In-depth characterization of vaccine-induced neoantigen-specific T cells in patients with IDH1-mutant glioma undergoing personalized peptide vaccination by Martin Glas, Florian Battke, Dirk Hadaschik, Martin Schulze, Saskia Biskup, David Reardon, Christina Kyzirakos, Simone Kayser, Oliver Bartsch, Armin Rabsteyn, Henning Zelba, Borong Shao, Annekathrin Reinhardt, Carsten Greve, Lisa Oenning, Pauline Latzer, Tabea Riedlinger, Julian Wünsche, Johannes Harter, Magdalena Feldhahn, Yannick Bantel, Janina Johänning, Jiri Ködding, Olga Maksimovic, Veit Scheble, Alexandra M Miller, Michael Castro, Deborah T Blumenthal

“…Extracellular CD154 staining was used to sort mutIDH1-specific CD4+T cells.Immunomonitoring revealed that the vaccines were immunogenic and induced mainly CD4 but also CD8 T cell responses. Vaccine-induced immune responses were robust and polyfunctional. …”
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Identification and analysis of miRNA - mRNA regulatory modules associated with resistance to bacterial leaf streak in rice by Baowei Wu, Xiaoyu Zhang, Jialiang Zhao, Bohong Zeng, Zhibin Cao

“…By conducting miRNA sequencing and transcriptome sequencing on both Dular and 9311 before and after BLS inoculation, we identified 19 miRNAs that were significantly downregulated at both 12 and 24 h post-inoculation in Dular, and 9 miRNAs that were significantly upregulated at the same time points in 9311. …”
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A-to-I RNA editing of CYP18A1 mediates transgenerational wing dimorphism in aphids by Bin Zhu, Rui Wei, Wenjuan Hua, Lu Li, Wenlin Zhang, Pei Liang

“…Adenosine (A) to inosine (I) RNA editing is a post-transcriptional modification that extends transcriptome variety without altering the genome, playing essential roles in numerous biological and physiological processes. …”
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Chemical quantification of N-acyl alanine methyl ester (NAME) production and impact on temporal gene expression patterns in Roseovarius tolerans EL-164 by Janina Leinberger, Diana Koteska, Judith Boldt, Jörn Petersen, Sahana Shivaramu, Jürgen Tomasch, Stefan Schulz, Thorsten Brinkhoff

“…By comparing the transcriptomes of pre- and post-metabolite-spikes, we identified three clusters of differentially expressed genes with distinct temporal expression patterns. …”
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Overexpression of the ABA Synthesis Gene OsABA2 Enhances Seed Storability in Rice by Yongxiang Liao, Pengfei Jiang, Mingming Zhang, Fangli Jin, Mengyuan Li, Jiazhi Dong, Daiming Guo, Yingxiu Liao, Asif Ali, Saira Saleem, Xiangyang Zhang, Qinggui Jiang, Su Liu, Hongyu Zhang, Xiaoqiong Chen, Kangxi Du, Hao Zhou, Duo Xia, Peizhou Xu, Xianjun Wu

“…For practical application, Gang46B—a hybrid rice parental line with poor storability—significantly improved its post-aging germination rates. These findings demonstrate that the overexpression of OsABA2 enhances seed storability by regulating ABA biosynthesis pathway and associated oxidative response. …”
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The translatome of glioblastoma by Fleur M. G. Cornelissen, Zhaoren He, Edward Ciputra, Richard R. deHaas, Ammarina Beumer‐Chuwonpad, David Noske, W. Peter Vandertop, Sander R. Piersma, Connie R. Jiménez, Cornelis Murre, Bart A. Westerman

“…We investigated inter‐cell‐line differences through differential expression analysis at both the translatome and transcriptome levels. Translational changes post‐radiotherapy were assessed at 30 and 60 min. …”
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DTC-m6Am: A Framework for Recognizing N6,2′-O-dimethyladenosine Sites in Unbalanced Classification Patterns Based on DenseNet and Attention Mechanisms by Hui Huang, Fenglin Zhou, Jianhua Jia, Huachun Zhang

“…Background: m6Am is a specific RNA modification that plays an important role in regulating mRNA stability, translational efficiency, and cellular stress response. m6Am’s precise identification is essential to gain insight into its functional mechanisms at transcriptional and post-transcriptional levels. …”
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Down-regulation of colon mucin production induced by Eimeria pragensis infection in mice by Yulia Dwi Setia, Yulia Dwi Setia, Mio Kokubo-Tanaka, Ryusei Tanaka, Akemi Yoshida, Eiji Nagayasu, Parnian Ahmadi, Parnian Ahmadi, Parnian Ahmadi, Ayako Yoshida, Ayako Yoshida, Haruhiko Maruyama

“…Colon tissues were collected at 3, 8, and 13 days post-infection (dpi) to assess pathological changes. …”
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Sperm Membrane: Molecular Implications and Strategies for Cryopreservation in Productive Species by Macarena Castro, Karla Leal, Felipe Pezo, María José Contreras

“…Similarly, the addition of lipid-based supplements contributes to membrane stabilization, improving post-thaw sperm viability and functionality. Moreover, the application of omics technologies, such as transcriptomics and proteomics, has facilitated a deeper understanding of molecular damage and protective responses, paving the way for the development of tailored, species-specific protocols. …”
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Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques by Hayden N. Brochu, Elise Smith, Sangmi Jeong, Michelle Carlson, Scott G. Hansen, Jennifer Tisoncik-Go, Lynn Law, Louis J. Picker, Michael Gale, Xinxia Peng

“…We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals. Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.IMPORTANCEThe human immunodeficiency virus (HIV) has infected millions of people worldwide. …”
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CYP1B1 knockout enhanced IFN-γ production is required but not sufficient for protection of cigarette smoke-exposed mice against lethal influenza virus infection by Wenxin Wu, Jeremy S. Alexander, J. Leland Booth, Magdalena Chlebicz, Craig A. Miller, Chao Xu, Susan Kovats, Susan Kovats, Jordan P. Metcalf, Jordan P. Metcalf, Jordan P. Metcalf

“…We used an in-vivo mouse model to assess the hypothesis that CYP1B1 modifies innate immune responses to CS and alters survival during IAV infection.MethodsWe measured CYP1B1 induction in bronchial epithelial cells in smokers and nonsmokers obtained by bronchoscopy by whole transcriptome analysis. …”
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Decoding ARF4 and EIF5B-Based Prognostic Signatures and Immune Landscape Following Insufficient Radiofrequency Ablation in Hepatocellular Carcinoma: Through Multi-Omics and Experim... by Zhang Y, Lu Y, Zheng S, Luo W, Tan M, Luo B

“…These findings suggest they could serve as viable therapeutic targets aimed at mitigating HCC recurrence post-RFA. Keywords: inadequate radiofrequency ablation, HCC, ARF4, EIF5B, biomarker…”
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Molecular mechanisms underlying age-dependent effects of rearing system on the goose testicular development and semen quality by Shenqiang Hu, Xiaopeng Li, Enhua Qing, Junqi Wang, Qingliang Chen, Yang Song, Jiasen Chen, Jiwei Hu, Liang Li, Jiwen Wang

“…In the present study, the testicular morphological, histological, and transcriptomic responses of three goose breeds to the two dryland rearing systems (i.e., cage rearing system, CRS and net-floor mixed rearing system, MRS) were systematically analyzed and compared. …”
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Genome-Wide Identification of <i>G3BP</i> Family in U’s Triangle <i>Brassica</i> Species and Analysis of Its Expression in <i>B. napus</i> by Alain Tseke Inkabanga, Qiheng Zhang, Shanshan Wang, Yanni Li, Jingyi Chen, Li Huang, Xiang Li, Zihan Deng, Xiao Yang, Mengxin Luo, Lingxia Peng, Keran Ren, Yourong Chai, Yufei Xue

“…We then analyzed their gene structure, protein motifs, gene duplication type, phylogeny, subcellular localization, SSR loci, and upstream miRNAs. Based on transcriptome data, we analyzed the expression patterns of <i>B. napus G3BP</i> (<i>BnaG3BP</i>) genes in various tissues/organs in response to <i>Sclerotinia</i> disease, blackleg disease, powdery mildew, dehydration, drought, heat, cold, and ABA treatments, and its involvement in seed traits including germination, α-linolenic acid content, oil content, and yellow seed. …”
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OsNUDX23 regulates early seed germination by modulating ROS balance and starch metabolism in rice by Xing Dai, Xing Dai, Wenwen Kong, Feiyan Wu, Zijie Pan, Lei Gao, Beixin Mo, Yu Yu, Weigui Luo

“…Down-regulation of genes involved in starch and sucrose metabolism was observed in Osnudx23 mutants during post-imbibition, accompanied with accumulated starch content. …”
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Immunomodulatory effects of intratumoral cowpea mosaic virus and calreticulin nanoparticles in canine tumors: early results by Akansha Singh, Jessica Fernanda Affonso de Oliveira, Jessica Fernanda Affonso de Oliveira, Jessica Fernanda Affonso de Oliveira, Jessica Schrader, Deepan Kishore, Sri Vidhya Chandrasekar, Steven Fiering, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Nicole F. Steinmetz, Ashish Ranjan

“…Post-treatment NanoString and flow cytometry analyses revealed a shift in the tumor microenvironment toward a more immunostimulatory state, marked by increased neutrophils and CD8+ T cells. …”
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Proteomics and integrative omic approaches for understanding host–pathogen interactions and infectious diseases by Pierre M Jean Beltran, Joel D Federspiel, Xinlei Sheng, Ileana M Cristea

“…Further expanding the understanding of proteome organization during an infection, we discuss methods that characterize the regulation of host and pathogen proteomes through alterations in protein abundance, localization, and post‐translational modifications. Finally, we highlight bioinformatic tools available for analyzing such proteomic datasets, as well as novel strategies for integrating proteomics with other omic tools, such as genomics, transcriptomics, and metabolomics, to obtain a systems‐level understanding of infectious diseases.…”
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The interplay between transcription and mRNA degradation in Saccharomyces cerevisiae by Subhadeep Das, Debasish Sarkar, Biswadip Das

“…The cellular transcriptome is shaped by both the rates of mRNA synthesis in the nucleus and mRNA degradation in the cytoplasm under a specified condition. …”
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Early pharmacological blockade of the CXCL12-CXCR4 axis attenuates vertebral hypercalcification in a zebrafish model of pseudoxanthoma elasticum by Jianjian Sun, Jichang Huang, Renjie Zhang, Shubin Zhang, Tao P. Zhong, Ping Zhu

“…Three mutant types (Type1-Type3, T1-T3) stratified by calcification severity, exhibited reduced levels of the calcification inhibitors vitamin K1 (VK1) and carboxylated matrix Gla protein (cMGP), which were inversely correlated with the severity of calcification. Vertebral transcriptomics revealed dysregulated pathways related to ossification, bone remodeling-associated extracellular matrix (ECM), and immune responses, with the CXCL12-CXCR4 axis identified as a pivotal signaling hub. …”
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Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum. by Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee

“…Approximately one-third of the total sRNAs were produced from the gene region, and sRNAs with an antisense direction or 5'-U were involved in post-transcriptional gene regulation by reducing the stability of the corresponding gene transcripts. …”
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