Automated homologue matching of human G-banded chromosomes.

Two sets of human G-banded chromosomes were employed to test a computer algorithm for homologue matching. One set was produced at the Rigshospitalet, Copenhagen, and the other at the University of Texas M. D. Anderson Hospital. Employing a cross-correlation measure to select candidate homologue mates for each chromosome resulted in correct matches in 91.1% of the cases in the Anderson set and 93.1% in the Denmark set. To identify each chromosome and to give a measure of classification accuracy when performed by humans, five cytogeneticists were asked to independently karyotype the 49 cells in the Anderson set. Agreement between two cytogeneticists was measured by the kappa statistic. If all chromosomes that could not be identified by any given cytogeneticist were removed from the comparison, kappa values were found to be in the vicinity of 0.95. With such unidentifiable chromosomes included as a separate class, the kappa values were closer to 0.89.

Mutagenic and cytogenetic analyses of organic extracts of simulated runoffs from model coal piles.

The use of coal as a fuel in utility and other industries in the United States is increasing. Typically, these utilities store their coal outdoors in large piles, and rainfall on the piles produces a runoff containing hazardous inorganic and organic materials. Four coals of varying sulfur contents, all used for fuel in the United States, were tested. Organic materials were extracted from simulated runoffs of model coal piles and were tested for mutagenicity with a Salmonella/microsomal assay and for clastogenicity and cytotoxicity in Chinese hamster ovary cells. The extracts of the high-sulfur coals and the lignite were more mutagenic and clastogenic than extracts from the low-sulfur coal.

Gene amplification in human tumor cells.

Some tumor cells contain additional DNA sequences that are microscopically observed as HSR or dm. Dm contain repeated sequences. Homogeneous staining regions and dm may be present in the same cell, and both may vary in size and number. HSR or dm are not the result of culture conditions or in vivo treatment. Confusion of dm with acentric fragments or diplococci should be avoided. HSR may be either C band negative or positive. The amplified sequences of HSR are not necessarily located at the normal chromosome sites of these genes in diploid cells. It is assumed that HSR is transcriptionally active in tumor cells as it is in drug resistant cells. The specific gene products of HSR or dm are unknown. HSR and dm may change the response of the cell to cancer chemotherapeutic drugs.

Studies of mammalian chromosome replication. II. Evidence for the existence of defined chromosome replicating units.

Sister chromatids of metaphase chromosomes can be differentially stained if the cells have replicated their DNA semiconservatively for two cell cycles in a medium containing 5-bromodeoxyuridine (BrdU). When prematurely condensed chromosomes (PCC) are induced in cells during the second S phase after BrdU is added to the medium, the replicated chromosome segments show sister chromatid differential (SCD) staining. Employing this PCC-SCD system on synchronous and asynchronous Chinese hamster ovary (CHO) cells, we have demonstrated that the replication patterns of the CHO cells can be categorized into G1/S, early, early-mid, mid-late, and late S phase patterns according to the amount of replicated chromosomes. During the first 4 h of the S phase, the replication patterns show SCD staining in chains of small chromosome segments. The amount of replicated chromosomes increase during the mid-late and late S categories (last 4 h). Significantly, small SCD segments are also present during these later intervals of the S phase. Measurements of these replicated segments indicate the presence of characteristic chromosome fragment sizes between 0.2 to 1.2 micrometers in all S phase cells except those at G1/S which contain no SCD fragments. These small segments are operationally defined as chromosome replicating units of chromosomal replicons. They are interpreted to be composed of clusters of molecular DNA replicons. The larger SCD segments in the late S cells may arise by the joining of adjacent chromosomal replicons. Further application of this PCC-SCD method to study the chromosome replication process of two other rodents, Peromyscus eremicus and Microtus agrestis, with peculiar chromosomal locations of heterochromatin has demonstrated an ordered sequence of chromosome replication. The euchromatin and heterochromatin of the two species undergo two separate sequences of decondensation, replication, and condensation during the early-mid and mid-late intervals respectively of the S phase. Similar-sized chromosomal replicons are present in both types of chromatin. These data suggest that mammalian chromosomes are replicated in groups of replicating units, or chromosomal replicons, along their lengths. The organization and structure of these chromosomal replicons with respect to those of the interphase nucleus and metaphase chromosomes are discussed.

Nucleolar activity in differentiated cells after stimulation.

Initiation of nucleolar organizer region (NOR) activity was observed by using the silver staining method at various times after activation or stimulation of differentiated cells. Two methods were used: (1) activation of human lymphocytes by treatment with phytohemagglutinin (PHA), and (2) cell-cell fusion of chick erythrocytes with squirrel monkey cells. An increase in NOR activity in lymphocytes was seen as early as 4 h after PHA treatment and between 10 and 22 h in the chick erythrocytes after fusion. In both systems, as the size of the dormant cell nucleus increased, the amount of silver staining increased until the silver-stained area approached that of cycling cells.

Studies of mammalian chromosome replication. I. BrdU-induced differential staining patterns in interphase and metaphase chromosomes.

The patterns of differential staining based on the effects of BrdU-substitution in chromosomal DNA have been examined in both metaphase chromosomes and prematurely condensed chromosomes (PCC) of interphase Chinese hamster cells. Results indicate that differential staining may be obtained in chromosomes from all stages of the cell cycle and correspond to the semi-conservation mode of DNA replication. Such fidelity of differential staining in both interphase and metaphase chromosomes suggests that components essential for induction of differential staining are present throughout the cell cycle and chromosomes may contain similar structures and organization throughout the cycle.

Cytogenetic toxicity of cyclophosphamide and its metabolites in vitro.

The effects of cyclophosphamide and three of its known metabolites (nitrogen mustard, acrolein, and nor-nitrogen mustard on chromosome breakage and sister chromatid exchange (SCE) were analyzed in vitro with and without the presence of a metabolic activating system (liver S9). We confirmed that cyclophosphamide induced chromosome breakage and SCE only in the presence of S9. After metabolism, cyclophosphamde was more active than the other agents in inducing SCE. Thus, the agent(s) directly responsible for this induction of a high SCE rate was not analyzed in this study. On the other hand, acrolein was most toxic to cell proliferation and most active in inducing chromosome breakage. The cytogenetic toxicity of these agents in comparison with their mutagenic and therapeutic activities is discussed.

Nonrandom distribution of chromosomal aberrations induced by three chemicals.

The G-band locations of 3244 breakpoints induced by cis-platinum (II) diamminedichloride (PDD), 1460 breakpoints induced by cytosine arabinoside (ara-C), and 1257 breakpoints induced by triethylenemelamine (TEM) in human lymphocyte chromosomes were identified. The breakpoints induced by each of these chemicals demonstrated a significantly nonrandom distribution within the human karyotype. The overall pattern of the interarm distribution was dependent upon the chemical used, but certain chromosomes arms exhibited similar responses to all 3 chemicals. Comparison of the frequencies of breakpoints within individual G-bands indicated that (1) certain bands were susceptible to damage induced by all 3 chemicals; (2) certain bands were resistant to damage by all 3 chemicals; (3) certain bands demonstrated variable susceptibility to induced damage dependent upon the chemical agent; and (4) other bands demonstrated near expected frequencies of damage (by length) to all 3 agents.

Improved method for cytogenetic studies of solid tumors.

Solid human tumors were dissociated with collagenase, cultured for 16-48 hours, and harvested for cytogenetic preparation. Of the 19 tumors used, 14 showed sufficient numbers of metaphases to be useful for chromosome analysis.

Cytological analyses of 14p+ variant by means of N-banding and combinations of silver staining and chromosome bandings.

An inherited human karyological variant (14p+) has been studied with a number of cytochemical techniques. The short arm of this variant chromosome 14 is nearly as long as the long arm, giving the chromosome a submetacentric to metacentric appearance. In conventionally Giemsa-stained preparations, maximum of three secondary constrictions can be observed the marker arm. The secondary constrictions are silver-positive in Ag-NOR preparations. However, the entire arm stains deeply in N-banded preparations. The 14p+ arm is also Q-negative, C-negative, G-negative, and R-positive with an almost homogeneous texture. The difference between N-banding and silver staining is interpreted as the result of gene activities of the ribosomal cistrons.

Nucleolus organizer regions in two species of Bovidae.

Silver-staining of nucleolar organizer regions (NORs) in somatic cells of Holstein cattle (Bos taurus) and European buffalo Murrah type (Bubalus bubalus) indicates that the NORs are located in the telomeres of chromosomes 2,3,4,11, and 29 of cattle and chromosomes 3,4,6,23, and 24 of buffalo. Chromosome identification was by Q-banding. Analysis of 326 metaphase cells showed a mean value of 7.7 +/- 1.2 for Ag-NORs with a range between 4 and 10 for cattle. In all of the cells examined, either one or both homologues of chromosome 29 showed telomeric silver staining for cattle. Meiotic preparations showed not more than 5 clusters of silver grains in the pachytene stage of cattle.

Combination of silver and fluorescent staining for metaphase chromosomes.

A convenient and reliable method for simulatneous visualization of silver staining (Ag-NOR) of the nucleolus organizers and fluorescent bandings in metaphase chromosomes is described. Studies employing this combined procedure on human chromosomes revealed that the Ag-NOR patterns may be characteristic for each chromosome of each individual.

Genome analysis of Peromyscus (Rodentia, Cricetidae) VII. Localization of satellite DNA sequences and cytoplasmic poly(A) RNA sequences of P. eremicus on metaphase chromosomes.

A satellite DNA fraction from P. eremicus, having a buoyant density of 1.705 g/ml in neutral CsCl density gradients, was isolated. In situ hybridization experiments, using 3H-RNA complementary to this DNA fraction indicated that the short (heterochromatic) arms of most of the autosomes contained this sequence. Conversely, in situ hybridization using 3H-complementary DNA (cDNA) synthesized from the cytoplasmic poly (A) RNA of P. eremicus (comprising a substantial fraction of total messenger RNA) showed that the number of silver grains in the long arms (euchromatin) was significantly higher than that in the short arms. The X chromosomes showed a distinct localization pattern of both sequences.

Aanlysis of the frequency and distribution of sister chromatid exchanges in cultured human lymphocytes.

Lymphocytes from 20 notmal subjects (11 male and 9 female) were examined for the frequency and location of sister chromatid exchanges (SCE) by the BrdU--Giemsa method. The mean frequency of SCE was 6.37 with little significant variation. One subject had a high number of exchanges in chromosome 1 while the remainder showed a random distribution of exchanges between chromosomes. The frequency of exchanges generally increased with chromosome length. However, chromosome 1, 2 and the B group had more exchanges than expected while the E, F and G grous had less than expected. The distribution of exchanges in chromosomes 1, 2 and the B group was non-random with a concentration of exchanges below the centromere and to a lesser extent on the distal portion of the long arm. The majority of exchanges appeared to occur at the junction between the dark and light G bands. It is suggested that the concentration of exchanges may reflect differences in BrdU incorporation along the length of the chromosome.

Studies of the squirel monkey, Saimiri sciureus, genome. II. C-band characterization and DNA replication patterns.

Cytological analysis of a squirrel monkey indicates a considerable degree of chromosomal polymorphism. DNA synthetic patterns reveal late synthesis in chromosomal segments that are C-band negative and asynchrony in DNA replication between homologs. Location of a satellite DNA with a CsCl neutral buoyant density of 4.691 g/ml was mainly in the noncentromeric constitutive heterochromatin.

Human nucleolus organizers: the satellites or the stalks?

A silver-staining technique specific for demonstrating nucleolus organizer regions (NOR) showed that the achromatic stalks of the 10 acrocentric autosomes of the human complement represent the NORs. Some variability in number of stained stalks is observed from cell-to-cell and from individual-to-individual. The silver-stained masses may extend beyond the stalks and cover the satellites, especially in chromosomes with short stalks or minute satellites.

Studies of the squirrel monkey, Saimiri sciureus, genome. I. Cytological characterization of chromosomal heterozygosity.

Chromosomal banding analyses have revealed two nonhomologous pericentric inversions in the telocentric group of chromosomes of a squirrel monkey, Saimiri sciureus. This individual is probably an intersubspecific hybrid whose parents originated from different geographical locations. The C-banding pattern shows polymorphism in location and amount of constitutive heterochromatin in at least four pairs of chromosomes. Ammoniacal silver (Ag-AS) staining specific for locating the nucleolar organizers indicates that these are located on only one pair of chromosomes and that there is a difference in the size of the nucleolus organizer regions between the homologs of this pair.

Sister chromatid differential staining pattern in prematurely condensed chromosomes.

Application of sister chromatid differential (SCD) procedure on G1, S and G2 prematurely condensed chromosomes (PCC) of cells in the second and third cycle of DNA replication in medium containing BrdU reveals differential staining patterns characteristic of their respective stages in the cell cycle. These findings also suggest a structural similarity between PCC and metaphase chromosomes.