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PubMed2003

Transplanted bone marrow regenerates liver by cell fusion.

Results from several experimental systems suggest that cells from one tissue type can form other tissue types after transplantation. This could be due to the presence of multipotential or several types of adult stem cells in donor tissues, or alternatively, to fusion of donor and recipient cells. In a model of tyrosinaemia type I, mice with mutations in the fumarylacetoacetate hydrolase gene (Fah-/-) regain normal liver function after transplantation of Fah+/+ bone marrow cells, and form regenerating liver nodules with normal histology that express Fah. Here we show that these hepatic nodules contain more mutant than wild-type Fah alleles, and that their hepatocytes express both donor and host genes, consistent with polyploid genome formation by fusion of host and donor cells. Using bone marrow cells marked with integrated foamy virus vectors that express green fluorescent protein, we identify common proviral junctions in hepatic nodules and haematopoietic cells. We also show that the haematopoietic donor genome adopts a more hepatocyte-specific expression profile after cell fusion, as the wild-type Fah gene was activated and the pan-haematopoietic CD45 marker was no longer expressed.

Animals↗

PubMed2001

p53 displacement from centrosomes and p53-mediated G1 arrest following transient inhibition of the mitotic spindle.

Growing evidence indicates a central role for p53 in mediating cell cycle arrest in response to mitotic spindle defects so as to prevent rereplication in cells in which the mitotic division has failed. Here we report that a transient inhibition of spindle assembly induced by nocodazole, a tubulin-depolymerizing drug, triggers a stable activation of p53, which can transduce a cell cycle inhibitory signal even when the spindle-damaging agent is removed and the spindle is allowed to reassemble. Cells transiently exposed to nocodazole continue to express high levels of p53 and p21 in the cell cycle that follows the transient exposure to nocodazole and become arrested in G(1), regardless of whether they carry a diploid or polyploid genome after mitotic exit. We also show that p53 normally associates with centrosomes in mitotic cells, whereas nocodazole disrupts this association. Together these results suggest that the induction of spindle damage, albeit transient, interferes with the subcellular localization of p53 at specific mitotic locations, which in turn dictates cell cycle arrest in the offspring of such defective mitoses.

Anaphase↗

PubMed1996

Fur regulates the expression of iron-stress genes in the cyanobacterium Synechococcus sp. strain PCC 7942.

A homologue of the 'ferric uptake regulation' gene (fur) was isolated from the cyanobacterium Synechococcus sp. strain PCC 7942 by an Escherichia coli-based 'in vivo repression assay'. The assay uses a reporter-gene construct containing the promoter region of the iron-regulated cyanobacterial gene isiA, fused to the coding region for chloramphenicol acetyltransferase. The isolated gene codes for a protein that has 41% sequence similarity (36% identity) to Fur from E. coli and contains the putative iron-binding motif found in the Fur proteins of purple bacteria. No significant similarity was found to the DxtR repressor that regulates the expression of toxin and siderophore production in Gram-positive bacteria. Insertional mutagenesis of the cloned cyanobacterial fur gene led to the creation of heteroallelic mutants that showed iron-deficiency symptoms in iron-replete medium, including the constitutive production of flavodoxin and of hydroxamate siderophores. Failure to eliminate wild-type copies of the fur gene from the polyploid genome of Synechococcus 7942 implies that in this cyanobacterium Fur may have essential functions in addition to the regulation of genes involved in iron scavenging or photosynthetic electron transport.

Amino Acid Sequence↗

PubMed1999

ORC localization in Drosophila follicle cells and the effects of mutations in dE2F and dDP.

We isolated mutations in Drosophila E2F and DP that affect chorion gene amplification and ORC2 localization in the follicle cells. In the follicle cells of the ovary, the ORC2 protein is localized throughout the follicle cell nuclei when they are undergoing polyploid genomic replication, and its levels appear constant in both S and G phases. In contrast, when genomic replication ceases and specific regions amplify, ORC2 is present solely at the amplifying loci. Mutations in the DNA-binding domains of dE2F or dDP reduce amplification, and in these mutants specific localization of ORC2 to amplification loci is lost. Interestingly, a dE2F mutant predicted to lack the carboxy-terminal transcriptional activation and RB-binding domain does not abolish ORC2 localization and shows premature chorion amplification. The effect of the mutations in the heterodimer subunits suggests that E2F controls not only the onset of S phase but also origin activity within S phase.

Animals↗

PubMed2004

Plastid transformation in higher plants.

Plastids of higher plants are semi-autonomous organelles with a small, highly polyploid genome and their own transcription-translation machinery. This review provides an overview of the technology for the genetic modification of the plastid genome including: vectors, marker genes and gene design, the use of gene knockouts and over-expression to probe plastid function and the application of site-specific recombinases for excision of target DNA. Examples for applications in basic science include the study of plastid gene transcription, mRNA editing, photosynthesis and evolution. Examples for biotechnological applications are incorporation of transgenes in the plastid genome for containment and high-level expression of recombinant proteins for pharmaceutical and industrial applications. Plastid transformation is routine only in tobacco. Progress in implementing the technology in other crops is discussed.

DNA, Plant↗

PubMed2006

High-resolution radiation hybrid map of wheat chromosome 1D.

Physical mapping methods that do not rely on meiotic recombination are necessary for complex polyploid genomes such as wheat (Triticum aestivum L.). This need is due to the uneven distribution of recombination and significant variation in genetic to physical distance ratios. One method that has proven valuable in a number of nonplant and plant systems is radiation hybrid (RH) mapping. This work presents, for the first time, a high-resolution radiation hybrid map of wheat chromosome 1D (D genome) in a tetraploid durum wheat (T. turgidum L., AB genomes) background. An RH panel of 87 lines was used to map 378 molecular markers, which detected 2312 chromosome breaks. The total map distance ranged from approximately 3,341 cR(35,000) for five major linkage groups to 11,773 cR(35,000) for a comprehensive map. The mapping resolution was estimated to be approximately 199 kb/break and provided the starting point for BAC contig alignment. To date, this is the highest resolution that has been obtained by plant RH mapping and serves as a first step for the development of RH resources in wheat.

Chromosome Breakage↗

PubMed2000

Contributions of plant molecular systematics to studies of molecular evolution.

Dobzhansky stated that nothing in biology makes sense except in the light of evolution. A close corollary, and the central theme of this paper, is that everything makes a lot more sense in the light of phylogeny. Systematics is in the midst of a renaissance, heralded by the widespread application of new analytical approaches and the introduction of molecular techniques. Molecular phylogenetic analyses are now commonplace, and they have provided unparalleled insights into relationships at all levels of plant phylogeny. At deep levels, molecular studies have revealed that charophyte green algae are the closest relatives of the land plants and suggested that liverworts are sister to all other extant land plants. Other studies have suggested that lycopods are sister to all other vascular plants and clarified relationships among the ferns. The impact of molecular phylogenetics on the angiosperms has been particularly dramatic--some of the largest phylogenetic analyses yet conducted have involved the angiosperms. Inferences from three genes (rbcL, atpB, 18S rDNA) agree in the major features of angiosperm phylogeny and have resulted in a reclassification of the angiosperms. This ordinal-level reclassification is perhaps the most dramatic and important change in higher-level angiosperm taxonomy in the past 200 years. At lower taxonomic levels, phylogenetic analyses have revealed the closest relatives of many crops and 'model organisms' for studies of molecular genetics, concomitantly pointing to possible relatives for use in comparative studies and plant breeding. Furthermore, phylogenetic information has contributed to new perspectives on the evolution of polyploid genomes. The phylogenetic trees now available at all levels of the taxonomic hierarchy for angiosperms and other green plants should play a pivotal role in comparative studies in diverse fields from ecology to molecular evolution and comparative genetics.

Evolution, Molecular↗

PubMed1982

[Growth of cardiac muscle cells during rat adaptation to altitude hypoxia].

The weight of the right heart ventricle in 1.5-month-old rats kept after birth in the mountains of 3400 m altitude is higher and its muscle cell cytoplasm mass is much larger compared to those in 1.5-month-old animals raised at 800 m altitude. The hypertrophy of cells is not due to their polyploidization. Only a small increase in the relative number of polyploid cells takes place under high altitude hypoxia. The weight of the right ventricle and myocyte mass in 3-month-old rats kept 1.5-3 months after the birth at 3400 m altitude also increases, although this augmentation is significantly less than in the animals grown in the mountains for 1.5 months immediately after the birth. The myocyte ploidy of adult animals adapted to hypoxia does not essentially differ from that of 1.5- and 3-month-old control rats: about 80 per cent of these cells are polyploid. Thus, the growth of cardiac myocytes under the heart hyperfunction in the case of high altitude hypoxia proceeds mainly on the ground of the stable polyploid genome, as well as normal ontogenetic growth of these cells.

Adaptation, Physiological↗

PubMed2005

An hypothesis about genome structures in mammalian polyploid cells based on a new concept that genome is fractal of six hierarchies.

A new model for the spatial configurations of DNA is proposed to solve the problem of DNA loss in mammalian polyploid cells. The ordinary concept that chromosomes are situated independently in nuclei cannot account well for the DNA loss in polyploid cells. A new concept about the DNA configurations in diploid cells is constructed based on observations that have been reported. Briefly, the DNA structure is self-similar fractal with a unit of opposite-handed twin-circles. In human diploid cells, DNA is constructed with six hierarchies whose sizes are 32(5), 32(4), 32(3), 32(2), 32(1) and 32(0) with a unit of 200 DNA base pairs, corresponding to a genome, a chromosome, a chromosome band, a replicon, a rosette loop (a gene) and a nucleosome, respectively. A model assuming particular spatial configurations of chromosomes in polyploid cells is deduced from this new concept about chromosome configurations in diploid cells. It can account satisfactorily for the problem of DNA loss in polyploid cells. When cell division is inhibited and DNA synthesis progresses, replicated DNA will be stacked. When inhibitors are removed, the polyploidized cells may return to the initial ploidy, because the stacked DNA loops have not been linked. When the stacked DNA twin-loops are linked with a proper configuration, the cells may become polyploid cells. There is a distinct difference in genome structure between polyploidized and polyploid cells. The homologous chromosomes of polyploid cells are arrayed mirror-symmetrically and they can come close to each other in the folded structure. If DNA synthesis is bypassed at the paired homologous chromosomes, DNA content is lost at every cell division. As the DNA loss progresses, the chromosome configuration of polyploid cells deviates gradually from mirror-symmetry and the DNA loss ceases, resulting in the establishment of semi-stable hypoploid.

Animals↗

PubMed1999

Rapid structural and epigenetic changes in polyploid and aneuploid genomes.

Recent work with plants has demonstrated that genome instability can be triggered by a change in chromosome number arising from either whole genome duplications (polyploidy) or loss/gain of individual chromosomes (aneuploidy). This genome instability is manifested as rapid structural and epigenetic alterations that can occur somatically or meiotically within a few generations after heteroploid formation. The intrinsic instability of newly formed polyploid and aneuploid genomes has relevance for genome evolution and human carcinogenesis, and points toward recombinational and epigenetic mechanisms that sense and respond to chromosome numerical changes.

Aneuploidy↗

PubMed2026

Deciphering the mosaic genome of sugarcane cultivars through polyploid admixture inference with AdmixPoly.

BACKGROUND: Characterizing population structure and admixture events between ancestral groups plays a key role in understanding the evolutionary history of species and crops. Most tools for inferring admixture have been developed for diploids and are not suitable for polyploids, in particular those with high and mixed ploidy such as Saccharum. RESULTS: Here we present AdmixPoly, an R-package designed to infer admixture in polyploid species both at the genome-wide scale and locally along chromosomes. We compare AdmixPoly with state-of-the-art methods using simulations, demonstrating its precision and computational efficiency. Notably, local admixture inference in complex scenarios, such as high ploidy levels, large numbers of ancestral groups and alleles per marker is enabled through efficient approximations of emission and transition probabilities within a hidden Markov model framework. We apply this approach to characterize the contributions of wild Saccharum species to the complex polyploid genome of modern sugarcane cultivars. A panel of wild and cultivated Saccharum accessions is genotyped for 80K genomic regions, each revealing approximately 50 read-scale haplotypes. CONCLUSIONS: The results reveal that most of the approximately 12 copies of each basic chromosome in modern cultivars are derived from the domesticated species Saccharum officinarum, with one to four copies typically contributed by distinct subgroups of the wild species Saccharum spontaneum. In addition, contributions from an unknown wild Saccharum group originating from the Pacific were identified in most cultivars. The conserved pattern of these introgressions suggests that they can be traced back to the early stages of sugarcane breeding approximately a century ago.

Saccharum↗

PubMed2005

Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana.

We review here the progress that has been achieved using molecular cytogenetics to analyze the genome structure of sugarcane (Saccharum spp) and banana (Musa spp), two crops that are polyploid, of interspecific origin and with chromosomes not distinguishable by their gross morphology. In Saccharum, molecular cytogenetics enabled us to determine the basic chromosome number of two species, Saccharum officinarum and S. spontaneum, involved in the origin of modern cultivars, to quantify the proportion of chromosomes of these species in the genome of modern cultivars, to assess the extent of interspecific chromosome recombination and to clarify the origin of the related species S. barberi. These techniques are also used to monitor introgression with related genera. In Musa, GISH enabled us to differentiate the four genomes involved in banana cultivars and allowed us to determine the genome constitution of several cultivars. FISH was used to analyze the distribution of repeated sequences along the genome.

Chromosomes, Plant↗

PubMed2005

Genome relationships in polyploid Poa pratensis and other Poa species inferred from phylogenetic analysis of nuclear and chloroplast DNA sequences.

The genus Poa comprises approximately 500 species that occur throughout the world, including the widely grown Kentucky bluegrass (P. pratensis L.). Hybridization and polyploidization have played a prominent role in the evolution of this complex genus, but limited information is available regarding genome relationships in Poa. Thus, we amplified, cloned, and compared the DNA sequences of 2 nuclear genes (CDO504 and thioredoxin-like protein) and 2 chloroplast genome loci (ndhF and trnT-trnF) from 22 Poa species. Four distinct classes of sequences corresponding to 4 putative homoeologous loci from each nuclear gene were found within polyploid P. pratensis. Nuclear sequences from 15 other Poa species were found to group with at least 1 P. pratensis homoeolog, whereas 6 species displayed sequences not present in P. pratensis. The nuclear genome phylogenies presented here show the first evidence of diverse and related genomes in the genus Poa.

Cell Nucleus↗

PubMed2000

Pairing affinities of the B- and G-genome chromosomes of polyploid wheats with those of Aegilops speltoides.

Chromosome pairing at metaphase I was studied in different interspecific hybrids involving Aegilops speltoides (SS) and polyploid wheats Triticum timopheevii (AtAtGG), T. turgidum (AABB), and T. aestivum (AABBDD) to study the relationships between the S, G, and B genomes. Individual chromosomes and their arms were identified by means of C-banding. Pairing between chromosomes of the G and S genomes in T. timopheevii x Ae. speltoides (AtGS) hybrids reached a frequency much higher than pairing between chromosomes of the B and S genomes in T. turgidum x Ae. speltoides (ABS) hybrids and T. aestivum x Ae. speltoides (ABDS) hybrids, and pairing between B- and G-genome chromosomes in T. turgidum x T. timopheevii (AAtBG) hybrids or T. aestivum x T. timopheevii (AAtBGD) hybrids. These results support a higher degree of closeness of the G and S genomes to each other than to the B genome. Such relationships are consistent with independent origins of tetraploid wheats T. turgidum and T. timopheevii and with a more recent formation of the timopheevi lineage.

Animals↗

PubMed2004

[Chromosome maps of trilliaceae: II. A study of the genome composition in polyploid species of the genus Trillium by fluorescence nucleotide base-specific staining of heterochromatic chromosome regions].

Chromosome banding with nucleotide base-specific fluorochromes chromomycin A3 (CMA) and Hoechst 33258 (H33258) was used to study the karyotypes and to construct cytological maps for diploid Trillium camschatcense (2n = 10), tetraploid T. tschonoskii (2n = 20), hexaploid T. rhombifolium (2n = 30), and a triploid T. camschatcense x T. tschonoskii hybrid (T. x hagae, 2n = 15). With H33258, species- and genome-specific patterns with numerous AT-rich heterochromatin bands were obtained for each of the four forms; CMA revealed a few small, mostly telomeric GC-rich bands. In T. tschonoskii, the two subgenomes were similar to each other and differed from the T. camschatcense genome; on this evidence, the species was considered to be a segmental allotetraploid. In T. x hagae, one T. camschatcense and both T. tschonoskii subgenomes were identified. The subgenomes of T. rhombifolium only partly corresponded to the T. camschatcense and T. tschonoskii genomes, in contrast to the morphologically identical Japanese species T. hagae. This was assumed to indicate that allohexaploids T. rhombifolium and T. hagae originated independently at different times; i.e., their origin is polyphyletic. Based on the chromosome maps, a new nomenclature was proposed for the Trillium genomes examined: K1K1 for T. camschatcense, T1T1T2T2 for T. tschonoskii, T1T1T2T2 for T. x hagae, and K1RK1RT1RT1RT2RT2R for T. rhombifolium.

Chromosome Mapping↗

PubMed1985

Chromosome banding in Amphibia. IX. The polyploid karyotypes of Odontophrynus americanus and Ceratophrys ornata (Anura, Leptodactylidae).

The somatic and meiotic chromosomes of the South American leptodactylid toads Odontophrynus americanus, Ceratophyrys ornata, and C. cranwelli were analysed both with conventional staining and differential banding techniques. The karyotypes of O. americanus were tetraploid; those of C. ornata octaploid. Ceratophrys cranwelli is a diploid species whose karyotype displays great similarities with that of C. ornata. The high frequency of multivalent pairing configurations in the meioses of O. americanus and C. ornata indicate that these animals were of autopolyploid origin. The conventionally stained somatic chromosomes of O. americanus can be arranged into sets of four similar chromosomes (quartets); those of C. ornata, into sets of eight similar chromosomes (octets). The banding patterns revealed heterogeneity within some quartets of O. americanus, dividing each of them into two pairs of homologous chromosomes. In analogy, some octets of C. ornata can be subdivided into two quartets of chromosomes with homologous bands. These structural heterogeneities within the quartets and octets are interpreted as a "diploidization" of the polyploid karyotypes. Diploidization leads to genomes that are polyploid with respect to the amount of genetic material and diploid with respect to chromosomal characteristics and the level of gene expression. In tetraploid O. americanus, the number of nucleolus organizer regions (NORs) and their DNA content is proportional to the degree of ploidy. In contrast, up to eight NORs have been deleted in the octoploid C. ornata. These NOR losses are discussed as a possible reason for the reduction of genetic activity in polyploid genomes.

Animals↗

PubMed1994

New 18S.26S ribosomal RNA gene loci: chromosomal landmarks for the evolution of polyploid wheats.

Three new 18S.26S rRNA gene loci were identified in common wheat by sequential N-banding and in situ hybridization (ISH) analysis. Locus Nor-A7 is located at the terminal area of the long arm of 5A in both diploid and polyploid wheats. Locus Nor-B6 is located in N-band 1BL2.5 of the long arm of chromosome 1B in Triticum turgidum and Triticum aestivum. ISH sites, similar to Nor-B6, were also detected on the long arms of chromosomes 1G in Triticum timopheevii and 1S in Aegilops speltoides, but their locations on the chromosomes were different from that of Nor-B6, indicating possible chromosome rearrangements in 1GL and 1BL during evolution. The third new locus, Nor-D8, was only found on the short arm of chromosome 3D in the common wheat Wichita. The loss of rRNA gene locus Nor-A3 and gain of repetitive DNA sequence pSc119 on the terminal part of 5AS suggest a structural modification of 5AS. Comparative studies of the location of the 18S.26S rRNA gene loci in polyploid wheats and putative A and B (G) genome progenitor species support the idea that: (1) Triticum monococcum subsp. urartu is the donor of both the A and A(t) genome of polyploid wheats. (2) Ae. speltoides is closer to the B and G genome of polyploid wheats than Aegilops longissima and is the most probable progenitor of these two genomes.

Biological Evolution↗

PubMed1992

Chloroplast heteroplasmicity is stabilized by an amber-suppressor tryptophan tRNA(CUA).

Photosynthesis-deficient mutants of the green alga Chlamydomonas reinhardtii were previously shown to arise from nonsense mutations within the chloroplast rbcL gene, which encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39). Photosynthesis-competent revertants of these nonsense mutants have often been found to be stably heteroplasmic, giving rise to both mutant and revertant cells during mitotic or meiotic divisions under nonselective growth conditions. It was proposed that the stable heteroplasmicity might arise from a balanced polymorphism of suppressor and wild-type alleles of a tRNA gene maintained within the polyploid chloroplast genome. In the present study, we have focused on determining the molecular basis for the heteroplasmicity of one such revertant, named R13-3C, which was recovered from the 18-7G amber (UAG) mutant. Restriction-enzyme analysis and DNA sequencing showed that the amber mutation is still present in the rbcL gene of the revertant strain. In contrast, DNA sequencing of the suspected tRNA(Trp) gene of the revertant revealed a mutation that would change its CCA anticodon to amber-specific CUA. This mutation was found to be heteroplasmic, being present in only 70% of the tRNA(Trp) gene copies. Under nonselective conditions, the suppressor mutation was lost from cells that also lost the revertant phenotype. We conclude that stable heteroplasmicity can arise as a balanced polymorphism of organellar alleles. This observation suggests that additional tRNA suppressors may be identified due to their heteroplasmic nature within polyploid genomes.

Animals↗