Fluorescence polarization in homogeneous nucleic acid analysis II: 5'-nuclease assay.

When the temperature and viscosity of the solvent is held constant, the degree of fluorescence polarization (FP) detected when a fluorescent dye is excited by plane polarized light depends mostly on the molecular weight of the dye molecule. By monitoring the FP of a fluorescent dye molecule, one can detect significant changes in the molecular weight of a fluorescent molecule without separation or purification. The 5'-nuclease (TaqMan) assay is a robust single nucleotide polymorphism genotyping method where an allele-specific probe that binds to a perfectly complementary target is cleaved by the 5'-nuclease activity of Taq DNA polymerase. Because the TaqMan probe is labeled with a fluorescent dye, it has high FP value when intact but a low FP value after cleavage. In this study, we compared the results of the 5'-nuclease assay based on standard fluorescence intensity readings and FP readings when genotyping 90 individuals with 20 single nucleotide polymorphisms. Our results show that FP is just as robust and reliable as the standard fluorescence detection method. Use of FP detection makes it possible to reduce the cost of TaqMan probes by abrogating the need for a fluorescence quencher.

Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28.

Linkage disequilibrium (LD), or the non-random association of alleles, is poorly understood in the human genome. Population genetic theory suggests that LD is determined by the age of the markers, population history, recombination rate, selection and genetic drift. Despite the uncertainties in determining the relative contributions of these factors, some groups have argued that LD is a simple function of distance between markers. Disease-gene mapping studies and a simulation study gave differing predictions on the degree of LD in isolated and general populations. In view of the discrepancies between theory and experimental observations, we constructed a high-density SNP map of the Xq25-Xq28 region and analysed the male genotypes and haplotypes across this region for LD in three populations. The populations included an outbred European sample (CEPH males) and isolated population samples from Finland and Sardinia. We found two extended regions of strong LD bracketed by regions with no evidence for LD in all three samples. Haplotype analysis showed a paucity of haplotypes in regions of strong LD. Our results suggest that, in this region of the X chromosome, LD is not a monotonic function of the distance between markers, but is more a property of the particular location in the human genome.

The homozygous complete hydatidiform mole: a unique resource for genome studies.

The most frequent type of complete hydatidiform mole is a 46, XX homozygote formed by the fertilization of an empty ovum by a single haploid sperm that later duplicates its chromosomes to give a diploid tumor. The homozygous nature of these complete hydatidiform moles makes them unique resources for human genome studies. They can serve as homozygous controls in the development of single nucleotide polymorphism (SNP) markers and provide a way to obtain long-range haplotypes that are useful in population studies. The use of a homozygous control makes it possible to estimate the allele frequencies of the SNP markers in any population by sequencing pooled DNA samples. In this report, we present evidence of homozygosity of a complete hydatidiform mole using 20 diallelic markers distributed across the genome. Furthermore, its usefulness as a homozygous control in SNP development and as a resource for long-range haplotype determination is demonstrated using 11 newly discovered loci in the BRCA2 region on chromosome 13q12-q13.

Improved enzyme immunosorbent assay for mouse prolactin using penicillinase as label.

Enzyme immunosorbent assay (EIA) for mouse prolactin was established by modifying a method originally developed for human prolactin by Shrivastav et al. This simple, sensitive, rapid, and reproducible assay utilizes penicillinase as the labeling enzyme, rabbit anti-mouse prolactin antibody (Ab) and goat anti-rabbit Ig Ab as the first and second antibodies. Prolactin reference preparations and enzyme-conjugated prolactin were mixed with the first Ab and incubated for 0.5 h at 4 degrees C (24-48 h for serum samples). Then, the sample mixture was transferred to the wells of microtiter plate coated with the second Ab. After being kept at room temperature for 2 h, the plate was washed and filled with substrate solution (penicillin V). Absorbance at 620 nm was measured with an ELISA reader to quantitate the amount of conjugated prolactin bound to the second Ab. The prolactin levels obtained by this assay exhibited good correlation with those measured by radioimmunoassay (RIA) (y = 0.95x + 9.14, r = 0.943), and the sensitivity of EIA was equivalent to that of RIA (1.7 ng/ml). The CVs of intra-assay and inter-assay by EIA for mouse serum samples ranged comparably to those by RIA.

Calorie consumption level influences development of C3H/Ou breast adenocarcinoma with indifference to calorie source.

To analyze simultaneously the influence attributable to calorie consumption level and percentage of dietary fat on the spontaneous development of mammary adenocarcinoma, virgin female C3H/Ou mice were separated into five dietary groups. Four groups of mice were fed purified diets either ad libitum (16-18 kcal/mouse/day) or restricted 40% in calorie consumption (10-11 kcal/mouse/day), and diets contained either 4.5%, 7.5%, 67%, or 68% calories from fat. Mice that consumed isocaloric diets developed breast malignancy at a comparable pace. Consuming a diet in which fats were present only at levels sufficient to satisfy the threshold requirement of essential fatty acids, 4.5-7.5% of the total calories, or alternatively where dietary fat represented greater than 67% of the total calories consumed, did not significantly alter the tendency for breast tumor development. The pace and frequency with which tumors occurred reflected the host's level of calorie consumption. Mice consuming a high caloric diet, low or high in fat, tended to have a shortened latency to breast tumor formation, an increased incidence of breast tumors, elevated serum prolactin levels, elevated levels of antibodies to mouse mammary tumor virus, and elevated circulating immune complex levels.