Generation and Functional Characteristics of CRISPR/Cas9-Edited <i>PtrPHOTs</i> Triple-Gene Mutants in Poplar by Hongtao Yao, Jiyao Cheng, Yuning Jing, Siran Zhu, Chong Wang, Yuxiang Cheng

“…Using CRISPR/Cas9 gene editing technology, triple-gene mutations in the <i>PtrPHOT1/2.1/2.2</i> (<i>PtrPHOTs</i>) were generated, providing initial insights into the functions of PHOTs in trees. …”
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Comprehensive identification, stress responses and protein-protein interactions of the ferredoxin gene family in the fast-growing tree species Paulownia fortunei by Xin Mao, Haibo Yang, Mengmeng Ji, Pingluo Xu, Guoqiang Fan

“…All members contain a 2Fe-2 S domain and light-responsive elements, displaying high conservation among subfamily members. Transcriptome analysis and real-time quantitative PCR (qRT-PCR) assays indicated that photosynthetic ferredoxins PfFd1 and PfFd2 play important roles in the response of Paulownia fortunei to droughts, salt and pathogen stresses. …”
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Inter-Relationship Between Melanoma Vemurafenib Tolerance Thresholds and Metabolic Pathway Choice by Pratima Nangia-Makker, Madison Ahrens, Neeraja Purandare, Siddhesh Aras, Jing Li, Katherine Gurdziel, Hyejeong Jang, Seongho Kim, Malathy P Shekhar

“…Our data demonstrate that drug tolerance thresholds play a direct role in driving metabolic shifts towards specific routes, thus providing a new basis for delineating VemR melanomas for metabolism-targeting therapies.…”
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Insights into the senescent mechanisms of harvested strawberry fruit at the physiological, molecular and metabolic levels by Boqian Yan, Ye Wang, Yuan Bai, Ziyang Liu, Huijun Liu, Xiangning Chen, Yuanyue Shen, Liusheng Duan

“…Finally, a physiological, molecular and metabolic model for strawberry fruit senescence is proposed, providing comprehensive insights into the preservative mechanisms.…”
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Music therapy as a preventive intervention for postpartum depression: modulation of synaptic plasticity, oxidative stress, and inflammation in a mouse model by Qiang Fu, Rui Qiu, Tongtong Yao, Liming Liu, Yaobo Li, Xiaodong Li, Wen Qi, Yuewen Chen, Yong Cheng

“…These findings suggest that music therapy prevents PPD by modulating oxidative stress, inflammation, and synaptic integrity, providing robust preclinical evidence for its potential as a natural preventive intervention for PPD. …”
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Human PBMC-based humanized mice exhibit myositis features and serve as a drug evaluation model by Akiko Nishidate, Kana Takemoto, Yuki Imura, Mikako Murase, Ryu Yamanaka, Manami Kikuchi, Junpei Anan, Sayuka Kato, Airi Akatsuka, Sachiko Mochizuki, Yuzo Koda

“…Transplantation of CD8+ T cell-depleted hPBMC leads to a significant reduction in polymyositis-like symptoms, in agreement with previous studies demonstrating CD8+ T cells as the main pathologic drivers of polymyositis. Furthermore, the transcriptome analysis of muscle tissue from hPBMC mice reveal extensive upregulation of characteristic genes of polymyositis, providing further support that hPBMC mice accurately reflect the pathophysiology of myositis in humans. …”
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Deep-Sea Cold Seep Campylobacterota: Diversity, Growth, Metabolic Characteristics, and Nutrient Production by Xiaoman Yan, Qinglei Sun, Ke Xu, Jintao Zhuo, Yuanyuan Sun, Guowei Qian, Xin Zhang, Li Sun

“…However, the nutrients that these bacteria can provide to their hosts are unclear. To date, research on Campylobacterota in cold seeps is very limited. …”
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Molecular Mechanisms Underlying Substance Transport, Signal Transduction, and Anti-Stress Regulation, as Well as Anti-Alkaline Regulation via <i>Bursicon</i> in the Cerebral Gangli... by Meiyao Wang, Jun Zhou, Jiachun Ge, Gangchun Xu, Yongkai Tang

“…In particular, the brain (cerebral ganglion for crustaceans) serves as a vital regulatory organ in response to environmental stress; (2) Methods: In this study, a comparative transcriptome approach was employed to investigate the key regulatory genes and molecular regulatory mechanisms in the cerebral ganglion of <i>E. sinensis</i> under alkaline stress. (3) Results: The results demonstrated that the cerebral ganglion of <i>E. sinensis</i> exhibited a positive response to acute alkaline stress. …”
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Bioinformatics and experimental validation identify biomarkers for diagnosing Alzheimer’s disease by Hui Liu, Hui Liu, Chenye Li, Congchen Zhai, Congchen Zhai, Mei Li, Lan Ma

“…Therefore, this study aims to identify potential biomarkers for AD using bioinformatics, providing new insights into its diagnosis.MethodsThis study utilized the transcriptome dataset GSE63060 from the Gene Expression Omnibus (GEO) and applied bioinformatics approaches to identify candidate genes. …”
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Targeting PDK1: A novel approach to combat hypoxia‐induced epithelial‐mesenchymal transition in chronic rhinosinusitis with nasal polyps by Sicen Pan, Mengyan Zhuang, Xiangdong Wang, Qinqin Zhang, Ting He, Ying Li, Jian Jiao, Luo Zhang

“…This study aims to elucidate the mechanisms driving EMT under hypoxic conditions in CRSwNP. Methods Transcriptome and proteome analyses of hypoxia‐treated human nasal epithelial cells (HNECs) were performed to identify key molecules and pathways. …”
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Interspecific Hybridization Enhanced Tolerance to Salinity and Cadmium Stress Through Modifying Biochemical, Physiological, and Resistance Gene Levels, Especially in Polyploid Rice... by Lixia Sun, Fozia Ghouri, Jiacheng Jin, Minghui Zhong, Weicong Huang, Zijun Lu, Jinwen Wu, Xiangdong Liu, Muhammad Qasim Shahid

“…Transcriptome analysis revealed several genes associated with heterosis and stress, including OsEAF6, which is associated with heterosis, and OsCIPK14, which is involved in defense signalling pathways. …”
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Global surveillance of circulating microRNA for diagnostic and prognostic assessment of acute myocardial infarction based on the plasma small RNA sequencing by Xiaomin Wang, Yaojun Lu, Ruiping Zhao, Bing Zhu, Jian Liu, Qiang Yue, Rina Wu, Shuwen Han, Yuanyuan Gao, Juan Chen, Jie Gong, Danna He, Teng Xu, Jianchao Ying

“…Previous studies revealed that several miRNAs exhibited the capacity for diagnosis and prognosis of AMI, the reasons why these circulating miRNAs are concerned as targets for investigation are quite cryptogenic, presumably due to the lack of clues provided by global surveillance at the transcriptome level, and the current data for some miRNAs are controversial and inconsistent among independent studies. …”
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Deep Learning for Multi-Tissue Cancer Classification of Gene Expressions (GeneXNet) by Tarek Khorshed, Mohamed N. Moustafa, Ahmed Rafea

“…These methods fall short in taking advantage of genome-wide next generation sequencing technologies which provide a snapshot of the whole transcriptome rather than a predetermined subset of genes. …”
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Gene ontology defines pre-post- hatch energy dynamics in the complexus muscle of broiler chickens by Jonathan Dayan, Zehava Uni

“…Although considered a key player during hatching, with activity that imposes a substantial metabolic demand, data are still limited. The study provides a bioenergetic and transcriptomic analyses during the pre-post-hatching period. …”
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Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development by Huawei Feng, Wenjuan Fan, Min Liu, Jiaqian Huang, Bosheng Li, Qing Sang, Baoxing Song

“…This ability provides great power to annotate the single nucleus clusters. …”
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Immunoinformatic Analysis to Identify Proteins to Be Used as Potential Targets to Control Bovine Anaplasmosis by Sergio D. Rodríguez-Camarillo, Rosa E. Quiroz-Castañeda, Hugo Aguilar-Díaz, José E. Vara-Pastrana, Diego Pescador-Pérez, Itzel Amaro-Estrada, Fernando Martínez-Ocampo

“…Omics sciences and new technologies to sequence full genomes provide valuable data that are revealed only after detailed bioinformatic analysis is performed. …”
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Chromosomal scale assembly and functional annotation of the apicomplexan parasite Eimeria acervulina by Subodh K. Srivastava, Carolyn C. Parker, Peter C. Thompson, Matthew S. Tucker, Benjamin M. Rosenthal, Asis Khan, Matthew J. Valente, Mark C. Jenkins

“…A total of 7,621 genes were predicted using a pipeline of BRAKER3, GeneMark-ETP and AUGUSTUS, of which 4,647 (60.97%) have a predicted Pfam function and 1,962 (25.74%) have Gene Ontology (GO) terms matching molecular, biological, and functional classes. Stage-specific transcriptome analysis revealed 9,761 transcripts. This genome assembly and transcriptome analysis provides the foundation for identifying biologically important candidates for anticoccidial drug and vaccine development.…”
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Genome-Wide Analysis Reveals Copy Number Variant Gene <i>TGFBR3</i> Regulates Pig Back Fat Deposition by Chunlei Zhang, Huan Yang, Qinglei Xu, Mingzheng Liu, Xiaohuan Chao, Jiahao Chen, Bo Zhou

“…In this study, whole-genome CNV detection was performed using next-generation sequencing data from LW and MZ pigs, and transcriptome data from back fat tissue of 180-day-old LW and MZ pigs were integrated for expression quantitative trait loci (eQTL) analysis. …”
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GEDG: gene expression database of grape by Wen Sun, Siyu Chen, Lina Tan, Yanglin Liu, Xinyuan Zhang, Yan Xiang, Han Zheng, Hanwei Yan

“…The primary objective of GEDG is to expand and utilize transcriptome data to better understand stress responses in grapes. …”
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Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis. by Daichi Susaki, Takamasa Suzuki, Daisuke Maruyama, Minako Ueda, Tetsuya Higashiyama, Daisuke Kurihara

“…Here, we visualized the living dynamics of female gametophyte development and performed transcriptome analysis of individual cell types to assess the cell fate specifications in Arabidopsis thaliana. …”
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