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Sheng Wu Gong Cheng Xue Bao = Chinese... Sep 2018Cyanobacteria are a phylum of bacteria which are believed to be the oldest photosynthetic prokaryotic microorganisms on earth. The phylogenetic group of cyanobacteria... (Review)
Review
Cyanobacteria are a phylum of bacteria which are believed to be the oldest photosynthetic prokaryotic microorganisms on earth. The phylogenetic group of cyanobacteria was thought to be one of the prokaryotes that contain monoploid, oligoploid and polyploid species, and one obstacle to engineering cyanobacteria is their polyploidy genome. In recent years, the ploidy level of cyanobacteria was found to be influenced by growth phase and by multiple genetic and environmental factors. In the present article, we reviewed the progress, analytical methods and influencing factors on the cyanobacterial ploidy, and discussed the significance of cyanobacterial polyploidy regarding to environmental ecology and biotechnology. Based on this observation, the future research directions in this field are prospected.
Topics: Cyanobacteria; Phylogeny; Ploidies; Polyploidy
PubMed: 30255673
DOI: 10.13345/j.cjb.170513 -
Nature Communications Oct 2022Ploidy changes are frequent in nature and contribute to evolution, functional specialization and tumorigenesis. Analysis of model organisms of different ploidies...
Ploidy changes are frequent in nature and contribute to evolution, functional specialization and tumorigenesis. Analysis of model organisms of different ploidies revealed that increased ploidy leads to an increase in cell and nuclear volume, reduced proliferation, metabolic changes, lower fitness, and increased genomic instability, but the underlying mechanisms remain poorly understood. To investigate how gene expression changes with cellular ploidy, we analyzed isogenic series of budding yeasts from 1N to 4N. We show that mRNA and protein abundance scales allometrically with ploidy, with tetraploid cells showing only threefold increase in protein abundance compared to haploids. This ploidy-dependent sublinear scaling occurs via decreased rRNA and ribosomal protein abundance and reduced translation. We demonstrate that the activity of Tor1 is reduced with increasing ploidy, which leads to diminished rRNA gene repression via a Tor1-Sch9-Tup1 signaling pathway. mTORC1 and S6K activity are also reduced in human tetraploid cells and the concomitant increase of the Tup1 homolog Tle1 downregulates the rDNA transcription. Our results suggest that the mTORC1-Sch9/S6K-Tup1/TLE1 pathway ensures proteome remodeling in response to increased ploidy.
Topics: Humans; Proteome; Tetraploidy; Haploidy; Transcription Factors; RNA, Ribosomal; Ribosomal Proteins; DNA, Ribosomal; Mechanistic Target of Rapamycin Complex 1; RNA, Messenger
PubMed: 36261409
DOI: 10.1038/s41467-022-33904-7 -
Histology and Histopathology Oct 1999We reviewed the literature concerning the history of determination of the ploidy of human megakaryocytes and its relationship with diseases. The ploidy of rabbit... (Review)
Review
We reviewed the literature concerning the history of determination of the ploidy of human megakaryocytes and its relationship with diseases. The ploidy of rabbit megakaryocytes was analyzed by microspectrophotometry in 1964, and the analysis of the ploidy in human megakaryocytes was first performed in 1968. Presently, microphotometry and flow cytometry are the primary methods for the evaluation of the ploidy, but they have their merits and demerits. In the ploidy of human megakaryocytes, a peak has often been reported at 16N in healthy individuals, and the next peaks have been observed at 32N and 8N. The results of ploidy analyses have been reported by many investigators to be comparable between patients with idiopathic thrombocytopenic purpura and normal subjects, but various shifts of the peaks have also been documented. The ploidy is often reported to shift to a larger ploidy class in polycythemia vera and essential thrombocythemia, but it has invariably been reported to shift to a smaller class in chronic myelogenous leukemia. In reactive thrombocytosis, the ploidy pattern was reported to be the same as that in normal individuals by some investigators but to shift to a larger ploidy by others. These differences are considered to be due to heterogeneity of the subjects. In myelodysplastic syndrome, the ploidy shifts mostly to a smaller class, but it may show various patterns. We also reviewed the ploidy in other rare hematological disorders, the relationships of the ploidy with diabetes mellitus and atherosclerotic disorders, and its changes in the ontogeny. Details of the mechanism of polyploidization and its biological significance remain unknown, and further advances in the studies of these topics are anticipated.
Topics: Animals; Hematologic Diseases; Humans; Megakaryocytes; Ploidies; Rabbits
PubMed: 10506938
DOI: 10.14670/HH-14.1223 -
Current Biology : CB May 2021In a new paper in this issue, Murawski and Brynildsen define chromosomal ploidy as an important characteristic for persistence following fluoroquinolone treatment....
In a new paper in this issue, Murawski and Brynildsen define chromosomal ploidy as an important characteristic for persistence following fluoroquinolone treatment. Bacteria carrying two chromosomes are more likely to repair DNA damage through homologous recombination compared with cells containing a single chromosome.
Topics: Anti-Bacterial Agents; DNA Damage; Diploidy; Homologous Recombination; Ploidies
PubMed: 34033776
DOI: 10.1016/j.cub.2021.03.072 -
Trends in Plant Science Dec 2017Mixed-ploidy species harbor a unique form of genomic and phenotypic variation that influences ecological interactions, facilitates genetic divergence, and offers... (Review)
Review
Mixed-ploidy species harbor a unique form of genomic and phenotypic variation that influences ecological interactions, facilitates genetic divergence, and offers insights into the mechanisms of polyploid evolution. However, there have been few attempts to synthesize this literature. We review here research on the cytotype distribution, diversity, and dynamics of intensively studied mixed-ploidy species and consider the implications for understanding mechanisms of polyploidization such as cytotype formation, establishment, coexistence, and post-polyploid divergence. In general, mixed-ploidy species are unevenly represented among families: they exhibit high cytotype diversity, often within populations, and frequently comprise rare and odd-numbered ploidies. Odd-ploidies often occur in association with asexuality. We highlight research hypotheses and opportunities that take advantage of the unique properties of ploidy variation.
Topics: Chromosomes, Plant; Genetic Variation; Plants; Ploidies; Polyploidy
PubMed: 29054346
DOI: 10.1016/j.tplants.2017.09.011 -
Oncogene Oct 2010After DNA or spindle damage, p53-defective tumor cells undergo a complex cycle of reversible polyploidy. How this process occurs and more importantly, why, has recently... (Review)
Review
After DNA or spindle damage, p53-defective tumor cells undergo a complex cycle of reversible polyploidy. How this process occurs and more importantly, why, has recently become the focus of several research groups, prompting this review in which we discuss two related phenomena that accompany the reversible polyploidy of tumor cells: the induction of meiosis genes such as MOS and the decrease in genomic instability observed during the reversion from polyploidy to para-diploidy. The reversible polyploidy likely provides the means through which the balance between increased chromosome instability (CIN), driving genetic variation and decreased CIN, necessary for perpetuating these malignant clones, is maintained. These concepts are integrated with recent findings that many meiotic and self-renewal genes become activated during reversible polyploidy and lead us to the hypothesis that tumor cell immortality may be achieved through germline-like transmission.
Topics: Aneuploidy; Animals; Gene Expression Regulation, Neoplastic; Genes, mos; Humans; Neoplasms; Ploidies
PubMed: 20676137
DOI: 10.1038/onc.2010.310 -
Developmental Cell Feb 2018There is mounting circumstantial evidence that ploidy, a cell's relative DNA content, is in part responsible for the differential cardiac regenerative capacity observed...
There is mounting circumstantial evidence that ploidy, a cell's relative DNA content, is in part responsible for the differential cardiac regenerative capacity observed between regenerative and non-regenerative organisms. In this issue of Developmental Cell, González-Rosa et al. (2018) provide direct evidence that polyploid cardiomyocytes have reduced proliferative and regenerative potential.
Topics: Heart; Myocytes, Cardiac; Ploidies; Regeneration
PubMed: 29486188
DOI: 10.1016/j.devcel.2018.02.004 -
Genes Jul 2023is the fastest-growing bacterium, with a doubling time of approximately 12-14 min. It has a high potential for basic research and biotechnological applications, e.g.,... (Review)
Review
is the fastest-growing bacterium, with a doubling time of approximately 12-14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of . Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in and will guide the optimization of molecular biological characterization and biotechnological applications.
Topics: DNA Copy Number Variations; Vibrio; Chromosomes; Ploidies
PubMed: 37510340
DOI: 10.3390/genes14071437 -
Genes Apr 2023Polyploidy, the duplication of the entire genome within a single cell, is a significant characteristic of cells in many tissues, including the liver. The quantification...
Polyploidy, the duplication of the entire genome within a single cell, is a significant characteristic of cells in many tissues, including the liver. The quantification of hepatic ploidy typically relies on flow cytometry and immunofluorescence (IF) imaging, which are not widely available in clinical settings due to high financial and time costs. To improve accessibility for clinical samples, we developed a computational algorithm to quantify hepatic ploidy using hematoxylin-eosin (H&E) histopathology images, which are commonly obtained during routine clinical practice. Our algorithm uses a deep learning model to first segment and classify different types of cell nuclei in H&E images. It then determines cellular ploidy based on the relative distance between identified hepatocyte nuclei and determines nuclear ploidy using a fitted Gaussian mixture model. The algorithm can establish the total number of hepatocytes and their detailed ploidy information in a region of interest (ROI) on H&E images. This is the first successful attempt to automate ploidy analysis on H&E images. Our algorithm is expected to serve as an important tool for studying the role of polyploidy in human liver disease.
Topics: Humans; Eosine Yellowish-(YS); Hematoxylin; Deep Learning; Liver; Ploidies; Polyploidy
PubMed: 37107679
DOI: 10.3390/genes14040921 -
Genome Biology Mar 2024Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for...
Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information, scAbsolute achieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome duplications. We demonstrate scAbsolute's capabilities using experimental cell multiplets, a FUCCI cell cycle expression system, and a benchmark against state-of-the-art methods. scAbsolute provides a robust foundation for single-cell DNA sequencing analysis across different technologies and has the potential to enable improvements in a number of downstream analyses.
Topics: Benchmarking; Cell Cycle; Cell Division; Ploidies; Sequence Analysis, DNA
PubMed: 38438920
DOI: 10.1186/s13059-024-03204-y