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Modeling DNA methyltransferase function to predict epigenetic correlation patterns in healthy and cancer cells.
Proc Natl Acad Sci U S A
January 2025
Department of Chemical Engineering, Stanford University, Stanford, CA 94305.
DNA methylation is a crucial epigenetic modification that orchestrates chromatin remodelers that suppress transcription, and aberrations in DNA methylation result in a variety of conditions such as cancers and developmental disorders. While it is understood that methylation occurs at CpG-rich DNA regions, it is less understood how distinct methylation profiles are established within various cell types. In this work, we develop a molecular-transport model that depicts the genomic exploration of DNA methyltransferase within a multiscale DNA environment, incorporating biologically relevant factors like methylation rate and CpG density to predict how patterns are established.
View Article and Find Full Text PDFDecoupling Individual Host Response and Immune Cell Engager Cytotoxic Potency.
ACS Nano
January 2025
Aix-Marseille Univ., CNRS, INSERM, LAI, Centuri Living Systems, 13009 Marseille, France.
Immune cell engagers are molecular agents, usually antibody-based constructs, engineered to recruit immune cells against cancer cells and kill them. They are versatile and powerful tools for cancer immunotherapy. Despite the multiplication of engagers tested and accepted in the clinic, how molecular and cellular parameters influence their actions is poorly understood.
View Article and Find Full Text PDFMultiscale Finite Element Modeling of Human Ear for Acoustic Wave Transmission into Cochlea and Hair Cells Fatigue Failure.
J Biomech Eng
January 2025
School of Aerospace and Mechanical Engineering, University of Oklahoma, 865 Asp Ave, Norman, OK 73019, USA.
Hearing loss is highly related to acoustic injuries and mechanical damage of ear tissues. The mechanical responses of ear tissues are difficult to measure experimentally, especially cochlear hair cells within the organ of Corti (OC) at microscale. Finite element (FE) modeling has become an important tool for simulating acoustic wave transmission and studying cochlear mechanics.
View Article and Find Full Text PDFIdentifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models.
J Chem Inf Model
January 2025
School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
The accurate identification of protein-nucleotide binding residues is crucial for protein function annotation and drug discovery. Numerous computational methods have been proposed to predict these binding residues, achieving remarkable performance. However, due to the limited availability and high variability of nucleotides, predicting binding residues for diverse nucleotides remains a significant challenge.
View Article and Find Full Text PDFPrediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers.
PLoS Comput Biol
January 2025
Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
Quantification of intrahepatic covalently closed circular DNA (cccDNA) is a key for evaluating an elimination of hepatitis B virus (HBV) in infected patients. However, quantifying cccDNA requires invasive methods such as a liver biopsy, which makes it impractical to access the dynamics of cccDNA in patients. Although HBV RNA and HBV core-related antigens (HBcrAg) have been proposed as surrogate markers for evaluating cccDNA activity, they do not necessarily estimate the amount of cccDNA.
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