Functional Roles of the Seagrass (<i>Zostera marina</i>) Holobiont Change with Plant Development by Sam Gorvel, Bettina Walter, Joe D. Taylor, Richard K. F. Unsworth

“…This study provides a novel functional analysis of microbial communities in seagrass (<i>Zostera marina</i>) rhizosphere and endosphere, comparing seedlings and mature plants. …”
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Identification of exosome-related genes in NSCLC via integrated bioinformatics and machine learning analysis by Zhenjie Sun, Tianyu Du, Guosheng Yang, Yinghuan Sun, Xuyang Xiao

“…The present study identified 59 exosome-associated differentially expressed genes (EA-DEGs) from the Gene Expression Omnibus (GEO) and GeneCards databases. Functional analysis indicated the involvement of the EA-DEGs in NSCLC-related pathways, including the cell cycle, DNA replication, and the immune response. …”
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Oysters in transition: hermaphrodite oysters display unique DNA methylation patterns in gill tissue by Sophie Valk, Marc Engelsma, Hendrik-Jan Megens, Pauline Kamermans, Albertinka J. Murk, Reindert Nijland

“…A total of 9,654 regions and 2,576 genes were differentially methylated between male, female, and hermaphrodite oysters. Functional analysis of differentially methylated genes indicated an association with energy homeostasis and metabolic processes, implying a remodeling of the energy balance. …”
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Identification of genes related to fatty acid metabolism in type 2 diabetes mellitus by Ji Yang, Yikun Zhou, Jiarui Zhang, Yongqin Zheng, Jundong He

“…Differential expression analysis, WGCNA, machine learning algorithms, diagnostic analysis, and validation were employed to identify key feature genes. Functional analysis, ceRNA network construction, immune microenvironment assessment, and drug prediction were conducted to explore the underlying molecular mechanisms. …”
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Genome-Wide Identification and Expression Analysis of the LbDof Transcription Factor Family Genes in <i>Lycium barbarum</i> by Yuchang Wang, Hongrui Wang, Weinan Li, Guoli Dai, Jinhuan Chen

“…Furthermore, the study offers a comprehensive genomic and functional analysis of <i>LbDof</i> genes, highlighting their potential roles in stress adaptation and fruit maturation. …”
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Comparative omics directed gene discovery and rewiring for normal temperature-adaptive red pigment synthesis by polar psychrotrophic fungus Geomyces sp. WNF-15A by Haoyu Long, Jiawei Zhou, Yanna Ren, Jian Lu, Nengfei Wang, Haifeng Liu, Xiangshan Zhou, Menghao Cai

“…A CRISPR-Cas9 gene-editing system was established for functional analysis of these genes. Deficiency of scaffold1.t692 and scaffold2.t704 with unknown functions highly improved AGRP synthesis at all tested temperatures. …”
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Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data by Ahmad Firoz, Adeel Malik, Sanjay Kumar Singh, Vivekanand Jha, Amjad Ali

“…The objective of this study was to explore the role of differentially expressed glycogenes (DEGGs) in three major tissues such as brain, muscle, and liver using mouse RNA-seq data, and we identified 579, 501, and 442 DEGGs for brain versus liver (BvL579), brain versus muscle (BvM501), and liver versus muscle (LvM442) groups. DAVID functional analysis suggested inflammatory response, glycosaminoglycan metabolic process, and protein maturation as the enriched biological processes in BvL579, BvM501, and LvM442, respectively. …”
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Development of reliable transgenic systems for inducing in vitro-cultured hematopoietic cell proliferation in Cherax quadricarinatus by Yaqi Zhao, Jinwu Wang, Liu Song, Ting Xue, Yifu Xu, Zhenxin Zhao, Zhenmin Bao, Huarong Guo

“…In summary, this study presented a reliable transgenic system for gene functional analysis in shrimp and crayfish, laying the foundation for the development of immortalized cell lines in crustaceans.…”
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Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF Genes Involved in Vegetative Organs Development in Switchgrass by Jianli Wang, Zhenying Wu, Zhongbao Shen, Zetao Bai, Peng Zhong, Lichao Ma, Duofeng Pan, Ruibo Zhang, Daoming Li, Hailing Zhang, Chunxiang Fu, Guiqing Han, Changhong Guo

“…The comprehensive analysis, described here, will facilitate the future functional analysis of ARF genes in grasses.…”
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Microarray Gene Expression Analysis of Murine Tumor Heterogeneity Defined by Dynamic Contrast-Enhanced MRI by Nick G. Costouros, Dominique Lorang, Yantian Zhang, Marshall S. Miller, Felix E. Diehn, Stephen M. Hewitt, Michael V. Knopp, King C. P. Li, Peter L. Choyke, H. Richard Alexander, Steven K. Libutti

“…Using DCE-MRI in a murine subcutaneous tumor model, we were able to perform pharmacokinetic functional analysis of a tumor, coregistration of MRI images with histological cross-sections, immunohistochemistry, laser capture microdissection, and genetic profiling of tumor heterogeneity based on pharmacokinetic parameters. …”
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Proteomic Approach to Study the Effect of <i>Pneumocystis jirovecii</i> Colonization in Idiopathic Pulmonary Fibrosis by Jonás Carmona-Pírez, Rocío Salsoso, Eléna Charpentier, Cinta Olmedo, Francisco J. Medrano, Lucas Román, Carmen de la Horra, Yaxsier de Armas, Enrique J. Calderón, Vicente Friaza

“…We recruited nine participants from the Virgen del Rocio University Hospital (Seville, Spain). iTRAQ and bioinformatics analyses were performed to identify differentially expressed proteins (DEPs), including a functional analysis of DEPs and of the protein–protein interaction networks built using the STRING database. …”
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Composition and diversity of rumen mycobiota in Jiani yaks (Bos grunniens jiani): insights into microbial ecology and functions by Yangji Cidan, Jia Wang, Hongzhuang Wang, Chang Xu, Yanbin Zhu, Muhammad Kasib Khan, Wangdui Basang, Kun Li

“…At the genus level, Rhodotorula, Kluyveromyces, Comoclathris, Arthrinium, Cladophialophora, Seimatosporium, Lambertella, and Sphacelotheca in 14 rib yaks, and Orpinomyces, Ustilago, Fusarium, Aspergillus, Caecomyces, Alternaria, Trichoderma and Acremonium in 15 rib yaks were found to be significantly (p < 0.05) different. Predictive functional analysis based on ruminal fungal DNA sequences from 15‑rib yaks (DLf) demonstrated that genes involved in energy metabolism were upregulated. …”
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Microbiota Dysbiosis in <i>Mytilus chilensis</i> Is Induced by Hypoxia, Leading to Molecular and Functional Consequences by Milton Montúfar-Romero, Diego Valenzuela-Miranda, Valentina Valenzuela-Muñoz, María F. Morales-Rivera, Cristian Gallardo-Escárate

“…Notably, there was a decrease in dominant bacterial taxa such as Rhodobacterales, while opportunistic pathogens such as <i>Vibrio</i> and <i>Aeromonas</i> exhibited increased abundance. Functional analysis indicated a decline in critical microbial functions associated with nutrient metabolism and immune support, potentially jeopardizing the health and survival of the host. …”
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Preparation of Whey Protein Hydrolysates and Their Impact on the Functional Properties of Infant Formula: A Review of Research Progress by Shuang LIU, Meixin LI, Shanshan LI, Ling KONG, Limin ZHEN, Zhiwei CHEN

“…Future research aspects emphasize the potential of whey protein hydrolysates, particularly in activity prediction and functional analysis when integrates with multi-omics approaches. …”
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A Comprehensive Transcriptomic and Proteomics Analysis of Candidate Secretory Proteins in Rose Grain Aphid, <i>Metopolophium dirhodum</i> (Walker) by Atsbha Gebreslasie Gebrekidan, Yong Zhang, Julian Chen

“…However, to verify the expression of these secretory genes and characterize the biological function of salivary proteins further investigation should be geared towards gene expression and functional analysis.…”
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Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes by Xueyan Peng, Shu Li, Wenjun Dou, Mingxin Li, Andrey A. Gontcharov, Zhanwu Peng, Bao Qi, Qi Wang, Yu Li

“…The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. …”
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Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.) by Yuzhu Huo, Wangdan Xiong, Kunlong Su, Yu Li, Yawen Yang, Chunxiang Fu, Zhenying Wu, Zhen Sun

“…Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.…”
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Telomere-related gene risk model predicts prognostic and immune microenvironment alterations in prostate cancer by Danfeng Zhao, Zhenjie Zang, Haodong Li, Ruiyu Li, Guanbo Wang, Keqin Zhang, Tongxiang Diao, Qiang Fu

“…Additionally, two hub genes were utilized to create risk models, with ROC curves confirming their predictive efficacy for 3-, 5-, and 10-year survival rates in patients. Functional analysis of these genes was conducted, and NPY siRNA transfection notably inhibited proliferation in LNCaP and DU145 cells. …”
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The identification of a blood circular RNA signature that differentiates Chikungunya virus infection by Xue Bai, Hanlin Yan, Guoxia Wen, Shaoxun Yuan, Wanjun Gu, Wanjun Gu, Wanjun Gu

“…Furthermore, this blood circRNA signature was correlated with viral load in patients with CHIKV infection. Functional analysis implicated that these biomarker circRNAs were involved in the activation and regulation of immune processes against CHIKV infection.ConclusionCollectively, our findings indicated that peripheral blood circRNAs were potential biomarkers for the early diagnosis of CHIKV infection.…”
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Unveiling the hidden allies of industrial chicory—a metagenomic exploration of rhizosphere microbiota and their impact on productivity and plant health by Lalie Leclercq, Lalie Leclercq, Sony Debarre, Emily Lloret, Bernard Taminiau, Georges Daube, Caroline Rambaud, Caroline Rambaud, Djamel Drider, Ali Siah, Bruno Desprez, Bruno Desprez, Jean-Louis Hilbert, Jean-Louis Hilbert, Anca Lucau-Danila, Anca Lucau-Danila

“…Moreover, the plant demonstrated an ability to repel pathogens and adapt to local microbial communities by selectively favoring beneficial microorganisms according to local stresses and nutritional needs.DiscussionOur study represents a comprehensive taxonomic and functional analysis of the Cichorium intybus rhizosphere microbiome, underscoring the pivotal role of soil composition and land-use history. …”
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