Self-diffusion of Rod-like Viruses Through Smectic Layer

We report the direct visualization at the scale of single particles of mass transport between smectic layers, also called permeation, in a suspension of rod-like viruses. Self-diffusion takes place preferentially in the direction normal to the smectic layers, and occurs by quasi-quantized steps of one rod length. The diffusion rate corresponds with the rate calculated from the diffusion in the nematic state with a lamellar periodic ordering potential that is obtained experimentally.Comment: latex, 4 pages, 4 figures, accepted in Phys. Rev. Let

Numerical calculations of the phase diagram of cubic blue phases in cholesteric liquid crystals

We study the static properties of cubic blue phases by numerically minimising the three-dimensional, Landau-de Gennes free energy for a cholesteric liquid crystal close to the isotropic-cholesteric phase transition. Thus we are able to refine the powerful but approximate, semi-analytic frameworks that have been used previously. We obtain the equilibrium phase diagram and discuss it in relation to previous results. We find that the value of the chirality above which blue phases appear is shifted by 20% (towards experimentally more accessible regions) with respect to previous estimates. We also find that the region of stability of the O5 structure -- which has not been observed experimentally -- shrinks, while that of BP I (O8-) increases thus giving the correct order of appearance of blue phases at small chirality. We also study the approach to equilibrium starting from the infinite chirality solutions and we find that in some cases the disclination network has to assemble during the equilibration. In these situations disclinations are formed via the merging of isolated aligned defects.Comment: 16 pages, 5 figures. Accepted for publication in Phys. Rev.

Isotropic-nematic phase transition in suspensions of filamentous virus and the neutral polymer Dextran

We present an experimental study of the isotropic-nematic phase transition in an aqueous mixture of charged semi-flexible rods (fd virus) and neutral polymer (Dextran). A complete phase diagram is measured as a function of ionic strength and polymer molecular weight. At high ionic strength we find that adding polymer widens the isotropic-nematic coexistence region with polymers preferentially partitioning into the isotropic phase, while at low ionic strength the added polymer has no effect on the phase transition. The nematic order parameter is determined from birefringence measurements and is found to be independent of polymer concentration (or equivalently the strength of attraction). The experimental results are compared with the existing theoretical predictions for the isotropic-nematic transition in rods with attractive interactions.Comment: 8 Figures. To be published in Phys. Rev. E. For more information see http://www.elsie.brandeis.ed

Development of a subacute ruminal acidosis risk score and its prediction using milk mid-infrared spectra in early-lactation cows

peer reviewe

Spectral phase encoding for data storage and addressing

We propose to use a broad-bandwidth laser source for storing and retrieving multiple holograms in a photorefractive material. Each storage address is defined by a specific spectral encoding of the reference beam. The validity of the spectral encoding method is tested in a preliminary experiment

Mineralizable nitrogen and denitrification enzyme activity drive nitrate concentrations in well-drained stony subsoil under lucerne (Medicago sativa L.)

Nitrogen (N) inputs to agricultural systems contribute substantially to soil nitrate (NO₃¯) concentrations, which increase NO₃¯ leaching and contamination of groundwater. The influence of soil microbes in regulating NO₃¯ concentrations in the topsoil are well studied but it is often assumed that microbial regulation of NO₃¯ concentrations in the subsoil is negligible. The aim of this study was to test this assumption by determining the relationships between microbial properties and NO₃¯ concentrations in both the subsoil and the topsoil. We measured the size of the mineralizable N (Nm) pool, microbial properties (microbial biomass, bacterial richness), nitrifier gene abundance (amoA gene copy number), denitrifier gene abundance (nirK and nirS gene copy number), denitrifier enzyme activity and NO₃¯ concentrations in the topsoil and the subsoil in a well-drained stony soil under an established lucerne crop. We used structural equation modelling (SEM) to identify and compare the linkages of microbial properties with NO₃¯ concentrations at each depth. In the topsoil, we found higher Nm, gene abundance, denitrification enzyme activity, bacterial richness, and microbial biomass than those in the subsoil, but there were no relationships between these variables and NO₃¯ concentrations in the topsoil (the SEM model explained 0.06% of the variability in NO₃¯ concentrations). In contrast, in the subsoil, NO₃¯ concentrations were strongly correlated with bacterial amoA abundance and denitrification enzyme activity, with both variables associated significantly with Nm. We found that bacterial richness was also associated with Nm in the subsoil. Our findings highlight that microbial properties are associated with NO₃¯ concentrations in the subsoil (the SEM model explained 82% the variability in NO₃¯ concentrations) and this suggest that nitrification and denitrification may contribute to regulating NO₃¯ concentrations in the subsoil. Our findings also suggest that denitrification contributes to reducing NO₃¯ concentrations in the subsoil. We conclude that studies addressing drivers of NO₃¯ leaching need to consider the potential for microbially-mediated attenuation (or an increase) in NO₃¯ concentrations throughout the soil profile

Regenerative agriculture in Aotearoa New Zealand - research pathways to build science-based evidence and national narratives.

fals

Prediction of metabolic clusters in early lactation dairy cows using models based on 2 milk biomarkers

The aim of this study was to describe metabolism of early-lactation dairy cows by clustering cows based on glucose, insulin-like growth factor I (IGF-I), free fatty acid, and beta-hydroxybutyrate (BHB) using the k-means method. Predictive models for metabolic clusters were created and validated using 3 sets of milk biomarkers (milk metabolites and enzymes, glycans on the immuno-gamma globulin fraction of milk, and Fourier-transform mid-infrared spectra of milk). Metabolic clusters are used to identify dairy cows with a balanced or imbalanced metabolic profile. Around 14 and 35 d in milk, serum or plasma concentrations of BHB, free fatty acids, glucose, and IGF-I were determined. Cows with a favorable metabolic profile were grouped together in what was referred to as the "balanced" group (n = 43) and were compared with cows in what was referred to as the "other balanced" group (n = 64). Cows with an unfavorable metabolic profile were grouped in what was referred to as the "imbalanced" group (n = 19) and compared with cows in what was referred to as the "other imbalanced" group (n = 88). Glucose and IGF-I were higher in balanced compared with other balanced cows. Free fatty acids and BHB were lower in balanced compared with other balanced cows. Glucose and IGF-I were lower in imbalanced compared with other imbalanced cows. Free fatty acids arid BHB were higher in imbalanced cows. Metabolic clusters were related to production parameters. There was a trend for a higher daily increase in fat- and protein-corrected milk yield in balanced cows, whereas that of imbalanced cows was higher. Dry matter intake and the daily increase in dry matter intake were higher in balanced cows and lower in imbalanced cows. Energy balance was continuously higher in balanced cows and lower in imbalanced cows. Weekly or twice-weekly milk samples were taken and milk metabolites and enzymes (milk glucose, glucose-6-phosphate, BHB, lactate dehydrogenase, N-acetyl-beta-D-glucosaminidase, isocitrate), immunogamma globulin glycans (19 peaks), and Fourier-transform mid-infrared spectra (1,060 wavelengths reduced to 15 principal components) were determined. Milk biomarkers with or without additional cow information (days in milk, parity, milk yield featurs) were used to create predictive models for the metabolic clusters. Accuracy for prediction of balanced (80%) and imbalanced (88%) cows was highest using milk metabolites and enzymes combined with days in milk and parity. The results and models of the present study are part of the GplusE project and identify novel milk-based phenotypes that may be used as predictors for metabolic and performance traits in early-lactation dairy cows

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs

Modulation of the vertical particle transfer efficiency in the oxygen minimum zone off Peru

The fate of the organic matter (OM) produced by marine life controls the major biogeochemical cycles of the Earth's system. The OM produced through photosynthesis is either preserved, exported towards sediments or degraded through remineralisation in the water column. The productive eastern boundary upwelling systems (EBUSs) associated with oxygen minimum zones (OMZs) would be expected to foster OM preservation due to low O2 conditions. But their intense and diverse microbial activity should enhance OM degradation. To investigate this contradiction, sediment traps were deployed near the oxycline and in the OMZ core on an instrumented moored line off Peru. Data provided high-temporal-resolution O2 series characterising two seasonal steady states at the upper trap: suboxic ([O2]  50%) and remineralisation (intermediate Teff 20  50%) has been reported in summer and winter associated with extreme limitation in O2 concentrations or OM quantity for OM degradation. However, higher levels of O2 or OM, or less refractory OM, at the oxycline, even in a co-limitation context, can decrease the OMZ transfer efficiency to below 50%. This is especially true in summer during intraseasonal wind-driven oxygenation events. In late winter and early spring, high oxygenation conditions together with high fluxes of sinking particles trigger a shutdown of the OMZ transfer (Teff < 6%). Transfer efficiency of chemical elements composing the majority of the flux (nitrogen, phosphorus, silica, calcium carbonate) follows the same trend as for carbon, with the lowest transfer level being in late winter and early spring. Regarding particulate isotopes, vertical transfer of δ15N suggests a complex pattern of 15N impoverishment or enrichment according to Teff modulation. This sensitivity of OM to O2 fluctuations and particle concentration calls for further investigation into OM and O2-driven remineralisation processes. This should include consideration of the intermittent behaviour of OMZ towards OM demonstrated in past studies and climate projections