The Edinburgh human metabolic network reconstruction and its functional analysis

A better understanding of human metabolism and its relationship with diseases is an important task in human systems biology studies. In this paper, we present a high-quality human metabolic network manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from literature. The network contains nearly 3000 metabolic reactions, which were reorganized into about 70 human-specific metabolic pathways according to their functional relationships. By analysis of the functional connectivity of the metabolites in the network, the bow-tie structure, which was found previously by structure analysis, is reconfirmed. Furthermore, the distribution of the disease related genes in the network suggests that the IN (substrates) subset of the bow-tie structure has more flexibility than other parts

Spin 3 cubic vertices in a frame-like formalism

Till now most of the results on interaction vertices for massless higher spin fields were obtained in a metric-like formalism using completely symmetric (spin-)tensors. In this, the Lagrangians turn out to be very complicated and the main reason is that the higher the spin one want to consider the more derivatives one has to introduce. In this paper we show that such investigations can be greatly simplified if one works in a frame-like formalism. As an illustration we consider massless spin 3 particle and reconstruct a number of vertices describing its interactions with lower spin 2, 1 and 0 ones. In all cases considered we give explicit expressions for the Lagrangians and gauge transformations and check that the algebra of gauge transformations is indeed closed.Comment: 17 pades, no figure

Higher spin interactions with scalar matter on constant curvature spacetimes: conserved current and cubic coupling generating functions

Cubic couplings between a complex scalar field and a tower of symmetric tensor gauge fields of all ranks are investigated on any constant curvature spacetime of dimension d>2. Following Noether's method, the gauge fields interact with the scalar field via minimal coupling to the conserved currents. A symmetric conserved current, bilinear in the scalar field and containing up to r derivatives, is obtained for any rank r from its flat spacetime counterpart in dimension d+1, via a radial dimensional reduction valid precisely for the mass-square domain of unitarity in (anti) de Sitter spacetime of dimension d. The infinite collection of conserved currents and cubic vertices are summarized in a compact form by making use of generating functions and of the Weyl/Wigner quantization on constant curvature spaces.Comment: 35+1 pages, v2: two references added, typos corrected, enlarged discussions in Subsection 5.2 and in Conclusion, to appear in JHE

Asymptotic W-symmetries in three-dimensional higher-spin gauge theories

We discuss how to systematically compute the asymptotic symmetry algebras of generic three-dimensional bosonic higher-spin gauge theories in backgrounds that are asymptotically AdS. We apply these techniques to a one-parameter family of higher-spin gauge theories that can be considered as large N limits of SL(N) x SL(N) Chern-Simons theories, and we provide a closed formula for the structure constants of the resulting infinite-dimensional non-linear W-algebras. Along the way we provide a closed formula for the structure constants of all classical W_N algebras. In both examples the higher-spin generators of the W-algebras are Virasoro primaries. We eventually discuss how to relate our basis to a non-primary quadratic basis that was previously discussed in literature.Comment: 61 page

Classical integrability and quantum aspects of the AdS(3) x S(3) x S(3) x S(1) superstring

In this paper we continue the investigation of aspects of integrability of the type IIA AdS(3) x S(3) x S(3) x S(1) and AdS(3) x S(3) x T(4) superstrings. By constructing a one parameter family of flat connections we prove that the Green-Schwarz string is classically integrable, at least to quadratic order in fermions, without fixing the kappa-symmetry. We then compare the quantum dispersion relation, fixed by integrability up to an unknown interpolating function h(lambda), to explicit one-loop calculations on the string worldsheet. For AdS(3) x S(3) x S(3) x S(1) the spectrum contains heavy, as well as light and massless modes, and we find that the one-loop contribution differs depending on how we treat these modes showing that similar regularization ambiguities as appeared in AdS(4)/CFT(3) occur also here.Comment: 29 pages; v2: updated references and acknowledgmen

Anaerobic utilization of pectinous substrates at extremely haloalkaline conditions by Natranaerovirga pectinivora gen. nov., sp. nov., and Natranaerovirga hydrolytica sp. nov., isolated from hypersaline soda lakes

Anaerobic enrichments at pH 10, with pectin and polygalacturonates as substrates and inoculated with samples of sediments of hypersaline soda lakes from the Kulunda Steppe (Altai, Russia) demonstrated the potential for microbial pectin degradation up to soda-saturating conditions. The enrichments resulted in the isolation of six strains of obligately anaerobic fermentative bacteria, which represented a novel deep lineage within the order Clostridiales loosely associated with the family Lachnospiraceae. The isolates were rod-shaped and formed terminal round endospores. One of the striking features of the novel group is a very narrow substrate spectrum for growth, restricted to galacturonic acid and its polymers (e.g. pectin). Acetate and formate were the final fermentation products. Growth was possible in a pH range from 8 to 10.5, with an optimum at pH 9.5–10, and in a salinity range from 0.2 to 3.5 M Na+. On the basis of unique phenotypic properties and distinct phylogeny, the pectinolytic isolates are proposed to be assigned to a new genus Natranaerovirga with two species N. hydrolytica (APP2T=DSM24176T=UNIQEM U806T) and N. pectinivora (AP3T=DSM24629T=UNIQEM U805T)

Maxwell-like Lagrangians for higher spins

We show how implementing invariance under divergence-free gauge transformations leads to a remarkably simple Lagrangian description of massless bosons of any spin. Our construction covers both flat and (A)dS backgrounds and extends to tensors of arbitrary mixed-symmetry type. Irreducible and traceless fields produce single-particle actions, while whenever trace constraints can be dispensed with the resulting Lagrangians display the same reducible, multi-particle spectra as those emerging from the tensionless limit of free open-string field theory. For all explored options the corresponding kinetic operators take essentially the same form as in the spin-one, Maxwell case.Comment: 77 pages, revised version. Erroneous interpretation and proof of the gauge-fixing procedure for mixed-symmetry fields corrected. As a consequence, the mixed-symmetry, one-particle Lagrangians are to be complemented with conditions on the divergences of the fields; all other conclusions unchanged. Additional minor changes including references added. To appear in JHE

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art ‘meta-omic’ techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments

Half-integer Higher Spin Fields in (A)dS from Spinning Particle Models

We make use of O(2r+1) spinning particle models to construct linearized higher-spin curvatures in (A)dS spaces for fields of arbitrary half-integer spin propagating in a space of arbitrary (even) dimension: the field potentials, whose curvatures are computed with the present models, are spinor-tensors of mixed symmetry corresponding to Young tableaux with D/2 - 1 rows and r columns, thus reducing to totally symmetric spinor-tensors in four dimensions. The paper generalizes similar results obtained in the context of integer spins in (A)dS.Comment: 1+18 pages; minor changes in the notation, references updated. Published versio

Strings in AdS_4 x CP^3: finite size spectrum vs. Bethe Ansatz

We compute the first curvature corrections to the spectrum of light-cone gauge type IIA string theory that arise in the expansion of $AdS_4\times \mathbb{CP}^3$ about a plane-wave limit. The resulting spectrum is shown to match precisely, both in magnitude and degeneration that of the corresponding solutions of the all-loop Gromov--Vieira Bethe Ansatz. The one-loop dispersion relation correction is calculated for all the single oscillator states of the theory, with the level matching condition lifted. It is shown to have all logarithmic divergences cancelled and to leave only a finite exponentially suppressed contribution, as shown earlier for light bosons. We argue that there is no ambiguity in the choice of the regularization for the self-energy sum, since the regularization applied is the only one preserving unitarity. Interaction matrices in the full degenerate two-oscillator sector are calculated and the spectrum of all two light magnon oscillators is completely determined. The same finite-size corrections, at the order 1/J, where $J$ is the length of the chain, in the two-magnon sector are calculated from the all loop Bethe Ansatz. The corrections obtained by the two completely different methods coincide up to the fourth order in $\lambda' =\lambda/J^2$. We conjecture that the equivalence extends to all orders in $\lambda$ and to higher orders in 1/J.Comment: 32 pages. Published version; journal reference adde