Observation of two-orbital spin-exchange interactions with ultracold SU(N)-symmetric fermions

We report on the direct observation of spin-exchanging interactions in a two-orbital SU(N)-symmetric quantum gas of ytterbium in an optical lattice. The two orbital states are represented by two different (meta-)stable electronic configurations of fermionic Yb-173. A strong spin-exchange between particles in the two separate orbitals is mediated by the contact interaction between atoms, which we characterize by clock shift spectroscopy in a 3D optical lattice. We find the system to be SU(N)-symmetric within our measurement precision and characterize all relevant scattering channels for atom pairs in combinations of the ground and the excited state. Elastic scattering between the orbitals is dominated by the antisymmetric channel, which leads to the strong spin-exchange coupling. The exchange process is directly observed, by characterizing the dynamic equilibration of spin imbalances between two large ensembles in the two orbital states, as well as indirectly in atom pairs via interaction shift spectroscopy in a 3D lattice. The realization of a stable SU(N)-symmetric two-orbital Hubbard Hamiltonian opens the route towards experimental quantum simulation of condensed-matter models based on orbital interactions, such as the Kondo lattice model.Comment: Correction: In the original version of this preprint the assignment of states with symmetric electronic wavefunction (|eg+>) and with antisymmetric electronic wavefunction (|eg->) to the observed spectral lines was inverted. This has been corrected in the current version. The results of the paper remain unchanged, with the exchange coupling being inverted to a ferromagnetic exchang

Observation of an orbital interaction-induced Feshbach resonance in 173-Yb

We report on the experimental observation of a novel inter-orbital Feshbach resonance in ultracold 173-Yb atoms, which opens the possibility of tuning the interactions between the 1S0 and 3P0 metastable state, both possessing vanishing total electronic angular momentum. The resonance is observed at experimentally accessible magnetic field strengths and occurs universally for all hyperfine state combinations. We characterize the resonance in the bulk via inter-orbital cross-thermalization as well as in a three-dimensional lattice using high-resolution clock-line spectroscopy.Comment: 5 pages, 4 figure

Enzymatic reduction and oxidation of fibre-bound azo-dyes

A new customer and environmental friendly method of hair bound dye decolouration was developed. Biotransformation of the azo-dyes Flame Orange and Ruby Red was studied using different oxidoreductases. The pathways of azo dye conversion by these enzymes were investigated and the intermediates and metabolites were identified and characterised using UV–vis spectroscopy, high-performance liquid chromatography (HPLC) and mass spectrometry (MS). Laccase from Pycnoporus cinnabarinus, manganese peroxidase (MnP) from Nematoloma frowardii and the novel Agrocybe aegerita peroxidase (AaP) were found to use a similar mechanism to convert azo dyes. They N-demethylated the dyes and concomitantly polymerized them to some extent. On the other hand the mechanism for cleavage of the azo bond by azo-reductases of Bacillus cereus and B. subtilis was based on reduction of the azo bond at the expense of NAD(P)H

Self-sustained enzymatic cascade for the production of 2, 5-furandicarboxylic acid from 5-methoxymethylfurfural

Background: 2, 5-Furandicarboxylic acid is a renewable building block for the production of polyfurandicarboxylates, which are biodegradable polyesters expected to substitute their classical counterparts derived from fossil resources. It may be produced from bio-based 5-hydroxymethylfurfural or 5-methoxymethylfurfural, both obtained by the acidic dehydration of biomass-derived fructose. 5-Methoxymethylfurfural, which is produced in the presence of methanol, generates less by-products and exhibits better storage stability than 5-hydroxymethylfurfural being, therefore, the industrial substrate of choice. Results: In this work, an enzymatic cascade involving three fungal oxidoreductases has been developed for the production of 2, 5-furandicarboxylic acid from 5-methoxymethylfurfural. Aryl-alcohol oxidase and unspecific peroxygenase act on 5-methoxymethylfurfural and its partially oxidized derivatives yielding 2, 5-furandicarboxylic acid, as well as methanol as a by-product. Methanol oxidase takes advantage of the methanol released for in situ producing H2O2 that, along with that produced by aryl-alcohol oxidase, fuels the peroxygenase reactions. In this way, the enzymatic cascade proceeds independently, with the only input of atmospheric O2, to attain a 70% conversion of initial 5-methoxymethylfurfural. The addition of some exogenous methanol to the reaction further improves the yield to attain an almost complete conversion of 5-methoxymethylfurfural into 2, 5-furandicarboxylic acid. Conclusions: The synergistic action of aryl-alcohol oxidase and unspecific peroxygenase in the presence of 5-methoxymethylfurfural and O2 is sufficient for the production of 2, 5-furandicarboxylic acid. The addition of methanol oxidase to the enzymatic cascade increases the 2, 5-furandicarboxylic acid yields by oxidizing a reaction by-product to fuel the peroxygenase reactions

The Using of Pseudomonas Cells for Bioremediation of Oil Contaminating Soils

The article describes results on the oxidation of crude-oil by bacteria of genus Pseudomonas: Ps. mendocina H-3, Ps. sp. H-7, Ps. stutzeri H-10, Ps. aeruginosa H-14, Ps. alcaligenes H-15 and Ps. sp. H-16. These microorganisms isolated from oil-contaminated soils in Kazakhstan were found to be capable of growing on crude oil components and oxidizing the hydrocarbons to different extent. Therefore, they may be useful for the bioremediation of oil-polluted soils and waters

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost andduringmushroomformation.The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation aremore highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics

Oxidoreductases on their way to industrial biotransformations

Fungi produce heme-containing peroxidases and peroxygenases, flavin-containing oxidases and dehydrogenases, and different copper-containing oxidoreductases involved in the biodegradation of lignin and other recalcitrant compounds. Heme peroxidases comprise the classical ligninolytic peroxidases and the new dye-decolorizing peroxidases, while heme peroxygenases belong to a still largely unexplored superfamily of heme-thiolate proteins. Nevertheless, basidiomycete unspecific peroxygenases have the highest biotechnological interest due to their ability to catalyze a variety of regio- and stereo-selective monooxygenation reactions with H2O2 as the source of oxygen and final electron acceptor. Flavo-oxidases are involved in both lignin and cellulose decay generating H2O2 that activates peroxidases and generates hydroxyl radical. The group of copper oxidoreductases also includes other H2O2 generating enzymes - copper-radical oxidases - together with classical laccases that are the oxidoreductases with the largest number of reported applications to date. However, the recently described lytic polysaccharide monooxygenases have attracted the highest attention among copper oxidoreductases, since they are capable of oxidatively breaking down crystalline cellulose, the disintegration of which is still a major bottleneck in lignocellulose biorefineries, along with lignin degradation. Interestingly, some flavin-containing dehydrogenases also play a key role in cellulose breakdown by directly/indirectly "fueling" electrons for polysaccharide monooxygenase activation. Many of the above oxidoreductases have been engineered, combining rational and computational design with directed evolution, to attain the selectivity, catalytic efficiency and stability properties required for their industrial utilization. Indeed, using ad hoc software and current computational capabilities, it is now possible to predict substrate access to the active site in biophysical simulations, and electron transfer efficiency in biochemical simulations, reducing in orders of magnitude the time of experimental work in oxidoreductase screening and engineering. What has been set out above is illustrated by a series of remarkable oxyfunctionalization and oxidation reactions developed in the frame of an intersectorial and multidisciplinary European RTD project. The optimized reactions include enzymatic synthesis of 1-naphthol, 25-hydroxyvitamin D3, drug metabolites, furandicarboxylic acid, indigo and other dyes, and conductive polyaniline, terminal oxygenation of alkanes, biomass delignification and lignin oxidation, among others. These successful case stories demonstrate the unexploited potential of oxidoreductases in medium and large-scale biotransformations

Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1

A Gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-FP) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. The organism, designated strain IF1, was identified as a member of the genus Arthrobacter on the basis of 16S ribosomal RNA gene sequence analysis. Arthrobacter strain IF1 was able to mineralize 4-FP up to concentrations of 5 mM in batch culture. Stoichiometric release of fluoride ions was observed, suggesting that there is no formation of halogenated dead-end products during 4-FP metabolism. The degradative pathway of 4-FP was investigated using enzyme assays and identification of intermediates by gas chromatography (GC), GC–mass spectrometry (MS), high-performance liquid chromatography, and liquid chromatography–MS. Cell-free extracts of 4-FP-grown cells contained no activity for catechol 1,2-dioxygenase or catechol 2,3-dioxygenase, which indicates that the pathway does not proceed through a catechol intermediate. Cells grown on 4-FP oxidized 4-FP, hydroquinone, and hydroxyquinol but not 4-fluorocatechol. During 4-FP metabolism, hydroquinone accumulated as a product. Hydroquinone could be converted to hydroxyquinol, which was further transformed into maleylacetic acid and β-ketoadipic acid. These results indicate that the biodegradation of 4-FP starts with a 4-FP monooxygenase reaction that yields benzoquinone, which is reduced to hydroquinone and further metabolized via the β-ketoadipic acid pathway

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide

Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register $\beta$-sheets, the primary structural component of amyloid fibrils, is a first step towards describing \emph{in vivo} protein aggregation and interactions between synthetic materials and proteins. Using all atom molecular simulations in implicit solvent we illustrate the effects of nanoparticle size, shape, and volume fraction on oligomer formation of an amyloidogenic peptide from the transthyretin protein. Surprisingly, we find that inert spherical crowding particles destabilize in-register $\beta$-sheets formed by dimers while stabilizing $\beta$-sheets comprised of trimers and tetramers. As the radius of the nanoparticle increases crowding effects decrease, implying smaller crowding particles have the largest influence on the earliest amyloid species. We explain these results using a theory based on the depletion effect. Finally, we show that spherocylindrical crowders destabilize the ordered $\beta$-sheet dimer to a greater extent than spherical crowders, which underscores the influence of nanoparticle shape on protein aggregation