Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates

Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log2 fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose

Charge and orbital order in half-doped manganites

An explanation is given for the charge order, orbital order and insulating state observed in half-doped manganese oxides, such as Nd$_{1/2}$Sr$_{1/2}$MnO$_{3}$. The competition between the kinetic energy of the electrons and the magnetic exchange energy drives the formation of effectively one-dimensional ferromagnetic zig-zag chains. Due to a topological phase factor in the hopping, the chains are intrinsically insulating and orbital-ordered. Most surprisingly, the strong Coulomb interaction between electrons on the same Mn-ion leads to the experimentally observed charge ordering. For doping less than 1/2 the system is unstable towards phase separation into a ferromagnetic metallic and charge-ordered insulating phase.Comment: To appear in Phys. Rev. Lett., 4 pages, 4 figure

Double-exchange via degenerate orbitals

We consider the double-exchange for systems in which doped electrons occupy degenerate orbitals, treating the realistic situation with double degenerate $e_g$ orbitals. We show that the orbital degeneracy leads in general to formation of anisotropic magnetic structures and that in particular, depending on the doping concentration, the layered magnetic structures of the A-type and chain-like structures of the C-type are stabilized. The phase-diagram that we obtain provides an explanation for the experimentally observed magnetic structures of some over-doped (electron-doped) manganites of the type Nd$_{1-x}$Sr$_x$MnO$_3$, Pr$_{1-x}$Sr$_x$MnO$_3$ and Sm$_{1-x}$Ca$_x$MnO$_3$ with $x > 0.5$.Comment: 4 pages, 1 figur

Laser Intensity Dependence of Photoassociation in Ultracold Metastable Helium

Photoassociation of spin-polarized metastable helium to the three lowest rovibrational levels of the J=1, $0_u^+$ state asymptoting to 2$s {}^{3}$S$_{1}+2p {}^{3}$P$_{0}$ is studied using a second-order perturbative treatment of the line shifts valid for low laser intensities, and two variants of a non-perturbative close-coupled treatment, one based upon dressed states of the matter plus laser system, and the other on a modified radiative coupling which vanishes asymptotically, thus simulating experimental conditions. These non-perturbative treatments are valid for arbitrary laser intensities and yield the complete photoassociation resonance profile. Both variants give nearly identical results for the line shifts and widths of the resonances and show that their dependence upon laser intensity is very close to linear and quadratic respectively for the two lowest levels. The resonance profiles are superimposed upon a significant background loss, a feature for this metastable helium system not present in studies of photoassociation in other systems, which is due to the very shallow nature of the excited state $0_u^+$ potential. The results for the line shifts from the close-coupled and perturbative calculations agree very closely at low laser intensities.Comment: 14 pages, 7 figures, title altered, text reduce

Cold collisions of OH and Rb. I: the free collision

We have calculated elastic and state-resolved inelastic cross sections for cold and ultracold collisions in the Rb($^1 S$) + OH($^2 \Pi_{3/2}$) system, including fine-structure and hyperfine effects. We have developed a new set of five potential energy surfaces for Rb-OH($^2 \Pi$) from high-level {\em ab initio} electronic structure calculations, which exhibit conical intersections between covalent and ion-pair states. The surfaces are transformed to a quasidiabatic representation. The collision problem is expanded in a set of channels suitable for handling the system in the presence of electric and/or magnetic fields, although we consider the zero-field limit in this work. Because of the large number of scattering channels involved, we propose and make use of suitable approximations. To account for the hyperfine structure of both collision partners in the short-range region we develop a frame-transformation procedure which includes most of the hyperfine Hamiltonian. Scattering cross sections on the order of $10^{-13}$ cm$^2$ are predicted for temperatures typical of Stark decelerators. We also conclude that spin orientation of the partners is completely disrupted during the collision. Implications for both sympathetic cooling of OH molecules in an environment of ultracold Rb atoms and experimental observability of the collisions are discussed.Comment: 20 pages, 16 figure

Non-inhibitory levels of oxygen during cultivation increase freeze-drying stress tolerance in Limosilactobacillus reuteri DSM 17938

The physiological effects of oxygen on Limosilactobacillus reuteri DSM 17938 during cultivation and the ensuing properties of the freeze-dried probiotic product was investigated. On-line flow cytometry and k-means clustering gating was used to follow growth and viability in real time during cultivation. The bacterium tolerated aeration at 500mL/min, with a growth rate of 0.74 +/- 0.13h(-1) which demonstrated that low levels of oxygen did not influence the growth kinetics of the bacterium. Modulation of the redox metabolism was, however, seen already at non-inhibitory oxygen levels by 1.5-fold higher production of acetate and 1.5-fold lower ethanol production. A significantly higher survival rate in the freeze-dried product was observed for cells cultivated in presence of oxygen compared to absence of oxygen (61.8%+/- 2.4% vs. 11.5%+/- 4.3%), coinciding with a higher degree of unsaturated fatty acids (UFA:SFA ratio of 10 for air sparged vs. 3.59 for N-2 sparged conditions.). Oxygen also resulted in improved bile tolerance and boosted 5 ' nucleotidase activity (370U/L vs. 240U/L in N-2 sparged conditions) but lower tolerance to acidic conditions compared bacteria grown under complete anaerobic conditions which survived up to 90min of exposure at pH 2. Overall, our results indicate the controlled supply of oxygen during production may be used as means for probiotic activity optimization of L. reuteri DSM 17938

Non-inhibitory levels of oxygen during cultivation increase freeze-drying stress tolerance in Limosilactobacillus reuteri DSM 17938

The physiological effects of oxygen on Limosilactobacillus reuteri DSM 17938 during cultivation and the ensuing properties of the freeze-dried probiotic product was investigated. On-line flow cytometry and k-means clustering gating was used to follow growth and viability in real time during cultivation. The bacterium tolerated aeration at 500 ml/min, with a growth rate of 0.74 ± 0.13 h-1 which demonstrated that low levels of oxygen did not influence the growth kinetics of the bacterium. Modulation of the redox metabolism was, however, seen already at non-inhibitory oxygen levels by 1.5-fold higher production of acetate and 1.5-fold lower ethanol production. A significantly higher survival rate in the freeze-dried product was observed for cells cultivated in presence of oxygen compared to absence of oxygen (61.8 ± 2.4 % vs 11.5 ± 4.3 %), coinciding with a higher degree of unsaturated fatty acids (UFA:SFA ratio of 10 for air sparged vs 3.59 for N2 sparged conditions.). Oxygen also resulted in improved bile tolerance and boosted 5’nucleotidase activity (370 U/L vs 240 U/L in N2 sparged conditions) but lower tolerance to acidic conditions compared bacteria grown under complete anaerobic conditions which survived up to 90 min of exposure at pH 2. Overall, our results indicate the controlled supply of oxygen during production may be used as means for probiotic activity optimisation of L. reuteri DSM 17938

de Sitter Supersymmetry Revisited

We present the basic $\mathcal{N} =1$ superconformal field theories in four-dimensional de Sitter space-time, namely the non-abelian super Yang-Mills theory and the chiral multiplet theory with gauge interactions or cubic superpotential. These theories have eight supercharges and are invariant under the full $SO(4,2)$ group of conformal symmetries, which includes the de Sitter isometry group $SO(4,1)$ as a subgroup. The theories are ghost-free and the anti-commutator $\sum_\alpha\{Q_\alpha, Q^{\alpha\dagger}\}$ is positive. SUSY Ward identities uniquely select the Bunch-Davies vacuum state. This vacuum state is invariant under superconformal transformations, despite the fact that de Sitter space has non-zero Hawking temperature. The $\mathcal{N}=1$ theories are classically invariant under the $SU(2,2|1)$ superconformal group, but this symmetry is broken by radiative corrections. However, no such difficulty is expected in the $\mathcal{N}=4$ theory, which is presented in appendix B.Comment: 21 pages, 2 figure

The D^{2k} R^4 Invariants of N=8 Supergravity

The existence of a linearized SUSY invariant for N=8 supergravity whose gravitational components are usually called R^4 was established long ago by on-shell superspace arguments. Superspace and string theory methods have also established analogous higher dimensional D^{2k} R^4 invariants. However, very little is known about the SUSY completions of these operators which involve other fields of the theory. In this paper we find the detailed component expansion of the linearized R^4 invariant starting from the corresponding superamplitude which generates all component matrix elements of the operator. It is then quite straightforward to extend results to the entire set of D^{2k} R^4 operators.Comment: 17 page

All-sky convolution for polarimetry experiments

We discuss all-sky convolution of the instrument beam with the sky signal in polarimetry experiments, such as the Planck mission which will map the temperature anisotropy and polarization of the cosmic microwave background (CMB). To account properly for stray light (from e.g. the galaxy, sun, and planets) in the far side-lobes of such an experiment, it is necessary to perform the beam convolution over the full sky. We discuss this process in multipole space for an arbitrary beam response, fully including the effects of beam asymmetry and cross-polarization. The form of the convolution in multipole space is such that the Wandelt-Gorski fast technique for all-sky convolution of scalar signals (e.g. temperature) can be applied with little modification. We further show that for the special case of a pure co-polarized, axisymmetric beam the effect of the convolution can be described by spin-weighted window functions. In the limits of a small angle beam and large Legendre multipoles, the spin-weight 2 window function for the linear polarization reduces to the usual scalar window function used in previous analyses of beam effects in CMB polarimetry experiments. While we focus on the example of polarimetry experiments in the context of CMB studies, we emphasise that the formalism we develop is applicable to anisotropic filtering of arbitrary tensor fields on the sphere.Comment: 8 pages, 1 figure; Minor changes to match version accepted by Phys. Rev.