Magic Angle Spinning Effects on Longitudinal NMR Relaxation: 15N in L-Histidine

Solid-state magnetic resonance is a unique technique that can reveal the dynamics of complex biological systems with atomic resolution. Longitudinal relaxation is a mechanism that returns longitudinal nuclear magnetization to its thermal equilibrium by incoherent processes. The measured longitudinal relaxation rate constant however represents the combination of both incoherent and coherent contributions to the change of nuclear magnetization. This work demonstrates the effect of magic angle spinning rate on the longitudinal relaxation rate constant in two model compounds: L-histidine hydrochloride monohydrate and glycine serving as proxies for isotopically-enriched biological materials. Most notably, it is demonstrated that the longitudinal 15N relaxation of the two nitrogen nuclei in the imidazole ring in histidine is reduced by almost three orders of magnitude at the condition of rotational resonance with the amine, while the amine relaxation rate constant is increased at these conditions. The observed phenomenon may have radical implications for the solid-state magnetic resonance in biophysics and materials, especially in the proper measurement of dynamics and as a selective serial transfer step in dynamic nuclear polarization

Wood lignocellulosic stabilizers : effect of their characteristics on stability and rheological properties of emulsions

Lignocellulosic materials from the forest industry have shown potential to be used as sustainable hydrocolloids to stabilize emulsions for many applications in life science and chemical industries. However, the effect of wood species and recovery method on the product’s properties and ability to stabilize emulsions of isolated lignocellulosic compounds is not well understood. Hemicelluloses, abundant lignocellulosic side stream, exhibit differences in their water solubility, anionic character, lignin content, and degree of acetylation. Here, we explored stability and rheological properties of model emulsions (5% hexadecane and 1% stabilizer, w/w) stabilized by different grades of sprucewood galactoglucomannan (GGM) and birchwood glucuronoxylan (GX) hemicelluloses. The results were compared to known soluble, insoluble, charged, and non-charged cellulosic stabilizers, namely methyl cellulose (MC), carboxymethyl cellulose (CMC), anionic- and nonionic-cellulose nanocrystals (aCNC and dCNC). The results showed that GX emulsions were highly stable compared to GGM emulsions, and that deacetylation and lignin removal markedly reduced emulsion stability of GGM. Carboxymethylation to increase anionic characters enhanced the emulsion stabilization capacity of GGM, but not that of GX. Investigating flow behaviors of emulsions indicated that hemicelluloses primarily stabilize emulsions by adsorption of insoluble particles, as their flow behaviors were similar to those of cellulose nanocrystals rather than those of soluble celluloses. Understanding the impact of the variations in composition and properties of hemicellulose stabilizers to stabilize emulsions allows tailoring of their recovery processes to obtain desirable hydrocolloids for different applications.Peer reviewe

Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities

Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO2 production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea

Dataset for: Fast simulations of multidimensional NMR spectra of proteins and peptides

To simulate full multidimensional NMR spectra of peptides and proteins in a reasonable time frame, a strategy for separating the time-consuming full-density matrix calculations from the chemical shift prediction and calculation of coupling patterns is presented. The simulation setup uses SIMPSON to calculate TOCSY transfer amplitudes and average distances as a source for NOESY transfer amplitudes. Simulated ¹H 1D, 2D TOCSY, and 2D NOESY NMR spectra of peptides with sequence PAGYN and NFGAIL and of ubiquitin are presented. In all cases, the simulations lasted from a few seconds to tens of seconds on a normal laptop computer

Core Scientific Dataset Model: A lightweight and portable model and file format for multi-dimensional scientific data

International audienceThe Core Scientific Dataset (CSD) model with JavaScript Object Notation (JSON) serialization is presented as a lightweight, portable, and versatile standard for intra-and interdisciplinary scientific data exchange. This model supports datasets with a p-component dependent variable, {U 0 ,. .. , U q ,. .. , U p 1 }, discretely sampled at M unique points in a d-dimensional independent variable (X 0 ,. .. X k ,. .. X d 1) space. Moreover, this sampling is over an orthogonal grid, regular or rectilinear, where the principal coordinate axes of the grid are the independent variables. It can also hold correlated datasets assuming the different physical quantities (dependent variables) are sampled on the same orthogonal grid of independent variables. The model encapsulates the dependent variables' sampled data values and the minimum metadata needed to accurately represent this data in an appropriate coordinate system of independent variables. The CSD model can serve as a re-usable building block in the development of more sophisticated portable scientific dataset file standards