The multipurpose cell factory Aspergillus niger can be engineered to produce hydroxylated collagen by Tom Morris, Friederike Gerstl, Sascha Jung, Timothy C. Cairns, Vera Meyer

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Exploring associations between metabolites and gene transcripts of common bean (Phaseolus vulgaris L.) in response to rust (Uromyces appendiculatus) infection by Penny Makhumbila, Molemi Rauwane, Hangwani Muedi, Ntakadzeni E. Madala, Sandiswa Figlan

“…The metabolome and transcriptome integration approach employed in this study provides insights on molecular mechanisms underlying U. appendiculatus response in P. vulgaris’ key developmental stages.…”
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CiNAC2 positively regulates drought stress tolerance by promoting superoxide dismutase activity in pecan (Carya illinoinensis) by Bingbing Yang, Chaochen Yang, Juanjuan Chen, Huadong Ren, Kailiang Wang, Linxiu Liu, Xiaohua Yao

“…Weighted gene co-expression network analysis of the transcriptome data was used to screen for a key drought-responsive gene, CiNAC2, which was overexpressed in Arabidopsis thaliana for functional validation. …”
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A proteotranscriptomic approach to dissect the molecular landscape of human retinoblastoma by Julian Wolf, Rozina Ida Hajdu, Stefaniya Boneva, Ira Godbole, Lucas Stürzbecher, Claudia Auw-Haedrich, Wolf A. Lagrèze, Hansjürgen Agostini, Thomas Reinhard, Stefan Tholen, Oliver Schilling, Günther Schlunck, Bertram Bengsch, Clemens Lange

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Multi-omics analysis of potential metabolic networks linking peripheral metabolic changes to inflammatory retinal conditions in STZ-induced early diabetic retinopathy by Xiaonan Zhang, Yan Liu, Mengxue Xia, Manwen Yang, Yingjie Wu, Fang Zhang

“…This study employed an integrative approach, combining retinal and serum transcriptomic and metabolomic profiles with genome-wide association study (GWAS) data, to identify peripheral metabolites potentially linking early retinal lesions. …”
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Common antimicrobials disrupt early zebrafish development through immune-cardiac signaling by Yueyue Liu, Chen Wang, Zhiyou Fu, Yingchen Bai, Guomao Zheng, Fengchang Wu

“…All tested chemicals, except CX, cause significant teratogenic effects. Transcriptomic analysis reveals substantial disruptions in immune-related coagulation cascades and mitogen-activated protein kinase signaling pathways. …”
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Exploring RNA cargo in extracellular vesicles for pleural mesothelioma detection by Agnieszka Kraft, Michaela B. Kirschner, Vanessa Orlowski, Manuel Ronner, Caroline Bodmer, Valentina Boeva, Isabelle Opitz, Mayura Meerang

“…In this study, we characterized the transcriptomic profile of EVs secreted by PM primary cells and explored their potential as a biomarker source for PM detection. …”
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Dual roles of Anisakis pegreffii proteins in macrophage immune dynamics by Min-hao Zeng, Min-hao Zeng, Min-hao Zeng, Sarah Alsobaie, Xiao-xu Wang, Shan Li, Fahad M. Aldakheel, Mourad A. M. Aboul-Soud, Wei-bin Liu

“…The analysis of ABP and glycoprotein - induced immune responses provides key insights into Anisakiasis pathogenesis and may help develop new treatments.…”
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Multicohort analysis identifies conserved transcriptional interactions between humans and Plasmodium falciparum by Bárbara Fernandes Silva, Nágila Isleide Silva, Pedro Felipe Loyola Souza, Tiago Paiva Guimarães, Luiz Gustavo Gardinassi

“…We analyzed nine public dual-transcriptomes acquired from whole blood of individuals infected with P. falciparum. …”
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The mechanism by which oriented polypropylene packaging alleviates postharvest ‘Black Spot’ in radish root (Raphanus sativus) by Zixin Lin, Bihong Feng, Shibei Fang, Xi Pang, Huafeng Liang, Shuzhi Yuan, Xiaodi Xu, Jinhua Zuo, Xiaozhen Yue, Qing Wang

“…Appearance and physiological parameters were assessed and transcriptomic and metabolomic analyses were conducted to identify the key molecular and biochemical factors contributing to the disorder and strategies for delaying its onset and development. …”
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Deep Pseudogene Categorization and Genome-Wide Transcription Prediction Using GANP-Based Feature Selection and TabNet Interpretability by Zeeshan Ahmed, Kashif Munir, Muhammad Usama Tanveer, Syed Rizwan Hassan, Ateeq Ur Rehman, Habib Hamam

“…Tested on a large-scale curated transcriptomic dataset, our framework achieves an accuracy of 96%, surpassing traditional machine learning models. …”
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Integrated multi-omics identify key signalling pathways for notochord lumenogenesis in ascidian Ciona savignyi by Jin Zhang, Zicheng Tan, Qishu Qin, Hongzhe Peng, Wenjie Shi, Haiyan Yu, Bo Dong

“…Here, we performed tissue-specific transcriptomic sequencing for the isolated Ciona notochord tissue, in which 10 551 genes in total were identified. …”
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Response of heterotrophic nitrifying/aerobic denitrifying strain Pseudomonas stutzeri YXH-102 to hypersaline stress by Youming Wang, Zhichun Wang, Yangfan Hu, Dexun Zou, Korakot Sombatmankhong, Wen Wang, Bo Yu

“…Results: Comparative transcriptomic analysis revealed 268 differentially expressed genes (DEGs) in response to a 10 % NaCl shock, with 86 upregulated and 182 downregulated. …”
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Titanium ions promote tomato growth and increase stress resistance by Yu-Bo Ma, Wen-Lin Li, Ji-Han Li, Meng-Jiao Li, Xin-Yu Li, Chun-Mei Wei, Cai-Xia Li, Yan Wang, Yun Zhao, Xin-Rong Ma

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Comprehensive Physiology, Cytology, and Transcriptomics Studies Reveal the Regulatory Mechanisms Behind the High Calyx Abscission Rate in the Bud Variety of Korla Pear (<i>Pyrus si... by Xian’an Yang, Shiwei Wang, Zhenbin Jiang, Cuifang Zhang, Long Zhao, Yutong Cui

“…The obtained results provide reliable data for the screening of candidate genes for calyx shedding and analysis of the regulatory mechanism behind a high calyx shedding rate, providing a theoretical basis upon which the calyx shedding rate of fruits can be improved through genetic improvement.…”
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Integrative single-cell and spatial transcriptomics uncover ELK4-mediated mechanisms in NDUFAB1+ tumor cells driving gastric cancer progression, metabolic reprogramming, and immune... by Yuwei Sun, Wenyang Nie, Zhikai Xiahou, Xiaojing Wang, Wenjia Liu, Zongkai Liu, Zhiheng Lin, Zhaidong Liu

“…The findings underscored the importance of developing specific therapeutic targets, targeting metabolic reprogramming, and overcoming immune evasion, providing new theoretical foundations.…”
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Screening and comparison of in vitro-induced resistant and clinically resistant Stenotrophomonas maltophilia strains for eravacycline resistance-related genes by Jie Wu, Jiarong Song, Junchang Cui

“…ObjectiveTo identify genes related to eravacycline resistance in Stenotrophomonas maltophilia (Sm) and to provide a theoretical basis for the study of eravacycline resistance mechanisms in Sm and the development of new antibiotics.MethodsThe study employed an integrated omics approach: (1) In vitro antimicrobial susceptibility profiling via broth microdilution to determine baseline MICs for eravacycline and comparator drugs; (2) Induction of resistance in clinical Sm isolates (WJ_4, WJ_14, WJ_18) with low eravacycline MICs through serial passage in escalating drug concentrations; (3) Transcriptome sequencing (RNA-seq) and whole-genome sequencing (WGS) of in vitro-induced resistant strains (WJ_4a, WJ_14a, WJ_18a) and a clinical high-MIC isolate (WJ_97); (4) Bioinformatics analyses, including differential gene expression screening (with |log2(fold change)| &gt; 2 and FDR-adjusted p &lt; 0.05), SNP detection via GATK, and copy number variation (CNV) quantification using CCNE-acc to identify and compare resistance-related genetic alterations.ResultsStable eravacycline-resistant strains were successfully induced, exhibiting 8- to 32-fold MIC increases. …”
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Single-cell analysis reveals the spatiotemporal effects of long-term electromagnetic field exposure on the liver by Mingming Zhang, Zhichun Lv, Lingping Zhao, Quan Zeng, Yunqiang Wu, Junnian Zhou, Jiafei Xi, Xuetao Pei, Haiyang Wang, Changyan Li, Wen Yue

“…Notably, hepatocytes, endothelial cells, and monocytes showed higher sensitivity to electromagnetic radiation, with their lipid metabolic functions, immune regulation functions, and intrinsic functions disturbed, respectively. Moreover, transcriptomic alterations were predominantly observed in the hepatocytes and endothelial cells in peri-portal regions, suggesting a zonation-related sensitivity to EMF within the liver.ConclusionOur study provided a spatiotemporal visualization of EMF-induced alterations in hepatic cells, which ultimately elucidated the biological effects of EMF exposure.…”
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A Genome-Wide Alternative Splicing Analysis of <i>Gossypium arboreum</i> and <i>Gossypium raimondii</i> During Fiber Development by Jianfeng Hao, Xingpeng Wen, Yuxian Zhu

“…In this study, we comparatively analyzed <i>G. arboreum</i> and <i>G. raimondii</i> AS events during fiber development using transcriptome data and identified 9690 and 7617 AS events that were distributed in 6483 and 4859 genes, respectively. …”
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Virtual Screening and Meta-Analysis Approach Identifies Factors for Inversion Stimulation (Fis) and Other Genes Responsible for Biofilm Production in <i>Pseudomonas aeruginosa</i>:... by Promise M. Emeka, Lorina I. Badger-Emeka, Krishnaraj Thirugnanasambantham

“…The present study uses a meta-analysis of a transcriptomics dataset to identify important genes and pathways in biofilm formation of <i>P. aeruginosa</i> induced keratitis. …”
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