Systems genomics of metabolic phenotypes in wild-type Drosophila melanogaster.

Systems biology is an approach to dissection of complex traits that explicitly recognizes the impact of genetic, physiological, and environmental interactions in the generation of phenotypic variation. We describe comprehensive transcriptional and metabolic profiling in Drosophila melanogaster across four diets, finding little overlap in modular architecture. Genotype and genotype-by-diet interactions are a major component of transcriptional variation (24 and 5.3% of the total variation, respectively) while there were no main effects of diet (<1%). Genotype was also a major contributor to metabolomic variation (16%), but in contrast to the transcriptome, diet had a large effect (9%) and the interaction effect was minor (2%) for the metabolome. Yet specific principal components of these molecular phenotypes measured in larvae are strongly correlated with particular metabolic syndrome-like phenotypes such as pupal weight, larval sugar content and triglyceride content, development time, and cardiac arrhythmia in adults. The second principal component of the metabolomic profile is especially informative across these traits with glycine identified as a key loading variable. To further relate this physiological variability to genotypic polymorphism, we performed evolve-and-resequence experiments, finding rapid and replicated changes in gene frequency across hundreds of loci that are specific to each diet. Adaptation to diet is thus highly polygenic. However, loci differentially transcribed across diet or previously identified by RNAi knockdown or expression QTL analysis were not the loci responding to dietary selection. Therefore, loci that respond to the selective pressures of diet cannot be readily predicted a priori from functional analyses.

Characterization of anthocyanins and anthocyanidins in purple-fleshed sweetpotatoes by HPLC-DAD/ESI-MS/MS.

Purple-fleshed sweetpotatoes (PFSP) can be a healthy food choice for consumers and a potential source for natural food colorants. This study aimed to identify anthocyanins and anthocyanidins in PFSP, and to evaluate the effect of thermal processing on these polyphenolic compounds. Freeze-dried powder of raw and steamed samples of three PFSP varieties were extracted with acidified methanol using a Dionex ASE 200 accelerated solvent extractor. Seventeen anthocyanins were identified by HPLC-DAD/ESI-MS/MS for Stokes Purple and NC 415 varieties with five major compounds: cyanidin 3-caffeoylsophoroside-5-glucoside, peonidin 3-caffeoylsophoroside-5-glucoside, cyanidin 3-caffeoyl-p-hydroxybenzoylsophoroside-5-glucoside, peonidin 3-caffeoyl-p-hydroxybenzoyl-sophoroside-5-glucoside, and peonidin-caffeoyl-feruloylsophoroside-5-glucoside. Okinawa variety showed 12 pigments with 3 major peaks identified as cyanidin 3-caffeoylsophoroside-5-glucoside, cyanidin 3-(6'',6'''-dicaffeoylsophoroside)-5-glucoside and cyanidin 3-(6''-caffeoyl-6'''-feruloylsophoroside)-5-glucoside. Steam cooking had no significant effect on total anthocyanin content or the anthocyanin pigments. Cyanidin and peonidin, which were the major anthocyanidins in the acid hydrolyzed extracts, were well separated and quantified by HPLC with external standards. Cyanidin and peonidin, which contribute to the blue and red hues of PFSP, can be simply quantified by HPLC after acid hydrolysis of the anthocyanins.

Mercury(II) bioaccumulation and antioxidant physiology in four aquatic insects.

We examined Hg(II) bioaccumulation and compartmentalization patterns in conjunction with antioxidant responses in four aquatic insect species: two caddisflies (Chimarra sp. and Hydropsyche betteni) and two mayflies (Maccaffertium modestum and Isonychia sp). Total antioxidant capabilities differed among unexposed larvae, with both caddisfly species exhibiting elevated antioxidant activities relative to the mayflies. We were able to account for these differences by examining the constitutive activities of catalase (CAT), glutathione peroxidase (GPx), glutathione S-transferase (GST), and superoxide dismutase (SOD), in the four species. We also examined levels of reduced and oxidized glutathione and cysteine in the insects. Glutathione peroxidase and SOD were the most responsive to Hg exposure, with GPx catalytic activity increasing between 50 and 310%. Superoxide dismutase activity decreased between 35 and 50%. This SOD suppression was shown to be dose-dependent in both caddisflies, butthe strength of this suppression did not appear to be related to rates of uptake. Surprisingly, little Hg (<10%) was found in the heat-stable cytosolic protein subcellular compartment in each of the four species, suggesting that Hg was not well detoxified. By combining bioaccumulation studies with other physiological measures, we can begin to better understand the consequences of trace metal pollutants in nature.

Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster.

Although most genetic association studies are performed with the intention of detecting nucleotide polymorphisms that are correlated with a complex trait, transcript abundance should also be expected to associate with diseases or phenotypes. We performed a scan for such quantitative trait transcripts in adult female heads of the fruit fly (Drosophila melanogaster) that might explain variation for nicotine resistance. The strongest association was seen for abundance of ornithine aminotransferase transcripts, implicating detoxification and neurotransmitter biosynthesis as mediators of the quantitative response to the drug. Subsequently, genetic analysis and metabolite profiling confirmed a complex role for ornithine and GABA levels in modification of survival time upon chronic nicotine exposure. Differences between populations from North Carolina and California suggest that the resistance mechanism may be an evolved response to environmental exposure.

Plasma and urinary phyto-oestrogens as biomarkers of intake: validation by duplicate diet analysis.

Estimating intake of phyto-oestrogens (PO) is difficult because there is inadequate information on the PO content of foods. Development of a biomarker of intake is therefore necessary for carrying out epidemiological studies. We aimed to validate a newly constructed PO database, containing more than 600 values assigned to foods by using duplicate diet analysis, and to investigate the relationships between measured PO intake, urinary excretion and plasma concentrations of PO. Fourteen subjects with estimated dietary intakes of PO ranging from 0 to 44 mg/d, measured by 7 d weighed intake, completed a duplicate diet collection over 24 h. Concurrently, a 24 h urine collection, validated using p-aminobenzoic acid, was obtained and one timed spot plasma sample taken. Duplicate diets, complete urine collections and plasma samples were analysed for total genistein and daidzein using liquid chromatography-MS to determine PO intake. The potential for 24 h urinary excretion and plasma PO concentrations to reflect dietary intake was investigated. Mean estimated and measured dietary PO intakes were 12.3 and 11.0 mg/d respectively. The correlation between estimated intake and measured intake of PO was highly significant (r 0.98, P<0.001). Urinary excretion (24 h) and plasma concentrations of PO were significantly related to measured dietary PO intake (r 0.97, P<0.001 and r 0.92, P<0.001 respectively). The relationship between 24 h urinary PO excretion and timed plasma concentrations was also significant (r 0.99, P<0.001). These findings validate the PO database and indicate that 24 h urinary excretion and timed plasma concentrations can be used as biomarkers of PO intake.