New insights into the transcription factor regulatory networks driving peel coloration under hormone induction analyzed by transcriptomics and metabolomics in tangor ‘Murcot’ by Yang Chen, Yang Chen, Lei Yang, Lei Yang, Shuang Li, Min Wang, Jianjun Yu, Wenqin Bai, Wenqin Bai, Wenqin Bai, Lin Hong, Lin Hong

“…Of these, two novel transcription factors, the ethylene-responsive transcription factor ABR1 and the HD-Zip transcription factor ATHB7, were uncovered through both transcriptomic analysis and weighted gene co-expression network analysis. …”
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Understanding Human Cerebral Malaria through a Blood Transcriptomic Signature: Evidences for Erythrocyte Alteration, Immune/Inflammatory Dysregulation, and Brain Dysfunction by Sandrine Cabantous, Belco Poudiougou, Aurélie Bergon, Abdoulaye Barry, Aboubacar A. Oumar, Abdoulaye M. Traore, Christophe Chevillard, Ogobara Doumbo, Alain Dessein, Sandrine Marquet

“…We have performed a whole transcriptomic analysis of blood samples from Malian children with CM or uncomplicated malaria (UM). …”
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Dietary Cholesterol Supplementation Inhibits the Steroid Biosynthesis but Does Not Affect the Cholesterol Transport in Two Marine Teleosts: A Hepatic Transcriptome Study by Ziling Song, Haiyan Xiong, Xiaoxue Meng, Qiang Ma, Yuliang Wei, Yanlu Li, Jian Liu, Mengqing Liang, Houguo Xu

“…In order to evaluate the effects of dietary cholesterol supplementation (D-CHO-S) on fish physiology, a liver transcriptome analysis was performed following a feeding experiment on turbot and tiger puffer with different levels of dietary cholesterol. …”
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Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. by Prabhakar Rajan, Caroline Dalgliesh, Phillippa J Carling, Thomas Buist, Chaolin Zhang, Sushma N Grellscheid, Kelly Armstrong, Jacqueline Stockley, Cedric Simillion, Luke Gaughan, Gabriela Kalna, Michael Q Zhang, Craig N Robson, Hing Y Leung, David J Elliott

“…Although several microarray-based studies have identified androgen-regulated genes, here we identify in-parallel global androgen-dependent changes in both gene and alternative mRNA isoform expression by exon-level analyses of the LNCaP transcriptome. While genome-wide gene expression changes correlated well with previously-published studies, we additionally uncovered a subset of 226 novel androgen-regulated genes. …”
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Integrated transcriptome and metabolome analyses reveals the mechanisms of function loss of Lr29 leaf rust resistance gene at high temperatures in wheat by Liwen Wang, Yang Yu, Hang Li, Mingzhu Lu, Shubo Cao, Ziqi Li, Haoyuan Song, Laszlo Purnhauser, Jinlong Li, Jiajie Wu

“…We also found that, at high temperatures, Lr29 downregulated the genes and metabolites associated with glycolysis and the tricarboxylic acid (TCA) cycle, while genes and metabolites related to the shikimic acid pathway were upregulated. …”
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Single-cell and spatial transcriptomic analyses revealing tumor microenvironment remodeling after neoadjuvant chemoimmunotherapy in non-small cell lung cancer by Xiaolu Cui, Siyuan Liu, He Song, Jingjing Xu, Yanbin Sun

“…A total of 16 lung cancer tissue samples were collected from a cohort of 12 NSCLC patients and subjected to single-cell RNA and spatial transcriptome sequencing. Our data demonstrated that the distribution of CD4 + Treg T cells and mCAFs indicated an immunosuppressive tumor microenvironment, while the accumulation of CD4 + Th17 T cells and iCAFs could act as a positive marker for the sensitivity to chemoimmunotherapy. …”
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Integrated Multi-Omics of the Longissimus Dorsal Muscle Transcriptomics and Metabolomics Reveals Intramuscular Fat Accumulation Mechanism with Diet Energy Differences in Yaks by Jingying Deng, Pengjia Bao, Ning Li, Siyuan Kong, Tong Wang, Minghao Zhang, Qinran Yu, Xinyu Cao, Jianlei Jia, Ping Yan

“…Meat quality assessment showed that the meat quality of the High-energy diet group (1.53 MJ/Kg, G) and the Medium-energy diet group (1.38 MJ/Kg, Z) were significantly improved compared with that of the Low-energy diet group (0.75 MJ/Kg, C), in which IMF content in the LD of yaks in G group was significantly higher (<i>p</i> < 0.05) compared with Z and C groups. Further analysis by combined transcriptomics and lipid metabolomics revealed that the differences in IMF deposition mainly originated from the metabolism of lipids, such as TG (triglycerides, TG), PS (phosphatidylserine, PS), and LPC (lysophosphatidylcholine, LPC), and were influenced by <i>SFRP4</i>, <i>FABP4</i>, <i>GADD45A</i>, <i>PDGFRA</i>, <i>RBP4</i>, and <i>DGAT2</i> genes, further confirming the importance of lipid–gene interactions in IMF deposition. …”
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Transcriptomic profiling reveals SARS-CoV-2-infected humanized MHC mice recapitulate human post vaccination immune responses by Siyue Li, Siyue Li, Xuelian Han, Ruolan Hu, Ruolan Hu, Keyu Sun, Min Li, Yuan Wang, Guangyu Zhao, Mengzhe Li, Huahao Fan, Huahao Fan, Huahao Fan, Huahao Fan, Qi Yin

“…Comparative analysis with human whole blood RNA-seq datasets revealed that hMHC mice exhibit both high reproducibility in transcriptomic profiles and significant similarity to human immune responses across innate and adaptive immunity. …”
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No detectable impact of chronic oral lactic acid exposure on honey bee health: Insights from survival, lactate accumulation and head transcriptome by Caroline Vilarem, Vincent Piou, Lucie Bouly, Frédéric Julien, Rachel Fourdin, Nathalie Vialaneix, Matthias Zytnicki, Angélique Vétillard

“…No lactate accumulation was detected in any of the honey bee organs analysed. Furthermore, transcriptomic analysis on the bees’ heads revealed no differences in gene expression. …”
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Transcriptomic profiles of monocyte-derived macrophages exposed to SARS-CoV-2 VOCs reveal immune-evasion escape driven by delta by Alessia Gallo, Josè Camilla Sammartino, Roberta Vazzana, Roberto Giambruno, Claudia Carcione, Nicola Cuscino, Salvatore Castelbuono, Vitale Miceli, Matteo Bulati, Daniele Lilleri, Irene Cassaniti, Pier Giulio Conaldi, Fausto Baldanti

“…Surprisingly, our data showed that macrophages exposed to the Delta variant exhibited a transcriptional profile more similar to the naïve control group, while macrophages exposed to the Omicron variant showed intermediate differentially expressed genes (DEGs) between the two groups. …”
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The comprehensive transcriptomic atlas of porcine immune tissues and the peripheral blood mononuclear cell (PBMC) immune dynamics reveal core immune genes by Qingyao Zhao, Jiahao Wang, Fuping Ma, Quanzhen Chen, Huatao Liu, Jinyan Yang, Siqian Chen, Yongjie Tang, Siyuan Mi, Lulu Wang, Xini Wang, Guohong Liu, Kai Xing, Ying Yu, Chuduan Wang

“…However, comprehensive systematic studies on transcriptome of porcine immune tissues are still rare. …”
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A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle by Mollie M. Green, Hunter R. Ford, Alexandra P. Tegeler, Oscar J. Benitez, Bradley J. Johnson, Clarissa Strieder-Barboza

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Immune Dysregulation and Trophoblastic Dysfunction as a Potential Cause of Idiopathic Recurrent Pregnancy Loss by Sara Vasconcelos, Ana Costa Braga, Ioannis Moustakas, Bruno Cavadas, Mariana Santos, Carla Caniçais, Carla Ramalho, Susana M. Chuva de Sousa Lopes, Cristina Joana Marques, Sofia Dória

“…Gene ontology (GO) analysis of downregulated genes implicated hormonal and endocrine processes, consistent with STB reduction, while upregulated genes were associated with MHC protein complex and immune system processes, aligning with EVT increases. …”
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Synergistic Response Mechanisms in Rice Seedlings Exposed to Brown Planthopper Infestation and High-Temperature Stress by Danyun Cao, Yuchen Ping, Yiru Lin, Jinyan Hu, Zimeng Wang, Wei Yuan, Tongtong Li, Linxin Liu, Bo Zhang, Shijiao Xiong, Cong Dang, Dawei Xue

“…This result can be elucidated by the subsequent transcriptome analysis. Differentially expressed genes (DEGs) following high-temperature treatment were enriched in metabolic processes and phenylpropanoid biosynthesis pathways, thereby enhancing rice resistance to BPH. …”
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Subpopulation-specific gene expression in Lachancea thermotolerans uncovers distinct metabolic adaptations to wine fermentation by Javier Vicente, Santiago Benito, Domingo Marquina, Antonio Santos

“…Understanding the gene expression differences linked to lactic acid production could allow a more rational address of biological acidification while optimizing yeast-specific nutritional requirements during fermentation. …”
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Integration of volatile and non-volatile metabolites and the transcriptome reveals the formation mechanisms of differential aroma compounds between Pyrus communis and Pyrus pyrifol... by Jiao Wang, Jiao Wang, Xianping Guo, Xianping Guo, Zhongying Wu, Zhongying Wu, Dongsheng Wang, Dongsheng Wang, Peng Guo, Yongping Han, Hui Jiang, Zhenzhen Lü

“…However, there is a lack of systematic research on this subject.MethodsAn analysis of volatile and non-volatile metabolites was combined with transcriptome analysis to explore the formation mechanism of differential aroma compounds between three P. communis and three P. pyrifolia cultivars.ResultsIn this study, a total of 510 volatile compounds were identified in the six cultivars. …”
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Silver carp muscle hydrolysate ameliorated atherosclerosis and liver injury in apoE-/- mice: the modulator effects on enterohepatic cholesterol metabolism by Kai Wang, Zixin Fu, Yuqing Tan, Hui Hong, Jianping Wu, Yongkang Luo

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Effects of exogenous insulin supplementation on lipid metabolism in peripartum obese dairy cows by Yuanyin Guo, Yihan Zhao, Ziang Wei, Jie Cao

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Combined metabolic phenotypes and gene expression profiles revealed the formation of terpene and ester volatiles during white tea withering process by Xuming Deng, Jun Wu, Tao Wang, Haomin Dai, Jiajia Chen, Bo Song, Shaoling Wu, Chenxi Gao, Yan Huang, Weilong Kong, Weijiang Sun

“…To study the mechanism underlying aroma changes during the white withering, we herein conducted volatile metabolomics and transcriptomics of the young leaves from the 'Fuding Dahaocha' tea cultivar. …”
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Combined Effects of Magnetized Irrigation and Water Source on Italian Lettuce (<i>Lactuca sativa</i> L. var. <i>ramosa</i> Hort.) Growth and Gene Expression by Xueying Yao, Xiaofan Wang, Mingshan Qu, Yibo Wei, Feifei Shan, Youli Li

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