Automation of routine clinical chromosome analysis. I. Karyotyping by machine

An automated karyotyping system suitable for widespread use in clinical laboratories is described. The software is implemented on a general-purpose, commercially available image analyzer (Magiscan 2) using TV input from a conventional research microscope with minimal modification. The analysis is automatic, but operator interaction is used to resolve difficulties. Extensive experience with a routine clinical workload shows that the system is robust and easy to use and that its use results in a substantially increased laboratory throughput.     

Metaphase chromosome structure. Involvement of topoisomerase II

SCI is a prominent, 170,000 Mr, non-histone protein of HeLa metaphase chromosomes. This protein binds DNA and was previously identified as one of the major structural components of the residual scaffold structure obtained by differential protein extraction from isolated chromosomes. The metaphase scaffold maintains chromosomal DNA in an organized, looped conformation. We have prepared a polyclonal antibody against the SC1 protein. Immunolocalization studies by both fluorescence and electron microscopy allowed identification of the scaffold structure in gently expanded chromosomes. The micrographs show an immunopositive reaction going through the kinetochore along a central, axial region that extends the length of each chromatid. Some micrographs of histone-depleted chromosomes provide evidence of the substructural organization of the scaffold; the scaffold appears to consist of an assembly of foci, which in places form a zig-zag or coiled arrangement. We present several lines of evidence that establish the identity of SC1 as topoisomerase II. Considering the enzymic nature of this protein, it is remarkable that it represents 1% to 2% of the total mitotic chromosomal protein. About 60% to 80% of topoisomerase II partitions into the scaffold structure as prepared from isolated chromosomes, and we find approximately three copies per average 70,000-base loop. This supports the proposed structural role of the scaffold in the organization of the mitotic chromosome. The dual enzymic and apparent structural function of topoisomerase II (SC1) and its location at or near the base of chromatin loops allows speculation as to its involvement in the long-range control of chromatin structure.     

Metaphase chromosome structure: evidence for a radial loop model.

Electron micrographs of thin sections of metaphase chromosomes isolated from HeLa cells provide new insight into the higher-order arrangement of the nucleoprotein fiber. Micrographs obtained from chromosomes swollen by chelation of the divalent cation are particularly revealing. Under these conditions, chromosomes swell in width by a factor of about 4 and the basic, thick nucleoprotein fiber (200–300 Å) relaxes to the thin fiber (100 Å), which is probably a linear array of nucleosomes. Cross sections show a central area from which the fibers emerge in a radial fashion, often forming loops which are 3–4 μm long. Chromosomes fixed in the presence of 1 mM MgCl₂ are more compact, having an average chromatid diameter of about 1 μm, and consist of the thick (200–300 Å) fiber. Radial loops of about 0.6 μm can be observed frequently in these chromosomes, although the loops are more difficult to visualize due to the compactness of the structure and the material contaminating the periphery. Chromosomes isolated with the help of hexylene glycol are extremely compact (diameter about 0.6 μm) but quite free of cytoplasmic material. They consist of a 500 Å fiber that forms rather regular projections at the periphery. These projections appear to be loops of the thick fiber (200–300 Å), possibly shortened by twisting into a short supercoil. The chromatin loops observed in the intact chromosomes are thought to be structurally related to the DNA loops observed previously in the histone-depleted chromosomes (Paulson and Laemmli, 1977). In this paper, we discuss a model in which the nucleoprotein fiber is folded into loops which are arranged in the chromatid in radial fashion, in such a way that their bases become the central axis of the chromatid.     

Variation within teosinte. II. numerical analysis of chromosome knob data

Principal components analysis of 46 chromosome knob positions and B chromosomes for 61 accessions of annual teosinte (in 12 groups) and 207 accessions of maize (in 87 groups) produced results which did not entirely agree with previous groupings. Teosintes of northwest and southeast Guatemala (races Huehuetenango and Guatemala) were widely separated from maize and from all other teosintes; however, teosintes of east Mexico-Distrito Federal (race Chalco) were also widely separated from maize and other teosintes. Teosintes of south Chihuahua (race Nobogame) grouped separately from other teosintes, suggesting that race Nobogame is not simply a northern extreme of race Central Plateau. Teosintes of east Michoacan and west Mexico (recently grouped into the Balsas race) grouped together but separately from other teosintes. The latter teosintes may merit special designation in a racial taxonomic system. Only the Central Plateau teosintes consistently overlapped with maize OTU's for the first few principal components. Even in that case there was no consistent association between the Central Plateau teosintes and any specific race of maize.     

A reappraisal of the stathmokinetic technique. II. Metaphase degeneration and its correction

The rate at which proliferating cells enter mitosis is an important cytokinetic measure. It is estimated by the metaphase arrest (or stathmokinetic) technique. This technique depends on the persistence of arrested metaphases in the tissue in question. But arrested metaphases do not, in fact, persist for long; some estimates of the rate at which cells are entering mitosis, based on a count of metaphases, are therefore underestimates. This paper presents a mathematical analysis of this phenomenon and a method of calculating the initial metaphase index from the depleted index at any given time.     

Metaphase chromosome accumulation and flow karyotypes in rice (Oryza sativa L.) root tip meristem cells.

Highly efficient cell synchronization and metaphase chromosome accumulation in rice root tip cells were achieved. Flow cytometric analysis was performed for obtaining optimal parameters to synchronize the cell cycles. High mitotic indices (about 57.6% in root tip meristemic area) were obtained by treating seedlings with 0.5 cm length using 0.5 mM hydroxyurea at 30 degrees C for 4 h, incubating in a hydroxyurea-free solution for 30 min, and then treating with 0.3 microM trifluralin for 3 h. After trifluralin treatment, incubation in distilled water for 15 min reduced chromosome clumping on metaphase spread. Uniformity of seed germination at the time of treatment is a critical parameter for obtaining high metaphase index. Isolated rice chromosomes were suitable for flow cytometric analysis and chromosome sorting. The morphology of flow sorted metaphase chromosomes was intact.     

Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research

The contribution of balanced chromosomal rearrangements to complex disorders remains unclear because they are not detected routinely by genome-wide microarrays and clinical localization is imprecise. Failure to consider these events bypasses a potentially powerful complement to single nucleotide polymorphism and copy-number association approaches to complex disorders, where much of the heritability remains unexplained. To capitalize on this genetic resource, we have applied optimized sequencing and analysis strategies to test whether these potentially high-impact variants can be mapped at reasonable cost and throughput. By using a whole-genome multiplexing strategy, rearrangement breakpoints could be delineated at a fraction of the cost of standard sequencing. For rearrangements already mapped regionally by karyotyping and fluorescence in situ hybridization, a targeted approach enabled capture and sequencing of multiple breakpoints simultaneously. Importantly, this strategy permitted capture and unique alignment of up to 97% of repeat-masked sequences in the targeted regions. Genome-wide analyses estimate that only 3.7% of bases should be routinely omitted from genomic DNA capture experiments. Illustrating the power of these approaches, the rearrangement breakpoints were rapidly defined to base pair resolution and revealed unexpected sequence complexity, such as co-occurrence of inversion and translocation as an underlying feature of karyotypically balanced alterations. These findings have implications ranging from genome annotation to de novo assemblies and could enable sequencing screens for structural variations at a cost comparable to that of microarrays in standard clinical practice.     

Complete DNA sequence of yeast chromosome II.

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.     

Analysis of the Phospholipid Profile of Metaphase II Mouse Oocytes Undergoing Vitrification

Oocyte freezing confers thermal and chemical stress upon the oolemma and various other intracellular structures due to the formation of ice crystals. The lipid profiles of oocytes and embryos are closely associated with both, the degrees of their membrane fluidity, as well as the degree of chilling and freezing injuries that may occur during cryopreservation. In spite of the importance of lipids in the process of cryopreservation, the phospholipid status in oocytes and embryos before and after freezing has not been investigated. In this study, we employed mass spectrometric analysis to examine if vitrification has an effect on the phospholipid profiles of mouse oocytes. Freshly prepared metaphase II mouse oocytes were vitrified using copper grids and stored in liquid nitrogen for 2 weeks. Fresh and vitrified-warmed oocytes were subjected to phospholipid extraction procedure. Mass spectrometric analyses revealed that multiple species of phospholipids are reduced in vitrified-warmed oocytes. LIFT analyses identified 31 underexpressed and 5 overexpressed phospholipids in vitrified mouse oocytes. The intensities of phosphatidylinositol (PI) {18∶2/16∶0} [M−H]− and phosphatidylglycerol (PG) {14∶0/18∶2} [M−H]− were decreased the most with fold changes of 30.5 and 19.1 in negative ion mode, respectively. Several sphingomyelins (SM) including SM {d38∶3} [M+H]+ and SM {d34∶0} [M+K]+ were decreased significantly in positive ion mode. Overall, the declining trend of multiple phospholipids demonstrates that vitrification has a marked effect on phospholipid profiles of oocytes. These results show that the identified phospholipids can be used as potential biomarkers of oocyte undergoing vitrification and will allow for the development of strategies to preserve phospholipids during oocyte cryopreservation.     

Metaphase I bonds,crossing-over frequency,and genetic length of specific chromosome arms of rye

Using a Giemsa C-banding procedure three chromosome pairs (3, 6 and 7) have been identified in meiosis of the F1 of a cross between two rye inbred lines. Two of these chromosome pairs (3 and 7) were heterozygous for a prominent telomeric heterochromatic band. The comparison between the frequencies of the different meiotic configurations at metaphase I, anaphase I and metaphase II presented by these two chromosome pairs has allowed the estimation of the chiasma frequency and the genetic length of the chromosome arms 3 short and 7 long.     

The Impact of Myeloperoxidase and Activated Macrophages on Metaphase II Mouse Oocyte Quality

Myeloperoxidase (MPO), an abundant heme-containing enzyme present in neutrophils, monocytes, and macrophages, is produced in high levels during inflammation, and associated with poor reproductive outcomes. MPO is known to generate hypochlorous acid (HOCl), a damaging reactive oxygen species (ROS) utilizing hydrogen peroxide (H₂O₂) and chloride (Cl^-). Here we investigate the effect of activated immune cells and MPO on oocyte quality. Mouse metaphase II oocytes were divided into the following groups: 1) Incubation with a catalytic amount of MPO (40 nM) for different incubation periods in the presence of 100 mM Cl^- with and without H₂O₂ and with and without melatonin (100 μM), at 37°C (n = 648/648 total number of oocytes in each group for oocytes with and without cumulus cells); 2) Co-cultured with activated mouse peritoneal macrophage and neutrophils cells (1.0 x 10⁶ cells/ml) in the absence and presence of melatonin (200 μM), an MPO inhibitor/ROS scavenger, for different incubation periods in HTF media, at 37°C (n = 200/200); 3) Untreated oocytes incubated for 4 hrs as controls (n = 73/64). Oocytes were then fixed, stained and scored based on the microtubule morphology and chromosomal alignment. All treatments were found to negatively affect oocyte quality in a time dependent fashion as compared to controls. In all cases the presence of cumulus cells offered no protection; however significant protection was offered by melatonin. Similar results were obtained with oocytes treated with neutrophils. This work provides a direct link between MPO and decreased oocyte quality. Therefore, strategies to decrease MPO mediated inflammation may influence reproductive outcomes.     

Influence on clinical practice of routine intra-partum fetal monitoring.

An attempt has been made to monitor by continuous fetal heart rate according all women admitted in labour. Altogether 85% of the 1070 patients delivered at one hospital were monitored in 1973 and 92% in 1974. Perinatal mortality fell significantly from levels in preceding years to 15-8 and 11-7 per 1000 births, respectively, in 1973 and 1974. The fall was primarily due to the elimination of intra-partum stillbirths and a significant reduction in neonatal mortality. The incidence of caesarean sections also fell from 9-7% in 1973 to 5-8% in 1974. All patients should be monitored because it is impossible to predict reliably intra-partum fetal distress from maternal "high-risk" factors present before the onset of labour.     

Genetic analysis of the mitochondrial rho-mutability in Saccharomyces. II. Disomy for chromosome IV and spontaneous rho-mutability

The disomy for chromosome IV in the strains studied led to: reduction in the red pigmentation of ade1 mutant colonies; a decrease in spontaneous rho- mutant frequency, and impairment of sporulation in hybrids descended from disomic parents. The nuclear srm1 mutation decreasing the spontaneous rho- mutability promoted the spontaneous extra chromosome loss in the disomics for chromosome IV. This result suggests a close connection between the spontaneous rho- mutability and mitotic chromosome stability.     

Automatic classification of chromosomes as part of a routine system for clinical analysis

A procedure for automatic classification of G-banded human chromosomes has been implemented on a semiautomated system for routine clinical analysis. Chromosomes represented by their density profiles are described by so-called weighted density distributions (WDDs) by application of a number of weighting functions and classified by a parametric discriminant analysis. During 16 mo of routine use of the system, 2,794 metaphases (127,925 chromosomes) from amniotic fluid have been karyotyped by the system with an error rate of 8-9%. This corresponds to 4-5 errors per metaphase. These errors can immediately be corrected by the operator on a displayed karyogram with a light pen.     

Detection of X chromosome aneuploidy using Southern blot analysis during routine population-based screening for fragile X syndrome

We report herein two cases where detection of X chromosome aneuploidy (cytogenetically proved 45,X/46XX and 47,XXX) was made possible by molecular diagnosis during population-based carrier screening for Fragile X syndrome, using Southern blot analysis. This study emphasizes the value of molecular analysis for gene dosage to suggest chromosomal aneuploidy.     

Randomised controlled trial of routine hospital clinic care versus routine general practice care for type II diabetics.

Two hundred patients with type II diabetes were entered into a randomised controlled trial lasting five years to compare routine care of this condition by a hospital diabetic clinic with routine care in general practice. Fewer patients in the group being cared for by their general practitioner (general practice group) were regularly reviewed or had regular estimations of blood glucose concentration. More patients in the general practice group than in the hospital group were admitted to hospital for medical reasons during the study (25 (24%) compared with 17 (18%] and more patients in the general practice group died (18) than did in the hospital group (6). At the end of the study mean concentrations of haemoglobin A1 were higher in the general practice group (10.4%) than in the hospital group (9.5%). Routine care in general practice for patients with type II diabetes was less satisfactory than care by the hospital diabetic clinic.