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JOURNAL ARTICLE
Kaiqing Yang, Jialin Tan, Gengbo Jiang, Zhuobiao Ni, Qingqi Lin, Yuanqing Chao, Zhepu Ruan, Rongliang Qiu
A Gram-stain-negative, rod-shaped, non-motile, catalase-positive, denitrifying bacterium, designated strain Y-1T , was isolated from an aeration tank of a sewage treatment plant in China and characterized using polyphasic taxonomic approaches. Strain Y-1T could grow at 10-37 °C (optimum 25 °C), at pH 5.0-10.0 (optimum 7.0) and in the presence of 0-3.0% (w/v) NaCl (optimum 0.5%). The phylogenetic tree based on the 16S rRNA gene sequences revealed that strain Y-1T was a member of genus Diaphorobacter, and showed the highest sequence similarities with Diaphorobacter oryzae RF3T (97...
April 23, 2024: Current Microbiology
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JOURNAL ARTICLE
Melissa R Budicini, Valerie J Rodriguez-Irizarry, Robert W Maples, Julie K Pfeiffer
UNLABELLED: RNA viruses lack proofreading in their RNA polymerases and therefore exist as genetically diverse populations. By exposing these diverse viral populations to selective pressures, viruses with mutations that confer fitness advantages can be enriched. To examine factors important for viral tropism and host restriction, we passaged murine norovirus (MNV) in a human cell line, HeLa cells, to select mutant viruses with increased fitness in non-murine cells. A major determinant of host range is expression of the MNV receptor CD300lf on mouse cells, but additional host factors may limit MNV replication in human cells...
April 23, 2024: Journal of Virology
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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
#4
JOURNAL ARTICLE
Aleksander Sulkowski, Clément Bouton, Chad Swanson
Vertebrate genomes contain lower than expected frequencies of the CpG dinucleotide. Consequently, many vertebrate viruses have evolved to mimic this composition, possibly in order to evade host antiviral defences (Greenbaum et al., 2008). For example, the antiviral protein ZAP binds CpGs in viral single stranded RNA with specific spacing requirements (Gonçalves-Carneiro et al., 2022), though CpGs are also likely depleted in viral genomes due to other selective pressures (Forni et al., 2023). Increasing CpG abundance by synonymous recoding could facilitate attenuation of viruses without compromising their epitope antigenicity by changing non-CpG codons to alternatives containing CpG without changing the overall amino acid sequence (Gonçalves-Carneiro et al...
April 3, 2024: Journal of Open Source Software
#5
JOURNAL ARTICLE
Hongyu Lu, Jia Zhang, Yixin Cao, Shuming Wu, Xingyan Wang, Yurong Bai, Chang Zhao, Jun Zhu, Yuan Wei, Runting Yin
MiRNAs are a class of small non-coding RNAs, which regulate gene expression post-transcriptionally by partial complementary base pairing. Aberrant miRNA expressions have been reported in tumor tissues and peripheral blood of cancer patients. Bioinformatic tools could improve efficiency of miRNA research, while current bioinformatic tools are in lack of sufficient accuracy. In recent years, artificial intelligence algorithms such as machine learning and deep learning have been widely used in the bioinformatical tools...
April 16, 2024: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
#6
JOURNAL ARTICLE
Jeeyeon Lee, Eun-Ae Kim, Jieun Kang, Yee Soo Chae, Ho Yong Park, Byeongju Kang, Soo Jung Lee, In Hee Lee, Ji-Young Park, Nora Jee-Young Park, Jin Hyang Jung
Hormone receptor (HR)-positive breast cancer can become aggressive after developing hormone-treatment resistance. This study elucidated the role of long non-coding RNA (lncRNA) SOX2OT in tamoxifen-resistant (TAMR) breast cancer and its potential interplay with the tumor microenvironment (TME). TAMR breast cancer cell lines TAMR-V and TAMR-H were compared with the luminal type A cell line (MCF-7). LncRNA expression was assessed via next-generation sequencing, RNA extraction, lncRNA profiling, and quantitative RT-qPCR...
April 22, 2024: BMC molecular and cell biology
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JOURNAL ARTICLE
Talita Ferreira Marques Aguiar, Maria Prates Rivas, Edson Mario de Andrade Silva, Sara Ferreira Pires, Gustavo Dib Dangoni, Taiany Curdulino Macedo, Alexandre Defelicibus, Bruna Durães de Figueiredo Barros, Estela Novak, Lilian Maria Cristofani, Vicente Odone, Monica Cypriano, Silvia Regina Caminada de Toledo, Isabela Werneck da Cunha, Cecilia Maria Lima da Costa, Dirce Maria Carraro, Israel Tojal, Tiago Antônio de Oliveira Mendes, Ana Cristina Victorino Krepischi
Hepatoblastoma stands as the most prevalent liver cancer in the pediatric population. Characterized by a low mutational burden, chromosomal and epigenetic alterations are key drivers of its tumorigenesis. Transcriptome analysis is a powerful tool for unraveling the molecular intricacies of hepatoblastoma, shedding light on the effects of genetic and epigenetic changes on gene expression. In this study conducted in Brazilian patients, an in-depth whole transcriptome analysis was performed on 14 primary hepatoblastomas, compared to control liver tissues...
April 22, 2024: Biochemical Genetics
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JOURNAL ARTICLE
Wenzhao Wang, Chang Liu, Dong He, Guidong Shi, Ping Song, Boqing Zhang, Tian Li, Jianlu Wei, Yunpeng Jiang, Liang Ma
Spinal cord injury (SCI) is a complex problem in modern medicine. Fibroblast activation and fibroscarring after SCI impede nerve recovery. Non-coding RNA plays an important role in the progression of many diseases, but the study of its role in the progression of spinal fibrosis is still emerging. Here, we investigated the function of circular RNAs, specifically antisense to the cerebellar degeneration-related protein 1 (CDR1as), in spinal fibrosis and characterized its molecular mechanism and pathophysiology...
April 20, 2024: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
#9
JOURNAL ARTICLE
Lingyu Ran, Wei Li, Huhai Zhang, Jie Lin, Longyin Zhu, Huanping Long, Lunli Xiang, Liping Chen, Qixuan Li, Yuhan Hu, Min Gong, Hongwen Zhao, Bin Xiao
Introduction Focal segmental glomerulosclerosis (FSGS) is a common glomerulopathy with unclear mechanism. The demand for FSGS clinical diagnostic biomarkers has not yet been met. Circular RNA (circRNA) is a novel non-coding RNA with multiple functions, but its diagnostic value for FSGS remains unexplored. This study aimed to identify circRNAs that could aid in early clinical diagnosis and to investigate their mechanisms in podocyte injury. Methods The signature of plasma circRNAs for FSGS was identified by circRNA microarray...
April 22, 2024: Kidney & Blood Pressure Research
#10
JOURNAL ARTICLE
YiPing Qin, JiHua Ren, HaiBo Yu, Xin He, ShengTao Cheng, WeiXian Chen, Zhen Yang, FengMing Sun, ChunDuo Wang, SiYu Yuan, Peng Chen, DaiQing Wu, Fang Ren, AiLong Huang, Juan Chen
Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers...
April 22, 2024: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
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JOURNAL ARTICLE
Norisuke Kano, Takeo Miki, Yurina Uehara, Daisuke Ori, Taro Kawai
Interleukin-6 (IL-6) plays a crucial role in various cellular functions, including the innate and adaptive immune responses. Dysregulated expression of IL-6 is associated with hyperinflammation and chronic inflammatory diseases. In this study, we aimed to identify the enhancer regions responsible for robust Il6 mRNA expression in murine macrophages. Through comprehensive genome-wide ChIP-seq and ATAC-seq analyses, we identified two distinct clusters, termed E1 and E2 regions, located at -144 kb to -163 kb relative to the Il6 transcription start site in lipopolysaccharide (LPS)-activated murine macrophages...
April 22, 2024: International Immunology
#12
REVIEW
Longze Zhang, Yanyang Wang, Jianmei Gao, Xue Zhou, Minglei Huang, Xianyao Wang, Zhixu He
Esophageal cancer (EC) is a common form of malignant tumor in the digestive system that is classified into two types: Esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinoma. ESCC is known for its early onset of symptoms, which can be difficult to identify, as well as its rapid progression and tendency to develop drug resistance to chemotherapy and radiotherapy. These factors contribute to the high incidence of disease and low cure rate. Therefore, a diagnostic biomarker and therapeutic target need to be identified for ESCC...
June 2024: Oncology Letters
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JOURNAL ARTICLE
Yuanchen Lan, Liyuan Yu, Zhiai Hu, Shujuan Zou
The dynamic balance between bone formation and bone resorption is a critical process of bone remodeling. The imbalance of bone formation and bone resorption is closely associated with the occurrence and development of various bone-related diseases. Under both physiological and pathological conditions, non-coding RNAs (ncRNAs) play a crucial regulatory role in protein expression through either inhibiting mRNAs translation or promoting mRNAs degradation. Circular RNAs (circRNAs) are a type of non-linear ncRNAs that can resist the degradation of RNA exonucleases...
March 20, 2024: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
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JOURNAL ARTICLE
Eko Fuji Ariyanto
No abstract text is available yet for this article.
2024: Frontiers in Pharmacology
#15
Tong Su, Nhu Trang, Jonathan Zhu, Lingbo Kong, Darin Cheung, Vita Chou, Lauren Ellis, Calvin Huang, Nichelle Camden, Colleen A McHugh
Non-coding RNA (ncRNA) gene products are involved in diverse biological processes including splicing, epigenetic regulation, gene expression, proliferation, and metabolism. The biological mechanisms by which ncRNAs contribute to cell survival remain poorly understood. We found that the Growth Regulator Antisense 1 (GRAS1) long non-coding RNA (lncRNA) transcript promotes growth in multiple human cell types by protecting against DNA damage. Knockdown of GRAS1 induced DNA damage and cell death, along with significant expression changes in DNA damage response, intrinsic apoptotic signaling, and cellular response to environmental stimulus genes...
April 11, 2024: bioRxiv
#16
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
#17
JOURNAL ARTICLE
FanJing Jing, YunYan Shi, Dong Jiang, Xiao Li, JiaLin Sun, XiaoLei Zhang, Qie Guo
Sorafenib is an important treatment strategy for advanced hepatocellular carcinoma (HCC). Unfortunately, drug resistance has become a major obstacle in sorafenib application. In this study, whole transcriptome sequencing (WTS) was conducted to compare the paired differences between non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), and mRNAs, in sorafenib-resistant and parental cells. The overlap of differentially expressed ncRNAs (DENs) between the SMMC7721/S and Huh7/S cells and their parental cells was determined...
April 30, 2024: Heliyon
#18
JOURNAL ARTICLE
Chang Meng, Juan Li, Xiang Wang, Yicen Ying, Zhihua Li, Aixiang Wang, Xuesong Li
This study aims to develop a prognostic signature based on m6A-related lncRNAs for clear cell renal cell carcinoma (ccRCC). Differential expression analysis and Pearson correlation analysis were used to identify m6A-related lncRNAs associated with patient outcomes in The Cancer Genome Atlas (TCGA) database. Our approach led to the development of an m6A-related lncRNA risk score (MRLrisk), formulated using six identified lncRNAs: NFE4, AL008729.2, AL139123.1, LINC02154, AC124854.1 and ARHGAP31-AS1. Higher MRLrisk was identified as a risk factor for patients' prognosis in ccRCC...
April 21, 2024: Cancer Investigation
#19
JOURNAL ARTICLE
Moringin, an isothiocyanate modulates multiple cellular signalling molecules in breast cancer cells.
Ankit Srivastava, Shruti Mishra, Avadhesh, Anusmita Shekher, Vipin Rai, Anupam Dhasmana, Jayanta Das, Daniele Perenzoni, Renato Iori, Subash C Gupta
Prohibitin (PHB) is a pleiotropic molecule with a variety of known functions and subcellular locations. PHB's function in breast cancer is poorly understood. Herein, we report that PHB is expressed in cancer types of diverse origin including breast cancer. The cancer patients with changes in PHB were reported to have significantly reduced 'overall survival' in comparison to the cases without alterations in PHB. The expression of PHB was increased by H2 O2 and also by Moringin (MG), which is an isothiocyanate derived from the seeds of Moringa oleifera...
April 19, 2024: Cellular Signalling
#20
JOURNAL ARTICLE
Michael Camerino, William Chang, Ales Cvekl
BACKGROUND: Nuclear organization of interphase chromosomes involves individual chromosome territories, "open" and "closed" chromatin compartments, topologically associated domains (TADs) and chromatin loops. The DNA- and RNA-binding transcription factor CTCF together with the cohesin complex serve as major organizers of chromatin architecture. Cellular differentiation is driven by temporally and spatially coordinated gene expression that requires chromatin changes of individual loci of various complexities...
April 20, 2024: Epigenetics & Chromatin
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