Gene clusters are common features of prokaryotic genomes also present in eukaryotes. Most clustered genes known are involved in the biosynthesis of secondary metabolites. Although horizontal gene transfer is a primary source of prokaryotic gene cluster (operon) formation and has been reported to occur in eukaryotes, the predominant source of cluster formation in eukaryotes appears to arise de novo or through gene duplication followed by neo- and sub-functionalization or translocation. Here we aim to provide an overview of the current knowledge and open questions related to plant gene cluster functioning, assembly, and regulation. We also present potential research approaches and point out the benefits of a better understanding of gene clusters in plants for both fundamental and applied plant science.
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http://dx.doi.org/10.1016/j.tplants.2014.01.013 | DOI Listing |
JNCI Cancer Spectr
January 2025
Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany.
Li-Fraumeni syndrome is a cancer predisposition syndrome caused by pathogenic TP53 germline variants and associated with a high lifelong cancer risk. We analysed the German LFS registry that contains data on 304 individuals. Cancer phenotypes were correlated with variants grouped according to their ability to transactivate target genes in a yeast assay using a traditional (non-functional, partially-functional) and a novel (clusters A, B, C) classification of variants into different groups.
View Article and Find Full Text PDFmBio
January 2025
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
Unlabelled: Bacterial typing at whole-genome scales is now feasible owing to decreasing costs in high-throughput sequencing and the recent advances in computation. The unprecedented resolution of whole-genome typing is achieved by genotyping the variable segments of bacterial genomes that can fluctuate significantly in gene content. However, due to the transient and hypervariable nature of many accessory elements, the value of the added resolution in outbreak investigations remains disputed.
View Article and Find Full Text PDFJ Transl Med
January 2025
Laboratory of Gene Engineering and Genomics, School of Basic Medical Sciences, Chengde Medical University, Chengde, 067000, China.
Objective: This study aims to elucidate the primary signaling communication among papillary craniopharyngioma (PCP) tumor cells.
Methods: Five samples of PCP were utilized for single-cell RNA sequencing. The most relevant ligand and receptor interactions among different cells were calculated using the CellChat package in R software.
Genome Med
January 2025
Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
Background: Mixed infection with multiple strains of the same pathogen in a single host can present clinical and analytical challenges. Whole genome sequence (WGS) data can identify signals of multiple strains in samples, though the precision of previous methods can be improved. Here, we present MixInfect2, a new tool to accurately detect mixed samples from Mycobacterium tuberculosis short-read WGS data.
View Article and Find Full Text PDFBMC Genomics
January 2025
Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524013, China.
Background: The Leizhou Black Goat (LZBG), a prominent breed in tropical China's meat goat industry, frequently exhibits inherent muscle atrophy and malnutrition-related traits. Particularly, muscles critical for support, such as the legs, often display severe symptoms. This study aimed to investigate the differential genes and signaling pathways influencing muscle development and atrophy across various muscle locations in LZBG from a muscular atrophy-affected family.
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