Molecular dynamics simulations of CXCL-8 and its interactions with a receptor peptide, heparin fragments, and sulfated linked cyclitols

CXCL-8 (Interleukin 8) is a CXC chemokine with a central role in the human immune response. We have undertaken extensive in silico analyses to elucidate the interactions of CXCL-8 with its various binding partners, which are crucial for its biological function. Sequence and structure analyses showed that residues in the thirdq β-sheet and basic residues in the heparin binding site are highly variable, while residues in the second β-sheet are highly conserved. Molecular dynamics simulations in aqueous solution of dimeric CXCL-8 have been performed with starting geometries from both X-ray and NMR structures showed shearing movements between the two antiparallel C-terminal helices. Dynamic conservation analyses of these simulations agreed with experimental data indicating that structural differences between the two structures at quaternary level arise from changes in the secondary structure of the N-terminal loop, the 310-helix, the 30s, 40s, and 50s loops and the third β-sheet, resulting in a different interhelical separation. Nevertheless, the observation of these different states indicates that CXCL-8 has the potential to undergo conformational changes, and it seems likely that this feature is relevant to the mode of binding of glycosaminoglycan (GAG) mimetics such as cyclitols. Simulations of the receptor peptide fragment−CXCL-8 complex identified several specific interactions of the receptor peptide with CXCL-8 that could be exploited in the structure-based design of competitive peptides and nonpeptidic molecules targeting CXCL-8 for combating inflammatory diseases. Simulations of the CXCL-8 dimer complexed with a 24-mer heparin fragment and of the CXCL-8−receptor peptide complex revealed that Arg60, Lys64, and Arg68 in the dimer bind to cyclitols in a horseshoe pattern, defining a region which is spatially distinct from the receptor binding site. There appears to be an optimum number of sulfates and an optimum length of alkyl spacers required for the interaction of cyclitol inhibitors with the dimeric form of CXCL-8. Calculation of the binding affinities of cyclitol inhibitors reflected satisfactorily the ranking of experimentally determined inhibitory potencies. The findings of these molecular modeling studies will help in the search for inhibitors which can modulate various CXCL-8 biological activities and serve as an excellent model system to study CXC-inhibitor interactions.

Legumes or nitrification inhibitors to reduce {N2O} emissions from subtropical cereal cropping systems in Oxisols?

The DAYCENT biogeochemical model was used to investigate how the use of fertilizers coated with nitrification inhibitors and the introduction of legumes in the crop rotation can affect subtropical cereal production and {N2O} emissions. The model was validated using comprehensive multi-seasonal, high-frequency dataset from two field investigations conducted on an Oxisol, which is the most common soil type in subtropical regions. Different N fertilizer rates were tested for each N management strategy and simulated under varying weather conditions. DAYCENT was able to reliably predict soil N dynamics, seasonal {N2O} emissions and crop production, although some discrepancies were observed in the treatments with low or no added N inputs and in the simulation of daily {N2O} fluxes. Simulations highlighted that the high clay content and the relatively low C levels of the Oxisol analyzed in this study limit the chances for significant amounts of N to be lost via deep leaching or denitrification. The application of urea coated with a nitrification inhibitor was the most effective strategy to minimize {N2O} emissions. This strategy however did not increase yields since the nitrification inhibitor did not substantially decrease overall N losses compared to conventional urea. Simulations indicated that replacing part of crop N requirements with N mineralized by legume residues is the most effective strategy to reduce {N2O} emissions and support cereal productivity. The results of this study show that legumes have significant potential to enhance the sustainable and profitable intensification of subtropical cereal cropping systems in Oxisols.

Nitrification (DMPP) and urease (NBPT) inhibitors had no effect on pasture yield, nitrous oxide emissions nor nitrate leaching under irrigation in a hot-dry climate

Modern dairy farming in Australia relies on substantial inputs of fertiliser nitrogen (N) to underpin economic production. However, N lost from dairy systems represents an opportunity cost and can pose a number of environmental risks. Nitrogen cycle inhibitors can be co-applied with N fertilisers to slow the conversion of urea to NH4+ to reduce losses via volatilisation, and slow the conversion of NH4+ to NO3- to minimize leaching of NO3- and gaseous losses via nitrification and denitrification. In a field campaign in a high input ryegrass-kikuyu pasture system we compared the soil N pools, losses and pasture production between a) urea coated with the nitrification inhibitor (3,4-dimethyl pyrazole phosphate - DMPP) b) urea coated with the urease inhibitor (N-(n-butyl) thiophosphoric triamide - NBPT) and c) standard urea. There was no treatment effect (P>0.05) on soil mineral N, pasture yield, N2O flux nor leaching of NO3- cf. standard urea. We hypothesise that at our site, because gaseous losses were highly episodic (rainfall was erratic and displayed no seasonal rainfall nor soil wetting pattern) that there was a lack of coincidence of N application and conditions conducive to gaseous losses, thus the effectiveness of the inhibitor products was minimal and did not result in an increase in pasture yield. There remains a paucity of knowledge on N cycle inhibitors in relation to their effective use in field system to increase N use efficiency. Further research is required to define under what field conditions inhibitor products are effective in order to be able to provide accurate advice to managers of nitrogen in production systems.

Marked increase in proton pump inhibitors use in Australia

Objectives: To examine the trends in the prescribing of subsidised proton pump inhibitors (PPIs) and histamine receptor antagonists (H2RAs), in the Australian population from 1995 to 2006 to encourage discussion regarding appropriate clinical use. PPIs and H2RAs are the second highest drug cost to the publicly subsidised Pharmaceutical Benefits Scheme (PBS). Design: Government data on numbers of subsidised scripts, quantity and doses for PPIs and H2RAs were analysed by gender and age, dose and indication. Main outcome measure: Drug utilisation as DDD [defined daily dose]/1000 population/day. Results: The use of combined PPIs increased by 1318%. Utilisation increased substantially after the relaxation of the subsidised indications for PPIs in 2001. Omeprazole had the largest market share but was substituted by its S-enantiomer esomeprazole after its introduction in 2002. There was considerable use in the elderly with the peak use being in those aged 80 years and over. The utilisation of H2RAs declined 72% over 12 years. Conclusions: PPI use has increased substantially, not only due to substitution of H2RAs but to expansion in the overall market. Utilisation does not appear to be commensurate with prevalence of gastro-oesophageal reflux disease (GORD) nor with prescribing guidelines for PPIs, with significant financial costs to patients and PBS. This study encourages clinical discussion regarding quality use of these medicines. © 2010 John Wiley & Sons, Ltd.

Single layer graphene film by ethanol chemical vapor deposition: Highly efficient growth and clean transfer method

The choice of ethanol (C2H5OH) as carbon source in the Chemical Vapor Deposition (CVD) of graphene on copper foils can be considered as an attractive alternative among the commonly used hydrocarbons, such as methane (CH4) [1]. Ethanol, a safe, low cost and easy handling liquid precursor, offers fast and efficient growth kinetics with the synthesis of fullyformed graphene films in just few seconds [2]. In previous studies of graphene growth from ethanol, various research groups explored temperature ranges lower than 1000 °C, usually reported for methane-assisted CVD. In particular, the 650–850 °C and 900 °C ranges were investigated, respectively for 5 and 30 min growth time [3, 4]. Recently, our group reported the growth of highly-crystalline, few-layer graphene by ethanol-CVD in hydrogen flow (1– 100 sccm) at high temperatures (1000–1070 °C) using growth times typical of CH4-assisted synthesis (10–30 min) [5]. Furthermore, a synthesis time between 20 and 60 s in the same conditions was explored too. In such fast growth we demonstrated that fully-formed graphene films can be grown by exposing copper foils to a low partial pressure of ethanol (up to 2 Pa) in just 20 s [6] and we proposed that the rapid growth is related to an increase of the Cu catalyst efficiency due weak oxidizing nature of ethanol. Thus, the employment of such liquid precursor, in small concentrations, together with a reduced time of growth and very low pressure leads to highly efficient graphene synthesis. By this way, the complete coverage of a copper catalyst surface with high spatial uniformity can be obtained in a considerably lower time than when using methane.

Sinteractivity, proton conductivity and chemical stability of BaZr 0.7In0.3O3-δ for solid oxide fuel cells (SOFCs)

In3+ was used as dopant for BaZrO3 proton conductor and 30 at%-doped BaZrO3 samples (BaZr0.7In 0.3O3-δ, BZI) were prepared as electrolyte materials for proton-conducting solid oxide fuel cells (SOFCs). The BZI material showed a much improved sinteractivity compared with the conventional Y-doped BaZrO 3. The BZI pellets reached almost full density after sintering at 1600 °C for 10 h, whereas the Y-doped BaZrO3 samples still remained porous under the same sintering conditions. The conductivity measurements indicated that BZI pellets showed smaller bulk but improved grain boundary proton conductivity, when compared with Y-doped BaZrO3 samples. A total proton conductivity of 1.7 × 10-3 S cm -1 was obtained for the BZI sample at 700 °C in wet 10% H 2 atmosphere. The BZI electrolyte material also showed adequate chemical stability against CO2 and H2O, which is promising for application in fuel cells.

Engineered protease inhibitors based on sunflower trypsin inhibitor-1 (SFTI-1) provide insights into the role of sequence and conformation in Laskowski mechanism inhibition

Laskowski inhibitors regulate serine proteases by an intriguing mode of action that involves deceiving the protease into synthesizing a peptide bond. Studies exploring naturally occurring Laskowski inhibitors have uncovered several structural features that convey the inhibitor's resistance to hydrolysis and exceptional binding affinity. However, in the context of Laskowski inhibitor engineering, the way that various modifications intended to fine-tune an inhibitor's potency and selectivity impact on its association and dissociation rates remains unclear. This information is important as Laskowski inhibitors are becoming increasingly used as design templates to develop new protease inhibitors for pharmaceutical applications. In this study, we used the cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), as a model system to explore how the inhibitor's sequence and structure relate to its binding kinetics and function. Using enzyme assays, MD simulations and NMR spectroscopy to study SFTI variants with diverse sequence and backbone modifications, we show that the geometry of the binding loop mainly influences the inhibitor's potency by modulating the association rate, such that variants lacking a favourable conformation show dramatic losses in activity. Additionally, we show that the inhibitor's sequence (including both the binding loop and its scaffolding) influences its potency and selectivity by modulating both the association and the dissociation rates. These findings provide new insights into protease inhibitor function and design that we apply by engineering novel inhibitors for classical serine proteases, trypsin and chymotrypsin and two kallikrein-related peptidases (KLK5 and KLK14) that are implicated in various cancers and skin diseases.