Statistical and machine learning methods for analysis of multiplex protein data from a novel proximity extension assay in patients with ST-elevation myocardial infarction.

Using data from patients with ST-elevation myocardial infarction (STEMI), we explored how machine learning methods can be used for analysing multiplex protein data obtained from proximity extension assays. Blood samples were obtained from 48 STEMI-patients at admission and after three months. A subset of patients also had blood samples obtained at four and 12 h after admission. Multiplex protein data were obtained using a proximity extension assay. A random forest model was used to assess the predictive power and importance of biomarkers to distinguish between the acute and the stable phase. The similarity of response profiles was investigated using K-means clustering. Out of 92 proteins, 26 proteins were found to significantly distinguish the acute and the stable phase following STEMI. The five proteins tissue factor pathway inhibitor, azurocidin, spondin-1, myeloperoxidase and myoglobin were found to be highly important for differentiating between the acute and the stable phase. Four of these proteins shared response profiles over the four time-points. Machine learning methods can be used to identify and assess novel predictive biomarkers as showcased in the present study population of patients with STEMI.

Effect of red light on the development and quality of mammalian embryos.

PURPOSE: To assess irradiance and total energy dose from different microscopes during the in-vitro embryonic developmental cycle in mouse and pig and to evaluate its effect on embryonic development and quality in pig. METHOD: Spectral scalar irradiance (380-1050 nm) was measured by a fiber-optic microsensor in the focal plane of a dissection microscope, an inverted microscope and a time-lapse incubation system. Furthermore, the effect of three different red light levels was tested in the time-lapse system on mouse zygotes for 5 days, and on porcine zona-intact and zona-free parthenogenetically activated (PA) embryos for 6 days. RESULTS: The time-lapse system used red light centered at 625 nm and with a lower irradiance level as compared to the white light irradiance levels on the dissection and inverted microscopes, which included more energetic radiation <550 nm. Even after 1000 times higher total energy dose of red light exposure in the time-lapse system, no significant difference was found neither in blastocyst development of mouse zygotes nor in blastocyst rates and total cell number of blastocysts of porcine PA embryos. CONCLUSIONS: Our results indicate that red light (625 nm, 0.34 W/m(2)) used in the time-lapse incubation system does not decrease the development and quality of blastocysts in both mouse zygotes and porcine PA embryos (both zona-intact and zona-free).

Metabolomic signatures of inbreeding at benign and stressful temperatures in Drosophila melanogaster.

While the population genetics of inbreeding is fairly well understood, the effects of inbreeding on the physiological and biochemical levels are not. Here we have investigated the effects of inbreeding on the Drosophila melanogaster metabolome. Metabolite fingerprints in males from five outbred and five inbred lines were studied by nuclear magnetic resonance spectroscopy after exposure to benign temperature, heat stress, or cold stress. In both the absence and the presence of temperature stress, metabolite levels were significantly different among inbred and outbred lines. The major effect of inbreeding was increased levels of maltose and decreased levels of 3-hydroxykynurenine and a galactoside [1-O-(4-O-(2-aminoethyl phosphate)-beta-d-galactopyranosyl)-x-glycerol] synthesized exclusively in the paragonial glands of Drosophila species, including D. melanogaster. The metabolomic effect of inbreeding at the benign temperature was related to gene expression data from the same inbred and outbred lines. Both gene expression and metabolite data indicate that fundamental metabolic processes are changed or modified by inbreeding. Apart from affecting mean metabolite levels, inbreeding led to an increased between-line variation in metabolite profiles compared to outbred lines. In contrast to previous observations revealing interactions between inbreeding and environmental stress on gene expression patterns and life-history traits, the effect of inbreeding on the metabolite profile was similar across the different temperature treatments.

Inbreeding by environmental interactions affect gene expression in Drosophila melanogaster.

Genomewide gene expression patterns were investigated in inbred and noninbred Drosophila melanogaster lines under benign and stressful (high temperature) environmental conditions in a highly replicated experiment using Affymetrix gene chips. We found that both heat-shock protein and metabolism genes are strongly affected by temperature stress and that genes involved in metabolism are differentially expressed in inbred compared with noninbred lines, and that this effect is accentuated after heat stress exposure. Furthermore we show that inbreeding and temperature stress cause increased between-line variance in gene expression patterns. We conclude that inbreeding and environmental stress both independently and synergistically affect gene expression patterns. Interactions between inbreeding and the environment are often observed at the phenotypic level and our results reveal some of the genes that are involved at the individual gene level. Our observation of several metabolism genes being differentially expressed in inbred lines and more so after exposure to temperature stress, together with lower fitness in the investigated inbred lines, supports the hypothesis that superiority of heterozygous individuals partly derives from increased metabolic efficiency.

Genome-wide analysis on inbreeding effects on gene expression in Drosophila melanogaster.

The deleterious consequences of inbreeding, especially in the form of inbreeding depression, are well known. However, little is known about how inbreeding affects genome-wide gene expression. Here, we show that inbreeding changes transcription levels for a number of genes. Gene expression profiles of Drosophila melanogaster lines inbred to F approximately = 0.67 at different rates changed relative to those of noninbred lines, but the rate of inbreeding did not significantly affect gene expression patterns. Genes being differentially expressed with inbreeding are disproportionately involved in metabolism and stress responses, suggesting that inbreeding acts like an environmental stress factor.