Spectral characterizations of sandglass graphs

a b s t r a c t The sandglass graph is obtained by appending a triangle to each pendant vertex of a path. It is proved that sandglass graphs are determined by their adjacency spectra as well as their Laplacian spectra

novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model

To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/

Spectral characterizations of sandglass graphs

The sandglass graph is obtained by appending a triangle to each pendant vertex of a path. It is proved that sandglass graphs are determined by their adjacency spectra as well as their Laplacian spectra. (C) 2009 Elsevier Ltd. All rights reserved

Subcellular Targeting of Bacterial CusF Enhances Cu Accumulation and Alters Root to Shoot Cu Translocation in Arabidopsis

Copper (Cu) is an important environmental pollutant that exerts harmful effects on all living organisms when in excess. In an effort to remove this toxin in situ, a bacterial Cu-binding protein gene CusF was engineered to target CusF for secretion to the cell wall and vacuoles and for accumulation in the cytoplasm. Analysis of transgenic Arabidopsis plants showed that CusF was functionally active and that plants expressing cell wall-(CusF(cw) transgenic lines) or vacuole-targeted CusF (CusF(vac) transgenic lines) were more resistant to Cu excess than untransformed plants and plants with cytoplasmic CusF (CusF(cyto) transgenic lines). Under short-term (48 h) exposure to Cu excess, CusFcw transgenic lines showed up to 2-fold increased Cu accumulation in roots compared with the untransformed plants; however, CusFcyto lines and the wild-type plants had similar Cu concentrations in both roots and shoots. Under long-term (40 d) exposure to Cu excess, all transgenic lines accumulated more Cu (up to 3-fold) in roots than the untransformed plants, whereas only CusFcyto lines showed a marked increase (similar to 3-fold of the wild-type plants) of Cu accumulation in shoots. In addition, expression of CusF in the cytosol dramatically enhanced Cu transport from roots to shoots when compared with plants with secretory pathway-targeted CusF. Our results demonstrate the feasibility of Cu tolerance and accumulation by engineering Cu-binding proteins targetable to subcellular compartments and provide new insights into the multifaceted mechanisms of Cu partitioning between roots and shoots

Engineering metal-binding sites of bacterial CusF to enhance Zn/Cd accumulation and resistance by subcellular targeting

The periplasmic protein CusF acts as a metallochaperone to mediate Cu resistance in Escherichia coli. CusF does not contain cysteine residues and barely binds to divalent cations. Here, we addressed effects of cysteine-substitution mutant (named as mCusF) of CusF on zinc/cadmium (Zn/Cd) accumulation and resistance. We targeted mCusF to different subcellular compartments in Arabidopsis. We found that plants expressing vacuole-targeted mCusF were more resistant to excess Zn than WT and plants with cell wall-targeted or cytoplasmic mCusF. Under long-term exposure to excess Zn, all transgenic lines accumulated more Zn (up to 2.3-fold) in shoots than the untransformed plants. Importantly, plants with cytoplasmic mCusF showed higher efficiency of Zn translocation from root to shoot than plants with secretory pathway-targeted-mCusF. Furthermore, the transgenic lines exhibited enhanced resistance to Cd and significant increase in root-to-shoot Cd translocation. We also found all transgenic plants greatly improved manganese (Mn) and iron (Fe) homeostasis under Cd exposure. Our results demonstrate heterologous expression of mCusF could be used to engineer a new phytoremediation strategy for Zn/Cd and our finding also deepen our insights into mechanistic basis for relieving Cd toxicity in plants through proper root/shoot partitioning mechanism and homeostatic accumulation of Mn and Fe. (C) 2015 Elsevier B.V. All rights reserved

Epalrestat Stimulated Oxidative Stress, Inflammation, and Fibrogenesis in Mouse Liver

Epalrestat (EPS), an aldose reductase inhibitor, is widely prescribed to manage diabetic neuropathy. It is generally believed that EPS is beneficial to diabetic patients because it can protect endothelial cells, Schwann cells, or other neural cells from oxidative stress. However, several clinical studies revealed that EPS therapy led to liver dysfunction, which limited its clinical applications. Currently, the underlying mechanism by which EPS causes liver dysfunction is unknown. This study aimed to investigate the mechanism responsible for EPS-induced liver injury. In mouse liver, EPS 1) increased oxidative stress, indicated by increased expression of manganese superoxide dismutase, Ho-1, and Nqo1, 2) induced inflammation, indicated by infiltration of inflammatory cells, and induced expression of tumor necrosis factor-alpha, CD11b, and CD11c, as well as 3) predisposed to induce fibrosis, evidenced by increased mRNA and protein expression of early profibrotic biomarker genes procollagen I and alpha-smooth muscle actin, and by increased collagen deposition. In cultured mouse and human hepatoma cells, EPS treatment induced oxidative stress, decreased cell viability, and triggered apoptosis evidenced by increased Caspase-3 cleavage/activation. In addition, EPS increased mRNA and protein expression of cytoglobin in mouse liver, indicating that EPS activated hepatic stellate cells (HSCs). Furthermore, EPS treatment in cultured human HSCs increased cell viability. In summary, EPS administration induced oxidative stress and inflammation in mouse liver, and stimulated liver fibrogenesis. Therefore, cautions should be exercised during EPS therapy

The relationship of retinal vessel diameters and fractal dimensions with blood pressure and cardiovascular risk factors.

BACKGROUND: This study aimed to investigate the correlation between quantitative retinal vascular parameters such as central retinal arteriolar equivalent (CRAE) and retinal vascular fractal dimension (D(f)), and cardiovascular risk factors in the Chinese Han population residing in the in islands of southeast China. METHODOLOGY/PRINCIPLE FINDINGS: In this cross-sectional study, fundus photographs were collected and semi-automated analysis software was used to analyze retinal vessel diameters and fractal dimensions. Cardiovascular risk factors such as relevant medical history, blood pressure (BP), lipids, and blood glucose data were collected. Subjects had a mean age of 51.9 ± 12.0 years and included 812 (37.4%) males and 1,357 (62.6%) females. Of the subjects, 726 (33.5%) were overweight, 226 (10.4%) were obese, 272 (12.5%) had diabetes, 738 (34.0%) had hypertension, and 1,156 (53.3%) had metabolic syndrome. After controlling for the effects of potential confounders, multivariate analyses found that age (β = 0.06, P = 0.008), sex (β = 1.33, P = 0.015), mean arterial blood pressure (β = -0.12, P<0.001), high-sensitivity C-reactive protein (β = -0.22, P = 0.008), and CRVE (β = 0.23, P<0.001) were significantly associated with CRAE. Age (β = -0.0012, P < 0.001), BP classification (prehypertension: β = -0.0075, P = 0.014; hypertension: β = -0.0131, P = 0.002), and hypertension history (β = -0.0007, P = 0.009) were significantly associated with D(f). CONCLUSIONS/SIGNIFICANCE: D(f) exhibits a stronger association with BP than CRAE. Thus, D(f) may become a useful indicator of cardiovascular risk