CBE—Life Sciences Education CBE-LSE CBE-LSE CBE-LSE Developmental Biology
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| http://dx.doi.org/10.1187/cbe.07-12-0106 | DOI Listing |
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Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes.
BMC Mol Cell Biol
January 2025
Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
Background: During the latter stages of their development, mammalian oocytes under dramatic chromatin reconfiguration, transitioning from a non-surrounded nucleolus (NSN) to a surrounded nucleolus (SN) stage, and concomitant transcriptional silencing. Although the NSN-SN transition is known to be essential for developmental competence of the oocyte, less is known about the accompanying molecular changes. Here we examine the changes in the transcriptome and DNA methylation during the NSN to SN transition in mouse oocytes.
View Article and Find Full Text PDFZIC1 is a context-dependent medulloblastoma driver in the rhombic lip.
Nat Genet
January 2025
Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma).
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 PDFCord blood platelet-rich plasma: proteomics analysis for ophthalmic applications.
Clin Proteomics
January 2025
Ophthalmology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli, 1, 00168, Rome, Italy.
Our objective is to determine the protein and complements constituents of Cord blood Platelet-rich plasma (CB-PRP), based on the hypothesis that it contains beneficial components capable of arresting or potentially decelerating the advancement of atrophic age-related macular degeneration (dry-AMD), with the support of radiomics. Two distinct pools of CB-PRP were assessed, each pool obtained from a total of 15 umbilical cord-blood donors. One aliquot of each pool respectively was subjected to proteomic analysis in order to enhance the significance of our findings, by identifying proteins that are shared between the two sample pools and gaining insights into the pathways they are associated with.
View Article and Find Full Text PDFDeciphering the core shunt mechanism in Arabidopsis cuticular wax biosynthesis and its role in plant environmental adaptation.
Nat Plants
January 2025
State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China.
Plant cuticular waxes serve as highly responsive adaptations to variable environments. Aliphatic waxes consist of very-long-chain (VLC) compounds produced from 1-alcohol- or alkane-forming pathways. The existing variation in 1-alcohols and alkanes across Arabidopsis accessions revealed that 1-alcohol amounts are negatively correlated with aridity factors, whereas alkanes display the opposite behaviour.
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