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1.
mBio ; 12(3)2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33975937

RESUMO

The thermotolerant multidrug-resistant ascomycete Candida auris rapidly emerged since 2009 causing systemic infections worldwide and simultaneously evolved in different geographical zones. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in C. auris and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses. We find that C. auris and multiple other species in the Clavispora/Candida clade shared a conserved small regional GC-poor centromere landscape lacking pericentromeres or repeats. Further, a centromere inactivation event led to karyotypic alterations in this species complex. Interspecies genome analysis identified several structural chromosomal changes around centromeres. In addition, centromeres are found to be rapidly evolving loci among the different geographical clades of the same species of C. auris Finally, we reveal an evolutionary trajectory of the unique karyotype associated with clade 2 that consists of the drug-susceptible isolates of C. aurisIMPORTANCECandida auris, the killer fungus, emerged as different geographical clades, exhibiting multidrug resistance and high karyotype plasticity. Chromosomal rearrangements are known to play key roles in the emergence of new species, virulence, and drug resistance in pathogenic fungi. Centromeres, the genomic loci where microtubules attach to separate the sister chromatids during cell division, are known to be hot spots of breaks and downstream rearrangements. We identified the centromeres in C. auris and related species to study their involvement in the evolution and karyotype diversity reported in C. auris We report conserved centromere features in 10 related species and trace the events that occurred at the centromeres during evolution. We reveal a centromere inactivation-mediated chromosome number change in these closely related species. We also observe that one of the geographical clades, the East Asian clade, evolved along a unique trajectory, compared to the other clades and related species.


Assuntos
Candida/genética , Centrômero/genética , Centrômero/metabolismo , Cromossomos/genética , Evolução Molecular , Genoma Fúngico , Antifúngicos/farmacologia , Candida/classificação , Candida/efeitos dos fármacos , Candidíase/microbiologia , Centrômero/classificação , Cromossomos/classificação , Genômica , Virulência
2.
mBio ; 12(1)2021 01 26.
Artigo em Inglês | MEDLINE | ID: mdl-33500338

RESUMO

How to achieve protein diversity by genome and transcriptome processing is essential for organismal complexity and adaptation. The present work identifies that the macronuclear genome of Halteria grandinella, a cosmopolitan unicellular eukaryote, is composed almost entirely of gene-sized nanochromosomes with extremely short nongenic regions. This challenges our usual understanding of chromosomal structure and suggests the possibility of novel mechvanisms in transcriptional regulation. Comprehensive analysis of multiple data sets reveals that Halteria transcription dynamics are influenced by: (i) nonuniform nanochromosome copy numbers correlated with gene-expression level; (ii) dynamic alterations at both the DNA and RNA levels, including alternative internal eliminated sequence (IES) deletions during macronucleus formation and large-scale alternative splicing in transcript maturation; and (iii) extremely short 5' and 3' untranslated regions (UTRs) and universal TATA box-like motifs in the compact 5' subtelomeric regions of most chromosomes. This study broadens the view of ciliate biology and the evolution of unicellular eukaryotes, and identifies Halteria as one of the most compact known eukaryotic genomes, indicating that complex cell structure does not require complex gene architecture.


Assuntos
Cromossomos/genética , Cilióforos/genética , Genoma , Macronúcleo/genética , Transcriptoma , Cromossomos/classificação , Filogenia
3.
Braz. J. Pharm. Sci. (Online) ; 57: e19033, 2021. tab, graf
Artigo em Inglês | LILACS | ID: biblio-1345461

RESUMO

Previously, we evaluated the effect of trichostatin A (TSA) on the expression of DNA methyltransferase 1 (DNMT1) in Hepatocellular Carcinoma (HCC). Fragile histidine triad (FHIT) and WW domain-containing oxidoreductase (WWOX) are two of the most common down-regulated genes in many cancers located on chromosome 3p14.2 and 16q23.3-24.1 respectively. The aim of the current study was to assess the effect of TSA on these genes expression, cell growth, and apoptosis in HCC WCH 17 cell. The cells were seeded and treated with TSA at different times. Then, MTT assay, flow cytometry, and qRT-PCR were achieved to determine viability, apoptosis and gene expression respectively. Cell growth was significantly inhibited, 92 to 36% after 24 h, 86 to 28% after 48 h, and 78 to 24% after 72 h. The results of flow cytometry confirmed that TSA increased apoptosis compared to the control group, the apoptosis percentage increased to 12%, 16%, and 18% in comparison to control groups (2%). Significant up-regulation of the genes was observed in all treated groups. We concluded that re-expression of silenced WWOX and FHIT genes could be achieved by TSA resulting in cell growth inhibition and apoptosis induction in WCH 17 cell.


Assuntos
Apoptose/fisiologia , Carcinoma Hepatocelular/patologia , Oxidorredutase com Domínios WW , Crescimento/fisiologia , Cromossomos/classificação , Citometria de Fluxo/instrumentação , Neoplasias/classificação
4.
Genes (Basel) ; 11(6)2020 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-32521831

RESUMO

The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68-86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) probes for chromosomes GGA11-28 for Columbina passerina, Columbina talpacoti, Patagioenas cayennensis, Geotrygon violacea and Geotrygon montana. Streptopelia decaocto was only investigated with paints because BACs for GGA10-28 had been previously analyzed. We also performed phylogenetic analyses in order to trace the evolutionary history of this family in light of chromosomal changes using our wcp data with chicken probes and from Zenaida auriculata, Columbina picui, Columba livia and Leptotila verreauxi, previously published. G-banding was performed on all these species. Comparative chromosome paint and G-banding results suggested that at least one interchromosomal and many intrachromosomal rearrangements had occurred in the diversification of Columbidae species. On the other hand, a high degree of conservation of microchromosome organization was observed in these species. Our cladistic analysis, considering all the chromosome rearrangements detected, provided strong support for L. verreauxi and P. cayennensis, G. montana and G. violacea, C. passerina and C. talpacoti having sister taxa relationships, as well as for all Columbidae species analyzed herein. Additionally, the chromosome characters were mapped in a consensus phylogenetic topology previously proposed, revealing a pericentric inversion in the chromosome homologous to GGA4 in a chromosomal signature unique to small New World ground doves.


Assuntos
Cromossomos/genética , Columbidae/genética , Análise Citogenética , Passeriformes/genética , Animais , Evolução Biológica , Galinhas/genética , Inversão Cromossômica/genética , Coloração Cromossômica/métodos , Cromossomos/classificação , Columbidae/classificação , Columbiformes/genética , Cariótipo , Passeriformes/classificação , Filogenia , Sintenia/genética
5.
Genes (Basel) ; 11(3)2020 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-32131436

RESUMO

The genus Crocidura represents a remarkable model for the study of chromosome evolution. This is the case of the lesser white-toothed shrew (Crocidura suaveolens), a representative of the Palearctic group. Although continuously distributed from Siberia to Central Europe, C. suaveolens is a rare, habitat-specialist species in the southwesternmost limit of its distributional range, in the Gulf of Cádiz (Iberian Peninsula). In this area, C. suaveolens is restricted to genetically isolated populations associated to the tidal marches of five rivers (Guadiana, Piedras, Odiel, Tinto and Guadalquivir). This particular distributional range provides a unique opportunity to investigate whether genetic differentiation and habitat specialization was accompanied by chromosomal variation. In this context, the main objective of this study was to determinate the chromosomal characteristics of the habitat-specialist C. suaveolens in Southwestern Iberia, as a way to understand the evolutionary history of this species in the Iberian Peninsula. A total of 41 individuals from six different populations across the Gulf of Cádiz were collected and cytogenetically characterized. We detected four different karyotypes, with diploid numbers (2n) ranging from 2n = 40 to 2n = 43. Two of them (2n = 41 and 2n = 43) were characterized by the presence of B-chromosomes. The analysis of karyotype distribution across lineages and populations revealed an association between mtDNA population divergence and chromosomal differentiation. C. suaveolens populations in the Gulf of Cádiz provide a rare example of true karyotypic polymorphism potentially associated to genetic isolation and habitat specialization in which to investigate the evolutionary significance of chromosomal variation in mammals and their contribution to phenotypic and ecological divergence.


Assuntos
Cromossomos/genética , Eutérios/genética , Evolução Molecular , Cariótipo , Animais , Cromossomos/classificação , DNA Mitocondrial/genética , Ecossistema , Europa (Continente) , Deriva Genética , Variação Genética/genética , Genética Populacional , Humanos , Cariotipagem , Filogenia , Musaranhos/genética , Sibéria , Áreas Alagadas
6.
BMC Med Genomics ; 11(Suppl 5): 0, 2018 11 20.
Artigo em Inglês | MEDLINE | ID: mdl-30453954

RESUMO

BACKGROUND: While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge. METHODS: We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods. RESULTS: We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs). CONCLUSION: Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.


Assuntos
Cromossomos/genética , Algoritmos , Povo Asiático/classificação , Povo Asiático/genética , População Negra/classificação , População Negra/genética , Cromossomos/classificação , Estudo de Associação Genômica Ampla , Humanos , Polimorfismo de Nucleotídeo Único , População Branca/classificação , População Branca/genética
7.
Cytogenet Genome Res ; 153(1): 46-53, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29130975

RESUMO

The number of sequenced lepidopteran genomes is increasing rapidly. However, the corresponding assemblies rarely represent whole chromosomes and generally also lack the highly repetitive W sex chromosome. Knowledge of the karyotypes can facilitate genome assembly and further our understanding of sex chromosome evolution in Lepidoptera. Here, we describe the karyotypes of the Glanville fritillary Melitaea cinxia (n = 31), the monarch Danaus plexippus (n = 30), and the African queen D. chrysippus (2n = 60 or 59, depending on the source population). We show by FISH that the telomeres are of the (TTAGG)n type, as found in most insects. M. cinxia and D. plexippus have "conventional" W chromosomes which are heterochromatic in meiotic and somatic cells. In D. chrysippus, the W is inconspicuous. Neither telomeres nor W chromosomes are represented in the published genomes of M. cinxia and D. plexippus. Representation analysis in sequenced female and male D. chrysippus genomes detected an evolutionarily old autosome-Z chromosome fusion in Danaus. Conserved synteny of whole chromosomes, so called "macro synteny", in Lepidoptera permitted us to identify the chromosomes involved in this fusion. An additional and more recent sex chromosome fusion was found in D. chrysippus by karyotype analysis and classical genetics. In a hybrid population between 2 subspecies, D. c. chrysippus and D. c. dorippus, the W chromosome was fused to an autosome that carries a wing colour locus. Thus, cytogenetics and the present state of genome data complement one another to reveal the evolutionary history of the species.


Assuntos
Borboletas/genética , Genoma/genética , Cariótipo , Sintenia/genética , Telômero/genética , Animais , Mapeamento Cromossômico , Cromossomos/classificação , Cromossomos/genética , Feminino , Hibridização in Situ Fluorescente , Masculino
9.
Cytogenet Genome Res ; 145(3-4): 201-17, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26112092

RESUMO

Mitotic chromosomes of 16 species of the frog genus Xenopus were prepared from kidney and lung cell cultures. In the chromosomes of 7 species, high-resolution replication banding patterns could be induced by treating the cultures with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT) in succession, and in 6 of these species the BrdU/dT-banded chromosomes could be arranged into karyotypes. In the 3 species of the clade with 2n = 20 and 4n = 40 chromosomes (X. tropicalis, X. epitropicalis, X. new tetraploid 1), as well as in the 3 species with 4n = 36 chromosomes (X. laevis, X. borealis, X. muelleri), the BrdU/dT-banded karyotypes show a high degree of homoeology, though differences were detected between these groups. Translocations, inversions, insertions or sex-specific replication bands were not observed. Minor replication asynchronies found between chromosomes probably involve heterochromatic regions. BrdU/dT replication banding of Xenopus chromosomes provides the landmarks necessary for the exact physical mapping of genes and repetitive sequences. FISH with an X. laevis 5S rDNA probe detected multiple hybridization sites at or near the long-arm telomeric regions in most chromosomes of X. laevis and X. borealis, whereas in X. muelleri, the 5S rDNA sequences are located exclusively at the long-arm telomeres of a single chromosome pair. Staining with the AT base pair-specific fluorochrome quinacrine mustard revealed brightly fluorescing heterochromatic regions in the majority of X. borealis chromosomes which are absent in other Xenopus species.


Assuntos
Bandeamento Cromossômico/métodos , Cromossomos/genética , Xenopus/genética , Animais , Bromodesoxiuridina , Células Cultivadas , Cromossomos/classificação , Cromossomos/ultraestrutura , Replicação do DNA , DNA Satélite/análise , Feminino , Hibridização in Situ Fluorescente/métodos , Cariotipagem/métodos , Masculino , Metáfase , Poliploidia , Sequências Repetitivas de Ácido Nucleico , Especificidade da Espécie , Terminologia como Assunto , Xenopus/classificação , Xenopus laevis/genética
10.
Cytogenet Genome Res ; 145(3-4): 187-91, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25871511

RESUMO

Xenopus laevis (XLA) is an allotetraploid species which appears to have undergone whole-genome duplication after the interspecific hybridization of 2 diploid species closely related to Silurana/Xenopus tropicalis (XTR). Previous cDNA fluorescence in situ hybridization (FISH) experiments have identified 9 sets of homoeologous chromosomes in X. laevis, in which 8 sets correspond to chromosomes 1-8 of X. tropicalis (XTR1-XTR8), and the last set corresponds to a fusion of XTR9 and XTR10. In addition, recent X. laevis genome sequencing and BAC-FISH experiments support this physiological relationship and show no gross chromosome translocation in the X. laevis karyotype. Therefore, for the benefit of both comparative cytogenetics and genome research, we here propose a new chromosome nomenclature for X. laevis based on the phylogenetic relationship and chromosome length, i.e. XLA1L, XLA1S, XLA2L, XLA2S, and so on, in which the numbering of XLA chromosomes corresponds to that in X. tropicalis and the postfixes 'L' and 'S' stand for 'long' and 'short' chromosomes in the homoeologous pairs, which can be distinguished cytologically by their relative size. The last chromosome set is named XLA9L and XLA9S, in which XLA9 corresponds to both XTR9 and XTR10, and hence, to emphasize the phylogenetic relationship to X. tropicalis, XLA9_10L and XLA9_10S are also used as synonyms.


Assuntos
Cromossomos/classificação , Terminologia como Assunto , Xenopus laevis/genética , Animais , Bandeamento Cromossômico , Cromossomos/genética , Cromossomos/ultraestrutura , Feminino , Hibridização Genética/genética , Hibridização in Situ Fluorescente , Metáfase , Filogenia , Especificidade da Espécie , Tetraploidia , Xenopus/classificação , Xenopus laevis/classificação
11.
PLoS Negl Trop Dis ; 8(9): e3182, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25233228

RESUMO

BACKGROUND: Previous studies have stressed the genetic divergence and high pathogenicity of strains of T. gondii from French Guiana. Although strains from coastal, human adapted environments (so called anthropized) resemble those found in other regions of the Caribbean, strains collected from inland jungle environment are genetically quite diverse. To better understand the composition of these distinct strain types, we undertook a more in depth analysis of T. gondii strains from French Guiana including profiling of chromosome 1a (Chr1a), which is often shared as a single monomorphic haplotype among lineages that are otherwise genetically distinct. METHODOLOGY/PRINCIPAL FINDINGS: Comparison of intron sequences from selectively neutral genes indicated that anthropized strains were most closely related to clonal type III strains from North America, although wider RFLP analysis revealed that they are natural hybrids. In contrast, strains isolated from the jungle were genetically very diverse. Remarkably, nearly all anthropized strains contained the monomorphic version of Chr1a while wild stains were extremely divergent. The presence of the monomorphic Chr1a strongly correlated with greater transmission in domestic cats, although there were several exceptions, indicating that other factors also contribute. Anthropized strains also varied in their virulence in laboratory mice, and this pattern could not be explained by the simple combination of previously identified virulence factors, indicating that other genetic determinants influence pathogenicity. CONCLUSIONS/SIGNIFICANCE: Our studies underscore the marked genetic separation of anthropized and wild strains of T. gondii in French Guiana and provide additional evidence that the presence of Chr1a is associated with successful expansion of widely different lineages within diverse geographic areas. The predominance of Chr1a among strains in the anthropized environment suggests that it may confer an advantage for transmission in this environment, and thus potentially contribute to the spread of pathogenecity determinants.


Assuntos
Cromossomos/classificação , Variação Genética , Toxoplasma/genética , Toxoplasmose Animal/parasitologia , Animais , Animais Domésticos , Sequência de Bases , Gatos , Guiana Francesa , Haplótipos , Humanos , Íntrons , Camundongos , Filogenia , Polimorfismo de Fragmento de Restrição , Seleção Genética , Toxoplasma/fisiologia , Toxoplasmose Animal/epidemiologia , Virulência/genética
12.
J Appl Genet ; 55(3): 397-401, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24664789

RESUMO

The development of new molecular techniques (array CGH, M-FISH, SKY-FISH, etc.) has led to great advancements in the entire field of molecular cytogenetics. However, the application of these methods is still very limited in farm animals. In the present study, we report, for the first time, the production of 13 river buffalo (Bubalus bubalis, 2n = 50) chromosome-specific painting probes, generated via chromosome microdissection and the DOP-PCR procedure. A sequential multicolor-FISH approach is also proposed on the same slide for the rapid identification of river buffalo chromosome/arms, namely, 1p-1q, 2p-2q, 3p-3q, 4p-4q, 5p-5q, 18, X, and Y, using both conventional and late-replicating banded chromosome preparations counterstained by DAPI. The provided 'bank' of chromosome-specific painting probes is useful for any further cytogenetic investigation not only for the buffalo breeds, but also for other species of the family Bovidae, such as cattle, sheep, and goats, for chromosome abnormality diagnosis, and, more generally, for evolutionary studies.


Assuntos
Búfalos/classificação , Búfalos/genética , Bovinos , Bandeamento Cromossômico , Cromossomos/genética , Hibridização in Situ Fluorescente/métodos , Animais , Cromossomos/classificação , Sondas de DNA , Cariotipagem , Especificidade da Espécie
13.
Tsitologiia ; 56(10): 779-84, 2014.
Artigo em Russo | MEDLINE | ID: mdl-25711088

RESUMO

Automated chromosome classification is an essential task in cytogenetics of animals and plants. Until now the automatic karyotyping systems were obtained only for human chromosomes. The main aim of this study was to develop the automatic pig chromosome classifier using image processing software "VideoTest-Karyo 3.1". To solve this problem 1578 chromosomes from 47 metaphases were used. The constructed classifier was checked with the use of additional sample of metaphases classified in fully automatic regime: error rate was 8.2%, this corresponds to 3.12 ± 0.26 errors per metaphase plate (these values are within acceptable limits for such kind of studies). In further studies the extra sample of pig acrocentric chromosomes was added to classifier up to 1807 chromosomes. This addition reduced the error rate up to 6.1%, which correspondes to 2.78 ± 0.18 errors per metaphase plate. It should be underlined that the revealed errors can immediately be corrected by an operator on every stage of analysis. The classifier was also verified using the chromosomes of boar with rcp(1p-; 11p+) in fully automatic regime and routine stained metaphases of Siberian minipigs with rob(16;17) in semi automatic regime. In both cases the chromosomes were identified correctly. The area of application of obtained pig automatic chromosome classifier is discussed.


Assuntos
Cromossomos/classificação , Cariotipagem/veterinária , Software , Sus scrofa/genética , Animais , Automação Laboratorial/instrumentação , Bandeamento Cromossômico , Feminino , Processamento de Imagem Assistida por Computador , Cariotipagem/instrumentação , Cariotipagem/métodos , Masculino , Metáfase
14.
In. Cardellá Rosales, Lidia; Hernández Fernández, Rolando. Bioquímica médica. Tomo II Componentes celulares y genética molecular. La Habana, ECIMED, 2.ed; 2014. , ilus, tab, graf.
Monografia em Espanhol | CUMED | ID: cum-61278
15.
Arq. bras. med. vet. zootec ; 65(1): 213-220, fev. 2013. graf, tab
Artigo em Português | LILACS | ID: lil-667558

RESUMO

Mapeou-se quantitative trait loci (QTL) associados a características de desempenho nos cromossomos 1, 2, 3, 12, 14, 15 e X de suínos pertencentes a uma população F2, formada a partir do cruzamento entre dois machos da raça naturalizada brasileira Piau e 18 fêmeas comerciais (Landrace x Large White x Pietrain). O mapa genético de ligação da população foi construído após a genotipagem dos animais para 35 marcadores microssatélites. As estimativas do conteúdo de informação polimórfica indicaram que os marcadores microssatélites foram adequados para as análises de QTL. Os dados foram analisados pelo mapeamento por intervalo usando-se o programa GridQTL. Encontraram-se seis QTL, sendo que o QTL genômico para idade ao abate atingiu a significância de 5% de probabilidade. As informações dos QTL detectados neste estudo são úteis para identificar genes que podem ser usados em conjunto com os métodos convencionais de seleção, aumentar a acurácia deles e prover uma compreensão dos fenótipos produtivos de suínos.


The accomplishment of the present study had the objective of mapping Quantitative Trait Loci (QTL) related to performance traits in a F2 pig population developed by mating two Brazilian Piau breed sires with 18 dams from a commercial line (Landrace × Large White × Pietrain). The linkage map for this population was constructed after genotyping the animals for 35 microsatellite markers. Estimates of polymorphic information content indicated that the microsatellite markers were appropriate for QTL analyses. The genotypes were analyzed by interval mapping using the GridQTL program. A total of six QTL were found, of which the QTL for slaughter age (days) was significant at the 5% genome-wise level. The information of the significant QTL detected in this study is useful for future fine-mapping studies for the identification of genes. Such information can be used together with traditional methods in breeding programs or even for a better understanding of the phenotypes of swine production.


Assuntos
Animais , Genômica/classificação , Mapeamento Cromossômico/veterinária , Suínos/genética , Cromossomos/classificação , Loci Gênicos , Técnicas de Genotipagem/veterinária
16.
BMC Bioinformatics ; 14 Suppl 16: S13, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24564477

RESUMO

BACKGROUND: Identification of good metaphase spreads is an important step in chromosome analysis for identifying individuals with genetic disorders. The process of finding suitable metaphase chromosomes for accurate clinical analysis is, however, very time consuming since they are selected manually. The selection of suitable metaphase chromosome spreads thus represents a major bottleneck for conventional cytogenetic analysis. Although many algorithms have been developed for karyotyping, none have adequately addressed the critical bottleneck of selecting suitable chromosome spreads. In this paper, we present a software tool that uses a simple rule-based system to efficiently identify metaphase spreads suitable for karyotyping. RESULTS: The chromosome shapes can be classified by the software into four main classes. The first and the second classes refer to individual chromosomes with straight and skewed shapes, respectively. The third class is characterized as those chromosomes with overlapping bodies and the fourth class is for the non-chromosome objects. Good metaphase spreads should largely contain chromosomes of the first and the second classes, while the third class should be kept minimal. Several image parameters were examined and used for creating rule-based classification. The threshold value for each parameter is determined using a statistical model. We observed that the Gaussian model can represent the empirical probability density function of the parameters and, hence, the threshold value can be easily determined. The proposed rules can efficiently and accurately classify the individual chromosome with > 90% accuracy. CONCLUSIONS: The software tool, termed MetaSel, was developed. Using the Gaussian-based rules, the tool can be used to quickly rank hundreds of chromosome spread images so as to assist cytogeneticists to perform karyotyping effectively. Furthermore, MetaSel offers an intuitive, yet comprehensive, workflow to assist karyotyping, including tools for editing chromosome (split, merge and fix) and a karyotyping editor (moving, rotating, and pairing homologous chromosomes). The program can be freely downloaded from "http://www4a.biotec.or.th/GI/tools/metasel".


Assuntos
Cromossomos/classificação , Processamento de Imagem Assistida por Computador/métodos , Cariotipagem/métodos , Metáfase , Software , Algoritmos , Humanos , Modelos Estatísticos , Distribuição Normal
17.
Zoolog Sci ; 29(10): 709-13, 2012 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23030344

RESUMO

Robertsonian (Rb) karyotypic polymorphism in Apodemus speciosus has interested many researchers with particular referece to the genetic divergence between Rb and non-Rb populations. Failure to find morphologic, biochemical, or genetic differences in previous studies reveals the necessity of focusing on loci on Rb chromosomes, which can be characterized by FISH mapping with DNA probes. In an Rb heterozygote, DNA probes from laboratory mouse chromosomes (MMUs) 1 and 10 were simultaneously hybridized to the long arm of a metacentric and a medium-sized acrocentric chromosome and to the short arm of the metacentric and a small acrocentric chromosome, respectively. Four additional probes derived from each of MMUs 1 and 10 were mapped to the long and short arms, respectively, of the Rb chromosome identified by the above markers. Homologies between the long arm of the Rb chromosome and MMU 1 and between the short arm and MMU 10 were supported by all ten markers, which were dispersed along nearly the entire lengths of the Rb chromosomes. These results indicate that the long and short arms of the Rb chromosomes are homologous to Apodemus speciosus chromosomes 12 and 19 (defined in a previous study), respectively. This ten-marker series can be useful for detecting chromosome-specific divergence between the two karyotypic populations at the gene level.


Assuntos
Cromossomos/classificação , Hibridização in Situ Fluorescente/veterinária , Murinae/genética , Translocação Genética , Animais , Citogenética , Marcadores Genéticos , Variação Genética , Cariótipo
18.
Artigo em Inglês | MEDLINE | ID: mdl-22688796

RESUMO

Cytogenetics is the study of normal and abnormal chromosomes. Every species is characterized by a given number of chromosomes that can be recognized by their specific shape. The chromosomes are arranged according to standard classification schemes for the respective species. While pre- and postnatal chromosome analyses investigate the constitutional karyotype, tumor cytogenetics is focused on the detection of clonal acquired, tumor-associated chromosome aberrations. Cytogenetic investigations in dogs are of great value especially for breeders dealing with fertility problems within their pedigrees, for veterinarians and last but not least for the dog owners. Dogs and humans share a variety of genetic diseases, including cancer. Thus, the dog has become an increasingly important model for genetic diseases. However, cytogenetic analyses of canine cells are complicated by the complex karyotype of the dog. Only just 15 years ago, a standard classification scheme for the complete canine karyotype was established. For chromosome analyses of canine cells the same steps of chromosome preparation are used as in human cytogenetics. There are few reports about cytogenetic changes in non-neoplastic cells, involving predominantly the sex chromosomes. Cytogenetic analyses of different entities of canine tumors revealed that, comparable to human tumors, tumors of the dog are often characterized by clonal chromosome aberrations, which might be used as diagnostic and prognostic markers. The integration of modern techniques (molecular genetic approaches, adaptive computer programs) will facilitate and complete conventional cytogenetic studies. However, conventional cytogenetics is still non-replaceable.


Assuntos
Aberrações Cromossômicas/veterinária , Cromossomos/classificação , Análise Citogenética/veterinária , Doenças do Cão/genética , Cães/genética , Animais , Cruzamento/métodos , Cruzamento/normas , Modelos Animais de Doenças , Doenças do Cão/diagnóstico , Feminino , Fertilidade/genética , Humanos , Hibridização in Situ Fluorescente/veterinária , Cariotipagem/veterinária , Masculino , Neoplasias/diagnóstico , Neoplasias/genética , Neoplasias/veterinária , Análise de Sequência com Séries de Oligonucleotídeos/veterinária , Linhagem , Prognóstico
19.
Genetica ; 138(11-12): 1181-9, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21052786

RESUMO

We analyze the prevalence of B chromosomes in 1,601 species of orthopteran insects where chromosome number and shape are known. B chromosomes have been reported in 191 of these species. Bs are not uniformly distributed among orthopteran superfamilies, with evident hotspots in the Pyrgomorphoidea (32.3% of species carrying Bs), Grylloidea (14.9%), Acridoidea (14.6%) and Tetrigoidea (14.3%). As expected under the theory of centromeric drive, we found a correlation between B chromosome presence and A chromosome shape-Bs are more frequent in karyotypes with more acrocentric A chromosomes. We also found that Bs are less common in species with high chromosome numbers and appear to be most common at the modal chromosome number (2n = 24). Study effort, measured for each genus, was not associated with B prevalence, A chromosome shape or A chromosome number. Our results thus provide support for centromeric drive as an important and prevalent force in the karyotypic evolution of Orthoptera, just as it appears to be in mammals. We suggest that centromeric drive may provide a mechanistic explanation for White's principle of karyotypic orthoselection.


Assuntos
Centrômero/genética , Cromossomos/genética , Cariotipagem , Ortópteros/genética , Animais , Evolução Biológica , Cromossomos/classificação , Feminino , Modelos Logísticos , Especificidade da Espécie
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