Picosecond time-resolved energy transfer within C-phycocyanin aggregates of Mastigocladus laminosus

We have investigated by picosecond absorption experiments how the size of C-phycocyanin aggregates from Mastigocladus laminosus influences the excitation energy transfer kinetics. Going from C-phycocyanin monomers to trimers the lifetime of the faster energy transfer component decreased from 57 ± 4 to 27 ± 4 ps over most of the wavelength range (580–645 nm) studied. This change was interpreted as the opening of fast transfer channels (α-84 → β-84 and/or β-84 → β-84) between two adjacent monomers in the trimeric unit. The 57 ps lifetime is probably due mainly to the β-155 → β-84 energy transfer step. The intermediate lifetime decreased from about 300 ps in the monomer to 100–120 ps in the trimer. The former is believed to be dominated by the equilibration process α-84 a3 β-84, while the latter probably represents the time required for the excitation energy to reach thermodynamic equilibrium within the trimer. The lifetime of the longest components was about 1 ns in both systems. This indicates that the chromophores in these C-phycocyanin complexes are more exposed to non-radiative processes (like, for instance, isomerization) compared to the chromophores in intact phycobilisomes, where this lifetime typically is about 1.8 ns. The anisotropy relaxation closely followed the isotropic lifetimes in both systems. The anisotropy after the initial fast relaxation, r(∞), was 0.29 ± 0.04 in monomers and decreased to 0.15 ± 0.03 in trimers. Measurements of the steady-state fluorescence excitation anisotropy gave the same results within the experimental error

A parallel multistate framework for atomistic non-equilibrium reaction dynamics of solutes in strongly interacting organic solvents

We describe a parallel linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM. Forces are obtained using the Hellman-Feynmann relationship, giving continuous gradients, and excellent energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to CCSD(T)-F12 electronic structure theory, we built a 64-state MS-EVB model designed to study the F + CD3CN -> DF + CD2CN reaction in CD3CN solvent. This approach allows us to build a reactive potential energy surface (PES) whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We use our PES to run MD simulations, and examine a range of transient observables which follow in the wake of reaction, including transient spectra of the DF vibrational band, time dependent profiles of vibrationally excited DF in CD3CN solvent, and relaxation rates for energy flow from DF into the solvent, all of which agree well with experimental observations. Immediately following deuterium abstraction, the nascent DF is in a non-equilibrium regime in two different respects: (1) it is highly excited, with ~23 kcal mol-1 localized in the stretch; and (2) not yet Hydrogen bonded to the CD3CN solvent, its microsolvation environment is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of its microsolvation environment results in a red shift. These two competing effects result in a post-reaction relaxation profile distinct from that observed when DF vibration excitation occurs within an equilibrium microsolvation environment. The parallel software framework presented in this paper should be more broadly applicable to a range of complex reactive systems.Comment: 58 pages and 29 Figure

The metabolic syndrome adds utility to the prediction of mortality over its components: The Vietnam Experience Study

Background\ud The metabolic syndrome increases mortality risk. However, as “non-affected” individuals may still have up to two risk factors, the utility of using three or more components to identify the syndrome, and its predictive advantage over individual components have yet to be determined.\ud \ud Methods\ud Participants, male Vietnam-era veterans (n = 4265) from the USA, were followed-up from 1985/1986 for 14.7 years (61,498 person-years), and all-cause and cardiovascular disease deaths collated. Cox's proportional-hazards regression was used to assess the effect of the metabolic syndrome and its components on mortality adjusting for a wide range of potential confounders.\ud \ud Results\ud At baseline, 752 participants (17.9%) were identified as having metabolic syndrome. There were 231 (5.5%) deaths from all-causes, with 60 from cardiovascular disease. After adjustment for a range of covariates, the metabolic syndrome increased the risk of all-cause, HR 2.03, 95%CI 1.52, 2.71, and cardiovascular disease mortality, HR 1.92, 95%CI 1.10, 3.36. Risk increased dose-dependently with increasing numbers of components. The increased risk from possessing only one or two components was not statistically significant. The adjusted risk for four or more components was greater than for only three components for both all-cause, HR 2.30, 95%CI 1.45, 3.66 vs. HR 1.70, 95%CI 1.11, 2.61, and cardiovascular disease mortality, HR 3.34, 95%CI 1.19, 9.37 vs. HR 2.81, 95%CI 1.07, 7.35. The syndrome was more informative than the individual components for all-cause mortality, but could not be assessed for cardiovascular disease mortality due to multicollinearity. Hyperglycaemia was the individual strongest parameter associated with mortality.\ud \u

Thromboinflammatory changes in plasma proteome of pregnant women with PCOS detected by quantitative label-free proteomics

Polycystic ovary syndrome (PCOS) is the most common endocrinological disorder of fertile-aged women. Several adverse pregnancy outcomes and abnormalities of the placenta have been associated with PCOS. By using quantitative label-free proteomics we investigated whether changes in the plasma proteome of pregnant women with PCOS could elucidate the mechanisms behind the pathologies observed in PCOS pregnancies. A total of 169 proteins with >= 2 unique peptides were detected to be differentially expressed between women with PCOS (n = 7) and matched controls (n = 20) at term of pregnancy, out of which 35 were significant (p-value <0.05). A pathway analysis revealed that networks related to humoral immune responses, inflammatory responses, cardiovascular disease and cellular growth and proliferation were affected by PCOS. Classification of cases and controls was carried out using principal component analysis, orthogonal projections on latent structure-discriminant analysis (OPLS-DA), hierarchical clustering, self-organising maps and ROC-curve analysis. The most significantly enriched proteins in PCOS were properdin and insulin-like growth factor II. In the dataset, properdin had the best predictive accuracy for PCOS (AUC=1). Additionally, properdin abundances correlated with AMH levels in pregnant women.Peer reviewe

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius.IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities

Tri-critical point and suppression of the Shastry-Sutherland phase in Ce2_{2}Pd2_{2}Sn by Ni doping

Structural, magnetization and heat capacity measurements were performed on Ce$_2$(Pd$_{1-x}$Ni$_x$)$_2$Sn ($0 \leq x \leq 0.25$) alloys, covering the full range of the Mo$_2$FeB$_2$ structure stability. In this system, the two transitions observed in Ce$_2$Pd$_2$Sn (at $T_N=4.8$\,K and $T_C=2.1$\,K respectively) converge into a tri-critical point at $T_{cr}\approx 3.4$\,K for $x\approx 0.3$, where the intermediate antiferromagnetic AF phase is suppressed. The $T_N(x)$ phase boundary decrease is due to an incipient Kondo screening of the Ce-4f moments and local atomic disorder in the alloy. Both mechanisms affect the formation of Ce-magnetic dimers on which the Shastry-Sutherland lattice (SSL) builds up. On the contrary, the $T_C(x)$ transition to the ferromagnetic ground state increases as a consequence of the weakening of the AF-SSL phase. Applied magnetic field also suppresses the AF phase like in the stoichiometric compound.Comment: 6 pages, 8 figure

On the minimum transport required to passively suppress runaway electrons in SPARC disruptions

In [V.A. Izzo et al 2022 Nucl. Fusion 62 096029], state-of-the-art modeling of thermal and current quench (CQ) MHD coupled with a self-consistent evolution of runaway electron (RE) generation and transport showed that a non-axisymmetric (n = 1) in-vessel coil could passively prevent RE beam formation during disruptions in SPARC, a compact high-field tokamak projected to achieve a fusion gain Q > 2 in DT plasmas. However, such suppression requires finite transport of REs within magnetic islands and re-healed flux surfaces; conservatively assuming zero transport in these regions leads to an upper bound of RE current ~1 MA compared to ~8.7 MA of pre-disruption plasma current. Further investigation finds that core-localized electrons, within r/a < 0.3 and with kinetic energies 0.2-15 MeV, contribute most to the RE plateau formation. Yet only a relatively small amount of transport, i.e. a diffusion coefficient ~18 $\mathrm{m^2/s}$, is needed in the core to fully mitigate these REs. Properly accounting for (i) the CQ electric field's effect on RE transport in islands and (ii) the contribution of significant RE currents to disruption MHD may help achieve this

Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway

Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies