Application of logistic regression to case-control association studies involving two causative loci

Models in which two susceptibility loci jointly influence the risk of developing disease can be explored using logistic regression analysis. Comparison of likelihoods of models incorporating different sets of disease model parameters allows inferences to be drawn regarding the nature of the joint effect of the loci. We have simulated case-control samples generated assuming different two-locus models and then analysed them using logistic regression. We show that this method is practicable and that, for the models we have used, it can be expected to allow useful inferences to be drawn from sample sizes consisting of hundreds of subjects. Interactions between loci can be explored, but interactive effects do not exactly correspond with classical definitions of epistasis. We have particularly examined the issue of the extent to which it is helpful to utilise information from a previously identified locus when investigating a second, unknown locus. We show that for some models conditional analysis can have substantially greater power while for others unconditional analysis can be more powerful. Hence we conclude that in general both conditional and unconditional analyses should be performed when searching for additional loci.     

Regulatory interactions between two actin nucleators, Spire and Cappuccino

Spire and Cappuccino are actin nucleation factors that are required to establish the polarity of Drosophila melanogaster oocytes. Their mutant phenotypes are nearly identical, and the proteins interact biochemically. We find that the interaction between Spire and Cappuccino family proteins is conserved across metazoan phyla and is mediated by binding of the formin homology 2 (FH2) domain from Cappuccino (or its mammalian homologue formin-2) to the kinase noncatalytic C-lobe domain (KIND) from Spire. In vitro, the KIND domain is a monomeric folded domain. Two KIND monomers bind each FH2 dimer with nanomolar affinity and strongly inhibit actin nucleation by the FH2 domain. In contrast, formation of the Spire-Cappuccino complex enhances actin nucleation by Spire. In Drosophila oocytes, Spire localizes to the cortex early in oogenesis and disappears around stage 10b, coincident with the onset of cytoplasmic streaming.     

Bacterial evolution through the selective loss of beneficial Genes. Trade-offs in expression involving two loci

The loss of preexisting genes or gene activities during evolution is a major mechanism of ecological specialization. Evolutionary processes that can account for gene loss or inactivation have so far been restricted to one of two mechanisms: direct selection for the loss of gene activities that are disadvantageous under the conditions of selection (i.e., antagonistic pleiotropy) and selection-independent genetic drift of neutral (or nearly neutral) mutations (i.e., mutation accumulation). In this study we demonstrate with an evolved strain of Escherichia coli that a third, distinct mechanism exists by which gene activities can be lost. This selection-dependent mechanism involves the expropriation of one gene's upstream regulatory element by a second gene via a homologous recombination event. Resulting from this genetic exchange is the activation of the second gene and a concomitant inactivation of the first gene. This gene-for-gene expression tradeoff provides a net fitness gain, even if the forfeited activity of the first gene can play a positive role in fitness under the conditions of selection.     

Subunit interactions of Glycera dibranchiata hemoglobin.

The coelomic cells of the polychaete annelid Glycera dibranchiata contain two hemoglobins. The monomer hemoglobin fraction is composed of one major component and two minor components as determined by starch gel electrophoresis and isoelectrofocusing, but is homogeneous as to subunit size as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The polymer hemoglobin fraction has and initial molecular weight of Mn = 125,000 as determined by osmometry, but exhibits an increased state of aggregation upon storage. The quaternary structure of the polymer is constituted of monomeric subunits in a non-covalent state of aggregation as demonstrated by its subunit dissociation inthe presence of propyl urea. The oxygen affinity of the polymer is lower than the monomer but increases with deaggregation. The Bohr effect is present only in the polymer. Cooperativity is also characteristic of the polymer and is pH-dependent. Interestingly, cooperativity increases with intermediate states of polymer deaggregation. By far, the main organic phosphate component of the coelomic red cells is ATP accompanied by small amounts of ADP and GTP. No modulating effect of ATP on the oxygen equilibrium of either polymer or total hemolysate was found.     

Fat body: a site of hemoglobin synthesis in Chironomus thummi (diptera)

Fourth instar larvae of Chironomus thummi were permitted to incorporate labeled amino acids and/or sigma-aminolevulinic acid (sigma-ALA) in vivo and in organ culture. The products secreted into the hemolymph or into the culture medium were examined by acrylamide gel electrophoresis. Nine electrophoretic bands can be resolved as hemoglobins without staining. When gels are sliced for scintillation counting, incorporated amino acids and sigma-ALA are shown to be associated primarily with the same nine hemoglobin bands, suggesting that hemoglobins are assembled and secreted. Staining of gels with Coomassie brilliant blue reveals that there are several bands in addition to the visible hemoglobins. These bands incorporate amino acids, but not sigma-ALA, suggesting that they are non-heme proteins. The results of culturing isolated salivary glands, gut, and fat body demonstrate that the fat body is the major site of hemoglobin synthesis and secretion. Labeled products of the gut represent about 5% of the total hemoglobins produced by the tissues, while no hemoglobins are produced by the salivary glands. Although nine hemoglobins are visibly resolved on gels, labeling techniques reveal as many as 14 hemoglobins. This is the first demonstration of hemoglobin synthesis by specific tissues in culture in an invertebrate.     

Leaf surface waxbloom in Pisum sativum influences predation and intra-guild interactions involving two predator species

Suppression of shared prey populations by insect predators can be influenced by interactions among these predators (intra-guild interactions). Intra-guild interactions among predators attacking herbivores may be influenced by plant characteristics, but this possibility has not been examined. Plant surface waxes are a ubiquitous and variable morphological feature that are known to affect insect predator behavior, and potentially in- fluence inter-predator interactions. To test this possibility we measured the effectiveness of individual and multiple predators on Pisum sativum L. lines with either wild-type crystalline waxes (normal waxbloom) or with reduced waxbloom resulting from a genetic mutation. On caged five-node plants of each line, reduction in populations of Acyrthosiphon pisum (Harris) (Homoptera: Aphidae) by individuals or pairs of second-instar Hippodamia con- vergens Guerin de Meneville (Coleoptera: Coccinellidae), and second-instar Chrysoperla plorabunda (Fitch) (Neuroptera: Chrysopidae), was significantly greater on the reduced waxbloom plants. Intra-specific interference by H. convergens depended on plant waxbloom type. Pairs of H. convergens larvae were no more effective than individuals of this species at reducing aphid populations on normal waxbloom plants, indicating interference, but were additive in their reduction of aphids on reduced waxbloom plants, indicating no interference. In contrast, pairs of C. plorabunda apparently interfered regardless of plant waxbloom type; pairs were no more effective at reducing aphids than individuals of this species. Heterospecific pairs of H. convergens and C. plorabunda were more effective on reduced waxbloom plants and showed no evidence of interference on either waxbloom type. Differences in behavior of the two predator species provided a partial explanation for the asymmetrical effect on intraspecific interactions in the two species. H. conver- gens spent significantly more time walking and less time ”scrambling” (ineffective locomotion) on reduced waxbloom plants than on normal waxbloom plants, and distributed these activities differently among plant parts on the two waxbloom types. In contrast, C. plorabunda spent the same amount of time walking and scrambling on each waxbloom type, although they distributed this walking and scrambling differently among plant parts of the two waxbloom types. The stronger influence of plant waxbloom on H. convergens behavior is consistent with the difference in intra-specific interference for this species on the two waxbloom types. The mechanisms of intra-specific interference by H. convergens on normal waxbloom plants and by C. plorabunda on both waxbloom types were not determined. Received: 14 July 1999 / Accepted: 10 January 2000     

Linkage of albino and hemoglobin beta-chain loci in the rabbit

Genetic linkage between the albino (c) and hemoglobin beta-chain (Hb beta) genes in rabbits was demonstrated by means of segregation data from one full-sib family. The map distance was estimated at 9 +/- 6 cM, which is similar to the 8 cM previously estimated between the same pair of loci in both mice and rats. The interspecies conservation of the chromosome segment comprising c and Hb beta thus extends outside the rodent family. Indications that it also may be conserved in man are discussed.     

Genomic imprinting of two antagonistic loci

We present a model that considers the coevolution of genomic imprinting at a growth factor locus and an antagonistic growth suppressor locus. With respect to the two loci considered independently, our model makes the familiar predictions that an imprinted growth factor locus will only be expressed from the paternally derived allele and an imprinted growth suppressor locus only from the maternally derived allele. In addition, our coevolutionary model allows us to make predictions regarding the sequence of evolutionary events necessary for generating such a system. We conclude that imprinting at the growth factor locus preceded the evolution of growth suppressor function at the second locus, which in turn preceded imprinting at that locus. We then discuss the consistency of these predictions with currently available comparative data on the insulin-like growth factor 2 insulin-like growth factor 2 receptor system of mammals.