Combined in silico and 19F NMR analysis of 5-fluorouracil metabolism in yeast at low ATP conditions.

The cytotoxic effect of 5-fluorouracil (5-FU) on yeast cells is thought to be mainly via a misincorporation of fluoropyrimidines into both RNA and DNA, not only DNA damage via inhibition of thymidylate synthase (TYMS) by fluorodeoxyuridine monophosphate (FdUMP). However, some studies on Saccharomyces cerevisiae show a drastic decrease in ATP concentration under oxidative stress, together with a decrease in concentration of other tri- and diphosphates. This raises a question if hydrolysis of 5-fluoro-2-deoxyuridine diphosphate (FdUDP) under oxidative stress could not lead to the presence of FdUMP and the activation of so-called ‘thymine-less death’ route. We attempted to answer this question with in silico modeling of 5-FU metabolic pathways, based on new experimental results, where the stages of intracellular metabolism of 5-FU in Saccharomyces cerevisiae were tracked by a combination of 19F and 31P NMR spectroscopic study. We have identified 5-FU, its nucleosides and nucleotides, and subsequent di- and/or triphosphates. Additionally, another wide 19F signal, assigned to fluorinated unstructured short RNA, has been also identified in the spectra. The concentration of individual metabolites was found to vary substantially within hours,however,theinitialsteady-statewaspreservedonlyforanhour,untiltheATPconcentration dropped by a half, which was monitored independently via 31P NMR spectra. After that, the catabolic process leading from triphosphates through monophosphates and nucleosides back to 5-FU was observed. These results imply careful design and interpretation of studies in 5-FU metabolism in yeast

Lie superalgebras and irreducibility of A_1^(1)-modules at the critical level

We introduce the infinite-dimensional Lie superalgebra ${\mathcal A}$ and construct a family of mappings from certain category of ${\mathcal A}$-modules to the category of A_1^(1)-modules of critical level. Using this approach, we prove the irreducibility of a family of A_1^(1)-modules at the critical level. As a consequence, we present a new proof of irreducibility of certain Wakimoto modules. We also give a natural realizations of irreducible quotients of relaxed Verma modules and calculate characters of these representations.Comment: 21 pages, Late

Hox-controlled reorganisation of intrasegmental patterning cues underlies Drosophila posterior spiracle organogenesis

10 páginas, 8 figuras. Material complementario del artículo esta disponible en http://dev.biologists.org/cgi/content/full/132/13/3093/DC1Hox proteins provide axial positional information and control segment morphology in development and evolution. Yet how they specify morphological traits that confer segment identity and how axial positional information interferes with intrasegmental patterning cues during organogenesis remain poorly understood. We have investigated the control of Drosophila posterior spiracle morphogenesis, a segment-specific structure that forms under Abdominal-B (AbdB) Hox control in the eighth abdominal segment (A8). We show that the Hedgehog (Hh), Wingless (Wg) and Epidermal Growth Factor Receptor (Egfr) pathways provide specific inputs for posterior spiracle morphogenesis and act in a genetic network made of multiple and rapidly evolving Hox/signalling interplays. A major function of AbdB during posterior spiracle organogenesis is to reset A8 intrasegmental patterning cues, first by reshaping wg and rhomboid expression patterns, then by reallocating the Hh signal and later by initiating de novo expression of the posterior compartment gene engrailed in anterior compartment cells. These changes in expression patterns confer axial specificity to otherwise reiteratively used segmental patterning cues, linking intrasegmental polarity and acquisition of segment identity.This work was supported by the `Centre National de la Recherche Scientifique' (CNRS), grants from `la Ligue Nationale Contre Le Cancer (équipe labellisée La Ligue)', `l'Association pour la Recherche contre le Cancer' (ARC), The Royal Society, The Welcome Trust, the `Minesterio de education y ciencia (BFU 2004 0 96) and ARC and EMBO long term fellowships to S. Merabet.Peer reviewe

Cyclotomic Gaudin models: construction and Bethe ansatz

This is a pre-copyedited author produced PDF of an article accepted for publication in Communications in Mathematical Physics, Benoit, V and Young, C, 'Cyclotomic Gaudin models: construction and Bethe ansatz', Commun. Math. Phys. (2016) 343:971, first published on line March 24, 2016. The final publication is available at Springer via http://dx.doi.org/10.1007/s00220-016-2601-3 © Springer-Verlag Berlin Heidelberg 2016To any simple Lie algebra $\mathfrak g$ and automorphism $\sigma:\mathfrak g\to \mathfrak g$ we associate a cyclotomic Gaudin algebra. This is a large commutative subalgebra of $U(\mathfrak g)^{\otimes N}$ generated by a hierarchy of cyclotomic Gaudin Hamiltonians. It reduces to the Gaudin algebra in the special case $\sigma = \text{id}$. We go on to construct joint eigenvectors and their eigenvalues for this hierarchy of cyclotomic Gaudin Hamiltonians, in the case of a spin chain consisting of a tensor product of Verma modules. To do so we generalize an approach to the Bethe ansatz due to Feigin, Frenkel and Reshetikhin involving vertex algebras and the Wakimoto construction. As part of this construction, we make use of a theorem concerning cyclotomic coinvariants, which we prove in a companion paper. As a byproduct, we obtain a cyclotomic generalization of the Schechtman-Varchenko formula for the weight function.Peer reviewe

Structure of the Head of the Bartonella Adhesin BadA

Trimeric autotransporter adhesins (TAAs) are a major class of proteins by which pathogenic proteobacteria adhere to their hosts. Prominent examples include Yersinia YadA, Haemophilus Hia and Hsf, Moraxella UspA1 and A2, and Neisseria NadA. TAAs also occur in symbiotic and environmental species and presumably represent a general solution to the problem of adhesion in proteobacteria. The general structure of TAAs follows a head-stalk-anchor architecture, where the heads are the primary mediators of attachment and autoagglutination. In the major adhesin of Bartonella henselae, BadA, the head consists of three domains, the N-terminal of which shows strong sequence similarity to the head of Yersinia YadA. The two other domains were not recognizably similar to any protein of known structure. We therefore determined their crystal structure to a resolution of 1.1 Å. Both domains are β-prisms, the N-terminal one formed by interleaved, five-stranded β-meanders parallel to the trimer axis and the C-terminal one by five-stranded β-meanders orthogonal to the axis. Despite the absence of statistically significant sequence similarity, the two domains are structurally similar to domains from Haemophilus Hia, albeit in permuted order. Thus, the BadA head appears to be a chimera of domains seen in two other TAAs, YadA and Hia, highlighting the combinatorial evolutionary strategy taken by pathogens

Effects of noise on convergent game learning dynamics

We study stochastic effects on the lagging anchor dynamics, a reinforcement learning algorithm used to learn successful strategies in iterated games, which is known to converge to Nash points in the absence of noise. The dynamics is stochastic when players only have limited information about their opponents' strategic propensities. The effects of this noise are studied analytically in the case where it is small but finite, and we show that the statistics and correlation properties of fluctuations can be computed to a high accuracy. We find that the system can exhibit quasicycles, driven by intrinsic noise. If players are asymmetric and use different parameters for their learning, a net payoff advantage can be achieved due to these stochastic oscillations around the deterministic equilibrium.Comment: 17 pages, 8 figure

Structure of a Burkholderia pseudomallei Trimeric Autotransporter Adhesin Head

Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region.Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 A resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs.The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

A Bacterial Acetyltransferase Destroys Plant Microtubule Networks and Blocks Secretion

The eukaryotic cytoskeleton is essential for structural support and intracellular transport, and is therefore a common target of animal pathogens. However, no phytopathogenic effector has yet been demonstrated to specifically target the plant cytoskeleton. Here we show that the Pseudomonas syringae type III secreted effector HopZ1a interacts with tubulin and polymerized microtubules. We demonstrate that HopZ1a is an acetyltransferase activated by the eukaryotic co-factor phytic acid. Activated HopZ1a acetylates itself and tubulin. The conserved autoacetylation site of the YopJ / HopZ superfamily, K289, plays a critical role in both the avirulence and virulence function of HopZ1a. Furthermore, HopZ1a requires its acetyltransferase activity to cause a dramatic decrease in Arabidopsis thaliana microtubule networks, disrupt the plant secretory pathway and suppress cell wall-mediated defense. Together, this study supports the hypothesis that HopZ1a promotes virulence through cytoskeletal and secretory disruption

Cryo-EM structure of lysenin pore elucidates membrane insertion by an aerolysin family protein

Lysenin from the coelomic fluid of the earthworm Eisenia fetida belongs to the aerolysin family of small β-pore-forming toxins (β-PFTs), some members of which are pathogenic to humans and animals. Despite efforts, a high-resolution structure of a channel for this family of proteins has been elusive and therefore the mechanism of activation and membrane insertion remains unclear. Here we determine the pore structure of lysenin by single particle cryo-EM, to 3.1 Å resolution. The nonameric assembly reveals a long β-barrel channel spanning the length of the complex that, unexpectedly, includes the two pre-insertion strands flanking the hypothetical membrane-insertion loop. Examination of other members of the aerolysin family reveals high structural preservation in this region, indicating that the membrane-insertion pathway in this family is conserved. For some toxins, proteolytic activation and pro-peptide removal will facilitate unfolding of the pre-insertion strands, allowing them to form the β-barrel of the channel