Genome‐derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry

Metabolic network models describing growth of Escherichia coli on glucose, glycerol and acetate were derived from a genome scale model of E. coli. One of the uncertainties in the metabolic networks is the exact stoichiometry of energy generating and consuming processes. Accurate estimation of biomass and product yields requires correct information on the ATP stoichiometry. The unknown ATP stoichiometry parameters of the constructed E. coli network were estimated from experimental data of eight different aerobic chemostat experiments carried out with E. coli MG1655, grown at different dilution rates (0.025, 0.05, 0.1, and 0.3 h^?1) and on different carbon substrates (glucose, glycerol, and acetate). Proper estimation of the ATP stoichiometry requires proper information on the biomass composition of the organism as well as accurate assessment of net conversion rates under well‐defined conditions. For this purpose a growth rate dependent biomass composition was derived, based on measurements and literature data. After incorporation of the growth rate dependent biomass composition in a metabolic network model, an effective P/O ratio of 1.49 ± 0.26 mol of ATP/mol of O, K_X (growth dependent maintenance) of 0.46 ± 0.27 mol of ATP/C‐mol of biomass and m_ATP (growth independent maintenance) of 0.075 ± 0.015 mol of ATP/C‐mol of biomass/h were estimated using a newly developed Comprehensive Data Reconciliation (CDR) method, assuming that the three energetic parameters were independent of the growth rate and the used substrate. The resulting metabolic network model only requires the specific rate of growth, µ, as an input in order to accurately predict all other fluxes and yields. Biotechnol. Bioeng. 2010;107: 369–381. © 2010 Wiley Periodicals, Inc.     

Using a mammalian cell cycle simulation to interpret differential kinase inhibition in anti-tumour pharmaceutical development

Systems biology needs to show practical relevance to commercial biological challenges such as those of pharmaceutical development. The aim of this work is to design and validate some applications in anti-cancer therapeutic development. The test system was a group of novel cyclin-dependent kinase (CDK) inhibitors synthesised by Cyclacel Ltd. The measured in vitro IC50s of each compound were used as input data to a proprietary cell cycle model developed by Physiomics plc. The model was able to predict over three orders of magnitude the cytotoxicity of each compound without model adaptation to specific cancer cell types. This pattern matched the experimentally determined data. One class of compounds was predicted to cause an increase of the cell cycle length with a non-linear dose-response curve. Further work will use apoptosis and DNA replication simulations to look at overall cell effects.     

Antimicrobial bioassay of Colchicum luteum Baker

The methanolic extract of the corms of Colchicum luteum Baker (Liliaceae) and its subsequent fractions in different solvent systems were screened for antibacterial and antifungal activities. The crude extract and all the fractions demonstrated moderate to excellent antifungal activities against tested pathogens in antifungal bioassay. Excellent antifungal activity was shown against trichophyton longifusus, up to 75%, and microsporum canis, up to 85%, while the crude extract and subsequent fractions showed mild to moderate activities in an antibacterial bioassay with maximum antibacterial activity 58% against Bacillus subtilis.     

In silico proteomic characterization of human epidermal growth factor receptor 2 (HER-2) for the mapping of high affinity antigenic determinants against breast cancer

Multiple different approaches are being used to activate the immune system against breast cancer. Vaccine therapy in general follows the principle that injections of various substances ultimately result in the presentation of tumor peptides to the patient’s immune system. We proposed a potential in silico DNA vaccine against breast cancer by integrating high affinity T cell (MHC-I and MHC-II) and B cell (continuous and discontinuous) epitopes. The matching of the HLA haplotype and antigen was performed to provide the appropriate peptide epitope suitable for majority of the patients. The immunogenic nature of the antigenic construct was also enhanced by the administration of consensus epitopes. The potency of DNA vaccines depends on the efficient expression and presentation of the encoded antigen of interest and the chances of efficient expression of our antigenic construct in host organism was also verified by in silico approaches. An attempt was made to overcome the limited potency of the DNA vaccine by targeting DNA to professional antigen-presenting cells (APCs). A higher immune response theoretically corresponds to a higher survival rate of patients. Therefore, optimization studies were also employed to enhance the immunogenicity of proposed in silico DNA vaccine.     

Quantum chemical modeling study of adsorption of benzoic acid on anatase TiO2 nanoparticles

The semi-empirical MSINDO method has been used to investigate the mode of adsorption of benzoic acid on the nano anatase TiO(2) (100) surface. The (100) surface is modeled with a Ti(36)O(90)H(36) cluster. Molecular dynamics simulations for the adsorption behavior of benzoic acid indicate it is linked to the TiO(2) surface through interactions from the oxygen atoms of the carboxylic acid moiety with surface titanium atoms. The benzoic acid may be positioned with its aromatic ring either parallel or perpendicular relative to the surface, however the perpendicular adsorption mode is more stable. The calculated substrate-surface interaction energy is influenced by the number of linkages between the substrate and the surface as well as the degree of hydrogen bonding between the acid hydrogen and lattice oxygen atom. The greater stability of the perpendicular adsorption orientation is ascribed to the higher number of linkages between the substrate and the surface. It is concluded that the simplified model is sufficiently detailed to elucidate surface interactions.     

Inhibition of alpha-synuclein fibrillization by dopamine is mediated by interactions with five C-terminal residues and with E83 in the NAC region

The interplay between dopamine and alpha-synuclein (AS) plays a central role in Parkinson's disease (PD). PD results primarily from a severe and selective devastation of dopaminergic neurons in substantia nigra pars compacta. The neuropathological hallmark of the disease is the presence of intraneuronal proteinaceous inclusions known as Lewy bodies within the surviving neurons, enriched in filamentous AS. In vitro, dopamine inhibits AS fibril formation, but the molecular determinants of this inhibition remain obscure. Here we use molecular dynamic (MD) simulations to investigate the binding of dopamine and several of its derivatives onto conformers representative of an NMR ensemble of AS structures in aqueous solution. Within the limitations inherent to MD simulations of unstructured proteins, our calculations suggest that the ligands bind to the (125)YEMPS(129) region, consistent with experimental findings. The ligands are further stabilized by long-range electrostatic interactions with glutamate 83 (E83) in the NAC region. These results suggest that by forming these interactions with AS, dopamine may affect AS aggregation and fibrillization properties. To test this hypothesis, we investigated in vitro the effects of dopamine on the aggregation of mutants designed to alter or abolish these interactions. We found that point mutations in the (125)YEMPS(129) region do not affect AS aggregation, which is consistent with the fact that dopamine interacts non-specifically with this region. In contrast, and consistent with our modeling studies, the replacement of glutamate by alanine at position 83 (E83A) abolishes the ability of dopamine to inhibit AS fibrillization.     

Bio-separation, speciation and determination of chromium in water using partially pyrolyzed olive pomace sorbent

Speciation of Cr(III)/Cr(VI) from water using olive pomace (OP) was improved by partial pyrolysis of OP. The sorbents were characterized by physicochemical techniques. Sorption of Cr(III) on raw and partially pyrolyzed OP sorbents followed Freundlich isotherm and second-order rate kinetics. OP pyrolyzed at 150 °C (sorbent OP-150) exhibited maximum sorption capacity, favorability and the lowest sorption energy. Sorption was exothermic and spontaneous for the raw-OP and OP pyrolyzed at 100 or 150 °C; but endothermic and non-spontaneous for OP pyrolyzed at 200, 250, 300 or 400 °C. A speciation method of chromium was proposed, in which Cr(III) was selectively retained at pH 3 on sorbent OP-150; while total Cr was determined after reduction of Cr(VI). The method was selective with a detection limit for Cr(III) of 1.58 μg L⁻¹. The method was applied on natural and industrial waters (recoveries >97.7%, RSD’s <9%) and on tobacco leaves certified reference material (INCT-PVTL-6).     

Ultraviolet irradiation induces the accumulation of chondroitin sulfate, but not other glycosaminoglycans, in human skin

Ultraviolet (UV) light alters cutaneous structure and function. Prior work has shown loss of dermal hyaluronan after UV-irradiation of human skin, yet UV exposure increases total glycosaminoglycan (GAG) content in mouse models. To more fully describe UV-induced alterations to cutaneous GAG content, we subjected human volunteers to intermediate-term (5 doses/week for 4 weeks) or single-dose UV exposure. Total dermal uronyl-containing GAGs increased substantially with each of these regimens. We found that UV exposure substantially increased dermal content of chondroitin sulfate (CS), but not hyaluronan, heparan sulfate, or dermatan sulfate. UV induced the accumulation of both the 4-sulfated (C4S) and 6-sulfated (C6S) isoforms of CS, but in distinct distributions. Next, we examined several CS proteoglycan core proteins and found a significant accumulation of dermal and endothelial serglycin, but not of decorin or versican, after UV exposure. To examine regulation in vitro, we found that UVB in combination with IL-1α, a cytokine upregulated by UV radiation, induced serglycin mRNA in cultured dermal fibroblasts, but did not induce the chondroitin sulfate synthases. Overall, our data indicate that intermediate-term and single-dose UVB exposure induces specific GAGs and proteoglycan core proteins in human skin in vivo. These molecules have important biologic functions and contribute to the cutaneous response to UV.     

Speciation of antimony in natural waters : the determination of Sb(III) and Sb(V) by continuous flow hydride generation-atomic absorption spectrometry

Abstract

A new procedure for the speciation of dissolved antimony is described. This makes use of complexation with citrate to prevent, preferentially, the formation of hydride from Sb(V) and allow the selective determination of Sb(III) to be made by continuous flow hydride generation - atomic absorption spectrometry. When the citric acid (12% m/V) is replaced by potassium iodide (3% m/V), total antimony is determined and the concentration of Sb(V) can be obtained by difference. The determination of the antimony species is dominated in this new procedure by the complexation of Sb(V) with citrate and the effect of pH is limited to a minor, re-inforcing role. This permits acidification to be made with hydrochloric acid. The principal interfering species in the determination of total antimony and Sb(III) is Fe³⁺, with Fe²⁺, Cu²⁺ and Ni²⁺ showing lesser effects on Sb(III). The technique is applied successfully to synthetic mixtures and to natural waters from the environment of a disused antimony mine.

The characteristic concentration obtained for antimony was 0.7 ng mL^–1 and the detection limit 1 ng mL^–1.     

Optimizing the Sensing Efficiency of Plasmonic Based Gas Sensor

Plasmonics - This paper investigates the behavior of the surface plasmon polaritons (SPPs) on dielectric-metal interface using Ag thin film on glass substrate. The Kretschman configuration, which...