Integrated visualization of a multi-omics study of starvation in mouse intestine

Summary Our understanding of complex biological processes can be enhanced by combining different kinds of high-throughput experimental data, but the use of incompatible identifiers makes data integration a challenge. We aimed to improve methods for integrating and visualizing different types of omics data. To validate these methods, we applied them to two previous studies on starvation in mice, one using proteomics and the other using transcriptomics technology. We extended the PathVisio software with new plugins to link proteins, transcripts and pathways. A low overall correlation between proteome and transcriptome data was detected (Spearman rank correlation: 0.21). At the level of individual genes, correlation was highly variable. Many mRNA/protein pairs, such as fructose biphosphate aldolase B and ATP Synthase, show good correlation. For other pairs, such as ferritin and elongation factor 2, an interesting effect is observed, where mRNA and protein levels change in opposite directions, suggesting they are not primarily regulated at the transcriptional level. We used pathway diagrams to visualize the integrated datasets and found it encouraging that transcriptomics and proteomics data supported each other at the pathway level. Visualization of the integrated dataset on pathways led to new observations on gene-regulation in the response of the gut to starvation. Our methods are generic and can be applied to any multi-omics study. The PathVisio software can be obtained at http://www.pathvisio.org. Supplemental data are available at http://www.bigcat.unimaas.nl/data/jib-supplemental/, including instructions on reproducing the pathway visualizations of this manuscript.

Linkage Groups of Protein-Coding Genes in Western Palearctic Water Frogs Reveal Extensive Evolutionary Conservation

Among progeny of a hybrid (Rana shqiperica × R. lessonae) × R lessonae, 14 of 22 loci form four linkage groups (LGs): (1) mitochondrial aspartate aminotransferase, carbonate dehydratase-2, esterase 4, peptidase D; (2) mannosephosphate isomerase, lactate dehydrogenase-B, sex, hexokinase-1, peptidase B; (3) albumin, fructose-biphosphatase-1, guanine deaminase; (4) mitochondrial superoxide dismutase, cytosolic malic enzyme, xanthine oxidase. Fructose-biphosphate aldolase-2 and cytosolic aspartate aminotransferase possibly form a fifth LG. Mitochondrial aconitate hydratase, α-glucosidase, glyceraldehyde-3+hosphate dehydrogenase, phosphogluconate dehydrogenase, and phosphoglucomutase-2 are unlinked to other loci. All testable linkages (among eight loci of LGs 1, 2, 3, and 4) are shared with eastern Palearctic water frogs. Including published data, 44 protein loci can be assigned to 10 of the 13 chromosomes in Holarctic Rana. Of testable pairs among 18 protein loci, agreement between Palearctic and Nearctic Rana is complete (125 unlinked, 14 linked pairs among 14 loci of five syntenies), and Holarctic Rana and Xenopus laevis are highly concordant (125 shared nonlinkages, 13 shared linkages, three differences). Several Rana syntenies occur in mammals and fish. Many syntenies apparently have persisted for 60–140 × 106 years (frogs), some even for 350–400 × 106 years (mammals and teleosts).

Changes associated with glycolytic-enzyme binding in the equatorial X-ray-diffraction pattern of glycerinated rabbit psoas muscle

The binding of fructose biphosphate aldolase to the thin filaments of glycerinated rabbit psoas muscle produces a significant change in its low-angle X-ray-diffraction pattern. The intensity of the (11) reflection relative to that of the (10) reflection increases by 26 +/- 3% (mean +/- S.E.M.), which is consistent with the increase in the mass of the thin filaments produced by enzyme binding. A similar effect is found with a mixture of aldolase and glyceraldehyde 3-phosphate dehydrogenase. The significance of the change in intensity is considered with reference to the interpretation of the equatorial patterns obtained from muscles in different physiological states. The magnitude of the increase in the relative intensity of the (11) reflection is lower than that observed between relaxed and contracting muscle and does not bring into question the interpretation linking changes in these patterns to cross-bridge movement. However, the effect due to enzyme binding may be important when making detailed interpretations of these changes. It may also be related to an unusual pattern sometimes observed in cardiac muscle.

The specific activity of aldolase in the livers of old and young rats

The catalytic activity of liver fructose-biphosphate aldolase (EC 4.1.2.13) of young and old rats in units per manomole sequence has been calculated. No evidence of the accumulation with age of altered enzyme molecules of low catalytic activity was obtained. This is contrary to results obtained using mice and rabbits and indicates that the accumulation of altered enzymes may not always be associated with aging. The possibility that altered proteins are formed, but do not accumulate, cannot be ruled out.