Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

Background

It has been reported in the quantitative trait locus (QTL) literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases.Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach.We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster.

Results

Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis.

Conclusion

We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

     

Pulmonary embolization causes hypoxemia by redistributing regional blood flow without changing ventilation

To explore mechanisms of hypoxemia after acutepulmonary embolism, we measured regional pulmonary blood flow andalveolar ventilation before and after embolization with 780-µm beadsin five anesthetized, mechanically ventilated pigs. Regionalventilation and perfusion were determined in~2.0-cm³ lung volumes by using1-µm-diameter aerosolized and 15-µm-diameter injected fluorescentmicrospheres. Hypoxemia after embolization resulted from increasedperfusion to regions with low ventilation-to-perfusion ratios.Embolization caused an increase in perfusion heterogeneity and a fallin the correlation between ventilation and perfusion. Correlationbetween regional ventilation pre- and postembolization was greater thancorrelation between regional perfusion pre- and postembolization. Themajority of regional ventilation-to-perfusion ratio heterogeneity wasattributable to changes in regional perfusion. Regional perfusionredistribution without compensatory changes in regional ventilation isresponsible for hypoxemia after pulmonary vascular embolization in pigs.

     

Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny

Phylogenetic analyses of closely related species should use information from multiple, independent genes with relatively high rates of sequence evolution. To investigate species for which there are few prior sequence data for single-copy nuclear (scnDNA) genes, primers for gene amplification can be designed to highly conserved regions of exons in order to amplify both coding (exons) and noncoding (introns) sequences. We have explored this approach in a phylogenetic analysis of six species of pinnipeds that, together with terrestrial carnivore outgroups, encompass divergence times < or = 40-50 Mya. We sequenced one intron from each of the aldolase A (ALD-A), aldolase C (ALD-C), and histone H2AF genes; one exon from the major-histocompatibility-complex DQA gene; a H2AF processed pseudogene (psi H2AF); and, for comparison with the nuclear genes, the 5' portion of the mitochondrial DNA (mtDNA) control region. The pinniped psi H2AF genes were found to be of limited use because they were paralogous with the gene in the outgroup. The rate of silent substitution in scnDNA (primarily introns) was 5-10-fold lower than that for mtDNA control region I, and scnDNA sequence divergence increased linearly with time < or = 40-50 Mya. Alleles at three polymorphic scnDNA loci (ALD-A, H2AF, and DQA) in the southern elephant seal were paraphyletic with respect to the allele from the closely related northern elephant seal, while the more numerous mtDNA alleles were monophyletic. This we attribute to the consequences of a higher mutation rate rather than to a lower effective population size of mtDNA compared with scnDNA. Within the short (i.e., < 500-bp) sequences of individual scnDNA sequences, phylogenetically informative variation was insufficient to obtain robust phylogenies. However, the combined scnDNA sequences produced a well-supported phylogeny congruent with that derived from mtDNA. This analysis illustrates the high resolution of mtDNA sequences compared with a similar length of scnDNA sequence, but it also demonstrates the utility of combining information from multiple short scnDNA sequences obtained using broadly applicable primers.      

Exchange diffusion of dopamine induced in planar lipid bilayer membranes by the ionophore X537A

The ionophore X537A causes a large increase in the [(14)C]dopamine (a catecholamine) permeability of planar bilayer membranes. Dopamine transport increases linearly with the ionophore concentration. At relatively high concentrations in the presence of dopamine, the ionophore omdices a conductance which is nearly ideally selective for the dopamine cation. However, the total dopamine flux as determined in tracer experiments is not affected by an electric field and is over 10(5) times larger than predicted from the estimated dopamine conductance. Increasing the dopamine concentration on the side containing radioactive dopamine (the cis side) saturates the dopamine transport. This saturation is relieved by trans addition of nonradioactive dopamine, tyramine, H(+), or K(+). With unequal concentrations of dopamine cis and trans (49 and 12.5 mM), the unidirectional dopamine fluxes are equal. Increasing H(+) cis and trans decreases dopamine transport. It is concluded that at physiological pH, the X537A-induced transport of dopamine occurs via an electrically silent exchange diffusion of dopamine cation with another cation (e.g., dopamine(+), H(+), or K(+)). X537A induces a Ca(++)-independent release of catecholamines from sympathetic nerves by interfering with intracellular storage within storage vesicles (R.W. Holz. 1975. Biochim. Biophys. Acta. 375:138-152). It is suggested that X537A causes an exchange of intravesicular catecholamine with a cytoplasmic cation (perhaps K(+) or H(+)) across the storage vesicle membrane.     

Effects of chronic modification of dietary fat and carbohydrate on the insulin, corticosterone and metabolic responses of rats fed acutely with glucose, fructose or ethanol

1. Male rats were fed for 14 days on powdered diets containing (by weight) 53% of starch, or on diets in which 20g of starch per 100g of diet was replaced by lard or corn oil. They were then fed acutely by stomach tube with a single dose of glucose, fructose or ethanol of equivalent energy contents, or with 0.15m-NaCl. The serum concentrations of corticosterone, insulin, glucose, glycerol, triacylglycerol and cholesterol were measured up to 6h after this treatment. 2. Feeding saline (0.9% NaCl) acutely to the rats maintained on the three powdered diets produced a small transient increase in circulating corticosterone that was similar to that in rats maintained on the normal 41B pelleted diet. 3. Feeding glucose acutely to the rats on the powdered diets produced peak concentrations of corticosterone that were 2–3-fold higher than those seen in rats maintained on the 41B diet. The duration of this response increased in the order starch diet<lard diet<corn-oil diet. This abnormal corticosterone response to glucose feeding appeared to be responsible for an increased activity in phosphatidate phosphohydrolase in the livers of rats fed the starch and lard diets of 2.9- and 4.9-fold respectively. The latter increase was similar to that produced by ethanol, whereas glucose did not increase the phosphohydrolase activity in the liver of rats maintained on the 41B diet. 4. Feeding fructose acutely produced even more marked increases than glucose in the concentrations of circulating corticosterone in rats given the powdered diets, but unlike glucose did not increase circulating insulin. The duration of the corticosterone response again increased in the order starch diet<lard diet<corn-oil diet. The concentrations of circulating glucose were increased by fructose feeding in rats maintained on these diets, but they were not altered in the rats maintained on the 41B pellets. A prolonged increase in serum corticosterone concentrations was also observed when fructose was fed to rats maintained on pelleted diets enriched with corn oil or beef tallow rather than with starch or sucrose. However, these effects were less marked than those seen with rats fed on the powdered diets. 5. These results are discussed in relation to the mechanism whereby high dietary fat exaggerates the effects of ethanol, fructose and sorbitol in stimulating triacylglycerol synthesis in the liver.     

News from the Biological Stain Commission No. 5

In this fifth issue of News from the Biological Stain Commission (BSC), under the heading of Regulatory Affairs, the BSC's International Affairs Committee provides more information from the meeting of the International Standards Organization ISO/TC 212 Committee that took place on June 2–4, 2008 at Vancouver, Canada. In addition, we give an update on the current situation regarding the supplies of hematoxylin.     

Benzidine-based dyes: effects of industrial practices,regulations, and world trade on the biological stains market

One of the most sweeping changes in the dye industry since the advent of synthetic dyes grew out of the health risks associated with benzidine. Dyes made from benzidine and its derivatives were used around the world until adverse health effects become incontrovertible. Workers and family members of workers involved in production and use of benzidine-based dyes had a high incidence of bladder cancer. Following publication of several reports documenting this health hazard, dye makers in the USA, Europe, and Japan phased these dyes out of production in the 1970s. Government regulations lent legal support for these voluntary initiatives. Two strategies subsequently evolved to compensate: developed nations brought alternative substances to market while emerging countries increased production of carcinogenic dyes and sold them at discount prices around the world. Nearly all dye manufacturing now has moved away from nations whose costs of production and compliance rendered them unable to compete. The purpose of this brief review is to publicize the health risks associated with dyes made from benzidine and its congeners, and to alert all companies and end users handling these dyes for biomedical applications that composition of the product and lot-to-lot variability may be problematic because of the manufacturing and distribution practices of the countries where they are produced.     

Dye–tissue interactions: mechanisms,quantification and bonding parameters for dyes used in biological staining

Staining of tissues by dyes is accomplished through various types of bonds, some of which have been poorly defined in traditional biological literature. Here, basic principles of bonding are reviewed to establish uniform terminology and definitions consistent with the field of chemistry. The concept of charge – its presence or absence, magnitude, extent of delocalization and potential for being displaced by outside forces – underlies all bonding phenomena. These same attributes influence solubility and resistance to extraction during dehydration of tissue sections. Covalent bonds involve shared electrons; they are very strong and essentially irreversible under conditions encountered during staining. Polar covalent bonds within dye molecules generate partial atomic charges that create the potential for hydrogen bonding. This is measured by the hydrogen bonding parameter (h), the number of groups bearing charges within the ranges ?0.15 to ?0.50 eV or +0.15 to +0.30 eV. The potential for ionic bonding is indicated by net charge (Z), while the strength of such bonds is a function of charge site geometry on both bonding partners. Charge delocalization owing to conjugation, electron influencing groups, and resonance creates soft charge sites in which the ionic charge is spread over a large volume. Poorly delocalized charges or point charges are hard (small in volume). Firm bonds result from hard-hard or soft-soft pairs. Hard-soft combinations are weak, readily displaced in competitive interactions, and disrupted by solvents. Coordinate bonds with certain metals are involved with mordant staining and metal chelation dyes. Three different van der Waals attractions comprise the remainder of bonding types, all involving dipoles: Keesom (dipole-dipole) forces, Debye (dipole-induced dipole) forces and London (induced dipole-induced dipole) forces. Potentials for engaging in any of these is quantified by measures of polarity (dipole moment, d), polarizability (crudely with π atoms describing the size of the conjugated system, or more directly with α), hydrophobicity (with the octanol-water partition coefficient, log P or the more convenient Hydrophobic Index, HI), and the number of halogen atoms (X). By using molecular modeling software, quantitative measures of bonding potential (bonding parameters) have been determined for over 400 dyes.     

Effects of fixation on routine,special and immunohistochemical stains: introduction to a symposium for the Biological Stain Commission

Orcein was first proposed as an elastic fiber stain by Taenzer in 1890, and has proved very useful for the purpose. It is an important constituent of the author's “Quad” stain. Unfortunately not all orcein samples have proved equally satisfactory, whether they are derived from the lichens from which the dye was originally prepared or have been manufactured by a synthetic process. At the present time several brands are available, and two of the brands of the synthetic product investigated have not proved to be the same thing; one of the latter proves only fair as an elastin stain, the other is one of the best samples the author has ever tried.     

Efficient design of the diaphragm: distribution of blood flow relative to mechanical advantage.

The mammalian diaphragm is composed of two separate muscles (costal and crural) connected by a central tendon that serves as a piston head for drawing air into the lungs. The two muscles are described as having different embryological origins, segmental innervations, and mechanical functions [De Troyer A, Sampson M, Sigrist S, and Macklem PT. Science 213: 237-238, 1981; De Troyer A, Sampson M, Sigrist S, and Macklem PT. J Appl Physiol 53: 30-39, 1982]. On the basis of regional blood flow measurements, the two muscles appear to be nonuniformly recruited at rest, but we anticipated that the two muscles would become uniformly recruited at heavy exercise to efficiently support the high energy requirements of ventilation. We used fluorescent microspheres to measure regional blood flow within the two muscles as an index of muscle recruitment from rest to heavy treadmill exercise in well-trained foxhounds. However, the heterogeneity of blood flow at rest persisted as exercise workloads were increased. Blood flow per gram of muscle remained twofold greater in ventral than dorsal regions of both muscles from rest to heavy exercise. This pattern was matched by a twofold greater regional mechanical advantage in ventral than dorsal regions of the two muscles measured anatomically. Hence blood flow was preferentially and efficiently distributed to those regions capable of generating the greatest inspiratory power independent of muscle mass. The two muscles were recruited from rest to heavy exercise as a single functional unit, not as two muscles under separate control.