A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour.

High-density SNP microarrays ("SNP chips") are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high-density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.

The limited role of myocardial fluorine-18 fluorodeoxyglucose imaging in candidates for cardiac transplantation: a planar imaging study.

This study compares the incidence and extent of hibernating myocardium (defined by myocardial perfusion/metabolism mismatch) in 28 cardiac transplant candidates with ischaemic cardiomyopathy and in 16 other patients with coronary artery disease (CAD) undergoing viability assessment. It then reviews the impact of myocardial perfusion metabolism imaging on management decisions in the transplant candidates at 6 months after scintigraphy. Each patient underwent a planar myocardial thallium-201 and fluorine-18 fluorodeoxyglucose scan on a modified gamma camera. Perfusion/metabolism mismatch was sized semi-quantitatively and each patient was assigned a global mismatch score. Transplant candidates had a lower left ventricular ejection fraction (LVEF) (P < 0.0002) and extent of hibernation myocardium (lower global mismatch score: P = 0.005) than other CAD patients but the difference in respect of mismatch frequency (8/28 vs 9/16 patients) did not reach statistical significance. Transplant candidates with LVEF < 20% had a lower global mismatch score (P < 0.02) than those with an LVEF > or = 20%. Interestingly two of three other CAD patients with LVEF < 20% had a moderate mismatch. Follow-up studies revealed the lack of impact of metabolic imaging as none of the three transplant candidates who eventually underwent revascularisation had hibernating myocardium and transplantation was offered to one of only two candidates with more than one minor mismatch. Thus metabolic imaging in potential transplant candidates may be of limited value because of the very low extent of hibernating myocardium, particularly if LVEF is below 20% and where clinical decisions are often based on many other factors.

Planar cardiac F-18 fluorodeoxyglucose imaging with a conventional gamma camera.

OBJECTIVE: To examine the potential of an adapted gamma camera to image cardiac uptake of the positron emitting glucose analogue fluorine-18 fluorodeoxyglucose (FDG). DESIGN: Postprandial studies were performed in 19 patients (mean age, 56 +/- 9 years) with coronary disease and resting cardiac dysfunction who had undergone a routine clinical 7 min/view planar thallium-201 (Tl-201) stress reinjection or rest redistribution study. A glucose/insulin protocol was used and, an hour after FDG injection, 15-minute static planar myocardial images were acquired in the four views used for Tl-201 scanning. RESULTS: The diagnostic quality of FDG images was at least as good as that of their Tl-201 counterparts, with less liver background in all but one FDG study. In the left anterior oblique 45 degrees view uncorrected global myocardial FDG and stress Tl-201 counts were similar, but the FDG study had significantly higher peak myocardial to background ratios. CONCLUSION: Assessing regional cardiac FDG uptake and myocardial perfusion seems feasible with conventional gamma camera technology, providing a widely available and cost effective means of detecting hibernating myocardium. Similar equipment may appreciably reduce the need for positron emission tomography in a range of clinical conditions.

The relationship between development of lung inflammation and changes in bone marrow populations in guinea-pigs following inhaled antigen challenge.

Sensitised guinea-pigs were exposed to aerosolised antigen. The resultant cellular infiltration into the lung was assessed in lung tissue and bronchoalveolar lavage fluid 6, 24, 72 h and 7 days later. An early neutrophil infiltration peaking at 6 h was succeeded by eosinophil migration which persisted for 7 days, at which time some of the eosinophils appeared immature. The lung eosinophilia was accompanied by an initial fall in eosinophilic cells in the bone marrow, followed by an increase in this population. Treatment with dexamethasone (25 mg/kg i.p.) given daily for 7 days after antigen challenge reduced the lung eosinophilia and observed bone marrow changes.

DNA sequence dependent binding modes of 4',6-diamidino-2-phenylindole (DAPI).

The interactions of DAPI with natural DNA and synthetic polymers have been investigated by hydrodynamic, DNase I footprinting, spectroscopic, binding, and kinetic methods. Footprinting results at low ratios (compound to base pair) are similar for DAPI and distamycin. At high ratios, however, GC regions are blocked from enzyme cleavage by DAPI but not by distamycin. Both poly[d(G-C)]2 and poly[d(A-T)]2 induce hypochromism and shifts of the DAPI absorption band to longer wavelengths, but the effects are larger with the GC polymer. NMR shifts of DAPI protons in the presence of excess AT and GC polymers are significantly different, upfield for GC and mixed small shifts for AT. The dissociation rate constants and effects of salt concentration on the rate constants are also quite different for the AT and the GC polymer complexes. The DAPI dissociation rate constant is larger with the GC polymer but is less sensitive to changes in salt concentration than with the AT complex. Binding of DAPI to the GC polymer and to poly[d(A-C)].poly[d(G-T)] exhibits slight negative cooperativity, characteristic of a neighbor-exclusion binding mode. DAPI binding to the AT polymer is unusually strong and exhibits significant positive cooperativity. DAPI has very different effects on the bleomycin-catalyzed cleavage of the AT and GC polymers, a strong inhibition with the AT polymer but enhanced cleavage with the GC polymer. All of these results are consistent with two totally different DNA binding modes for DAPI in regions containing consecutive AT base pairs versus regions containing GC or mixed GC and AT base pair sequences. The binding mode at AT sites has characteristics which are similar to those of the distamycin-AT complex, and all results are consistent with a cooperative, very strong minor groove binding mode. In GC and mixed-sequence regions the results are very similar to those observed with classical intercalators such as ethidium and indicate that DAPI intercalates in DNA sequences which do not contain at least three consecutive AT base pairs.

The interaction with DNA of unfused aromatic systems containing terminal piperazino substituents. Intercalation and groove-binding.

A number of unfused tricyclic aromatic intercalators have shown excellent activity as amplifiers of the anticancer activity of the bleomycins and the 4',6-diphenylpyrimidines, 2a and 2b, with terminal basic functions (4-methylpiperazino groups) have been synthesized to test the structural requirements for amplifier-DNA interactions. The terminal piperazine rings are bulky, have limited flexibility, and are twisted out of the phenyl ring plane in both 2a and 2b. With 2a the pyrimidine is unsubstituted at position 5 and the conformation predicted by molecular mechanics calculations has a 25-30 degrees twist between the phenyl and pyrimidine ring planes. With 2b the 5-position is substituted with a methyl group and this causes a larger twist angle (50-60 degrees) between the phenyl and pyrimidine planes. These conformational variations lead to markedly different DNA interactions for 2a and 2b. Absorption, CD and NMR spectral, viscometric, flow dichroism and kinetics results indicate that 2a binds strongly to DNA by intercalation while 2b binds more weakly in a groove complex. The general structure and conformation of 2a, a slightly twisted, unfused-aromatic system with terminal piperazino groups is more similar to groove-binding agents such as Hoechst 33258 than to intercalators. The fact that 2a forms a strong intercalation complex with DNA is unusual but in agreement with studies on other amplifiers of anticancer drug action. Molecular modeling studies provide a second unusual feature of the 2a intercalation complex. While most well-characterized intercalators bind with their bulky and/or cationic substitutents in the DNA minor groove, the cationic piperazino groups of 2a are too large to bind in the minor groove in an intercalation complex but can form strong interactions with DNA in the major groove. The tricyclic aromatic ring system of 2a stacks well with adjacent base-pairs in the major-groove complex and the piperazino groups have good electrostatic and van der Waals interactions with the DNA backbone.

The interaction of unfused polyaromatic heterocycles with DNA: intercalation, groove-binding and bleomycin amplification.

A number of unfused-aromatic cations have been found to bind to DNA by intercalation and to amplify the bleomycin catalysed cleavage of DNA. These molecules are more similar in structure to unfused minor-groove binding compounds such as netropsin and DAPI than to fused-ring intercalators such as proflavine. An analysis of DAPI interactions with specific sequence DNA polymers has indicated that the binding modes for the molecule are sequence dependent: minor groove binding in sequences of three or more AT base pairs and intercalation in mixed or pure GC base pair sequences. As with other unfused intercalators which bind with their cationic side chains in the major groove, the amidinium groups of DAPI are in the major groove in the GC intercalation complex. DAPI is, thus, a good bleomycin amplifier in GC sequences but its minor-groove binding mode in AT sequences leads to bleomycin inhibition.

Interaction of unfused tricyclic aromatic cations with DNA: a new class of intercalators.

Unfused tricyclic aromatic ring systems 1-6 with one or two cationic side chains have been synthesized and their interactions with DNA and synthetic polymers probed with a variety of techniques. Molecular mechanics calculations indicate that the torsional angle between ring planes in the minimum energy conformation of the tricyclic molecules can range from 0 degree to as high as 50 degrees depending on the type of rings and substituents. Viscometric titrations with linear and supercoiled DNA, linear dichroism, and NMR studies indicated that all compounds with torsional angles of approximately 20 degrees or less bind to DNA by intercalation. The more highly twisted intercalators caused significant perturbation of DNA structure. Unfused intercalators with twist angles of approximately 20 degrees have reduced binding constants, suggesting that they could not form an optimum interaction with the DNA base pairs. Unfused intercalators with twist less than 20 degrees formed strong complexes with DNA. The structures of these unfused intercalators are more analogous to typical groove-binding molecules, and an analysis of their interaction with DNA provides a better understanding of the subtle differences between intercalation and groove-binding modes for aromatic cations. The results indicate that intercalation and groove-binding modes should be viewed as two potential wells on a continuous energy surface. The results also suggest design strategies for intercalators that can optimally complement DNA base pair propeller twist or that can induce bends in DNA at the intercalation site.