Article
Biochemistry & Molecular Biology
Yulong Song, Xiuju He, Wenbing Yang, Yaoxing Wu, Jun Cui, Tian Tang, Rui Zhang
Summary: This study developed an editing identification pipeline specifically for RNA viruses and constructed an atlas of A-to-I RNA editing sites in SARS-CoV-2 from diverse samples. The findings showed that A-to-I editing was dynamically regulated, varied between tissue and cell types, and correlated with the intensity of innate immune response. Additionally, editing hotspots were observed, including recoding sites in the spike gene that affect viral infectivity and antigenicity. The study also provided evidence that RNA editing accelerated SARS-CoV-2 evolution in humans during the epidemic.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Sijia Wu, Mengyuan Yang, Pora Kim, Xiaobo Zhou
Summary: A-to-I RNA editing plays a crucial role in the pathogenesis of Alzheimer's disease (AD) and the establishment of the ADeditome database provides valuable insights for identifying therapeutic target genes. Through functional annotation of 1676 363 editing sites in 1524 samples, key editing events influencing AD progression were identified.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Oncology
Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
Summary: RNA editing, induced by ADAR, plays a crucial regulatory role in metazoans, affecting multiple cellular processes and functions. Despite the development of bioinformatics tools for identifying editing sites, the lack of widely accepted standards and challenges in tumor sample analysis still exist. Numerous editing sites have been reported in non-coding regions, impacting the biosynthesis of ncRNAs.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Zhao Zhang, Mei Luo, Qiang Li, Yuan Liu, Charles Lussier, Jian Zhang, Youqiong Ye, An-Yuan Guo, Leng Han
Summary: This study systematically investigates the impact of enhancer RNAs (eRNAs) on cancer and provides a multidimensional data portal for further research.
Article
Biochemistry & Molecular Biology
Yoav Shoshan, Noa Liscovitch-Brauer, Joshua J. C. Rosenthal, Eli Eisenberg
Summary: RNA editing by ADAR enzymes converts adenosines into inosines, altering protein-coding sequences and diversifying the proteome; recoding is abundant in neural tissues of coleoid cephalopods with over-representation of nonsynonymous edits; shared, strongly recoded sites in coleoids have been selected for proteome diversification, suggesting that an editable A is more beneficial than an uneditable A or a genomically encoded G.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Cell Biology
David Rodriguez Morales, Mirolyuba Ilieva, Sarah Rennie, Shizuka Uchida
Summary: Adenosine to inosine (A-to-I) RNA editing is a common RNA modification in mammalian transcriptomes. Upregulated RNA editing enzymes, adenosine deaminase acting on RNAs (ADARs), suggest that monitoring RNA editing patterns could be useful as diagnostic biomarkers for diseases. This article provides an overview of epitranscriptomics and focuses on the detection and analysis of A-to-I RNA editing using bioinformatic tools in RNA-seq data sets, while briefly reviewing its involvement in disease progressions. The authors argue for routine detection of RNA editing patterns in RNA-based data sets to accelerate the identification of disease-related RNA editing targets.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chia-Yu Shih, Yun-Chi Chen, Heng-Yi Lin, Chia-Ying Chu
Summary: The DEAD-box proteins, including DDX6, are RNA-binding proteins that play a role in post-transcriptional regulation of gene expression. DDX6 has functions in translational repression, miRNA-mediated gene silencing, and RNA decay in the cytoplasm. Its nuclear function was previously unknown until this study discovered its interaction with ADAR1, a protein involved in RNA editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Eddie Park, Yan Jiang, Lili Hao, Jingyi Hui, Yi Xing
Summary: The study suggests a mechanism where RNA editing variability can influence the phenotypes of complex traits and diseases by altering the stability and steady-state level of critical RNA molecules.
Editorial Material
Biochemistry & Molecular Biology
Juan F. Diaz F. Quiroz, Louise D. D. Siskel, Joshua J. C. Rosenthal
Summary: Adenosine deamination by ADAR enzymes edits genetic information in mRNA. Researchers have developed two systems to redirect ADAR activity for therapeutic purposes. Currently, this technology is mainly used for correcting genetic mutations, but we argue that it can be used to modulate cell physiology in a temporary manner, particularly in the nervous system, for therapeutic advantages.
Article
Biology
Tram Anh Nguyen, Jia Wei Joel Heng, Yan Ting Ng, Rui Sun, Shira Fisher, Gokce Oguz, Pornchai Kaewsapsak, Shifeng Xue, Bruno Reversade, Adaikalavan Ramasamy, Eli Eisenberg, Meng How Tan
Summary: This study identified millions of editing events in Xenopus with high accuracy and systematically mapped the editome across developmental stages, adult organs, and species. The highest deamination activity was observed in early embryogenesis and in the ovary. Editing events showed poor conservation across different Xenopus species. The findings suggest that species-specific editing may play a role in the unique physiology or environmental adaptation of each animal.
Article
Chemistry, Multidisciplinary
Xu Zhou, Ramkrishna Mitra, Fei Hou, Shunheng Zhou, Lihong Wang, Wei Jiang
Summary: Adenosine-to-inosine RNA editing plays a critical role in cancer therapy response. A comprehensive identification of drug resistance-related RNA editing events and understanding of their mechanism is lacking. This study identifies 7157 differential editing sites (DESs) from 98,127 informative RNA editing sites in tumor tissues and reveals various editing patterns in resistant samples. RNA-binding proteins are found to potentially regulate these editing events. DESs are significantly enriched in 3'-UTRs and their impact on miRNA regulations is explored. Genes associated with DESs are involved in drug resistance-related functions. A convenient online resource for retrieving DESs is built. These findings provide insights into the landscape and regulatory mechanism of RNA editing in drug resistance and offer new therapeutic targets for reversing drug resistance.
Article
Chemistry, Multidisciplinary
Steve D. Knutson, Robert A. Arthur, H. Richard Johnston, Jennifer M. Heemstra
Summary: The study presents an EndoV-linked immunosorbency assay (EndoVLISA) for rapid measurement of global A-to-I editing signatures in cellular RNA. The method is cost-effective, straightforward, and suitable for disease detection and drug development applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Sijia Wu, Qiuping Xue, Mengyuan Yang, Yanfei Wang, Pora Kim, Xiaobo Zhou, Liyu Huang
Summary: A-to-I RNA editing diversifies the human transcriptome, potentially contributing to neurodegenerative pathogenesis. Genetic variants play a key role in the variability of A-to-I RNA editing. Through comprehensive analysis of genetic and transcriptomic data, we identified 95,198 RNA editing quantitative trait loci and highlighted several RNA-binding proteins that may be involved in genetic control of A-to-I RNA editing. These genetic variants also contribute to the variability of other molecular phenotypes associated with RNA editing. The findings provide valuable insights into the understanding of neurodegenerative pathogenesis related to A-to-I RNA editing.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Toxicology
Akin Cayir
Summary: Epigenetic modifications, including RNA editing, can be influenced by environmental stimuli and are linked with adverse health outcomes; over 150 reversible RNA modifications have been identified, indicating dynamic features of modification; the RNA editing field is expanding and requires more empirical evidence for diseases and toxicology.
CRITICAL REVIEWS IN TOXICOLOGY
(2021)
Article
Oncology
Ji Wen, Michael Rusch, Samuel W. Brady, Ying Shao, Michael N. Edmonson, Timothy Shaw, Brent B. Powers, Liqing Tian, John Easton, Charles G. Mullighan, Tanja Gruber, David Ellison, Jinghui Zhang
Summary: This study identified 722 unique RNA editing sites in coding regions across pediatric cancers, with 70% being nonsynonymous recoding variants. The majority of editing sites were canonical A-to-I or C-to-U sites. RNA editing was enriched in brain tumors compared to other cancers, with a focus on glutamate receptors and ion channels involved in neurotransmitter signaling.
Article
Agriculture, Dairy & Animal Science
Zijie Xu, Xianwei Wang, Xingya Song, Qingming An, Dahui Wang, Zijing Zhang, Xiaoting Ding, Zhi Yao, Eryao Wang, Xian Liu, Baorui Ru, Zejun Xu, Yongzhen Huang
Summary: This study found that the CCSER1 gene copy number variation is differentially distributed among goat breeds and is significantly associated with body weight and heart girth traits. The expression pattern of the CCSER1 gene also varies among different tissues in goats.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Computer Science, Software Engineering
Yubo Zhang, Shuang Han, Zhongxin Zhang, Jianyang Wang, Hongbo Bi
Summary: In this paper, a network framework CF-GAN is proposed to address the issues of insufficient embedding of generated images in text description semantics, incomplete target object, and insufficient texture structure. The proposed framework includes two modules, FFERM and MBRM, which fine-grain the generated images through deep fusion.
Review
Food Science & Technology
Ruixuan Geng, Yanan Wang, Jingjing Fang, Yuhan Zhao, Mengjie Li, Seong-Gook Kang, Kunlun Huang, Tao Tong
Summary: The largest organ of the human body, the skin, expresses various chemosensory receptors including odorant receptors (ORs), which are involved in skin biological processes and diseases such as wound healing, hair growth, and melanin regulation.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Plant Sciences
Min Jia, Sheng-Qi Zhu, Ya-Hui Wang, Jie-Xia Liu, Shan-Shan Tan, Hui Liu, Sheng Shu, Jian-Ping Tao, Ai-Sheng Xiong
Summary: This study investigated the effects of different storage conditions on celery morphological characteristics, anatomical features, and antioxidant accumulation. The results showed that storing celery in darkness at low temperature was the optimal condition for maintaining its morphological characteristics and preserving antioxidant accumulation. Additionally, the genes GDP-d-mannose pyrophosphorylase and l-galactose dehydrogenase were found to play a crucial role in the accumulation of ascorbic acid in celery.
Article
Computer Science, Artificial Intelligence
Jianming Zhang, Yaoqi He, Wenjun Feng, Jin Wang, Neal N. Xiong
Summary: In this work, we combine hand-crafted features and deep features to improve the representation ability of object appearance. We propose a new background-aware and spatial-temporal regularized correlation filters model (BSTCF) to model both the background and variations over time. Experimental results demonstrate the superior performance of the proposed tracking algorithm.
APPLIED INTELLIGENCE
(2023)
Article
Materials Science, Multidisciplinary
Xingkun Dong, Xiangjun Jiang, Yanping Wang, Peng Li, Fengqun Pan
Summary: In this study, a beam element model with tension-compression asymmetry is constructed using the improved Brinson model. The computational effectiveness of the beam element is verified by comparing the calculated results with experimental results. Additionally, a new mechanical property analysis model for shape memory alloy bolted joints is proposed and solved iteratively using the bisection method. The proposed model provides a more efficient and precise calculation method compared to traditional methods.
JOURNAL OF INTELLIGENT MATERIAL SYSTEMS AND STRUCTURES
(2023)
Article
Forestry
Qiliang Zhu, Kun Yan, Yufeng Dong, Yanping Wang
Summary: Sexual dimorphism of plants influences the differences in morphology and physiology between males and females. This study found that the rhizosphere soils of female poplars had less total carbon but more nutrients compared to soils of males. However, the alpha-diversity of rhizosphere bacterial communities was higher under male plants. The co-occurrence network of bacterial communities in soil under male trees was more diverse and complex. These findings suggest that male poplars may have better environmental adaptability.
JOURNAL OF FORESTRY RESEARCH
(2023)
Article
Nanoscience & Nanotechnology
Chengyu Lu, Jing Zheng, Tonu Yoshitomi, Naoki Kawazoe, Yingnan Yang, Guoping Chen
Summary: Matrix stiffness has an impact on the adipogenic differentiation of hMSCs with controlled morphology. Both cell spreading area and hydrogel stiffness play a synergistic role in adipogenic differentiation, while cell elongation does not affect it. Actin filament alignment is strongly related to adipogenic differentiation.
ACS APPLIED BIO MATERIALS
(2023)
Article
Chemistry, Physical
Jing Niu, Yu-Ting Miao, Wei David Wang, Meng-Tong Ruan, Zhi-Peng Wang, Hua-Dong Xue, Si-Min Yu, Chong Liu, Jian-Feng Wu, Wei Wang
Summary: The crucial role of surface ethoxy species, i.e., equilibrium with ethene in the primary step and further alkylation to form the C-C bond, was confirmed for the first time through a selective C-13-labeling protocol and a multitechnique approach during the adsorption of ethene on zeolite H-Y.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Article
Environmental Sciences
Wuli Li, Xirun Zong, Yi-Sheng He, Tiantian Meng, Ying Tang, Qi Yang, Qing Huang, Yuanyin Wang, Song Li, Hai-Feng Pan
Summary: Evidence suggests a possible association between ambient air pollutants and oral diseases. The present study aimed to investigate the relationship between short-term exposure to air pollution and outpatient visits for pulpitis. The results showed that exposure to NO2, PM2.5, and CO were positively correlated with an increased risk of pulpitis outpatient visits, while exposure to O-3 was associated with a decreased risk. Age and season were found to be effect modifiers of these associations.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Chemistry, Analytical
Jin-Ling Pu, Pei-Hong Tong, Yong-Juan Meng, Jian-Ping LI
Summary: A bilayer-structured ZIF-8 composite was synthesized as a molecularly imprinted electrochemiluminescence sensor for the detection of dopamine. The composite material consisted of an inner layer, loaded with a luminescent probe, and an outer layer with recognition function. The sensor showed a linear relationship between the electrochemiluminescence intensity change and dopamine concentration, with a detection limit of 4.8 x 10^-15 mol/L. It was successfully applied to the detection of dopamine in human serum samples.
CHINESE JOURNAL OF ANALYTICAL CHEMISTRY
(2023)
Correction
Chemistry, Multidisciplinary
Hui Chen, Qiannan Wu, Yanfei Wang, Qinfeng Zhao, Xuan Ai, Yucheng Shen, Xiaoxin Zou
CHEMICAL COMMUNICATIONS
(2023)
Article
Microbiology
Huan Du, Jie Pan, Cuijing Zhang, Xilan Yang, Cheng Wang, Xiaolan Lin, Jinhui Li, Wan Liu, Haokui Zhou, Xiaoli Yu, Shuming Mo, Guoqing Zhang, Guoping Zhao, Wu Qu, Chengjian Jiang, Yun Tian, Zhili He, Yang Liu, Meng Li
Summary: The study compares the microbial features of mangrove ecosystems in China and South America, finding analogous assembly patterns and key functional guilds. The entire communities exhibit significant distance-decay patterns and are strongly influenced by stochastic processes, while the assembly of specialists may be related to the behaviors of organisms in the mangrove ecosystems. Sulfate-reducing prokaryotes dominate the mangrove microbiomes and play important roles in maintaining community structure and functions.
MICROBIOLOGY SPECTRUM
(2023)
Article
Energy & Fuels
Ming Yang, Wanyu Ge, Zirui Liu, Qiang Yue, Jun Zhang, Yanping Lv, Hao Wu
Summary: Alkali-assisted Mo doped Ni-Mn layered double hydroxides exhibit high catalytic activity in the urea oxidation reaction, achieving high current density and specific current activity. Both indirect electrochemical and direct urea oxidation processes occur when using Mo-NiMnLDH-OH as catalyst. This study provides a new approach for developing efficient catalysts for UOR.
Article
Radiology, Nuclear Medicine & Medical Imaging
Yanping Wang, Yuexiang Li, Guang Lin, Qirui Zhang, Jing Zhong, Yan Zhang, Kai Ma, Yefeng Zheng, Guangming Lu, Zhiqiang Zhang
Summary: This study investigates the feasibility of deep learning-based diagnostic models to detect and assess the severity of lower-extremity fatigue fractures on plain radiographs. The results demonstrate that the models have achieved satisfactory performance in detecting and grading fatigue fractures, providing assistance to radiologists in the radiological diagnosis of such fractures.
EUROPEAN RADIOLOGY
(2023)
