A simple visualization technique to understand the system dynamics in bioreactors

In this article, we present a graph theoretic method to visualize and analyze the system behavior under different operating conditions. The system attributes (or variables) are the nodes in the graphs, and partial correlation between a pair of attributes defines the distance between corresponding nodes, resulting in a fully connected graph. Then, the redundant links are reduced using Pathfinder Network Scaling technique to uncover the latent network structure. We use a simulated biological reactor dataset in normal and faulty operation to validate our method. The method is general and can be used to analyze several different systems.     

Microwave assisted Wolff rearrangement: A facile method for the synthesis of Fmoc-β-amino acids

Summary The Wolff rearrangement of α-diazoketones, derived from Fmoc-α-amino acids, under no base conditions on exposure to microwave irradiation for 40 to 60 sec to Fmoc-β-amino acids with retention of configuration in good yield (91–95%) is described.     

Synthesis and biological evaluation of nitrogen-containing benzophenone analogues as TNF-α and IL-6 inhibitors with antioxidant activity

A series of nitrogen-containing benzophenone analogues were synthesized by Mannich reaction and evaluated for the inhibition of pro-inflammatory cytokines, TNF-α and IL-6. DPPH (1,1-diphenyl-2-picryl hydrazine) radical scavenging activity and its kinetics were studied to determine the antioxidant potential of the test samples. All the synthesized compounds exhibited promising activity against IL-6 in a range of 81–89%, 09–42% at 10 and 1 μM, respectively, concentration. Exceptionally, the compound 20e was observed to be an effective inhibitor of TNF-α (54%) and IL-6 (97%), (47%) at 10 and 1 μM concentrations with minimum toxicity (22%) against CCK-8 cells. With few exceptions, all other compounds were found to be excellent inhibitors of IL-6 and moderate to excellent inhibitors of TNF-α, however the toxicity profiles of these compounds need to be ameliorated in further optimization studies. Amongst the tested compounds, 16a, 17g, 18f, 18g, 19g and 20e were found to possess significant antioxidant activity.     

MicroRNA-146a modulates human bronchial epithelial cell survival in response to the cytokine-induced apoptosis

MicroRNA plays an important role in cell differentiation, proliferation and cell death. The current study found that miRNA-146a was up-regulated in human bronchial epithelial cells (HBECs) in response to stimulation by TGF-ß1 plus cytomix (a mixture of IL-1ß, IFN-γ and TNF-α). TGF-ß1 plus cytomix (TCM) induced apoptosis in HBECs (3.4 ± 0.6% of control vs 83.1 ± 4.0% of TCM treated cells, p < 0.01), and this was significantly blocked by the miRNA-146a mimic (8.8 ± 1.5%, p < 0.01). In contrast, a miRNA-146a inhibitor had only a modest effect on cell survival but appeared to augment the induction of epithelial-mesenchymal transition (EMT) in response to the cytokines. The MicroRNA-146a mimic appears to modulate HBEC survival through a mechanism of up-regulating Bcl-XL and STAT3 phosphorylation, and by this mechanism it could contribute to tissue repair and remodeling.     

Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks

The identification of cellular responses to damage can promote mechanistic insight into stress signalling. We have screened a library of 3968 Escherichia coli gene-deletion mutants to identify 99 gene products that modulate the toxicity of the alkylating agent methyl methanesulfonate (MMS). We have developed an ontology mapping approach to identify functional categories over-represented with MMS-toxicity modulating proteins and demonstrate that, in addition to DNA re-synthesis (replication, recombination, and repair), proteins involved in mRNA processing and translation influence viability after MMS damage. We have also mapped our MMS-toxicity modulating proteins onto an E. coli protein interactome and identified a sub-network consisting of 32 proteins functioning in DNA repair, mRNA processing, and translation. Clustering coefficient analysis identified seven highly connected MMS-toxicity modulating proteins associated with translation and mRNA processing, with the high connectivity suggestive of a coordinated response. Corresponding results from reporter assays support the idea that the SOS response is influenced by activities associated with the mRNA-translation interface.     

Synthesis, spectral characterization and in vitro biological studies of Co(II), Ni(II) and Cu(II) complexes with 1,2,4-triazole Schiff bases

A series of metal complexes of cobalt(II), nickel(II) and copper(II) have been synthesized with newly derived biologically active ligands. These ligands were synthesized by the condensation of 3-substituted-4-amino-5-hydrazino-1,2,4-triazole and 8-formyl-7-hydroxy-4-methylcoumarin. The probable structure of the complexes has been proposed on the basis of elemental analyses and spectral (IR, Uv-Vis, magnetic, ESR, FAB-mass and thermal studies) data. Electro chemical study of the complexes is also reported. All these complexes are non-electrolytes in DMF and DMSO. All the ligands and their Co(II), Ni(II) and Cu(II) complexes were screened for their antibacterial (Escherichia coli, Staphylococcus aureus, Staphylococcus pyogenes and Pseudomonas aeruginosa) and antifungal (Aspergillus niger, Aspergillus flavus and cladosporium) activities by MIC method. The brine shrimp bioassay was also carried out to study their in vitro cytotoxic properties.     

Graft copolymers of starch and its application in textiles

The graft copolymerization of styrene (ST), methyl methacrylate (MMA)/butyl acrylate (BA) with starch was carried chemically using ferrous ion-peroxide redox system. The grafting was performed at 60 °C and the monomer ratios of ST/MMA and ST/BA was varied with their % composition as 80/20, 50/50 and 20/80 parts by weight. The effect of initiator concentration, starch concentration and the monomer ratio on the grafting efficiency was studied. The grafted starch granules (GSG) were further analyzed for their particle size, bulk density and by sizing on cotton yarn for its physico-mechanical properties such as tensile strength, elongation at break, etc. The rheological properties of the resulting granular product in water as well as the starch graft copolymer emulsion were studied.     

Preparation and Evaluation of Miconazole Nitrate-Loaded Solid Lipid Nanoparticles for Topical Delivery

The purpose of this study was to prepare miconazole nitrate (MN) loaded solid lipid nanoparticles (MN-SLN) effective for topical delivery of miconazole nitrate. Compritol 888 ATO as lipid, propylene glycol (PG) to increase drug solubility in lipid, tween 80, and glyceryl monostearate were used as the surfactants to stabilize SLN dispersion in the SLN preparation using hot homogenization method. SLN dispersions exhibited average size between 244 and 766 nm. All the dispersions had high entrapment efficiency ranging from 80% to 100%. The MN-SLN dispersion which showed good stability for a period of 1 month was selected. This MN-SLN was characterized for particle size, entrapment efficiency, and X-ray diffraction. The penetration of miconazole nitrate from the gel formulated using selected MN-SLN dispersion as into cadaver skins was evaluated ex-vivo using franz diffusion cell. The results of differential scanning calorimetry (DSC) showed that MN was dispersed in SLN in an amorphous state. The MN-SLN formulations could significantly increase the accumulative uptake of MN in skin over the marketed gel and showed a significantly enhanced skin targeting effect. These results indicate that the studied MN-SLN formulation with skin targeting may be a promising carrier for topical delivery of miconazole nitrate.     

Dynamic ��-Helix Structure of Micelle-bound Human Amylin

Amylin is an endocrine hormone that regulates metabolism. In patients afflicted with type 2 diabetes, amylin is found in fibrillar deposits in the pancreas. Membranes are thought to facilitate the aggregation of amylin, and membrane-bound oligomers may be responsible for the islet β-cell toxicity that develops during type 2 diabetes. To better understand the structural basis for the interactions between amylin and membranes, we determined the NMR structure of human amylin bound to SDS micelles. The first four residues in the structure are constrained to form a hairpin loop by the single disulfide bond in amylin. The last nine residues near the C terminus are unfolded. The core of the structure is an α-helix that runs from about residues 5–28. A distortion or kink near residues 18–22 introduces pliancy in the angle between the N- and C-terminal segments of the α-helix. Mobility, as determined by ¹⁵N relaxation experiments, increases from the N to the C terminus and is strongly correlated with the accessibility of the polypeptide to spin probes in the solution phase. The spin probe data suggest that the segment between residues 5 and 17 is positioned within the hydrophobic lipid environment, whereas the amyloidogenic segment between residues 20 and 29 is at the interface between the lipid and solvent. This orientation may direct the aggregation of amylin on membranes, whereas coupling between the two segments may mediate the transition to a toxic structure.Type 2 diabetes affects over 100 million people worldwide (1) and is thought to cost upward of $130 billion dollars a year to treat in the United States alone (2). The endocrine hormone amylin (also known as islet amyloid polypeptide) appears to have key roles in diabetes pathology (3–5). The normal functions of amylin include the inhibition of glucagon secretion, slowing down the emptying of the stomach, and inducing a feeling of satiety through the actions of the hormone on neurons of the hypothalamus in the brain (5). The effects of amylin are exerted in concert with those of insulin and reduce the level of glucose in the blood (3, 5). Circulating amylin levels increase in a number of pathological conditions, including obesity, syndrome X, pancreatic cancer, and renal failure (3). Amylin levels together with insulin are raised initially in type 2 diabetes but fall as the disease progresses to a stage where the pancreatic islets of Langerhans β-cells that synthesize amylin no longer function (3).One of the hallmarks of type 2 diabetes, found in 90% of patients, is the formation of extracellular amyloid aggregates composed of amylin (3–5). The amyloid deposits accumulate in the interstitial fluid between islet cells and are usually juxtaposed with the β-cell membranes (3). Aggregates of amylin are toxic when added to cultures of β-cells, so that the amyloid found in situ may be responsible for β-cell death as type 2 diabetes progresses (6, 7). Genetic evidence that amylin is directly involved in pathology includes a familial S20G mutation that leads to early onset of the disease (8) and produces an amylin variant that aggregates more readily (9).As with all amyloids it is unclear whether fibrillar structures or soluble oligomers are responsible for pathology. A recurrent theme for amyloidogenic proteins is that toxicity appears to be exerted through membrane-bound oligomers that form pores and disrupt ion balance across membranes (4, 10–13). Experimental evidence for such oligomers has been found for the amyloid-β (Aβ)² peptides (14), which cause Alzheimer disease, and for α-synuclein (αS), the protein involved in Parkinson disease (15), a particular interest of our laboratory. The similar toxic effects exerted by these amyloidogenic molecules may have a common structural and physical basis. Detailed structural models are available for Aβ (16) and αS (17) bound to SDS micelle mimetics of membranes. For amylin there are models of peptide fragments 1–19 (18), 20–29 (19), and 17–29 (20) bound to micelles but as of yet no model of the complete hormone. This turns out to be particularly important as the interplay between structure and dynamics in amylin only comes to light when considering the whole molecule.Here we report the solution structure of human amylin bound to SDS micelles. We complement the structure with information on dynamics and on the immersion of amylin into micelles.