Effect Of Ploidy Research Articles

Ploidy influences cellular responses to gross chromosomal rearrangements in saccharomyces cerevisiae

BackgroundGross chromosomal rearrangements (GCRs) such as aneuploidy are key factors in genome evolution as well as being common features of human cancer. Their role in tumour initiation and progression has not yet been completely elucidated and the effects of additional chromosomes in cancer cells are still unknown. Most previous studies in which Saccharomyces cerevisiae has been used as a model for cancer cells have been carried out in the haploid context. To obtain new insights on the role of ploidy, the cellular effects of GCRs were compared between the haploid and diploid contexts.ResultsA total number of 21 haploid and diploid S. cerevisiae strains carrying various types of GCRs (aneuploidies, nonreciprocal translocations, segmental duplications and deletions) were studied with a view to determining the effects of ploidy on the cellular responses. Differences in colony and cell morphology as well as in the growth rates were observed between mutant and parental strains. These results suggest that cells are impaired physiologically in both contexts. We also investigated the variation in genomic expression in all the mutants. We observed that gene expression was significantly altered. The data obtained here clearly show that genes involved in energy metabolism, especially in the tricarboxylic acid cycle, are up-regulated in all these mutants. However, the genes involved in the composition of the ribosome or in RNA processing are down-regulated in diploids but up-regulated in haploids. Over-expression of genes involved in the regulation of the proteasome was found to occur only in haploid mutants.ConclusionThe present comparisons between the cellular responses of strains carrying GCRs in different ploidy contexts bring to light two main findings. First, GCRs induce a general stress response in all studied mutants, regardless of their ploidy. Secondly, the ploidy context plays a crucial role in maintaining the stoichiometric balance of the proteins: the translation rates decrease in diploid strains, whereas the excess protein synthesized is degraded in haploids by proteasome activity.

Genetic variation within and between populations of hermaphroditic Bulinus truncatus tetraploid freshwater snails of the Albertine Rift, East Africa

Genetic variability within and among Bulinus truncatus of the Albertine Rift freshwater bodies were assessed to investigate the degree of inbreeding and gene flow in the snail populations. The effect of ploidy on the genetic structuring of B. truncatus is also described. We characterized the genetic structure of seven B. truncatus populations from Lake Albert, Lake Kivu, and Katosho swamp in Tanzania using five polymorphic microsatellite loci. Genetic differentiation was quantified using pairwise FST values and Nei’s standard genetic distances. Different alleles were observed across all loci and genetic diversity was low although it varied greatly across populations; observed heterozygosity was, however, higher than the expected heterozygosity in three of the populations studied. Significant heterozygote deficiencies were observed coupled with significant linkage disequilibria in five populations for all the five loci examined in this study. We found significant genetic differentiation among the seven freshwater bodies; private alleles were observed across all loci indicating restricted or absence of gene flow between populations. Limited snail dispersal and the reproductive biology of B. truncatus are the major forces shaping the genetic variation observed. Low genetic variation within B. truncatus populations exposes them to a high parasite infection risk as predicted in the Red Queen hypothesis.

Effect of triploidy on growth and ionoregulatory performance in ocean-type Chinook salmon: A quantitative genetics approach

The use of triploid salmon for aquaculture is attractive as they do not mature sexually, limiting losses associated with poor flesh quality in mature fish and posing less genetic risk to wild stocks if they escape. Inconsistent survival and growth performance in triploid fish, however, has limited their implementation. In our study, ocean-type Chinook salmon (Oncorhynchus tshawytscha) were bred using replicated 3×3 factorial mating designs to create 18 families to test whether triploidization resulted in changes in growth and ionoregulation performance in freshwater and seawater. Eggs were pressure shocked after fertilization to create triploid offspring in a subset of each family. In spring, freshwater fish were sampled for size and gill Na+, K+-ATPase activity. Plasma chloride and cortisol were measured following a 24-h saltwater challenge. Growth performance was monitored for a further four months following transfer to sea water. We found significant effects of ploidy and sire (paternal effect) on smolt weight, as well as on gill Na+, K+-ATPase activity, although the latter did not correspond with performance in a 24-h saltwater challenge. Following four months of ocean growth, diploid animals were consistently larger, with greater circulating levels of insulin-like growth factor-1 than triploid sibs, although specific growth rates did not differ. Conversely, gill Na+, K+-ATPase activity at that time was significantly higher in triploid than diploid fish. When the phenotypic variance for the various traits was partitioned, triploids exhibited significantly greater additive genetic variance and maternal effects across all traits relative to diploid fish — indicating that gene dosage effects were primarily additive. The strong family effect indicates that genotype has a substantial role in determining the effects of ploidy manipulation on ionoregulatory and growth performance in Chinook salmon.

Effect of Stock Density and Ploidy in Jundia, Rhamdia quelen, Larvae Performance

The performance (growth and survival) of diploid and triploid jundia, Rhamdia quelen, was evaluated at six different stocking densities (10, 60, 110, 160, 210, 260 larvae/liter) during 31 days after rearing in an intensive larviculture system. Triploid fish exhibited a significantly higher survival rate than diploids at all stocking densities (27.1 ± 4.3% vs. 12.1 ± 3.3%; P < 0.01). Survival was not affected by stocking density (P > 0.05). Length gain was not affected by either ploidy or stocking density. Diploid fish gained more weight than triploids (P < 0.05), though this difference could result from lower fish densities in diploid treatments resulting from the higher mortality rate of diploid fish. This hypothesis is strengthened by the higher biomass present in triploid treatments (P < 0.01).

Transcript levels of ten caste-related genes in adult diploid males of Melipona quadrifasciata (Hymenoptera, Apidae): a comparison with haploid males, queens and workers

In Hymenoptera, homozygosity at the sex locus results in the production of diploid males. In social species, these pose a double burden by having low fitness and drawing resources normally spent for increasing the work force of a colony. Yet, diploid males are of academic interest as they can elucidate effects of ploidy (normal males are haploid, whereas the female castes, the queens and workers, are diploid) on morphology and life history. Herein we investigated expression levels of ten caste-related genes in the stingless bee Melipona quadrifasciata, comparing newly emerged and 5-day-old diploid males with haploid males, queens and workers. In diploid males, transcript levels for dunce and paramyosin were increased during the first five days of adult life, while those for diacylglycerol kinase and the transcriptional co-repressor groucho diminished. Two general trends were apparent, (i) gene expression patterns in diploid males were overall more similar to haploid ones and workers than to queens, and (ii) in queens and workers, more genes were up-regulated after emergence until day five, whereas in diploid and especially so in haploid males more genes were down-regulated. This difference between the sexes may be related to longevity, which is much longer in females than in males.

Ploidy effects on hatchery survival, deformities, and performance in Atlantic salmon ( Salmo salar)

The production of sterile triploid Atlantic salmon ( Salmo salar) may help address the increasing pressure on the industry to reduce potential breeding between farmed escapees and wild fish populations. However, many previous studies have observed poor performance at sea in triploid stocks (growth, survival, and deformity). This may result from poor early hatchery performance and a strong parental effect. Therefore, in the present study, two year classes (2007 and 2008) of mixed sex fish were created (10 males:10 females) to examine ploidy interactions on hatchery performance. Egg batches were divided in two at fertilisation with one group subjected to a hydrostatic pressure shock to induce triploidy. Triploid rate was confirmed at 100% in all groups, verified by red blood cell nucleus length measurements. Survival to hatch did not differ between ploidy. However, reduced survival was found to strongly correlate with gamete quality. During the hatchery phase ploidy significantly affected size at hatch, with diploids generally larger than triploids. Growth advantage of diploids over triploids was only maintained for 6 weeks post-first feeding, with triploids generally out-growing their diploid siblings by the end of the hatchery phase. Deformity prevalence in first feeding stages was generally low (mean < 2%), with no overall effect of ploidy. Our findings show that triploid salmon can perform as well if not better than their diploid siblings. The low incidence of deformity during the hatchery and freshwater phases is also a significant improvement over previous reports in triploid salmon stocks.

Responses of diploid and triploid Pacific oysters Crassostrea gigas to Vibrio infection in relation to their reproductive status

Several Vibrio species are known to be pathogenic to the Pacific oyster Crassostrea gigas. Survival varies according to pathogen exposure and high mortality events usually occur in summer during gametogenesis. In order to study the effects of gametogenetic status and ploidy (a factor known to affect reproduction allocation in oysters) on vibriosis survival, we conducted two successive experiments. Our results demonstrate that a common bath challenge with pathogenic Vibrio splendidus and Vibrio aestuarianus on a mixture of mature, spawning and non-mature oysters can lead to significant mortality. Previous bath challenges, which were done using only non-mature oysters, had not produced mortality. Immunohistochemical analyses showed the affinity of Vibrio for gonadic tissues, highlighting the importance of sexual maturity for vibriosis infection processes in oysters. Mortality rate results showed poor repeatability between tanks, however, in this bath challenge. We then tested a standardized and repeatable injection protocol using two different doses of the same combination of two Vibrio species on related diploid and triploid oysters at four different times over a year. Statistical analyses of mortality kinetics over a 6-day period after injection revealed that active gametogenesis periods correspond to higher susceptibility to vibriosis and that there is a significant interaction of this seasonal effect with ploidy. However, no significant advantage of triploidy was observed. Triploid oysters even showed lower survival than diploid counterparts in winter. Results are discussed in relation to differing energy allocation patterns between diploid and triploid Pacific oysters.

The effect of ploidy and sexual maturation on the resistance of erythrocytes to haemolysis in rainbow trout ( Oncorhynchus mykiss)

The abilities of triploid and diploid red blood cells to face an osmotic challenge were investigated. Erythrocytes from triploid rainbow trout were significantly more resistant to osmotic lysis than those from immature diploids of the same age. This observation could be related to the initial cell's shape and size and to the difference in cell surface area-to-volume ratio. Comparison of changes in intracellular ionic concentration (K +, Cl −) associated with cell volume regulatory processes did not indicate any mechanistic explanation for this difference in osmotic resistance. This difference gradually disappeared during diploid sexual maturation. The early acquisition of high resistance to haemolysis by triploid erythrocytes is surprising since diploids appear to require time consuming and complex physiological changes to achieve a similar capability. Therefore, triploid cells appear as interesting models for investigation into cell physiology.

EVALUATION OF ELEVATED PLOIDY AND ASEXUAL REPRODUCTION AS ALTERNATIVE EXPLANATIONS FOR GEOGRAPHIC PARTHENOGENESIS IN EUCYPRIS VIRENS OSTRACODS

Transitions from sexual to asexual reproduction are often coupled with elevations in ploidy. As a consequence, the importance of ploidy per se for the maintenance and spread of asexual populations is unclear. To examine the effects of ploidy and asexual reproduction as independent determinants of the success of asexual lineages, we sampled diploid sexual, diploid asexual, and triploid asexual Eucypris virens ostracods across a European wide range. Applying nuclear and mitochondrial markers, we found that E. virens consists of genetically highly differentiated diploid sexual populations, to the extent that these sexual clades could be considered as cryptic species. All sexual populations were found in southern Europe and North Africa and we found that both diploid asexual and triploid asexual lineages have originated multiple times from several sexual lineages. Therefore, the asexual lineages show a wide variety of genetic backgrounds and very strong population genetic structure across the wide geographic range. Finally, we found that triploid, but not diploid, asexual clones dominate habitats in northern Europe. The limited distribution of diploid asexual lineages, despite their shared ancestry with triploid asexual lineages, strongly suggests that the wider geographic distribution of triploids is due to elevated ploidy rather than to asexuality.

Effects of Ploidy and Recombination on Evolution of Robustness in a Model of the Segment Polarity Network

Many genetic networks are astonishingly robust to quantitative variation, allowing these networks to continue functioning in the face of mutation and environmental perturbation. However, the evolution of such robustness remains poorly understood for real genetic networks. Here we explore whether and how ploidy and recombination affect the evolution of robustness in a detailed computational model of the segment polarity network. We introduce a novel computational method that predicts the quantitative values of biochemical parameters from bit sequences representing genotype, allowing our model to bridge genotype to phenotype. Using this, we simulate 2,000 generations of evolution in a population of individuals under stabilizing and truncation selection, selecting for individuals that could sharpen the initial pattern of engrailed and wingless expression. Robustness was measured by simulating a mutation in the network and measuring the effect on the engrailed and wingless patterns; higher robustness corresponded to insensitivity of this pattern to perturbation. We compared robustness in diploid and haploid populations, with either asexual or sexual reproduction. In all cases, robustness increased, and the greatest increase was in diploid sexual populations; diploidy and sex synergized to evolve greater robustness than either acting alone. Diploidy conferred increased robustness by allowing most deleterious mutations to be rescued by a working allele. Sex (recombination) conferred a robustness advantage through “survival of the compatible”: those alleles that can work with a wide variety of genetically diverse partners persist, and this selects for robust alleles.

Microsatellite instability and DNA ploidy in colorectal cancer

Appropriate stratification tools for targeted surveillance after resection for colorectal cancer (CRC) are lacking. The objective of the current study was to investigate the effect of microsatellite instability (MSI) and DNA ploidy on surveillance after surgery. The authors evaluated 186 consecutive, population-based patients with stage I through III CRC who underwent surgery with curative intent and who entered a systematic surveillance program. MSI was analyzed with polymerase chain reaction for 5 known quasimonomorphic markers (BAT-26, BAT-25, NR-21, NR-24, and NR-27), and DNA ploidy was analyzed with automated cytometry. Recurrence, recurrence-free survival (RFS), and disease-specific survival (DSS) were evaluated by univariate and multivariate statistical tests. Patients with MSI (20%) were significantly younger than patients without MSI (median age, 61 years vs 67 years; P=.016). Proximal location (adjusted odds ratio [AOR], 5.4; 95% confidence interval [95% CI], 2.1-14.1 [P=.001]), large tumor size (>or=5 cm: AOR, 3.5; 95% CI, 1.3-9.6 [P=.015]), and poor tumor differentiation (AOR, 6.6; 95% CI, 2-21.8 [P=.002]) were associated with MSI. MSI conveyed an increased risk for locoregional recurrence (OR, 2.9; 95% CI, 1.2-7 [P=.016]), with a trend toward a shorter time to recurrence (P=.060). Neither MSI status nor DNA ploidy predicted distant metastasis, RFS, or DSS. Lymph node status was the best predictor of distant spread (AOR, 3.9; 95% CI, 2-7.9 [P<.001]) and DSS (hazard ratio, 4.9; 95% CI, 2.6-9 [P<.001]). Patients who had microsatellite instable tumors were at increased risk for locoregional recurrence, whereas lymph node status was the best predictor of distant metastasis. Clinical surveillance and choice of modality (ie, endoscopy vs radiologic imaging) may be improved when patients are stratified according to these cancer features.

Comparative growth performances of diploid and triploid Chinese shrimp Fenneropenaeus chinensis (Osbeck, 1765) under different salinities

This study aimed at evaluating the ploidy effects on growth performances of Chinese shrimp (Fenneropenaeus chinensis Osbeck, 1765) reared in different salinities under laboratory conditions. In the acute salinity experiment, there was no difference (P > 0.05) in tolerance observed in triploid and diploid shrimp due to abrupt salinity changes. The lethal salinity for 50% of the individuals in 96 h at 23-25 degrees C was about 2 g L(-1) in both triploids and diploids. While for the chronic salinity experiment, statistical analyses confirmed that the differences in growth performances including the specific growth rate (SGR), the feeding rate (FR), feed conversion efficiency (FCE) and intermoult period (IP) between triploid and diploid were related to salinity. Diploid shrimp reared in 20 g L(-1) exhibited highest SGR (P < 0.05), while triploids performed well in 20 and 30 g L(-1) salinities (P < 0.05). Based on the survival and growth data, the optimal salinity for the culture of diploid F. chinensis should be 20 g L(-1) and for triploids it should be between 20 and 30 g L(-1).

The ploidy effects in plant gene expression: Progress, problems and prospects

Polyploidy and haploid are widely employed in the studies of genetics and evolution, and great progress has been made in these fields, inspiring the enthusiasm of scientists to explore the ploidy effects in gene expression. In this paper, we review the gene expression and its regulation in polyploids, especially in autopolyploids. We summarize some limitations in previous reports on polyploidy gene expression and its regulation, especially the limitations in the research materials. We propose an idea to create homologous ploidy series with twin-seedlings and to employ high-throughput techniques to investigate the polyploidy transcriptome and its regulation.

Indirect Effects of Ploidy Suggest X Chromosome Dose, Not the X:A Ratio, Signals Sex in Drosophila

In the textbook view, the ratio of X chromosomes to autosome sets, X:A, is the primary signal specifying sexual fate in Drosophila. An alternative idea is that X chromosome number signals sex through the direct actions of several X-encoded signal element (XSE) proteins. In this alternative, the influence of autosome dose on X chromosome counting is largely indirect. Haploids (1X;1A), which possess the male number of X chromosomes but the female X:A of 1.0, and triploid intersexes (XX;AAA), which possess a female dose of two X chromosomes and the ambiguous X:A ratio of 0.67, represent critical tests of these hypotheses. To directly address the effects of ploidy in primary sex determination, we compared the responses of the signal target, the female-specific SxlPe promoter of the switch gene Sex-lethal, in haploid, diploid, and triploid embryos. We found that haploids activate SxlPe because an extra precellular nuclear division elevates total X chromosome numbers and XSE levels beyond those in diploid males. Conversely, triploid embryos cellularize one cycle earlier than diploids, causing premature cessation of SxlPe expression. This prevents XX;AAA embryos from fully engaging the autoregulatory mechanism that maintains subsequent Sxl expression, causing them to develop as sexual mosaics. We conclude that the X:A ratio predicts sexual fate, but does not actively specify it. Instead, the instructive X chromosome signal is more appropriately seen as collective XSE dose in the early embryo. Our findings reiterate that correlations between X:A ratios and cell fates in other organisms need not implicate the value of the ratio as an active signal.

Differential attack on diploid, tetraploid, and hexaploid Solidago altissima L. by five insect gallmakers

Genetic variation among plants can influence host choice and larval performance in insect herbivores. Ploidy (cytotype) variation is a particularly dramatic form of plant genetic variation, and where diploid and polyploid cytotypes of a species occur in sympatry, they may provide herbivores with choices that are distinguished by profound and genome-wide genetic differences. We tested for non-random attack by five gallmaking insect herbivores on diploid, tetraploid, and hexaploid cytotypes of the goldenrod Solidago altissima L., working in seven midwestern US populations where the ploidies co-occur on spatial scales relevant to insect host choice. For four of the five herbivores, attack was non-random with respect to ploidy at one or more sites. Ploidy effects on attack were complex: the ploidy subjected to highest attack varied both across herbivores within sites and (for most herbivores) across sites within herbivores. Ploidy effects on attack will alter rates of encounter between insect herbivores-either increasing or decreasing the likelihood of two herbivores sharing a host plant ramet, compared with the case with no effects of ploidy. Plant ploidy variation appears likely to have a major impact on insect community organization, and perhaps on plant-herbivore coevolution, but that impact is likely to be spatially heterogeneous.

Flesh qualities and muscle fiber characteristics in triploid and diploid rainbow trout

Summary Analyzed with regard to their slaughter weights and flesh quality 78-month-old diploid and triploid rainbow trout (full sibs) were reared together in a pond after tagging at an age of 12 months. Triploids had higher body weights and carcass percentages than diploids (6 kg vs 4 kg and 66% vs 52%). Triploid fish also displayed lower electrical conductivity values and darker (L* value) and redder (a* value) flesh color. The fillets of the triploid trout contained more crude fat and less moisture than the diploids (6% vs 3% and 68% vs 74%, respectively). No effect of ploidy was found with regard to the protein contents. Triploid rainbow trout had larger mean white and intermediate muscle fiber areas than diploid fish in the dorsal and pelvic fin regions. In the pelvic fin part, the white muscle fiber areas were larger than in the dorsal fin part. In conclusion, adult triploid rainbow trout grow faster especially by fiber hypertrophy and have better flesh quality parameters than diploid fish.

The influence of ploidy on saltwater adaptation, acute stress response and immune function following seawater transfer in non-smolting rainbow trout

We investigated the effect of ploidy on osmoregulatory, stress and immune responses in non-smolting rainbow trout during saltwater adaptation. Sibling groups of diploid and triploid trout were acclimated in freshwater (FW) and then subjected to abrupt transfer to full strength (35 ppt) saltwater (SW) or back to FW. Fish were sampled pre-stress, and 1, 3, 6, 12, 24, 48, 72 and 168 h post-stress. Overall mortality in SW was less than 5% in either ploidy, with no mortality in FW. Significant elevations in plasma osmolality and gill ATPase were observed within 1–3 h of SW transfer, but retuned to basal levels within 72 h indicative of rapid saltwater adaptation and did not differ between ploidy. Furthermore, FW–SW transfer also caused significant and sustained elevations in total blood haemoglobin, plasma IGF-I, cortisol, glucose, total white blood cell counts, increased plasma but decreased mucus lysozyme, and enhanced head kidney macrophage respiratory burst activity. Conversely, FW–FW transfer evoked more transient and less elevated responses, more typical of primary and secondary responses to a single stressor. We conclude that the more elevated levels in these parameters are a function of saltwater adaptation as well as the generic stress response, and that this did not differ between ploidy. Strong positive correlations were found between plasma IGF-I and cortisol, and with osmolality, glucose and WBC, while a negative correlation was found with plasma lysozyme irrespective of ploidy. Overall, the current results suggest that triploidy does not affect the ability of non-smolting trout to adapt to full strength seawater under optimum conditions, and that the osmotic and stress response to such transfer is similar to diploids.

Effect of triploidy on quality traits of shi drum (Umbrina cirrosa L.) until the second rearing year

Carcass and flesh morphometric, reological and chemical traits of triploid (3n) and diploid (2n) shi drum (Umbrina cirrosa L.) were evaluated through 7 months. Three age groups, 17-, 21- and 24-month-old fish, were investigated. The effects of ploidy were statistically evaluated and the weight of fish was included in the model as a covariate because triploids grew less than diploids. As expected, fish weight was found to be significantly correlated with all the investigated morphometric traits, but showed a negative correlation with some chemical (pH) and colour traits (lightness) of raw fillet. In comparison with controls, triploid shi drums were characterized by different morphological traits that involved a slender body shape. In triploids, a reduction in condition factor, backbone weight, dressing index and an increase in the agility index were also recorded. When the commercial size (i.e. over 300 g) was achieved, triploids exhibited larger coelomatic and fillet (dorsal white muscle) fat deposition than diploids. Among reological traits, colour and texture were affected by ploidy; raw fillet lightness and cooked flesh tenderness were higher among triploids in all the investigated age groups. As fish were fed with a restricted feeding regimen, fillet fat deposition was supposed to be limited. Thus, the effects of ploidy on reological traits may be only partially explained by lipid fillet amount and are supposed to be more related to different fibre muscle architecture.

P-233: Oct3A and Oct3B immunostaining patterns in human 3PN zygotes and aneuploid embryos diagnosed by preimplantation genetic diagnosis (PGD): Embryonic chromosome status can be independent of developmental competence

The effects of ploidy and the parental genome composition on Oct-4 expression was previously studied in murne parthenogenic embryos and suggested that Oct-4 is necessary but not sufficient for developmental potency. The impact of parental genome on Oct-4 expression of human preimplantation embryos requires elucidation. To address the issue, we assessed Oct3A and Oct3B protein patterns in human embryos that developed from 3 pronuclear (3PN) zygotes or embryos with chromosome anomalies as diagnosed by PGD.

Defining Ploidy-Specific Thresholds in Array Comparative Genomic Hybridization to Improve the Sensitivity of Detection of Single Copy Alterations in Cell Lines

Array comparative genomic hybridization (CGH) is being widely used to screen for recurrent genomic copy number alterations in neoplasms, with imbalances typically detected through the application of gain and loss thresholds. Review of array CGH publications for the year 2005 showed that a wide range of thresholds are used. However, the effect of sample ploidy on the sensitivity of these thresholds for single copy alterations (SCAs) has not been evaluated. Here, we describe a method to evaluate the detection accuracy of thresholds for detecting SCAs in cell line array CGH data. By applying a hidden Markov model-based method, we segmented array CGH data from well-karyotyped cell lines and generated ploidy-specific sensitivity-specificity plots, from which we identified optimum thresholds relevant to sample ploidy. We demonstrate that commonly used nonploidy-specific thresholds are suboptimal in their ability to call SCAs, particularly when applied to hypertriploid or tetraploid cell lines. We conclude that the use of ploidy-specific thresholds improves the sensitivity of thres-hold-based array CGH for detecting SCAs in cell lines. Because polyploidy is a common feature of cancer cells, the application of ploidy-specific thresholds to cell lines (and potentially to clinical samples) may improve the detection sensitivity of SCAs of biological significance.