Article
Biotechnology & Applied Microbiology
Zhenyu Shao, Yang Han, Dan Zhou
Summary: Through comprehensive bioinformatic analyses, this study reveals that previous observations of extensive and strand-biased 5-methylcytosine (5mC) in mitochondrial DNA (mtDNA) are likely artifacts caused by a combination of factors including inefficient bisulfite conversion, low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). By establishing an optimized procedure for library preparation and data analysis of bisulfite sequencing, the researchers demonstrate an even distribution of 5mC signals across mtDNA and an average methylation level similar to background noise.
Article
Medicine, General & Internal
Dae-Yeon Kim, Hee-Tae Cheong, Chang-Six Ra, Kazuhiro Kimura, Bae Dong Jung
Summary: The study revealed that inhibition of UCP2 expression in Hep3B cells was due to methylation of the promoter region, and treatment with 5-aza could increase UCP2 expression, which may have implications for cancer treatment.
INTERNATIONAL JOURNAL OF MEDICAL SCIENCES
(2021)
Article
Cell Biology
Xubin Zheng, Qiong Wu, Haonan Wu, Kwong-Sak Leung, Man-Hon Wong, Xueyan Liu, Lixin Cheng
Summary: This study introduced the most prevalent methods for processing bisulfite sequencing data and evaluated the consistency of the data acquired from different measurements in liver cancer. Differential methylated genes measured by various bisulfite sequencing assays and 450 k beadchip were consistently hypo-methylated in liver cancer with high functional similarity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Hossein Dehdari, Fatemeh Moradian, Ali Barzegar, Mohammed Ali Ebirahimzadeh
Summary: This study found that increased transcription of CYP1A1 in breast cancer is correlated with hypermethylation of a specific CpG block and upregulation of antiapoptotic protein BCL-2. The hypermethylation of this CpG block may serve as a potential biomarker for diagnosis and progression of breast cancer.
EXPERIMENTAL CELL RESEARCH
(2022)
Article
Chemistry, Applied
Xiaoshan Guo, Dandan Huang, Guangqin Jing, Jianrong Feng, Shuhua Zhu
Summary: Exogenous NO can alleviate the decrease in DNA methylation induced by cold stress and enhance the cold resistance of peaches. This study provides important insights into the effects of low temperature on fruit and the mechanisms of cold resistance.
Article
Biochemistry & Molecular Biology
Veronika N. Laine, Bernice Sepers, Melanie Lindner, Fleur Gawehns, Suvi Ruuskanen, Kees van Oers
Summary: The field of molecular biology is rapidly advancing and there is a growing interest in studying ecological epigenetics, particularly in wild vertebrates. This review provides a practical guide for researchers studying DNA methylation variation in wild vertebrates, discussing technical aspects, limitations, and data analysis methods.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Chemistry, Multidisciplinary
Neng-Bin Xie, Min Wang, Tong-Tong Ji, Xia Guo, Jiang-Hui Ding, Bi-Feng Yuan, Yu-Qi Feng
Summary: The study presents an engineered deaminase-mediated sequencing (EDM-seq) method for the quantitative detection of 5hmC in DNA at single-nucleotide resolution. The method uses an engineered A3A protein to deaminate C and 5mC, while leaving 5hmC unaffected, allowing for the direct and quantitative detection of 5hmC in DNA.
Article
Biochemistry & Molecular Biology
Antonella Sarnataro, Giulia De Riso, Sergio Cocozza, Antonio Pezone, Barbara Majello, Stefano Amente, Giovanni Scala
Summary: DNA methylation is an important epigenetic modification that influences gene regulation, genomic imprinting, and genome stability. EpiStatProfiler is an R package that allows the analysis of CpG and non-CpG epialleles based on bisulfite sequencing data, with additional features for genomic annotation and analysis. It is the first package to provide functionalities specifically for epiallele composition analysis from any type of bisulfite sequencing experiment.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Mauricio Penuela, Jenny Johana Gallo-Franco, Jorge Finke, Camilo Rocha, Anestis Gkanogiannis, Thaura Ghneim-Herrera, Mathias Lorieux
Summary: This study investigates the association between recombination rates and DNA methylation in two commercial rice varieties, revealing negative and positive correlations between them, as well as the significant impact of the centromere region. Furthermore, machine learning regression models are developed to predict recombination rates using methylated cytosines in the CHH context.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Fabio Coppede, Utsa Bhaduri, Andrea Stoccoro, Vanessa Nicoli, Eleonora Di Venere, Giuseppe Merla
Summary: The central objective of combining discovery science with biomedical applications is to benefit patients and reduce the global disease burden. The conversion of DNA methylation (DNAm) from a biological process to a diagnostic tool is a prime example of this transformation, which took nearly a century. In recent years, DNAm studies have been standardized in clinical applications more than ever before, offering great potential for diagnosing various diseases associated with epigenetic alterations. DNAm detection plays a role in noninvasive prenatal testing and indicates prenatal risk factors in very preterm infants. In the field of cancer, liquid biopsy-based DNAm profiling provides valuable epigenetic biomarkers for early-stage diagnosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Athanasios Dalakouras, Ioannis Ganopoulos
Summary: Exogenous RNA molecules can trigger RNA interference in plants, and high-pressure spraying of dsRNAs can induce de novo methylation of promoter sequences in plants.
Article
Plant Sciences
Fangming Zhu, Mingyan Li, Manwen Yan, Fei Qiao, Xuefei Jiang
Summary: DNA methylation plays a crucial role in plants' response to osmotic stress, with genes related to plant hormone synthesis, signal transduction, osmoregulatory substance, and antioxidant enzymes rapidly responding. Additionally, demethylation of key enzyme genes can alleviate the inhibition of cell growth caused by osmotic stress.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Billy T. Lau, Alison Almeda, Marie Schauer, Madeline McNamara, Xiangqi Bai, Qingxi Meng, Mira Partha, Susan M. Grimes, HoJoon Lee, Gregory M. Heestand, Hanlee P. Ji
Summary: We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes, enabling longitudinal monitoring of cancer patients during treatment. This approach generated significantly more reads compared to existing methods and allowed us to determine the origin of individual reads. By leveraging the methylomes of matched tumors and immune cells, we characterized the cfDNA methylomes of cancer patients.
Article
Biotechnology & Applied Microbiology
Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Mark D. Robinson
Summary: ARPEGGIO is a workflow for analyzing epigenetic data in allopolyploids, utilizing the EAGLE-RC read classification algorithm to address sequence similarity challenges among parental genomes. This workflow offers automation and a complete set of analyses starting from raw WGBS data to outputting a list of genes showing differential methylation, ensuring reproducibility with simple set up and interpretation. ARPEGGIO stands out as the only workflow supporting polyploid data, as shown through its performance evaluation and agreement with published results.
Review
Biotechnology & Applied Microbiology
Hao Lv, Fu-Ying Dao, Dan Zhang, Hui Yang, Hao Lin
Summary: DNA modification is crucial in regulating gene expression in cell development, with advances in DNA sequencing technology allowing for the resolution of different modifications at a genome-wide scale. This has led to the discovery of new insights into the complexity and functions of multiple methylations. The review discusses various mapping approaches and the development of future sequencing technologies for improving detection resolution.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)