Ensemble modeling of SARS-CoV-2 immune dynamics in immunologically naïve rhesus macaques predicts that potent, early innate immune responses drive viral elimination by Catherine Byrne, Joshua T. Schiffer

“…Among the numerous genes potentially contributing to the innate response, we identified IFI27 as most closely linked to viral load decline. …”
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Molecular characterisation of influenza B virus from the 2017/18 season in primary models of the human lung reveals improved adaptation to the lower respiratory tract by Duygu Merve Çalışkan, Sriram Kumar, Saskia Hinse, Klaus Schughart, Rainer Wiewrodt, Stefan Fischer, Vera Krueger, Karsten Wiebe, Peter Barth, Alexander Mellmann, Stephan Ludwig, Linda Brunotte

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Genome-Wide Identification and Abiotic Stress Response Analysis of C2H2 Zinc Finger Protein Genes in Foxtail Millet (<i>Setaria italica</i>) by Qian Zhao, Yingxin Zhang, Xiangyu Xing, Shuyao Li, Ruidong Sun, Weilong Zhang, Jun Zhang, Liangyu Jiang, Zhenyuan Zang, Ming Gao, Jian Zhang

“…Transcriptome profiling and qPCR validation in the YuGu 56 cultivar identified several stress-responsive candidates, including <i>SiC2H2-35</i> and <i>SiC2H2-58</i> (salt tolerance), as well as <i>SiC2H2-23</i> (5.19-fold induction under salt stress) and <i>SiC2H2-32</i> (5.47-fold induction under drought). …”
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RNA-sequencing studies suggest that microRNAs and alternative splicing of pre-mRNAs modulate immune and inflammatory responses in Holstein cattle infected with Mycobacterium avium... by Gerard Badia-Bringué, Marta Alonso-Hearn

“…As bioinformatic tools continue to develop, microRNAs (miRNAs) and alternative splicing (AS) have emerged as important contributors to host responses during infections. Although RNA-Seq enables AS analysis, most transcriptomic studies still emphasize gene-level expression due to the complexity of AS workflows, the need for deeper sequencing, and incomplete transcript annotations, even in humans. …”
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A panoramic view of cotton resistance to Verticillium dahliae: From genetic architectures to precision genomic selection by Xiaojun Zhang, Shiming Liu, Peng Wu, Wanying Xu, Dingyi Yang, Yuqing Ming, Shenghua Xiao, Weiran Wang, Jun Ma, Xinhui Nie, Zhan Gao, Junyuan Lv, Fei Wu, Zhaoguang Yang, Baoxin Zheng, Ping Du, Jiangmei Wang, Hao Ding, Jie Kong, Alifu Aierxi, Yu Yu, Wei Gao, Zhongxu Lin, Chunyuan You, Keith Lindsey, Nataša Štajner, Maojun Wang, Jiahe Wu, Shuangxia Jin, Xianlong Zhang, Longfu Zhu

“…Verticillium wilt (VW), caused by Verticillium dahliae (V. dahliae), is one of the most devastating diseases affecting crop production worldwide. …”
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Exploring the Efficacy and Potential Mechanisms of Topical <i>Periplaneta americana</i> (L.) Extract in Treating Androgenetic Alopecia in a Mouse Model: A Systems Pharmacology and... by Tangfei Guan, Xin Yang, Canhui Hong, Peiyun Xiao, Yongshou Yang, Chenggui Zhang, Zhengchun He

“…Androgenetic alopecia (AGA), the most prevalent form of hair loss worldwide, faces significant therapeutic challenges due to high costs and limited efficacy of current interventions, necessitating safer and more effective solutions. …”
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Genome-Wide Identification of <i>PP2C</i> Gene Family in Oat (<i>Avena sativa</i> L.) and Its Functional Analyses in Response to ABA and Abiotic Stresses by Panpan Huang, Kuiju Niu, Jikuan Chai, Wenping Wang, Yanming Ma, Yanan Cao, Guiqin Zhao

“…Plant protein phosphatase 2C (PP2C) represents the largest and most functionally diverse group of protein phosphatases in plants, playing pivotal roles in regulating metabolic processes, hormone signaling, stress responses, and growth regulation. …”
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Genome-Wide Identification and Characterization of Heat Shock Proteins in the Stored-Product Pest <i>Rhyzopertha dominica</i> (Fabricius): Phylogenetic, Structural, and Stress-Indu... by Yueliang Bai, Yanzhu Xie, Junji Yao, Fangfang Zeng, Dianxuan Wang

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Genome-Wide Identification of Cucumber <i>Lhc</i> Genes’ Family and Their Expression Analysis by Yongmei Miao, Kaijing Zhang

“…Analysis of the <i>cis</i>-acting elements in <i>CsLhc</i> promoters revealed their potential involvement in stress responses. Transcriptome data indicated that <i>CsLhcs</i> are minimally expressed in male flowers and roots, but highly expressed in other organs. …”
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EGR1 mRNA expression levels and polymorphisms are associated with slaughter performance in chickens by Mao Ye, Xiaohuan Chao, Chutian Ye, Lijin Guo, Zhexia Fan, Xuerong Ma, Aijun Liu, Weiming Liang, Shuya Chen, Cheng Fang, Xiquan Zhang, Qingbin Luo

“…The selection of breeds with excellent slaughtering performance and high meat production performance has become one of the most important selective breeding goals. In our previous study, we conducted transcriptome sequencing on chicken breast tissues with high and low breast muscle rates and found higher early growth response protein 1 (EGR1) expression in breast tissues with a low breast muscle ratio, thus hypothesizing that the EGR1 gene is involved in the growth and development process of chicken muscle tissues. …”
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Identification of <i>AP2/ERF</i> Transcription Factors and Characterization of <i>AP2/ERF</i> Genes Related to Low-Temperature Stress Response and Fruit Development in Luffa by Jianting Liu, Haifeng Zhong, Chengjuan Cao, Yuqian Wang, Qianrong Zhang, Qingfang Wen, Haisheng Zhu, Zuliang Li

“…Plant-specific APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factors are involved in the regulation of genes associated with the growth and developmental processes of numerous plants. …”
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Lack of IFN-γ response of human uterine myometrium-derived MSCs significantly improve multiple IBD parameters compared to bone marrow MSCs: Implications for anti-TNFα-refractory pa... by Li-Tzu Wang, Hsiu-Huan Wang, Shih-Sheng Jiang, Chia-Chih Chang, Pei-Ju Hsu, Ko-Jiunn Liu, Huey-Kang Sytwu, B. Linju Yen, Men-Luh Yen

“…Overall, UtMSCs outperformed BMMSCs in improving microbiota, avoiding IFN-γ responses, and modulating overall Th responses, suggesting this MSC source may offer more significant effectiveness for IBD and Th1/Th17-mediated conditions. …”
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An Intelligent and Conductive Hydrogel with Multiresponsive and ROS Scavenging Properties for Infection Prevention and Anti‐Inflammatory Treatment Assisted by Electrical Stimulatio... by Tao Zhang, Zongwu Meng, Haoyu Yu, Ping Ding, Tianhan Kai

“…The HEPP not only adeptly controls high ROS levels, but also enhances the regulation of inflammation in the wound area via electrical stimulation (ES), thereby promoting healing that is supported by the immune response. Studies conducted in vitro, along with transcriptomic analyses, indicate that ES primarily mitigates inflammation by regulating Interleukin‐6 (IL‐6) and tumor necrosis factor‐α (TNF‐α). …”
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Identification and Analysis of Endoplasmic-Reticulum-Stress- and Salt-Stress-Related Genes in <i>Solanum tuberosum</i> Genome: <i>StbZIP60</i> Undergoes Splicing in Response to Sal... by Peiyan Guan, Dongbo Zhao, Chenxi Zhang, Zhennan Qiu, Qingshuai Chen, Inna P. Solyanikova, Peinan Sun, Peipei Cui, Ru Yu, Xia Zhang, Yanmei Li, Linshuang Hu

“…We identified 29 genes involved in ER stress response in the potato genome. Transcriptome data analysis showed that the expression levels of related genes were significantly different in different tissues. …”
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Combining explainable machine learning, demographic and multi-omic data to inform precision medicine strategies for inflammatory bowel disease. by Laura-Jayne Gardiner, Anna Paola Carrieri, Karen Bingham, Graeme Macluskie, David Bunton, Marian McNeil, Edward O Pyzer-Knapp

“…Our approach models IBD drug response while also identifying its most predictive features as part of a transparent ML precision medicine strategy.…”
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Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus. by Hung-Che Lin, Guillermo Vidal-Diez de Ulzurrun, Sheng-An Chen, Ching-Ting Yang, Rebecca J Tay, Tomoyo Iizuka, Tsung-Yu Huang, Chih-Yen Kuo, A Pedro Gonçalves, Siou-Ying Lin, Yu-Chu Chang, Jason E Stajich, Erich M Schwarz, Yen-Ping Hsueh

“…A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. …”
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Molecular effects of clinically relevant chemotherapeutic agents on choline phospholipid metabolism in triple negative breast cancer cells by Caitlin M. Tressler, Kanchan Sonkar, Menglin Cheng, Vinay Ayyappan, Ruoqing Cai, Kristine Glunde

“…The presented metabolic and transcriptomic findings support that the GPC/PC ratio and PtdC-phospholipases and -lysophospholipases could be further developed for assessing the response to chemotherapy treatment in TNBC patients.Statement of Significance: We show that the glycerophosphocholine-to-phosphocholine ratio and phosphatidylcholine-specific-phospholipases and -lysophospholipases are reliable markers for assessing the response to several chemotherapeutic agents, which could help with selecting correct treatments for TNBC patients.…”
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Characterization of temporal expression of immune genes in female locust challenged by fungal pathogen, Aspergillus sp. by Muhammad Saad Waqas, Xiao Xu, Pengfei Zhang, Jin Guo, Shaojing Hu, Yinwei You, Long Zhang

“…MethodsWe conducted transcriptomic analyses of the locust Locusta migratoria under Aspergillus oryzae infection to clarify temporal variation in its molecular immune response. …”
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Identification of Gene Targets for the Sprouting Inhibitor CIPC by Thomas M. Grand, James K. Pitman, Alexander L. Williams, Lisa M. Smith, Andrew J. Fleming

“…Despite its ban from 2020 in the EU, isopropyl N‐(3‐chlorophenyl) carbamate (also known as chlorpropham or CIPC) remains the most widely used suppressant worldwide. However, the mechanism of action of CIPC remains obscure. …”
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Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock by Connor Reynolds, Joshua Colmer, Hannah Rees, Ehsan Khajouei, Rachel Rusholme-Pilcher, Hiroshi Kudoh, Antony N. Dodd, Anthony Hall

“…However, understanding clock function at the transcriptome level and its response to the environment requires assaying across high resolution time-course experiments. …”
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