Modelling of sawtooth-induced fast ion transport in positive and negative triangularity in TCV

Internal kinks are a common magneto hydro-dynamic (MHD) instability observed in tokamak operation when the q profile in the plasma core is close to unity. This MHD instability impacts both the transport of the bulk plasma (current, particle and energy transport) and minority species, such as fast ions. In TCV (R 0 /a = 0.88 m/0.25 m) the fast ion population is generated in the plasma by neutral beam tangential injection of energies up to 28 keV. TCV features 16 active shaping coils permitting a great flexibility in plasma shape, including negative triangularity (δ) configurations that show surprisingly high confinement. This study focuses on the transport of fast ions induced by sawteeth, by comparing two triangularity cases and simulation results with experimental data. Comparison of two equilibria with opposite δ shows that the fast ion drifts are larger for δ < 0. Furthermore, the sawtooth-induced transport in this case is larger than δ > 0 in similar conditions. Comparison with experimental data confirms the dominance of the modification of thermal kinetic profiles following the sawtooth crash in explaining drops in the neutron rates and FIDA signals. Additional fast ion diffusion, however, improves the interpretation of the experimental data. For δ < 0, the amplitude of the perturbation better representing the experimental data is larger. Finaly, an exploratory study for 50 keV particles (soon available in TCV) shows that the situation does not worsen for such particles.

Understanding the Surface Characteristics of Biochar and Its Catalytic Activity for the Hydrodeoxygenation of Guaiacol

Biochar (BCR) was obtained from the pyrolysis of a palm-oil-empty fruit bunch at 773 K for 2 h and used as a catalyst for the hydrodeoxygenation (HDO) of guaiacol (GUA) as a bio-oil model compound. Brunauer–Emmet–Teller surface area analysis, NH3 and CO2-temperature-programmed desorption, scanning electron microscope–dispersive X-ray spectroscopy, CHN analysis and X-ray fluorescence spectroscopy suggested that macroporous and mesoporous structures were formed in BCR with a co-presence of hydrophilic and hydrophobic sites and acid–base behavior. A combination of infrared, Raman and inelastic neutron scattering (INS) was carried out to achieve a complete vibrational assignment of BCR. The CH–OH ratio in BCR is ~5, showing that the hydroxyl functional groups are a minority species. There was no evidence for any aromatic C–H stretch modes in the infrared, but they are clearly seen in the INS and are the majority species, with a ratio of sp3–CH:sp2–CH of 1:1.3. The hydrogen bound to sp2–C is largely present as isolated C–H bonds, rather than adjacent C–H bonds. The Raman spectrum shows the characteristic G band (ideal graphitic lattice) and three D bands (disordered graphitic lattice, amorphous carbon, and defective graphitic lattice) of sp2 carbons. Adsorbed water in BCR is present as disordered layers on the surface rather than trapped in voids in the material and could be removed easily by drying prior to catalysis. Catalytic testing demonstrated that BCR was able to catalyze the HDO of GUA, yielding phenol and cresols as the major products. Phenol was produced both from the direct demethoxylation of GUA, as well as through the demethylation pathway via the formation of catechol as the intermediate followed by deoxygenation.

Emergent transcriptional adaption facilitates convergent succession within a synthetic community

Taxonomic convergence is common in bacterial communities but its underlying molecular mechanism remains largely unknown. We thus conducted a time-series transcriptional analysis of a convergent two-species synthetic community that grew in a closed broth-culture system. By analyzing the gene expression and monitoring the community structure, we found that gene expression mainly changed in the early stage, whereas community structure significantly changed in the late stage. The significant change of gene expression occurred even at the very beginning, which was designated as “0 h effect”, suggesting the effect of species interaction on gene expression was inevitable. Besides, the effect of interaction on gene expression has a “population effect”, which means that majority species have greater impact on gene expressions of minority species than vice versa. Furthermore, gene set enrichment analysis revealed that among a total of 63 unique pathways (occupying about 50% of all the metabolic pathways in both species), 40 (63%) were consistently suppressed, 16 (25%) were conditionally expressed, and only 7 (11%) were consistently activated. Overall, they were strictly regulated by both time and initial structures. Therefore, we proposed that microorganism responses and the induced gene expression changes play important roles in the process of community succession.

Ruminant Milk-Derived Extracellular Vesicles: A Nutritional and Therapeutic Opportunity?

Milk has been shown to contain a specific fraction of extracellular particles that are reported to resist digestion and are purposefully packaged with lipids, proteins, and nucleic acids to exert specific biological effects. These findings suggest that these particles may have a role in the quality of infant nutrition, particularly in the early phase of life when many of the foundations of an infant’s potential for health and overall wellness are established. However, much of the current research focuses on human or cow milk only, and there is a knowledge gap in how milk from other species, which may be more commonly consumed in different regions, could also have these reported biological effects. Our review provides a summary of the studies into the extracellular particle fraction of milk from a wider range of ruminants and pseudo-ruminants, focusing on how this fraction is isolated and characterised, the stability and uptake of the fraction, and the reported biological effects of these fractions in a range of model systems. As the individual composition of milk from different species is known to differ, we propose that the extracellular particle fraction of milk from non-traditional and minority species may also have important and distinct biological properties that warrant further study.

Sub-millisecond conformational transitions of short single-stranded DNA lattices by photon correlation single-molecule FRET

Thermally-driven conformational fluctuations (or 'breathing') of DNA plays important roles in the function and regulation of the 'macromolecular machinery of genome expression.' Fluctuations in double-stranded (ds) DNA are involved in the transient exposure of pathways to protein binding sites within the DNA framework, leading to the binding of functional and regulatory proteins to single-stranded (ss) DNA templates. These interactions often require that the ssDNA sequences, as well as the proteins involved, assume transient conformations critical for successful binding. Here we use microsecond-resolved single-molecule F&oumlrster Resonance Energy Transfer (smFRET) experiments to investigate the backbone fluctuations of short (ss) oligo- oligo(dT)n templates within DNA constructs that can also serve as models for ss-dsDNA junctions. Such junctions, as well as the attached ssDNA sequences, are involved in the binding of ssDNA binding (ssb) proteins that control and integrate the mechanisms of DNA replication complexes. We have used these data to determine multi-order time-correlation functions (TCFs) and probability distribution functions (PDFs) that characterize the kinetic and thermodynamic behavior of the system. We find that the oligo(dT)n tails of ss-dsDNA constructs inter-convert, on sub-millisecond time-scales, between three macrostates with distinctly different end-to-end distances. These are: (i) a 'compact' macrostate that represents the dominant species at equilibrium; (ii) a 'partially extended' macrostate that exists as a minority species; and (iii) a 'highly extended' macrostate that is present in trace amounts. We propose a model for ssDNA secondary structure that advances our understanding of how spontaneously formed nucleic acid conformations may facilitate the activities of ssDNA associating proteins.

The role of excitons in 3D and 2D lead halide perovskites

Excitons in lead halide perovskites often go unnoticed as minority species, yet they account for almost all of light emission.

Molecular recognition of S-nitrosothiol substrate by its cognate protein denitrosylase

Protein S-nitrosylation mediates a large part of nitric oxide's influence on cellular function by providing a fundamental mechanism to control protein function across different species and cell types. At steady state, cellular S-nitrosylation reflects dynamic equilibria between S-nitrosothiols (SNOs) in proteins and small molecules (low-molecular-weight SNOs) whose levels are regulated by dedicated S-nitrosylases and denitrosylases. S-Nitroso-CoA (SNO-CoA) and its cognate denitrosylases, SNO-CoA reductases (SCoRs), are newly identified determinants of protein S-nitrosylation in both yeast and mammals. Because SNO-CoA is a minority species among potentially thousands of cellular SNOs, SCoRs must preferentially recognize this SNO substrate. However, little is known about the molecular mechanism by which cellular SNOs are recognized by their cognate enzymes. Using mammalian cells, molecular modeling, substrate-capture assays, and mutagenic analyses, we identified a single conserved surface Lys (Lys-127) residue as well as active-site interactions of the SNO group that mediate recognition of SNO-CoA by SCoR. Comparing SCoRK127Aversus SCoRWT HEK293 cells, we identified a SNO-CoA–dependent nitrosoproteome, including numerous metabolic protein substrates. Finally, we discovered that the SNO-CoA/SCoR system has a role in mitochondrial metabolism. Collectively, our findings provide molecular insights into the basis of specificity in SNO-CoA–mediated metabolic signaling and suggest a role for SCoR-regulated S-nitrosylation in multiple metabolic processes.

Complete Genome Sequence of a Reference Stock of Simian Immunodeficiency Virus RNA (SIVmac251/32H/L28) Determined by Deep Sequencing

A reference preparation for simian immunodeficiency virus (SIV) RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats, including minority species, were determined. This information will inform SIV research investigations and aid evaluation and development of amplification assays for SIV RNA quantification.

Complete Genome Sequence of the WHO International Standard for HIV-2 RNA Determined by Deep Sequencing

The World Health Organization (WHO) International Standard for HIV-2 RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats (LTRs), including minority species, were assigned subtype A. This information will aid design, development, and evaluation of HIV-2 RNA amplification assays.