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NaP-TRAP reveals the regulatory grammar in 5'UTR-mediated translation regulation during zebrafish development.
Nat Commun
December 2024
Department of Genetics, Yale University, Yale School of Medicine, New Haven, 06510, CT, USA.
The cis-regulatory elements encoded in an mRNA determine its stability and translational output. While there has been a considerable effort to understand the factors driving mRNA stability, the regulatory frameworks governing translational control remain more elusive. We have developed a novel massively parallel reporter assay (MPRA) to measure mRNA translation, named Nascent Peptide Translating Ribosome Affinity Purification (NaP-TRAP).
View Article and Find Full Text PDFThe survival of B cells is compromised in kidney disease.
Nat Commun
December 2024
Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
Antibody-mediated protection against pathogens is crucial to a healthy life. However, the recent SARS-CoV-2 pandemic has shown that pre-existing comorbid conditions including kidney disease account for compromised humoral immunity to infections. Individuals with kidney disease are not only susceptible to infections but also exhibit poor vaccine-induced antibody response.
View Article and Find Full Text PDFEnvironment-Organism Feedbacks Drive Changes in Ecological Interactions.
Ecol Lett
January 2025
Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
Ecological interactions are foundational to our understanding of community composition and function. While interactions are known to change depending on the environmental context, it has generally been assumed that external environmental factors are responsible for driving these dependencies. Here, we derive a theoretical framework which instead focuses on how intrinsic environmental changes caused by the organisms themselves alter interaction values.
View Article and Find Full Text PDFR3Design: deep tertiary structure-based RNA sequence design and beyond.
Brief Bioinform
November 2024
AI Lab, Research Center for Industries of the Future, Westlake University, Zhejiang 310058, China.
The rational design of Ribonucleic acid (RNA) molecules is crucial for advancing therapeutic applications, synthetic biology, and understanding the fundamental principles of life. Traditional RNA design methods have predominantly focused on secondary structure-based sequence design, often neglecting the intricate and essential tertiary interactions. We introduce R3Design, a tertiary structure-based RNA sequence design method that shifts the paradigm to prioritize tertiary structure in the RNA sequence design.
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