On the Fourier refinement of protein structures

The situation normally encountered in the high-resolution refinement of protein structures is one in which the inaccurate positions of P out of a total of N atoms are known whereas those of the remaining atoms are unknown. Fourier maps with coefficients (FN -- F'P) × exp (i[alpha]'P) and (mFN -- nF'P) exp (i[alpha]'P), where FN is the observed structure factor and F'P and [alpha]'P are the magnitude and the phase angle of the calculated structure factor corresponding to the inaccurate atomic positions, are often used to correct the positions of the P atoms and to determine those of the Q unknown atoms. A general theoretical approach is presented to elucidate the effect of errors in the positions of the known atoms on the corrected positions of the known atoms and the positions of the unknown atoms derived from such maps. The theory also leads to the optimal choice of parameters used in the different syntheses. When the errors in the positions of the input atoms are systematic, their effects are not taken care of automatically by the syntheses.

Genetic Structure of Cochliobolus sativus Populations Sampled from Roots and Leaves of Barley and Wheat in North Dakota

Common root rot (CRR) and spot blotch, caused by Cochliobolus sativus (Ito and Kurib.) Drechsl. ex Dast., are important diseases of barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) worldwide. However, the population biology of C. sativus is still poorly understood. In this study, the genetic structure of three C. sativus populations, consisting of isolates sampled respectively from barley leaves (BL), barley roots (BR) and wheat roots (WR) in North Dakota, was analysed with amplified fragment length polymorphism (AFLP) markers. A total of 127 AFLP loci were generated among 208 C. sativus isolates analysed with three primer combinations. Gene diversity (H = 0.277-0.335) were high in all three populations. Genetic variation among C. sativus individuals within population accounted for 74%, whereas 26% of the genetic variation was explained among populations. Genetic differentiation was high (empty set PT = 0.261, corrected G ''(st)= 0.39), whereas gene flow (Nm) ranged from 1.27 to 1.56 among the three populations analysed. The multilocus linkage disequilibrium (LD) ((r) over bard = 0.0760.117) was moderate in C. sativus populations. Cluster analyses indicate that C. sativus populations differentiated according to the hosts (barley and wheat) and tissues (root and leaf) although generalists also exist in North Dakota. Crop breeding may benefit from combining genes for resistance against both specialists and generalists of C. sativus.

Fluorescent probe and NMR studies of the aggregation of bile salts in aqueous solution

The binding of the fluorescent probes 1-anilino-8-naphthalene sulfonate and dansyl cadaverine to the sodium salts of cholic, deoxycholic and dehydrocholic acids has been investigated. Enhanced probe solubilisation accompanies aggregation. Monitoring of fluorescence intensities as a function of bile salt concentration permits the detection of primary micelle formation, as well as secondary association. The transition concentrations obtained by fluorescence are in good agreement with values determined for the critical micelle concentrations, by other methods. Differences in the behaviour of cholate and deoxycholate have been noted. Fluorescence polarisation studies of 1,6-diphenyl-1,3,5-hexatriene solubilised in bile salt micelles suggest a higher microviscosity for the interior of the deoxycholate micelle as compared to cholate. 1H NMR studies of deoxycholate over the range 1–100 mg/ml suggest that micelle formation leads to a greater immobilisation of the C18 and C19 methyl groups as compared to the C21 methyl group. Well resolved 13C resonances are observed for all three steroids even at high concentration. Both fluorescence and NMR studies confirm that dehydrocholate does not aggregate.

How weed control and fertilisation influence tree physiological processes and growth at early establishment in an exotic F1 hybrid pine plantation of subtropical Australia

Purpose This study investigated how nitrogen (N) nutrition and key physiological processes varied under changed water and nitrogen competition resulting from different weed control and fertilisation treatments in a 2-year-old F1 hybrid (Pinus elliottii Engelm var. elliottii × P. caribaea var. hondurensis Barr. ex Golf.) plantation on a grey podzolic soil type, in Southeast Queensland. Materials and methods The study integrated a range of measures including growth variables (diameter at ground level (DGL), diameter at breast height (DBH) and height (H)), foliar variables (including foliar N concentration, foliar δ13C and δ15N) and physiological variables (including photosynthesis (An), stomatal conductance (gs), transpiration (E), intrinsic water use efficiency (WUEi) (A/gs) and xylem pressure potential (ΨXPP)) to better understand the mechanisms influencing growth under different weed control and fertilisation treatments. Five levels of weed control were applied: standard (routine), luxury, intermediate, mechanical and nil weed control, all with routine fertilisation plus an additional treatment, routine weed control and luxury fertilisation. Relative weed cover was assessed at 0.8, 1.1 and 1.6 years after plantation establishment to monitor the effectiveness of weed control treatments. Soil investigation included soil ammonium (NH4 +-N), nitrate (NO3 −-N), potentially mineralizable N (PMN), gravimetric soil moisture content (MC), hot water extractable organic carbon (HWETC), hot water extractable total N (HWETN), total C, total N, stable C isotope composition (δ13C), stable N isotope composition (δ15N), total P and extractable K. Results and discussion There were significant relationships between foliar N concentrations and relative weed cover and between tree growth and foliar N concentration or foliar δ15N, but initial site preparation practices also increased soil N transformations in the planting rows reducing the observable effects of weed control on foliar δ15N. A positive relationship between foliar N concentration and foliar δ13C or photosynthesis indicated that increased N availability to trees positively influenced non-stomatal limitations to photosynthesis. However, trees with increased foliar N concentrations and photosynthesis were negatively related to xylem pressure potential in the afternoons which enhanced stomatal limitations to photosynthesis and WUEi. Conclusions Luxury and intermediate weed control and luxury fertilisation positively influenced growth at early establishment by reducing the competition for water and N resources. This influenced fundamental key physiological processes such as the relationships between foliar N concentration, A n, E, gs and ΨXPP. Results also confirmed that time from cultivation is an important factor influencing the effectiveness of using foliar δ15N as an indicator of soil N transformations.

Effects of weed control and fertilization at early establishment on tree nitrogen and water use in an exotic F1 hybrid pine of subtropical Australia

Purpose We investigated the effects of weed control and fertilization at early establishment on foliar stable carbon (δ13C) and nitrogen (N) isotope (δ15N) compositions, foliar N concentration, tree growth and biomass, relative weed cover and other physiological traits in a 2-year old F1 hybrid (Pinus elliottii var. elliottii (Engelm) × Pinus caribaea var. hondurensis (Barr. ex Golf.)) plantation grown on a yellow earth in southeast Queensland of subtropical Australia. Materials and methods Treatments included routine weed control, luxury weed control, intermediate weed control, mechanical weed control, nil weed control, and routine and luxury fertilization in a randomised complete block design. Initial soil nutrition and soil fertility parameters included (hot water extractable organic carbon (C) and total nitrogen (N), total C and N, C/N ratio, labile N pools (nitrate (NO3 −) and ammonium (NH4 +)), extractable potassium (K+)), soil δ15N and δ13C. Relative weed cover, foliar N concentrations, tree growth rate and physiological parameters including photosynthesis, stomatal conductance, photosynthetic nitrogen use efficiency, foliar δ15N and foliar δ13C were also measured at early establishment. Results and discussion Foliar N concentration at 1.25 years was significantly different amongst the weed control treatments and was negatively correlated to the relative weed cover at 1.1 years. Foliar N concentration was also positively correlated to foliar δ15N and foliar δ13C, tree height, height growth rates and tree biomass. Foliar δ15N was negatively correlated to the relative weed cover at 0.8 and 1.1 years. The physiological measurements indicated that luxury fertilization and increasing weed competition on these soils decreased leaf xylem pressure potential (Ψxpp) when compared to the other treatments. Conclusions These results indicate how increasing N resources and weed competition have implications for tree N and water use at establishment in F1 hybrid plantations of southeast Queensland, Australia. These results suggest the desirability of weed control, in the inter-planting row, in the first year to maximise site N and water resources available for seedling growth. It also showed the need to avoid over-fertilisation, which interfered with the balance between available N and water on these soils.

Wind drift of snowfall between the radar volume and ground

This study evaluates how the advection of precipitation, or wind drift, between the radar volume and ground affects radar measurements of precipitation. Normally precipitation is assumed to fall vertically to the ground from the contributing volume, and thus the radar measurement represents the geographical location immediately below. In this study radar measurements are corrected using hydrometeor trajectories calculated from measured and forecasted winds, and the effect of trajectory-correction on the radar measurements is evaluated. Wind drift statistics for Finland are compiled using sounding data from two weather stations spanning two years. For each sounding, the hydrometeor phase at ground level is estimated and drift distance calculated using different originating level heights. This way the drift statistics are constructed as a function of range from radar and elevation angle. On average, wind drift of 1 km was exceeded at approximately 60 km distance, while drift of 10 km was exceeded at 100 km distance. Trajectories were calculated using model winds in order to produce a trajectory-corrected ground field from radar PPI images. It was found that at the upwind side from the radar the effective measuring area was reduced as some trajectories exited the radar volume scan. In the downwind side areas near the edge of the radar measuring area experience improved precipitation detection. The effect of trajectory-correction is most prominent in instant measurements and diminishes when accumulating over longer time periods. Furthermore, measurements of intensive and small scale precipitation patterns benefit most from wind drift correction. The contribution of wind drift on the uncertainty of estimated Ze (S) - relationship was studied by simulating the effect of different error sources to the uncertainty in the relationship coefficients a and b. The overall uncertainty was assumed to consist of systematic errors of both the radar and the gauge, as well as errors by turbulence at the gauge orifice and by wind drift of precipitation. The focus of the analysis is error associated with wind drift, which was determined by describing the spatial structure of the reflectivity field using spatial autocovariance (or variogram). This spatial structure was then used with calculated drift distances to estimate the variance in radar measurement produced by precipitation drift, relative to the other error sources. It was found that error by wind drift was of similar magnitude with error by turbulence at gauge orifice at all ranges from radar, with systematic errors of the instruments being a minor issue. The correction method presented in the study could be used in radar nowcasting products to improve the estimation of visibility and local precipitation intensities. The method however only considers pure snow, and for operational purposes some improvements are desirable, such as melting layer detection, VPR correction and taking solid state hydrometeor type into account, which would improve the estimation of vertical velocities of the hydrometeors.

Divide-and-Correct Algorithm for Division in a Negative Base

A divide-and-correct algorithm is described for multiple-precision division in the negative base number system. In this algorithm an initial quotient estimate is obtained from suitable segmented operands; this is then corrected by simple rules to arrive at the true quotient.

Suomen maankuoren kivilajikoostumuksen tulkinta seismisistä aineistoista

Aim of this study is to investigate composition of the crust in Finland using seismic wide-angle velocity models and laboratory measurements on P- and S-wave velocities of different rock types. The velocities adopted from wide-angle velocity models were compared with laboratory velocities of different rock types corrected for the crustal PT conditions in the study area. The wide-angle velocity models indicate that the P-wave velocity does not only increase step-wise at boundaries of major crustal layers, but there is also gradual increase of velocity within the layers. On the other hand, the laboratory measurements of velocities indicate that no single rock type is able to provide the gradual downward increasing trends. Thus, there must be gradual vertical changes in rock composition. The downward increase of velocities indicates that the composition of the crust becomes gradually more mafic with increasing depth. Even though single rock types cannot simulate the wide-angle model velocities, it can be done with a mixture of rock types. There are a large number of rock type mixtures giving the correct P-wave velocities. Therefore, the inverse solution of rock types and their proportions from velocities is a non-unique problem if only P-wave velocities is available. Amount of the possible rock type mixtures can be limitted using S-wave velocities, reflection seismic results and other geological and geophysical results of the study area. Crustal model FINMIX-2 is presented in this study and it suggest that the crustal velocity profiles can be simulated with rock type mixtures, where the upper crust consists of felsic gneisses and granitic-granodioritic rocks with a minor contribution of quartzite, amphibolite and diabase. In the middle crust the amphibolite proportion increases. The lower crust consists of tonalitic gneiss, mafic garnet granulite, hornblendite, pyroxenite and minor mafic eclogite. This composition model is in agreement with deep crustal kimberlite-hosted xenolith data in eastern Finland and reflectivity of the FIRE (Finnish Reflection Experiment). According to FINMIX-2 model the Moho is deeper and the crustal composition is a more mafic than an average global continental model would suggest. Composition models of southern Finland are quite similar than FINMIX-2 model. However, there are minor differencies between the models, which indicates areal differences of composition. Models of northern Finland shows that the crustal thickness is smaller than southern Finland and composition of the upper crust is different. Density profiles calculated from the lithological models suggest that there is practically no density contrast at Moho in areas of the high-velocity lower crust. This implies that crustal thickness in the central Fennoscandian Shield may have been controlled by the densities of the lower crustal and upper mantle rocks.

Autoxidation of conjugated linoleic acid methyl ester in the presence of α-tocopherol: the hydroperoxide pathway

The autoxidation of conjugated linoleic acid (CLA) is poorly understood in spite of increasing interest in the beneficial biological properties of CLA and growing consumption of CLA-rich foods. In this thesis, the autoxidation reactions of the two major CLA isomers, 9-cis,11-trans-octadecadienoic acid and 10-trans,12-cis-octadecadienoic acid, are investigated. The results contribute to an understanding of the early stages of the autoxidation of CLA methyl ester, and provide for the first time a means of producing and separating intact CLA methyl ester hydroperoxides as well as basic knowledge on lipid hydroperoxides and their hydroxy derivatives. Conjugated diene allylic monohydroperoxides were discovered as primary autoxidation products formed during autoxidation of CLA methyl esters in the presence and absence of α-tocopherol. This established that one of the autoxidation pathways of CLA methyl ester is the hydroperoxide pathway. Hydroperoxides were produced from the two major CLA methyl esters by taking advantage of the effect of α-tocopherol to promote hydroperoxide formation. The hydroperoxides were analysed and separated first as methyl hydroxyoctadecadienoates and then as intact hydroperoxides by HPLC. The isolated products were characterized by UV, GC-MS, and NMR techniques. In the presence of a high amount of α-tocopherol, the autoxidation of CLA methyl ester yields six kinetically-controlled conjugated diene monohydroperoxides and is diastereoselective in favour of one particular geometric isomer as a pair of enantiomers. The primary autoxidation products produced from the two major CLA isomers include new positional isomers of conjugated diene monohydroperoxides, the 8-, 10-, 12-, and 14-hydroperoxyoctadecadienoates. Furthermore, two of these new positional isomers have an unusual structure for a cis,trans lipid hydroperoxide where the allylic methine carbon is adjacent to the cis instead of the usual trans double bond. The 1H and 13C NMR spectra of nine isomeric methyl hydroxyoctadecadienoates and of ten isomeric methyl hydroperoxyoctadecadienoates including the unusual cis,trans hydroperoxides, i.e. Me 8-OOH-9c,11t and Me 14-OOH-10t,12c, were fully assigned with the aid of 2D NMR spectroscopy. The assigned NMR data enabled determination of the effects of the hydroxyl and hydroperoxyl groups on the carbon chemical shifts of CLA isomers, identification of diagnostic signals, and determination of chemical shift differences of the olefinic resonances that may help with the assignment of structure to as yet unknown lipid hydroperoxides either as hydroxy derivatives or as intact hydroperoxides. A mechanism for the hydroperoxide pathway of CLA autoxidation in the presence of a high amount of α-tocopherol was proposed based on the characterized primary products, their relative distribution, and theoretical calculations. This is an important step forward in CLA research, where exact mechanisms for the autoxidation of CLA have not been presented before. Knowledge of these hydroperoxide formation steps is of crucial importance for understanding the subsequent steps and the different pathways of the autoxidation of CLA. Moreover, a deeper understanding of the autoxidation mechanisms is required for ensuring the safety of CLA-rich foods. Knowledge of CLA oxidation and how it differs from the oxidation of nonconjugated polyunsaturated fatty acids may also be the key to understanding the biological mechanisms of CLA activity.

Aspects and Applications of Pulse Sequence Design for Solution-State Nuclear Magnetic Resonance Spectroscopy

NMR spectroscopy enables the study of biomolecules from peptides and carbohydrates to proteins at atomic resolution. The technique uniquely allows for structure determination of molecules in solution-state. It also gives insights into dynamics and intermolecular interactions important for determining biological function. Detailed molecular information is entangled in the nuclear spin states. The information can be extracted by pulse sequences designed to measure the desired molecular parameters. Advancement of pulse sequence methodology therefore plays a key role in the development of biomolecular NMR spectroscopy. A range of novel pulse sequences for solution-state NMR spectroscopy are presented in this thesis. The pulse sequences are described in relation to the molecular information they provide. The pulse sequence experiments represent several advances in NMR spectroscopy with particular emphasis on applications for proteins. Some of the novel methods are focusing on methyl-containing amino acids which are pivotal for structure determination. Methyl-specific assignment schemes are introduced for increasing the size range of 13C,15N labeled proteins amenable to structure determination without resolving to more elaborate labeling schemes. Furthermore, cost-effective means are presented for monitoring amide and methyl correlations simultaneously. Residual dipolar couplings can be applied for structure refinement as well as for studying dynamics. Accurate methods for measuring residual dipolar couplings in small proteins are devised along with special techniques applicable when proteins require high pH or high temperature solvent conditions. Finally, a new technique is demonstrated to diminish strong-coupling induced artifacts in HMBC, a routine experiment for establishing long-range correlations in unlabeled molecules. The presented experiments facilitate structural studies of biomolecules by NMR spectroscopy.

Late Transition Metal and Aluminum Complexes for the Polymerization of Ethene and Acrylates

Polyethene, polyacrylates and polymethyl acrylates are versatile materials that find wide variety of applications in several areas. Therefore, polymerization of ethene, acrylates and methacrylates has achieved a lot attention during past years. Numbers of metal catalysts have been introduced in order to control the polymerization and to produce tailored polymer structures. Herein an overview on the possible polymerization pathways for ethene, acrylates and methacrylates is presented. In this thesis iron(II) and cobalt(II) complexes bearing tri- and tetradentate nitrogen ligands were synthesized and studied in the polymerization of tertbutyl acrylate (tBA) and methyl methacrylate (MMA). Complexes are activated with methylaluminoxane (MAO) before they form active combinations for polymerization reactions. The effect of reaction conditions, i.e. monomer concentration, reaction time, temperature, MAO to metal ratio, on activity and polymer properties were investigated. The described polymerization system enables mild reaction conditions, the possibility to tailor molar mass of the produced polymers and provides good control over the polymerization. Moreover, the polymerization of MMA in the presence of iron(II) complex with tetradentate nitrogen ligands under conditions of atom transfer radical polymerization (ATRP) was studied. Several manganese(II) complexes were studied in the ethene polymerization with combinatorial methods and new active catalysts were found. These complexes were also studied in acrylate and methacrylate polymerizations after MAO activation and converted into the corresponding alkyl (methyl or benzyl) derivatives. Combinatorial methods were introduced to discover aluminum alkyl complexes for the polymerization of acrylates and methacrylates. Various combinations of aluminum alkyls and ligands, including phosphines, salicylaldimines and nitrogen donor ligands, were prepared in situ and utilized to initiate the polymerization of tBA. Phosphine ligands were found to be the most active and the polymerization MMA was studied with these active combinations. In addition, a plausible polymerization mechanism for MMA based on ESI-MS, 1H and 13C NMR is proposed.

Divide-and-Correct Algorithm for Division in a Negative Base

A divide-and-correct algorithm is described for multiple-precision division in the negative base number system. In this algorithm an initial quotient estimate is obtained from suitable segmented operands; this is then corrected by simple rules to arrive at the true quotient.

Robust features of future climate change impacts on sorghum yields in West Africa

West Africa is highly vulnerable to climate hazards and better quantification and understanding of the impact of climate change on crop yields are urgently needed. Here we provide an assessment of near-term climate change impacts on sorghum yields in West Africa and account for uncertainties both in future climate scenarios and in crop models. Towards this goal, we use simulations of nine bias-corrected CMIP5 climate models and two crop models (SARRA-H and APSIM) to evaluate the robustness of projected crop yield impacts in this area. In broad agreement with the full CMIP5 ensemble, our subset of bias-corrected climate models projects a mean warming of +2.8 °C in the decades of 2031–2060 compared to a baseline of 1961–1990 and a robust change in rainfall in West Africa with less rain in the Western part of the Sahel (Senegal, South-West Mali) and more rain in Central Sahel (Burkina Faso, South-West Niger). Projected rainfall deficits are concentrated in early monsoon season in the Western part of the Sahel while positive rainfall changes are found in late monsoon season all over the Sahel, suggesting a shift in the seasonality of the monsoon. In response to such climate change, but without accounting for direct crop responses to CO2, mean crop yield decreases by about 16–20% and year-to-year variability increases in the Western part of the Sahel, while the eastern domain sees much milder impacts. Such differences in climate and impacts projections between the Western and Eastern parts of the Sahel are highly consistent across the climate and crop models used in this study. We investigate the robustness of impacts for different choices of cultivars, nutrient treatments, and crop responses to CO2. Adverse impacts on mean yield and yield variability are lowest for modern cultivars, as their short and nearly fixed growth cycle appears to be more resilient to the seasonality shift of the monsoon, thus suggesting shorter season varieties could be considered a potential adaptation to ongoing climate changes. Easing nitrogen stress via increasing fertilizer inputs would increase absolute yields, but also make the crops more responsive to climate stresses, thus enhancing the negative impacts of climate change in a relative sense. Finally, CO2 fertilization would significantly offset the negative climate

Flaws in the current method for calculating methane emissions during dairy manure management in New Zealand

New Zealand's Greenhouse Gas Inventory (the NZ Inventory) currently estimates methane (CH4) emissions from anaerobic dairy effluent ponds by: (1) determining the total pond volume across New Zealand; (2) dividing this volume by depth to obtain the total pond surface area; and (3) multiplying this area by an observational average CH4 flux. Unfortunately, a mathematically erroneous determination of pond volume has led to an imbalanced equation and a geometry error was made when scaling-up the observational CH4 flux. Furthermore, even if these errors are corrected, the nationwide estimate still hinges on field data from a study that used a debatable method to measure pond CH4 emissions at a single site, as well as a potentially inaccurate estimation of the amount of organic waste anaerobically treated. The development of a new methodology is therefore critically needed.

Achieving a national sample of nursing homes: Balancing probability techniques and practicalities

Sampling design is critical to the quality of quantitative research, yet it does not always receive appropriate attention in nursing research. The current article details how balancing probability techniques with practical considerations produced a representative sample of Australian nursing homes (NHs). Budgetary, logistical, and statistical constraints were managed by excluding some NHs (e.g., those too difficult to access) from the sampling frame; a stratified, random sampling methodology yielded a final sample of 53 NHs from a population of 2,774. In testing the adequacy of representation of the study population, chi-square tests for goodness of fit generated nonsignificant results for distribution by distance from major city and type of organization. A significant result for state/territory was expected and was easily corrected for by the application of weights. The current article provides recommendations for conducting high-quality, probability-based samples and stresses the importance of testing the representativeness of achieved samples.