Condensin and cohesin display different arm conformations with characteristic hinge angles

Structural maintenance of chromosomes (SMC) proteins play central roles in higher-order chromosome dynamics from bacteria to humans. In eukaryotes, two different SMC protein complexes, condensin and cohesin, regulate chromosome condensation and sister chromatid cohesion, respectively. Each of the complexes consists of a heterodimeric pair of SMC subunits and two or three non-SMC subunits. Previous studies have shown that a bacterial SMC homodimer has a symmetrical structure in which two long coiled-coil arms are connected by a flexible hinge. A catalytic domain with DNA- and ATP-binding activities is located at the distal end of each arm. We report here the visualization of vertebrate condensin and cohesin by electron microscopy. Both complexes display the two-armed structure characteristic of SMC proteins, but their conformations are remarkably different. The hinge of condensin is closed and the coiled-coil arms are placed close together. In contrast, the hinge of cohesin is wide open and the coiled-coils are spread apart from each other. The non-SMC subunits of both condensin and cohesin form a globular complex bound to the catalytic domains of the SMC heterodimers. We propose that the "closed" conformation of condensin and the "open" conformation of cohesin are important structural properties that contribute to their specialized biochemical and physiological functions.     

In vivo dissection of the chromosome condensation machinery: reversibility of condensation distinguishes contributions of condensin and cohesin

The machinery mediating chromosome condensation is poorly understood. To begin to dissect the in vivo function(s) of individual components, we monitored mitotic chromosome structure in mutants of condensin, cohesin, histone H3, and topoisomerase II (topo II). In budding yeast, both condensation establishment and maintenance require all of the condensin subunits, but not topo II activity or phospho-histone H3. Structural maintenance of chromosome (SMC) protein 2, as well as each of the three non-SMC proteins (Ycg1p, Ycs4p, and Brn1p), was required for chromatin binding of the condensin complex in vivo. Using reversible condensin alleles, we show that chromosome condensation does not involve an irreversible modification of condensin or chromosomes. Finally, we provide the first evidence of a mechanistic link between condensin and cohesin function. A model discussing the functional interplay between cohesin and condensin is presented.     

Sex chromosome loss, micronuclei, sister chromatid exchange and aging: a study including 16 centenarians

In the present study we analysed the possible effect of age, sex and smoking on the mean values of micronucleus (MN) and sister chromatid exchange (SCE) frequencies on peripheral blood obtained from 38 subjects ranging in age from 16 to 63 years and 16 centenarians. The mean number of binucleated cells with micronuclei varied in function of age and sex (as demonstrated by the analysis of covariance (F=13.13; P<0.001), particularly evident was the increment observed in women with increasing age (interaction age/sex: F=5.53; P<0.05). Smoking habits had no effects on MN frequency (F=0.36; P>0.05). Sex (F=4.18; P<0.05) and smoking habits (F=14.64; P<0.001) influenced significantly SCE per cell frequencies, but age had no effects on them (F=2.45; P>0.05).The age-associated increase of sex chromosome loss was studied using fluorescence in situ hybridisation (FISH) on interphase nuclei.The loss of Y signals was observed in 10% of interphase cells from the centenarians males, that is six times more often than in the younger control men (1.6%). The frequency of X signal loss (1.7%) in young women was similar to that observed in male controls of the same age but the incidence of the X chromosome aneuploidy in centenarian females was appreciably higher (22%) than that found for the Y chromosome in males. These results were correlated with the data on MN formation and a positive correlation between the percentage of aneuploid cells (FISH) and MN values was observed (r=0.50; P<0.05).     

The analysis of data in studies of invertebrate reproduction. II. The analysis of oocyte size/frequency data,and comparison of different types of data

The measurement of oocyte sizes is the best method for examining reproductive cycles in the animals on which we have worked (mainly echinoderms and molluscs). The examination of standardised residuals in an R × C contingency table permits the detailed study of the growth of oocytes, and of differences in developmental stage both within and between samples. A nested design analysis of variance permits the quantification of the degree of seasonality in a species, and makes interspecific comparisons in the amount of inter- and intra-individual synchrony possible.

Comparisons between different types of data and methods of studying interpopulation differences in reproductive pattern are also reviewed.     

Loss of chromosome 1 in myxopapillary ependymoma suggests a region out of chromosome 22 as critical for tumour biology: a FISH analysis of four cases on touch imprint smears

OBJECTIVE: Ependymomas are glial tumours. They constitute approximately 5-10% of intracranial tumours and are tumours which can recur. Predictive factors of outcome in ependymomas are not well established. Karyotypic studies are relatively scarce and loss of chromosome 22 has been described to correlate with recurrence. We are unaware of any reports involving chromosome 1 aberrations in the malignant progression of ependymomas. METHODS: Cytogenetic analysis of four myxopapillary ependymomas was performed using double target fluorescent in situ hybridization (FISH), focusing on chromosomes 1 and 22. RESULTS: One patient's tumour had recurred. FISH was performed on 500 nuclei/tumours. All four cases showed a loss of chromosome 22q while only one showed an additional loss of chromosome 1p, and this was the one that recurred. CONCLUSIONS: We support the presence of a tumour suppressor gene on 1p associated with relapse in myxopapillary ependymomas and suggest that status of chromosome 1p by FISH may indicate a high-risk group of patients harbouring this tumour. More studies of this type are needed towards this direction as our results refer to a minimal number of individuals analysed.     

Direct analysis of radiation-induced chromosome fragments and rings in unstimulated human peripheral blood lymphocytes by means of the premature chromosome condensation technique

Development of the procedure to stimulate peripheral blood lymphocytes has greatly facilitated the understanding of chromosome aberration formation and repair mechanisms in human cells. Yet, because radiation induces far more initial chromosome breaks than are observed as aberrations in metaphase, it has not been possible to examine the kinetics of primary chromosome breakage and rejoining with this procedure. An improved method to induce premature chromosome condensation in unstimulated lymphocytes has been used to study primary chromosome breakage, rejoining, and ring formation at various times after irradiation with up to 800 rad of X-rays. The dose-response relations for chromosome fragments analyzed immediately or 1, 2, or 24 h after exposure were found to be linear. Rapid rejoining of chromosome fragments, which takes place in the first 3 h after X-ray exposure, was not correlated with a simultaneous increase in the formation of rings. The yield of rings per cell scored 24 h after irradiation, however, increased significantly and fit a linear quadratic equation. Both chromosome fragment rejoining and ring formation were completed about 6 h after irradiation. The frequency distributions of rings among cells followed a Poisson distribution, whereas chromosome fragments were overdispersed.     

Clinical findings and cytogenetic analysis of small supernumerary ring chromosomes 7: report of two new cases

Two new patients, mosaic for a small supernumerary ring chromosome 7 are described. There are only seven published reported concerning supernumerary ring chromosome 7 and we reviewed the previously reported cases in an attempt to establish genotype-phenotype correlations, which are particularly important for genetic counselling and clinical genetics. Our first case was a 20 months old girl who was referred for a mild motor developmental delay, an asymmetric facial appearance, a plagiocephaly and a short nose with anteverted nostrils. Our second case was a 9 years old boy who was referred for a IQ at the lower end of the normal range (? 80), obesity, hyperactivity and some dysmorphic features including hypertelorism and down slanting palpebral fissures. In both cases, chromosome analysis after G and R banding and FISH showed a small ring chromosome 7 in respectively 76% and 50% of consecutively scored metaphases. Both ring chromosomes were labelled by FISH using the Williams Syndrome locus probe (Elastin Gene D7S486). Comparison between these two cases and previously published cases allowed to delineate frequent clinical findings. A mild mental retardation was found in the majority of patients. which is an important data for genetic counselling.     

Evolution of X-Degenerate Y Chromosome Genes in Greater Apes: Conservation of Gene Content in Human and Gorilla,But Not Chimpanzee

Compared with the X chromosome, the mammalian Y chromosome is considerably diminished in size and has lost most of its ancestral genes during evolution. Interestingly, for the X-degenerate region on the Y chromosome, human has retained all 16 genes, while chimpanzee has lost 4 of the 16 genes since the divergence of the two species. To uncover the evolutionary forces governing ape Y chromosome degeneration, we determined the complete sequences of the coding exons and splice sites for 16 gorilla Y chromosome genes of the X-degenerate region. We discovered that all studied reading frames and splice sites were intact, and thus, this genomic region experienced no gene loss in the gorilla lineage. Higher nucleotide divergence was observed in the chimpanzee than the human lineage, particularly for genes with disruptive mutations, suggesting a lack of functional constraints for these genes in chimpanzee. Surprisingly, our results indicate that the human and gorilla orthologues of the genes disrupted in chimpanzee evolve under relaxed functional constraints and might not be essential. Taking mating patterns and effective population sizes of ape species into account, we conclude that genetic hitchhiking associated with positive selection due to sperm competition might explain the rapid decline in the Y chromosome gene number in chimpanzee. As we found no evidence of positive selection acting on the X-degenerate genes, such selection likely targets other genes on the chimpanzee Y chromosome. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Karyotype evolution in Tilapia: mitotic and meiotic chromosome analysis of Oreochromis karongae and O. niloticus x O. karongae hybrids

The karyotype of Oreochromis species is considered to be highly conserved, with a diploid chromosome complement of 2n = 44. Here we show, by analysis of mitotic and meiotic chromosomes, that the karyotype of O. karongae, one of the Lake Malawi chambo species, is 2n = 38. This difference in chromosome number does not prevent the production of inter-specific hybrids between O. niloticus (2n = 44) and O. karongae (2n = 38). Analysis of the meiotic chromosomes of the O. niloticus × O. karongae hybrids indicates that three separate chromosome fusion events have occurred in O. karongae. Comparison of the O. karongae and O. niloticus karyotypes suggests that these consist of one Robertsonian fusion and two fusions of a more complex nature.     

Use of NotI microarrays in analysis of epigenetic and structural changes in epithelial tumor genomes by the example of human chromosome 3

A new comparative genome hybridization technology using NotI microarrays is described (Karolinska Institute International Patent WO02/086163). The method is based on comparative genome hybridization of NotI-enriched probes from tumor and normal genomic DNA with radically new NotI microarrays. A total of 181 NotI-binding loci of human chromosome 3 were assayed in 200 human malignant tissue samples from various organs: kidney, lung, breast, ovary, cervix, and prostate. The most significant portion (above 30%) of aberrations (deletions and methylation) were detected in NotI sites located in the MINT24, BHLHB2, RPL15, RARbeta1, ITGA9, RBSP3, VHL, and ZIC4 genes. This indicates that they may be associated with cancer development. Methylation of these genomic loci was confirmed by methylation-specific PCR and bisulfite sequencing. The results confirm that the proposed method can contribute to cancer genomics.     

Structural Organization of the Human Genome: Distribution of Nucleotides,AluRepeats, and Exons in Chromosomes 21 and 22

Analysis of DNA sequences of the human chromosomes 21 and 22 performed using a specially designed MegaGene software allowed us to obtain the following results. Purine and pyrimidine nucleotide residues are unevenly distributed along both chromosomes, displaying maxima and minima (waves) with a period of about 3 Mbp. Distribution of G+C along both chromosomes has no distinct maxima and minima, however, chromosome 21 contains considerably less G+C than chromosome 22. Both exons and Alurepeats are unevenly distributed along chromosome 21: they are scarce in its left part and abundant in the right part, while MIR elements are quite monotonously spread along this chromosome. The Alurepeats show a wave-like distribution pattern similar for both repeat orientations. The number of the Alurepeats of opposite orientations was equal for both studied chromosomes, and this may be considered a new property of the human genome. The positive correlation between the exon and Aludistribution patterns along the chromosome, the concurrent distribution of Alurepeats in both orientations along the chromosome, and the equal copy numbers for Aluin direct and inverted orientations within an individual chromosome point to their important role in the human genome, and do not fit the notion that Alurepeats belong to parasitic (junk) DNA.     

Effect of low-level, 60-Hz electromagnetic fields on human lymphoid cells: I. Mitotic rate and chromosome breakage in human peripheral lymphocytes

Dividing human peripheral lymphocytes from 10 normal adults (5 males and 5 females) were exposed in vitro to low level 60-Hz electromagnetic fields for 69 hours. The current density of the electrical field was 30 microA/cm2, while the magnetic field was either 1 or 2 gauss. The cytological endpoints measured were mitotic rate and chromosome breakage. No statistically significant differences, indicative of a field effect, were observed between treated and control cells whether exposed to an electric field, a magnetic field, or to various combinations of the two.     

The evolution of the spindlin gene in birds: sequence analysis of an intron of the spindlin W and Z gene reveals four major divisions of the Psittaciformes

The Psittaciformes (parrots, parakeets) are among the most widely held captive birds. Yet, their evolution and their phylogenetic relationships have been relatively little studied. This paper describes the phylogenetic relationships between a number of Psittaciformes as derived from the sequences of the third intron of the Z-chromosomal and W-chromosomal spindlin genes. The Z-chromosomal sequences of the kakapo (Strigops habroptilus), the kea (Nestor notabilis), and the kaka (Nestor meridionalis) from New Zealand form a cluster which is the sister group to all other Psittaciformes. The results show further that the Z-chromosomal sequences of the other species can be divided into two groups based on the occurrence of a sequence element ACCCT. The group with the insert (A) is mainly from species with an Australasian geographical distribution and includes such species as the Lories (Lorius, etc.), the budgerigar (Melospittacus undulatus), and the rosellas (Platycercus). It also includes the African lovebirds (Agapornidae), which are the only representative of group A outside Australasia. Group B, without the insert, includes the neotropical parrots and parakeets such as the amazons (Amazona, etc.), the macaws (Ara, etc.), and the conures (Aratinga, etc.), the Australian Cacatuini and the African species such as the African grey parrot (Psittacus erithacus) as well as Coracopsis vasa from Madagascar and Psittrichas fulgidus from New Guinea. The W-chromosomal sequence data show that another division of the Psittacidae is found in the replacement of a pyrimidine-rich segment occurring in many non-psittacines as well as the kakapo (S. habroptilus), the kea (N. notabilis), the kaka (N. meridionalis), and the Cacatuini by a microsatellite consisting of a variable number of TATTA monomers in the other Psittaciformes. The results support a Gondwanan origin of the Psittaciformes and the suggestion that paleogeographic events were a major force in psittacine divergence.     

Cytogenetic analysis of Australian tiger beetles (Coleoptera: Cicindelidae): chromosome number, sex-determining system and localization of rDNA genes

The chromosomes of four species of Australian tiger beetle are documented. The male meioformulae of three species of Cicindela (tribe Cicindelini) were determined as follow: Cicindela cardinalba Sumlin 1987, n = 10 + X₁ X₂ X₃Y; C. sp. ( saetigera group) and Cicindela gillesensis Hudson 1994, n = 11 + X₁ X₂ X₃Y. The male meioformula of Megacephala whelani Sumlin 1992 (tribe Megacephalini) is n = 12 + XY. Fluorescence in situ hybridization (FISH) was used to localize the 18S-28S ribosomal gene clusters on male mitotic and meiotic chromosomes and nuclei using a polymerase chain reaction-amplified ribosomal probe. Fluorescence in mitosis and meiotic first prophase stages in the three Cicindela species showed that rDNA genes are in two of the four chromosomes that form the sex vesicle. In M. whelani hybridization in mitosis and first metaphase stages indicate that rDNA genes are in three, medium- to small-sized, autosomal pairs. Silver staining of male meiotic nuclei reveals the presence of active nucleolar organizing regions (NORs) in the sex vesicle of the three species of Cicindela . The cytogenetic and evolutionary implications of these findings are discussed.     

Cytogenetic analysis of Ctenostomini by C-banding and rDNA localization and its relevance to the knowledge of the evolution of tiger beetles (Coleoptera: Cicindelidae)

In this work, the first cytogenetic data on Neotropical Collyrinae is provided, by way of their karyotypes, C-banding and ribosomal genes (rDNA) localization using fluorescence in situ hybridization (FISH). The two species analysed, Ctenostoma (Procephalus) ornatum ornatum (male) and Ctenostoma (Euctenostoma) rugosum(female) showed, respectively, a diploid number of 17 and 18 chromosomes. C. ornatum ornatum has a multiple sex chromosome system ( n=7 + X₁X₂Y), and mitotic and meiotic metaphase cells showed rDNA gene labelling in the smallest autosomal pair. In this species, no C-bands were obtained, while C. rugosum seems to exhibit centromeric and/or interstitial C-bands in almost all chromosomes. The observation of a multiple sex chromosome system in Ctenostomini ensured the appearance of this characteristic in the hypothetical ancestral of Collyrinae and Cicindelini. The subfamily Collyrinae is not uniform in what concerns diploid chromosome number and rDNA gene localization, because C. ornatum ornatum possesses a lower chromosome number and autosomal rDNA genes when compared with the other Collyrinae species studied ( Neocollyris spp.). Independent events leading to the reduction in chromosome number might have taken place during the split of the Collyrinae into the tribes Ctenostomini and Collyrini.     

Determination of major pollutant and biogeochemical processes in an oil-contaminated aquifer using human health risk assessment and multivariate statistical analysis

Techniques for monitored natural attenuation usually produce large complex datasets that are difficult to interpret. Here, human health risk assessments and multivariate statistical analyses are combined to extract and analyze useful information from large monitoring datasets to identify the main pollutants in a petroleum-contaminated aquifer in northeast China and the main biogeochemical processes affecting the pollutants. The data included organic and inorganic geochemical species concentrations, physicochemical indicators, C and S stable isotope data collected for four years of more than 10 monitoring. The health risk assessment indicated that benzene was a representative pollutant. Cluster analysis classified the groundwater samples into two groups and indicated strong biodegradation occurred near the core and upgradient of the petroleum hydrocarbon plume. The factors explaining most variability were extracted by principal component analysis, which correlated with biodegradation and mineral dissolution processes. The factor scores and spatial distributions of hydrogeochemical and isotope indicators confirmed that biodegradation effects weakened and mineral dissolution strengthened upgradient to downgradient of the contaminated plume. The analysis method could be useful for rapidly studying pollution characteristics and identifying biodegradation processes in contaminated aquifersfrom large complex datasets. The results will provide a basis for developing an enhanced bioremediation scheme for the study site.     

Human disturbance and natural habitat: a biome level analysis of a global data set

This paper presents an analysis of conversion of natural habitat to human use on a global scale. Human disturbance of natural systems is classified in a three-category system and ranked using a Habitat Index based on remaining undisturbed and partially disturbed land. Data is analysed by biome and biogeographic province, allowing identification of the biomes and provinces which have been the most impacted by human activity. Temperate biomes are found to be generally more disturbed than tropical biomes. Four of the top five most disturbed biomes are temperate. Certain biomes and geographic areas stand out as conservation priorities, notably the islands of Southeast Asia, Mediterranean vegetation types, Temperate Broadleaf Forests and Tropical Dry Forests. Areas for which data deficiencies exist are identified.