Article
Biochemistry & Molecular Biology
Kai-Yuan Huang, Sheng-Long Kan, Ting-Ting Shen, Pin Gong, Yuan-Yuan Feng, Hong Du, Yun-Peng Zhao, Tao Wan, Xiao-Quan Wang, Jin-Hua Ran
Summary: This study investigated the evolutionary pattern of chloroplast RNA editing sites in gymnosperms based on genomic and transcriptomic data. The study revealed common and unique characteristics of chloroplast RNA editing sites in gymnosperms compared to other land plants. Additionally, GC content and plastomic size were found to be correlated with the number of chloroplast RNA editing sites in gymnosperms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Qiqi Jing, Weiwei Liu, Haoyun Jiang, Yaya Liao, Qiang Yang, Yuyun Xing
Summary: In this study, five ABEs were used to generate A-to-G (T-to-C) conversions in five genome loci in porcine fetal fibroblasts. Different editing efficiencies and activity windows were observed in these targeting regions using different editors. The strategy of two sgRNAs in one vector showed superior editing efficiency. ABE-mediated start-codon mutation in APOE resulted in the silencing of its protein expression and elimination of the majority of its mRNA. No off-target DNA site was detected, but substantial off-target RNA events were present in the ABE-edited cells.
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
Biochemistry & Molecular Biology
Chiara Ambrosini, Eliana Destefanis, Eyemen Kheir, Francesca Broso, Federica Alessandrini, Sara Longhi, Nicolo Battisti, Isabella Pesce, Erik Dassi, Gianluca Petris, Anna Cereseto, Alessandro Quattrone
Summary: BOOST is a gene-editing approach that rescues haploinsufficiency by modifying specific single nucleotides in the Kozak sequence. It has been found that many haploinsufficient genes are regulated by suboptimal Kozak sequences, and by changing these sequences, gene translation can be enhanced to treat these diseases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Jie Qiao, Yingying Chen, Haoyu Ge, Hao Xu, Xiaobing Guo, Ruishan Liu, Chenyu Li, Ruyan Chen, Jianjun Gou, Mantao Chen, Beiwen Zheng
Summary: This study identified a Citrobacter freundii isolate carrying IMP-4, NDM-1, OXA-1, and KPC-2 genes and conducted comprehensive research on its drug resistance mechanism, molecular transfer mechanism, and epidemiology. It revealed that these four resistance genes coexist on a novel transferable hybrid plasmid that carries multiple drug resistance genes and insertion sequences.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Francis A. Acquah, Blaine H. M. Mooers
Summary: Targeting the U-helix structure can lead to the development of safer and more efficient drugs for treating trypanosome infections, as this RNA editing pathway is absent in humans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Yan Guo, Yuri F. van der Heijden, Fernanda Maruri, Limin Jiang, Robert Morrison, Timothy R. Sterling
Summary: This study marks the first discovery of three RNA editing events in Mycobacterium tuberculosis, providing novel insights into gene expression regulation in this bacterium species.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Immunology
Jie Qiao, Haoyu Ge, Hao Xu, Xiaobing Guo, Ruishan Liu, Chenyu Li, Ruyan Chen, Beiwen Zheng, Jianjun Gou
Summary: This study aimed to explore the genetic characteristics of IMP-4 and SFO-1 co-producing MDR clinical isolates of Enterobacter hormaechei. The isolates were sensitive to meropenem, amikacin, and polymyxin B, but resistant to cephalosporins, aztreonam, piperacillin/tazobactam, and aminoglycosides.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Jiarui Li, Tomoko Oonishi, Guangyao Fan, Matomo Sakari, Toshifumi Tsukahara
Summary: This study presents a strategy to enhance the editing efficiency of site-directed RNA editing (SDRE) system by redirecting exogenous ADARs to specific sites using antisense RNA oligonucleotides.
APPLIED SCIENCES-BASEL
(2023)
Article
Multidisciplinary Sciences
Huaxia Shi, Ying Xu, Na Tian, Ming Yang, Fu-Sen Liang
Summary: The authors develop a chemically inducible and reversible RNA m6A modification editing platform that allows temporal control at specific sites of individual RNA transcripts.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Rui Tao, Yanhong Wang, Yun Hu, Yaoge Jiao, Lifang Zhou, Lurong Jiang, Li Li, Xingyu He, Min Li, Yamei Yu, Qiang Chen, Shaohua Yao
Summary: A novel prime editor, WT-PE, was designed in this study by fusing reverse transcriptase (RT) to nuclease wild-type Cas9, enabling efficient editing of large genomic fragments. The WT-PE system introduced a double strand break (DSB) and a single 3' extended flap in the target site, and coupled with paired prime editing guide RNAs (pegRNAs), it achieved bi-directional prime editing, allowing versatile and efficient large-scale genome editing. This WT-PE system has great potential for modeling or treating diseases related to large-fragment aberrations.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Multidisciplinary Sciences
Liang Li, Andi Jing, Minxin Xie, Sheng Li, Chonghua Ren
Summary: The American cockroach is an important hemimetabolous insect model for research, utilizing RNA interference as an essential tool for functional gene studies. RNAi operation in P. americana allows researchers to quickly obtain dysfunctional phenotypes, facilitating developmental and metamorphic research.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(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)
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
Shinzi Ogasawara, Ai Yamada
Summary: RNA editing has gained attention as a method for genetic information editing without damaging the genome. A new method called RNA overwriting, using the influenza A virus RNA-dependent RNA polymerase, has been developed, allowing both cleavage and extension for editing any type of RNA.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Allergy
Kyoung Yong Jeong, Jong Sun Lee, Ji Eun Yuk, Hangyeol Song, Hye Jung Lee, Kuan Jung Kim, Bum Joon Kim, Kook-Jin Lim, Kyung Hee Park, Jae-Hyun Lee, Jung-Won Park
Summary: This study identified a novel allergen, Bomb m 4, in silkworm pupa allergic patients and evaluated its diagnostic sensitivity. Bomb m 4 was found to be the major allergen in these patients. This study is of significance for the accurate diagnosis of silkworm pupa allergy.
CLINICAL AND EXPERIMENTAL ALLERGY
(2022)
Letter
Allergy
Da Woon Sim, Jong Sun Lee, Kyung Hee Park, Kyung Sik Kim, Kyoung Yong Jeong, Jae-Hyun Lee, Jung-Won Park
ALLERGY ASTHMA & IMMUNOLOGY RESEARCH
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Tai-Soon Yong, Ju Yeong Kim
Article
Biochemistry & Molecular Biology
Qing Xiong, Angel Tsz-Yau Wan, Xiaoyu Liu, Cathy Sin-Hang Fung, Xiaojun Xiao, Nat Malainual, Jinpao Hou, Lingyi Wang, Mingqiang Wang, Kevin Yi Yang, Yubao Cui, Elaine Lai-Han Leung, Wenyan Nong, Soo-Kyung Shin, Shannon Wing-Ngor Au, Kyoung Yong Jeong, Fook-Tim Chew, Jerome Ho-Lam Hui, Ting-Fan Leung, Anchalee Tungtrongchitr, Nanshan Zhong, Zhigang Liu, Stephen Kwok-Wing Tsui
Summary: This study examines the evolutionary origin, diverse lifestyles, and quick adaptation of astigmatic mites in human household environments using six high-quality assembled and annotated genomes. The research reveals that astigmatic mites evolved from Prostigmata, notorious plant pests, and rapidly diversified from soil oribatid mites. The study also highlights the rapid expansion of gene families via tandem gene duplications in astigmatic mites, providing genetic resources for adaptation to changing household environments. Additionally, massive horizontal gene transfer events occurred during the evolution of astigmatic mites, enabling detoxification and digestive functions and offering potential drug targets for pest control.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Medical Laboratory Technology
Ju Yeong Kim, Myung-Hee Yi, Myungjun Kim, Joon-Sup Yeom, Hyun Dong Yoo, Seong Min Kim, Tai-Soon Yong
Summary: This study reported the first case of B. mandrillaris-induced encephalitis in Korea. Molecular identification using TA cloning with the 18S rRNA gene confirmed the presence of the pathogen. This method can serve as a feasible and affordable diagnostic tool for detecting infectious agents.
ANNALS OF LABORATORY MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Kyoung Yong Jeong, Jung-Won Park
Summary: Oak pollen allergy is a common allergenic condition worldwide, causing pollinosis. While the molecular properties of some component allergens have been identified, research on others is still lacking. Neglecting to study some oak component allergens may be due to their high cross-reactivity with birch. However, utilizing these culprit allergen molecules could enhance diagnostic sensitivity and effectiveness of immunotherapy. Sensitization to oak and birch pollen often leads to pollen food allergy syndrome with fruits and vegetables as triggers. Acorns and wood dust from oak trees can also cause allergic diseases. This article summarizes the distribution, taxonomy, and molecular characteristics of allergenic oak trees, as well as cross-reactivity, clinical aspects for diagnosis and immunotherapy, with a focus on the situation in Korea.
CURRENT PROTEIN & PEPTIDE SCIENCE
(2022)
Article
Parasitology
Ju Yeong Kim, Jun Ho Choi, Sung-Hyun Nam, Robert Fyumagwa, Tai-Soon Yong
Summary: By deep sequencing of tsetse fly samples, different mammalian animals were identified as blood-meal sources, and two Trypanosoma species were detected in tsetse flies collected from the Serengeti National Park, Maswa Game Reserve, and Tarangire National Park in Tanzania.
PARASITES & VECTORS
(2022)
Article
Entomology
Hangyeol Song, Jongsun Lee, Kyoung Yong Jeong, Doo-Sung Cheon, Jung-Won Park
Summary: House dust mite is a common cause of atopic dermatitis in humans and dogs. Detection of serum IgE to allergens is commonly used for diagnosis, but cross-reactivity and non-specific reactivity can lead to misdiagnosis. By comparing human and canine IgE reactivities to mite component allergens, different sensitization patterns were found between allergic humans and dogs.
EXPERIMENTAL AND APPLIED ACAROLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Kyoung Yong Jeong
CURRENT PROTEIN & PEPTIDE SCIENCE
(2022)
Article
Parasitology
Soo Lim Kim, Jun Ho Choi, Myung-hee Yi, Seogwon Lee, Myungjun Kim, Singeun Oh, In-Yong Lee, Bo-Young Jeon, Tai-Soon Yong, Ju Yeong Kim
Summary: This study used NGS-based metabarcoding analysis to examine the gut microbiome of the striped field mouse and found that microbial composition varied with season and parasitic infection status. The results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs.
PARASITES & VECTORS
(2022)
Article
Immunology
Ju Yeong Kim, Myung-hee Yi, Myungjun Kim, Jun Ho Choi, Seogwon Lee, Tai-Soon Yong
Summary: This study examines the effect of antibiotic treatment on the bacterial concentration in house dust mites and its allergenic properties. It reveals that ampicillin treatment significantly reduces the bacterial content and lipopolysaccharide levels in the mites, but does not alter the concentration of major allergens. Furthermore, the extract from ampicillin-treated mites reduces allergic airway inflammation in human bronchial epithelial cells.
JOURNAL OF IMMUNOLOGY RESEARCH
(2023)
Article
Allergy
Jongsun Lee, Sung-Ryeol Kim, Jong Han Park, Kyung-Hee Park, Kyoung Yong Jeong, Jae-Hyun Lee, Chon-Sik Kang, Kyeong-Hoon Kim, Jung-Won Park
Summary: The omega 5D cultivar shows lower allergenicity in WDEIA patients, suggesting it may be a safe alternative for them.
ALLERGY ASTHMA & IMMUNOLOGY RESEARCH
(2022)