Biochemical and structural properties of Potato virus A VPg

The potato virus A (PVA) genome linked protein (VPg) is a multifunctional protein that takes part in vital infection cycle events such as replication and movement of the virus from cell to cell. VPg is attached to the 5´ end of the genome and is carried in the tip structure of the filamentous virus particle. VPg is also the last protein to be cleaved from the polyprotein. VPg interacts with several viral and host proteins and is phosphorylated at several positions. These features indicate a central role in virus epidemiology and a requirement for an efficient but flexible mechanism for switching between different functions. -- This study examines some of the key VPg functions in more detail. Mutations in the positively charged region from Ala38 to Lys44 affected the NTP binding, uridylylation, and in vitro translation inhibition activities of VPg, whereas in vivo translation inhibition was not affected. Some of the data generated in this study implicated the structural flexibility of the protein in functional activities. VPg lacks a rigid structure, which could allow it to adapt conformationally to different functions as needed. A major finding of this study is that PVA VPg belongs to the class of ´intrinsically disordered proteins´ (IDPs). IDPs are a novel protein class that has helped to explain the observed lack of structure. The existence of IDPs clearly shows that proteins can be functional and adapt a native fold without a rigid structure. Evidence for the intrinsic disorder of VPg was provided by CD spectroscopy, NMR, fluorescence spectroscopy, bioinformatic analysis, and limited proteolytic digestion. The structure of VPg resembles that of a molten globule-type protein and has a hydrophobic core domain. Approximately 50% of the protein is disordered and an α-helical stabilization of these regions has been hypothesized. Surprisingly, VPg structure was stabilized in the presence of anionic lipid vesicles. The stabilization was accompanied by a change in VPg structure and major morphological modifications of the vesicles, including a pronounced increase in the size and appearance of pore or plaque like formations on the vesicle surface. The most likely scenario seems to be an α-helical stabilization of VPg which induces formation of a pore or channel-like structure on the vesicle surface. The size increase is probably due to fusion or swelling of the vesicles. The latter hypothesis is supported by the evident disruption of the vesicles after prolonged incubation with VPg. A model describing the results is presented and discussed in relation to other known properties of the protein.

Properties of intramuscular connective tissue in pork and poultry with reference to weakening of structure

The most common connective tissue research in meat science has been conducted on the properties of intramuscular connective tissue (IMCT) in connection with eating quality of meat. From the chemical and physical properties of meat, researchers have concluded that meat from animals younger than physiological maturity is the most tender. In pork and poultry, different challenges have been raised: the structure of cooked meat has weakened. In extreme cases raw porcine M. semimembranosus (SM) and in most turkey M. pectoralis superficialis (PS) can be peeled off in strips along the perimysium which surrounds the muscle fibre bundles (destructured meat), and when cooked, the slices disintegrate. Raw chicken meat is generally very soft and when cooked, it can even be mushy. The overall aim of this thesis was to study the thermal properties of IMCT in porcine SM in order to see if these properties were in association with destructured meat in pork and to characterise IMCT in poultry PS. First a 'baseline' study to characterise the thermal stability of IMCT in light coloured (SM and M. longissimus dorsi in pigs and PS in poultry) and dark coloured (M. infraspinatus in pigs and a combination of M. quadriceps femoris and M. iliotibialis lateralis in poultry) muscles was necessary. Thereafter, it was investigated whether the properties of muscle fibres differed in destructured and normal porcine muscles. Collagen content and also solubility of dark coloured muscles were higher than in light coloured muscles in pork and poultry. Collagen solubility was especially high in chicken muscles, approx. 30 %, in comparison to porcine and turkey muscles. However, collagen content and solubility were similar in destructured and normal porcine SM muscles. Thermal shrinkage of IMCT occurred at approximately 65 °C in pork and poultry. It occurred at lower temperature in light coloured muscles than in dark coloured muscles, although the difference was not always significant. The onset and peak temperatures of thermal shrinkage of IMCT were lower in destructured than in normal SM muscles, when the IMCT from SM muscles exhibiting ten lowest and ten highest ultimate pH values were investigated (onset: 59.4 °C vs. 60.7 °C, peak: 64.9 °C vs. 65.7 °C). As the destructured meat was paler than normal meat, the PSE (pale, soft, exudative) phenomenon could not be ruled out. The muscle fibre cross sectional area (CSA), the number of capillaries per muscle fibre CSA and per fibre and sarcomere length were similar in destructured and normal SM muscles. Drip loss was clearly higher in destructured than in normal SM muscles. In conclusion, collagen content and solubility and thermal shrinkage temperature vary between porcine and poultry muscles. One feature in the IMCT could not be directly associated with weakening of the meat structure. Poultry breast meat is very homogenous within the species.

Synthesis of Azo Coupled Crown Ethers Containing Transition Metal and other Chromophoric Environments and Their Ion Complexation Properties

The crown ethers, 2,3-benzo-1,4,7,10,13-pentaoxa-cyclopentadeca-2-ene and 2,3, ll,12-dibenzo-l,4,7,10,13,16-hexaoxscyclooctadeca-2,11-diene are incorporated into H,N'-ethylenebis(acetylacetoneimino) nickel(II) and copper(II), phenol, and β-naphthol by diazo coupling reactions. The selective nature of the coupling reaction has-been demonstrated by the isolation of both asymmetric mono- and symmetric bis(glyoxalarylcrownhydrazoneimino) metal(II) complexes. An interesting binuclear complex containing two intramolecularly rearranged (glyoxal-hydrazonearylimino) metal(II) groups joined by 18-crown-6 result8 when bis(arenediazonium)-18-crown-6 is coupled with the metal(I1) Schiff bases. The substituted ethers form cationic salts with NaClO4, KCNS, NH4CNS, 14g(CNS)2 and Ca(CNS)2. All the synthesised ethers exhibit ion selectivity sequence as K+ > Na+ and Ca2+ > Mg2+.

Structure, energetics and diffusion properties of isomers of trimethyl benzene in beta zeolite: Uptake and Monte Carlo simulation study

A Monte Carlo study along with experimental uptake measurements of 1,2,3-trimethyl benzene, 1,2,4-trimethyl benzene and 1,3,5-trimethyl benzene (TMB) in beta zeolite is reported. The TraPPE potential has been employed for hydrocarbon interaction and harmonic potential of Demontis for modeling framework of the zeolite. Structure, energetics and dynamics of TMB in zeolite beta from Monte Carlo runs reveal interesting information about the diameter, properties of these isomers on confinement. Of the three isomers, 135TMB is supposed to have the largest diameter. It is seen TraPPE with Demontis potential predicts a restricted motion of 135TMB in the channels of zeolite beta.Experimentally, 135TMB has the highest transport diffusivity whereas MID results suggest this has the lowest self diffusivity. (C) 2009 Elsevier Inc. Ail rights reserved.

A chitotetrose specific lectin from Luffa acutangula :Physico-chemical properties and the assignment of orientation of sugars in the lectin binding site

A chitooligosaccharide specific lectin (Luffa acutangula agglutinin) has been purified from the exudate of ridge gourd fruits by affinity chromatography on soybean agglutininglycopeptides coupled to Sepharose-6B. The affinity purified lectin was found homogeneous by polyacrylamide gel electrophoresis, in sodium dodecyl sulphate-polyacrylamide gels, by gel filtration on Sephadex G-100 and by sedimentation velocity experiments. The relative molecular weight of this lectin is determined to be 48,000 ± 1,000 by gel chromatography and sedimentation equilibrium experiments. The sedimentation coefficient (S20, w) was obtained to be 4·06 S. The Stokes’ radius of the protein was found to be 2·9 nm by gel filtration. In sodium dodecyl sulphate-polyacrylamide gel electrophoresis the lectin gave a molecular weight of 24,000 in the presence as well as absence of 2-mercaptoethanol. The subunits in this dimeric lectin are therefore held by non-covalent interactions alone. The lectin is not a glycoprotein and circular dichroism spectral studies indicate that this lectin has 31% α-helix and no ß-sheet. The lectin is found to bind specifically to chitooligosaccharides and the affinity of the lectin increases with increasing oligosaccharide chain length as monitored by near ultra-violetcircular dichroism and intrinsic fluorescence titration. The values of ΔG, ΔΗ and ΔS for the binding process showed a pronounced dependence on the size of the oligosaccharide. The values for both ΔΗ and ΔS show a significant increase with increase in the oligosaccharide chain length showing that the binding of higher oligomers is progressively more favoured thermodynamically than chitobiose itself. The thermodynamic data is consistent with an extended binding site in the lectin which accommodates a tetrasaccharide. Based on the thermodynamic data, blue shifts and fluorescence enhancement, spatial orientation of chitooligosaccharides in the combining site of the lectin is assigned.

Microbes in the tailoring of barley malt properties

Microbes have a decisive role in the barley-malt-beer chain. A major goal of this thesis was to study the relationships between microbial communities and germinating grains during malting. Furthermore, the study provided a basis for tailoring of malt properties with natural, malt-derived microbes. The malting ecosystem is a dynamic process, exhibiting continous change. The first hours of steeping and kilning were the most important steps in the process with regard to microbiological quality. The microbial communities consisting of various types of bacteria, yeasts and filamentous fungi formed complex biofilms in barley tissues and were well-protected. Inhibition of one microbial population within the complex ecosystem led to an increase of non-suppressed populations, which must be taken into account because a shift in microbial community dynamics may be undesirable. Both bacterial and fungal communities should be monitored simultaneously. Using different molecular approaches we showed that the diversity of microbes in the malting ecosystem was greater than expected. Even some new microbial groups were found in the malting ecosystem. Suppression of Gram-negative bacteria during steeping was advanategous for grain germination and malt brewhouse performance. Fungal communities including both filamentous fungi and yeasts significantly contributed to the production of microbial beta-glucanases and xylanases, and were also involved in proteolysis. Well-characterized lactic acid bacteria (Lactobacillus plantarum VTT E-78076 and Pediococcus pentosaceus VTT E-90390) proved to be an effective way of balancing the microbial communities in malting. Furthermore, they had positive effects on malt characteristics and notably improved wort separation. Previously the significance of yeasts in the malting ecosystem has been largely underestimated. This study showed that yeast community was an important part of the industrial malting ecosystem. Yeasts produced extracellular hydrolytic enzymes with a potentially positive contribution to malt processability. Furthermore, several yeasts showed strong antagonistic activity against field and storage moulds. Addition of a selected yeast culture (Pichia anomala VTT C-04565) into steeping restricted Fusarium growth and hydrophobin production and thus prevented beer gushing. Addition of P. anomala C565 into steeping water tended to retard wort filtration, but the filtration was improved when the yeast culture was combined with L. plantarum E76. The combination of different microbial cultures offers a possibility to use ther different properties, thus making the system more robust. Improved understanding of complex microbial communities and their role in malting enables a more controlled process management and the production of high quality malt with tailored properties

Occurrence and properties of steryl ferulates and glycosides in wheat and rye

Cereal kernels are known to contain a number of minor components that possess beneficial health attributes. In this thesis rye and wheat were studied as sources of steryl ferulates and steryl glycosides and their behaviour in processing were evaluated. Further, enzymatic hydrolysis of these conjugates was studied, as well as the capacity of steryl ferulates to inhibit lipid oxidation at different temperatures. Steryl ferulates were shown to have a strong positive correlation with dietary fibre contents in milling fractions from the outer parts of the kernels obtained from a commercial scale mill. Highest contents of steryl ferulates were found in the bran in both cereals, with the content decreasing once moving towards the inner parts of the kernel. Variation in the contents of steryl ferulates was higher in wheat fractions than rye fractions. Steryl glycosides, on the other hand, had either negative or no correlation with dietary fibre, and the range of the steryl glycoside contents was much narrower than that of steryl ferulates in both cereals. There were significant differences in the sterol compositions of these steryl conjugates when compared with each other or with the total plant sterols in the corresponding fractions. Properties of steryl ferulates and steryl glycosides were evaluated after common processing methods and in enzymatic hydrolysis. Thermal and mechanical processing had only minor or no effects on the contents of steryl conjugates from rye and wheat bran. Enzymatic treatments on the other hand caused some changes, especially in the contents of glycosylated sterols. When steryl ferulates extracted from rye or wheat bran were subjected to enzymatic treatments by steryl esterase, significant differences in the rates of hydrolysis were observed between steryl ferulates from different sources with differing sterol compositions. Further, differences were also observed between enzymes from different sources. Steryl glycosides were shown to be hydrolysed by β-glucosidase (cellobiase) from A. niger, but less with β-glucosidases from other sources. Steryl ferulates showed good antioxidant activity at both moderate and high temperatures. In bulk and emulsion systems of methyl linoleate at 40°C steryl ferulates extracted from rye and wheat bran inhibited hydroperoxide formation much more effectively than synthetic steryl ferulates or those extracted from rice (γ-oryzanol), demonstrating that the sterol composition has an effect on the activity. At cooking (100°C) and frying temperatures (180°C) sitostanyl ferulate was shown to inhibit polymer formation significantly and, especially at 100°C, comparably to α-tocopherol. The rate of antioxidant degradation was slower for sitostanyl ferulate, showing higher heat stability than α-tocopherol. When evaluated as a mixture, no synergistic effect was observed between these two antioxidants. The data presented in this thesis provides information that may henceforth be applied when evaluating the intakes of steryl conjugates from cereal sources, as well as their possible influences as minor bioactive components. Wheat and rye both are good sources of steryl ferulates and steryl glycosides and, especially with steryl ferulates, what may be lost out to some other cereals on quantity is compensated with quality of the sterol composition.

Food and Indoor Air Isolated Bacillus Non-Protein Toxins: : Structures, Physico-Chemical Properties and Mechanisms of Effects on Eukaryotic Cells

We report here the structures and properties of heat-stable, non-protein, and mammalian cell-toxic compounds produced by spore-forming bacilli isolated from indoor air of buildings and from food. Little information is available on the effects and occurrence of heat-stable non-protein toxins produced by bacilli in moisture-damaged buildings. Bacilli emit spores that move in the air and can serve as the carriers of toxins, in a manner similar to that of the spores of toxic fungi found in contaminated indoor air. Bacillus spores in food cause problems because they tolerate the temperatures applied in food manufacture and the spores later initiate growth when food storage conditions are more favorable. Detection of the toxic compounds in Bacillus is based on using the change in mobility of boar spermatozoa as an indicator of toxic exposure. GC, LC, MS, and nuclear magnetic resonance NMR spectroscopy were used for purification, detection, quantitation, and analysis of the properties and structures of the compounds. Toxicity and the mechanisms of toxicity of the compounds were studied using boar spermatozoa, feline lung cells, human neural cells, and mitochondria isolated from rat liver. The ionophoric properties were studied using the BLM (black-lipid membrane) method. One novel toxin, forming ion channels permeant to K+ > Na+ > Ca2+, was found and named amylosin. It is produced by B. amyloliquefaciens isolated from indoor air of moisture-damaged buildings. Amylosin was purified with an RP-HPLC and a monoisotopic mass of 1197 Da was determined with ESI-IT-MS. Furthermore, acid hydrolysis of amylosin followed by analysis of the amino acids with the GS-MS showed that it was a peptide. The presence of a chromophoric polyene group was found using a NMR spectroscopy. The quantification method developed for amylosin based on RP-HPLC-UV, using the macrolactone polyene, amphotericin B (MW 924), as a reference compound. The B. licheniformis strains isolated from a food poisoning case produced a lipopeptide, lichenysin A, that ruptured mammalian cell membranes and was purified with a LC. Lichenysin A was identified by its protonated molecules and sodium- and potassium- cationized molecules with MALDI-TOF-MS. Its protonated forms were observed at m/z 1007, 1021 and 1035. The amino acids of lichenysin A were analyzed with ESI-TQ-MS/MS and, after acid hydrolysis, the stereoisomeric forms of the amino acids with RP-HPLC. The indoor air isolates of the strain of B. amyloliquefaciens produced not only amylosin but also lipopeptides: the cell membrane-damaging surfactin and the fungicidal fengycin. They were identified with ESI-IT-MS observing their protonated molecules, the sodium- and potassium-cationized molecules and analysing the MS/MS spectra. The protonated molecules of surfactin and fengycin showed m/z values of 1009, 1023, and 1037 and 1450, 1463, 1493, and 1506, respectively. Cereulide (MW 1152) was purified with RP-HPLC from a food poisoning strain of B. cereus. Cereulide was identified with ESI-TQ-MS according to the protonated molecule observed at m/z 1154 and the ammonium-, sodium- and potassium-cationized molecules observed at m/z 1171, 1176, and 1192, respectively. The fragment ions of the MS/MS spectrum obtained from the protonated molecule of cereulide at m/z 1154 were also interpreted. We developed a quantification method for cereulide, using RP-HPLC-UV and valinomycin (MW 1110, which structurally resembles cereulide) as the reference compound. Furthermore, we showed empirically, using the BLM method, that the emetic toxin cereulide is a specific and effective potassium ionophore of whose toxicity target is especially the mitochondria.

Valence states and magnetic properties of LaNi1-xMnxO3 (for 0≤x≤0.2 and x=0.5)

Single-phase LaNi1-xMnxO3 samples in the compositional range 00.05, but any motional enthalpy appears to remain small ( Delta Hm approximately=0). The x=0.1 sample exhibits ferrimagnetic spin glass behaviour below 40K, and the ferromagnetic interactions increase with manganese concentration. The oxide with x=0.50 is ferromagnetic with a well defined Curie temperature.

Integrating organic matter into banana plantation in North Queensland: the effects on soil properties

The major banana production areas in Australia are particularly sensitive to environments due to their close proximity to areas of World Heritage rainforest and the Great Barrier Reef catchment. Management of soil quality, nutrients and pesticides are vital to maintaining the integrity of these sensitive areas. Studies on cropping systems have suggested that integrating organic matter into ground cover management would improve the quality of soil under banana cultivation. In this study, an alternative management practice for bananas, which addresses the management of organic matter and fertiliser application, was assessed and compared to the conventional practice currently employed in the banana industry. Several chemical, physical and biological soil parameters were measured including: pH, electrical conductivity, water stable aggregates, bulk density, water filled pore space, porosity, water content, fluorescein diacetate hydrolyis (FDA) and beta-glucosidase activity. The alternative management practice did not have a significant impact of the production and growth of bananas but overall improved the quality of the soil. Although some differences were observed, the chemical and physical soil characteristics did not differ dramatically between the two management systems. The addition of organic matter resulted in the soil under alternative practice having higher FDA and beta-glucosidase levels, indicating higher microbial activity. The integration of organic matter into the management of bananas resulted in positive benefits on soil properties under bananas, however, methods of maintaining organic matter in the soil need to be further researched.

Multiangular Spectrometry and Optical Properties of Debris Covered Surfaces

Due to the recent development in CCD technology aerial photography is now slowly changing from film to digital cameras. This new aspect in remote sensing allows and requires also new automated analysis methods. Basic research on reflectance properties of natural targets is needed so that computerized processes could be fully utilized. For this reason an instrument was developed at Finnish Geodetic Institute for measurement of multiangular reflectance of small remote sensing targets e.g. forest understorey or asphalt. Finnish Geodetic Institute Field Goniospectrometer (FiGIFiGo) is a portable device that is operated by 1 or 2 persons. It can be reassembled to a new location in 15 minutes and after that a target's multiangular reflectance can be measured in 10 - 30 minutes (with one illumination angle). FiGIFiGo has effective spectral range approximately from 400 nm to 2000 nm. The measurements can be made either outside with sunlight or in laboratory with 1000 W QTH light source. In this thesis FiGIFiGo is introduced and the theoretical basis of such reflectance measurements are discussed. A new method is introduced for extraction of subcomponent proportions from reflectance of a mixture sample, e.g. for retrieving proportion of lingonberry's reflectance in observation of lingonberry-lichen sample. This method was tested by conducting a series of measurements on reflectance properties of artificial samples. The component separation method yielded sound results and brought up interesting aspects in targets' reflectances. The method and the results still need to be verified with further studies, but the preliminary results imply that this method could be a valuable tool in analysis of such mixture samples.