Chemical synthesis and structure elucidation of bovine K-casein (1-44)

The caseins (αs1, αs2, β, and κ) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1–44) of bovine κ-casein, the protein which maintains the micellar structure of the caseins. κ-Casein (1–44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro8 to Arg34. This is the first report which demonstrates extensive secondary structure within the casein class of proteins.

Beyond chemical dependency for managing plant-parasitic nematodes: Examples from the banana, pineapple and vegetable industries of tropical and subtropical Australia

Plant-parasitic nematodes are important pests of horticultural crops grown in tropical and subtropical regions of Australia. Burrowing nematode (Radopholus similis) is a major impediment to banana production and root-knot nematodes (predominantly Meloidogyne javanica and M. incognita) cause problems on pineapple and a range of annual vegetables, including tomato, capsicum, zucchini, watermelon, rockmelon, potato and sweet potato. In the early 1990s, nematode control in these industries was largely achieved with chemicals, with methyl bromide widely used on some subtropical vegetable crops, ethylene dibromide applied routinely to pineapples and non-volatile nematicides such as fenamiphos applied up to four times a year in banana plantations. This paper discusses the research and extension work done over the last 15 years to introduce an integrated pest management approach to nematode control in tropical and subtropical horticulture. It then discusses various components of current integrated pest management programs, including crop rotation, nematode monitoring, clean planting material, organic amendments, farming systems to enhance biological suppression of nematodes and judicious use of nematicides. Finally, options for improving current management practices are considered.

Physio-chemical assessment of beauty leaf (Calophyllum inophyllum) as second-generation biodiesel feedstock

Recently, second-generation (non-vegetable oil) feedstocks for biodiesel production are receiving significant attention due to the cost and social effects connected with utilising food products for the production of energy products. The Beauty leaf tree (Calophyllum inophyllum) is a potential source of non-edible oil for producing second-generation biodiesel because of its suitability for production in an extensive variety of atmospheric condition, easy cultivation, high fruit production rate, and the high oil content in the seed. In this study, oil was extracted from Beauty leaf tree seeds through three different oil extraction methods. The important physical and chemical properties of these extracted Beauty leaf oils were experimentally analysed and compared with other commercially available vegetable oils. Biodiesel was produced using a two-stage esterification process combining of an acid catalysed pre-esterification process and an alkali catalysed transesterification process. Fatty acid methyl ester (FAME) profiles and important physicochemical properties were experimentally measured and estimated using equations based on the FAME analysis. The quality of Beauty leaf biodiesels was assessed and compared with commercially available biodiesels through multivariate data analysis using PROMETHEE-GAIA software. The results show that mechanical extraction using a screw press produces oil at a low cost, however, results in low oil yields compared with chemical oil extraction. High pressure and temperature in the extraction process increase oil extraction performance. On the contrary, this process increases the free fatty acid content in the oil. A clear difference was found in the physical properties of Beauty leaf oils, which eventually affected the oil to biodiesel conversion process. However, Beauty leaf oils methyl esters (biodiesel) were very consistent physicochemical properties and able to meet almost all indicators of biodiesel standards. Overall this study found that Beauty leaf is a suitable feedstock for producing second-generation biodiesel in commercial scale. Therefore, the findings of this study are expected to serve as the basis for further development of Beauty leaf as a feedstock for industrial scale second-generation biodiesel production.

Extension of Chemical Phytotoxicity Testing Facility for Warm-Season Turfgrasses

The turf industry needs to access a range of more selective, effective and environmentally acceptable pesticides, which will help to address environmental concerns while maintaining the industry's internationally competitive status. This includes both new pesticides being developed globally for turf use and older generic chemicals previously registered for other agricultural purposes and now requiring extension of that registration for use in turf.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone H-1(alpha) and C-13' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to alpha-helical/beta-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

Chemical modification of Methionines of Ribonuclease a with O-Benzoquinone

The accessibility of methionines in RNAase A to reaction with OBQ has been studied at highly acidic pH. The differences between the rate constants of reactions of the methionine and methionines of RNAase A with OBQ is a reflection on the limited accessibility of methionines in the protein conformation. Nevertheless, at sufficiently high OBQ concentration, all the four methionines of the enzyme can be modified. At lower concentration of OBQ, a derivative may be prepared in which a specific methionine is modified. The introduced chromophore ionizes at around pH 3 in this derivative. The derivative has partial activity towards RNA which is enhanced on addition of S-protein.

Optical and chemical properties of polyterpenol thin films deposited via plasma-enhanced chemical vapor deposition

The development of novel organic polymer thin films is essential for the advancement of many emerging fields including organic electronics and biomedical coatings. In this study, the effect of synthesis conditions, namely radio frequency (rf) deposition power, on the material properties of polyterpenol thin films derived from nonsynthetic environmentally friendly monomer was investigated. At lower deposition powers, the polyterpenol films preserved more of the original monomer constituents, such as hydroxy functional groups; however, they were also softer and more hydrophilic compared to polymers fabricated at higher power. Enhanced monomer fragmentation and consequent reduction in the presence of the polar groups in the structure of the high-power samples reduced their optical band gap value from 2.95 eV for 10 W to 2.64 eV for 100 W. Regardless of deposition power, all samples were found to be optically transparent with smooth, defect-free, and homogenous surfaces.

Weed age affects chemical control of Conyza bonariensis in fallows

In the last decade, Conyza bonariensis has become a widespread and difficult-to-control weed in Australian broad-acre cropping, particularly in glyphosate-based zero-tilled fallows of the subtropical grain region. The first Australian populations of C. bonariensis, where it is known as flaxleaf fleabane, were confirmed resistant to glyphosate in 2010. Control with alternative herbicides in fallows has been inconsistent, with earlier research indicating that weed age could be a potential contributing factor. In two field experiments, the impact of weed age (one, two and three months) was measured on the efficacy of six non-selective herbicide mixtures and sequential applications for control in fallows. In another two experiments we evaluated 11 non-selective herbicides, mixtures and sequential applications applied to one and three month old weeds using higher rates on older weeds. When herbicide rates were consistent for different weed ages, efficacy was reduced only by an average of 1% when two month old weeds were treated compared to one month old weeds. However when applied to three month old weeds, efficacy of treatments was significantly (P < 0.001) reduced by 3-30%. When herbicide rates were increased, weed age had no adverse effect on efficacy, which ranged from 90 to 100%, for amitrole, glyphosate mixed with 2,4-D amine plus picloram, and three sequential application treatments of glyphosate mixtures followed with bipyridyl products. Thus, this problem weed can be controlled effectively and consistently at the rosette stage of one to two months old, or three month old weeds with several different treatments at robust rates. These effective glyphosate alternatives and sequential-application tactics will minimise replenishment of the soil seed-bank and further reduce the risk for further evolution of glyphosate resistance. (C) 2012 Elsevier Ltd. All rights reserved.

Physical characterization of plastic surfaces in wearing and cleanability research

Plastic surfaces are a group of materials used for many purposes. The present study was focused on methods for investigation of surface topography, wearing and cleanability of polyvinyl chloride (PVC) model surfaces and industrial plastic surfaces. Contact profilometry, scanning electron microscopy (SEM) and atomic force microscopy (AFM) are powerful methods for studying the topography of plastic surfaces. Although they have their own limitations, they are together an effective tool providing useful information on surface topography, especially when studying laboratory-made PVC model surfaces with known chemical compositions and structures. All examined laboratory-made PVC plastic surfaces examined in this work could be considered as smooth according to both AFM and profilometer measurements because height differences are in the nanoscale on every surface. Industrial plastic surfaces are a complex group of materials because of their chemical and topographical heterogeneity, but they are nevertheless important reference materials when developing cleaning and wearing methods. According to the results of this study the Soiling and Wearing Drum and the Frick-Taber methods are very useful when simulating three-body wearing of plastic surfaces. Both the investigated wearing methods can be used to compare the wearing of different plastic materials using appropriate evaluation methods of wearing and industrial use. In this study, physical methods were developed and adapted from other fields of material research to cleanability studies. The thesis focuses on the methodology for investigating the cleanability of plastic surfaces under realistic conditions, where surface topography and the effect of wear cleanability were among the major topics. A colorimetric method proved to be suitable for examining the cleanability of the industrial plastic surfaces. The results were utilized to evaluate the relationship between cleanability and the surface properties of plastic surfaces. The devices and methods used in the work can be utilized both in material research and product development.

Digestion capasity, nutrient digestibilities and physico-chemical conditions in the intestine influenced by the age of growing turkeys

Six experiments have been conducted to examine digestibility and feeding value of domestic Finnish fibre-rich cereals (barley and oats as compared to maize and wheat) and protein sources (rapeseed meal and cake, peas, faba beans, lupin seeds) for growing turkeys and to investigate effects of age of the birds (from 3 to 12 weeks of age) on digestion process and estimated nutrient digestibility and energy values. Besides, an objective of the study was to test applications of digestibility research methodology for turkeys. Total tract digestibility and apparent metabolizable energy (AME) was assayed in experimental cages using excreta collection, and a slaughter method was applied to sample small intestinal digesta for determination of apparent ileal crude protein digestibility (AICPD), jejuno-duodenal digesta viscosity and caecal volatile fatty acid (VFA) concentration. Digesta viscosity decreased and caecal VFA production increased with age of growing turkeys. Digesta retention times in the small intestine were generally longer in the older birds than in the younger ones. Crude fat digestibility and AME increased with age of growing turkeys, especially with viscous diets. AICPD seemed to decrease with age in most cases. Supplementation with β-gucanase-xylanase decreased viscosity, improved crude fat digestibility and metabolizable energy value and increased VFA production especially in barley-fed turkeys and especially in the young birds. Poor protein digestibility and low energy value of rapeseed meal and rapeseed cake decreased their feeding value for turkeys. In addition, a typical goitrogenic effect of rapeseed feeding was detected. Use of legume seeds as feed for growing turkeys is limited mostly by the low energy value in lupin seeds and the low ileal protein and amino acid digestibility in faba beans. Digestibility of fibre-rich protein sources was not improved with age of the turkeys. Euthanizing the turkeys for AICPD determination by carbon dioxide and bleeding led to lower digestibility values than mechanical stunning and cervical dislocation, suggesting inferiority of carbon dioxide stunning in experimental use. Comparison of AICPD and AME results obtained using different markers showed that considerable differences may occur, especially on total tract level, when acid-insoluble ash gave considerably lower AME values than titanium dioxide and chromic oxide.

Chemical characteristics and behaviour of sediment phosphorus in the northeastern Baltic Sea.

Chemical characteristics and behaviour of sediment phosphorus in the northeastern Baltic Sea Eutrophication is a severe environmental problem in the Baltic Sea, especially in the Gulf of Finland and the Archipelago Sea, and it is enhanced by the release of phosphorus (P) from bottom sediments. The release of P from sediment reserves largely depends on the occurrence of P in different chemical forms and on the prevailing conditions, especially on the presence of oxygen. This study examines the chemical character and the vertical distribution of sediment P in two shallow estuaries, in shallow coastal sediments overlain by oxic near-bottom water, and in poorly oxygenated open sea sediments in the northeastern Baltic Sea. The objective was to evaluate how much of the sediment P is buried and removed from the nutrient cycle, and how much of it is in forms that can be released from the sediment to the overlaying water over time. Relationships between the distribution of the different P forms and the chemical and physical properties of the sediment, sediment pore water, and near-bottom water were determined in order to examine the behaviour of P at the sediment-water interface. The results show that the chemical character of sediment P varied in the different areas. Generally, in the outer estuaries and in the organic-rich coastal areas in the eastern Gulf of Finland, the sediments were higher in P than the sediments in the poorly oxygenated open sea areas in the central and western Gulf. The estuary sediments that received erosion-transported material were characterised by P bound to hydrated oxides of iron and aluminum. Iron-bound P is sensitive to changes in redox-conditions, but part of it was buried in the estuaries, possibly because of high sedimentation rates and incomplete reduction of iron. The open sea sediments in the central and western Gulf of Finland were dominated by apatite-P, which was also abundant in the areas strongly affected by sediment transportation. The burial of sediment P was most effective in the areas rich in apatite-P, which is a relatively stable form of P in sediment. In the eastern Gulf of Finland, organic P forms predominated in the organic-rich sediments. A part of these P forms will be buried, while part will be degraded in the long term, releasing soluble P to the pore water. In the poorly oxygenated areas, iron compounds at the sediment surface are not able to retain P released during mineralisation of organic matter or reduction-induced dissolution of iron-compounds in deep sediment layers. However, in the shallow coastal areas overlain by oxic near-bottom water, the organic-rich surface sediment can also become temporarily reduced and release P from the sediment to the overlaying water. The considerable variation in the chemical composition of sediment P reserves in the northeastern Baltic Sea proved that it is an important factor and should be taken into account when evaluating the release of sediment P and the role of P reserves in bottom sediments in eutrophication.

Technicum - Chemical Lab

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Improved chemical control of Conyza bonariensis in wheat limits problems in the following fallow

Conyza bonariensis is a major weed infesting zero-tilled cropping systems in subtropical Australia, particularly in wheat and winter fallows. Uncontrolled C.bonariensis survives to become a problem weed in the following crops or fallows. As no herbicide has been registered for C.bonariensis in wheat, the effectiveness of 11 herbicides, currently registered for other broad-leaved weeds in wheat, was evaluated in two pot and two field experiments. As previous research showed that the age of C.bonariensis, and to a lesser extent, the soil moisture at spraying affected herbicide efficacy, these factors also were investigated. The efficacy of the majority of herbicide treatments was reduced when large rosettes (5-15cm diameter) were treated, compared with small rosettes (<5cm diameter). However, for the majority of herbicide treatments, the soil moisture did not affect the herbicide efficacy in the pot experiments. In the field, a delay in herbicide treatment of 2 weeks reduced the herbicide efficacy consistently across herbicide treatments, which was related to weed age but not to soil moisture differences. Across all the experiments, four herbicides controlled C.bonariensis in wheat consistently (83-100%): 2,4-D; aminopyralid + fluroxypyr; picloram + MCPA + metsulfuron; and picloram + high rates of 2,4-D. Thus, this problem weed can be effectively and consistently controlled in wheat, particularly when small rosettes are treated, and therefore C.bonariensis will have a less adverse impact on the following fallow or crop.

Computational studies on new chemical species in the gas-phase and the solid-state.

There is intense activity in the area of theoretical chemistry of gold. It is now possible to predict new molecular species, and more recently, solids by combining relativistic methodology with isoelectronic thinking. In this thesis we predict a series of solid sheet-type crystals for Group-11 cyanides, MCN (M=Cu, Ag, Au), and Group-2 and 12 carbides MC2 (M=Be-Ba, Zn-Hg). The idea of sheets is then extended to nanostrips which can be bent to nanorings. The bending energies and deformation frequencies can be systematized by treating these molecules as an elastic bodies. In these species Au atoms act as an 'intermolecular glue'. Further suggested molecular species are the new uncongested aurocarbons, and the neutral Au_nHg_m clusters. Many of the suggested species are expected to be stabilized by aurophilic interactions. We also estimate the MP2 basis-set limit of the aurophilicity for the model compounds [ClAuPH_3]_2 and [P(AuPH_3)_4]^+. Beside investigating the size of the basis-set applied, our research confirms that the 19-VE TZVP+2f level, used a decade ago, already produced 74 % of the present aurophilic attraction energy for the [ClAuPH_3]_2 dimer. Likewise we verify the preferred C4v structure for the [P(AuPH_3)_4]^+ cation at the MP2 level. We also perform the first calculation on model aurophilic systems using the SCS-MP2 method and compare the results to high-accuracy CCSD(T) ones. The recently obtained high-resolution microwave spectra on MCN molecules (M=Cu, Ag, Au) provide an excellent testing ground for quantum chemistry. MP2 or CCSD(T) calculations, correlating all 19 valence electrons of Au and including BSSE and SO corrections, are able to give bond lengths to 0.6 pm, or better. Our calculated vibrational frequencies are expected to be better than the currently available experimental estimates. Qualitative evidence for multiple Au-C bonding in triatomic AuCN is also found.

Quantum Chemical Studies of Intermolecular Interactions

This thesis studies the intermolecular interactions in (i) boron-nitrogen based systems for hydrogen splitting and storage, (ii) endohedral complexes, A@C60, and (iii) aurophilic dimers. We first present an introduction of intermolecular interactions. The theoretical background is then described. The research results are summarized in the following sections. In the boron-nitrogen systems, the electrostatic interaction is found to be the leading contribution, as 'Coulomb Pays for Heitler and London' (CHL). For the endohedral complex, the intermolecular interaction is formulated by a one-center expansion of the Coulomb operator 1/rab. For the aurophilic attraction between two C2v monomers, a London-type formula was derived by fully accounting for the anisotropy and point-group symmetry of the monomers.