Manganese-catalyzed oligomerizations of nucleotide analogs

Summary The synthesis of pyrophosphate-linked oligomers from the bis-phosphoimidazolides of deoxyadenosine and deoxyguanosine, as well as from acyclic analogs of these nucleosides, is catalyzed much more effectively by Mn(II) than by Mg(II). The presence of Mn(II) reduces the extent of cyclization of the monomer-bis-phosphoimidazolide and thereby increases the yields of oligomeric products. The Mn(II)-catalyzed oligomerization is less sensitive to the presence of a complementary polynucleotide template than is the Mg(II)-catalyzed reaction.Nucleic Acid-Like Structures VII. For the previous paper in this series see Visscher et al. (1989)     

Prebiotic Chemistry of Phosphonic Acids: Products Derived From Phosphonoacetaldehyde in the Presence of Formaldehyde

Phosphonoacetaldehyde (PAL), a phosphonic acid analogue of glycolaldehyde phosphate, reacts in the presence of formaldehyde under mildly basic conditions to produce several new products. The reaction proceeds in two stages: a fast aldol condensation of formaldehyde with PAL, and a slower reaction to produce products containing two phosphonic acid groups. We report on the derivatization, isolation by means of HPLC and characterization of these compounds. One of the products is of potential interest as a building block for a prebiotic informational polymer.     

Histopathologic and flow-cytometric analysis of neoplastic and benign "background" tissue in breast carcinoma resections.

Two-color, multiparametric synthesis phase fraction (SPF) analysis of cytokeratin-labeled epithelial cells was flow cytometrically performed on both benign (SPFb) and malignant tissue samples (if available, SPFt) from 132 mastectomy/lumpectomy specimens. These data were then correlated with clinicopathologic features, including (1) tumor differentiation, (2) the proportion of tumor comprised of duct carcinoma-in situ (DCIS), and (3) the histology of accompanying benign breast tissue, classified by predominant microscopic pattern as intact, normal terminal duct lobular units (NTDLU, 34% of cases), atrophic (AT, 33% of cases), proliferative fibrocystic (PFC, 26% of cases), and non-proliferative fibrocystic (NPFC, 7% of cases). SPFt was inversely correlated with extent of DCIS (DCIS = 0-20% tumor volume - 12.7% mean SPFt, vs. DCIS >20% tumor volume - 6.4% mean SPFt, p = 0.001). SPFt also correlated with the histology of background benign breast tissue (NTDLU - 14.8% mean SPFt vs. AT - 6.9% mean SPFt vs. PFC - 12.7% mean SPFt, p = 0.05) but it did not correlate with patient age or SPFb (overall mean = 0.73%). SPFb was correlated with patient age (>56 yr - 0.59% mean SPFb vs. <56 yr - 0.84% mean SPFb, p = 0.02), with background histology (NTDLU - 1.1% mean SPFb vs. AT - 0.43% mean SPFb vs. PFC - 0.70% mean SPFb, p < 0.02) and with the grade of the neoplasm (well/moderate - 0.58% mean vs. poorly differentiated - 0.85% mean, p = 0.04). Patients having a background of PFC were significantly older than patients with a background of NTDLU (45.2 yr vs. 60.2 yr, p = 0.01). We conclude: (1) breast carcinomas arising from a background of more actively cycling pre-involutional or proliferative fibrocystic epithelium have a greater proliferative fraction than tumors arising from atrophic epithelium, implying that the differentiation status of target cells may impact the effect(s) of tumorigenic events; (2) PFC may represent delayed, abnormal or interrupted involution rather than a hyperproliferative state relative to NTDLU, suggesting that it facilitates neoplasia by extending the period of exposure to promoter agents such as endogenous hormones, and (3) lower SPFt in breast neoplasia with more abundant "residual" DCIS may reflect a lengthier pre-invasive disease interval due to intrinsically less aggressive phenotype.     

Bias, precision and heritability of self-reported and clinically measured height in Australian twins

Many studies of quantitative and disease traits in human genetics rely upon self-reported measures. Such measures are based on questionnaires or interviews and are often cheaper and more readily available than alternatives. However, the precision and potential bias cannot usually be assessed. Here we report a detailed quantitative genetic analysis of stature. We characterise the degree of measurement error by utilising a large sample of Australian twin pairs (857 MZ, 815 DZ) with both clinical and self-reported measures of height. Self-report height measurements are shown to be more variable than clinical measures. This has led to lowered estimates of heritability in many previous studies of stature. In our twin sample the heritability estimate for clinical height exceeded 90%. Repeated measures analysis shows that 2–3 times as many self-report measures are required to recover heritability estimates similar to those obtained from clinical measures. Bivariate genetic repeated measures analysis of self-report and clinical height measures showed an additive genetic correlation >0.98. We show that the accuracy of self-report height is upwardly biased in older individuals and in individuals of short stature. By comparing clinical and self-report measures we also showed that there was a genetic component to females systematically reporting their height incorrectly; this phenomenon appeared to not be present in males. The results from the measurement error analysis were subsequently used to assess the effects of error on the power to detect linkage in a genome scan. Moderate reduction in error (through the use of accurate clinical or multiple self-report measures) increased the effective sample size by 22%; elimination of measurement error led to increases in effective sample size of 41%.     

Role of energy systems in two intermittent field tests in women field hockey players

The energetics of 2 field tests that reflect physical performance in intermittent sports (i.e., the Interval Shuttle Sprint Test [ISST] and the Interval Shuttle Run Test [ISRT]) were examined in 21 women field hockey players. The ISST required the players to perform 10 shuttle sprints starting every 20 seconds. During the ISRT, players alternately ran 20-m shuttles for 30 seconds and walked for 15 seconds with increasing speed. Anaerobic and aerobic power tests included Wingate cycle sprints and a .V(O2)max cycle test, respectively. Based on correlation and regression analyses, it was concluded that for the ISST, anaerobic energetic pathways contribute mainly to energy supply for peak sprint time, while aerobic energetic pathways also contribute to energy supply for total sprint time. Energy during the ISRT is supplied mainly by the aerobic energy system. Depending on the aspect of physical performance a coach wants to determine, the ISST or ISRT can be used.     

Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates

Array based DNA pooling techniques facilitate genome-wide scale genotyping of large samples. We describe a structured analysis method for pooled data using internal replication information in large scale genotyping sets. The method takes advantage of information from single nucleotide polymorphisms (SNPs) typed in parallel on a high density array to construct a test statistic with desirable statistical properties. We utilize a general linear model to appropriately account for the structured multiple measurements available with array data. The method does not require the use of additional arrays for the estimation of unequal hybridization rates and hence scales readily to accommodate arrays with several hundred thousand SNPs. Tests for differences between cases and controls can be conducted with very few arrays. We demonstrate the method on 384 endometriosis cases and controls, typed using Affymetrix Genechip© HindIII 50 K arrays. For a subset of this data there were accurate measures of hybridization rates available. Assuming equal hybridization rates is shown to have a negligible effect upon the results. With a total of only six arrays, the method extracted one-third of the information (in terms of equivalent sample size) available with individual genotyping (requiring 768 arrays). With 20 arrays (10 for cases, 10 for controls), over half of the information could be extracted from this sample.     

Predicting unobserved phenotypes for complex traits from whole-genome SNP data

Genome-wide association studies (GWAS) for quantitative traits and disease in humans and other species have shown that there are many loci that contribute to the observed resemblance between relatives. GWAS to date have mostly focussed on discovery of genes or regulatory regions habouring causative polymorphisms, using single SNP analyses and setting stringent type-I error rates. Genome-wide marker data can also be used to predict genetic values and therefore predict phenotypes. Here, we propose a Bayesian method that utilises all marker data simultaneously to predict phenotypes. We apply the method to three traits: coat colour, %CD8 cells, and mean cell haemoglobin, measured in a heterogeneous stock mouse population. We find that a model that contains both additive and dominance effects, estimated from genome-wide marker data, is successful in predicting unobserved phenotypes and is significantly better than a prediction based upon the phenotypes of close relatives. Correlations between predicted and actual phenotypes were in the range of 0.4 to 0.9 when half of the number of families was used to estimate effects and the other half for prediction. Posterior probabilities of SNPs being associated with coat colour were high for regions that are known to contain loci for this trait. The prediction of phenotypes using large samples, high-density SNP data, and appropriate statistical methodology is feasible and can be applied in human medicine, forensics, or artificial selection programs.     

Quantitative trait loci variation for growth and obesity between and within lines of pigs (Sus scrofa)

The hypothesis that quantitative trait loci (QTL) that explain variation between divergent populations also account for genetic variation within populations was tested using pig populations. Two regions of the porcine genome that had previously been reported to harbor QTL with allelic effects that differed between the modern pig and its wild-type ancestor and between the modern pig and a more distantly related population of Asian pigs were studied. QTL for growth and obesity traits were mapped using selectively genotyped half-sib families from five domesticated modern populations. Strong support was found for at least one QTL segregating in each population. For all five populations there was evidence of a segregating QTL affecting fatness in a region on chromosome 7. These findings confirm that QTL can be detected in highly selected commercial populations and are consistent with the hypothesis that the same chromosome locations that account for variation between populations also explain genetic variation within populations.