Molecular turn in Yersinia pestis pathogenesis: implications of the gppA frameshift for bacterial survival in human macrophage by Hongyan Chen, Shiyang Cao, Yazhou Zhou, Tong Wang, Yang Jiao, Yafang Tan, Yarong Wu, Yifan Ren, Yajun Song, Jing-Ren Zhang, Zongmin Du, Ruifu Yang

“…This adaptive evolution potentially explains why microtus Y. pestis strains exhibit attenuated virulence in humans in contrast to the lethal pathogenicity of non-microtus strains. Transcriptome analysis suggests that the disturbed balance of the ratio of ppGpp to pppGpp caused by GppA inactivation results in an upregulation of genes involved in the synthesis of branched-chain amino acids, which are essential for bacterial growth. …”
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Genetic and therapeutic heterogeneity shape the baseline and longitudinal immune ecosystem of ovarian clear cell carcinoma by Min Yu, Fei Xu, Xiaohua Wu, Jiajia Li, Xiaojun Chen, Lihua Chen, Jiaxin Chen, Mengdong Ni, Siyu Xia, Jiana Li, Chaohua Liu

“…Background Ovarian clear cell carcinoma (OCCC) is a rare and chemo-resistant subtype of ovarian cancer. While immunotherapy has demonstrated effectiveness in some OCCC cases, the mechanisms for heterogeneous immunoreactivity and potential combinatory strategies remain unclear.Methods Tumor samples from 13 patients with OCCC underwent single-cell mRNA-seq and TCR-seq to generate 1 40 683 cells transcriptome, while additionally 31 formalin-fixed paraffin-embedded samples were used for immunohistochemistry. …”
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Effects of Genetic Polymorphism in the <i>IFI27</i> Gene on Milk Fat Traits and Relevance to Lipid Metabolism in Bovine Mammary Epithelial Cells by Xinyi Jiang, Zhihui Zhao, Xuanxu Chen, Fengshuai Miao, Jing Li, Haibin Yu, Ping Jiang, Ziwei Lin

“…Haplotype frequency analysis showed that H5H5 was associated with lower milk fat content (<i>p</i> < 0.05), while milk from H5H6 animals had a higher fat content (<i>p</i> < 0.05). …”
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TGF-β3 Restrains Osteoclastic Resorption Through Autophagy by Hui Liao, Yiqin Pan, Yiming Liu, Yuxiao Li, Shiyi Huang, Shan Ding, Qi Xiang

“…Analysis of the full transcriptome of hPDLSCs (human periodontal ligament stem cells) revealed that the expression of RANKL was significantly up-regulated after TGF-β3 treatment during osteogenesis, which suggests its involvement in clock-controlled autophagy in bone metabolism. …”
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Action mechanism of a novel agrichemical quinofumelin against Fusarium graminearum by Qian Xiu, Xiaoru Yin, Yuanyuan Chen, Ziyang Zhang, Yushuai Mao, Tianshi Wang, Jie Zhang, Mingguo Zhou, Yabing Duan

“…However, there is currently no available information on its mechanism of action. Here, we used transcriptome and metabolome analysis to observe a co-enrichment pattern of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) within pyrimidine biosynthesis pathway (PBP), identifying down-regulation of dihydroorotate dehydrogenase (DHODH). …”
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Human cytomegalovirus UL23 inhibits immune cell migration and blocks antiviral immune cell responses by reducing the expression of chemokines CCL2 and CCL5 by Hankun Wang, Chunling Zhang, Moran Li, Wangchun Zhao, Jialin Wang, Yanhong Ran, Xiaoping Yang, Zemin Deng, Jun Chen, Hongjian Li

“…Viruses have also evolved multiple strategies to resist the host’s immune system while coexisting with the host. In this study, based on RNA sequencing transcriptome differential analysis, we found that HCMV encoded UL23 May specifically down-regulate chemokines Chemokine ligand 2 (CCL2) and Chemokine ligand 5 (CCL5). …”
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Overexpression of MYB transcription factor LrAN2 from Lycium ruthenicum activated the anthocyanin biosynthesis in the leaf and fruit of Lycium barbarum by Yunlong Liang, Wenyan Ma, Jinglei Hu, Yanyan Jiang, Shiming Li, Yun Li, Xuemei Bao, Dong Cao, Baolong Liu

“…The results showed that the stems, leaves, and fruits of transgenic plants were purple and contained significantly higher anthocyanin levels compared to the wild-type plants. Transcriptome analysis of leaf and fruit identified 5,832 differentially expressed genes (DEGs) in leaves and 2,029 DEGs in fruits, with 910 genes common to both tissues. …”
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Dynamic Alterations in DNA Methylation of CD4+ T Cells and Macrophages in a Murine Model of Tuberculous Pleural Infection Induced by BCG Vaccination by Ming‐Ming Shao, Qing‐Yu Chen, Xin Zhang, Shu‐Feng Dong, Rui‐Qi Wei, Huan‐Zhong Shi, Feng‐Shuang Yi

“…Notably, macrophages exhibited the most pronounced differences in DNA methylation profiles on Day 1, while CD4+ T cells demonstrated gradual changes over time. …”
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AmMADS47 of Agropyron mongolicum negatively regulates drought tolerance in rice by Bobo Fan, Bobo Fan, Hushuai Nie, Xiaolei Li, Yu Ma, Ersuo Lv, Jing Wu, Xiuxiu Yan, Yongqing Zhai, Yan Zhao, Jie Liu, Xiaohong Du, Yanhong Ma

“…Gene regulation in response to osmotic stress was analyzed in the three pathways, showing that, compared to WTD, OED exhibited up-regulation of a few drought-sensitive genes, while most genes positively regulating drought in WTD were down-regulated in OED. …”
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The role of CD47 in immune escape of colon cancer and its correlation with heterogeneity of tumor immune microenvironment by Qiu-Si Tian, ChunMei Zhang, Zhi-Jun Bao, ZhiGang Pei

“…Immunohistochemical analysis was performed on 90 samples, while the remaining 6 were subjected to multiplex immunofluorescence. …”
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ROS-Mediated Unfolded Protein Response Activation Drives Hepatocyte Apoptosis in Mesaconitine-Induced Liver Injury by Jin Tian, Yubin Zhuang, Yinuo Liu, Yihong Zheng, Xuyang Liu, Shiyu Lin, Chenhua Zheng, Zekai Wu

“…A global transcriptome analysis revealed the substantial upregulation of unfolded protein response (UPR)-associated genes, notably <i>hsp90b1</i>, <i>hspa5</i>, and <i>hspb9</i>, indicating that MA-induced oxidative stress triggered endoplasmic reticulum (ER) stress and subsequent UPR activation. …”
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CzcR-dependent reduction of catalase gene expression and induction of catalase activity in Pseudomonas aeruginosa during zinc excess by Ting Li, Zhifeng Mo, Yuying Zhao, Huiluo Cao, Shuo Sheng, Zeling Xu

“…Results In the study, comparative transcriptome analysis comprehensively described the CzcR-dependent and -independent gene regulatory pattern in P. aeruginosa during Zn excess, which revealed the counteractive co-regulation of two key H2O2-detoxifying catalase genes katA and katB through CzcR-dependent and -independent pathways in response to Zn excess. …”
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Role of KNDy neurons in puberty onset in male offspring following prenatal androgen exposure by Runfei Ge, Yun Zhang, Yongting Yuan, Tingting Li, GuiYu Qiu, Shuaijun Guo, Lianguo Fu

“…Hypothalamic samples of six male offspring rats at postnatal day (PND) 21 (n = 3 per group) were collected for transcriptome analysis. The time of puberty onset was recorded in 36 male offspring (n = 18 per group). …”
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Cysteine-Mediated Root Growth Promotion in Strawberry (<i>Fragaria × ananassa</i>) Induced by <i>TgSWO</i>-Overexpressing <i>Trichoderma</i> by Xiaohui Meng, Yuanhua Wang, Xu Zhang, Hongjun Yang, Yilei Lu, Ye Xu, Xiong Zhang, Zhiming Yan

“…Field-emission scanning electron microscopy (SEM) of the S-OE roots revealed denser hyphal colonization. Transcriptome analysis of S-OE showed a decrease in genes related to defense and detoxification, while genes for cell-wall growth and hormone signaling increased, shifting focus from defense to growth. …”
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A novel gene signature for predicting outcome in colorectal cancer patients based on tumor cell-endothelial cell interaction via single-cell sequencing and machine learning by Lina Pang, Qingxia Sun, Wenyue Wang, Mingjie Song, Ying Wu, Xin Shi, Xiaonan Shi

“…Specifically, Malignant Cluster01 subpopulations primarily served as signal senders, while Tip-like endothelial cells acted as receivers in PARs signaling. …”
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Unraveling the Multilayered Regulatory Networks of miRNAs and PhasiRNAs in <i>Ginkgo biloba</i> by Qixuan Wei, Ang Xu, Anqi Zhao, Lisha Shi, Qi Wang, Xiaoming Yang, Meiling Ming, Liangjiao Xue, Fuliang Cao, Fangfang Fu

“…We conducted an in-depth analysis of deep sequencing data from the gymnosperm <i>Ginkgo biloba</i>, encompassing sRNA, transcriptome, and degradome libraries. …”
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Integration of Bulk and Single-Cell RNA Sequencing to Identify RNA Modifications-Related Prognostic Signature in Ovarian Cancer by Wang S, Zheng Q, Chen L

“…Subsequent analyses covered enrichment analysis, immune microenvironment, mutation analysis, and chemotherapeutic drug sensitivity. …”
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Response of different cotton genotypes to salt stress and re-watering by Kang Zhao, Tao Yang, Bo Pang, Honggang Wang, Zhining Yang, Weiwei Liang, Cun Rui, Wengwei Gao

“…Transcriptome analysis was performed on cotton leaves under salt stress and re-watering conditions. …”
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Lipophilic Resazurin in Bioelectrochemical Systems: Role in Regulating Carbon Metabolic Pathways by Siyu Tan, Xiao Zhu, Xinxin Wang, Huangsheng Su, Zongqiang Zhu, Xiaobo Luo, John R. Reinfelder, Yundang Wu, Fangbai Li

“…Transcriptome analysis reveals significant upregulation of genes involved in the NADH‐dependent metabolic pathway (e.g., nuoHIJKLMN) and ATP synthesis (atpABDEFGH) under resazurin conditions. …”
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Microglia regulate cortical remyelination via TNFR1-dependent phenotypic polarization by Athena Boutou, Ilias Roufagalas, Katerina Politopoulou, Spyros Tastsoglou, Maya Abouzeid, Giorgos Skoufos, Laia Verdu de Juan, Jeong Hun Ko, Vasiliki Kyrargyri, Artemis G. Hatzigeorgiou, Christopher J. Barnum, Raymond J. Tesi, Jan Bauer, Hans Lassmann, Michael R. Johnson, Lesley Probert

“…Here, we show that microglia-specific deletion of tumor necrosis factor receptor 1 (TNFR1) and pharmacological inhibition of soluble TNF (solTNF) or downstream interleukin-1 receptor (IL-1R) allow maturation of highly activated disease-associated microglia with increased size and myelin phagocytosis capacity that accelerate cortical remyelination and motor recovery. Single-cell transcriptomic analysis of cortex at disease onset reveals that solTNF inhibition enhances reparative IL-10-responsive while preventing damaging IL-1-related signatures of disease-associated microglia. …”
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