Genome-Wide Characterization of the <i>SnRK</i> Gene Family in <i>Taxus</i> and Homologous Validation of <i>TaSnRK1.2</i> as a Central Regulator in Stress-Responsive Transcriptiona... by Pengjun Lu, Jianqiu Ji, Fangjuan Fan, Tao Liu, Zhenting Shi, Wentao Li, Chongbo Sun

“…Specifically, we identified <i>SnRK</i> genes through genomic analysis and assessed tissue-specific expression via transcriptomics, while regulatory networks were deciphered using WGCNA. …”
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Screening and comparison of in vitro-induced resistant and clinically resistant Stenotrophomonas maltophilia strains for eravacycline resistance-related genes by Jie Wu, Jiarong Song, Junchang Cui

“…Transcriptome analysis revealed consistent upregulation of efflux pump genes (smrA, smeD, smeE, smeF) across all induced strains. …”
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The involvement of PsTCP genes in hormone-mediated process of bud dormancy release in tree peony (Paeonia suffruticosa) by Qianqian Wang, Bole Li, Zefeng Qiu, Jiayi Ying, Xuyichen Jin, Zeyun Lu, Junli Zhang, Xia Chen, Xiangtao Zhu

“…Specifically, PsTCP14 was classified under Class I, while PsTCP3 and PsTCP4 were classified under Class II. …”
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Response mechanism of ethanol-tolerant Saccharomyces cerevisiae strain ES-42 to increased ethanol during continuous ethanol fermentation by Xue-Xue Ji, Quan Zhang, Bai-Xue Yang, Qing-Ran Song, Zhao-Yong Sun, Cai-Yun Xie, Yue-Qin Tang

“…Cells were collected at different ethanol concentrations (from 60 g/L to 100 g/L) for comparative transcriptomic analysis. Results During continuous fermentation, as ethanol concentration increased, the expression of genes associated with cytoplasmic ribosomes, translation, and fatty acid biosynthesis progressively declined, while the expression of genes related to heat shock proteins (HSPs) and ubiquitin-mediated protein degradation gradually increased. …”
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Environmental adaptation and reproductive mechanisms of Codium fragile subsp. fragile in the Bohai Bay by Jingjing Zi, Zhiying Wang, Lanping Ding

“…Additionally, the highest gamete release rate was observed at 25°C, salinity of 20, and light intensity of 1000 Lux, while optimal conditions for sporeling growth were 20°C, salinity of 30, and 1000 Lux. …”
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Explaining <i>Echis</i>: Proteotranscriptomic Profiling of <i>Echis carinatus carinatus</i> Venom by Salil Javed, Prasad Gopalkrishna Gond, Arpan Samanta, Ajinkya Unawane, Muralidhar Nayak Mudavath, Anurag Jaglan, Kartik Sunagar

“…For instance, the venom gland transcriptome and inter- and intra-population venom variation in <i>E. c. carinatus</i> have largely remained uninvestigated. …”
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Characterization of Immune Response Against <i>Mycobacterium marinum</i> Infection in Coho Salmon (<i>Oncorhynchus kisutch</i>) by Le Li, Danlei Xu, Xiaoqing Yu, Chunlei Gai, Haibin Ye, Jing Diao

“…Gene Ontology and KEGG enrichment analysis highlighted pathways such as cytokine–cytokine receptor interaction, metabolic pathways, and Toll-like receptor signaling in the kidney, while the DEGs in the liver were enriched in metabolic pathways, immune system processes, and stress and defense responses. …”
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Identification of key genes and metabolites for hydrogen gas-alleviated browning in Lanzhou lily scale by Xuejuan Pan, Chen Liang, Hongsheng Zhang, Xuemei Hou, Tong Wang, Zhuohui Zhang, Chunlei Wang, Weibiao Liao

“…In addition, H₂ fumigation increased the content of soluble sugars and soluble proteins while decreasing the content of total phenols. Metabolomic and transcriptomic analyses demonstrate that differentially expressed genes (DEGs) and differential metabolites (DAMs) were significantly enriched in pathways related to enzymatic and non-enzymatic browning. …”
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Auxin Controls Root Gravitropic Response by Affecting Starch Granule Accumulation and Cell Wall Modification in Tomato by Huabin Liu, Yue Wu, Jiahui Cai, Lele Xu, Cheng Zhou, Chengliang Wang

“…Treatment with the exogenous auxin NAA heightened starch synthesis, while exogenous application of the auxin biosynthesis inhibitor yucasin dampened starch synthesis in tomato roots. …”
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The chromosome-level genome of Hemerocallis middendorffii provides new insights into the floral scents and color biosynthesis in Chinese native daylily by Meiyu Sun, Baocai Han, Jianhua Xiao, Haiyan Yu, Yinli Jia, Shuhai Yuan, Juan Yao, Quan Xing, Dongqi Wu, Guofeng Sun, Jinzheng Zhang

“…The main terpenoids contributing to floral fragrance were linalool, 3-carene, nerolidol, and α-farnesene, while carotenoids and anthocyanidins were the main components of floral color. …”
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Regulatory mechanism of Haa1p and Hap4p in Saccharomyces cerevisiae to mixed acetic acid and formic acid when fermenting mixed glucose and xylose by Xin-Yu Xiao, Bo Li, Zi-Yuan Xia, Quan Zhang, Cai-Yun Xie, Yue-Qin Tang

“…Under these conditions, genes related to metabolic regulation, RNA processing, and transcription were significantly downregulated, while those involved in transport, ribosome biogenesis, genome stability, and sporulation were significantly upregulated. …”
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AozC, a zn(II)2Cys6 transcription factor, negatively regulates salt tolerance in Aspergillus oryzae by controlling fatty acid biosynthesis by Wenbin Yu, Zeying Zhao, Yufei Zhang, Yayi Tu, Bin He

“…Results Overexpression of AozC decreased growth rates in the presence of salt, while its knockdown enhanced growth, the number of spores, and biomass, particularly under conditions of 15% salt concentration, doubling these metrics compared to the wild type. …”
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Emission and Transcriptional Regulation of Aroma Variation in <i>Oncidium</i> Twinkle ‘Red Fantasy’ Under Diel Rhythm by Yan Chen, Shengyuan Zhong, Lan Kong, Ronghui Fan, Yan Xu, Yiquan Chen, Huaiqin Zhong

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Comparative gene expression analysis of Beauveria bassiana against Spodoptera frugiperda by Hamdy H. Aly, Yun Meng, Dun Wang

“…GO analysis revealed enrichment in cellular and catalytic activities, while KEGG pathways highlighted early-stage metabolic adaptations related to nutrient acquisition and energy metabolism. …”
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Arginine-Mediated Liver Immune Regulation and Antioxidant Defense in Largemouth Bass (<i>Micropterus salmoides</i>): Multi-Omics Insights into Metabolic Remodeling During <i>Nocard... by Yu-Long Sun, Shuai-Liang Zhang, Feng-Feng Zhou, Yuan-Xin Qian, Yang He, Run-Zhe Zhang, Fen Dong, Qiang Chen, Han-Ying Xu, Ji-Teng Wang, Yu-Ting Deng, Tao Han

“…The results demonstrated that arginine supplementation significantly reduced the expression of LPS-induced apoptosis-related genes (<i>bax</i>, <i>cas3</i>, <i>cas8</i>, and <i>cas9</i>) by up to 50% while increasing the expression of antioxidant genes (<i>gpx</i>, <i>GST</i>) by up to 700% at 24 h. …”
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Multi-omics exploration of chaperone-mediated immune-proteostasis crosstalk in vascular dementia and identification of diagnostic biomarkers by Wentong Li, Yiyi Zhang, Chuanhong Li, Mingyang Jiang, Dong Wang, Luomeng Chao, Luomeng Chao, Luomeng Chao, Yuxia Yang

“…Immune microenvironment analysis was conducted using CIBERSORT, while single-cell transcriptomics was analyzed within the Seurat framework.ResultsA total of 897 DEGs were identified, with functional enrichment analysis revealing significant involvement in T cell activation (p=2.84×10-3), neuroactive ligand-receptor interaction (p=6.01×10-4), and osteoclast differentiation (NES=2.83). …”
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Revealing VCAN as a Potential Common Diagnostic Biomarker of Renal Tubules and Glomerulus in Diabetic Kidney Disease Based on Machine Learning, Single-Cell Transcriptome Analysis a... by Li Jiang, Jie Jian, Xulin Sai, Xiai Wu

“…Mendelian randomization analysis confirmed that serum VCAN protein levels were a risky factor for DKD, while there was no reverse association. It exhibited the good diagnostic potential for estimated glomerular filtration rate and proteinuria in DKD. …”
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Characterization of the regulatory network and pathways in duodenum affecting chicken abdominal fat deposition by Zhijie Liu, Sibei Cheng, Xing Zhang, Miaomiao Yang, Jixiang Wei, Fei Ye, Zheng Ma, Huimin Kang, Zhengfen Zhang, Hua Li, Hai Xiang

“…The aforementioned genes including TMEM150C, REXO1, PIK3C2G, ppp1cb, PARP12, SERPINE2, LRAT, CYP1A1, INSR and APOA4, were proposed as candidate genes, while the miRNAs, including miR-107-y, miR-22-y, miR-25-y, miR-2404-x and miR-16-x, as well as lncRNAs such as ENSGALT00000100291, TCONS_00063508, TCONS_00061201 and TCONS_00079402 were the candidate regulators associated with chicken abdominal fat deposition. …”
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Over Time Changes in the Transcriptomic Profiles of Tomato Plants with or Without <i>Mi-1</i> Gene During Their Incompatible or Compatible Interactions with the Whitefly <i>Bemisia... by Susana Pascual, Clara I. Rodríguez-Álvarez, Irene López-Vidriero, José M. Franco-Zorrilla, Gloria Nombela

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Dysregulation of innate and adaptive lymphoid immunity may have implications for symptom attribution and predict responses to targeted therapies in neuropsychiatric systemic lupus... by Julius Lindblom, Guillermo Barturen, Lorenzo Beretta, Daniel Toro-Domínguez, Elena Carnero-Montoro, Maria Orietta Borghi, Jessica Castillo, Ellen Iacobaeus, Yvonne Enman, Chandra Mohan, Marta E. Alarcón-Riquelme, Dionysis Nikolopoulos, Ioannis Parodis, Jacques-Olivier Pers, Alain Saraux, Valérie Devauchelle-Pensec, Sandrine Jousse-Joulin, Bernard Lauwerys, Julie Ducreux, Anne-Lise Maudoux, Ana Tavares, Isabel Almeida, Miguel Angel Gonzalez-Gay Mantecón, Ricardo Blanco Alonso, Alfonso Corrales Martínez, Ignasi Rodríguez-Pintó, Gerard Espinosa, Rik Lories, Nicolas Hunzelmann, Doreen Belz, Niklas Baerlecken, Michael Zauner, Michaela Lehner, Eduardo Collantes, Ma Angeles Aguirre-Zamorano, Alejandro Escudero-Contreras, Ma Carmen Castro-Villegas, Norberto Ortego, María Concepción Fernández Roldán, Enrique Raya, Inmaculada Jiménez Moleón, Enrique de Ramon, Isabel Díaz Quintero, Pier Luigi Meroni, Tommaso Schioppo, Carolina Artusi, Carlo Chizzolini, Aleksandra Zuber, Donatienne Wynar, Attila Balog, Magdolna Deák, Márta Bocskai, Sonja Dulic, Gabriella Kádár, Falk Hiepe, Silvia Thiel, Manuel Rodriguez Maresca, Antonio López-Berrio, Rocío Aguilar-Quesada, Héctor Navarro-Linares

“…The interferon gene module was prominently upregulated in subgroup 1, while the B cell, T cell, and cytotoxic/natural killer (NK) cell modules were downregulated. …”
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