How a vicinal layer of solvent modulates the dynamics of proteins

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.     

Development of Interleukin-2 Loaded Chitosan-Based Nanogels Using Artificial Neural Networks and Investigating the Effects on Wound Healing in Rats

The aim of this study was to develop and characterize rh- IL-2 loaded chitosan-based nanogels for the healing of wound incision in rats. Nanogels were prepared using chitosan and bovine serum albumin (BSA) by ionic gelation method and high temperature application, respectively. Particle size, zeta potential, and polydispersity index were measured for characterization of nanogels. The morphology of nanogels was examined by using SEM and AFM. The IL-2 loading capacity of nanogels was determined using ELISA method. In vitro release of IL-2 from nanogels was performed using Franz diffusion cells. Artificial neural network (ANN) models were developed using selected input parameters (stirring rate, chitosan%, BSA%, TPP%) where particle size was an output parameter for IL-2 free nanogels. Wound healing effect of IL-2 loaded chitosan-TPP nanogel was evaluated by determining the malondialdehyde (MDA) and glutathione (GSH) levels of wound tissues in rats. The particle size of IL-2 loaded chitosan-TPP nanogels was found to be larger than that of IL-2 loaded BSA-based chitosan nanogels. Drug loading capacity of nanogels was found 100%?±?0.010 for both nanogels. IL-2 was released slowly after the initial burst effect. According to SEM and AFM imaging, BSA-chitosan nanogel particles were of nanometer size and presented a swelling tendency, and chitosan-TPP nanogel particles were found to be spherical and homogenously dispersed. IL-2 loaded chitosan-TPP nanogel was found suitable for improving wound healing because it decreased the MDA levels and increased the GSH levels wound tissues comparing to control group.     

Daily Variations in the Responses to Papaverine but not Theophylline in Rat Aorta

The presence of temporal patterns in the responses of vascular smooth muscle to relaxing agents have been known. The aim of this study was to examine the variations in the in vitro sensitivity of rat aorta to papaverine and theophylline in both endothelium-intact and -denuded rings. The animals were synchronized with a 12-h light: 12-h dark schedule. Rat thoracic aorta rings were obtained from animals sacrificed at six different times (09:00, 13:00, 17:00, 21:00, 01:00 and 05:00) of the day. Tissues were precontracted submaximally with phenylephrine and then were relaxed by papaverine (10^-8 - 10^-4 M) and theophylline (10^-7 &miknus; 10^-3 M) applied cumulatively. The responses to most of the concentrations and EC₅₀ values for papaverine demonstrated an ultradian rhythm with an 8 h periodicity. Time-dependent variations were not found in the responses to theophylline. The results are discussed in relation with the time-dependent differences in signal transducing mechanisms.     

The metagenomic basis of anammox metabolism in Candidatus 'Brocadia fulgida'

Anammox (anaerobic ammonium oxidation) coupled to nitrite reduction is an important step in the nitrogen cycle and has been recognized as an important sink for fixed nitrogen in the ocean. Still little is known about the genomic blueprint of different anammox species. In the present article, we discuss the important genes of anammox metabolism in Candidatus 'Brocadia fulgida' that were retrieved via a metagenomic approach.     

Efficacy of tar oil recovered during slow pyrolysis of macadamia nut shells

Decay and termite resistance of wood treated with tar oil obtained from a commercial pyrolysis process of macadamia nut shells was evaluated. Vacuum-treated pinewood specimens were subjected to two brown- and two white-rot fungi based on the soil-block test method specified by the American Wood Protection Association after a 10-day-leaching process. Treated specimens were also subjected to the subterranean termite attack according to Japanese Industrial Standards (JIS) for 3 weeks under laboratory conditions. In the study, growth inhibition of selected fungi with the tar oil was also tested in vitro. Treated wood specimens at a retention level of 460 kg m⁻³ showed good protection against all the fungi tested. Mass losses in leached specimens were less than those observed in unleached specimens. Similar results were seen when the specimens were subjected to termite attack. Inhibition tests showed that higher concentrations of the tar oil are critical for inhibition of the brown-rot fungi compared to the concentrations required to impede the white-rot and sap-staining fungi tested.     

Crosslinked aggregates of Rhizopus oryzae lipase as industrial biocatalysts: Preparation, optimization, characterization, and application for enantioselective resolution reactions

Lipase from Rhizopus oryzae (ROL) was immobilized as crosslinked enzyme aggregate (CLEA) via precipitation with ammonium sulfate and simultaneous crosslinking with glutaraldehyde. The optimum conditions of the immobilization process were determined. Lipase CLEAs showed a twofold increase in activity when Tween 80‐pretreated lipase was used for CLEA preparation. CLEAs were shown to have several advantages compared to free lipase. CLEAs were more stable at 50°C and 60°C as well as for a wide range of pH. After incubation at 50°C, CLEA showed 74% of initial activity whereas free enzyme was totally inactivated. Reduction of Schiff bases has been performed for the first time in the CLEA preparation process significantly improving the chemically modified CLEAs' reusability, thus providing an enzyme with high potential for recycling even under aqueous reaction conditions where enzyme leakage is, in general, one of the major problems. The CLEA retained 91% activity after 10 cycles in aqueous medium. The immobilized enzyme was used for kinetic resolution reactions. Results showed that immobilization had an enhancing effect on the conversion (c) as well as on the enantiomeric ratio (E). ROL CLEA displayed five times higher enantioselectivity for the hydrolysis of (R,S)‐1‐phenylethyl acetate and likewise 1.5 times higher enantioselectivity for the transesterification of racemic (R–S)‐1‐phenylethanol with vinylacetate. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 28: 937–945, 2012 This article was published online on June 26, 2012. An edit was subsequently requested. This notice is included in the online and print versions to indicate that both have been corrected [27 June 2012].     

Ladderane lipid distribution in four genera of anammox bacteria

Intact ladderane phospholipids and core lipids were studied in four species of anaerobic ammonium oxidizing (anammox) bacteria, each representing one of the four known genera. Each species of anammox bacteria contained C(18) and C(20) ladderane fatty acids with either 3 or 5 linearly condensed cyclobutane rings and a ladderane monoether containing a C(20) alkyl moiety with 3 cyclobutane rings. The presence of ladderane lipids in all four anammox species is consistent with their putative physiological role to provide a dense membrane around the anammoxosome, the postulated site of anammox catabolism. In contrast to the core lipids, large variations were observed in the distribution of ladderane phospholipids, i.e. different combinations of hydrophobic tail (ladderane, straight chain and methyl branched fatty acid) types attached to the glycerol backbone sn-1 position, in combination with different types of polar headgroup (phosphocholine, phosphoethanolamine or phosphoglycerol) attached to the sn-3 position. Intact ladderane lipids made up a high percentage of the lipid content in the cells of "Candidatus Kuenenia stuttgartiensis", suggesting that ladderane lipids are also present in membranes other than the anammoxosome. Finally, all four investigated species contained a C(27) hopanoid ketone and bacteriohopanetetrol, which, indicates that hopanoids are anaerobically synthesised by anammox bacteria.     

Isolation and characterization of a prokaryotic cell organelle from the anammox bacterium Kuenenia stuttgartiensis

Anaerobic ammonium oxidizing (anammox) bacteria oxidize ammonium with nitrite to nitrogen gas in the absence of oxygen. These microorganisms form a significant sink for fixed nitrogen in the oceans and the anammox process is applied as a cost‐effective and environment‐friendly nitrogen removal system from wastewater. Anammox bacteria have a compartmentalized cell plan that consists of three separate compartments. Here we report the fractionation of the anammox bacterium Kuenenia stuttgartiensis in order to isolate and analyze the innermost cell compartment called the anammoxosome. The subcellular fractions were microscopically characterized and all membranes in the anammox cell were shown to contain ladderane lipids which are unique for anammox bacteria. Proteome analyses and activity assays with the isolated anammoxosomes showed that these organelles harbor the energy metabolism in anammox cells. Together the experimental data provide the first thorough characterization of a respiratory cell organelle from a bacterium and demonstrate the essential role of the anammoxosome in the production of a major portion of the nitrogen gas in our atmosphere.     

Biological control potential of native entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) against Spodoptera cilium (Lepidoptera: Noctuidae) in turfgrass

In laboratory studies, we demonstrated that five native entomopathogenic nematode species/isolates caused 100% mortality of Spodoptera cilium larvae, a soil surface-feeding pest of turfgrass. At 25 infective juveniles/cm² applied to sod, two selected Turkish species, Steinernema carpocapsae and Heterorhabditis bacteriophora (Sarigerme isolate), averaged 77% and 29% larval mortality, respectively.