Genome-Wide Identification and Expression Analysis of <i>UBP</i> Genes in Peppers (<i>Capsicum annuum</i> L.) by Xuerui Chang, Tiantian Wang, Jiaxin Huang, Jia Xu, Yangyang Ruan, Yanping Liang, Jing Wang

“…By utilizing genomic and transcriptomic databases, we employed bioinformatics tools to identify <i>UBP</i> family members within pepper genomes and to analyze the expression profiles of <i>CaUBP</i> genes under various abiotic stresses, as well as in different tissues and organs. …”
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Prediction of new candidate proteins and analysis of sub-modules and protein hubs associated with seed development in rice (Oryza sativa) using an ensemble network-based systems bi... by M. R. P. De Silva, J. W. J. K. Weeraman, S. Piyatissa, P. C. Fernando

“…The predictions were validated using enrichment analysis and cross-checked with independent transcriptomic analysis results. The rice seed development sub-network was further analyzed for community and hub detection. …”
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Drought-induced molecular changes in crown of various barley phytohormone mutants by Anetta Kuczyńska, Martyna Michałek, Piotr Ogrodowicz, Michał Kempa, Natalia Witaszak, Michał Dziurka, Damian Gruszka, Agata Daszkowska-Golec, Iwona Szarejko, Paweł Krajewski, Krzysztof Mikołajczak

“…The objective of the present study was the elucidation of drought-induced molecular reactions in the crowns of different barley phytohormone mutants. We verified the hypothesis that defects of gibberellins, brassinosteroids, and strigolactones action affect the transcriptomic, proteomic, and hormonal response of barley crown to the transitory drought influencing plant development under stress. …”
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Pyroptosis-related lncRNAs are potential biomarkers for predicting prognoses and immune landscapes in patients with gastric adenocarcinoma by Haidu Hong, Yuancheng Huang, Zehong Yang, Xiaotao Jiang, Hong Liu

“…Abstract Objectives The purpose of this study was to investigate the significance of pyroptosis-related lncRNAs (PRlncRNA) in predicting prognoses and immune landscapes of patients with gastric adenocarcinoma (STAD). Methods Transcriptomic data and clinicopathological data were obtained from The Cancer Genome Atlas database. …”
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Joint analysis of germline genetic data from over 29,000 cases with suspected hereditary breast and ovarian cancer (HBOC) as part of the NASGE initiative by Jan Henkel, Andreas Laner, Melanie Locher, Tobias Wohlfrom, Birgit Neitzel, Kerstin Becker, Teresa Neuhann, Angela Abicht, Verena Steinke-Lange, Barbara Klink, Birgit Eichhorn, Winfried Schmidt, Daniel Berner, Anna Teubert, Anne Holtorf, Sarah Heinrich, Gabriele Wildhardt, Martin Schulze, Laura von der Heyden, Konstanze Hörtnagel, Daniela Steinberger, Saskia Kleier, Peter Lorenz, Ralf Glaubitz, Saskia Biskup, Elke Holinski-Feder

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Candida albicans and Staphylococcus aureus reciprocally promote their virulence factor secretion and pro-inflammatory effects by Raymond Pasman, Bastiaan P. Krom, Martijs J. Jonker, Wim C. de Leeuw, Gertjan Kramer, Stanley Brul, Sebastian A. J. Zaat, Jianbo Zhang, Jianbo Zhang

“…However, the effect of C. albicans–S. aureus co-existence on virulence factor secretion and pro-inflammatory effects remain elusive.MethodsWe systematically investigated the virulence factors released by C. albicans and S. aureus under different culturing conditions using proteomics. We characterized their pro-inflammatory effects in macrophages with transcriptomics and gene set enrichment analysis.Results and DiscussionWe showed that co-culturing of C. albicans and S. aureus promoted the secretion of 7 cytolytic, 11 proteolytic, and 3 lipolytic extracellular virulence factors (ECVFs) and impacted non-ECVFs, owing to Als1/Als3-mediated interactions, the presence of C. albicans, or its pH maintenance. …”
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Molecular subtyping and precision therapy for esophageal cancer by Guangkun Pei, Zhuoran Liang, Bianli Gu, Linlin Shi, Ze‐Xian Liu, Shegan Gao

“…Two main types of EC, Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC), differ significantly in their molecular characteristics and response to treatment. …”
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Proteasomal activation ameliorates neuronal phenotypes linked to FBXO11-deficiency by Anne Gregor, Laila Distel, Arif B. Ekici, Philipp Kirchner, Steffen Uebe, Mandy Krumbiegel, Soeren Turan, Beate Winner, Christiane Zweier

“…Interestingly, application of three different proteasome-activating substances could alleviate FBXO11-deficiency-associated phenotypes in both human neurons and flies. …”
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Internal in-frame translation generates Cas11b, which is important for effective interference in an archaeal CRISPR-Cas system by A-L. Sailer, J. Brendel, A. Chernev, A. Chernev, S. König, S. König, T. Bischler, T. Gräfenhan, H. Urlaub, H. Urlaub, U. Gophna, A. Marchfelder

“…CRISPR-Cas systems vary in their Cas protein composition and have therefore been divided into different classes and types. Type I systems of bacteria have been shown to contain the small protein Cas11 as part of the interference complex known as Cascade. …”
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scFocus: Detecting branching probabilities in single-cell data with SAC by Chunlin Chen, Zeyu Fu, Jiajia Yang, Huaqing Chen, Jiabao Huang, Shitian Qin, Chuhuai Wang, Xiaoqian Hu

“…Single-cell transcriptomics captures cell differentiation trajectories through changes in gene expression intensity. …”
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Implication of fibroblast growth factor 7 in ovarian cancer metastases and patient survival by Laura F. Mortan, Laura F. Mortan, Brooke A. Meelheim, Justin Garland, Justin Garland, Jacqueline A. Bohn, Zitha Redempta Isingizwe, Doris M. Benbrook, Doris M. Benbrook

“…Serum FGF7 protein levels above the median of 25 patients with ovarian cancer were associated with worse progression-free and overall survival (p = 0.005 and 0.019, respectively) independent of patient and tumor characteristics.ConclusionsIn comparison to ascites, tumors exhibit different transcriptomic profiles that identify candidate biomarkers and drug targets for predicting and preventing recurrence. …”
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Innate immune pathway activated mesenchymal stromal cells improve function and histologic outcomes in a rodent osteoarthritis model by Cody Plaisance, Lyndah Chow, Renata Impastato, Zoë J. Williams, Isabella Sabino, Katie J. Sikes, Kelly S. Santangelo, Steven Dow, Steven Dow, Lynn M. Pezzanite

“…Outcome parameters included voluntary gait activity, joint histology and RNA transcriptomic analyses of synovial tissues.ResultsWe found that activation of MSC via either innate immune pathway improved functional voluntary movement outcomes compared to treatment with non-activated MSC. …”
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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

“…Comparative replication kinetics in different cell lines provided further evidence for improved replication fitness, tolerance towards higher temperatures, and the development of immune evasion mechanisms by the 2018 IBV isolates. …”
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Evolution of cetacean-specific conserved non-coding elements suggests their role in the limb changes during secondary aquatic adaptation by Zhenhua Zhang, Zhenpeng Yu, Yujie Chong, Yao Liu, Jia Liu, Wenhua Ren, Shixia Xu, Guang Yang

“…A transgenic mouse was constructed to carry a cetacean-specific enhancer (i.e., hs1586), which exhibited a significant phenotypic difference in forelimb buds at embryonic day (E)10.5, supported by transcriptomic and epigenomic evidence. …”
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Comparative analysis of dorsal and tail skin reveals region-dependent heterogeneity in axolotl skin regeneration by Lieke Yang, Qian Chen, Jinman Li, Yan Hu, Yaoxin Liu, Binbin Lu, Shuaibin Pei, Tingyi Huang, Yanmei Liu, Ji-Feng Fei

“…Through comparative histological and transcriptomic analyses of full-thickness excisional wounds, we identify accelerated re-epithelialization and reduced collagen deposition in tail skin compared to dorsal wounds. …”
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Divergent multifunctional P450s-empowered biosynthesis of bioactive tripterifordin and cryptic atiserenoids in Aconitum implies convergent evolution by Fei Luo, Qian Zhou, Feilong Chen, Xinyu Liu, Tsan-Yu Chiu, Guo-Yuan Zhu, Ancheng C. Huang

“…Here, via mining the transcriptomes of Aconitum carmichaelii and Aconitum coreanum followed by functional validation, we discover nine TPSs capable of furnishing the ent-kaurene, ent-atiserene or 16α-hydroxy-ent-kaurene scaffold and 14 divergent P450s, of which eight are multifunctional, catalyzing oxidation at seven different sites of the scaffolds. …”
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The glycolytic characteristics of hepatocellular carcinoma and its interaction with the microenvironment: a comprehensive omics study by Dan Chen, Dandan Lin, Huling Li, Jiandong Yang, Lei Liu, Hanyuan Zhang, Dandan Tang, Kai Wang

“…Additionally, single-cell sequencing data (GSE202642) were used to analyze the significantly infiltrated cellular subpopulations in HCC and investigate the expression of prognostic markers across different cell types. Spatial transcriptomics and mass cytometry (CyTOF) data were used to examine the expression differences in immune cells across tumor, peritumoral, and control tissues. …”
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Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in Ataxia Telangiectasia by Sylvia N. Michki, Benjamin D. Singer, Javier V. Perez, Aaron J. Thomas, Valerie Natale, Kathryn A. Helmin, Jennifer Wright, Leon Cheng, Lisa R. Young, Howard M. Lederman, Sharon A. McGrath-Morrow

“…Conclusion Using a transcriptomic approach, we identified novel features and developed an inflammatory score to identify subsets of individuals with different inflammatory phenotypes in A-T. …”
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O-GlcNAcylation-related genes mediate tumor microenvironment characteristics and prediction of immunotherapy response in gastric cancer by Wang Wangwen, Lu Xi, Zhu Chengjun, Li Jie, Liu Yue, Yao Zhangchao, Li Xiaolin

“…We aim to identify molecular clusters related to O-GlcNAcylation and establish a novel scoring system for predicting prognosis and immunotherapy efficacy in patients with gastric cancer (GC). The transcriptomic and clinical data are obtained from XENA-UCSC and GEO databases. …”
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The Potential Role of C4 MYH11+ Fibroblasts and the MDK-SDC2 Ligand-Receptor Pair in Lung Adenocarcinoma: Implications for Prognosis and Therapeutic Strategies by Hongling Jia, Yanjie Bian, Jie Yuan, Yi Zhang, Shengyi Zhang

“…This study employed single-cell RNA sequencing (scRNA-seq) to analyze transcriptomic data from nine LUAD patients at different stages of tumor infiltration, aiming to elucidate the tumor microenvironment and key biological processes of LUAD. …”
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