Article
Chemistry, Analytical
Carlos H. S. Mendes, Maycom W. F. Silva, Severino Carlos B. Oliveira
Summary: The electrochemical oxidation of 5-methylcytosine was studied at glassy carbon electrode in aqueous solution, revealing a single, irreversible reaction step controlled by diffusion, generating intermediate radicals. C5 methylated pyrimidines are more easily oxidized and reactive compared to unmethylated bases. A new electroanalytical method using differential pulse voltammetry for quantification of DNA methylation was proposed, showing promising results for detection of 5-mCyt.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Weihua Qin, Clemens Steinek, Ksenia Kolobynina, Ignasi Forne, Axel Imhof, M. Cristina Cardoso, Heinrich Leonhardt
Summary: The reversible attachment of ubiquitin regulates the interaction, activity, and degradation of proteins. This study employs recombinant binding domains to investigate protein ubiquitination in living cells, using fluorescent ubiquitin binders to detect ubiquitination state. HP1 beta was identified as a novel ubiquitination target of UHRF1, and K48 and K63 linked protein ubiquitination were discriminated using specific ubiquitin binding domains. Complementation assays with split YFP and a cell cycle marker were used to detect the ubiquitination of p53 and its inhibition by Nutlin-3. Overall, the ubiF3H assay proves useful for probing specific protein ubiquitination and screening for regulators of this posttranslational modification.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Rui Yuan, Shilong Chen, Yongcui Wang
Summary: This study revealed methylation sites associated with EGFR inhibitor sensitivity genes through the correlation between DNA methylation and drug sensitivity, providing new therapeutic targets for understanding anti-EGFR-inhibitor resistance in lung cancer.
Article
Oncology
Chiara Herzog, Fatima Marin, Allison Jones, Iona Evans, Daniel Reisel, Elisa Redl, Lena Schreiberhuber, Sonia Paytubi, Beatriz Pelegrina, Alvaro Carmona, Paula Peremiquel-Trillas, Jon Frias-Gomez, Marta Pineda, Joan Brunet, Jordi Ponce, Xavier Matias-Guiu, Silvia de Sanjose, Laia Alemany, Adeola Olaitan, Michael Wong, Davor Jurkovic, Emma J. Crosbie, Adam N. Rosenthal, Line Bjorge, Michal Zikan, Lukas Dostalek, David Cibula, Karin Sundstrom, Joakim Dillner, Laura Costas, Martin Widschwendter
Summary: The study developed a noninvasive triage test for women with suspected endometrial cancer symptoms, aiming to improve early diagnosis and reduce the need for in-person visits. The test showed high sensitivity and specificity in detecting EC cases in different sample types and settings.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Jack M. Colicchio, Cynthia L. Amstutz, Nelson Garcia, Keerthana N. Prabhu, Thomas M. Cairns, Melis Akman, Thomas Gottilla, Twyla Gollery, Shawn L. Stricklin, Travis S. Bayer
Summary: Epigenetic variation plays a crucial role in determining plant phenotype and adaptation to the environment. However, tools for high resolution and low-cost profiling and comparison of the methylomes of multiple individual plants or groups of plants are currently lacking. In this study, a computational approach and R package (sounDMR) utilizing long read nanopore sequencing is described, enabling robust identification of differential methylation, assessment of variability within treatment groups, and identification of individual plants of interest. These findings demonstrate the accessibility of high resolution epigenetic profiling in plant breeding and biotechnology using cost-effective nanopore sequencing.
SCIENTIFIC REPORTS
(2023)
Article
Dermatology
Cristiana Banila, Daniel Green, Dimitris Katsanos, Joana Viana, Alice Osmaston, Angel Menendez Vazquez, Magnus Lynch, Shakiba Kaveh
Summary: This study demonstrates the feasibility and effectiveness of using tape stripping combined with whole-genome sequencing as a noninvasive approach to measuring DNA methylation changes in the skin. The method shows promise in discerning relevant methylation alterations in diverse patient cohorts, offering a potential avenue for identifying skin ageing biomarkers and evaluating treatment responses.
BRITISH JOURNAL OF DERMATOLOGY
(2023)
Article
Multidisciplinary Sciences
Zaka Wing-Sze Yuen, Akanksha Srivastava, Runa Daniel, Dennis McNevin, Cameron Jack, Eduardo Eyras
Summary: The study evaluated the performance of multiple tools in detecting CpG methylation from Nanopore sequencing, revealing a tradeoff between false positives and false negatives. The authors proposed a consensus approach, METEORE, to improve prediction accuracy, and provided Snakemake pipelines for reproducibility.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Keren Xu, Shaobo Li, Ivo S. Muskens, Natalina Elliott, Swe Swe Myint, Priyatama Pandey, Helen M. Hansen, Libby M. Morimoto, Alice Y. Kang, Xiaomei Ma, Catherine Metayer, Beth A. Mueller, Irene Roberts, Kyle M. Walsh, Steve Horvath, Joseph L. Wiemels, Adam J. Smith
Summary: The study revealed that accelerated epigenetic aging in the blood of Down syndrome (DS) patients begins prenatally and is associated with somatic GATA1 mutations. DS newborns showed a significant increase in DNAmSkinBloodClock, but were not associated with epigenetic gestational age acceleration.
Article
Genetics & Heredity
Joan Sabria-Back, Ana Monteagudo-Sanchez, Marta Sanchez-Delgado, Anne C. Ferguson-Smith, Olga Gomez, Africa Pertierra Cartada, Jair Tenorio, Julian Nevado, Pablo Lapunzina, Arrate Pereda Aguirre, Carles Gimenez Sevilla, Estefania Toro Toro, Guiomar Perez de Nanclares, David Monk
Summary: Kagami-Ogata syndrome (KOS14) and Temple syndrome (TS14) are associated with reciprocal alterations within the chr14q32 imprinted domain. A work-up strategy for preimplantation genetic testing (PGT) was presented to avoid the transmission of a causative micro-deletion. PGT was successfully offered to identify an unaffected embryo and transfer it, resulting in the birth of a healthy baby.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Biochemical Research Methods
Peixin Tian, Minhao Yao, Tao Huang, Zhonghua Liu
Summary: In this article, a novel method called CoxMKF is proposed for high-dimensional mediation analysis, which can achieve FDR control even in finite-sample settings, particularly advantageous when the sample size is not large. CoxMKF can overcome the randomness of unstable model-X knockoffs and has been shown to control FDR well in finite samples.
Article
Biochemical Research Methods
Christos Maniatis, Catalina Vallejos, Guido Sanguinetti
Summary: Single-cell multi-omics assays provide unprecedented opportunities to explore epigenetic regulation at the cellular level. However, high levels of technical noise and data sparsity often result in a lack of statistical power in correlative analyses. SCRaPL is a novel computational tool that addresses this issue by carefully modeling noise in the experimental systems.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Will T. Kaufhold, Wolfgang Pfeifer, Carlos E. Castro, Lorenzo Di Michele
Summary: The study utilizes metadynamics to sample the free energy landscapes of DNA nanostructures and demonstrates its ability to predict the mechanical response of DNA nanodevices. These findings are significant for the design and application of DNA nanostructures.
Article
Biochemical Research Methods
Hua Shi, Shuang Li, Xi Su
Summary: N6-methyladenine (6mA), a type of DNA methylation, has gained significant attention in recent years. Accurate identification of 6mA sites is crucial for understanding its biological activities and mechanisms in plant genomes. Traditional wet-lab experiments are time-consuming and labor-intensive, leading to the emergence of computational methods, particularly machine learning. However, current methods heavily rely on prior knowledge and large model scale, resulting in limited generalization performance. To address these limitations, researchers propose Plant6mA, a lightweight structure predictor based on Transformer encoder, which demonstrates superior generalization performance in predicting 6mA locations in plant genomes.
Article
Chemistry, Multidisciplinary
Bintian Zhang, Eathen Ryan, Xu Wang, Stuart Lindsay
Summary: Proteins, as molecular electronic components, have a long electronic decay length of around 10 nm, high contact resistance, and extreme sensitivity to chemical details of the contact. The conductance of even large bioelectronic assemblies is largely controlled by the conductance of the contacts. Using engineered streptavidin tetramers with defined ratios of active to dead monomers, researchers found a strong dependence of conductance on the separation of biotin molecules, indicating a short-range tunneling interaction within streptavidin. The presence of hexaglutamate tails on active monomers enhances conductance significantly through an electronic resonance effect in protein conductance.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Ya-Ling Tan, A-Qian Huang, Li-Juan Tang, Jian-Hui Jiang
Summary: The development of multiplexed droplet loop-mediated isothermal amplification (multiplexed dLAMP) technique, which allows simultaneous quantification of multiple targets, provides a highly sensitive digital nucleic acid method for rapid and effective detection of viruses and other pathogens. The technology not only has been successfully demonstrated in the laboratory, but also holds promise for digital detection of HCV and HIV RNA in clinical applications. With high precision and low detection limits, it offers a new approach for the prevention and control of infectious diseases.
