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Plants (Basel, Switzerland) Nov 2023Whole-genome duplication is a significant evolutionary mechanism in plants, with polyploid plants often displaying larger organs and enhanced adaptability to unfavorable...
A Comparative Analysis of Major Cell Wall Components and Associated Gene Expression in Autotetraploid and Its Donor Diploid Rice ( L.) under Blast and Salt Stress Conditions.
Whole-genome duplication is a significant evolutionary mechanism in plants, with polyploid plants often displaying larger organs and enhanced adaptability to unfavorable conditions compared to their diploid counterparts. The cell wall acts as a primary defense for plant cells against external stresses, playing an essential role in the plant's resistance to various stressors. In this study, we utilized both autotetraploid and its donor diploid rice ( L.) to analyze their phenotypic differences comparatively, the composition of key cell wall components, and the expression of related genes under normal conditions, as well as under stress from () and salt. Our findings indicated that autotetraploid rice exhibits significantly larger phenotypic characteristics under normal conditions than diploid rice. At the seedling stage, the lignin, cellulose, hemicellulose, and pectin levels in autotetraploid rice were markedly lower than in diploid rice. Additionally, 24 genes associated with major cell wall components showed differential expression between diploid and tetraploid rice. At the filling stage, the lignin and pectin content in autotetraploid rice were significantly higher than in diploid rice, while the levels of cellulose and hemicellulose were notably lower. Under stress or salt stress, autotetraploid rice showed smaller lesion areas and less wilting than diploid rice. The increased lignin content in autotetraploid rice under stress suggested a stronger adaptive capacity to adverse conditions. Compared to salt stress, stress induced more differential expression of genes related to major cell wall components. In this study, we explored the differences in the major cell wall components of diploid and homologous tetraploid rice under various treatment conditions. This study provides valuable insights into understanding the cell wall's adaptive mechanisms in autotetraploid rice when facing blast disease and salt stress, and it reveals the differential gene expression linked to these adaptive capabilities.
PubMed: 38068612
DOI: 10.3390/plants12233976 -
Nature Communications Apr 2024Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their...
Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.
Topics: Humans; Male; Prostatic Neoplasms; DNA Copy Number Variations; Single-Cell Analysis; Aneuploidy; Prostate; Clone Cells; Diploidy; Aged
PubMed: 38658552
DOI: 10.1038/s41467-024-47664-z -
Human Vaccines & Immunotherapeutics Dec 2023A serum-free, highly purified rabies vaccine produced in Vero cells is under development. The initial formulation, PVRV-NG, was evaluated in five Phase II studies and... (Randomized Controlled Trial)
Randomized Controlled Trial
Safety and immunogenicity of three dose levels of an investigational, highly purified Vero cell rabies vaccine: A randomized, controlled, observer-blinded, Phase II study with a simulated post-exposure regimen in healthy adults.
A serum-free, highly purified rabies vaccine produced in Vero cells is under development. The initial formulation, PVRV-NG, was evaluated in five Phase II studies and subsequently reformulated (PVRV-NG2). This multicenter, observer-blinded Phase II study investigated the safety and immune response of three different doses (antigen content) of PVRV-NG2 versus a licensed human diploid cell rabies vaccine (HDCV; Imovax rabies®). Healthy adults ( = 320) were randomized to receive PVRV-NG2 (low, medium, or high dose), PVRV-NG, or HDCV (2:2:2:1:1 ratio), according to a five-dose Essen simulated post-exposure regimen (Days [D] 0, 3, 7, 14, and 28). All participants received human rabies immunoglobulin intramuscularly on D0. Immunogenicity was assessed at D0, 14, 28, 42, and 6 months after the final injection using the rapid fluorescent focus inhibition test. Seroconversion rates were calculated as the percentage of participants achieving rabies virus neutralizing antibody titers ≥0.5 IU/mL. All analyses were descriptive. At each timepoint, geometric mean titers (GMTs) increased with antigen content (measured using an enzyme-linked immunosorbent assay). High-dose PVRV-NG2 GMTs were the highest at all timepoints, medium-dose PVRV-NG2 GMTs were similar to those with HDCV, and low-dose PVRV-NG2 GMTs were similar to PVRV-NG. The safety profile of PVRV-NG2 was comparable to PVRV-NG; however, fewer injection site reactions were reported with PVRV-NG2 or PVRV-NG (range 36.7-47.5%) than with HDCV (61.5%). This study demonstrated a dose-effect of antigen content at all timepoints. As post-exposure prophylaxis, the safety and immunogenicity profiles of the high-dose PVRV-NG2 group compared favorably with HDCV. Clinicaltrials.gov number: NCT03145766.
Topics: Animals; Chlorocebus aethiops; Humans; Adult; Rabies Vaccines; Rabies; Vero Cells; Rabies virus; Antibodies, Viral
PubMed: 37921410
DOI: 10.1080/21645515.2023.2275453 -
FEBS Open Bio Apr 2024The Egyptian Rousettus bat (Rousettus aegyptiacus) is a common fruit bat species that is distributed mainly in Africa and the Middle East. Bats serve as reservoir hosts...
The Egyptian Rousettus bat (Rousettus aegyptiacus) is a common fruit bat species that is distributed mainly in Africa and the Middle East. Bats serve as reservoir hosts for numerous pathogens. Human activities, such as hunting bats for food, managing vermin, and causing habitat loss, elevate the likelihood of transmission of bat pathogens to humans and other animals. Consequently, bat cell lines play a crucial role as research materials for investigating viral pathogens. However, the inherent limitation of finite cell division in primary cells necessitates the use of immortalized cells derived from various bat tissues. Herein, we successfully established six fibroblast cell lines derived from an infant bat heart and lungs and an elderly bat heart. Three of the six cell lines, called K4DT cells, were transduced by a combination of cell cycle regulators, mutant cyclin-dependent kinase 4, cyclin D1, and human telomerase reverse transcriptase. The other three cell lines, named SV40 cells, were transfected with simian virus 40 large T antigen. Transgene protein expression was detected in the transduced cells. All three K4DT cell lines and one lung-derived SV40 cell line were virtually immortalized and nearly maintained the normal diploid karyotypes. However, the two other heart-derived SV40 cell lines had aberrant karyotypes and the young bat-derived cell line stopped proliferating at approximately 40 population doublings. These bat cell lines are valuable for studying pathogen genomics and biology.
Topics: Animals; Humans; Aged; Chiroptera; Egypt; Cell Line
PubMed: 38373743
DOI: 10.1002/2211-5463.13781 -
Proceedings. Biological Sciences Feb 2024In bryophytes that alternate between haploid gametophytes and diploid sporophytes through sexual reproduction, sporophytes are often attached to and nurtured on the...
In bryophytes that alternate between haploid gametophytes and diploid sporophytes through sexual reproduction, sporophytes are often attached to and nurtured on the female gametophyte. A similar phenomenon is seen in Florideophyceae (a group of red algae). These systems in which a gametophyte (mother) invests nutrients in sporophytes (offspring) are ideal for studying the evolution of 'parental care' in non-animal organisms. Here, we propose a model of a haploid-diploid life cycle and examine the evolution of maternal investment in sporophytes focusing on two effects: the degree of paternal or maternal control of investment and the number of sporophytes. We find that when the female dominantly controls the investment, the evolutionarily stable level of investment is that which maximizes the expected reproductive success of the female gametophyte. The genomic conflict between maternal and paternal alleles complicates the evolutionary outcome; however, a greater male allelic effect and a higher number of sporophytes favour a higher energy investment, which may lead to evolutionary branching or run-away escalation of the investment level. This suggests that the selfishness of the paternal gene is the evolutionary driver of parental care and that complex structures such as fusion cells in red algae may have evolved to suppress it.
Topics: Diploidy; Haploidy; Plants; Bryophyta; Reproduction
PubMed: 38351800
DOI: 10.1098/rspb.2023.2351 -
PloS One 2023Recurrent polyploidization occurred in the evolutionary history of most Eukaryota. However, how neopolyploid detriment (sterility, gigantism, gene dosage imbalances) has...
Recurrent polyploidization occurred in the evolutionary history of most Eukaryota. However, how neopolyploid detriment (sterility, gigantism, gene dosage imbalances) has been overcome and even been bridged to evolutionary advantage (gene network diversification, mass radiation, range expansion) is largely unknown, particularly for animals. We used the parasitoid wasp Nasonia vitripennis, a rare insect system with heritable polyploidy, to begin addressing this knowledge gap. In Hymenoptera the sexes have different ploidies (haploid males, diploid females) and neopolyploids (diploid males, triploid females) occur for various species. Although such polyploids are usually sterile, those of N. vitripennis are reproductively capable and can even establish stable polyploid lines. To assess the effects of polyploidization, we compared a long-established polyploid line, the Whiting polyploid line (WPL) and a newly generated transformer knockdown line (tKDL) for fitness traits, absolute gene expression, and cell size and number. WPL polyploids have high male fitness and low female fecundity, while tKDL polyploids have poor male mate competition ability and high fertility. WPL has larger cells and cell number reduction, but the tKDL does not differ in this respect. Expression analyses of two housekeeping genes indicated that gene dosage is linked to sex irrespective of ploidy. Our study suggests that polyploid phenotypic variation may explain why some polyploid lineages thrive and others die out; a commonly proposed but difficult-to-test hypothesis. This documentation of diploid males (tKDL) with impaired competitive mating ability; triploid females with high fitness variation; and hymenopteran sexual dosage compensation (despite the lack of sex chromosomes) all challenges general assumptions on hymenopteran biology. We conclude that polyploidization is dependent on the duplicated genome characteristics and that genomes of different lines are unequally suited to survive diploidization. These results demonstrate the utility of N. vitripennis for delineating mechanisms of animal polyploid evolution, analogous to more advanced polyploid plant models.
Topics: Female; Male; Animals; Wasps; Triploidy; Polyploidy; Diploidy; Haploidy; Reproduction
PubMed: 37917617
DOI: 10.1371/journal.pone.0288278 -
Plant Biotechnology Journal Nov 2023Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to... (Review)
Review
Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to decipher their genome structures, evolutionary, and life secrets. Genome sequencing efforts showed that different cultivars, although Bt homeologs being more privileged in gene retention and gene expression. This subgenome bias, extended to sequence variation and point mutation, might be related to the long terminal repeat (LTR) explosions after tetraploidization, especially in At subgenomes. Except that, whole-genome sequences revealed many important genes, for example, fatty acids and triacylglycerols pathway, NBS-LRR (nucleotide-binding site-leucine-rich repeats), and seed size decision genes, were enriched after recursive polyploidization. Each ancestral polyploidy, with old ones having occurred hundreds of thousand years ago, has thousands of duplicated genes in extant genomes, contributing to genetic novelty. Notably, although full genome sequences are available, the actual At subgenome ancestor has still been elusive, highlighted with new debate about peanut origin. Although being an orphan crop lagging behind other crops in genomic resources, the genome sequencing achievement has laid a solid foundation for advancing crop enhancement and system biology research of peanut.
Topics: Arachis; Genome, Plant; Domestication; Chromosome Mapping; Biological Evolution; Polyploidy
PubMed: 37523347
DOI: 10.1111/pbi.14125 -
The Journal of Investigative Dermatology Nov 2023An effective healing response is critical to healthy aging. In particular, energy homeostasis has become increasingly recognized as a factor in effective skin...
An effective healing response is critical to healthy aging. In particular, energy homeostasis has become increasingly recognized as a factor in effective skin regeneration. ANT2 is a mediator of adenosine triphosphate import into mitochondria for energy homeostasis. Although energy homeostasis and mitochondrial integrity are critical for wound healing, the role played by ANT2 in the repair process had not been elucidated to date. In our study, we found that ANT2 expression decreased in aged skin and cellular senescence. Interestingly, overexpression of ANT2 in aged mouse skin accelerated the healing of full-thickness cutaneous wounds. In addition, upregulation of ANT2 in replicative senescent human diploid dermal fibroblasts induced their proliferation and migration, which are critical processes in wound healing. Regarding energy homeostasis, ANT2 overexpression increased the adenosine triphosphate production rate by activating glycolysis and induced mitophagy. Notably, ANT2-mediated upregulation of HSPA6 in aged human diploid dermal fibroblasts downregulated proinflammatory genes that mediate cellular senescence and mitochondrial damage. This study shows a previously uncharacterized physiological role of ANT2 in skin wound healing by regulating cell proliferation, energy homeostasis, and inflammation. Thus, our study links energy metabolism to skin homeostasis and reports, to the best of our knowledge, a previously unreported genetic factor that enhances wound healing in an aging model.
PubMed: 37211200
DOI: 10.1016/j.jid.2023.05.002 -
ELife Oct 2023Chromatin has been shown to undergo diffusional motion, which is affected during gene transcription by RNA polymerase activity. However, the relationship between...
Chromatin has been shown to undergo diffusional motion, which is affected during gene transcription by RNA polymerase activity. However, the relationship between chromatin mobility and other genomic processes remains unclear. Hence, we set out to label the DNA directly in a sequence unbiased manner and followed labeled chromatin dynamics in interphase human cells expressing GFP-tagged proliferating cell nuclear antigen (PCNA), a cell cycle marker and core component of the DNA replication machinery. We detected decreased chromatin mobility during the S-phase compared to G1 and G2 phases in tumor as well as normal diploid cells using automated particle tracking. To gain insight into the dynamical organization of the genome during DNA replication, we determined labeled chromatin domain sizes and analyzed their motion in replicating cells. By correlating chromatin mobility proximal to the active sites of DNA synthesis, we showed that chromatin motion was locally constrained at the sites of DNA replication. Furthermore, inhibiting DNA synthesis led to increased loading of DNA polymerases. This was accompanied by accumulation of the single-stranded DNA binding protein on the chromatin and activation of DNA helicases further restricting local chromatin motion. We, therefore, propose that it is the loading of replisomes but not their catalytic activity that reduces the dynamics of replicating chromatin segments in the S-phase as well as their accessibility and probability of interactions with other genomic regions.
Topics: Humans; Chromatin; DNA Replication; S Phase; Cell Cycle; DNA Helicases
PubMed: 37906089
DOI: 10.7554/eLife.87572 -
The Journal of Biological Chemistry May 2024About 18% of all human cancers carry a mutation in the KRAS gene making it among the most sought-after anticancer targets. However, mutant KRas protein has proved...
About 18% of all human cancers carry a mutation in the KRAS gene making it among the most sought-after anticancer targets. However, mutant KRas protein has proved remarkably undruggable. The recent approval of the first generation of RAS inhibitors therefore marks a seminal milestone in the history of cancer research. It also raises the predictable challenges of limited drug efficacies and acquired resistance. Hence, new approaches that improve our understanding of the tumorigenic mechanisms of oncogenic RAS within more physiological settings continue to be essential. Here, we have used the near-diploid hTERT RPE-1 cells to generate isogenic cell lines in which one of the endogenous KRAS alleles carries an oncogenic KRAS mutation at glycine 12. Cells with a KRAS, KRAS, or KRAS genotype, together with WT KRAS cells, reveal that oncogenic KRAS.G12X mutations increase cell proliferation rate and cell motility and reduced focal adhesions in KRAS cells. Epidermal growth factor -induced phosphorylation of ERK and AKT was comparable between KRAS, KRAS, KRAS, and KRAS cells. Interestingly, KRAS cells showed varying responses to distinct inhibitors with the KRAS and KRAS cells more sensitive to hydroxyurea and MEK inhibitors, U0126 and trametinib, but more resistant to PI3K inhibitor, PIK-90, than the KRAS cells. A combination of low doses of hydroxyurea and U0126 showed an additive inhibition on growth rate that was greater in KRAS than WT cells. Collectively, these cell lines will be a valuable resource for studying oncogenic RAS signaling and developing effective anti-KRAS reagents with minimum cytotoxicity on WT cells.
PubMed: 38796063
DOI: 10.1016/j.jbc.2024.107409