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Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.
J Hered
January 2025
Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, Copenhagen, 1353, Denmark.
The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species.
View Article and Find Full Text PDFMechanisms for DNA Interplay in Eukaryotic Transcription Factors.
Annu Rev Biophys
January 2025
1CREST Center for Cellular and Biomolecular Machines, University of California, Merced, California, USA; email:
Like their prokaryotic counterparts, eukaryotic transcription factors must recognize specific DNA sites, search for them efficiently, and bind to them to help recruit or block the transcription machinery. For eukaryotic factors, however, the genetic signals are extremely complex and scattered over vast, multichromosome genomes, while the DNA interplay occurs in a varying landscape defined by chromatin remodeling events and epigenetic modifications. Eukaryotic factors are rich in intrinsically disordered regions and are also distinct in their recognition of short DNA motifs and utilization of open DNA interaction interfaces as ways to gain access to DNA on nucleosomes.
View Article and Find Full Text PDFPD-L1-CD80 interactions are required for intracellular signaling necessary for dendritic cell migration.
Sci Adv
January 2025
Department of Medicine, Division of Gastroenterology and Hepatology, University of Colorado School of Medicine, Aurora, CO, USA.
Programmed cell death protein 1 (PD-1) and programmed death ligand 1 (PD-L1) interactions are targets for immunotherapies aimed to reinvigorate T cell function. Recently, it was documented that PD-L1 regulates dendritic cell (DC) migration through intracellular signaling events. In this study, we find that both preclinical murine and clinically available human PD-L1 antibodies limit DC migration.
View Article and Find Full Text PDFAn ecological-evolutionary perspective on the genomic diversity and habitat preferences of the .
Microb Genom
January 2025
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
Members of the phylum inhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of various lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes , , and were highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classes and showed preferences to non-soil habitats.
View Article and Find Full Text PDFFibroblast transcriptomics uncovers pathogenic genomic variants in individuals with exome-negative childhood onset epilepsy.
Epilepsia
January 2025
Applied Translational Neurogenomics Group, Vlaams Instituut voor Biotechnology (VIB) Center for Molecular Neurology, VIB, Antwerp, Belgium.
Objective: This study aims to improve genetic diagnosis in childhood onset epilepsy with neurodevelopmental problems by utilizing RNA sequencing of fibroblasts to identify pathogenic variants that may be missed by exome sequencing and copy number variation analysis.
Methods: We enrolled 41 individuals with childhood onset epilepsy and neurodevelopmental problems who previously had inconclusive genetic testing. Fibroblast samples were cultured and analyzed using RNA sequencing to detect aberrant expression, aberrant splicing, and monoallelic expression using the Detection of RNA Outlier Pipeline (DROP) pipeline.
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