In Silico screening of nonsteroidal anti-inflammatory drugs and their combined action on Prostaglandin H Synthase-1

The detailed kinetic model of Prostaglandin H Synthase-1 (PGHS-1) was applied to in silico screening of dose-dependencies for the different types of nonsteroidal anti-inflammatory drugs (NSAIDs), such as: reversible/irreversible, nonselective/selective to PGHS-1/PGHS-2 and time dependent/independent inhibitors (aspirin, ibuprofen, celecoxib, etc.) The computational screening has shown a significant variability in the IC50s of the same drug, depending on different in vitro and in vivo experimental conditions. To study this high heterogeneity in the inhibitory effects of NSAIDs, we have developed an in silico approach to evaluate NSAID action on targets under different PGHS-1 microenvironmental conditions, such as arachidonic acid, reducing cofactor, and peroxide concentrations. The designed technique permits translating the drug IC50, obtained in one experimental setting to another, and predicts in vivo inhibitory effects based on the relevant in vitro data. For the aspirin case, we elucidated the mechanism underlying the enhancement and reduction (aspirin resistance) of its efficacy, depending on PGHS-1 microenvironment in in vitro/in vivo experimental settings. We also present the results of the in silico screening of the combined action of sets of two NSAIDs (aspirin with ibuprofen, aspirin with celecoxib), and study the mechanism of the experimentally observed effect of the suppression of aspirin-mediated PGHS-1 inhibition by selective and nonselective NSAIDs. Furthermore, we discuss the applications of the obtained results to the problems of standardization of NSAID test assay, dependence of the NSAID efficacy on cellular environment of PGHS-1, drug resistance, and NSAID combination therapy

Use of Microwave Radiometry to Monitor Thermal Denaturation of Albumin

This study monitored thermal denaturation of albumin using microwave radiometry. Brightness Temperature, derived from Microwave Emission (BTME) of an aqueous solution of bovine serum albumin (0.1 mM) was monitored in the microwave frequency range 3.8–4.2 GHz during denaturation of this protein at a temperature of 56°C in a conical polypropylene cuvette. This method does not require fluorescent or radioactive labels. A microwave emission change of 1.5–2°C in the BTME of aqueous albumin solution was found during its denaturation, without a corresponding change in the water temperature. Radio thermometry makes it possible to monitor protein denaturation kinetics, and the resulting rate constant for albumin denaturation was 0.2 ± 0.1 min−1, which corresponds well to rate constants obtained by other methods

Compensatory effects in the PI3K/PTEN/AKT signaling network following receptor tyrosine kinase inhibition

Overcoming de novo and acquired resistance to anticancer drugs that target signaling networks is a formidable challenge for drug design and effective cancer therapy. Understanding the mechanisms by which this resistance arises may offer a route to addressing the insensitivity of signaling networks to drug intervention and restore the efficacy of anticancer therapy. Extending our recent work identifying PTEN as a key regulator of Herceptin sensitivity, we present an integrated theoretical and experimental approach to study the compensatory mechanisms within the PI3K/PTEN/AKT signaling network that afford resistance to receptor tyrosine kinase (RTK) inhibition by anti-HER2 monoclonal antibodies. In a computational model representing the dynamics of the signaling network, we define a single control parameter that encapsulates the balance of activities of the enzymes involved in the PI3K/PTEN/AKT cycle. By varying this control parameter we are able to demonstrate both distinct dynamic regimes of behavior of the signaling network and the transitions between those regimes. We demonstrate resistance, sensitivity, and suppression of RTK signals by the signaling network. Through model analysis we link the sensitivity-to-resistance transition to specific compensatory mechanisms within the signaling network. We study this transition in detail theoretically by variation of activities of PTEN, PI3K, AKT enzymes, and use the results to inform experiments that perturb the signaling network using combinatorial inhibition of RTK, PTEN, and PI3K enzymes in human ovarian carcinoma cell lines. We find good alignment between theoretical predictions and experimental results. We discuss the application of the results to the challenges of hypersensitivity of the signaling network to RTK signals, suppression of drug resistance, and efficacy of drug combinations in anticancer therapy

Treatment and Companion Diagnostics of Lower Back Pain Using Self-Controlled Energo-Neuroadaptive Regulator (SCENAR) and Passive Microwave Radiometry (MWR)

Evaluation of the effectiveness of treatment of nonspecific lower back pain (LBP) is currently largely based on the patient’s subjective feelings. The purpose of this study was to use passive microwave radiometry (MWR) as a tool for assessing the effectiveness of various treatment methods in patients with acute and subacute nonspecific LBP. Patients with a pain assessment on a visual analogue scale (VAS) of 6 to 10 points were divided into two groups: Group I included patients with pharmacological, syndrome-oriented treatment (n = 30, age 54.9 ± 2.3 years); Group II included a combination of pharmacotherapy with self-controlled energy-neuroadaptive regulation (SCENAR) (n = 25, age 52.8 ± 2.5 years). The analysis showed that the addition of SCENAR therapy (Group II) significantly potentiated the analgesic effect at the stages of treatment, and after 3 weeks, this had increased by more than two times, by 1.3 points on the VAS. There was also a significant decrease in the maximum internal temperature and normalization of the gradient of internal and skin temperatures, and a decrease in thermo-asymmetry, as assessed by temperature fields. Thermal asymmetry visualization allows the identification of the area of pathological muscle spasm and/or inflammation in the projection of the vertebral-motor segment for the possible targeted use of treatment methods such as percutaneous electro neurostimulation, massage, manual therapy, diagnostic and treatment blocks, etc. The MWR method also avoids unnecessary radiation exposure

Compartmentalization of the Edinburgh Human Metabolic Network

<p>Abstract</p> <p>Background</p> <p>Direct in vivo investigation of human metabolism is complicated by the distinct metabolic functions of various sub-cellular organelles. Diverse micro-environments in different organelles may lead to distinct functions of the same protein and the use of different enzymes for the same metabolic reaction. To better understand the complexity in the human metabolism, a compartmentalized human metabolic network with integrated sub-cellular location information is required.</p> <p>Results</p> <p>We extended the previously reconstructed Edinburgh Human Metabolic Network (EHMN) [Ma, et al. Molecular Systems Biology, 3:135, 2007] by integrating the sub-cellular location information for the reactions, adding transport reactions and refining the protein-reaction relationships based on the location information. Firstly, protein location information was obtained from Gene Ontology and complemented by a Swiss-Prot location keywords search. Then all the reactions in EHMN were assigned to a location based on the protein-reaction relationships to get a preliminary compartmentalized network. We investigated the localized sub-networks in each pathway to identify gaps and isolated reactions by connectivity analysis and refined the location information based on information from literature. As a result, location information for hundreds of reactions was revised and hundreds of incorrect protein-reaction relationships were corrected. Over 1400 transport reactions were added to link the location specific metabolic network. To validate the network, we have done pathway analysis to examine the capability of the network to synthesize or degrade certain key metabolites. Compared with a previously published human metabolic network (Human Recon 1), our network contains over 1000 more reactions assigned to clear cellular compartments.</p> <p>Conclusions</p> <p>By combining protein location information, network connectivity analysis and manual literature search, we have reconstructed a more complete compartmentalized human metabolic network. The whole network is available at <url>http://www.ehmn.bioinformatics.ed.ac.uk</url> and free for academic use.</p

Novel species identification and deep functional annotation of electrogenic biofilms, selectively enriched in microbial fuel cell (MFC) array

In this study, electrogenic microbial communities originating from a single source were multiplied using our custom-made, 96-well-plate- based microbial fuel cell (MFC) array. Developed communities operated under different pH conditions and produced currents up to 19.4 A/m3 (0.6 A/m2) within 2 days of inoculation. Microscopic observations [combined scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS)] revealed that some species present in the anodic biofilm adsorbed copper on their surface because of the bioleaching of the printed circuit board (PCB), yielding Cu2 + ions up to 600 mg/L. Beta- diversity indicates taxonomic divergence among all communities, but functional clustering is based on reactor pH. Annotated metagenomes showed the high presence of multicopper oxidases and Cu-resistance genes, as well as genes encoding aliphatic and aromatic hydrocarbon-degrading enzymes, corresponding to PCB bioleaching. Metagenome analysis revealed a high abundance of Dietzia spp., previously characterized in MFCs, which did not grow at pH 4. Binning metagenomes allowed us to identify novel species, one belonging to Actinotalea, not yet associated with electrogenicity and enriched only in the pH 7 anode. Furthermore, we identified 854 unique protein-coding genes in Actinotalea that lacked sequence homology with other metagenomes. The function of some genes was predicted with high accuracy through deep functional residue identification (DeepFRI), with several of these genes potentially related to electrogenic capacity. Our results demonstrate the feasibility of using MFC arrays for the enrichment of functional electrogenic microbial consortia and data mining for the comparative analysis of either consortia or their members

Application of air cathode microbial fuel cells for energy efficient treatment of dairy wastewater

Microbial Fuel Cells (MFCs) offer a promising new solution for wastewater treatment due to their advantageous characteristics: lower energy demand and less excess sludge compared to the conventional activated sludge wastewater treatment technology. In this study, two systems of single chamber air cathode MFCs with a working volume of 14 L were investigated for the energy efficient treatment of dairy wastewater. Biomass-originated carbon cathode and noble-metal free cathode catalyst were applied to meet the demand for a lower investment cost. Influent chemical oxygen demand (COD) was in the range of 900 to 3830 mg L⁻¹, while hydraulic retention time was ~ 2.4 days. Systems provided 156 mW m⁻³ and 170 mW m⁻³ maximum power densities and coulombic efficiencies of 11.5 % and 12.8 % in average. Organic removal efficiency of 71.1 ± 8.0 % was observed when influent COD was between 900 and 1500 mg L⁻¹, however effluent quality and removal efficiency (67.9 ± 12.6 %) deteriorated as influent COD was increased (1500 - 3830 mg L⁻¹). At high influent CODs (over 3000 mg L⁻¹), an organic elimination rate of 0.82 ± 0.11 kg COD m⁻³d⁻¹ was calculated, that can be considered as the upper limit of organic removal in the systems. Based on the results, MFCs may offer a potential solution for small-scale dairy factories for the pretreatment of their effluent to meet the criteria for wastewater discharge to sewer systems. The modular MFC design also facilitates to tailor the system to actual capacity requirements

Development of a New Hydrogel Anion Exchange Membrane for Swine Wastewater Treatment

We developed a proprietary anion exchange membrane (AEM) for wastewater treatment as an alternative to commercial products. Following the successful development of a hydrogel cation exchange membrane on a porous ceramic support, we used the same approach to fabricate an AEM. Different positively charged monomers and conditions were tested, and all AEMs were tested for nitrate and phosphate anion removal from buffers by electrodialysis. The best AEM was tested further with real swine wastewater for phosphate removal by electrodialysis and nitrate removal in a bioelectrochemical denitrification system (BEDS). Our new AEM showed better phosphate removal compared with a commercial membrane; however, due to its low permselectivity, the migration of cations was detected while operating a two-chambered biocathode BEDS in which the membrane was utilized as a separator. After improving the permselectivity of the membrane, the performance of our proprietary AEM was comparable to that of a commercial membrane. Because of the usage of a porous ceramic support, our AEM is self-supporting, sturdy, and easy to attach to various frames, which makes the membrane better suited for harsh and corrosive environments, such as swine and other animal farms and domestic wastewater