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PubMed2005

Evolution of Hox clusters in Salmonidae: a comparative analysis between Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss).

We studied the genomic organization of Hox genes in Atlantic salmon (Salmo salar) and made comparisons to that in rainbow trout (Oncorhynchus mykiss), another member of the family Salmonidae. We used these two species to test the hypothesis that the Hox genes would provide evidence for a fourth round of duplication (4R) of this gene family given the recent polyploid ancestry of the salmonid fish. Thirteen putative Hox clusters were identified and 10 of these complexes were localized to the current Atlantic salmon genetic map. Syntenic regions with the rainbow trout linkage map were detected and further homologies and homeologies are suggested. We propose that the common ancestor of Atlantic salmon and rainbow trout possessed at least 14 clusters of Hox genes, and additional clusters cannot be ruled out. Salmonid Hox cluster complements seem to be more similar to those of zebrafish (Danio rerio) than medaka (Oryzias latipes) or pufferfish (Sphoeroides nephelus and Takifugu rubripes), as both Atlantic salmon and rainbow trout have retained HoxCb ortholog, which has been lost in medaka and pufferfish but not in zebrafish. However, our data suggest that phylogenetically, the homologous genes within each cluster express mosaic relationships among the teleosts tested and, thus, leave unresolved the interfamilial relationships among these taxa.

Animals↗

PubMed2005

Gene duplication and the properties of biological networks.

Patterns of network connection of members of multigene families were examined for two biological networks: a genetic network from the yeast Saccharomyces cerevisiae and a protein-protein interaction network from Caenorhabditis elegans. In both networks, genes belonging to gene families represented by a single member in the genome ("singletons") were disproportionately represented among the nodes having large numbers of connections. Of 68 single-member yeast families with 25 or more network connections, 28 (44.4%) were located in duplicated genomic segments believed to have originated from an ancient polyploidization event; thus, each of these 28 loci was thus presumably duplicated along with the genomic segment to which it belongs, but one of the two duplicates has subsequently been deleted. Nodes connected to major "hubs" with a large number of connections, tended to be relatively sparsely interconnected among themselves. Furthermore, duplicated genes, even those arising from recent duplication, rarely shared many network connections, suggesting that network connections are remarkably labile over evolutionary time. These factors serve to explain well-known general properties of biological networks, including their scale-free and modular nature.

Animals↗

PubMed2004

Analysis of genomic and expressed major histocompatibility class Ia and class II genes in a hexaploid Lake Tana African 'large' barb individual (Barbus intermedius).

Expression of too many co-dominant major histocompatibility complex (MHC) alleles is thought to be detrimental to proper functioning of the immune system. Polyploidy of the genome will increase the number of expressed MHC genes unless they are prone to a silencing mechanism. In polyploid Xenopus species, the number of MHC class I and II genes has been physically reduced, as it does not increase with higher ploidy genomes. In the zebrafish some class II B loci have been silenced, as only two genomically bona fide loci, DAA/DAB and DEA/DEB, have been described. Earlier studies indicated a reduction in the number of genomic and expressed class II MHC genes in a hexaploid African 'large' barb. This prompted us to study the number of MHC genes present in the genome of an African 'large' barb individual (Barbus intermedius) in relation to those expressed, adopting the following strategy. Full-length cDNA sequences were generated from mRNA and compared with partial genomic class Ia and II sequences generated by PCR using the same primer set. In addition, we performed Southern hybridizations to obtain a verification of the number of class I and II B genes. Our study revealed three beta2-microglobulin, five class Ia, four class II A, and four class II B genes at the genomic level, which were shown to be expressed in the hexaploid barb individual. The class Ia and class II data indicate that the ploidy status does not correlate with the presence and expression of these MHC genes.

Amino Acid Sequence↗

PubMed2002

The development of low temperature inactive (Lti) baker's yeast.

The construction of a novel baker's yeast variety via traditional genetic techniques is described. The phenotype was designated "Lti" ("Low temperature inactive"). Lti mutations with the desired characteristics within a genetically well-defined haploid laboratory strain of Saccharomyces cerevisiae were isolated, and two different approaches were taken to obtain baker's yeast strains, which exhibit reduced fermenting activity at refrigeration temperatures. In a first approach, a chosen Lti strain carrying mutation lti9 was combined with other laboratory strains carrying defined MAL alleles. In a second approach, the same lti mutation was introduced in the genetic background of polyploid commercial baker's yeast strains that harbor important "industrial" properties. Lti strains arising from both approaches were characterized with specifically developed screening procedures. Strains of the "academic" Lti strain family displayed between 85% and 92% of the biomass yield of a commercial reference strain, whereas strains of the "industrial" Lti strain family showed a variation between 60% and 115%. Lti strains from both families varied strongly among each other in their activity in model doughs: at 8 degrees C they displayed activities between 5% and 30%, and at 30 degrees C between 40% and 113% of a commercial reference baker's yeast strain.

Biomass↗

PubMed2002

Saccharomyces bayanus var. uvarum in Tokaj wine-making of Slovakia and Hungary.

Using genetic hybridisation analysis and molecular karyotyping we revealed an association of Saccharomyces bayanus var. uvarum species with Tokaj wine-making. Along with identification of Saccharomyces strains isolated by E. Minárik in Slovakia, the composition of Tokaj populations in Hungary was studied. Twenty-eight Hungarian Saccharomyces strains were analysed in terms of karyotype. The majority of strains belong to S. bayanus var. uvarum. Two non-identified Saccharomyces strains were found to be polyploid according to their complex karyotype patterns.

DNA, Bacterial↗

PubMed2005

Direct mating between diploid sake strains of Saccharomyces cerevisiae.

Various auxotrophic mutants of diploid heterothallic Japanese sake strains of Saccharomyces cerevisiae were utilized for selecting mating-competent diploid isolates. The auxotrophic mutants were exposed to ultraviolet (UV) irradiation and crossed with laboratory haploid tester strains carrying complementary auxotrophic markers. Zygotes were then selected on minimal medium. Sake strains exhibiting a MATa or MATalpha mating type were easily obtained at high frequency without prior sporulation, suggesting that the UV irradiation induced homozygosity at the MAT locus. Flow cytometric analysis of a hybrid showed a twofold higher DNA content than the sake diploid parent, consistent with tetraploidy. By crossing strains of opposite mating type in all possible combinations, a number of hybrids were constructed. Hybrids formed in crosses between traditional sake strains and between a natural nonhaploid isolate and traditional sake strains displayed equivalent fermentation ability without any apparent defects and produced comparable or improved sake. Isolation of mating-competent auxotrophic mutants directly from industrial yeast strains allows crossbreeding to construct polyploids suitable for industrial use without dependence on sporulation.

Alcoholic Beverages↗

PubMed1996

Thrombopoietic activity of recombinant human interleukin 11 in cancer patients receiving chemotherapy.

Interleukin 11 (IL-11) is a newly identified hematopoietic growth factor that exerts its primary effect on megakaryocyte maturation and platelet production. It has a unique receptor, signaling by which is mediated by the glycoprotein (GP) 130 pathway. IL-11 is synergistic with stem-cell factor (c-kit ligand) in vitro, enhancing proliferation of primitive hematopoietic stem cells, and has been shown to be critical to the process of polyploidization and maturation. In preclinical models, IL-11 was shown to enhance platelet recovery following intensive chemotherapy, and in murine bone-marrow transplant models it accelerates the recovery of all hematopoietic lineages. Nonhuman primate studies have demonstrated a dose-related thrombopoietic effect; however, no myeloid effect has been observed. In clinical phase I trials, subcutaneous IL-11 was well tolerated and induced a dose-related thrombopoietic effect in women with breast cancer. IL-11 at doses of > 25 micrograms/kg per day appeared to reduce the severity of chemotherapy-induced thrombocytopenia. In a randomized phase II trial, IL-11 at 50 micrograms/kg reduced the requirement for platelet transfusions as compared with that in placebotreated controls. IL-11 is an interesting factor; however, further studies are needed to confirm its activity and are in progress.

Antineoplastic Agents↗

PubMed2002

[Anagrelide-induced changes of megakaryopoiesis during therapy of chronic myeloproliferative disorders with thrombocythemia].

Thrombocythemia in the course of chronic myeloproliferative disorders like chronic idiopathic myelofibrosis (cIMF) and of course essential thrombocythemia (ET), are characterized by life-threatening complications. In a number of clinical trials the recently introduced drug Agrylin((R)) has proven to be very effective. The normalization of the platelet count was related to an interference with megakaryocyte maturation leading to a left-shifting of this cell lineage and/or a reduced proliferation. However, until now no systematic study has been performed on the relationship between development of megakaryopoiesis and proliferative activity. In this investigation we included 10 patients with cIMF and 5 patients with ET that had received Agrylin((R)) for a period ranging between 6 and 70 months. Following therapy this cohort revealed a decrease in the platelet count from 1,104x10(9)/l at diagnosis to 485x10(9)/l. In this context we focused on an immunohistochemical and morphometric analysis of the CD61(+) megakaryopoiesis involving also endomitotic reduplication, by applying a double-immune incubation technique with the proliferating cell nuclear antigen (PCNA). Moreover, we determined the changes of fiber density during observation time. According to our results, the thrombocytopenic effect of Agrylin((R)) is based on an arrest in the dynamics of megakaryocyte maturation towards large (mature) platelet-shedding (polyploid) cells. This pathomechanism causes a significant increase in the number of promegakaryoblasts and megakaryoblasts. On the other hand, the total amount of CD61(+) megakaryocytic cells is not increased. Related to the peculiar cell biology of endomitotic reduplication during the maturation process and its different periods alloted to each single step, PCNA activity (late G1- and S-phase of the cell cycle) is found to be enhanced in the megakaryocyte precursors. Finally, no significant influence of Agrylin((R)) on the evolution of myelofibrosis is detectable and there is a general improvement of hematological data especially in cIMF.

Blood Platelets↗

PubMed2004

Production of intergeneric somatic hybrids between round kumquat (Fortunella japonica Swingle) and 'Morita navel' orange (Citrus sinensis Osbeck).

Intergeneric somatic hybrids between embryogenic callus-derived protoplasts of round kumquat (Fortunella japonica Swingle) and 'Morita navel' orange (Citrus sinensis Osbeck) were produced by electrofusion. Among the eight different fusion strains obtained, six showed normal morphology, whereas the remaining two showed malformation. All the regenerated plants were intermediate in leaf morphology and had thick and round leaves, which are typical characteristics of polyploids. Ploidy analyses by flow cytometry and chromosome counting in root-tip cells revealed that these plants are amphidiploid (2n=4x=36). Hybridity of the fusion products was confirmed by random amplified polymorphic DNA and cleaved amplified polymorphic sequence (CAPS) analyses. Furthermore, analyses of chloroplast (cp) and mitochondrial (mt) DNA by CAPS showed that these somatic hybrids contained cp- and mt-DNA of round kumquat without recombination in the regions analyzed.

Chimera↗

PubMed2004

Aminooxyacetic acid inhibits antheridiogenesis and development of Anemia phyllitidis gametophytes.

Cytomorphological studies of the development of young fern gametophytes (Anemia phyllitidis) have been used to investigate combined effects of gibberellic acid and ethylene on male sex expression. ACC (the key by-product in ethylene biosynthesis pathway) was found to exert a synergetic effect on the gibberellic acid-induced antheridia formation, and this phenomenon could be related with the specific stimulation of cell growth and activity of their differentiation. To complete and verify those observations male sex expression in the fern gametophytes treated with ACC-biosynthesis inhibitor was reinvestigated. Aminooxyacetic acid (AOA) restrained antheridia formation via inhibition of cell divisions. AOA influenced the arrangement and flexibility of cellulose microfibrils in the antheridial zone cells, thus affecting cell expansion. On the other hand, the level of DNA synthesis was not reduced. Transient increase in the number of S-phase cells, followed by the accumulation of G2-phase cells led to the enhancement of cell polyploidization. All these findings correspond with the previous observations and support participation of ethylene in gibberellic acid-induced male sex expression in ferns.

Amino Acids, Cyclic↗

PubMed2004

Multiple spindles and cellularization during microsporogenesis in an artificially induced tetraploid accession of Brachiaria ruziziensis (Gramineae).

The genus Brachiaria is characterized by a majority of polyploid accessions--mainly tetraploid--and apomictic reproduction. Sexuality is found among diploids. To overcome incompatibility barriers, accessions with the same ploidy level are necessarily used in hybridization. Thus, sexual diploid accessions were tetraploidized to be used as female genitors. This paper reports microsporogenesis in an artificially induced tetraploid accession of Brachiaria ruziziensis. Chromosome pairing at diakinesis ranged from univalents to tetravalents, with predominance of bivalents. Irregular chromosome segregation was frequent in both meiotic divisions. During the first division, multiple spindles showing different arrangements were recorded. The spindle position determined the plane of first cytokinesis and the number of chromosomes determined the size of the cell. Meiotic products were characterized by polyads with spores of different sizes. Pollen sterility was estimated at 61.38%. The limitations of using this accession in the breeding program are discussed.

Brachiaria↗

PubMed2005

Production of doubled haploids in durum wheat (Triticum turgidum L.) through isolated microspore culture.

The objective of this work was to produce doubled haploid plants from durum wheat through the induction of androgenesis. A microspore culture technique was developed and used to produce fertile doubled haploid plants of agronomic interest. Five cultivars, one selected line, plus a collection of 20 F(1) crosses between different genotypes of high breeding value were used. Studies on several factors such as pre-treatments and media components were carried out in order to develop a protocol to regenerate green haploid plantlets. Anthers were pre-treated in 0.7 M mannitol. Microspores, from anther maceration, were plated on a C(17) induction culture medium with ovary co-culture. The optimum regeneration medium J25-8 was used. From 35 microspore isolations, 407 green plantlets were obtained. With this technique mature embryos were obtained. Green plants were regenerated from all genotypes used and approximately 67% of them were spontaneously doubled haploids. Some haploids and a very few polyploids plants were obtained. From the 407 plants, 275 were completely fertile and gave enough seeds to be assayed in the field. This protocol could be used complementary to or instead of the intergeneric crossing with maize as an economically feasible method to obtain doubled haploids from most durum wheat genotypes.

Benzyl Compounds↗

PubMed2005

Differential expression of manganese superoxide dismutase sequence variants in near isogenic lines of wheat during cold acclimation.

Numerous sequence variants of wheat (Triticum aestivum L.) manganese superoxide dismutase (MnSOD) genes have been found. Quantitative real-time PCR was used to measure the expression levels of three MnSOD genes distinguished by a variable amino acid, and three genes distinguished by sequence variation in the 3' untranslated region (3' UTR), in wheat plants grown at 20 degrees C and cold-acclimated for 1-4 weeks at 2 degrees C. The amino acid variants did not differ significantly in expression levels, however, differential expression of genes differing in the 3' UTR was observed. Diploid wheat-related species also carried sequence variants of MnSOD, with differing levels of expression, suggesting diversification of the MnSOD gene family occurred prior to the polyploidization events of hexaploid wheat.

3' Untranslated Regions↗

PubMed2006

Occurrence of tetraploidy in Nicotiana attenuata plants after Agrobacterium-mediated transformation is genotype specific but independent of polysomaty of explant tissue.

Genotypes of Nicotiana attenuata collected from Utah and Arizona were transformed with 17 different vectors (14 unpublished vectors based on 3 new backbone vectors) using an Agrobacterium-mediated procedure to functionally analyze genes important for plant-insect interactions. None of the 51 T1-T3 transgenic Utah lines analyzed by the flow cytometry were tetraploid, as opposed to 18 of 33 transgenic Arizona lines (55%). Analysis of T0 regenerants transformed with the same vector carrying an inverted repeat (IR) N. attenuata pro-systemin construct confirmed the genotype dependency of tetraploidization: none of the 23 transgenic Utah lines were tetraploid but 31 (72%) of 43 transgenic Arizonas were tetraploid. We tested the hypothesis that the differences in polysomaty of the explant tissues accounted for genotype dependency of tetraploid formation by measuring polysomaty levels in different seedling tissues. Hypocotyls, cotyledons, and roots of Utah and Arizona genotypes contained similar percentages of 4C nuclei (61 and 60; 7 and 5; and 58 and 61%, respectively). Since we used hypocotyls as explant sources and the nonoccurrence of tetraploid Utah transformants does not correspond to the high percentage of 4C nuclei in Utah hypocotyls, we can rule out a direct relationship between tetraploid formation and polysomaty level. We hypothesize that the difference between the Utah and Arizona genotypes results from the failure of polyploid Utah callus to regenerate into fully competent plants. We propose that future work on post-transformation polyploidy concentrate on the processes that occur during callus formation and plant regeneration from callus.

Cotyledon↗

PubMed2005

An efficient adventitious shoot regeneration system for Zhanhua winter jujube (Zizyphus jujuba Mill.) using leaf explants.

The direct induction of adventitious shoots from leaf explants obtained from adult plants of Zhanhua winter jujube, an elite variety of Zizyphus jujuba Mill., is reported. The percentage of leaf explants producing shoots and the average number of shoots per explant were significantly improved when 10-day-old leaves were explanted onto Woody Plant Medium and maintained initially in the dark. The plant growth regulator thidiazuron (TDZ) was effective in stimulating shoot regeneration from leaf explants of Zhanhua winter jujube. The highest efficiency of shoot formation was observed with a 20-day culture in the dark on WPM containing 4.54 microM TDZ and 2.85 microM indoleacetic acid (IAA). The regenerated shoots were transferred to MS medium containing 0.89 microM benzyladenine and 5.77 microM gibberellic acid for growth. When the shoots were about 2 cm in height, they were transferred to Nitsch medium supplemented with 1.14 microM IAA and 2.46 microM indolebutyric acid to induce rooting. This system of adventitious shoot production from leaf explants of adult plants could be useful for the genetic engineering and polyploidization of winter jujube.

Agriculture↗

PubMed2026

Complete telomere-to-telomere genome assembly of Guazuma ulmifolia uncovers evolutionary mechanisms, drought adaptation, and flavonoid biosynthesis.

The first T2T reference genome of Guazuma ulmifolia is reported, which serves as a core genomic resource for stress adaptation research and stress-tolerant breeding in cacao wild relatives. Climate change, particularly increased incidence of drought, poses a major threat to food security. Understanding the genomic basis of environmental adaptation in crop wild relatives can provide valuable resources for improving stress resilience. Guazuma ulmifolia, a wild relative of Theobroma cacao with important ecological and medicinal value, lacks high-quality reference genomic resources. Here, we report the first telomere-to-telomere (T2T) chromosome-level genome assembly of G. ulmifolia, with a genome size of 311.31 Mb, contig N50 of 35.19 Mb, and 98.70% BUSCO completeness. Repetitive sequences constitute 27.43% of the G. ulmifolia genome, with LTR retrotransposons as the predominant class. Comparative genomic analyses revealed that genome-size variation among Malvaceae species is associated with differences in polyploidization history and TE dynamics. Ancestral karyotype reconstruction identified five lineage-specific chromosome fusion events distinguishing G. ulmifolia from T. cacao. Comparative analyses further identified tandem duplication-associated expansion of stress-related LEA and GST gene families, suggesting potential genomic features associated with stress responses. Flavonoid biosynthesis genes were largely conserved in copy number but showed tissue-specific expression patterns, providing candidate genes for investigating secondary metabolism. Together, this study establishes a high-quality T2T genome resource for exploring genome evolution, chromosome organization, and stress-related genomic features in Malvaceae.

Genome, Plant↗

PubMed2002

Persistence of neoangiogenesis and cardiomyocyte divisions in right ventricular myocardium of rats born and raised in hypoxic conditions.

Effects of chronic hypoxia on capillary and myocyte growth were examined in rats born and raised in a low pressure chamber (equivalent of 3500 m a.s.l.). The animals were sacrificed at the age of 3 months and their hearts were used to study right ventricular growth and vascularization. The results of our cytological and morphometric analysis suggest the persistence of capillary neogenesis in this particular model of cardiac hypertrophy. Under the optical microscope, we observed significant changes in capillary spatial patterns such as the presence of sinusoids and irregular capillary sprouts. This resulted in a significant shortening of the effective diffusion distance and in a slight decrease in the calculated diameter of the Krogh cylinder. Concomitant to the remodeling of the terminal capillary network, the right ventricular myocardium of hypoxic rats exhibited peculiar changes in myocyte cytology. The principal alteration consisted in the ectopic subsarcolemmal location of some of muscle cell nuclei which appeared enlarged and rounded, sometimes irregularly folded. At the E. M. level, they presented chromatine condensation, nucleolemmal folding and, occasionally, nuclear splitting. Irregular chromatin densifications at the equatorial position were also encountered but we never observed nucleolemmal dissolution or typical metaphase plaques which excludes the presence of mitotic division. Some of the marginalized nuclei were progressively excluded from original binucleate cells into small cytoplasmic processes that invaded the adjacent neo-formed pericapillar spaces and gave rise to small well-organized cardiomyocytes. This apparent fragmentation of cardiomyocytes may evoke the description of the apoptotic process which is believed to be stimulated in hypoxic tissues. However, we could not confirm that myocyte fragmentation that we describe is followed by shrinkage necrosis or by any mobilization of adjacent resident cells. Nuclear exclusions into pericapillary myocyte sprouts may, therefore, reflect amitotic divisions of polyploid cardiomyocytes which contribute to the persistence of hyperplasic growth in right ventricular myocardium in hearts of rats exposed to chronic hypoxia during their early postnatal life. Par analogie with our data, it can be expected that an appropriate stimulation of angiogenesis in hearts of adult animals attenuates some of cytological and functional drawbacks that accompany hypertrophic cardiomyopathies of other etiologies.

Age Factors↗

PubMed1998

Radiation-induced genetic instability: no association with changes in radiosensitivity or cell cycle checkpoints in C3H 10T1/2 mouse fibroblasts.

We investigated various phenotypic characteristics of radiation-induced morphologically transformed C3H 10T1/2 mouse fibroblasts. The cells were treated with 8 Gy x-rays, and type II/III foci were isolated. Cell lines were developed from these foci, and subsequently clones were established from these focal lines. The clones were examined for DNA content, radiosensitivity and inducible cell cycle arrests. Besides the morphological changes associated with the transformed state, the major difference between the isolated focal lines or derived clones and the parental C3H 10T1/2 line was one of ploidy. The transformed cells often displayed aneuploid and multiple polyploid populations. No change in the radiosensitivity of the transformed cells was observed. Furthermore, the two major radiation- and staurosporine-induced G1 and G2 cell cycle arrests observed in the parental cell line were also observed in the morphological transformants, suggesting that checkpoint function was normal.

Aneuploidy↗