Molecular biological methods for studying the gut microbiota : the EU human gut flora project

Seven European laboratories co-operated in a joint project (FAIR CT97-3035) to develop, refine and apply molecular methods towards facilitating elucidation of the complex composition of the human intestinal microflora and to devise robust methodologies for monitoring the gut flora in response to diet. An extensive database of 16S rRNA sequences for tracking intestinal bacteria was generated by sequencing the 16S rRNA genes of new faecal isolates and of clones obtained by amplification with polymerase chain reaction (PCR) on faecal DNA from subjects belonging to different age groups. The analyses indicated that the number of different species (diversity) present in the human gut increased with age. The sequence information generated, provided the basis for design of 16S rRNA-directed oligonucleotide probes to specifically detect bacteria at various levels of phylogenetic hierarchy. The probes were tested for their specificity and used in whole-cell and dot-blot hybridisations. The applicability of the developed methods was demonstrated in several studies and the major outcomes are described

Nonperturbative Description of Deep Inelastic Structure Functions in Light-Front QCD

We explore the deep inelastic structure functions of hadrons nonperturbatively in an inverse power expansion of the light-front energy of the probe in the framework of light-front QCD. We arrive at the general expressions for various structure functions as the Fourier transform of matrix elements of different components of bilocal vector and axial vector currents on the light-front in a straightforward manner. The complexities of the structure functions are mainly carried by the multi-parton wave functions of the hadrons, while, the bilocal currents have a dynamically dependent yet simple structure on the light-front in this description. We also present a novel analysis of the power corrections based on light-front power counting which resolves some ambiguities of the conventional twist analysis in deep inelastic processes. Further, the factorization theorem and the scale evolution of the structure functions are presented in this formalism by using old-fashioned light-front time-ordered perturbation theory with multi-parton wave functions. Nonperturbative QCD dynamics underlying the structure functions can be explored in the same framework. Once the nonperturbative multi-parton wave functions are known from low-energy light-front QCD, a complete description of deep inelastic structure functions can be realized.Comment: Revtex, 30 pages and no figur

Factorization Breaking in Dijet Photoproduction with a Leading Neutron

The production of dijets with a leading neutron in ep-interactions at HERA is calculated in leading order and next-to-leading order of perturbative QCD using a pion-exchange model. Differential cross sections for deep-inelastic scattering (DIS) and photoproduction are presented as a function of several kinematic variables. By comparing the theoretical predictions for DIS dijets to recent H1 data, the pion flux factor together with the parton distribution functions of the pion is determined. The dijet cross sections in photoproduction show factorization breaking if compared to the H1 photoproduction data. The suppression factor is S = 0.48 (0.64) for resolved (global) suppression.Comment: 16 pages, 5 figure

Static properties of nuclear matter within the Boson Loop Expansion

The use of the Boson Loop Expansion is proposed for investigating the static properties of nuclear matter. We explicitly consider a schematic dynamical model in which nucleons interact with the scalar-isoscalar sigma meson. The suggested approximation scheme is examined in detail at the mean field level and at the one- and two-loop orders. The relevant formulas are provided to derive the binding energy per nucleon, the pressure and the compressibility of nuclear matter. Numerical results of the binding energy at the one-loop order are presented for Walecka's sigma-omega model in order to discuss the degree of convergence of the Boson Loop Expansion.Comment: 40 pages, 13 figure

Higher twist and transverse momentum dependent parton distributions: a light-front hamiltonian approach

In order to study twist-3 and transverse momentum dependent parton distributions, we use light-front time-ordered pQCD at order $\alpha_s$ to calculate various distribution functions for a dressed quark target. This study enables us to investigate in detail the existing relations between twist-3 and transverse momentum dependent parton distributions. Our calculation shows explicitly that two versions of such relations, considered to be equivalent, occur in the literature which need to be distinguished. Moreover, we examine sum rules for higher twist distributions. While the Burkhardt-Cottingham sum rule for $g_2$ is fulfilled, the corresponding sum rule for $h_2$ is violated.Comment: 10 pages, REVTe

Immune sensing of Candida albicans requires cooperative recognition of mannans and glucans by lectin and Toll-like receptors

Peer reviewedPublisher PD

Combined quantification of the global proteome, phosphoproteome, and proteolytic cleavage to characterize altered platelet functions in the human Scott syndrome

The Scott syndrome is a very rare and likely underdiagnosed bleeding disorder associated with mutations in the gene encoding anoctamin-6. Platelets from Scott patients are impaired in various Ca(2+)-dependent responses, including phosphatidylserine exposure, integrin closure, intracellular protein cleavage, and cytoskeleton-dependent morphological changes. Given the central role of anoctamin-6 in the platelet procoagulant response, we used quantitative proteomics to understand the underlying molecular mechanisms and the complex phenotypic changes in Scott platelets compared with control platelets. Therefore, we applied an iTRAQ-based multi-pronged strategy to quantify changes in (1) the global proteome, (2) the phosphoproteome, and (3) proteolytic events between resting and stimulated Scott and control platelets. Our data indicate a limited number of proteins with decreased (70) or increased (64) expression in Scott platelets, among those we confirmed the absence of anoctamin-6 and the strong up-regulation of aquaporin-1 by parallel reaction monitoring. The quantification of 1566 phosphopeptides revealed major differences between Scott and control platelets after stimulation with thrombin/convulxin or ionomycin. In Scott platelets, phosphorylation levels of proteins regulating cytoskeletal or signaling events were increased. Finally, we quantified 1596 N-terminal peptides in activated Scott and control platelets, 180 of which we identified as calpain-regulated, whereas a distinct set of 23 neo-N termini was caspase-regulated. In Scott platelets, calpain-induced cleavage of cytoskeleton-linked and signaling proteins was downregulated, in accordance with an increased phosphorylation state. Thus, multipronged proteomic profiling of Scott platelets provides detailed insight into their protection against detrimental Ca(2+)-dependent changes that are normally associated with phosphatidylserine exposure

"Object Categorization: Reversals and Explanations of the Basic-Level Advantage" (Rogers & Patterson, 2007): A simplicity account

T. T. Rogers and K. Patterson (2007), in their article “Object Categorization: Reversals and Explanations of the Basic-Level Advantage” (Journal of Experimental Psychology: General, 136, 451–469), reported an impressive set of results demonstrating a reversal of the highly robust basic-level advantage both in patients with semantic dementia and in healthy individuals engaged in a speeded categorization task. To explain their results, as well as the usual basic-level advantage seen in healthy individuals, the authors employed a parallel distributed processing theory of conceptual knowledge. In this paper, we introduce an alternative way of explaining the results of Rogers and Patterson, which is premised on a more restricted set of assumptions born from standard categorization theory. Specifically, we provide evidence that their results can be accounted for based on the predictions of the simplicity model of unsupervised categorization

Strange quark matter in a chiral SU(3) quark mean field model

We apply the chiral SU(3) quark mean field model to investigate strange quark matter. The stability of strange quark matter with different strangeness fraction is studied. The interaction between quarks and vector mesons destabilizes the strange quark matter. If the strength of the vector coupling is the same as in hadronic matter, strangelets can not be formed. For the case of beta equilibrium, there is no strange quark matter which can be stable against hadron emission even without vector meson interactions.Comment: 19 pages, 8 figure

Eutectic colony formation: A phase field study

Eutectic two-phase cells, also known as eutectic colonies, are commonly observed during the solidification of ternary alloys when the composition is close to a binary eutectic valley. In analogy with the solidification cells formed in dilute binary alloys, colony formation is triggered by a morphological instability of a macroscopically planar eutectic solidification front due to the rejection by both solid phases of a ternary impurity that diffuses in the liquid. Here we develop a phase-field model of a binary eutectic with a dilute ternary impurity and we investigate by dynamical simulations both the initial linear regime of this instability, and the subsequent highly nonlinear evolution of the interface that leads to fully developed two-phase cells with a spacing much larger than the lamellar spacing. We find a good overall agreement with our recent linear stability analysis [M. Plapp and A. Karma, Phys. Rev. E 60, 6865 (1999)], which predicts a destabilization of the front by long-wavelength modes that may be stationary or oscillatory. A fine comparison, however, reveals that the assumption commonly attributed to Cahn that lamella grow perpendicular to the envelope of the solidification front is weakly violated in the phase-field simulations. We show that, even though weak, this violation has an important quantitative effect on the stability properties of the eutectic front. We also investigate the dynamics of fully developed colonies and find that the large-scale envelope of the composite eutectic front does not converge to a steady state, but exhibits cell elimination and tip-splitting events up to the largest times simulated.Comment: 18 pages, 18 EPS figures, RevTeX twocolumn, submitted to Phys. Rev.