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| http://dx.doi.org/10.1016/j.cell.2014.11.001 | DOI Listing |
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Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams.
Commun Biol
January 2025
Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA.
Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam (Tridacna maxima) genome to demonstrate how symbiosis has left complex signatures in an animal's genome.
View Article and Find Full Text PDFProtein quality control machinery: regulators of condensate architecture and functionality.
Trends Biochem Sci
January 2025
Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; Department of Biology, Syracuse University, Syracuse, NY 13244, USA; Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA; Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA. Electronic address:
Protein quality control (PQC) mechanisms including the ubiquitin (Ub)-proteasome system (UPS), autophagy, and chaperone-mediated refolding are essential to maintain protein homeostasis in cells. Recent studies show that these PQC mechanisms are further modulated by biomolecular condensates that sequester PQC components and compartmentalize reactions. Accumulating evidence points towards the PQC machinery playing a pivotal role in regulating the assembly, disassembly, and viscoelastic properties of several condensates.
View Article and Find Full Text PDFRsWOX13 promotes taproot development by activating cell division and expansion and sucrose metabolism in radish.
Plant Physiol Biochem
December 2024
National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Sanya Institute, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, PR China; College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China. Electronic address:
Radish is an important annual root vegetable crop, whose yield is largely dependent on taproot thickening and development. However, the regulatory network of WOXs-mediated taproot development remains poorly understood in radish. Herein, the RsWOX13 was classified in an ancient clade of the WOX gene family that harbors a conserved homeodomain.
View Article and Find Full Text PDFSMORE: spatial motifs reveal patterns in cellular architecture of complex tissues.
Genome Biol
January 2025
Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, 90095, CA, USA.
Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential arrangements of cells and examine their associated gene expression specializations. Applied to retina, brain, and embryonic tissue maps, SMORE identifies novel spatial motifs, including one that offers a new mechanism of action for type 1b bipolar cells.
View Article and Find Full Text PDFDecoupled peak property learning for efficient and interpretable electronic circular dichroism spectrum prediction.
Nat Comput Sci
January 2025
AI for Science (AI4S)-Preferred Program, Peking University Shenzhen Graduate School, Shenzhen, China.
Electronic circular dichroism (ECD) spectra contain key information about molecular chirality by discriminating the absolute configurations of chiral molecules, which is crucial in asymmetric organic synthesis and the drug industry. However, existing predictive approaches lack the consideration of ECD spectra owing to the data scarcity and the limited interpretability to achieve trustworthy prediction. Here we establish a large-scale dataset for chiral molecular ECD spectra and propose ECDFormer for accurate and interpretable ECD spectrum prediction.
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