Development of a human DNA quantitation system.

The AluQuant Human DNA Quantitation System has been developed for human-specific quantitation of forensic samples. This system uses probes specific to repetitive genetic elements allowing quantitation without target amplification. Target immobilization is unnecessary with employment of solution hybridization. The AluQuant Human DNA Quantitation System uses a series of enzymatic reactions to produce a luminescent signal proportional to the quantity of human DNA present. This report demonstrates a range of quantitation from 0.1-50 ng of human DNA. Signal from non-human DNAs tested was insignificant and addition of non-human DNAs into a human sample did not alter quantitation. Lastly, the system was unaffected by degradation of sample through sonication. The AluQuant Human DNA Quantitation System is a simple and sensitive method for quantitating the concentration of human DNA in forensic samples.

Reuse of denaturing polyacrylamide gels for short tandem repeat analysis.

Denaturing polyacrylamide gel electrophoretic analysis of amplified polymorphic short tandem repeat (STR) loci using fluorescent markers is a mainstay of forensic and paternity testing. To reduce the drawback of preparing gels or using expensive precast gels, we have developed a simple and rapid method to reuse gels between 2 and 8 times over a period of several days. Following the initial electrophoresis and scan, the original samples are removed from the gel by a 1-1.5-h reverse-electrophoresis step. This step heats the gel for the next set of samples and can be performed several days after the initial electrophoresis. Sample bands remain sharp on subsequent runs, but edge effects (frowning of the outside lanes) become progressively worse and ultimately limit gel reuse. Well distortions and separation of the gel from the plates become problems if the gel is used more than twice. However, degassing the gel solution and bonding the gel to both plates eliminate these problems. Precast gels also can be used multiple times. Using this technique, we have successfully analyzed samples amplified with a nine-locus multiplex system and characterized the separated products using a fluorescent scanner and software.

A novel and simple method to assay the activity of individual protein kinases in a crude tissue extract.

Protein kinases and phosphatases play an important role in a variety of cellular functions. Thus, it is of interest to develop an assay system that can be used to quantify the activity of individual enzymes specifically in a crude cellular extract, is simple to perform, and is amenable to automation. Here we report on the development of a protein kinase assay that addresses these points and circumvents the pitfalls of existing methodologies. The assay is based on the high affinity and strong binding of streptavidin toward biotin-linked peptide substrates. The biotinylated peptide substrate is phosphorylated by the cognate protein kinase using [gamma-32P]ATP under optimal enzyme condition, and the phosphorylated peptide product is then captured by a streptavidin-linked disk. After removal of free [gamma-32P]ATP, the 32P incorporated into the peptide substrate can be used as an expression of enzyme activity. In contrast to the commonly used phosphocellulose method, only the phospho-, biotinylated peptide (and not other phosphorylated proteins present in the extract) will bind to the disks, thus giving a true estimate of enzymatic activity. In addition to specificity, this assay does not require the peptide substrate to contain basic amino acids or to be modified by the addition of basic amino acid residues as required for the phosphocellulose method which may result in altered specificity of the substrate.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosomal sublocalization of the 2;13 translocation breakpoint in alveolar rhabdomyosarcoma.

A characteristic balanced reciprocal chromosomal translocation [t(2;13)(q35;q14)] has been identified in more than 50% of alveolar rhabdomyosarcomas. As the first step in characterization of the genes involved in this translocation, we constructed somatic cell hybrids that retained either the derivative chromosome 2 or the derivative chromosome 13 without a normal chromosome 13 homologue. Ten linked DNA probes known to be located within bands 13q13-q14 were mapped relative to the breakpoint on chromosome 13, allowing localization of the breakpoint region between two loci separated by 5.5 cM. A long-range restriction map extending approximately 2,300 kb around these loci failed to provide evidence of rearrangement. Additionally, we confirmed that the FMS-like tyrosine kinase gene (FLT), previously localized to 13q12 by in situ hybridization, is located proximal to the breakpoint, and we demonstrated that FLT is not a target for disruption by this tumor-specific translocation.

The gene for aromatase (P450arom) in the chicken is located on the long arm of chromosome 1.

An 125I-labeled partial cDNA for the chicken aromatase P450 was used for in situ hybridization to chromosomes from primary chicken embryo fibroblast cultures. The results indicate that the gene that encodes aromatase is located on the long arm of chromosome 1 at approximately position 0.16.

Molecular evaluation of abnormalities of the short arm of chromosome 1 in neuroblastoma.

Cytogenetic analyses have documented the consistent deletion of part of the short arm of chromosome 1 in neuroblastoma cells suggesting the presence of a suppressor gene in this chromosomal region. To determine, the smallest region of deletion overlap at the molecular level on independently derived tumors and to define the location of the breakpoints more precisely, Southern analyses were performed on a somatic cell hybrid panel containing the normal and altered chromosomes 1 from seven neuroblastoma lines. By this method we were able to analyze a panel of 20 cloned sequences and two isozymes to determine the location of the breakpoints. Our findings indicate that the proximal breakpoints of chromosome 1 deletions ranged over a distance of more than 50 cM with the most distal deletion breakpoint occurring between MYCL1 and D1S57. In addition, using restriction fragment length polymorphisms, it was determined that in at least three of the five cell lines in which MYCL1 was deleted from a chromosome 1, the gene was translocated to another chromosome thus retaining the diploid complement. We propose that the neuroblastoma susceptibility gene is located distal to MYCL1 and that there is another gene which is linked to MYCL1 that may be involved in this neoplasm.

Excision of N-myc from chromosome 2 in human neuroblastoma cells containing amplified N-myc sequences.

Amplification of one of three growth-stimulating myc genes is a common method by which many tumor types gain a proliferative advantage. In metastatic human neuroblastoma, the amplification of the N-myc locus, located on chromosome 2, is a dominant feature of this usually fatal pediatric cancer. Of the many models proposed to explain this amplification, all incorporate as the initial step either disproportionate overreplication of the chromosomal site or recombination across a loop structure. The original locus is retained within the chromosome in the overreplication models but is excised in the recombination models. To test these models, we have used somatic cell hybrids to separate and analyze the chromosomes 2 from a neuroblastoma cell line containing in vivo amplified N-myc. Our results demonstrate that N-myc is excised from one of the chromosomes, suggesting that deletion is a requisite part of gene amplification in a naturally occurring system.

Agarose gel electrophoresis in isozyme separation and visualization.

Isozyme analysis of rodent-human somatic cell hybrids has been used frequently to detect specific human chromosomes. The majority of these isozyme systems employs starch gels, the use of which can be laborious when screening large numbers of cell lines. We describe the development of two procedures to detect the long arms of human chromosomes 1 and 2 in Chinese hamster-human cell hybrids by a rapid and reproducible method using 1-mm-thick agarose gels. Detection of human chromosome 1q was accomplished by screening for human fumarate hydratase activity, whose gene has been mapped to 1q42.1. Detection of chromosome 2q was performed by screening for the isozyme isocitrate dehydrogenase 1, which has been localized to 2q32-qter. These systems provide a basis for the further development of procedures for detecting chromosome-specific isozyme markers in agarose gels.

Molecular analysis of chromosome 1 abnormalities in neuroblastoma.

Tumor cells from 70% of neuroblastoma patients contain a deletion of part of the short arm of chromosome 1, indicating that this chromosomal region includes a gene involved in tumor formation. To more precisely evaluate the boundaries and mechanisms involved in generating these deletions, we have examined four neuroblastoma cell lines using a combination of somatic cell hybridization, isozyme analysis, and nucleic acid hybridization employing both standard and restriction fragment length polymorphic probes. The data suggest that the truncation of chromosome 1 in these neuroblastomas was most likely due to a complex translocation and deletion mechanism rather than a simple unbalanced translocation or terminal or interstitial deletion. This conclusion is supported by the frequent removal of MYCL from the altered chromosome 1 to another chromosome. Furthermore, the data suggest that the frequency of breakpoints previously assigned by karyotypic analysis to bands other than 1p32 in neuroblastomas may be overestimated. Finally, this study identified a breakpoint at 1p32 that was localized between the genes JUN and MYCL for one neuroblastoma thus establishing the order of these genes as centromere, JUN, MYCL, telomere. We conclude that the observed breakpoints within chromosome 1p in human neuroblastoma are not as variable as previously described and suggest the results of this study provide evidence for the involvement of specific DNA sequences within 1p32 in the generation of neuroblastoma.

Use of somatic cell hybrids to analyze role of specific enzymes in daunorubicin cytotoxicity.

Through the use of drug-adapted tissue culture cells, correlations have been observed between the level of specific enzymes and drug resistance. Drug resistance, however, may be due to multiple factors. To test whether the activity of daunorubicin reductase or NADPH diaphorase independently influences in vitro daunorubicin-induced cytotoxicity, we developed somatic cell hybrid clones to partially isolate these factors. This was accomplished by fusing daunorubicin-resistant myeloblast cells obtained from a patient with monosomy 7 leukemia to a daunorubicin-sensitive Chinese hamster cell line. The in vitro cytotoxicity of daunorubicin was compared in hybrid clones having variable enzyme activities; the concentrations of daunorubicin that inhibited the growth of clones by 50% did not differ by more than 2-fold, whereas daunorubicin reductase activities and NADPH diaphorase isozyme activities differed by more than 100- and 15-fold, respectively. These large differences in enzymatic activity were obtained in part by the suppression of specific hamster genes, indicating a regulatory control mechanism for xenobiotic enzymes. Our findings suggest that in this system substantial intercellular variation in the activity of these xenobiotic enzymes does not independently influence cellular resistance to daunorubicin.

Analysis of JHM central nervous system infections in rats.

Intracerebral inoculation of murine coronavirus JHM into 2- to 3-day-old Wistar Furth rats causes an acute encephalomyelitis, while inoculations at 10 days of age usually result in hind leg paralysis. To examine the distribution of viral antigens within this infected central nervous system (CNS) tissue, we used the avidin-biotin-peroxidase method to detect monoclonal and polyclonal antibodies bound to JHM structural proteins; in addition we used the Western blot technique to detect viral proteins. Our study demonstrated the following characteristics: Infected neuronal and glial cells produced viral nucleocapsid and E2 glycoprotein. The synthesis of these viral structural proteins was not restricted to cells in any particular part of the central nervous system. While JHM E2 proteins could be detected in individual cells of JHM-infected CNS tissue, the relative level of detectable E2 protein in the total CNS tissue of infected rats was reduced by more than 13-fold compared with JHM-infected tissue culture cells. Hippocampus neuronal cells provided a sensitive indication of JHM infection. These cells invariably contained antigens in both acutely and chronically infected animals. The distribution of cells containing viral antigens differed markedly for JHM-induced acute encephalitis and chronic demyelinating disease. Acutely infected brains had large lesions containing low levels of viral antigen scattered throughout the brain. One percent to ten percent of histologically normal cells in many parts of the brain contained viral antigens; in addition, more neuronal cells than glial cells were observed to be antigen-positive. The hippocampus appeared normal with hematoxylin-eosin staining; however, a scattered infection of neuronal cells was apparent.(ABSTRACT TRUNCATED AT 250 WORDS)

Transformation of mouse bone marrow cells by transfection with a human oncogene related to c-myc is associated with the endogenous production of macrophage colony stimulating factor 1.

We recently derived a series of transformed cell lines by transfecting mouse bone marrow cells highly enriched for macrophage progenitors with a newly described human gene, R-myc, which has homology to the c-myc oncogene. In this report, we show that these lines share some features characteristic of cells of the mononuclear phagocyte lineage. Specifically, all cell lines had macrophage- or monocytelike morphology, contained nonspecific esterase, were phagocytic for latex beads, secreted lysozyme, bore the Mac-1 antigen, and contained a minority of cells with Fc receptors. However, only a single monocytelike clone had appreciable numbers of cells which bore complement receptor 1, and none were phagocytic for antibody or complement-coated particles, or constitutively secreted Interleukin-1. All these cell lines secreted a growth factor capable of supporting the in vitro proliferation of bone marrow macrophages. Radioimmunoassay and receptor binding studies indicate that this factor is colony stimulating factor 1.

Transcription of hematopoietic-associated oncogenes in childhood leukemia.

We have examined the transcriptional expression of the cellular homologues of several retrovirus-associated oncogenes, myc, rel, rasH, myb, src, and erb, in uncultured childhood leukemia and normal hematopoietic cells, as a first step in determining their normal function and possible association with human neoplasia. Cellular myc-specific RNA was detected in all 30 samples of hematopoietic tissue examined, including 18 leukemias of both the lymphoid and myeloid series, three lymphomas, five normal leukocytes, and four cell lines. Although the level of expression varied over a 25-fold range, no general pattern based on cell type or disease state was evident. In addition, in all cell types examined, a single-molecular-weight myc-specific RNA species was observed. Transcriptional expression of the rel and rasH genes showed a similar lack of specificity, with the rasH gene being expressed at a low uniform level in all cell types examined. myb expression was marginally detectable in most samples, although the myeloid leukemia cells possessed approximately 4-fold higher levels. The expression of src was relatively low in most samples, with markedly elevated levels in a few diverse leukemia samples. erb expression was undetectable in all but two acute myelogenous leukemia samples. Analysis of one patient who had high levels of myc, erb, and src expression before therapy revealed a dramatic reduction in erb and src expression but not myc expression while the patient was in remission. These results indicate that primary human leukemia cells, as well as normal leukocytes, do express the cell homologues to several retrovirus-associated oncogenes, that some leukemia cells express high levels of several oncogenes, and that some of these genes are differentially expressed in specific subpopulations of cells.

Chromosomal clustering of five defined endogenous retrovirus loci in White Leghorn chickens.

By using in situ hybridization, we localized three endogenous chicken retrovirus loci associated with the gs- chf- phenotype to distinct regions on chromosome 1. These three loci, ev4, ev5, and ev8, along with the two other known gs- chf--associated loci in White Leghorn chickens, ev1 and ev13, appear to be evenly distributed along chromosome 1, occurring approximately every 1.8 X 10(7) base pairs. The presence of all five loci on chromosome 1 represents a highly nonrandom distribution and all but eliminates a mechanism of independent random integration events for the generation of these loci.

5'-terminal deletions are a common feature of endogenous retrovirus loci located on chromosome 1 of White Leghorn chickens.

My previous studies demonstrated that chromosome 1 has all five of the endogenous retrovirus loci associated with nonexpression of viral proteins (gs- chf-) in White Leghorn chickens. The current study was done to localize the two defective endogenous retrovirus loci, ev3 and ev6, to determine whether nonexpression of the viral loci on chromosome 1 is a transcriptional prerequisite or a result of an underlying structural defect. The structure of ev6 is every similar to that of two other gs- chf- -associated loci, ev4 and ev5; all three contain a 5'-terminal deletion that eliminates the viral transcriptional promoter. Unlike the gs- chf- -associated loci, ev6 apparently uses an adjacent cell promoter to produce high levels of viral glycoprotein. The ev6 locus was located on the long arm of chromosome 1 by in situ hybridization, thus indicating that transcription of an endogenous retrovirus locus on chromosome 1 can occur. However, the 5'-terminal deletion in several viral loci on chromosome 1, but not on other chromosomes, suggests that the deletion may result from the events that generate or maintain these loci in the White Leghorn population. The additional finding of ev3, which has an internal deletion, on a microchromosome suggests that the mechanism that produced deletions in many chromosome 1 loci is specific for the 5' terminus.

Chromosomal localization of three endogenous retrovirus loci associated with virus production in White Leghorn chickens.

Proposed mechanisms for the generation of endogenous retrovirus loci have been examined by determining the chromosomal distribution of these loci by means of in situ hybridization. Unlike the clustering on chromosome 1 of five endogenous retrovirus loci associated with the gs- chf- phenotype A. Tereba and S. M. Astrin, submitted for publication), three loci associated with endogenous retrovirus production (V+ phenotype) were located on three separate chromosomes. ev2, which codes for the prototype endogenous RAV-0 genome in line 7(2) chickens, was localized near the middle of the long arm of chromosome 2, ev7, coding for a noninfectious, inducible genome present in line 15B chickens, was located near the end of the long arm of the Z chromosome. A third V+ locus, designated ev14, was detected near the middle of chromosome 3. This arrangement of V+ loci is consistent with an integration mechanism employing randomly distributed integration sites in the chicken genome. In addition, these data provide evidence suggesting that the gs- chf- -associated loci may have been generated by a different mechanism.