Magnetic ordering in GdNi2B2C revisited by resonant x-ray scattering: evidence for the double-q model

Recent theoretical efforts aimed at understanding the nature of antiferromagnetic ordering in GdNi2B2C predicted double-q ordering. Here we employ resonant elastic x-ray scattering to test this theory against the formerly proposed, single-q ordering scenario. Our study reveals a satellite reflection associated with a mixed-order component propagation wave vector, viz., (q_a,2q_b,0) with q_b = q_a approx= 0.55 reciprocal lattice units, the presence of which is incompatible with single-q ordering but is expected from the double-q model. A (3q_a,0,0) wave vector (i.e., third-order) satellite is also observed, again in line with the double-q model. The temperature dependencies of these along with that of a first-order satellite are compared with calculations based on the double-q model and reasonable qualitative agreement is found. By examining the azimuthal dependence of first-order satellite scattering, we show the magnetic order to be, as predicted, elliptically polarized at base temperature and find the temperature dependence of the "out of a-b plane" moment component to be in fairly good agreement with calculation. Our results provide qualitative support for the double-q model and thus in turn corroborate the explanation for the "magnetoelastic paradox" offered by this model.Comment: 8 pages, 5 figures. Submitted to Phys. Rev.

Genomic insights into the evolution of hybrid isoprenoid biosynthetic gene clusters in the MAR4 marine streptomycete clade

BackgroundConsiderable advances have been made in our understanding of the molecular genetics of secondary metabolite biosynthesis. Coupled with increased access to genome sequence data, new insight can be gained into the diversity and distributions of secondary metabolite biosynthetic gene clusters and the evolutionary processes that generate them. Here we examine the distribution of gene clusters predicted to encode the biosynthesis of a structurally diverse class of molecules called hybrid isoprenoids (HIs) in the genus Streptomyces. These compounds are derived from a mixed biosynthetic origin that is characterized by the incorporation of a terpene moiety onto a variety of chemical scaffolds and include many potent antibiotic and cytotoxic agents.ResultsOne hundred and twenty Streptomyces genomes were searched for HI biosynthetic gene clusters using ABBA prenyltransferases (PTases) as queries. These enzymes are responsible for a key step in HI biosynthesis. The strains included 12 that belong to the 'MAR4' clade, a largely marine-derived lineage linked to the production of diverse HI secondary metabolites. We found ABBA PTase homologs in all of the MAR4 genomes, which averaged five copies per strain, compared with 21 % of the non-MAR4 genomes, which averaged one copy per strain. Phylogenetic analyses suggest that MAR4 PTase diversity has arisen by a combination of horizontal gene transfer and gene duplication. Furthermore, there is evidence that HI gene cluster diversity is generated by the horizontal exchange of orthologous PTases among clusters. Many putative HI gene clusters have not been linked to their secondary metabolic products, suggesting that MAR4 strains will yield additional new compounds in this structure class. Finally, we confirm that the mevalonate pathway is not always present in genomes that contain HI gene clusters and thus is not a reliable query for identifying strains with the potential to produce HI secondary metabolites.ConclusionsWe found that marine-derived MAR4 streptomycetes possess a relatively high genetic potential for HI biosynthesis. The combination of horizontal gene transfer, duplication, and rearrangement indicate that complex evolutionary processes account for the high level of HI gene cluster diversity in these bacteria, the products of which may provide a yet to be defined adaptation to the marine environment

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

<p>Abstract</p> <p>Background</p> <p>Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR) relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model.</p> <p>Results</p> <p>We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of <it>Saccharomyces cerevisiae</it>.</p> <p>Conclusion</p> <p>The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.</p

Editorial: Towards a Unifying Pan-Arctic Perspective of the Contemporary and Future Arctic Ocean

An international symposium addressing pan-Arctic perspectives of the marine ecosystems of the Arctic Ocean took place in October 2017 and this editorial introduces the publications that derived from the conference. The symposium focused in particular upon physical forcing and biogeochemical cycling in surface waters of the Arctic Ocean, connectivity between surface and deep waters in the central basins and adjacent slopes and the ecology of the lesser-known shelf ecosystems. The symposium was the fourth in a sequence that has pan-Arctic integrations of Arctic Ocean ecosystems at its core. The series started in 2002 and its first volume was published under the title Structure and function of contemporary food webs on Arctic shelves (Wassmann, 2006). At the 2002-meeting, a suite of marine Arctic researchers from the main nations that work in the Arctic Ocean started applying the now-ubiquitous term pan-Arctic. The term underlined that the applied research goals and directions were more than a circumarctic perspective, but distinctly considered the entire expanse of the Arctic Ocean. Based upon this exercise, increased interest in the Arctic and some of the scientific endeavors of the 4th International Polar Year central projects and key oceanographers operating in the pan-Arctic region convened at the 2nd pan-Arctic integration symposium, entitled Arctic Marine Ecosystems in an Era of Rapid Climate Change in 2009 (Wassmann, 2011). After a decade of pan-Arctic research and building upon the foundation presented in Wassmann (2006, 2011) a 3rd conference was initiated in 2012, entitled Overarching perspectives of contemporary and future ecosystems in the Arctic Ocean (Wassmann, 2015). This Research Topic brings together 13 publications from the 4th pan-arctic integration symposium held in 2017, entitled Toward a Unifying Pan-Arctic Perspective of the Contemporary and Future Arctic Ocean. We, the editors of the Research Topic, are delighted with the breadth, quality and diversity of the papers. We introduce the essence of the publications under three, summarizing headlines • Physical connectivity, yet regionality • What shapes pan-Arctic primary production • The fate of production. Toward the end we incorporate the knowledge presented in this volume into the overall progress. and status of pan-Arctic marine ecosystem integration that has been achieved, so far, through the four pan-Arctic integration symposia

An axisymmetric time-domain spectral-element method for full-wave simulations: Application to ocean acoustics

The numerical simulation of acoustic waves in complex 3D media is a key topic in many branches of science, from exploration geophysics to non-destructive testing and medical imaging. With the drastic increase in computing capabilities this field has dramatically grown in the last twenty years. However many 3D computations, especially at high frequency and/or long range, are still far beyond current reach and force researchers to resort to approximations, for example by working in 2D (plane strain) or by using a paraxial approximation. This article presents and validates a numerical technique based on an axisymmetric formulation of a spectral finite-element method in the time domain for heterogeneous fluid-solid media. Taking advantage of axisymmetry enables the study of relevant 3D configurations at a very moderate computational cost. The axisymmetric spectral-element formulation is first introduced, and validation tests are then performed. A typical application of interest in ocean acoustics showing upslope propagation above a dipping viscoelastic ocean bottom is then presented. The method correctly models backscattered waves and explains the transmission losses discrepancies pointed out in Jensen et al. (2007). Finally, a realistic application to a double seamount problem is considered.Comment: Added a reference, and fixed a typo (cylindrical versus spherical

ZAC in GtoPdb v.2023.1

The zinc-activated channel (ZAC, nomenclature as agreed by the NC-IUPHAR Subcommittee for the Zinc Activated Channel) is a member of the Cys-loop family that includes the nicotinic ACh, 5-HT3, GABAA and strychnine-sensitive glycine receptors [2, 3, 5]. The channel is likely to exist as a homopentamer of 4TM subunits that form an intrinsic cation selective channel equipermeable to Na+, K+ and Cs+, but impermeable to Ca2+ and Mg2+ [5]. ZAC displays constitutive activity that can be blocked by tubocurarine, TTFB and high concentrations of Ca2+ [5]. Although denoted ZAC, the channel is more potently activated by H+ and Cu2+, with greater and lesser efficacy than Zn2+, respectively [5]. Orthologs of the human ZACN gene are present in a wide range of mammalian genomes, but notably not in the mouse or rat genomes. [2, 3]

ZAC in GtoPdb v.2021.3

The zinc-activated channel (ZAC, nomenclature as agreed by the NC-IUPHAR Subcommittee for the Zinc Activated Channel) is a member of the Cys-loop family that includes the nicotinic ACh, 5-HT3, GABAA and strychnine-sensitive glycine receptors [2, 3, 4]. The channel is likely to exist as a homopentamer of 4TM subunits that form an intrinsic cation selective channel equipermeable to Na+, K+ and Cs+, but impermeable to Ca2+ and Mg2+ [4]. ZAC displays constitutive activity that can be blocked by tubocurarine and high concentrations of Ca2+ [4]. Although denoted ZAC, the channel is more potently activated by H+ and Cu2+, with greater and lesser efficacy than Zn2+, respectively [4]. ZAC is present in the human, chimpanzee, dog, cow and opossum genomes, but is functionally absent from mouse, or rat, genomes [2, 3]

ZAC (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database

The zinc-activated channel (ZAC, nomenclature as agreed by the NC-IUPHAR Subcommittee for the Zinc Activated Channel) is a member of the Cys-loop family that includes the nicotinic ACh, 5-HT3, GABAA and strychnine-sensitive glycine receptors [1, 2, 3]. The channel is likely to exist as a homopentamer of 4TM subunits that form an intrinsic cation selective channel equipermeable to Na+, K+ and Cs+, but impermeable to Ca2+ and Mg2+ [3]. ZAC displays constitutive activity that can be blocked by tubocurarine and high concentrations of Ca2+ [3]. Although denoted ZAC, the channel is more potently activated by protons and copper, with greater and lesser efficacy than zinc, respectively [3]. ZAC is present in the human, chimpanzee, dog, cow and opossum genomes, but is functionally absent from mouse, or rat, genomes [1, 2]

Water Defluoridation: Nanofiltration vs Membrane Distillation

Nowadays, fluoride contamination of drinking water is a major problem for various countries, because high concentrations of fluoride pose a risk of dental and skeletal fluorosis. Over past years, membrane nanofiltration (NF) has been proposed as convenient defluoridation technology. However, NF cannot be applied to water systems with high fluoride concentration, and the disposal of the membrane concentrate remains an issue. In this work, we compared a commercial polyester NF membrane and a polypropylene hollow-fiber membrane distillation (MD) module for their ability to remove fluoride ions from water in the presence of hardness ions and organic fouling agents. The NF membrane can offer more than 10 times higher water productivity than MD, under realistic gradients of temperature and pressure, respectively. Despite that, after reaching a concentration factor of about 3, fouling and scaling caused the flux to drop to about 80% with respect to its initial value. Moreover, F- retention decreased from 90% to below 80%, thus providing a permeate of scarce quality. MD was operated in the direct-contact mode on a polypropylene hollow-fiber membrane, which was charged with a hot feed flow (average T = 58 °C) on one side and a cooled (20 °C) permeate flow of distilled water on the other side. The concentration of fluoride ions in the permeate was always below the detection limit of our electrode (0.2 ppm), regardless of the fluoride concentration in the feed. Moreover, the MD module showed higher resistance to fouling and scaling than NF, and CaF2 crystals were recovered from the MD concentrate after cooling. These results suggest that the synergic combination of the two techniques might be beneficial for the purification of fluoride-contaminated water systems: MD can be used to further concentrate the NF retentate, thus producing high-purity water and recovering CaF2 crystals.Fil: Moran Ayala, Lucia Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Paquet, Marie. University of Aalborg; DinamarcaFil: Janowska, Katarzyna. University of Aalborg; DinamarcaFil: Jamard, Paul. University of Aalborg; DinamarcaFil: Quist Jensen, Cejna A.. University of Aalborg; DinamarcaFil: Bosio, Gabriela Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Martire, Daniel Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Fabbri, Debora. Università di Torino; ItaliaFil: Boffa, Vittorio. University of Aalborg; Dinamarc

On the nature of nuclear dissipation, as a hallmark for collective dynamics at finite excitation

We study slow collective motion of isoscalar type at finite excitation. The collective variable is parameterized as a shape degree of freedom and the mean field is approximated by a deformed shell model potential. We concentrate on situations of slow motion, as guaranteed, for instance, by the presence of a strong friction force, which allows us to apply linear response theory. The prediction for nuclear dissipation of some models of internal motion are contrasted. They encompass such opposing cases as that of pure independent particle motion and the one of "collisional dominance". For the former the wall formula appears as the macroscopic limit, which is here simulated through Strutinsky smoothing procedures. It is argued that this limit hardly applies to the actual nuclear situation. The reason is found in large collisional damping present for nucleonic dynamics at finite temperature $T$. The level structure of the mean field as well as the $T$-dependence of collisional damping determine the $T$-dependence of friction. Two contributions are isolated, one coming from real transitions, the other being associated to what for infinite matter is called the "heat pole". The importance of the latter depends strongly on the level spectrum of internal motion, and thus is very different for "adiabatic" and "diabatic" situations, both belonging to different degrees of "ergodicity".Comment: 50 pages plus 10 figures, uuencoded postscript file