Article
Biochemical Research Methods
Kevin Sutanto, Marcel Turcotte
Summary: Non-coding RNAs (ncRNAs) are transcribed RNA elements that do not code for proteins but play important roles in biological processes and disorders. Their structure is closely associated with their functions and conservation. This study proposes the use of secondary structure fingerprints to improve classification accuracy by considering global and local structural matches. By combining these fingerprints with k-mers, a deep learning architecture achieved high accuracy, precision, and recall.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Endocrinology & Metabolism
Weihao Sun, Xinhui Zhang, Lei Wang, Guanyu Ren, Shuguang Piao, Chenghua Yang, Zhiyong Liu
Summary: The study investigated the histological changes and molecular mechanisms in cryptorchidism patients aged 20 to 40 years. Results showed a significant atrophy and decline in spermatogenic cells in the testes of patients with longer disease duration, with downregulation of genes related to sperm development and differentiation, providing insights into the decline in fertility in adult cryptorchidism.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Microbiology
Lorena Azevedo de Lima, Kristina Reinmets, Lars Keld Nielsen, Esteban Marcellin, Audrey Harris, Michael Kopke, Kaspar Valgepea
Summary: RNA sequencing (RNA-seq) is a widely used technique for transcriptome analysis, but the choice of library preparation kits can significantly impact the results. Different commercial products show significant differences in rRNA removal, strand specificity, and transcript abundance distribution. Selecting appropriate sample processing workflows and products is crucial for RNA-seq studies.
MICROBIOLOGY SPECTRUM
(2022)
Article
Medicine, Research & Experimental
Baolan Sun, Xi Cheng, Mu Zhang, Qin Shi, Xinxin Zhao, Xudong Wang, Yuquan Zhang
Summary: This study aimed to identify different transcriptome expression profiles involved in deep vein thrombosis (DVT), and to explore the diagnostic and therapeutic potential of circRNAs and mRNAs in DVT progression. By sequencing samples from a rat model of DVT, the study observed dynamic changes in circRNAs and mRNAs during DVT progression, and identified differentially expressed circRNAs and mRNAs associated with various functions and pathways. The findings suggest that dysregulated transcriptome profiles may offer mechanistic insights into DVT diagnosis and treatment.
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2023)
Article
Genetics & Heredity
Priyanka Banerjee, Wellison J. S. Diniz, Soren P. Rodning, Paul W. Dyce
Summary: Improving reproductive efficiency in beef heifers is crucial in the cow-calf industry. This study aimed to predict the future reproductive outcome of Angus-Simmental crossbred heifers using miRNA expression profiles from peripheral white blood cells at weaning.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Tianning Chen, Kailun Huo, Dece Kong, Shan Su, Tieyi Yang, Weiwei Zhang, Jin Shao
Summary: By studying peripheral blood samples from early postmenopausal women, we identified key lncRNAs that are associated with the progression of postmenopausal osteoporosis. One of the candidates, MIR22HG, was found to potentially serve as a miRNA precursor and regulate the FoxO signaling pathway in bone metabolism. These findings are of great significance for predicting and diagnosing early postmenopausal osteoporosis (PMOP).
Article
Biotechnology & Applied Microbiology
Zhu-Jun Shen, Ye-Chen Han, Mu-Wen Nie, Ruo-Lan Xiang, Hong-Zhi Xie
Summary: This study elucidated the roles of circRNAs in SMG dysfunction in hypertension by analyzing RNA-seq data. Differentially expressed circRNAs and mRNAs were found to be associated with the immune system and cell adhesion molecules, suggesting a crucial role in the development of SMG dysfunction. The ceRNA network analysis also highlighted the importance of the salivary secretion pathway in this mechanism.
Article
Neurosciences
Gangyi Feng, Jinghua Ou, Zhenzhong Gan, Xiaoyan Jia, Danting Meng, Suiping Wang, Patrick C. M. Wong
Summary: This study used functional MRI to investigate how the neural dynamics of different brain networks contribute to explaining individual differences in language learning. The research identified that certain brain regions represent newly acquired language knowledge and the connectivity between these regions is enhanced in more successful learners. The findings suggest that neural fingerprints derived from multiple neural network dynamics can explain not only the degree of success but also patterns of language learning across different components.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Jingting Shu, Yifan Liu, Yanju Shan, Gaige Ji, Xiaojun Ju, Yunjie Tu, Shiying Shi, Zhongwei Sheng, Ming Zhang, Jianmin Zou
Summary: This study investigated the miRNAs and related pathways involved in the development of Wooden Breast (WB) in modern commercial broiler chickens. Through small RNA sequencing, 23 significantly differentially expressed miRNAs were identified, indicating their involvement in biological processes and pathways related to energy metabolism, apoptosis, focal adhesion, and development of blood vessels. Four differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR), including gga-miR155, gga-miR-29c, and gga-miR-133.
Article
Cell Biology
Na Li, Qin Guo, Qiao Zhang, Bai-Jun Chen, Xiao-An Li, Yan Zhou
Summary: This study identified numerous differentially m(6)A methylated sites and genes in CRC, suggesting potential mechanisms of m(6)A-mediated gene expression regulation in colorectal cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
Jia Liu, Haiyan Lu, Silu Hu, Faping Wang, Xiaoju Tang, Huajing Wan, Fengming Luo
Summary: This study investigated the age-related molecular alterations of human airway by analyzing RNA sequencing data from airway brushing specimens. The results showed that the proportion of basal cells decreased with age, indicating a weakening of their self-renewal ability. The age-related genes were mainly involved in immune regulatory signaling pathways, suggesting that changes in immune function play critical roles in age-related airway diseases.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Yujie Ning, Feiyu Zhang, Shujin Li, Chaowei Wang, Yifan Wu, Sijie Chen, Yanli Liu, Feihong Chen, Xiong Guo, Xi Wang, Hongmou Zhao
Summary: This study investigates the role of extracellular vesicular miRNAs in knee osteoarthritis and identifies differentially expressed miRNAs and their target genes. The findings provide new insights into the pathogenesis of cartilage injury and knee osteoarthritis.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Biochemical Research Methods
Zerun Lin, Le Ou-Yang
Summary: In this paper, a multi-view contrastive learning model (DeepMCL) is proposed to infer gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data collected from multiple data sources or time points. The experimental results validate the effectiveness of our contrastive learning and attention mechanisms, demonstrating the effectiveness of our model in integrating multiple data sources for GRN inference.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Zerun Lin, Le Ou-Yang
Summary: The paper proposes a multi-view contrastive learning model, DeepMCL, for inferring gene regulatory networks from scRNA-seq data. By utilizing a deep Siamese convolutional neural network and attention mechanism, the model integrates information from multiple data sources, improving the accuracy of network inference.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Ming Du, Shuo Zhang, Xiaoxia Liu, Congjian Xu, Xiaoyan Zhang
Summary: Ovarian cancer is a cancer type characterized by copy number variations and large-scale chromosome alterations, which may serve as biomarkers for tumor metastasis and chemoresistance. Most ovarian cancer cell lines are aneuploid, with numerical complexity ranging from 5 to 12. A2780, COV434, and TOV21G were identified as diploid cell lines, while OV2944-HM1 and ID-8 were near-tetraploid. Gene expression profiles differed between diploid and aneuploid cell lines, with differentially expressed genes mainly involved in protein function regulation, TGF-beta signaling, and immune regulation. Chromosome 1 and 19 alterations may play a role in immune-related alterations and ovarian cancer progression, respectively. Further research is needed for verification.
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Eddy Albarran, David L. Wilson, Jun Ding, Eric T. Kool
Summary: Mitochondrial function declines with aging and neurodegeneration, largely due to accumulated mutations in mtDNA from deficient DNA repair. A fluorescent probe, UBER, was used to visualize mitochondrial BER activity, showing increased repair under oxidative stress and time delay between stress onset and BER initiation. Cells lacking MTH1 exhibited elevated demand for BER activity during extended stress, while absence of OGG1 limited glycosylation capacity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Biswarup Jash, Eric T. Kool
Summary: In this study, we investigated the acylation reactivity of RNA 2'-OH groups and identified the strong influence of steric and inductive effects on the reaction. These findings provide insights into new strategies for enhancing conjugation and mapping of RNA.
CHEMICAL COMMUNICATIONS
(2022)
Article
Microbiology
Mericien Venzon, Ritika Das, Daniel J. Luciano, Julia Burnett, Hyun Shin Park, Joseph Cooper Devlin, Eric T. Kool, Joel G. Belasco, E. Jane Albert Hubbard, Ken Cadwell
Summary: Microbial byproducts play a crucial role in the reproductive development of nematodes by affecting their fertility and hatching abilities through alterations in arginine and aldehyde levels.
CELL HOST & MICROBE
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Emily M. Harcourt, Yong Woong Jun, David L. Wilson, Emily D. Ledgerwood, Eric T. Kool
Article
Biochemistry & Molecular Biology
Yujeong Lee, Yoshiyuki Onishi, Lisa McPherson, Anna M. Kietrys, Marian Hebenbrock, Yong Woong Jun, Ishani Das, Shanthi Adimoolam, Debin Ji, Michael G. Mohsen, James M. Ford, Eric T. Kool
Summary: Impaired DNA repair activity is associated with increased cancer rates. This study found that certain tyrosine kinase inhibitors, such as nilotinib, can activate the repair enzyme MTH1, which cleanses oxidatively damaged nucleotides. Structural optimization resulted in compounds that strongly activate MTH1 and decrease mutagenic nucleotides in cellular DNA. These findings suggest that MTH1 activators may be a promising strategy to suppress tumorigenesis in individuals with elevated cancer risks.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yong Woong Jun, Emily M. Harcourt, Lu Xiao, David L. Wilson, Eric T. Kool
Summary: This article presents a convenient and versatile method for general fluorescence labeling of DNAs. It utilizes deaminated DNA bases and aminooxy-substituted rotor dyes to mark label positions and trap AP sites, resulting in high emission intensities for fluorescence labeling of oligonucleotides and dsDNA.
NATURE COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Yong Woong Jun, Eric T. Kool
Summary: DNA repair enzymes play a significant role in protecting cellular DNA from damage and are closely associated with cancer and inflammation pathways. The development of new tools and methods has greatly contributed to the study of these enzymes and their potential applications in diagnostics and therapies. This article provides an overview of the development of chemical tools for studying DNA repair processes and discusses the insights gained from their application. The article also highlights the importance of future research in the field of biomedicine and human health.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Beatriz Mateo-Victoriano, Ling Zhang, Govindi Samaranayake, Cassie Due, Clara Troccoli, Julia Zaias, Nagaraj Nagathihalli, Michael Mohsen, Eric Kool, Priyamvada Rai
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Lu Xiao, Linglan Fang, Sayantan Chatterjee, Eric T. Kool
Summary: RNA 2'-OH acylation is widely used for structure mapping and conjugation, and depends on selective reactions with unpaired nucleotides. We prepared a range of structurally diverse acylimidazole reagents and used deep sequencing to study their reactivity and selectivity in a variety of RNA structures. Our results demonstrate that the reagent scaffold significantly affects reactivity profiles and highlight new acylating agents with altered selectivity, including compounds that show elevated selectivity within loops and reduced off-target reactivity in loop closing base pairs. We also discovered a simple reagent that is cell permeable and can map RNA structure in the presence of protein contacts, and describe reagents with elevated selectivity within small loops for site-selective labeling.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Sayantan Chatterjee, Ryuta Shioi, Eric T. Kool
Summary: The nucleophilic reactivity of RNA 2'-OH groups has been applied in various RNA-related processes. In this study, it is discovered that activated small-molecule sulfonyl species can retain their reactivity in water. Reactions with ribose 2'-OH show high yields, especially for aryl sulfonyltriazole species. Additionally, an azide-substituted sulfonyltriazole reagent is developed for labeling RNA via click chemistry.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Yong Woong Jun, Melis Kant, Erdem Coskun, Takamitsu A. A. Kato, Pawel Jaruga, Elizabeth Palafox, Miral Dizdaroglu, Eric T. T. Kool
Summary: High-temperature cooking damages DNA in food, which can then enter the cellular DNA and lead to genetic risks.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Linglan Fang, Lu Xiao, Yong Woong Jun, Yoshiyuki Onishi, Eric T. T. Kool
Summary: The presence of a hydroxyl group at the 2'-position in ribose makes RNA susceptible to hydrolysis. In this study, reversible 2'-OH acylation was presented as a general strategy to preserve RNA stability. High-yield polyacylation of 2'-hydroxyls effectively protected RNAs from degradation, and subsequent treatment with nucleophilic reagents removed acylation adducts and recovered a wide range of RNA functions.
Article
Chemistry, Multidisciplinary
Ryuta Shioi, Lu Xiao, Sayantan Chatterjee, Eric T. Kool
Summary: The reactivity of RNA 2'-OH groups with acylating agents has been studied for high-yield conjugation of RNA strands. This study focuses on the stereoselectivity of chiral acylimidazoles in RNA reactions. The results reveal that positional selectivity and reactivity vary greatly with local RNA macro-chirality, and the chirality of the reagents has a significant impact on their reactivity. This study demonstrates new chemical strategies for selective RNA modification and probing.
Article
Biochemical Research Methods
Reema Baskar, Amy F. Chen, Patricia Favaro, Warren Reynolds, Fabian Mueller, Luciene Borges, Sizun Jiang, Hyun Shin Park, Eric T. Kool, William J. Greenleaf, Sean C. Bendall
Summary: Master transcription factors regulate cell states by driving gene-expression programs, and their abundance affects cell fate at the chromatin level. InTAC-seq method allows the study of the relationship between protein abundance and gene regulation in cells.
CELL REPORTS METHODS
(2022)
Article
Chemistry, Multidisciplinary
Sergio M. Marques, Michaela Slanska, Klaudia Chmelova, Radka Chaloupkova, Martin Marek, Spencer Clark, Jiri Damborsky, Eric T. Kool, David Bodnar, Zbynek Prokop
Summary: HaloTag labeling technology has revolutionized protein chemistry and cellular biology, and a systematic analysis of different ligands has led to the discovery of an optimal protein tag selection protocol, eliminating the need for expensive and complex protein engineering.