RNA interference suppression of genes in glycosyl transferase families 43 and 47 in wheat starchy endosperm causes large decreases in arabinoxylan content

The cell walls of wheat (Triticum aestivum) starchy endosperm are dominated by arabinoxylan (AX), accounting for 65% to 70% of the polysaccharide content. Genes within two glycosyl transferase (GT) families, GT43 (IRREGULAR XYLEM9 [IRX9] and IRX14) and GT47 (IRX10), have previously been shown to be involved in the synthesis of the xylan backbone in Arabidopsis, and close homologs of these have been implicated in the synthesis of xylan in other species. Here, homologs of IRX10 TaGT47_2 and IRX9 TaGT43_2, which are highly expressed in wheat starchy endosperm cells, were suppressed by RNA interference (RNAi) constructs driven by a starchy endosperm-specific promoter. The total amount of AX was decreased by 40% to 50% and the degree of arabinosylation was increased by 25% to 30% in transgenic lines carrying either of the transgenes. The cell walls of starchy endosperm in sections of grain from TaGT43_2 and TaGT47_2 RNAi transgenics showed decreased immunolabeling for xylan and arabinoxylan epitopes and approximately 50% decreased cell wall thickness compared with controls. The proportion of AX that was water soluble was not significantly affected, but average AX polymer chain length was decreased in both TaGT43_2 and TaGT47_2 RNAi transgenics. However, the long AX chains seen in controls were absent in TaGT43_2 RNAi transgenics but still present in TaGT47_2 RNAi transgenics. The results support an emerging picture of IRX9-like and IRX10-like proteins acting as key components in the xylan synthesis machinery in both dicots and grasses. Since AX is the main component of dietary fiber in wheat foods, the TaGT43_2 and TaGT47_2 genes are of major importance to human nutrition.

Aerosol scattering and absorption during the EUCAARI-LONGREX flights of the Facility for Airborne Atmospheric Measurements (FAAM) BAe-146: can measurements and models agree?

Scattering and absorption by aerosol in anthropogenically perturbed air masses over Europe has been measured using instrumentation flown on the UK’s BAe-146-301 large Atmospheric Research Aircraft (ARA) operated by the Facility for Airborne Atmospheric Measurements (FAAM) on 14 flights during the EUCAARI-LONGREX campaign in May 2008. The geographical and temporal variations of the derived shortwave optical properties of aerosol are presented. Values of single scattering albedo of dry aerosol at 550 nm varied considerably from 0.86 to near unity, with a campaign average of 0.93 ± 0.03. Dry aerosol optical depths ranged from 0.030 ± 0.009 to 0.24 ± 0.07. An optical properties closure study comparing calculations from composition data and Mie scattering code with the measured properties is presented. Agreement to within measurement uncertainties of 30% can be achieved for both scattering and absorption,but the latter is shown to be sensitive to the refractive indices chosen for organic aerosols, and to a lesser extent black carbon, as well as being highly dependent on the accuracy of the absorption measurements. Agreement with the measured absorption can be achieved either if organic carbon is assumed to be weakly absorbing, or if the organic aerosol is purely scattering and the absorption measurement is an overestimate due to the presence of large amounts of organic carbon. Refractive indices could not be inferred conclusively due to this uncertainty, despite the enhancement in methodology compared to previous studies that derived from the use of the black carbon measurements. Hygroscopic growth curves derived from the wet nephelometer indicate moderate water uptake by the aerosol with a campaign mean f (RH) value (ratio in scattering) of 1.5 (range from 1.23 to 1.63) at 80% relative humidity. This value is qualitatively consistent with the major chemical components of the aerosol measured by the aerosol mass spectrometer, which are primarily mixed organics and nitrate and some sulphate.

Large deviations of Rouse polymer chain: first passage problem

The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional Kramers' problem, which presents rich and unexpected behavior. We first perform direct and forward-flux sampling (FFS) simulations, and measure the mean first-passage time $\tau(z)$ for the free end to reach a certain distance $z$ away from the origin. The results show that the mean FP time is getting faster if the Rouse chain is represented by more beads. Two scaling regimes of $\tau(z)$ are observed, with transition between them varying as a function of chain length. We use these simulations results to test two theoretical approaches. One is a well known asymptotic theory valid in the limit of zero temperature. We show that this limit corresponds to fully extended chain when each chain segment is stretched, which is not particularly realistic. A new theory based on the well known Freidlin-Wentzell theory is proposed, where dynamics is projected onto the minimal action path. The new theory predicts both scaling regimes correctly, but fails to get the correct numerical prefactor in the first regime. Combining our theory with the FFS simulations lead us to a simple analytical expression valid for all extensions and chain lengths. One of the applications of polymer FP problem occurs in the context of branched polymer rheology. In this paper, we consider the arm-retraction mechanism in the tube model, which maps exactly on the model we have solved. The results are compared to the Milner-McLeish theory without constraint release, which is found to overestimate FP time by a factor of 10 or more.

Global climatology of surface water temperatures of large lakes by remote sensing

Lake surface water temperatures (LSWTs) of 246 globally distributed large lakes were derived from Along-Track Scanning Radiometers (ATSR) for the period 1991–2011. The climatological cycles of mean LSWT derived from these data quantify on a global scale the responses of large lakes' surface temperatures to the annual cycle of forcing by solar radiation and the ambient meteorological conditions. LSWT cycles reflect the twice annual peak in net solar radiation for lakes between 1°S to 12°N. For lakes without a lake-mean seasonal ice cover, LSWT extremes exceed air temperatures by 0.5–1.7 °C for maximum and 0.7–1.9 °C for minimum temperature. The summer maximum LSWTs of lakes from 25°S to 35°N show a linear decrease with increasing altitude; −3.76 ± 0.17 °C km−1 (inline image = 0.95), marginally lower than the corresponding air temperature decrease with altitude −4.15 ± 0.24 °C km−1 (inline image = 0.95). Lake altitude of tropical lakes account for 0.78–0.83 (inline image) of the variation in the March to June LSWT–air temperature differences, with differences decreasing by 1.9 °C as the altitude increases from 500 to 1800 m above sea level (a.s.l.) We define an ‘open water phase’ as the length of time the lake-mean LSWT remains above 4 °C. There is a strong global correlation between the start and end of the lake-mean open water phase and the spring and fall 0 °C air temperature transition days, (inline image = 0.74 and 0.80, respectively), allowing for a good estimation of timing and length of the open water phase of lakes without LSWT observations. Lake depth, lake altitude and distance from coast further explain some of the inter-lake variation in the start and end of the open water phase.

New insights into the compressibility and high-pressure stability of Ni(CN)2: a combined study of neutron diffraction, Raman spectroscopy, and inelastic neutron scattering

Nickel cyanide is a layered material showing markedly anisotropic behaviour. High-pressure neutron diffraction measurements show that at pressures up to 20.1 kbar, compressibility is much higher in the direction perpendicular to the layers, c, than in the plane of the strongly chemically bonded metal-cyanide sheets. Detailed examination of the behaviour of the tetragonal lattice parameters, a and c, as a function of pressure reveal regions in which large changes in slope occur, for example, in c(P) at 1 kbar. The experimental pressure dependence of the volume data is fitted to a bulk modulus, B0, of 1050 (20) kbar over the pressure range 0–1 kbar, and to 124 (2) kbar over the range 1–20.1 kbar. Raman spectroscopy measurements yield additional information on how the structure and bonding in the Ni(CN)2 layers change with pressure and show that a phase change occurs at about 1 kbar. The new high-pressure phase, (Phase PII), has ordered cyanide groups with sheets of D4h symmetry containing Ni(CN)4 and Ni(NC)4 groups. The Raman spectrum of phase PII closely resembles that of the related layered compound, Cu1/2Ni1/2(CN)2, which has previously been shown to contain ordered C≡N groups. The phase change, PI to PII, is also observed in inelastic neutron scattering studies which show significant changes occurring in the phonon spectra as the pressure is raised from 0.3 to 1.5 kbar. These changes reflect the large reduction in the interlayer spacing which occurs as Phase PI transforms to Phase PII and the consequent increase in difficulty for out-of-plane atomic motions. Unlike other cyanide materials e.g. Zn(CN)2 and Ag3Co(CN)6, which show an amorphization and/or a decomposition at much lower pressures (~100 kbar), Ni(CN)2 can be recovered after pressurising to 200 kbar, albeit in a more ordered form.

Synchrotron X-ray imaging via ultra-small-angle scattering: principles of quantitative analysis and application in studying bone integration to synthetic grafting materials

Optimized experimental conditions for extracting accurate information at subpixel length scales from analyzer-based X-ray imaging were obtained and applied to investigate bone regeneration by means of synthetic beta-TCP grafting materials in a rat calvaria model. The results showed a 30% growth in the particulate size due to bone ongrowth/ingrowth within the critical size defect over a 1-month healing period.

Resonant neutrino scattering: An impossible experiment?

The experimental feasibility was investigated for the resonant scattering of monoenergetic neutrinos emitted in the two-body beta decay. A simple general formula shows that the resonance cross section can be as large as of the order of 10(-17) cm(2). The Mossbauer setup using a solid crystal was examined with a focus on the electronic structure of the emitter and the absorber. Based on realistic calculations, we show that interactions of valence electrons in the solid lead to a level broadening of the atomic ground state, which considerably suppresses the resonant scattering of neutrinos. (C) 2010 Elsevier B.V. All rights reserved.

Challenging measurement of the (16)O+(27)Al elastic and inelastic angular distributions up to large angles

The (16)O+(27)Al elastic and inelastic angular distributions have been measured in a broad angular range (13 degrees < theta(lab) < 52 degrees) at about 100 MeV incident energy. The use of the MAGNEX large acceptance magnetic spectrometer and of the ray-reconstruction analysis technique has been crucial in order to provide, in the same experiment, high-resolution energy spectra and cross-section measurements distributed over more than seven orders of magnitude down to hundreds of nb/sr. (C) 2011 Elsevier B.V. All rights reserved.

Resilience of protein-protein interaction networks as determined by their large-scale topological features

The relationship between the structure and function of biological networks constitutes a fundamental issue in systems biology. Particularly, the structure of protein-protein interaction networks is related to important biological functions. In this work, we investigated how such a resilience is determined by the large scale features of the respective networks. Four species are taken into account, namely yeast Saccharomyces cerevisiae, worm Caenorhabditis elegans, fly Drosophila melanogaster and Homo sapiens. We adopted two entropy-related measurements (degree entropy and dynamic entropy) in order to quantify the overall degree of robustness of these networks. We verified that while they exhibit similar structural variations under random node removal, they differ significantly when subjected to intentional attacks (hub removal). As a matter of fact, more complex species tended to exhibit more robust networks. More specifically, we quantified how six important measurements of the networks topology (namely clustering coefficient, average degree of neighbors, average shortest path length, diameter, assortativity coefficient, and slope of the power law degree distribution) correlated with the two entropy measurements. Our results revealed that the fraction of hubs and the average neighbor degree contribute significantly for the resilience of networks. In addition, the topological analysis of the removed hubs indicated that the presence of alternative paths between the proteins connected to hubs tend to reinforce resilience. The performed analysis helps to understand how resilience is underlain in networks and can be applied to the development of protein network models.

Adsorption of anionic amphiphilic polyelectrolytes onto amino-terminated solid surfaces

The adsorption behavior of several amphiphilic polyelectrolytes of poly(maleic anhydride-alt-styrene) functionalized with naphthyl and phenyl groups, onto amino-terminated silicon wafer has been studied by means of null- ellipsometry, atomic force microscopy (AFM) and contact angle measurements. The maximum of adsorption, Gamma(plateau), varies with the ionic strength, the polyelectrolyte structure and the chain length. Values of Gamma(plateau) obtained at low and high ionic strengths indicate that the adsorption follows the ""screening-reduced adsorption"" regime. Large aggregates were detected in solution by means of dynamic light scattering and fluorescence measurements. However. AFM indicated the formation of smooth layers and the absence of aggregates. A model based on a two-step adsorption behavior was proposed. In the first one, isolated chains in equilibrium with the aggregates in solution adsorbed onto amino-terminated surface. The adsorption is driven by electrostatic interaction between protonated surface and carboxylate groups. This first layer exposes naphtyl or phenyl groups to the solution. The second layer adsorption is now driven by hydrophobic interaction between surface and chains and exposes carboxylate groups to the medium, which repel the forthcoming chain by electrostatic repulsion. Upon drying some hydrophobic naphtyl or phenyl groups might be oriented to the air, as revealed by contact angle measurements. Such amphiphilic polyelectrolyte layers worked well for the building-up of multilayers with chitosan. (C) 2010 Elsevier Ltd. All rights reserved.

New insights on surface-enhanced Raman scattering based on controlled aggregation and spectroscopic studies, DFT calculations and symmetry analysis for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine adsorbed onto citrate-stabilized gold nanoparticles

Asystematic study on the surface-enhanced Raman scattering (SERS) for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine (bptz) adsorbed onto citrate-modified gold nanoparticles (cit-AuNps) was carried out based on electronic and vibrational spectroscopy and density functional methods. The citrate/bptz exchange was carefully controlled by the stepwise addition of bptz to the cit-AuNps, inducing flocculation and leading to the rise of a characteristic plasmon coupling band in the visible region. Such stepwise procedure led to a uniform decrease of the citrate SERS signals and to the rise of characteristic peaks of bptz, consistent with surface binding via the N heterocyclic atoms. In contrast, single addition of a large amount of bptz promoted complete aggregation of the nanoparticles, leading to a strong enhancement of the SERS signals. In this case, from the distinct Raman profiles involved, the formation of a new SERS environment became apparent, conjugating the influence of the local hot spots and charge-transfer (CT) effects. The most strongly enhanced vibrations belong to a(1) and b(2) representations, and were interpreted in terms of the electromagnetic and the CT mechanisms: the latter involving significant contribution of vibronic coupling in the system. Copyright (C) 2010 John Wiley & Sons, Ltd.

Using Polycarbonate Membranes as Templates for the Preparation of Au Nanostructures for Surface-Enhanced Raman Scattering

Polycarbonate membranes (PCM) of various pores sizes (400, 200, 100 and 50 nm) were used as templates for gold deposition. The electrodeposition from gold ions resulted in the formation of gold nanotubes when large pores size PCMs (400 and 200 nm) were used. On the other hand, gold nanowires were predominant for the PCMs with smaller pores size (100 and 50 nm). Surface-enhanced Raman scattering (SERS) from the probe molecule 4-mercaptopyridine (4-MPy) was obtained from all these nanostructures. The SERS efficiency of the substrates produced using the PC M templates were compared to two commonly used SERS platforms: a roughened gold electrode and gold nanostructures electrodeposited through organized polystyrene spheres (PSS). The SERS signal of the probe molecule increased as the pore diameter of the PCM template decreased. Moreover, the SERS efficiency from the nanostructures produced using 50 nm PCM templates was four and two times better than the signal from the roughened gold electrode and the PSS template, respectively. The SERS substrates prepared using PCM templates were more homogenous over a larger area (ca. 1 cm(2)), presented better spatial and sample to sample reproducibility than the other substrates. These results show that SERS substrates prepared using PCM templates are promising for the fabrication of planar SERS platforms for analytical/bioanalytical applications.

Fine root isotropy in Eucalyptus grandis plantations. Towards the prediction of root length densities from root counts on trench walls

The objectives of the study were to assess changes in fine root anisotropy and specific root lengths throughout the development of Eucalyptus grandis ( W. Hill ex Maiden) plantations and to establish a predictive model of root length density (RLD) from root intercept counts on trench walls. Fine root densities (<1 mm in diameter) were studied in 6-, 12-, 22-, 28-, 54-, 68- and 72-month-old E. grandis plantations established on deep Ferralsols in southern Brazil. Fine root intercepts were counted on 3 faces of 90-198 soil cubes (1 dm(3) in volume) in each stand and fine root lengths (L) were measured inside 576 soil cubes, sampled between the depths of 10 cm and 290 cm. The number of fine root intercepts was counted on one vertical face perpendicular to the planting row (N(t)), one vertical face parallel to the planting row (N(l)) and one horizontal face (N(h)), for each soil cube sampled. An overall isotropy of fine roots was shown by paired Student's t-tests between the numbers of fine roots intersecting each face of soil cubes at most stand ages and soil depths. Specific root lengths decreased with stand age in the upper soil layers and tended to increase in deep soil layers at the end of the rotation. A linear regression established between N(t) and L for all the soil cubes sampled accounted for 36% of the variability of L. Such a regression computed for mean Nt and L values at each sampling depth and stand age explained only 55% of the variability, as a result of large differences in the relationship between L and Nt depending on stand productivity. The equation RLD=1.89*LAI*N(t), where LAI was the stand leaf area index (m(2) m(-2)) and Nt was expressed as the number of root intercepts per cm(2), made it possible to predict accurately (R(2)=0.84) and without bias the mean RLDs (cm cm(-3)) per depth in each stand, for the whole data set of 576 soil cubes sampled between 2 years of age and the end of the rotation.

Motile sperm organelle morphology examination (MSOME): intervariation study of normal sperm and sperm with large nuclear vacuoles

Background: Although the motile sperm organelle morphology examination (MSOME) was developed only as a selection criterion, its application as a method for classifying sperm morphology may represent an improvement in evaluation of semen quality, with potential clinical repercussions. The present study aimed to evaluate individual variations in the motile sperm organelle morphology examination (MSOME) analysis after a time interval.Methods: Two semen samples were obtained from 240 men from an unselected group of couples undergoing infertility investigation and treatment. Mean time interval between the two semen evaluations was 119 +/- 102 days. No clinical or surgical treatment was realized between the two observations. Spermatozoa were analyzed at greater than or equal to 8400 x magnification by inverted microscope equipped with DIC/Nomarski differential interference contrast optics. At least 200 motile spermatozoa per semen sample were evaluated and percentages of normal spermatozoa and spermatozoa with large nuclear vacuoles (LNV/one or more vacuoles occupying >50% of the sperm nuclear area) were determined. A spermatozoon was classified as morphologically normal when it exhibited a normal nucleus (smooth, symmetric and oval nucleus, width 3.28 +/- 0.20 mu m, length 4.75 +/- 0.20 mu m/absence of vacuoles occupying >4% of nuclear area) as well as acrosome, post-acrosomal lamina, neck and tail, besides not presenting cytoplasm around the head. One examiner, blinded to subject identity, performed the entire study.Results: Mean percentages of morphologically normal and LNV spermatozoa were identical in the two MSOME analyses (1.6 +/- 2.2% vs. 1.6 +/- 2.1% P = 0.83 and 25.2 +/- 19.2% vs. 26.1 +/- 19.0% P = 0.31, respectively). Regression analysis between the two samples revealed significant positive correlation for morphologically normal and for LNV spermatozoa (r = 0.57 95% CI: 0.47-0.65 P < 0.0001 and r = 0.50 95% CI: 0.38-0.58 P < 0.0001, respectively).Conclusions: The significant positive correlation and absence of differences between two sperm samples evaluated after a time interval with respect to normal morphology and LNV spermatozoa indicated that MSOME seems reliable (at least for these two specific sperm forms) for analyzing semen. The present result supports the future use of MSOME as a routine method for semen analysis.

Importance of lateral lagoons for the ichthyofauna in a large tropical reservoir

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