Number Of Genetic Backgrounds Research Articles

Little effect of HSP90 inhibition on the quantitative wing traits variation in Drosophila melanogaster.

Drosophila wings have been a model system to study the effect of HSP90 on quantitative trait variation. The effect of HSP90 inhibition on environmental buffering of wing morphology varies among studies while the genetic buffering effect of it was examined in only one study and was not detected. Variable results so far might show that the genetic background influences the environmental and genetic buffering effect of HSP90. In the previous studies, the number of the genetic backgrounds used is limited. To examine the effect of HSP90 inhibition with a larger number of genetic backgrounds than the previous studies, 20 wild-type strains of Drosophila melanogaster were used in this study. Here I investigated the effect of HSP90 inhibition on the environmental buffering of wing shape and size by assessing within-individual and among-individual variations, and as a result, I found little or very weak effects on environmental and genetic buffering. The current results suggest that the role of HSP90 as a global regulator of environmental and genetic buffering is limited at least in quantitative traits.

Combining the Dihydrofolate Reductase Protein-Fragment Complementation Assay with Gene Deletions to Establish Genotype-to-Phenotype Maps of Protein Complexes and Interaction Networks.

Systematically measuring the impact of gene deletion on protein-protein interactions is a promising approach to reveal the structural bases of protein interaction networks and to allow a better understanding of how genotypes translate into phenotypes. Genetic and protein-interaction tools in yeast now allow us to explore this third dimension of protein-protein interaction networks. Because it is scalable and quantitative, the protein-fragment complementation assay (PCA) using dihydrofolate reductase (DHFR) as the reporter protein provides an exceptionally powerful tool for such a purpose. Here, we describe a fully automated protocol that combines DHFR PCA for protein-protein interaction measurement and synthetic genetic array (SGA) technology for introducing mutant and other alleles into PCA strains using genetic crosses. In this, PCA strains are crossed with strains carrying a gene deletion and SGA markers, and the recombinant haploid progeny are selected by SGA. The resulting haploid strains, each expressing a DHFR-fragment fusion protein in a gene-specific haploid deletion background, are crossed to measure the interaction between the two recombinant proteins by PCA in a diploid homozygous deletion background. This approach can be used to measure a single protein interaction in a large array of genetic backgrounds or a large number of protein interactions in a small number of genetic backgrounds.

Discovery and characterization of spontaneous mouse models of craniofacial dysmorphology

Craniofacial abnormalities are among the most common features of human genetic syndromes and disorders. The etiology of these conditions is often complex, influenced by both genetic context and the environment. Frequently, craniofacial abnormalities present as part of a syndrome with clear comorbid phenotypes, providing additional insight into mechanisms of the causative gene or pathway. The mouse has been a key tool in our understanding of the genetic mechanisms of craniofacial development and disease, and can provide excellent models for human craniofacial abnormalities. While powerful genetic engineering tools in the mouse have contributed significantly our understanding of craniofacial development and dysmorphology, forward genetic approaches provide an unbiased means to identify new genes and pathways. Moreover, spontaneous mutations can occur on any number of genetic backgrounds, potentially revealing critical genes that require a specific genetic context. Here we report discovery and phenotyping of 43 craniofacial mouse models, derived primarily from a screen for spontaneous mutations in production colonies at the Jackson Laboratory. We identify the causative gene for 33 lines, including novel genes in pathways not previously connected to craniofacial development, and novel alleles of known genes that present with unique phenotypes. Together with our detailed characterization, this work provides a valuable gene discovery resource for the craniofacial community, and a rich source of mouse models for further investigation.

The effects of multilocus balancing selection on neutral variability.

We studied the effect of multilocus balancing selection on neutral nucleotide variability at linked sites by simulating a model where diallelic polymorphisms are maintained at an arbitrary number of selected loci by means of symmetric overdominance. Different combinations of alleles define different genetic backgrounds that subdivide the population and strongly affect variability. Several multilocus fitness regimes with different degrees of epistasis and gametic disequilibrium are allowed. Analytical results based on a multilocus extension of the structured coalescent predict that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. Our simulation results show that although variability increases with the number of genetic backgrounds that are maintained in the population, it is reduced by random fluctuations in the frequencies of those backgrounds and does not reach high levels even in very large populations. We also show that previous results on balancing selection in single-locus systems do not extend to the multilocus scenario in a straightforward way. Different patterns of linkage disequilibrium and of the frequency spectrum of neutral mutations are expected under different degrees of epistasis. Interestingly, the power to detect balancing selection using deviations from a neutral distribution of allele frequencies seems to be diminished under the fitness regime that leads to the largest increase of variability over the neutral case. This and other results are discussed in the light of data from the Mhc.

Leaf-to-shoot apex movement of symplastic tracer is restricted coincident with flowering in Arabidopsis.

Classical experiments in plant physiology showed that leaves are the source of signals that control the development of flowers from shoot meristems. Additional physiological and genetic experiments have indicated some of the molecules (e.g., gibberellins, cytokinins, and sucrose) that promote flowering in mustards including Arabidopsis. These small hydrophilic molecules are likely to move to the shoot apex symplastically via the phloem and/or via cell-to-cell movement through plasmodesmata. To analyze potential changes in the symplastic trafficking of small molecules during the induction of flowering in Arabidopsis, we measured changes in the flow of symplastic tracers from the leaf to the shoot apex. We previously found that the onset of flowering is coincident with an evident decrease in the leaf-to-shoot trafficking of symplastic tracer molecules; this decrease in trafficking is transitory and resumes when floral development is established. Here we provide detailed analyses of symplastic connectivity during floral induction by monitoring tracer movement under different photoperiodic induction conditions and in a number of genetic backgrounds with altered flowering times. In all cases, the correlation between flowering and the reduction of symplastic tracer movement holds true. The lack of tracer movement during the induction of flowering may represent a change in plasmodesmal selectivity at this time or that a period of reduced symplastic communication is associated with floral induction.

Sequences of the waxy loci of wheat: utility in analysis of waxy proteins and developing molecular markers.

The waxy proteins from a number of genetic backgrounds of wheat and its progenitors were analyzed by SDS-PAGE. The deduced amino acid sequences of the waxy proteins of three diploid progenitor species indicated several key amino acid substitutions, which could explain the differences observed in the electrophoretic mobilities of the wheat waxy proteins. A slight difference observed in the apparent molecular weight of the WX-A1 protein of diploid and polyploid wheat was explained by amino acid substitutions or variations in predicted protein structures. Further, twelve different partial genomic clones, representing the individual waxy loci of the various diploid, tetraploid and hexaploid wheats, were isolated and compared. The results indicated significant variations in intron 4 and led to identification of sequences unique to the individual waxy genes and genomes of wheat and its proposed progenitors. The sequence variations observed have a great potential for development as molecular markers for identification of specific waxy loci and study of the various waxy mutants of wheat.

The effect of adaptive mutagenesis on genetic variation at a linked, neutral locus.

Based on recent studies in single-celled organisms, it has been argued that a fitness benefit associated with a mutation will increase the probability of that mutation occurring. This increase is independent of mutation rates at other loci and is called adaptive mutagenesis. We modeled the effect of adaptive mutagenesis on populations of haploid organisms with adaptive mutation rates ranging from 0 to 1 x 10(-5). Allele frequencies at the selected locus and a neutral linked locus were tracked. We also observed the amount of linkage disequilibrium during the selective sweep and the final heterozygosity after the sweep. The presence of adaptive mutagenesis increases the number of genetic backgrounds carrying the new fitter allele, making the outcomes more representative of the population before the selection. Therefore, more neutral genetic variation is preserved in simulations with adaptive mutagenesis than in those without it due to hitchhiking. Since adaptive mutagenesis is time-dependent, it can generate mutants when other mechanisms of mutation cannot. In addition, adaptive mutagenesis has the potential to confound both phylogeny construction and the detection of natural selection from patterns of nucleotide variation.

Attempts to engineer an Escherichia coli DNA-binding protein as a tool for affinity purification of heterologous proteins

Restriction sites were introduced into the Escherichia coli melR gene that facilitated the fusion of other proteins to MelR. Both β-galactosidase and the constant domain of the human IgG kappa light chain were fused to MelR. However, whilst unmodified MelR could be over-expressed, neither MelR fusion protein was over-produced. Addition of an extra domain to MelR leads to reduced expression in a number of genetic backgrounds.

Catabolite repression gene of Escherichia coli.

A catabolite repression gene (cat) which alters the sensitivity of Escherichia coli to catabolite repression has been mapped by transduction and shown to be located between the pyrC and purB genes. When the cat-1 mutation was studied in a number of genetic backgrounds, the results showed that this mutation affects the synthesis of more than one catabolic enzyme but does not completely eliminate catabolic repression under all conditions. It is suggested that this mutation may cause a block in the accumulation of the catabolite effector. Our experiments show that this effector is not glucose-6-phosphate.