Decoding post-transcriptional gene expression controls in trypanosomatids using machine learning [version 2; peer review: 2 approved] by David Horn, Michele Tinti

“…We suggest a model whereby UTRs control the rate of translation initiation, while favoured codons increase the rate of translation elongation, thereby reducing mRNA turnover.…”
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Phosphorus Alleviates Cadmium Damage by Reducing Cadmium Accumulation and Enhancing Antioxidant Enzymes at the Vegetative Phase in Soybean by Sen Jia, Xiang Zhao, Junxia Huang, Xingdong Yao, Futi Xie

“…This study aimed to explore the interactive effects of Cd and phosphate on soybeans at the physiological, transcriptomic, and metabolic levels using a multi-omics approach. …”
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RBM47 functions as an anti-oncogene by regulating expression and alternative splicing of cell proliferation and apoptosis associated genes in colorectal cancer cells by Guangshi Liu, Tao Li, Peng Li, Suyan Wei, Kamuran Abulizi

“…Abstract Transcriptional and post-transcriptional regulation mediated by RNA binding proteins (RBPs) have essential influence on the progression of colorectal cancer (CRC), while the underlying mechanisms need to be clarified. …”
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TPS genes expression pattern and terpenoids content in the leaves and flowers of Chimonanthus praecox and C. salicifolius by Wei Zou, Chang Liu, Han Wang, Rui-Yang Shen, Meng-Cheng Ji, Cui-Hua Gu, Li-Yuan Yang

“…We identified 63 and 48 TPS genes from the genomes of C. praecox and C. salicifolius. Transcriptome analysis showed that TPS-b subfamily genes (related to monoterpene synthesis) showed high expression levels in flowers and leaves, while TPS-a subfamily genes (related to sesquiterpene synthesis) showed strong expression in leaves. …”
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Rhythm profiling using COFE reveals multi-omic circadian rhythms in human cancers in vivo. by Bharath Ananthasubramaniam, Ramji Venkataramanan

“…Moreover, rhythms in the transcriptome were strongly associated with the cancer-relevant proteome. …”
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Deciphering the prognostic significance of WDR77 in gliomas: a comprehensive analysis by Hanwen Lu, Bingchang Zhang, Wenhua Li, Zhanxiang Wang

“…A total of 699 glioma samples from the TCGA database were used as the training cohort, while 1018 samples from CGGA were used as the validation cohort. …”
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A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy. by Nadia Khan, Nadia Khan, Barry Schoenike, Trina Basu, Heidi Grabenstatter, Genesis Rodriguez, Caleb Sindic, Margaret Johnson, Eli Wallace, Rama Maganti, Raymond Dingledine, Avtar Roopra

“…Complex neurological conditions can give rise to large scale transcriptomic changes that drive disease progression. …”
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(p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms by Florian Engelhardt, Kathryn Turnbull, Melisa Gür, Mathias Müsken, Matthias Preusse, Susanne Häussler, Mohammad Roghanian

“…Initial increases in (p)ppGpp reduce growth and metabolism while suppressing motility and pyocyanin production. …”
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Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire. by Ivy K Brown, Nathan Dyjack, Mindy M Miller, Harsha Krovi, Cydney Rios, Rachel Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P O'Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A Seibold, James Scott-Browne, Radleigh G Santos, R Lee Reinhardt

“…Using IL-4-reporter mice to identify responding CD4+ T cells to Nippostrongylus brasiliensis infection, T cell receptor sequencing paired with novel clustering algorithms revealed a broadly reactive and clonally diverse CD4+ T cell response. While the most prevalent clones and clonotypes exhibited some tissue selectivity, most were observed to reside in both the lung and lung-draining lymph nodes. …”
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Roles of P-body factors in Candida albicans filamentation and stress response. by Melissa A Tosiano, Frederick Lanni, Aaron P Mitchell, C Joel McManus

“…Hyphal growth is strongly associated with virulence in the human fungal pathogen Candida albicans. While hyphal transcriptional networks have been the subject of intense study, relatively little is known about post-transcriptional regulation. …”
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Protocol to estimate the heritability of drug response with GxEMM and identify gene-drug interactions with TxEWAS by Michal Sadowski, Andy W. Dahl, Noah Zaitlen

“…We describe steps for estimating the heritability of drug response with gene-environment interaction mixed model (GxEMM) and identifying gene-drug interactions with gene-environment interaction transcriptome-wide association study (TxEWAS). While the protocol describes application to drug treatments, this framework can be used to characterize the genetic basis of any covariate’s effect.For complete details on the use and execution of this protocol, please refer to Sadowski et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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Adverse predictive value of ASPM on lung adenocarcinoma overall survival depended on chemotherapy status by Yan Zheng, Baichen Sun, Zhiling Qu

“…Objective Transcriptome and proteome analyses may yield inconsistent predictions regarding tumor prognosis. …”
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Construction and Evaluation of a Rat Model of Abnormal Uterine Bleeding by LIAN Hui, JIANG Yanling, LIU Jia, ZHANG Yuli, XIE Wei, XUE Xiaoou, LI Jian

“…Serum and uterine tissue samples were collected from the model group at 0, 12, 24, 36, and 48 h after mifepristone administration, while the normal control group was sampled at 36 h. …”
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Dose-dependent effects of gamma radiation on the early zebrafish development and gene expression. by Selma Hurem, Leonardo Martín Martín, Dag Anders Brede, Eystein Skjerve, Rasoul Nourizadeh-Lillabadi, Ole Christian Lind, Terje Christensen, Vidar Berg, Hans-Christian Teien, Brit Salbu, Deborah Helen Oughton, Peter Aleström, Jan Ludvig Lyche

“…The survival observed at 96 hours post fertilization (hpf) in the 38 mGy/h group was significantly lower, while other groups showed no significant difference compared to controls. …”
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Genome-wide identification of starch metabolism gene families in Potentilla anserina and the expression pattern in response to abiotic stress factors by Yangmiao Jiao, Qin He, Xu Li, Yang Chen, Tingting Tian, Liang Cao, Zaiqi Zhang

“…In the tuberous roots, when compared with the control conditions, 2 AMYs and 4 BAMs were upregulated, while 3 BAMs were downregulated, meanwhile, the contents of maltose and glucose-6-phosphate (G6P) were decreased, while the content of glucose-1-phosphate (G1P) was increased under drought treatment. …”
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Nucleus Pulposus Cells Induce M2 Polarization of RAW264.7 via CX3CL1/CX3CR1 Pathway and M2 Macrophages Promote Proliferation and Anabolism of Nucleus Pulposus Cells by Xiao-Tao Wu, Bo-Wen Wan, Xin-Min Feng, Yu-Ping Tao, Yong-Xiang Wang, Hui-Hui Sun

“…M2 polarized macrophages can further promote NP cell viability, proliferation, and anabolism, while inhibit NP cell apoptosis and catabolism.…”
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Co-exposure to ozone and polystyrene nanoplastic exacerbates cognitive impairment and anxiety-like behavior by regulating neuronal pyroptosis in mice by Anqi Dai, Xudong Liu, Yinuo Chen, Yougang Wang, Haomin Qi, Yan Zeng, Jinquan Li

“…Ozone (O3) and nanoplastics (NPs) are pervasive environmental pollutants that frequently co-occur in our heavily industrialized era. While it has been documented that exposure to O3 or NPs individually has neurotoxic effects, studies investigating their combined impact and the hazardous mechanisms resulting from co-exposure are limited. …”
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PARP inhibitors elicit a cellular senescence mediated inflammatory response in homologous recombination proficient cancer cells by Misato Kamii, Ryo Kamata, Hitoshi Saito, Gaku Yamamoto, Chiaki Mashima, Toyohiro Yamauchi, Takehiro Nakao, Yuta Sakae, Tomoko Yamamori-Morita, Kazuki Nakai, Yumi Hakozaki, Masataka Takenaka, Aikou Okamoto, Akihiro Ohashi

“…Abstract Poly (ADP-ribose) polymerase (PARP) inhibitors have improved the prognosis of homologous recombination deficient (HRD) ovarian cancer (OC), while effective therapeutic strategies for HR-proficient (HRP) OC still need to be established. …”
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Genetic prioritisation of candidate drug targets for glaucoma through multi-trait and multi-omics integration by Jianqi Chen, Yangjiani Li, Yingting Zhu, Zhidong Li, Shitong Huang, Wenzhi Huang, Yuyao Ling, Jingying Liang, Yunxia Leng, Yehong Zhuo

“…We employed proteome and transcriptome Mendelian randomization (MR) and colocalisation to identify potential therapeutic targets, glaucoma endophenotype MR to explore the potential mechanisms of identified associations, and phenome-wide MR to investigate possible adverse effects of candidate targets. …”
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Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade by Natalia Nenasheva, Clara Pitzschel, Cynthia N. Webster, Alexander J. Hart, Jill L. Wegrzyn, Mia M. Bengtsson, Katharina J. Hoff

“…For gene prediction, BRAKER2 was employed in the absence of transcriptomic data, while BRAKER3 was utilised when transcriptome short read data were available from the Sequence Read Archive. …”
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