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Deep mutational scanning of the Trypanosoma brucei developmental regulator RBP6 reveals an essential disordered region influenced by positive residues.
Nat Commun
January 2025
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06536, USA.
To regain infectivity, Trypanosoma brucei, the pathogen causing Human and Animal African trypanosomiasis, undergoes a complex developmental program within the tsetse fly known as metacyclogenesis. RNA-binding protein 6 (RBP6) is a potent orchestrator of this process, however, an understanding of its functionally important domains and their mutational constraints is lacking. Here, we perform deep mutational scanning of the entire RBP6 primary structure.
View Article and Find Full Text PDFIdentification and characterization of GRAS genes in passion fruit (Passiflora edulis Sims) revealed their roles in development regulation and stress response.
Plant Cell Rep
January 2025
Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, College of Life Sciences, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
Twenty-nine GRAS genes were identified in passion fruit, the N-terminal regions and 3D (three-dimensional) structures were closely related with their tissue-specific expression patterns. Candidate PeGRASs for enhancing stress resistance were identified. Passion fruit (Passiflora edulis Sims) is a tropical fruit crop with significant edible and ornamental value, but its growth and development are highly sensitive to environmental conditions.
View Article and Find Full Text PDFIdentification, molecular characterization and expression patterns of Cathepsin L in Yesso scallop (Patinopecten yessoensis) shell-infested by Polydora.
Comp Biochem Physiol B Biochem Mol Biol
January 2025
Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, China.
Patinopecten yessoensis (Yesso scallop), one of the most important aquaculture molluscs in China, has recently suffered severe Polydora disease, causing economic losses. Cathepsin L (CatL), a cysteine protease, has important functions in immune responses in vertebrates and invertebrates. However, little is known regarding the structure and function of CatL in scallops.
View Article and Find Full Text PDFA multi-modal transformer for cell type-agnostic regulatory predictions.
Cell Genom
January 2025
The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA; The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:
Sequence-based deep learning models have emerged as powerful tools for deciphering the cis-regulatory grammar of the human genome but cannot generalize to unobserved cellular contexts. Here, we present EpiBERT, a multi-modal transformer that learns generalizable representations of genomic sequence and cell type-specific chromatin accessibility through a masked accessibility-based pre-training objective. Following pre-training, EpiBERT can be fine-tuned for gene expression prediction, achieving accuracy comparable to the sequence-only Enformer model, while also being able to generalize to unobserved cell states.
View Article and Find Full Text PDFBio-nanopore technology for biomolecules detection.
Adv Biotechnol (Singap)
December 2024
School of Food Science and Technology, State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, Jiangsu, China.
Bio-nanopore technology holds great promise in biomacromolecule detection, with its high throughput and low cost positioning it as an ideal detection tool. This technology employs a unique detection mechanism that utilizes nanoscale pores to rapidly and sensitively convert biological molecules interactions into electrical signals, enabling real-time, single-molecule detection with exceptional sensitivity. This review focuses on the latest advancements in this technology across various domains, including DNA and RNA sequencing, protein detection, and small molecule identification.
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