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PubMedDate not supplied

Improved estimation of the proportion of triploids in populations with diploid and triploid individuals.

We consider the estimation of the proportion of triploids in populations of plants or animals in which diploid and triploid individuals coexist, using data from electrophoretic analysis of isozyme or microsatellite markers. Individuals that have three distinct alleles at a locus are unambiguously triploid. However, other individuals cannot be classified with certainty as diploid or triploid, unless allelic dosage can be determined reliably. This is impossible for microsatellite markers, and for many isozyme markers. We therefore present a maximum likelihood method of estimating the proportion of triploids based only on the presence or absence of different alleles.

Alleles↗

PubMed2006

Mechanisms and rates of birth and death of dispersed duplicated genes during the evolution of a multigene family in diploid and tetraploid wheats.

A family of 5 genes that evolved within the past 1.9 Myr in diploid wheat was characterized. The ancestral gene, ALP-A1, is on chromosome 1A and encodes an aci-reductone dioxygenase-like protein. The duplicated genes ALP-A2, ALP-A3, ALP-A4.1, and ALP-A4.2 acquired complete coding sequences but lost the original promoter. They are on chromosomes 4A, 2A, 6A and 6A, respectively, and evolved sequentially, the youngest duplicated gene always producing the next duplicate. It is shown that dispersed gene duplication rate consists of the primary rate (duplications of ancestral genes) and the secondary rate (duplications of genes that had been generated by recent duplications). The primary rate was 2.5 x 10(-3) gene(-1) Myr(-1) in diploid wheat. The secondary rate was 5.2 x 10(-2) gene(-1) Myr(-1) in the ALP family. The 20-fold acceleration of the secondary rate was caused by the insertion of the ALP-A2 gene into a novel type transposon. Only the ALP-A1 and ALP-A3 genes are transcribed. The transcription of ALP-A3 is directed by a promoter within a DNA fragment similar to a CACTA type of DNA transposons, making ALP-A3 a new gene. The ALP-A3 transcript is longer than that of the ALP-A1. The half-life of ALP duplicated genes was estimated to be 0.87 Myr. Strong purifying selection acting on the ancestral gene ALP-A1 was undiminished by the evolution of duplicated genes. The evolution of the ALP family shows that repeated elements facilitate both gene duplication and expression of duplicated genes and highlights their importance for the evolution of gene repertoire in large plant genomes.

Amino Acid Sequence↗

PubMed1995

Synergism between gonadotrophins and vinblastine relative to the frequencies of metaphase I, diploid and aneuploid mouse oocytes.

Ovulated oocytes are used to obtain estimates of germ cell aneuploidy following in vivo treatment with various chemicals. Such studies commonly use exogenous gonadotrophins to increase the number of ovulated oocytes and to induce ovulation during specific time periods. However, the gonadotrophin dosages have not been evaluated relative to the possibility that synergistic and antagonistic interactions may exist between the hormones and the chemical being studied. We, therefore, studied the interactions of different hormone dosages (5 IU pregnant mare's serum (PMS) and 2.5 IU human chorionic gonadotrophin (HCG), 7.5 IU PMS and 5 IU HCG, and 10 IU PMS and 7.5 IU HCG) alone (controls) and in combination with 0.2 mg/kg of the aneugen vinblastine sulfate (VBS) relative to the number of oocytes ovulated, the frequencies of metaphase I (MI), diploid and aneuploid oocytes. The results indicated that the proportions of oocytes ovulated were not significantly (P > 0.05) different among the various control and VBS groups. VBS, however, resulted in significantly (P < 0.01) higher levels of MI oocytes than in controls. In the VBS-treated females, higher frequencies (P < 0.05) of MI oocytes were found in the 7.5 IU PMS and 5 IU HCG and 10 IU PMS and 7.5 IU HCG groups as compared to the 5 IU PMS and 2.5 IU HCG group. The frequencies of diploid oocytes did not differ significantly (P > 0.05) within the control of VBS groups; whereas, when comparisons were made between each control and VBS group, only the difference between the 5 IU PMS and 2.5 IU HCG groups was significant (P < 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

Aneuploidy↗

PubMed1999

Increased frequencies of diploid sperm detected by multicolour FISH after treatment of rats with carbendazim without micronucleus induction in peripheral blood erythrocytes.

The purpose of the present study was to determine the effect of a single oral dose of carbendazim (CARB) on the frequencies of numerical chromosome aberrations in sperm and on micronuclei in peripheral blood erythrocytes of rats. Dual colour FISH on epididymal sperm of rats treated 31 days before sacrifice (0, 50, 150, 450 and 800 mg/kg body wt CARB in corn oil), corresponding to exposure during late pachytene, revealed a clear induction of diploid sperm. Induction of aneuploid sperm was not observed. Although the absolute frequencies of diploidy were low, ranging from 0.03% in the control group to 0.22% in the highest dose group, the observed dose-response relationship was highly significant. In sperm of rats killed 50 days after treatment with CARB (corresponding to exposure of spermatogonial stem cells) the effect was no longer apparent. In a second experiment, in addition to more dose groups in the low dose range, the peripheral blood micronucleus assay was incorporated. Results of triple colour FISH on epididymal sperm of rats treated with CARB (0-800 mg/kg body wt) again showed induction of diploid, but not of aneuploid sperm. Induction was less prominent than in the first experiment, but the dose-response relationship for diploidy was again significant. In blood samples drawn from the tail vein 48 h after treatment with CARB induction of micronuclei in peripheral blood erythrocytes was not observed, whereas the micronucleus frequency was significantly increased after a single i. p. dose of mitomycin C (3 mg/kg body wt). In conclusion, the present results show that CARB induces diploidy in sperm, without an accompanying induction of micronuclei in erythrocytes. This finding suggests that in rats the peripheral blood micronucleus assay is a less sensitive indicator for the genotoxic potential of CARB than the epididymal sperm aneuploidy/diploidy assay.

Administration, Oral↗

PubMedDate not supplied

Formation of nucleolar polymorphisms in trisomic chickens and subsequent microevolution of rRNA gene clusters in diploids.

Variations in nucleolar size are common in animals and man, yet the basis and significance of this variation are not well understood. In this report, we describe the generation de novo of individuals that express nucleolar size variations (polymorphisms) and the underlying basis for this phenotype in a vertebrate animal system (Gallus domesticus). Individuals that express nucleolar size polymorphisms were produced from mating chickens trisomic for the nucleolar organizer (NO) chromosome; 10%-18% of progeny demonstrated nucleolar polymorphisms. These progeny were incorporated into a diploid genetic line in which the polymorphic trait was observed to segregate in Mendelian fashion. An even more dramatic nucleolar size polymorphism (one macro- plus one micronucleolus) evolved in one diploid family over the course of only two generations. These individuals were used to ascertain that the polymorphic-nucleoli phenotype was expressed in tissues derived from the three primary embryonic cell layers in embryos and neonates. Image analysis was conducted on cells of these birds to quantitate the size differences between macro- and micronucleoli (5 mu2 versus 1 mu2, respectively). Finally, these birds were studied with the technique of in situ hybridization, which showed that gene number differences between homologous NO chromosomes (i.e., heterozygosity for rRNA gene copy number), underlies the polymorphic-nucleoli phenotype. Thus, the chicken emerges as an experimental system through which heterozygosity for the rRNA gene copy number can be induced, easily identified, transmitted, and expressed in all somatic tissues.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMedDate not supplied

An extraordinarily low diploid chromosome number in the reptile Gonatodes taniae (Squamata, Gekkonidae).

Mitotic and meiotic chromosomes of the gekkonid lizard Gonatodes tanieae from Venezuela were analyzed with conventional staining, differential banding techniques, and in situ hybridization using a synthetic telomeric DNA probe. The karyotype of this species is distinguished by the extraordinarily reduced diploid chromosome number of 2n = 16, which is the lowest value known for reptiles. In contrast to most other reptilian species, G. taniae has exclusively bi-armed (meta- and submetacentric) macrochromosomes and no microchromosomes. Examination of the mitotic chromosomes with AT and GC base pair-specific fluorochromes shows the absence of multiple banding patterns in euchromatic regions. The n = 8 diakinetic bivalents of male meiosis present terminal, subterminal, interstitial, and pericentromeric chiasmata. Comparison of the karyotypes of G. taniae and G. vittatus (also collected in Venezuela), and with those of three other Gonatodes species, indicates that the exceptional diploid number of 2n = 16 is the result of repeated centric fusions. In addition to the telomeres, all pericentromeric regions of the G. taniae chromosomes contain considerable amounts of the (TTAGGG)n telomeric sequence. These are probably not only relics of the centric fusions, but also a major component of the highly repetitive DNA in the C band-positive heterochromatin.

Animals↗

PubMed1995

Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.

Molecular techniques allow the survey of a large number of linked polymorphic loci in random samples from diploid populations. However, the gametic phase of haplotypes is usually unknown when diploid individuals are heterozygous at more than one locus. To overcome this difficulty, we implement an expectation-maximization (EM) algorithm leading to maximum-likelihood estimates of molecular haplotype frequencies under the assumption of Hardy-Weinberg proportions. The performance of the algorithm is evaluated for simulated data representing both DNA sequences and highly polymorphic loci with different levels of recombination. As expected, the EM algorithm is found to perform best for large samples, regardless of recombination rates among loci. To ensure finding the global maximum likelihood estimate, the EM algorithm should be started from several initial conditions. The present approach appears to be useful for the analysis of nuclear DNA sequences or highly variable loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci.

Algorithms↗

PubMed1996

Diploid expression of human leukocyte antigen class I and class II molecules on spermatozoa and their cyclic inverse correlation with inhibin concentration.

A diploid expression of class I and class II human leukocyte antigens (HLA) has been found in purified spermatozoa by using double fluorescence labeling cytofluorometry and relevant monoclonal antibodies; this expression has been confirmed for the first time by the analysis of specific HLA mRNA and metabolic 35S labeling followed by immunoprecipitation, which demonstrates an active ongoing translation of HLA proteins in germinal cells. Long-living mRNA coming from diploid germinal cells may be translated to HLA molecules in spermatozoa. This translation is controlled (or at least inversely correlated) by a testicular hormone (inhibin) in a cyclic fashion. Remarkably, serum levels of inhibin, synthesized by Leydig and Sertoli cells, follow a 12- to 13-day cycle, with a peak level at Day 6; this is probably controlled by FSH (not cyclic in males) and other testicular and/or unknown hormones. Peak levels of inhibin concur with the lower density and percentage of spermatozoa expressing both HLA class I and II molecules (close to 3% by cytofluorometry); lowest levels of inhibin coincide with the highest numbers (35-40%) of spermatozoa positive for both HLA molecules and a higher surface density. These observations could put to an end a disconcerting and long-lasting controversy on the expression/non-expression of HLA antigens on spermatozoa. The possibility that HLA-bearing spermatozoa are more capacitated for fertilization than those that do not bear HLA, and the implications of our results on male fertility control are also discussed.

Antibodies, Monoclonal↗

PubMed1987

Rabies pre-exposure prophylaxis using intradermal human diploid cell vaccine: immunologic efficacy and cost-effectiveness in a university medical center and a review of selected literature.

The authors studied the antigenicity of intradermal human diploid cell rabies vaccine administered to 40 laboratory workers considered to be at-risk at the University of Virginia Medical Center. A 1-year postvaccination serology was determined for 20 of those 40, all of whom demonstrated an antirabies titer greater than or equal to 1:50 by the raped fluorescent focus inhibition test. By 2 years' postvaccination, 5 of 40 subjects had "unprotective levels" (less than 1:5), whereas 35 had titers greater than or equal to 1:5, and none had a titer greater than or equal to 1:50. Booster doses given to four subjects whose titers had declined produced a 1-month postvaccination antirabies titer greater than or equal to 1:50 in all cases. Vaccine administration by the intradermal rather than the intramuscular route resulted in a cost savings of $120 (U.S.) per employee. This data indicate that the intradermal administration of human diploid cell vaccine for rabies pre-exposure prophylaxis achieves an immunologic response thought to be protective while providing a substantial cost savings when compared with the intramuscular route of administration. Those who receive primary pre-exposure rabies vaccination should have serologic confirmation of immunologic protection every 2 years with a booster dose given to subjects demonstrating a titer less than 1:5.

Adolescent↗

PubMed2000

Adaptive dynamics in diploid, sexual populations and the evolution of reproductive isolation.

Evolutionary branching is the process whereby an initially monomorphic population evolves to a point where it undergoes disruptive selection and splits up into two phenotypically diverging lineages. We studied evolutionary branching in three models that are ecologically identical but that have different genetic systems. The first model is clonal, the second is sexual diploid with additive genetics on a single locus and the third is like the second but with an additional locus for mate choice. Evolutionary branching occurred under exactly the same ecological circumstances in all three models. After branching the evolutionary dynamics may be qualitatively different. In particular, in the diploid, sexual models there can be multiple evolutionary outcomes whereas in the corresponding clonal model there is only one. We showed that evolutionary branching favours the evolution of (partial) assortative mating and that this in turn effectively restores the results from the clonal model by rendering the alternative outcomes unreachable except for the one that also occurs in the clonal model. The evolution of assortative mating during evolutionary branching can be interpreted as the initial phase of sympatric speciation with phenotypic divergence and partial reproductive isolation.

Adaptation, Physiological↗

PubMed1981

Varicella-zoster virus infection of diploid and chemically transformed guinea-pig embryo cells: factors influencing virus replication.

Factors influencing the replication of varicella-zoster virus (VZV) in guinea-pig embryo cells were evaluated using both diploid cells (GPEC) and a chemically transformed cell line (GPT). Wild-type and vaccine strains of VZV were successfully isolated and serially propagated in GPEC prepared from early gestation whole embryos (less than 2 cm in length). Low passage GPEC (less than or equal to 5 subcultivations) were more susceptible to VZV infection than high passage GPEC (greater than 5 subcultivations), and guinea-pig cells were consistently less permissive than human diploid cells. Cell-free virus was produced from VZV-infected GPEC cultures by sonication and peak yields of 10(3) p.f.u./ml were obtained. In addition, we report the isolation and propagation of VZV, as well as production of cell-free virus, in GPT. Both GPEC and GPT cells were less susceptible to VZV infection than human cells. However, viral replication was enhanced by incubation of VZV-infected GPT cultures at 32 degree C rather than 36 degree C.

Animals↗

PubMed1981

Naturally occurring diploid isolates of Aspergillus nidulans.

Six wild isolates belonging to heterokaryon compatibility group A of the Birmingham Aspergillus nidulans collection were shown to be diploid. Five were proven heterozygous for a naturally occurring conditional lethal haploid genotype. It is considered unlikely that these diploids arose by mutation in storage. Consequently, somatic diploidy is a regular occurrence in the natural population of this saprophytic species.

Aspergillus nidulans↗

PubMed1986

RecE-dependent lysogenic induction in the absence of repressor in Bacillus subtilis non-complementing diploids.

The RecE protein of Bacillus subtilis, known to be required for induction of the SOS response and of phi 105 prophage, was shown to be involved in mitomycin C induction of B. subtilis diploid lysogens carrying a silent phi 105 prophage in their unexpressed chromosome. These stable non-complementing diploid lysogens, formed by protoplast fusion and regeneration, did not synthesize repressor, so that the induction observed must have resulted from RecE-dependent activation of the prophage rather than from RecE-dependent inactivation of repressor. Mitomycin C treatment does not induce permanent expression of the silent chromosome, so the activation seems to be temporary, perhaps reflecting the action of an SOS function under RecE control.

Bacillus subtilis↗

PubMed1994

Characterization of thermosensitive autolytic mutants from diploid Saccharomyces cerevisiae.

In order to carry out a systematic search for mutants affected in cell integrity, the diploid strain Saccharomyces cerevisiae D1 was subjected to mutagenesis with ethyl methane sulphonate (EMS), and mutant clones were screened for thermosensitive autolytic phenotypes. The screening was based on examination of cell populations, from individual mutant clones, stained with propidium iodide to establish the proportion of cells lysing under non-permissive conditions by means of flow cytometry. Osmotic remediation of the autolytic phenotype in the presence of 1 M sorbitol was also checked. Out of 13,300 clones surviving mutagenesis, 34 were confirmed to be thermosensitive autolytic and 7 of them showed some osmotic complementation with regard to growth and cell lysis. The osmotic remediation in the other strains was negligible or affected only one of the two parameters. The expression of the mutant phenotype in the strains isolated led to a sporulation defect (40% of the strains) and significant alterations in morphology, such as cells in chains (35%), altered buds (25%) that eventually might elongate, round unbudded and highly vacuolated cells (12%) and large-sized cells (12%). These observations show that alterations in functions related to cell integrity can be correlated with an altered morphology. Genetic analysis of the mutant strains that could sporulate showed that in many instances the mutant phenotype was the result of more than one mutation, the mutations being individually recessive. However, at least one mutant strain, 933, carried a single mendelian mutation that was dominant in the diploid but haploid segregants were non-viable. Dominance of this mutation was also confirmed in tetraploids obtained by means of protoplast fusion.

Autolysis↗

PubMed1999

Loss of heterozygosity, by mitotic gene conversion and crossing over, causes strain-specific adenine mutants in constitutive diploid Candida albicans.

Molecular evidence is provided in this paper to elucidate a long-standing intriguing phenomenon in fungal genetics: that many natural isolates of the constitutive diploid organism Candida albicans yield strain-specific, recessive mutants at a reproducible frequency that is as high as a few percent of the surviving cells after exposure to UV irradiation or other mutagens. Southern hybridization analysis and DNA sequence data indicated that C. albicans CA12, a clinical isolate, is heterozygous for the ADE2 gene, carrying one functional and one null allele. Sequence analysis of the null allele revealed the presence of a 1.3 kb deletion, which locates between two AATC repeats and spans the promoter and coding regions of the gene. The adenine auxotrophic mutants, which were readily isolated after UV irradiation of C. albicans CA12, were proved to be the segregants of mitotic recombination as they remained as diploid, not hemizygous or haploid, cells and were homozygous for ade2. Analysis of reciprocal products of the mitotic recombination detected that the process of loss of heterozygosity was mediated by mitotic crossing over (reciprocal exchange of genetic information) as well as gene conversion (non-reciprocal exchange of genetic information).

Adenine↗

PubMed2025

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing.

Human cell lines are fundamental tools in biomedical research and are widely used in disease modeling, drug development, and many other domains. Here, we present chromosome-level, phased diploid genome assemblies of two popular human cell lines: the BJ foreskin fibroblast line and the IMR-90 fetal lung fibroblast line. Our high-quality assemblies, generated using long-read and Hi-C sequencing data, reveal substantial structural variation, including more than 50,000 insertions, deletions, duplications, and inversions compared to the recent T2T-CHM13v2.0 reference. Our assemblies provide detailed maps of genetic variation, enabling more accurate variant calling and the ability to phase reads when using newly generated or historical sequencing data on these cell lines or their derivatives. All assemblies and associated data have been made available as a resource for the research community. We envision that diploid genome assembly will become a cornerstone approach for personalized medicine in the near future.

Journal Article↗

PubMed2003

Evolutionary advantage of diploidal over polyploidal sexual reproduction.

We modify the Penna model for biological aging, which is based on the mutation-accumulation theory, in order to verify if there would be any evolutionary advantage of triploid over diploid organisms. We show that this is not the case, and that diploidal sex is always better than that involving three individuals.

Age Factors↗

PubMed2005

Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops).

The Hardness (Ha) locus controls grain hardness in hexaploid wheat (Triticum aestivum) and its relatives (Triticum and Aegilops species) and represents a classical example of a trait whose variation arose from gene loss after polyploidization. In this study, we investigated the molecular basis of the evolutionary events observed at this locus by comparing corresponding sequences of diploid, tertraploid, and hexaploid wheat species (Triticum and Aegilops). Genomic rearrangements, such as transposable element insertions, genomic deletions, duplications, and inversions, were shown to constitute the major differences when the same genomes (i.e., the A, B, or D genomes) were compared between species of different ploidy levels. The comparative analysis allowed us to determine the extent and sequences of the rearranged regions as well as rearrangement breakpoints and sequence motifs at their boundaries, which suggest rearrangement by illegitimate recombination. Among these genomic rearrangements, the previously reported Pina and Pinb genes loss from the Ha locus of polyploid wheat species was caused by a large genomic deletion that probably occurred independently in the A and B genomes. Moreover, the Ha locus in the D genome of hexaploid wheat (T. aestivum) is 29 kb smaller than in the D genome of its diploid progenitor Ae. tauschii, principally because of transposable element insertions and two large deletions caused by illegitimate recombination. Our data suggest that illegitimate DNA recombination, leading to various genomic rearrangements, constitutes one of the major evolutionary mechanisms in wheat species.

Chromosome Mapping↗