TIM-3 and NKG2A. …”
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IL1RAP is an immunotherapeutic target for normal karyotype triple-mutated acute myeloid leukemia by Arnaud Métois, Marie-Eve Bordeleau, Louis Theret, Azadeh Hajmirza, Ossama Moujaber, Jean-François Spinella, Jalila Chagraoui, Nadine Mayotte, Isabel Boivin, Éric Audemard, Léo Aubert, Véronique Lisi, Banafsheh Khakipoor, Azer Farah, Éric Bonneil, Alma Robert, Julie Lippens, Anna Moraitis, François Béliveau, Albert Feghaly, Geneviève Boucher, Richard Marcotte, Patrick Gendron, Pierre Thibault, Sébastien Lemieux, Guillaume Richard-Carpentier, Vincent-Philippe Lavallée, Josée Hébert, Philippe P. Roux, Guy Sauvageau

“…Transcriptome analysis was carried out on the 691 primary AML samples, and single-cell RNA sequencing was conducted on 23 primary AML samples. …”
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Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases by Alba Segarra‐Casas, Cristina Domínguez‐González, Daniel Natera‐de Benito, Solange Kapetanovic, Aurelio Hernández‐Laín, Berta Estévez‐Arias, Laura Llansó, Carlos Ortez, Cristina Jou, Itxaso Martí‐Carrera, Arístides López‐Márquez, Maria José Rodríguez, Laura González‐Mera, Velina Nedkova, Roberto Fernández‐Torrón, Benjamín Rodríguez‐Santiago, Cecília Jimenez‐Mallebrera, Raul Juntas‐Morales, Adolfo López‐de Munain, Jordi Surrallés, Andrés Nascimento, Eduard Gallardo, Montse Olivé, Pia Gallano, Lidia González‐Quereda

“…Here, we implemented transcriptome analysis of muscle biopsies as a complementary diagnostic tool for patients with muscle disease but no definitive genetic diagnosis after exome sequencing. …”
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Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses by Sarah Buddle, Leysa Forrest, Naomi Akinsuyi, Luz Marina Martin Bernal, Tony Brooks, Cristina Venturini, Charles Miller, Julianne R. Brown, Nathaniel Storey, Laura Atkinson, Timothy Best, Sunando Roy, Sian Goldsworthy, Sergi Castellano, Peter Simmonds, Heli Harvala, Tanya Golubchik, Rachel Williams, Judith Breuer, Sofia Morfopoulou, Oscar Enrique Torres Montaguth

“…Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. …”
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Characterization of full-length long noncoding RNAs and identification of virus-responsive lncRNAs in Sogatella furcifera by Yawen Ban, Yawen Ban, Ting Cui, Ting Cui, Lifei Zhao, Lifei Zhao, Xue Li, Xue Li, Qing Bai, Qing Bai, Qingfa Wu, Qingfa Wu

“…Stage-specific lncRNAs were predominantly expressed during embryogenesis (e.g., 93 transcripts between 0 and 72 h post-oviposition) and molting (e.g., 16 in pre-ecdysis), while sex-biased expression patterns emerged after 24 h. …”
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Emu-miR-10a-5p in Echinococcus multilocularis-derived-extracellular vesicles alleviates airway inflammation in mice with allergic asthma by inhibiting macrophage M2a polarization t... by Yunzhuo Xin, Yunzhuo Xin, Rou Wen, Rou Wen, Rou Wen, Dong Song, Jing Xiao, Jing Xiao, Xiaoping Gao, Mei Yin, Yanli Bai, Jie Wang, Jie Wang, Xiangyu Zhou, Jiaqing Zhao, Jiaqing Zhao, Jiaqing Zhao

“…The gene expression changes in MH-S cells after transfect with emu-miR-10a-5p mimics was analyzed through transcriptome sequencing. We established a mouse model of ovalbumin (OVA)-induced allergic asthma. …”
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Bridging the Gap: Biofilm-mediated establishment of Bacillus velezensis on Trichoderma guizhouense mycelia by Jiyu Xie, Xinli Sun, Yanwei Xia, Lili Tao, Taimeng Tan, Nan Zhang, Weibing Xun, Ruifu Zhang, Ákos T. Kovács, Zhihui Xu, Qirong Shen

“…To resolve this contradiction, we developed an inoculation method, that allows B. velezensis colonization of T. guizhouense hyphae and performed a transcriptome analysis. During colonization of the fungal hyphae, B. velezensis SQR9 upregulates expression of biofilm related genes (e.g. eps, tasA, and bslA) that is distinct from free-living cells. …”
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Overexpression of the ABA Synthesis Gene OsABA2 Enhances Seed Storability in Rice by Yongxiang Liao, Pengfei Jiang, Mingming Zhang, Fangli Jin, Mengyuan Li, Jiazhi Dong, Daiming Guo, Yingxiu Liao, Asif Ali, Saira Saleem, Xiangyang Zhang, Qinggui Jiang, Su Liu, Hongyu Zhang, Xiaoqiong Chen, Kangxi Du, Hao Zhou, Duo Xia, Peizhou Xu, Xianjun Wu

“…Correspondingly, the contents of hydrogen peroxide and malondialdehyde were lower, whereas catalase activity and total antioxidant capacity were higher in OsABA2-OE lines after artificial aging treatments. Comparative transcriptome analysis further revealed that the overexpression of OsABA2 may enhance seed storability by modulating the expression of ROS scavenging genes. …”
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Mechanistic insights into JSS1_004-mediated antagonism of the DndBCDE-FGH restriction system and engineering applications by Yu He, Susu Jiang, Fang Wang, Junwu Bi, Siting Li, Fuliang Yin, Shi Chen, Chao Chen, Lianrong Wang

“…Notably, JSS1_004 exhibits pleiotropic effects on host physiology, including repressing the dndBCDE-FGH operon confirmed by transcriptome. ChIP-seq analysis further revealed that JSS1_004 binding to promoter regions and coding sequences of genes associated with protein synthesis machinery, including tRNA, rRNA, and ribosomal subunit genes (SSU/LSU), thereby hijacking the host’s translational apparatus. …”
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LncRNA PELATON regulates Th2 cell differentiation by miR-10b-5p/GATA3 axis in allergic rhinitis by Zhen Liu, MD, Yumei Li, PhD, Xiangkun Zhao, MM, Qi Sun, MD, Yu Zhang, MD, Yaqi Wang, MM, Han Fang, MD, Yujuan Yang, MD, Yakui Mou, MD, Xicheng Song, MD

“…Spearman's correlation analysis was used to calculate the correlation between the 2 variables. …”
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CircSLC22A3 inhibits the invasion and metastasis of ESCC via the miR-19b-3p/TRAK2 axis and by reducing the stability of m6A-modified ACSBG1 mRNA by Yingjie Pan, Hang Yang, Jiayi Zhang, Ruolan Zhang, Yun Liu, Jun Bie, Qiaoling Chen, Yan Qiao, Kang Liu, Guiqin Song

“…Downstream miR-19b-3p and target gene TRAK2 were screened by bioinformatics analysis and RT-qPCR, with binding confirmed via luciferase reporter assays. …”
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Lycium barbarum glycopeptide ameliorates aging phenotypes and enhances cardiac metabolism by activating the PINK1/Parkin-mediated mitophagy pathway in D-galactose-induced mice by Tianchan Peng, Jian Xiang, Yun Tian, Xiaogen Tang, Lina Wang, Lijuan Gao, Oscar Junhong Luo, Li’an Huang, Guobing Chen

“…Results: LbGp treatment improved the aging phenotypes of D-galactose-induced mice, with a pronounced enhancement in cardiac function compared to neurocognitive and skeletal muscle functions. Transcriptome analysis indicated that LbGp ameliorated energy metabolism in the heart. …”
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Identification of a PANoptosis-related gene signature reveals therapeutic potential of SFRP2 in pulmonary arterial hypertension by Li Li, Mukamengjiang Juaiti

“…Gene expression was further validated using a rat PAH model and pulmonary artery fibroblasts (PAAFs), while hub gene functions were investigated at the cellular level through Western blot, CCK-8, and flow cytometry assays.ResultsThrough integrated transcriptomic analysis, SFRP2 was identified as a feature gene related to PAH and PANoptosis. …”
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