Modeling Gene Networks in Saccharomyces cerevisiae

Detailed and innovative analysis of gene regulatory network structures may reveal novel insights to biological mechanisms. Here we study how gene regulatory network in Saccharomyces cerevisiae can differ under aerobic and anaerobic conditions. To achieve this, we discretized the gene expression profiles and calculated the self-entropy of down- and upregulation of gene expression as well as joint entropy. Based on these quantities the uncertainty coefficient was calculated for each gene triplet, following which, separate gene logic networks were constructed for the aerobic and anaerobic conditions. Four structural parameters such as average degree, average clustering coefficient, average shortest path, and average betweenness were used to compare the structure of the corresponding aerobic and anaerobic logic networks. Five genes were identified to be putative key components of the two energy metabolisms. Furthermore, community analysis using the Newman fast algorithm revealed two significant communities for the aerobic but only one for the anaerobic network. David Gene Functional Classification suggests that, under aerobic conditions, one such community reflects the cell cycle and cell replication, while the other one is linked to the mitochondrial respiratory chain function

Bisleuconothine A potentiates the effect of hyperbaric oxygen therapy against traumatic brain injury by enhancing P2X4 protein expressions

Purpose: To investigate the effect of bisleuconothine A (BA), alone and in combination with hyperbaric oxygen (HO), on traumatic brain injury (TBI) in rats. Methods: Traumatic brain injury (TBI) was induced by dropping a 200-g weight of steel on the left anterior frontal areas of Sprague-Dawley rats. The synergistic effect of BA and HO was determined by assessing neurological score, as well as parameters of oxidative stress and inflammation, expressions of P2X4 protein and other proteins, and levels of reactive oxygen species (ROS) in the brain tissues of TBI rats. Results: Neurological function score, levels of inflammatory mediators and oxidative stress parameters were significantly reduced in rats treated with BA alone, and in those treated with a combination of BA and HO, when compared with untreated TBI rats (p < 0.01). Moreover, treatment with BA alone, and BA-HO combination attenuated the altered protein expressions of P2X4, Akt, PI3K and TLR-4 in the TBI rats, and also upregulated the mRNA expression of P2X4 in the brain tissue, when compared with untreated TBI rats (p < 0.01). Conclusion: These results suggest that BA, when used alone or in combination with HO, reduces neuronal injury through upregulation of the protein expression of P2X4 in rats with traumatic brain injury. Thus, BA may be used clinically with HO therapy for the management of traumatic injury. Keywords: Bisleuconothine A, Hyperbaric oxygen, Neuronal injury, Oxidative stress, Inflammatory mediator

Cascading Failure Mechanism in Biological Systems

We establish the genes correlation networks of three species under different physiological states, normal soybean and those with root rot disease, anaerobic and aerobic growth of yeast and prostate cancer of human, based on the gene expression profiles. After investigating these networks using a cascading failure model, we find that the dynamic stability of the networks under different states differ significantly. Furthermore, the structural key genes which contribute greatly to these differences are identified. Finally, the biological functions of the key genes which may result in the root rot disease of soybean are annotated. This helps to reveal the relevant functional mechanisms that might be responsible for the changes and thus provides a useful tool toward understanding the mechanisms of various life processes

Network Structure Analysis Identifying Key Genes of Autism and Its Mechanism

Identifying the key genes of autism is of great significance for understanding its pathogenesis and improving the clinical level of medicine. In this paper, we use the structural parameters (average degree) of gene correlation networks to identify genes related to autism and study its pathogenesis. Based on the gene expression profiles of 82 autistic patients (the experimental group, E) and 64 healthy persons (the control group, C) in NCBI database, spearman correlation networks are established, and their average degrees under different thresholds are analyzed. It is found that average degrees of C and E are basically separable at the full thresholds. This indicates that there is a clear difference between the network structures of C and E, and it also suggests that this difference is related to the mechanism of disease. By annotating and enrichment analysis of the first 20 genes (MD-Gs) with significant difference in the average degree, we find that they are significantly related to gland development, cardiovascular development, and embryogenesis of nervous system, which support the results in Alter et al.’s original research. In addition, FIGF and CSF3 may play an important role in the mechanism of autism

Recyclable iron(II) caffeine-derived ionic salt catalyst in the Diels–Alder reaction of cyclopentadiene and alpha,beta-unsaturated N-acyloxazolidinones in dimethyl carbonate

Iron(II) triflate was used in combination with caffeine-derived salts as recyclable catalysts for the Diels–Alder reaction run in dimethyl carbonate (DMC) as a green solvent. The catalyst was prepared as an ionic salt from a xanthinium salt and Fe(OTf)2. Various substrates including α,β-unsaturated carbonyl and N-acyloxazolidinone derivatives were reacted with cyclopentadiene using this recyclable catalyst. The use of a low catalyst loading (1 mol%) afforded high yields (up to 99%) of the corresponding cycloadducts. The recycling and the efficiency of the catalyst were demonstrated for several runs

Fifth-Order Mapped Semi-Lagrangian Weighted Essentially Nonoscillatory Methods Near Certain Smooth Extrema

Fifth-order mapped semi-Lagrangian weighted essentially nonoscillatory (WENO) methods at certain smooth extrema are developed in this study. The schemes contain the mapped semi-Lagrangian finite volume (M-SL-FV) WENO 5 method and the mapped compact semi-Lagrangian finite difference (M-C-SL-FD) WENO 5 method. The weights in the more common scheme lose accuracy at certain smooth extrema. We introduce mapped weighting to handle the problem. In general, a cell average is applied to construct the M-SL-FV WENO 5 reconstruction, and the M-C-SL-FD WENO 5 interpolation scheme is proposed based on an interpolation approach. An accuracy test and numerical examples are used to demonstrate that the two schemes reduce the loss of accuracy and improve the ability to capture discontinuities

Study of Mn incorporation into SAPO framework: synthesis, characterization and catalysis in chloromethane conversion to light olefins

MnAPSO-34 molecular sieve has been synthesized with triethylamine as the template, characterized with XRD, XRF, P-31, Al-27 and Si-21 NMR and FT-IR techniques and compared with SAPO-34. The template decomposition and removal have been investigated with TG-DTG-DSC coupled with mass spectrometer. Mn incorporation generates a negligible difference On the chemical shift in P-31 and Al-27 MAS NMR, while an effect on the intensity of resonance peaks is revealed. Si-29 MAS NMR study has demonstrated that Mn incorporation favors the Si island formation, which may give rise to the stronger acidic sites. The thermal analysis (TG-DSC) on template removal in a diluted oxygen atmosphere, leading to the formation Of CO2, NO and H2O, showed, besides a low temperature endothermic weight loss due to the desorption of water, two weight losses (200-400 and 400-600 degrees C) for SAPO-34 and MnAPSO-34, suggesting two different chemical location environments of template molecules in these two molecular sieves. The quantity of template removed at higher temperature range is much higher in MnAPSO-34, indicating stronger template-framework interaction and stronger acidity after calcination. The acid difference caused by Mn incorporation has also been evidenced by ammonia adsorption evaluated by FT-IR. Chloromethane transformation was carried out over MnAPSO-34 and SAPO-34 and the catalytic performance showed that both molecular sieves are very active and selective catalyst for light olefins production. MnAPSO-34 demonstrated higher activity and light olefins selectivity. (c) 2005 Elsevier Inc. All rights reserved