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PubMed1984

Genetic system of Schwanniomyces alluvius determined by diad analysis of fusion products.

The genetics of Schwanniomyces alluvius, a yeast that secretes alpha-amylase, were investigated. No mating types have been detected in this haploid organism. Hybrids were produced by protoplast fusion, and these were subjected to diad analysis by using two-spored asci. Results showed that the diploidy introduced by cell fusion persists through successive spore generations. It was concluded that in this organism, sporulation is preceded by the fusion of mitotic products, regardless of the ploidy of the latter. Routine procedures for constructing novel strains would, no doubt, be hampered by this failure of the sporulation process to restore haploidy. Nevertheless, chromosomal instability of hybrids, as indicated both by heterogeneity of fusion products and by a high frequency of morbidity among their segregants, may permit the use of classical genetic techniques for strain construction.

Ascomycota↗
PubMed2000

Population genetics and evolution of genomic imprinting.

At a small number of mammalian loci, only one of the two copies of a gene is expressed. Just which copy is expressed depends on the sex of the parent from which that copy was inherited. Such genes are said to be imprinted. The functional haploidy implied by imprinting has a number of population genetic consequences. Moreover, since diploidy is widely believed to be advantageous, the evolution of this non-Mendelian form of expression requires an explanation. Here I examine some of the theoretical and mathematical models investigating these two aspects of imprinting. For instance, the dynamics and equilibrium properties of many models of natural selection at imprinted loci are formally equivalent to models without imprinting. And different approaches to modeling the problem of the evolution of imprinting reveal the weakness of several of the apparent predictions of various verbal hypotheses about why imprinting has evolved.

Animals↗
PubMed2005

Mechanisms of fungal speciation.

The objective of this review is to provide a synthesis of speciation theory, of what is known about mechanisms of speciation in fungi and from this, what is expected, and of ideas on how speciation can be elucidated in more fungal systems. The emphasis is on process rather than pattern. Phylogeographic studies in some groups, such as the agarics, demonstrate predominantly allopatric speciation, often through vicariance, as seen in many plants and animals. The variety of life history factors in fungi suggests, however, a diversity in speciation mechanisms that is borne out in comparison of some key examples. Life history features in fungi with a bearing on speciation include genetic mechanisms for intra- and interspecies interactions, haploidy as monokaryons, dikaryons, or coenocytes, distinctive types of propagules with distinctive modes of dispersal, as well as characteristic relationships to the substrate or host as specialized or generalist saprotrophs, parasites or mutualists with associated opportunities and selective pressures for hybridization. Approaches are proposed for both retrospective, phylogeographic determination of speciation mechanisms, and experimental studies with the potential for genomic applications, particularly in examining the relationship between adaptation and reproductive isolation.

Biological Evolution↗
PubMed2004

Mismatch repair gene PMS2: disease-causing germline mutations are frequent in patients whose tumors stain negative for PMS2 protein, but paralogous genes obscure mutation detection and interpretation.

The MutLalpha heterodimer formed by mismatch repair (MMR) proteins MLH1 and PMS2 is a major component of the MMR complex, yet mutations in the PMS2 gene are rare in the etiology of hereditary nonpolyposis colorectal cancer. Evidence from five published cases suggested that contrary to the Knudson principle, PMS2 mutations cause hereditary nonpolyposis colorectal cancer or Turcot syndrome only when they are biallelic in the germline or abnormally expressed. As candidates for PMS2 mutations, we selected seven patients whose colon tumors stained negative for PMS2 and positive for MLH1 by immunohistochemistry. After conversion to haploidy, truncating germline mutations of PMS2 were found in two patients (2192delTAACT and deletion of exon 8). These mutations abrogated PMS2 protein in germline cells by Western analysis. In two additional patients, PMS2 protein from one allele also was abrogated. Novel or previously described missense variants of PMS2 were detected, but their pathogenicity is undetermined. We detected and characterized a new transcript, PMS2CL, showing 98% sequence identity with exons 9 and 11-15 of PMS2 and emanating from a locus close to PMS2 in chromosome 7p. Its predicted protein product was not detected. Thus, in addition to several previously described PMS2-related genes resembling the 5' end of PMS2, at least one related gene resembles the 3' end of PMS2. In conclusion, both detectable and presently undefined germline mutations are deleterious and produce susceptibility to cancer by the two-hit mechanism. Paralogous genes interfere with mutation detection, resulting in underdiagnosis of PMS2 mutations. Mutation detection in PMS2 requires haploid DNA.

Adaptor Proteins, Signal Transducing↗
PubMed1977

F-bodies as Y chromosome markers in mature human sperm heads: a quantitative approach.

It is generally accepted that at least some Y chromosomes in human mature sperm heads are represented in preparations by fluorescent F-bodies. From data consisting solely of F-body scorings and the visually estimated size of sperm heads from normal donors, a quantitative model is developed which permits simultaneous estimation of six parameters representing biological factors (the proportions of ploidy classes and of their sex-chromosome complements) and biassing factors (not all Y chromosomes represented by F-bodies, not all F-bodies representing Y chromosomes, and error in scoring ploidy from visual size). The analysis is statistically adequate and succeeds in predicting a variety of independently validated phenomena. The work may be regarded as a contribution to the integration of qualitative and quantitative evidence in the study of F-bodies. In all, 21,700 one-headed spermatozoa from 12 donors were scored. A mean of 54% spermatozoa lacking F-bodies was subject to a standard deviation between donors of 4.8, over and above binomial error. Analysis yielded the following estimates: 83.3% of diploid spermatozoa are XY, the remainder XX and YY in assumed equal number (this information assists analysis of the origin of embryonic triploidy); 2.4% of spermatozoa are diploid (this estimate does not compete in accuracy with direct estimates from DNA absorbance); only 83% of Y chromosomes are represented by F-bodies; 7% of haploid heads and 14% of diploids contain one or more "adventitious bodies" indistinguishable from true F-bodies. The visually scored head sizes "Small" and "Medium" correspond approximately with haploidy and diploidy; nearly all haploids are scored as Small, and 72% of the Medium are diploid. F-bodies are not thought at present to give a useful basis for estimating the presumably low incidence of sex-chromosome aneuploidy and nondisjunction. No such estimate has been attempted. The problem is overshadowed by not fully understood complicating factors of greater magnitude, which now appear to be a major subject of enquiry. Some implications and possible future developments are discussed.

Humans↗
PubMed1983

Spontaneous heteroploidy in one-cell mouse embryos.

First cleavage divisions were analyzed, after chromosome banding, in 321 zygotes recovered from superovulated, outbred ICR mice 33-35 h after injection of human chorionic gonadotropin. With 72.1% of all zygotes at metaphase and late prophase analyzed, there was 87% diploidy, 3.6% trisomy, 2.5% monosomy, 0.4% structural rearrangement, and 0.93% triploidy. Aneuploid zygotes in which there were 37 or 38 chromosomes accounted for 6.5% of the population with both haploid complements analyzable. In 45 diploid zygotes in which only one complement was analyzable, there was 93.4% haploidy, 2.2% disomy, and 4.4% hypoploidy. The chromosome most often involved in aneuploidy was the 19. The parental origin of the chromosome anomalies was determined on the basis of differential condensation of the chromosomes. The source of trisomy was shown to be the male in three and the female in five of the eight cases determined. This indicates a paternal contribution to trisomy and a female nondisjunction frequency of 1.5% (five of 321). For monosomy where the origin was identified in five of the cases, the male complement was implicated in three zygotes. The single break was seen in a sperm-derived chromosome. Two of the three triploids were dispermic and one was digynic. The outbred Swiss mouse might be a useful model for studying factors responsible for the induction of cytogenetic anomalies in early development of mammals.

Animals↗
PubMed1992

Evidence for genetic etiology of heteroploidy in embryos of the Japanese quail (Coturnix coturnix japonica).

The Japanese quail was used as an experimental system to detect the effects of genes that affect chromosome behavior and distribution. From a random-bred population, three inbred generations were produced by full-sib matings in 36 families. The expectation from such a breeding scheme was that embryos bearing aberrations induced by recessive mutant genes would cluster within families and recur in particular lineages. Chromosomal aberrations caused by errors during fertilization, cleavage mitosis, and gametogenesis were scored in 2,037 16- to 18-h embryos from 107 families. Comparisons of the observed frequencies among families and lineages and pedigree analysis indicated that four types of chromosome aberrations had a genetic basis: (1) triploidy and triploid chimerism; (2) haploidy and haploid chimerism; (3) diploid/tetraploid mosaicism; and (4) a new aberration, referred to as "atypical mitotic metaphase." Analysis of the sex-chromosome complements of the embryos indicated that triploidy resulted predominantly from diploid ova, haploid cell lines originated from supernumerary sperm nuclei, and tetraploid cell lines resulted from endoreduplication or failure of cytokinesis. Clustering of triploidy in particular lineages was due to dispermy or recurrent suppression of one or both meiotic divisions during oogenesis.

Animals↗
PubMed1991

Cytogenetic and molecular genetic studies of follicular and papillary thyroid cancers.

Cytogenetic studies have shown frequent clonal abnormalities in papillary carcinoma (PTC) and follicular carcinoma (FTC). Loss of heterozygosity (LOH) may suggest the presence of tumor suppressor genes and has not been reported in these neoplasms. These studies were undertaken to determine if consistent chromosomal abnormalities are associated with thyroid cancer, to determine likely regions for molecular genetic investigations, and to determine if there is allelic loss in thyroid tumors. Cytogenetic analysis of 26 PTC and 5 FTC showed clonal abnormalities in 9 and included -Y, +5, or inv(10)(q11.2q21.2) in PTC, and -Y or near haploidy in FTC. Using DNA probes specific for chromosomes 1, 3, 10, 16, and 17, we carried out restriction fragment length polymorphism analysis on 6 FTC, 3 follicular adenomas (FA), and 12 PTC. LOH of all informative loci on chromosome 3p was observed in all 6 FTC, but not in FA or PTC. No LOH was observed for loci mapped to chromosome 10 in PTC. Our results suggest: cytogenetic abnormalities of chromosome 10q are associated with PTC; cytogenetic and molecular abnormalities of chromosome 3 are associated with FTC; and a tumor suppressor gene may be present on the short arm of chromosome 3 important for the development or progression of FTC.

Adenocarcinoma↗
PubMed2005

Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens.

BACKGROUND: The moss Physcomitrella patens is an emerging plant model system due to its high rate of homologous recombination, haploidy, simple body plan, physiological properties as well as phylogenetic position. Available EST data was clustered and assembled, and provided the basis for a genome-wide analysis of protein encoding genes. RESULTS: We have clustered and assembled Physcomitrella patens EST and CDS data in order to represent the transcriptome of this non-seed plant. Clustering of the publicly available data and subsequent prediction resulted in a total of 19,081 non-redundant ORF. Of these putative transcripts, approximately 30% have a homolog in both rice and Arabidopsis transcriptome. More than 130 transcripts are not present in seed plants but can be found in other kingdoms. These potential "retained genes" might have been lost during seed plant evolution. Functional annotation of these genes reveals unequal distribution among taxonomic groups and intriguing putative functions such as cytotoxicity and nucleic acid repair. Whereas introns in the moss are larger on average than in the seed plant Arabidopsis thaliana, position and amount of introns are approximately the same. Contrary to Arabidopsis, where CDS contain on average 44% G/C, in Physcomitrella the average G/C content is 50%. Interestingly, moss orthologs of Arabidopsis genes show a significant drift of codon fraction usage, towards the seed plant. While averaged codon bias is the same in Physcomitrella and Arabidopsis, the distribution pattern is different, with 15% of moss genes being unbiased. Species-specific, sensitive and selective splice site prediction for Physcomitrella has been developed using a dataset of 368 donor and acceptor sites, utilizing a support vector machine. The prediction accuracy is better than those achieved with tools trained on Arabidopsis data. CONCLUSION: Analysis of the moss transcriptome displays differences in gene structure, codon and splice site usage in comparison with the seed plant Arabidopsis. Putative retained genes exhibit possible functions that might explain the peculiar physiological properties of mosses. Both the transcriptome representation (including a BLAST and retrieval service) and splice site prediction have been made available on http://www.cosmoss.org, setting the basis for assembly and annotation of the Physcomitrella genome, of which draft shotgun sequences will become available in 2005.

Alternative Splicing↗
PubMed1977

The culture of pig oocytes in minimal medium, and the influence of progesterone and estradiol-17beta on meiotic maturation.

Pig oocytes, with (intact) or without (denuded) adhering granulosa cells, were cultured for 33 to 35 h in minimal culture media containing bovine serum albumin and either progesterone or estradiol-17beta or both steroids. The incidence of maturation for intact oocytes in minimal medium was comparable, if not superior, to that observed by other investigators using complex culture media. No statistically significant stimulation of maturation by progesterone was observed for either intact or denuded oocytes. Estradiol-17beta at concentrations of 1.0 and 10.0 mug per ml inhibited the maturation of denuded oocytes, but the inhibition was overcome either by including progesterone in the medium or by subsequently culturing the inhibited oocytes in steriod-free medium. Chromosomal examination of air-dried oocytes indicated that intact and denuded oocytes cultured either in progesterone or estradiol-17beta exhibited an increased incidence of diploidy and hyperhaploidy at telophase I and metaphase II, but that oocytes cultured in media containing both progesterone and estradiol showed a higher incidence of normal haploidy than did control oocytes.

Animals↗
PubMed1978

Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox.

The 40,000-fold variation in eukaryote haploid DNA content is unrelated to organismic complexity or to the numbers of protein-coding genes. In eukaryote microorganisms, as well as in animals and plants, DNA content is strongly correlated with cell volume and nuclear volume, and with cell cycle length and minimum generation time. These correlations are simply explained by postulating that DNA has 2 major functions unrelated to its protein-coding capacity: (1) the control of cell volume by the number of replicon origins, and (2) the determination of nuclear volume by the overall bulk of the DNA: cell growth rates are determined by the cell volume and by the area of the nuclear envelope available for nucleocytoplasmic transport of RNA, which in turn depends on the nuclear volume and therefore on the DNA content. During evolution nuclear volume, and therefore DNA content, has to be adjusted to the cell volume to allow reasonable growth rates. The great diversity of cell volumes and growth rates, and therefore of DNA contents, among eukaryotes results from a varying balance in different species between r-selection, which favours small cells and rapid growth rates and therefore low DNA C-values, and K-selection which favours large cells and slow growth rates and therefore high DNA C-values. In multicellular organisms cell size needs to vary in different tissues: size differences between somatic cells result from polyteny, endopolyploidy, or the synthesis of nucleoskeletal RNA. Conflict between the need for large ova and small somatic cells explains why lampbrush chromosomes, nurse cells, chromatin diminution and chromosome elimination evolved. Similar evolutionary considerations clarify the nature of polygenes, the significance of the distribution of haploidy, diploidy and dikaryosis in life cycles and of double fertilization in angiosperms, and of heteroploidy despite DNA constancy in cultured cells, and other puzzles in eukaryote chromosome biology. Eukaryote DNA can be divided into genic DNA (G-DNA), which codes for proteins (or serves as recognition sites for proteins involved in transcription, replication and recombination), and nucleoskeletal DNA (S-DNA) which exists only because of its nucleoskeletal role in determining the nuclear volume (which it shares with G-DNA, and performs not only directly, but also indirectly by coding for nucleoskeletal RNA). Mechanistic and evolutionary implications of this are discussed.

Animals↗
PubMed2004

Co-infection weakens selection against epistatic mutations in RNA viruses.

Co-infection may be beneficial in large populations of viruses because it permits sexual exchange between viruses that is useful in combating the mutational load. This advantage of sex should be especially substantial when mutations interact through negative epistasis. In contrast, co-infection may be detrimental because it allows virus complementation, where inferior genotypes profit from superior virus products available within the cell. The RNA bacteriophage phi6 features a genome divided into three segments. Co-infection by multiple phi6 genotypes produces hybrids containing reassorted mixtures of the parental segments. We imposed a mutational load on phi6 populations by mixing the wild-type virus with three single mutants, each harboring a deleterious mutation on a different one of the three virus segments. We then contrasted the speed at which these epistatic mutations were removed from virus populations in the presence and absence of co-infection. If sex is a stronger force, we predicted that the load should be purged faster in the presence of co-infection. In contrast, if complementation is more important we hypothesized that mutations would be eliminated faster in the absence of co-infection. We found that the load was purged faster in the absence of co-infection, which suggests that the disadvantages of complementation can outweigh the benefits of sex, even in the presence of negative epistasis. We discuss our results in light of virus disease management and the evolutionary advantage of haploidy in biological populations.

Bacteriophage phi 6↗
PubMed2005

X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis.

Comparing patterns of molecular evolution between autosomes and sex chromosomes (such as X and W chromosomes) can provide insight into the forces underlying genome evolution. Here we investigate patterns of codon bias evolution on the X chromosome and autosomes in Drosophila and Caenorhabditis. We demonstrate that X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophila and Caenorhabditis. Furthermore, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years. We provide several lines of evidence that this elevation in codon bias is due exclusively to their chromosomal location and not to any other property of X-linked genes. We present two possible explanations for these observations. One possibility is that natural selection is more efficient on the X chromosome due to effective haploidy of the X chromosomes in males and persistently low effective numbers of reproducing males compared to that of females. Alternatively, X-linked genes might experience stronger natural selection for higher codon bias as a result of maladaptive reduction of their dosage engendered by the loss of the Y-linked homologs.

Animals↗
PubMed2001

The role of bone marrow transplantation in first remission of paediatric all.

Although intensive chemotherapy has improved event-free survival for most children with lymphoblastic leukaemia there remain up to 10% who have not benefited from this approach. These include infants, children with Ph1 positive leukaemia, with near-haploidy, and slow remitters in most of whom event free survival remains below 40%. Evaluation of the benefits of Bone Marrow Transplantation in high risk ALL is fraught with difficulties and to date has not produced clear evidence of benefit. The way forward lies in prospective evaluation of BMT in tightly defined subsets of highest risk children, a task which will require international collaboration.

Bone Marrow Transplantation↗
PubMed1999

Loss of heterozygosity and DNA ploidy point to a diverging genetic mechanism in the origin of peripheral and central chondrosarcoma.

Chondrosarcomas are malignant cartilaginous tumors arising centrally in bone (central chondrosarcoma), or secondarily within the cartilaginous cap of a hereditary or sporadic exostosis (peripheral chondrosarcoma). Loss of heterozygosity (LOH) was studied by microsatellite analysis at the loci harboring the EXT genes (implicated in hereditary multiple exostoses), the EXT-like genes, and at 9p21, 13q14, 17p13, and chromosome 10. Nineteen of 20 peripheral chondrosarcomas showed LOH at all loci tested, while only 3 of 12 central chondrosarcomas exhibited LOH, restricted to 9p21, 10, 13q14, and 17p13. LOH at 9p21 did not appear to involve the CDKN2A gene, as assessed by SSCP analysis. DNA flow cytometry demonstrated a wide variation in the ploidy status in peripheral chondrosarcomas (DNA indexes, 0.56-2.01), whereas central chondrosarcomas were predominantly peridiploid. Near-haploidy found in peripheral chondrosarcomas could explain part of the high LOH percentages. Ki-67 immunohistochemistry suggested a higher proliferation rate in peripheral chondrosarcomas. Our results indicate that peripheral chondrosarcomas, arising secondarily to an exostosis, may obtain genetic alterations during malignant transformation, with subsequent genetic instability as demonstrated by a high percentage of LOH and a wide variation in ploidy status. In contrast, peridiploidy and a low percentage of LOH in central tumors suggest that a different oncogenic molecular mechanism may be operative.

Adolescent↗
PubMed1999

Hypodiploidy with less than 45 chromosomes confers adverse risk in childhood acute lymphoblastic leukemia: a report from the children's cancer group.

We have determined the prognostic significance of hypodiploidy (<46 chromosomes) in a large cohort of children with acute lymphoblastic leukemia (ALL) treated by the Children's Cancer Group. Among 1,880 patients, 110 (5.8%) had hypodiploid karyotypes: 87 had 45 chromosomes, 15 had 33 to 44 chromosomes, none had 29 to 32 chromosomes, and 8 had 24 to 28 chromosomes (near-haploidy). Six-year event-free survival (EFS) estimates for patients with 45 chromosomes, 33 to 44 chromosomes, or 24 to 28 chromosomes were 65% (standard deviation [SD], 8%), 40% (SD, 18%), and 25% (SD, 22%), respectively (log rank, P =.002; test for trend, P =.0009). The combined hypodiploid group had worse outcome than nonhypodiploid patients, with 6-year EFS of 58% (SD, 7%) and 76% (SD, 2%), respectively (P <.0001). EFS for the subgroup with 45 chromosomes was similar to that of patients with pseudodiploidy (P =.43) or 47 to 50 chromosomes (P =.76). None of the patients with 24 to 28 chromosomes had a t(4;11), a t(9;22), or a t(1;19), and most received highly intensive therapy. The adverse risk associated with 33 to 44 and 24 to 28 chromosomes remained significant in multivariate analyses adjusted for important risk factors including age, white blood cell count, and Philadelphia chromosome status. Thus, hypodiploidy with less than 45 chromosomes, particularly 24 to 28 chromosomes, is a significant adverse risk factor despite treatment with contemporary intensive therapies.

Child↗
PubMedDate not supplied

Immunoglobulin allotypy of allophenic rabbits.

We obtained two allophenic rabbits formed by the manipulation of blastocysts from strains which differed by their coat colour and their immunoglobulin allotypic specificities. The phenotype of these two rabbits was a1,a2,a3,b4. They were chimeras for their lymphocytic system but not for their coat colour as they had the homogeneous brown coat colour of one of their parental strain. The IgG concentration in the serum of these allophenic rabbits was of the same order of magnitude as the IgG concentration in the serum of normal rabbits of the same age. Twenty-five weeks after birth, one of the allophenic rabbits expressed predominantly the a1 allotypic specificity (around 70% a1, 5% a2, 20% a3) which came from its brown parents, while the second one expressed predominantly the a3 allotypic specificity (around 2% a1, 20% a2, 60% a3) which came from its white parents. Each allotypically different IgG produced by these allophenic rabbits possessed the whole set of allotypic determinants found on IgG carrying the same specificity and produced by normal rabbits. We did not find significant signs of genetic information transfers from the cells of one parental strain to the cells of the other parental strain, or of eventual perturbations of the functional haploidy of the immunoglobulin-producing cells. As these allophenic rabbits only had different a series allotypic specificities, the probability of finding such signs was certainly low as they would have implied hybrid IgG molecules with two allotypically different heavy chains. We now have allophenic rabbits in which different a and b series allotypic specificities are involved and with which we will look for hybrid IgG molecules with heavy chains from one parental strain and light chains from the other parental strain. With these two rabbits we observed the "chimeric drift", namely the slow disappearance of constituants (here one allotypic specificity) coming from one parental strain. The first progeny tests carried out with these allophenic rabbits indicated that they did not seem to be chimeras at the germinal cell level. All their first offspring which were homogeneously brown and homozygous a1,b4 expressed the whole set of variants and determinants of the a1 or the b4 allotypic specificity.

Animals↗
PubMed2001

Phenotypic analysis of hMSH2 mutations in mouse cells carrying human chromosomes.

Conversion of diploidy to haploidy is a method that allows the generation of stable murine/human hybrid cell lines carrying selected human chromosomes in only a single copy. In this setting, it is possible to detect genetic mutations with greater sensitivity and reliability than in diploid cells. Using this method, we were able to identify mutations in the human mismatch repair (MMR) gene hMSH2 in hereditary nonpolyposis colon cancer families, which have escaped detection by the conventional methods. In this report, we show that such hybrid cell lines can also be a valuable tool in the study of the mutated MMR proteins, in particular the variants found in hereditary nonpolyposis colon cancer families that carry missense mutations and where it is unclear whether they predispose to colon cancer. This analysis is made possible by the fact that the human hMSH2 protein is able to complement the MMR defect in the host murine cell line.

Alleles↗