Allelic variation in gene expression identified through computational analysis of the dbEST database

Differential expression between the two alleles of an individual and between people with different genotypes has been commonly observed. Quantitative differences in gene expression between people may provide the genetic basis for the phenotypic difference between individuals and may be the primary cause of complex diseases. In this paper, we developed a computational method to identify genes that displayed allelic variation in gene expression in human EST libraries. To model allele-specific gene expression, we first identified EST libraries in which both A and B alleles were expressed and then identified allelic variation in gene expression based on the EST counts for each allele using a binomial test. Among 1107 SNPs that had a sufficient number of ESTs for the analysis, 524 (47%) displayed allelic variation in at least one cDNA library. We verified experimentally the allelic variation in gene expression for 6 of these SNPs. The frequency of allelic variation observed in EST libraries was similar to the previous studies using the SNP chip and primer extension method. We found that genes that displayed allelic variation were distributed throughout the human genome and were enriched in certain chromosome regions. The SNPs and genes identified in this study will provide a rich source for evaluating the effects of those SNPs and associated haplotypes in human health and diseases.     

Biogeography of the túngara frog, Physalaemus pustulosus: a molecular perspective

Physalaemus pustulosus, a small leptodactylid frog with South American affinities, ranges across northern South America through Middle America to southern Mexico. To investigate its geographic variation and evolutionary origins, we analysed the presumptive gene products of 14 allozyme loci and sequenced a portion of the mitochondrial COI gene from individuals sampled throughout the distribution. Generally, allozyme dissimilarities and sequence divergences are correlated with each other and with geographic proximity. The greatest discontinuity in genetic variation was found between populations in Middle America vs. South America + Panama. Based on two Bayesian MCMC (Markov chain Monte Carlo) divergence time estimates involving two independent temporal constraints, the timing of the separation of northern and southern túngara frog lineages is significantly older than the time since completion of the current Panama land bridge. P. pustulosus first invaded Middle America from South America about 6-10 million years ago giving rise to the northern lineage. The southern lineage then invaded Panama independently after land bridge completion. Despite millions of years of independent evolution, the multilocus allozyme data revealed that western Panama populations represent a contact zone containing individuals with alleles from both groups present.     

Biomass recycling and the origin of phenotype in fungal mycelia

Fungi are one of the most important and widespread components of the biosphere, and are essential for the growth of over 90% of all vascular plants. Although they are a separate kingdom of life, we know relatively little about the origins of their ubiquitous existence. This reflects a wider ignorance arising from their status as indeterminate organisms epitomized by extreme phenotypic plasticity that is essential for survival in complex environments. Here we show that the fungal phenotype may have its origins in the defining characteristic of indeterminate organisms, namely their ability to recycle locally immobilized internal resources into a mobilized form capable of being directed to new internal sinks. We show that phenotype can be modelled as an emergent phenomenon resulting from the interplay between simple local processes governing uptake and remobilization of internal resources, and macroscopic processes associated with their transport. Observed complex growth forms are reproduced and the sensitive dependence of phenotype on environmental context may be understood in terms of nonlinearities associated with regulation of the recycling apparatus.     

The ins and outs of sphingolipid synthesis

Sphingolipids are ubiquitous components of eukaryotic cell membranes, where they play important roles in intracellular signaling and in membrane structure. Even though the biochemical pathway of sphingolipid synthesis and its compartmentalization between the endoplasmic reticulum and Golgi apparatus have been known for many years, the molecular identity of the enzymes in this pathway has only recently been elucidated. Here, we summarize progress in the identification and characterization of the enzymes, the transport of ceramide from the endoplasmic reticulum to the Golgi apparatus, and discuss how regulating the synthesis of sphingolipids might impact upon their functions.     

Oral microbial communities in sickness and in health

The relationship between humans and their oral microflora begins shortly after birth and lasts a lifetime. Up until fairly recently, the associations between the host and oral bacteria were considered in terms of a multiplicity of single species interactions. However, it is becoming more apparent that the oral microbes comprise a complex community, and that oral health or disease depends on the interface between the host and the microbial community as a whole. Although it is important to continue studies of the pathogenic properties of specific microbes, these are relevant only in the context of the properties of the community within which they reside. Understanding the microbial communities that drive sickness or health is a key to combating human oral diseases.     

Androgen-induced mineralization by MC3T3-E1 osteoblastic cells reveals a critical window of hormone responsiveness

Despite their clinical importance for skeletal growth and homeostasis, the actions of androgens on osteoblastic cells are not well understood. MC3T3-E1 cells, a nontransformed murine preosteoblastic cell line, that traverse the stages of osteoblastic differentiation within 30 days in vitro, were exposed to mibolerone (an androgen receptor (AR) agonist) or 5alpha-dihydroxytestosterone (DHT) from days 3 to 30 post-plating. Cells exposed to this hormonal regimen exhibited a significant increase in mineralization (calcium deposition) compared to vehicle-treated cells. Delaying treatment for 4-11 days (treatment still completed on day 30 post-plating) enhanced mineralization further. Within 2 days post-plating, AR protein increased 7.2-fold in androgen-treated cells and 2.5-fold in vehicle-treated cells. MC3T3-E1 cells transfected with an androgen- and glucocorticoid-responsive reporter construct on day 1 post-plating followed by a 2 day exposure to DHT, mibolerone, or dexamethasone (dex; a glucocorticoid receptor agonist) exhibited reporter gene activation only with dex treatment. In contrast, delaying transfection and treatment for at least 1 day resulted in comparable androgen- and dex-mediated reporter gene transactivation. Therefore, the ability of MC3T3-E1 cells to respond to androgens is dependent on the timing of androgen administration.     

Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats

Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.     

Variation in tissue-specific gene expression among natural populations

Background

Variation in gene expression is extensive among tissues, individuals, strains, populations and species. The interactions among these sources of variation are relevant for physiological studies such as disease or toxic stress; for example, it is common for pathologies such as cancer, heart failure and metabolic disease to be associated with changes in tissue-specific gene expression or changes in metabolic gene expression. But how conserved these differences are among outbred individuals and among populations has not been well documented. To address this we examined the expression of a selected suite of 192 metabolic genes in brain, heart and liver in three populations of the teleost fish Fundulus heteroclitus using a highly replicated experimental design.

Results

Half of the genes (48%) were differentially expressed among individuals within a population-tissue group and 76% were differentially expressed among tissues. Differences among tissues reflected well established tissue-specific metabolic requirements, suggesting that these measures of gene expression accurately reflect changes in proteins and their phenotypic effects. Remarkably, only a small subset (31%) of tissue-specific differences was consistent in all three populations.

Conclusions

These data indicate that many tissue-specific differences in gene expression are unique to one population and thus are unlikely to contribute to fundamental differences between tissue types. We suggest that those subsets of treatment-specific gene expression patterns that are conserved between taxa are most likely to be functionally related to the physiological state in question.