Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

Epistasis refers to the interaction between genes. Although high-throughput epistasis data from model organisms are being generated and used to construct genetic networks(1-3), the extent to which genetic epistasis reflects biologically meaningful interactions remains unclear(4-6). We have addressed this question through in silico mapping of positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis. We found that negative epistasis occurs mainly between nonessential reactions with overlapping functions, whereas positive epistasis usually involves essential reactions, is highly abundant and, unexpectedly, often occurs between reactions without overlapping functions. We offer mechanistic explanations of these findings and experimentally validate them for 61 S. cerevisiae gene pairs.

Metabolic changes in rat prefrontal cortex and hippocampus induced by chronic morphine treatment studied ex vivo by high resolution H-1 NMR spectroscopy

Ex vivo H-1 NMR spectroscopy was used to measure changes in the concentrations of cerebral metabolites in the prefrontal cortex (PFC) and hippocampus of rats subjected to repeated morphine treatment known to cause tolerance/dependence. The results show th

An Automatic Classification Method of Metabolic Cycle Based on Biomimetic Pattern Recognition

Correct classification of different metabolic cycle stages to identification cell cycle is significant in both human development and clinical diagnostics. However, it has no perfect method has been reached in classification of metabolic cycle yet. This paper exploringly puts forward an automatic classification method of metabolic cycle based on Biomimetic pattern recognition (BPR). As to the three phases of yeast metabolic cycle, the correct classification rate reaches 90%, 100% and 100% respectively.

Effects of multistage coupling and disk flexibility on mistuned bladed disk dynamics

The effects ofdisk flexibility and multistage coupling on the dynamics of bladed disks with and without blade mistuning are investigated. Both free and forced responses are examined using finite element representations of example single and two-stage rotor models. The reported work demonstrates the importance of proper treatment of interstage (stage-to-stage) boundaries in order to yield adequate capture of disk-blade modal interaction in eigenfrequency veering regions. The modified disk-blade modal interactions resulting from interstage-coupling-induced changes in disk flexibility are found to have a significant impact on (a) tuned responses due to excitations passing through eigenfrequency veering regions, and (b) a design's sensitivity to blade mistuning. Hence, the findings in this paper suggest that multistage analyses may be required when excitations are expected to fall in or near eigenfrequency veering regions or when the sensitivity to blade mistuning is to be accounted for Conversely, the observed sensitivity to disk flexibility also indicates that the severity of unfavorable structural interblade coupling may be reduced significantly by redesigning the disk(s) and stage-to-stage connectivity. The relatively drastic effects of such modifications illustrated in this work indicate that the design modifications required to alleviate veering-related response problems may be less comprehensive than what might have been expected.

Assembly of the highest connectivity Wells-Dawson polyoxometalate coordination polymer: the use of organic ligand flexibility

Through tuning the length of flexible bis(triazole) ligands and different metal ion coordination geometries, four Wells-Dawson polyoxoanion-based hybrid compounds, [Cu-6(btp)(3)(P2W18O62)] center dot 3H(2)O (1) (btp = 1,3-bis(1,2,4-triazol-1-yl)propane), [Cu-6(btb)(3)((P2W18O62) center dot 2H(2)O (2), [Cu-3(btb)(6)(P2W18O62)] center dot 6H(2)O (btb = 1,4-bis(1,2,4-triazol-1-yl)butane) (3), and [Cu-3(btx)(5.5)((P2W18O62) center dot 4H(2)O (btx = 1,6-bis(1,2,4-triazol-1-yl)hexane) (4), were synthesized and structurally characterized. in compound 1, the metal-organic motif exhibits a ladder-like chain, which is further fused by the ennead-dentate [P2W18O62](6-) anions to construct a 3D structure. In compound 2, the metal-organic motif exhibits an interesting Cu-btb grid layer, and the ennead-dentate polyoxoanions are sandwiched by two Cu-btb layers to construct a 3D structure

Toxicological effects of cinnabar in rats by NMR-based metabolic profiling of urine and serum

Cinnabar, an important traditional Chinese mineral medicine, has been widely used as a Chinese patent medicine ingredient for sedative therapy. However, the pharmaceutical and toxicological effects of cinnabar, especially in the whole organism, were subjected to few investigations. In this study, an NMR-based metabolomics approach has been applied to investigate the toxicological effects of cinnabar after intragastrical administration (dosed at 0.5, 2 and 5 g/kg body weight) on male Wistar rats.

Poly[[(pentaethylenehexamine)manganese(II)] [hepta-mu-selenido-tritin(IV)]]: a tin-selenium net with remarkable flexibility

The title compound, {[Mn(C10H28N6)][Sn3Se7]}(n), consists of anionic (infinity){[Sn3Se7](2-)} layers interspersed by [Mn(peha)](2+) complex cations ( peha is pentaethylenehexamine). Pseudo-cubic (Sn3Se4) cluster units within each layer are held together to form a 6(3) net with a hole size of 8.74 x 13.87 angstrom. Weak N-H center dot center dot center dot Se interactions between the host inorganic frameworks and metal complexes extend the components into a three-dimensional network. The incorporation of metal complexes into the flexible anion layer dictates the distortion of the holes.

Metabolic profiling studies on the toxicological effects of realgar in rats by H-1 NMR spectroscopy

The toxicological effects of realgar after intragastrical administration (1 g/kg body weight) were investigated over a 21 day period in male Wistar rats using metabonomic analysis of H-1 NMR spectra of urine, serum and liver tissue aqueous extracts. Liver and kidney histopathology examination and serum clinical chemistry analyses were also performed. H-1 NMR spectra and pattern recognition analyses from realgar treated animals showed increased excretion of urinary Kreb's cycle intermediates, increased levels of ketone bodies in urine and serum, and decreased levels of hepatic glucose and glycogen, as well as hypoglycemia and hyperlipoidemia, suggesting the Perturbation of energy metabolism. Elevated levels of choline containing metabolites and betaine in serum and liver tissue aqueous extracts and increased serum creatine indicated altered transmethylation. Decreased urinary levels of trimethylamine-N-oxide, phenylacetylglycine and hippurate suggested the effects on the gut microflora environment by realgar.

Metabolic profiling of serum from gadolinium chloride-treated rats by H-1 NMR spectroscopy

Metabolic profiling of serum from gadolinium chloride (GdCl3, 10 and 50 mg/kg body weight, intraperitoneal [i.p.])-treated rats was investigated by the NMR spectroscopic-based metabonomic strategy. Serum samples were collected at 48, 96, and 168 h postdose (p.d.) after exposure to GdCl3. H-1 NMR spectra of serum were analyzed by pattern recognition using principal components analysis. The studies showed that there was a dose-related biochemical effect of GdCl3 treatment on the levels of a range of low-molecular weight compounds in serum. The liver damage induced by GdCl3 was characterized by the elevation of lactate, pyruvate, and creatine as well as the decrease of branched-chain amino acids (valine and isoleucine), alanine, glucose, and trimethylamine-N-oxide concentration in serum samples. The biochemical effects of GdCl3 in rats could be consulted when evaluating the biochemical profile of gadolinium-containing compounds that are being developed for nuclear magnetic resonance imaging.