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JOURNAL ARTICLE
Yumeng Wang, Shuqiang Li, Zihang Liu, Xuanzheng Li, Yifan Yu, Hao Liu
Liver hepatocellular carcinoma (LIHC) is a significant global health issue with limited treatment options. In this study, single-cell RNA sequencing (scRNA-seq) data were used to explore the molecular mechanisms of LIHC development and identify potential targets for therapy. The expression of peroxisome proliferator-activated receptors (PPAR)-related genes was analysed in LIHC samples, and primary cell populations, including natural killer cells, T cells, B cells, myeloid cells, endothelial cells, fibroblasts and hepatocytes, were identified...
April 2024: Journal of Cellular and Molecular Medicine
#2
JOURNAL ARTICLE
Farley M Kwok van der Giezen, Amy Viljoen, Leni Campbell-Clause, Nhan Trong Dao, Catherine Colas des Francs-Small, Ian Small
The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2...
April 23, 2024: Plant Journal
#3
JOURNAL ARTICLE
Yazhou Zhu, Ming Li, Zihua Li, Jiahui Song, Wei Zhao
OBJECTIVE: To explore the role of miRNA in liver damage caused by Echinococcus multilocularis infection. METHODS: Six female C57BL mice were randomly divided into two groups, the control group and the infection group. Mice in the control group were injected with 100 μL PBS through the hepatic portal vein, and mice in the infection group were infected with E. multilocularis via the hepatic portal vein to establish a mouse model of infection. Small RNA sequencing was performed for detecting the expression of miRNAs in the liver of mice infected with 2000 E...
April 2024: Immunity, Inflammation and Disease
#4
JOURNAL ARTICLE
Jens Sivkær Pettersen, Flemming Damgaard Nielsen, Patrick Rosendahl Andreassen, Jakob Møller-Jensen, Mikkel Girke Jørgensen
Two-component systems are key signal-transduction systems that enable bacteria to respond to a wide variety of environmental stimuli. The human pathogen, Streptococcus pneumoniae (pneumococcus) encodes 13 two-component systems and a single orphan response regulator, most of which are significant for pneumococcal pathogenicity. Mapping the regulatory networks governed by these systems is key to understand pneumococcal host adaptation. Here we employ a novel bioinformatic approach to predict the regulons of each two-component system based on publicly available whole-genome sequencing data...
June 2024: NAR genomics and bioinformatics
#5
JOURNAL ARTICLE
Xiaoxue Fan, Xuze Gao, He Zang, Zhitan Liu, Xin Jing, Xiaoyu Liu, Sijia Guo, Haibin Jiang, Ying Wu, Zhijian Huang, Dafu Chen, Rui Guo
In the present study, small RNA (sRNA) data from Ascosphaera apis were filtered from sRNA-seq datasets from the gut tissues of A. apis -infected Apis mellifera ligustica worker larvae, which were combined with the previously gained sRNA-seq data from A. apis spores to screen differentially expressed milRNAs (DEmilRNAs), followed by trend analysis and investigation of the DEmilRNAs in relation to significant trends. Additionally, the interactions between the DEmilRNAs and their target mRNAs were verified using a dual-luciferase reporter assay...
2024: Frontiers in Microbiology
#6
JOURNAL ARTICLE
Jianqi Yang, Jishun Tang, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang, Xiaofei Guo, Wenping Hu, Mingxing Chu
BACKGROUND: The pituitary directly regulates the reproductive process through follicle-stimulating hormone (FSH) and luteinizing hormone (LH). Transcriptomic research on the pituitaries of ewes with different FecB (fecundity Booroola) genotypes has shown that some key genes and lncRNAs play an important role in pituitary function and sheep fecundity. Our previous study found that ewes with FecB + + genotypes (without FecB mutation) still had individuals with more than one offspring per birth...
April 22, 2024: BMC Genomics
#7
JOURNAL ARTICLE
Ruth E Drury, Susana Camara, Irina Chelysheva, Sagida Bibi, Katherine Sanders, Salle Felle, Katherine Emary, Daniel Phillips, Merryn Voysey, Daniela M Ferreira, Paul Klenerman, Sarah C Gilbert, Teresa Lambe, Andrew J Pollard, Daniel O'Connor
The immune mechanisms mediating COVID-19 vaccine attenuation of COVID-19 remain undescribed. We conducted comprehensive analyses detailing immune responses to SARS-CoV-2 virus in blood post-vaccination with ChAdOx1 nCoV-19 or a placebo. Samples from randomised placebo-controlled trials (NCT04324606 and NCT04400838) were taken at baseline, onset of COVID-19-like symptoms, and 7 days later, confirming COVID-19 using nucleic amplification test (NAAT test) via real-time PCR (RT-PCR). Serum cytokines were measured with multiplexed immunoassays...
April 22, 2024: Nature Communications
#8
JOURNAL ARTICLE
Andreas Roller, Iakov I Davydov, Petra C Schwalie, Martha L Serrano-Serrano, Astrid Heller, Nicolas Staedler, Cláudia S Ferreira, Gabriele Dietmann, Irina Klaman, Alberto Valdeolivas, Konstanty Korski, Michael A Cannarile
BACKGROUND: The immune status of a patient's tumor microenvironment (TME) may guide therapeutic interventions with cancer immunotherapy and help identify potential resistance mechanisms. Currently, patients' immune status is mostly classified based on CD8+tumor-infiltrating lymphocytes. An unmet need exists for comparable and reliable precision immunophenotyping tools that would facilitate clinical treatment-relevant decision-making and the understanding of how to overcome resistance mechanisms...
April 22, 2024: Journal for Immunotherapy of Cancer
#9
JOURNAL ARTICLE
Xiaobin Xie, Yibo Wang, Fang Ma, Ruilin Ma, Leqiang Du, Xin Chen
High-temperature stress poses a significant environmental challenge for aquatic organisms, including tsinling lenok trout (Brachymystax lenok tsinlingensis). This study aimed to investigate the role of microRNAs (miRNAs) in inducing liver inflammation in tsinling lenok trout under high-temperature stress. Tsinling lenok trout were exposed to high-temperature conditions (24 °C) for 8 h, and liver samples were collected for analysis. Through small RNA sequencing, we identified differentially expressed miRNAs in the liver of high-temperature-stressed tsinling lenok trout compared to the control group (maintained at 16 °C)...
April 22, 2024: Marine Biotechnology
#10
JOURNAL ARTICLE
Yuan Wang, Xuanlin Li, Chenghong Zhu, Shijie Yi, Yan Zhang, Zhi Hong
BACKGROUND: Aphids (Hemiptera: Aphididae) are notorious sap-sucking insects that rampantly threaten agricultural production worldwide. Current management against aphids in the field heavily relies on chemical pesticides, which makes economical and eco-friendly methods urgently needed. Spray-induced gene silencing (SIGS) offers a powerful and precise approach to pest management. However, the high costs and instability of double-stranded RNA (dsRNA) regulators applied for downstream RNA interference (RNAi) still limit this strategy...
April 22, 2024: Pest Management Science
#11
Hope M Healey, Hayden B Penn, Clayton M Small, Susan Bassham, Vithika Goyal, Micah A Woods, William A Cresko
UNLABELLED: Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genomes revealed suggestive gene content differences and provide the opportunity for detailed genetic analyses. We created a single cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy...
April 9, 2024: bioRxiv
#12
Philipp Rentzsch, Aaron Kollotzek, Pejman Mohammadi, Tuuli Lappalainen
Differential expression (DE) analysis is a widely used method for identifying genes that are functionally relevant for an observed phenotype or biological response. However, typical DE analysis includes selection of genes based on a threshold of fold change in expression under the implicit assumption that all genes are equally sensitive to dosage changes of their transcripts. This tends to favor highly variable genes over more constrained genes where even small changes in expression may be biologically relevant...
April 10, 2024: bioRxiv
#13
Jing Liu, Federica Mosti, Hanzhi T Zhao, Jesus E Sotelo-Fonseca, Carla F Escobar-Tomlienovich, Davoneshia Lollis, Camila M Musso, Yiwei Mao, Abdull J Massri, Hannah M Doll, Andre M Sousa, Gregory A Wray, Ewoud Schmidt, Debra L Silver
Humans evolved an extraordinarily expanded and complex cerebral cortex, associated with developmental and gene regulatory modifications 1-3 . Human accelerated regions (HARs) are highly conserved genomic sequences with human-specific nucleotide substitutions. Although there are thousands of annotated HARs, their functional contribution to human-specific cortical development is largely unknown 4,5 . HARE5 is a HAR transcriptional enhancer of the WNT signaling receptor Frizzled8 (FZD8) active during brain development 6 ...
April 11, 2024: bioRxiv
#14
Yuyang Chen, Ruebena Dawes, Hyung Chul Kim, Sarah L Stenton, Susan Walker, Alicia Ljungdahl, Jenny Lord, Vijay S Ganesh, Jialan Ma, Alexandra C Martin-Geary, Gabrielle Lemire, Elston N D'Souza, Shan Dong, Jamie M Ellingford, David R Adams, Kirsten Allan, Madhura Bakshi, Erin E Baldwin, Seth I Berger, Jonathan A Bernstein, Natasha J Brown, Lindsay C Burrage, Kimberly Chapman, Alison G Compton, Chloe A Cunningham, Precilla D'Souza, Emmanuèle C Délot, Kerith-Rae Dias, Ellen R Elias, Carey-Anne Evans, Lisa Ewans, Kimberly Ezell, Jamie L Fraser, Lyndon Gallacher, Casie A Genetti, Christina L Grant, Tobias Haack, Alma Kuechler, Seema R Lalani, Elsa Leitão, Anna Le Fevre, Richard J Leventer, Jan E Liebelt, Paul J Lockhart, Alan S Ma, Ellen F Macnamara, Taylor M Maurer, Hector R Mendez, Stephen B Montgomery, Marie-Cécile Nassogne, Serena Neumann, Melanie O'Leary, Elizabeth E Palmer, John Phillips, Georgia Pitsava, Ryan Pysar, Heidi L Rehm, Chloe M Reuter, Nicole Revencu, Angelika Riess, Rocio Rius, Lance Rodan, Tony Roscioli, Jill A Rosenfeld, Rani Sachdev, Cas Simons, Sanjay M Sisodiya, Penny Snell, Laura St Clair, Zornitza Stark, Tiong Yang Tan, Natalie B Tan, Suzanna El Temple, David R Thorburn, Cynthia J Tifft, Eloise Uebergang, Grace E VanNoy, Eric Vilain, David H Viskochil, Laura Wedd, Matthew T Wheeler, Susan M White, Monica Wojcik, Lynne A Wolfe, Zoe Wolfenson, Changrui Xiao, David Zocche, John L Rubenstein, Eirene Markenscoff-Papadimitriou, Sebastian M Fica, Diana Baralle, Christel Depienne, Daniel G MacArthur, Joanna Mm Howson, Stephan J Sanders, Anne O'Donnell-Luria, Nicola Whiffin
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes 1 . Increasingly, large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a novel syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome 2 . We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 119 individuals with NDD...
April 9, 2024: medRxiv
#15
Jing Liu, Casie Curtin, Rahul Lall, Sarah Lane, Jakob Wieke, Abul Ariza, Leinal Sejour, Ioannis Vlachos, Beshay N Zordoky, Randall T Peterson, Aarti Asnani
BACKGROUND: Anthracyclines such as doxorubicin (Dox) are highly effective anti-tumor agents, but their use is limited by dose-dependent cardiomyopathy and heart failure. Our laboratory previously reported that induction of cytochrome P450 family 1 (Cyp1) enzymes contributes to acute Dox cardiotoxicity in zebrafish and in mice, and that potent Cyp1 inhibitors prevent cardiotoxicity. However, the role of Cyp1 enzymes in chronic Dox cardiomyopathy, as well as the mechanisms underlying cardioprotection associated with Cyp1 inhibition, have not been fully elucidated...
April 11, 2024: bioRxiv
#16
Dimitrios Pollalis, Constantin Georgescu, Jonathan D Wren, Grigor Tombulyan, Justin M Leung, Pein-An Lo, Clarisa Marie Bloemhof, Ryang Hwa Lee, EunHye Bae, Jeffrey K Bailey, Britney O Pennington, Amir I Khan, Kaitlin R Kelly, Ashley K Yeh, Kartik S Sundaram, Mark Humayun, Stain Louie, Dennis O Clegg, Sun Young Lee
Dysfunction of the retinal pigment epithelium (RPE) is a common shared pathology in major degenerative retinal diseases despite variations in the primary etiologies of each disease. Due to their demanding and indispensable functional roles throughout the lifetime, RPE cells are vulnerable to genetic predisposition, external stress, and aging processes. Building upon recent advancements in stem cell technology for differentiating healthy RPE cells and recognizing the significant roles of small extracellular vesicles (sEV) in cellular paracrine and autocrine actions, we investigated the hypothesis that the RPE-secreted sEV alone can restore essential RPE functions and rescue photoreceptors in RPE dysfunction-driven retinal degeneration...
April 13, 2024: bioRxiv
#17
JOURNAL ARTICLE
Lulu Ji, Xiaoli Zhang, Zhiguo Chen, Yuexiao Wang, Hengxuan Zhu, Yaru Nai, Yanyi Huang, Rujie Lai, Yu Zhong, Xiting Yang, Qiongtao Wang, Hanyang Hu, Lin Wang
BACKGROUND: p66Shc, as a redox enzyme, regulates reactive oxygen species (ROS) production in mitochondria and autophagy. However, the mechanisms by which p66Shc affects autophagosome formation are not fully understood. METHODS: p66Shc expression and its location in the trophoblast cells were detected in vivo and in vitro. Small hairpin RNAs or CRISPR/Cas9, RNA sequencing, and confocal laser scanning microscope were used to clarify p66Shc's role in regulating autophagic flux and STING activation...
April 20, 2024: Cell Communication and Signaling: CCS
#18
JOURNAL ARTICLE
Yuwei Duan, Bing Cai, Jing Guo, Chen Wang, Qingyun Mai, Yan Xu, Yang Zeng, Yue Shi, Boyan Wang, Chenhui Ding, Minghui Chen, Canquan Zhou, Yanwen Xu
BACKGROUND: Antral follicles consist of an oocyte cumulus complex surrounding by somatic cells, including mural granulosa cells as the inner layer and theca cells as the outsider layer. The communications between oocytes and granulosa cells have been extensively explored in in vitro studies, however, the role of oocyte-derived factor GDF9 on in vivo antral follicle development remains elusive due to lack of an appropriate animal model. Clinically, the phenotype of GDF9 variants needs to be determined...
April 20, 2024: Cell Communication and Signaling: CCS
#19
JOURNAL ARTICLE
Feng Gao, Shenghui Wu, Kang Zhang, Zhiming Xu, Fusheng Quan
Intestinal inflammation is a common digestive system disease. Milk-derived exosomes can participate in intercellular communication and transport a variety of bioactive components, and the microRNAs (miRNAs) they carry play important roles in a variety of biological processes in the body. At present, the preventive effect and mechanism of action of goat milk exosomes and their derived miRNAs on intestinal inflammation are still unclear. In this study, the protective effect of goat milk exosomes on LPS-induced intestinal inflammation was investigated using mouse intestinal inflammation model and IEC-6 cell inflammation model...
April 18, 2024: International Journal of Biological Macromolecules
#20
REVIEW
Sandra Kovachka, Yuquan Tong, Jessica L Childs-Disney, Matthew D Disney
RNA has diverse cellular functionality, including regulating gene expression, protein translation, and cellular response to stimuli, due to its intricate structures. Over the past decade, small molecules have been discovered that target functional structures within cellular RNAs and modulate their function. Simple binding, however, is often insufficient, resulting in low or even no biological activity. To overcome this challenge, heterobifunctional compounds have been developed that can covalently bind to the RNA target, alter RNA sequence, or induce its cleavage...
April 18, 2024: Trends in Pharmacological Sciences
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