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International Journal of Molecular... May 2024The increase in atmospheric CO concentration is a significant factor in triggering global warming. CO is essential for plant photosynthesis, but excessive CO can...
The increase in atmospheric CO concentration is a significant factor in triggering global warming. CO is essential for plant photosynthesis, but excessive CO can negatively impact photosynthesis and its associated physiological and biochemical processes. The tetraploid L., a superior and improved variety, exhibits high tolerance to abiotic stress. In this study, we investigated the physiological and proteomic response mechanisms of the tetraploid under high CO treatment. The results of our physiological and biochemical analyses revealed that a 5% high concentration of CO hindered the growth and development of the tetraploid and caused severe damage to the leaves. Additionally, it significantly reduced photosynthetic parameters such as n, s, r, and i, as well as respiration. The levels of chlorophyll (Chl a and b) and the fluorescent parameters of chlorophyll (, /, P, and ) also significantly decreased. Conversely, the levels of ROS (HO and O) were significantly increased, while the activities of antioxidant enzymes (SOD, CAT, GR, and APX) were significantly decreased. Furthermore, high CO induced stomatal closure by promoting the accumulation of ROS and NO in guard cells. Through a proteomic analysis, we identified a total of 1652 DAPs after high CO treatment. GO functional annotation revealed that these DAPs were mainly associated with redox activity, catalytic activity, and ion binding. KEGG analysis showed an enrichment of DAPs in metabolic pathways, secondary metabolite biosynthesis, amino acid biosynthesis, and photosynthetic pathways. Overall, our study provides valuable insights into the adaptation mechanisms of the tetraploid to high CO.
Topics: Carbon Dioxide; Robinia; Tetraploidy; Photosynthesis; Proteomics; Chlorophyll; Plant Proteins; Proteome; Plant Leaves; Reactive Oxygen Species; Gene Expression Regulation, Plant; Stress, Physiological; Antioxidants
PubMed: 38791300
DOI: 10.3390/ijms25105262 -
Genes May 2024Genomic imbalance in aneuploidy is often detrimental to organisms. To gain insight into the molecular basis of aneuploidies in humans, we analyzed transcriptome data...
Genomic imbalance in aneuploidy is often detrimental to organisms. To gain insight into the molecular basis of aneuploidies in humans, we analyzed transcriptome data from several autosomal and sex chromosome aneuploidies. The results showed that in human aneuploid cells, genes located on unvaried chromosomes are inversely or proportionally -modulated, while a subset of genes on the varied chromosomes are compensated. Less genome-wide modulation is found for sex chromosome aneuploidy compared with autosomal aneuploidy due to X inactivation and the retention of dosage sensitive regulators on both sex chromosomes to limit the effective dosage change. We also found that lncRNA and mRNA can have different responses to aneuploidy. Furthermore, we analyzed the relationship between dosage-sensitive transcription factors and their targets, which illustrated the modulations and indicates genomic imbalance is related to stoichiometric changes in components of gene regulatory complexes.In summary, this study demonstrates the existence of -acting effects and compensation mechanisms in human aneuploidies and contributes to our understanding of gene expression regulation in unbalanced genomes and disease states.
Topics: Humans; Aneuploidy; Gene Expression Regulation; RNA, Long Noncoding; Dosage Compensation, Genetic; Transcriptome; Transcription Factors; Genome, Human
PubMed: 38790266
DOI: 10.3390/genes15050637 -
Genes Apr 2024Genome-wide prenatal cell-free DNA (cfDNA) screening can be used to screen for a wide range of fetal chromosomal anomalies in pregnant patients. In this study, we...
Genome-wide prenatal cell-free DNA (cfDNA) screening can be used to screen for a wide range of fetal chromosomal anomalies in pregnant patients. In this study, we describe our clinical experience with a genome-wide cfDNA assay in screening for common trisomies, sex chromosomal aneuploidies (SCAs), rare autosomal aneuploidies (RAAs), and copy-number variations (CNVs) in about 6000 patients over a three-year period at our hospital's Prenatal Diagnostic Unit in Spain. Overall, 204 (3.3%) patients had a high-risk call, which included 76 trisomy 21, 21 trisomy 18, 7 trisomy 13, 29 SCAs, 31 RAAs, 31 CNVs, and 9 cases with multiple anomalies. The diagnostic outcomes were obtained for the high-risk cases when available, allowing for the calculation of positive predictive values (PPVs). Calculated PPVs were 95.9% for trisomy 21, 77.8% for trisomy 18, 66.7% for trisomy 13, 10.7% for RAAs, and 10.7% for CNVs. Pregnancy and birth outcomes were also collected for the majority of RAA and CNV cases. Adverse perinatal outcomes for some of these cases included preeclampsia, fetal growth restriction, preterm birth, reduced birth weight, and major congenital structural abnormalities. In conclusion, our study showed strong performance for genome-wide cfDNA screening in a large cohort of pregnancy patients in Spain.
Topics: Humans; Female; Pregnancy; Spain; Cell-Free Nucleic Acids; Adult; DNA Copy Number Variations; Prenatal Diagnosis; Trisomy; Chromosome Disorders; Aneuploidy; Noninvasive Prenatal Testing
PubMed: 38790198
DOI: 10.3390/genes15050568 -
Genes Apr 2024Cellular senescence is an irreversible growth arrest that acts as a barrier to cancer initiation and progression. Histone alteration is one of the major events during...
Cellular senescence is an irreversible growth arrest that acts as a barrier to cancer initiation and progression. Histone alteration is one of the major events during replicative senescence. However, little is known about the function of H3.3 in cellular senescence. Here we found that the downregulation of H3.3 induced growth suppression with senescence-like phenotypes such as senescence-associated heterochromatin foci (SAHF) and β-galactosidase (SA-β-gal) activity. Furthermore, H3.3 depletion induced senescence-like phenotypes with the p53/p21-depedent pathway. In addition, we identified miR-22-3p, tumor suppressive miRNA, as an upstream regulator of the (H3 histone, family 3B) gene which is the histone variant H3.3 and replaces conventional H3 in active genes. Therefore, our results reveal for the first time the molecular mechanisms for cellular senescence which are regulated by H3.3 abundance. Taken together, our studies suggest that H3.3 exerts functional roles in regulating cellular senescence and is a promising target for cancer therapy.
Topics: Cellular Senescence; Humans; Histones; Tumor Suppressor Protein p53; Fibroblasts; MicroRNAs; Diploidy; Down-Regulation; Heterochromatin
PubMed: 38790171
DOI: 10.3390/genes15050543 -
New Biotechnology Sep 2024Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of...
Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.
Topics: Metabolic Engineering; Beer; Saccharomyces; Flavoring Agents; Saccharomyces cerevisiae
PubMed: 38788897
DOI: 10.1016/j.nbt.2024.05.006 -
Biology Apr 2024This study aimed to understand the differences in the performance of diploid and tetraploid daylily cultivars under water deficit conditions, which are essential...
This study aimed to understand the differences in the performance of diploid and tetraploid daylily cultivars under water deficit conditions, which are essential indicators of drought tolerance. This research revealed that tetraploid daylilies performed better than diploid varieties in arid conditions due to their enhanced adaptability and resilience to water deficit conditions. The analysis of the results highlighted the need to clarify the specific physiological and molecular mechanisms underlying the enhanced drought tolerance observed in tetraploid plants compared to diploids. This research offers valuable knowledge for improving crop resilience and sustainable floricultural practices in changing environmental conditions. The morphological and physiological parameters were analyzed in 19 diploid and 21 tetraploid daylily cultivars under controlled water deficit conditions, and three drought resistance groups were formed based on the clustering of these parameters. In a high drought resistance cluster, 93.3% tetraploid cultivars were exhibited. This study demonstrates the significance of ploidy in shaping plant responses to drought stress. It emphasizes the importance of studying plant responses to water deficit in landscape horticulture to develop drought-tolerant plants and ensure aspects of climate change.
PubMed: 38785771
DOI: 10.3390/biology13050289 -
The Journal of Cell Biology Sep 2024Maintenance of ploidy depends on the mitotic kinase Aurora B, the catalytic subunit of the chromosomal passenger complex (CPC) whose proficient activity is supported by...
Maintenance of ploidy depends on the mitotic kinase Aurora B, the catalytic subunit of the chromosomal passenger complex (CPC) whose proficient activity is supported by HP1 enriched at inner centromeres. HP1 is known to associate with INCENP of the CPC in a manner that depends on the PVI motif conserved across HP1 interactors. Here, we found that the interaction of INCENP with HP1 requires not only the PVI motif but also its C-terminally juxtaposed domain. Remarkably, these domains conditionally fold the β-strand (PVI motif) and the α-helix from a disordered sequence upon HP1 binding and render INCENP with high affinity to HP1. This bipartite binding domain termed SSH domain (Structure composed of Strand and Helix) is necessary and sufficient to attain a predominant interaction of HP1 with INCENP. These results identify a unique HP1-binding module in INCENP that ensures enrichment of HP1 at inner centromeres, Aurora B activity, and thereby mitotic fidelity.
Topics: Humans; Aurora Kinase B; Binding Sites; Centromere; Chromobox Protein Homolog 5; Chromosomal Proteins, Non-Histone; HeLa Cells; Mitosis; Protein Binding
PubMed: 38781028
DOI: 10.1083/jcb.202312021 -
Reproductive Biology and Endocrinology... May 2024The best method for selecting embryos ploidy is preimplantation genetic testing for aneuploidies (PGT-A). However, it takes more labour, money, and experience. As such,...
BACKGROUND
The best method for selecting embryos ploidy is preimplantation genetic testing for aneuploidies (PGT-A). However, it takes more labour, money, and experience. As such, more approachable, non- invasive techniques were still needed. Analyses driven by artificial intelligence have been presented recently to automate and objectify picture assessments.
METHODS
In present retrospective study, a total of 3448 biopsied blastocysts from 979 Time-lapse (TL)-PGT cycles were retrospectively analyzed. The "intelligent data analysis (iDA) Score" as a deep learning algorithm was used in TL incubators and assigned each blastocyst with a score between 1.0 and 9.9.
RESULTS
Significant differences were observed in iDAScore among blastocysts with different ploidy. Additionally, multivariate logistic regression analysis showed that higher scores were significantly correlated with euploidy (p < 0.001). The Area Under the Curve (AUC) of iDAScore alone for predicting euploidy embryo is 0.612, but rose to 0.688 by adding clinical and embryonic characteristics.
CONCLUSIONS
This study provided additional information to strengthen the clinical applicability of iDAScore. This may provide a non-invasive and inexpensive alternative for patients who have no available blastocyst for biopsy or who are economically disadvantaged. However, the accuracy of embryo ploidy is still dependent on the results of next-generation sequencing technology (NGS) analysis.
Topics: Humans; Aneuploidy; Deep Learning; Retrospective Studies; Female; Preimplantation Diagnosis; Adult; Pregnancy; Blastocyst; Genetic Testing; Fertilization in Vitro
PubMed: 38778410
DOI: 10.1186/s12958-024-01230-w -
BMC Plant Biology May 2024Glehnia littoralis is a medicinal and edible plant species having commercial value and has several hundred years of cultivation history. Polyploid breeding is one of the...
BACKGROUND
Glehnia littoralis is a medicinal and edible plant species having commercial value and has several hundred years of cultivation history. Polyploid breeding is one of the most important and fastest ways to generate novel varieties. To obtain tetraploids of G. littoralis in vitro, colchicine treatment was given to the seeds and then were screened based on morphology, flow cytometry, and root tip pressing assays. Furthermore, transcriptome analysis was performed to identity the differentially expressed genes associated with phenotypic changes in tetraploid G. littoralis.
RESULTS
The results showed that 0.05% (w/v) colchicine treatment for 48 h was effective in inducing tetraploids in G. littoralis. The tetraploid G. littoralis (2n = 4x = 44) was superior in leaf area, leaf thickness, petiole diameter, SPAD value (Chl SPAD), stomatal size, epidermal tissues thickness, palisade tissues thickness, and spongy tissues thickness to the diploid ones, while the stomatal density of tetraploids was significantly lower. Transcriptome sequencing revealed, a total of 1336 differentially expressed genes (DEGs) between tetraploids and diploids. Chromosome doubling may lead to DNA content change and gene dosage effect, which directly affects changes in quantitative traits, with changes such as increased chlorophyll content, larger stomata and thicker tissue of leaves. Several up-regulated DEGs were found related to growth and development in tetraploid G. littoralis such as CKI, PPDK, hisD and MDP1. KEGG pathway enrichment analyses showed that most of DEGs were enriched in metabolic pathways.
CONCLUSIONS
This is the first report of the successful induction of tetraploids in G. littoralis. The information presented in this study facilitate breeding programs and molecular breeding of G. littoralis varieties.
Topics: Tetraploidy; Gene Expression Profiling; Phenotype; Transcriptome; Colchicine; Caryophyllales; Gene Expression Regulation, Plant; Plant Leaves
PubMed: 38778255
DOI: 10.1186/s12870-024-05154-w -
Nature Jun 2024Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions and allows the generalizability of laboratory findings to be...
Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions and allows the generalizability of laboratory findings to be assessed. One notable discovery made in natural isolates of Saccharomyces cerevisiae is that aneuploidy-an imbalance in chromosome copy numbers-is frequent (around 20%), which seems to contradict the substantial fitness costs and transient nature of aneuploidy when it is engineered in the laboratory. Here we generate a proteomic resource and merge it with genomic and transcriptomic data for 796 euploid and aneuploid natural isolates. We find that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins-especially subunits of protein complexes-show reduced expression, but the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage compensated, and average protein levels are shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and shows the utility of exploiting the natural diversity of species to attain generalizable molecular insights into complex biological processes.
Topics: Aneuploidy; Dosage Compensation, Genetic; Genetic Variation; Proteasome Endopeptidase Complex; Proteolysis; Proteome; Proteomics; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Ubiquitination; Gene Expression Profiling; Genomics
PubMed: 38778096
DOI: 10.1038/s41586-024-07442-9