A genomic view of food-related and probiotic Enterococcus strains

The study of enterococcal genomes has grown considerably in recent years. While special attentionis paid to comparative genomic analysis among clinical relevant isolates, in this study we performedan exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential tobe used as probiotics. Beyond common genetic features, we especially aimed to identify those thatare specific to enterococcal strains isolated from a certain food-related source as well as features presentin a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7different species, were examined and compared. Their phylogenetic relationship was reconstructedbased on orthologous proteins and whole genomes. Likewise, markers associated with a successfulcolonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clusteredregularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features.At the same time, a search for antibiotic resistance genes was carried out, since they are of bigconcern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteomeuniversally present among the genera and to determine that most of the accessory genes codefor hypothetical proteins, providing reasonable hints to support their functional characterization.Fil: Bonacina, Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Suárez, Nadia Elina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Hormigo, Daniel Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Fadda, Silvina G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; ArgentinaFil: Lechner, Marcus. University Marburg; AlemaniaFil: Saavedra, Maria Lucila. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Centro de Referencia Para Lactobacilos; Argentin

PROTECTIVE ROLE OF DIETARY BIOACTIVE COMPOUNDS: MECHANISMS AND HYPOTHESIS

Scientific evidences support the protective role of diets rich in fruit and vegetables against chronic diseases, like cancer and cardiovascular disease. In particular two classes of chemopreventive phytochemicals, i.e. isothiocyanates presence in Cruciferae and anthocyanins (ACNs) presence in berries and other colored fruits and vegetables, are considered in this thesis. Cruciferae and especially Brassica genus contain high concentration of constituents with antioxidant properties (e.g. carotenoids, vitamin C, folate) as well as glucosinolate precursors of isothiocyanates (ITCs) and indoles that modulate xenobiotic biotransformation enzymes, such as Glutathione S-Transferase (GST). The protective effect of broccoli (Brassica oleracea L. var. italica) was tested through two different study protocols: a regular-intake intervention study with daily consumption of one serving of steamed broccoli for 10 days and a single-meal study (i.e. single consumption of broccoli, 250g). Analyzed broccoli resulted to be a good source of antioxidant compounds (carotenoids, vitamin C) and glucosinolates as ITCs. Subjects involved in the study were young male smokers recruited on the basis of anthropometric characteristics, food habits and their GSTM1 genotype. Thirty subjects were enrolled for the regular-intake study. A single blind randomized cross-over experimental design was scheduled. Fasting blood samples were collected at the beginning and at the end of each treatment period (0, 10, 30, 40 days). Concentration of carotenoids, lutein, \u3b2-carotene and folate was assessed in plasma and serum samples. Lymphocytes were used for the determination of biomarkers of oxidative stress: cell resistance against oxidative stress, endogenous DNA damage (i.e. oxidized purines), in vitro DNA repair activity and mRNA expression of OGG1, NUDT1 and HO-1 levels. Cell protection against H2O2-induced DNA damage was higher after broccoli diet with respect to control diet in the whole group of subjects. Folate and lutein concentrations increased significantly after broccoli diet. Broccoli intake caused a more consistent and significant effect of protection against DNA damage in GSTM1 null (-27.6%) subjects compared to GSTM1 positive (-13.1%) individuals (p<0.05). Oxidized purines decreased significantly (p<0.05) after broccoli intake (-22.6%) while no effect of polymorphism was observed. DNA repair activity and OGG1, HO-1 and NUDT1 mRNA expression levels did not differ throughout the intervention study. Twelve volunteers were selected for the single-meal study. Fasting blood samples were collected before broccoli consumption and after 3, 6, 8 and 24 h from broccoli intake in order to evaluate: cell resistance to oxidative DNA damage, bioavailability of bioactive compounds (folate, lutein, \u3b2-carotene and vitamin C) and total GST activity. In particular, serum folate, plasma vitamin C and \u3b2-carotene concentrations significantly increased. Furthermore, plasma GST activity increased significantly in individuals with GSTM1 positive genotype at 6 h with respect to 3 h and 24 h but not compared to baseline. Interestingly, ex-vivo induced DNA damage was significantly reduced after 24 h from broccoli consumption. In conclusion, these two studies demonstrated that 10 days of consumption of steamed broccoli could improve defence against DNA damage, without affecting repair activity in young healthy smokers. Moreover, a single portion of steamed broccoli was able to decrease DNA damage and to modulate GST activity. Even if preliminary, our data suggest a \u201cdiet/genetic\u201d interaction. Delphinidin-3-glucoside (Dp-3-glc) and cyanidin-3-glucoside (Cy-3-glc) are two ACNs able to inhibit tumor cell proliferation. An in vitro study was designed to investigate the effect of Dp-3-glc and Cy-3-glc on the angiogenic and Dp-3-glc on the procoagulant activities of human microvascular endothelial cells (HMEC-1). HMEC-1 were incubated for up to 24h with culture media \ub1 ACNs (0.1, 1, 10, 100 \ub5M) alone or in combination with purified proangiogenic factor (VEGF), or bacterial endotoxin (LPS). Angiogenesis was evaluated by the capillary-like tube formation in Matrigel and the wound healing assay; while the pro-coagulant activity was tested by the thrombin generation (TG) assay and Tissue Factor (TF) expression as antigen, one-stage recalcification assay and mRNA quantitation. Results showed that Dp-3-glc was able to inhibit angiogenesis in resting cells and in VEGF-stimulated conditions at 100 \ub5M; interestingly, the inhibition of the migratory VEGF-dependent stimulus started at the Dp-3-glc concentration of 1 \ub5M. In the TG assay Dp-3-glc significantly contrasted with the pro-thrombotic stimulus of LPS starting from 10 \ub5M on HMEC-1 intact monolayer and TF expression at 100 \ub5M concentration. Differently, Cy-3-glc did not show any effect on angiogenesis. In conclusion, this study, in terms of anti-angiogenic and anti-coagulant properties of Dp-3-glc make this compound a potential cancer chemopreventive agent. Together our results, from both in vivo studies on humans and in vitro cell culture models, support potential health benefits derived from the intake of fruit (coloured berries) and vegetable (broccoli)

Abstract Canonical Inference

An abstract framework of canonical inference is used to explore how different proof orderings induce different variants of saturation and completeness. Notions like completion, paramodulation, saturation, redundancy elimination, and rewrite-system reduction are connected to proof orderings. Fairness of deductive mechanisms is defined in terms of proof orderings, distinguishing between (ordinary) "fairness," which yields completeness, and "uniform fairness," which yields saturation.Comment: 28 pages, no figures, to appear in ACM Trans. on Computational Logi

On the Expressivity and Applicability of Model Representation Formalisms

A number of first-order calculi employ an explicit model representation formalism for automated reasoning and for detecting satisfiability. Many of these formalisms can represent infinite Herbrand models. The first-order fragment of monadic, shallow, linear, Horn (MSLH) clauses, is such a formalism used in the approximation refinement calculus. Our first result is a finite model property for MSLH clause sets. Therefore, MSLH clause sets cannot represent models of clause sets with inherently infinite models. Through a translation to tree automata, we further show that this limitation also applies to the linear fragments of implicit generalizations, which is the formalism used in the model-evolution calculus, to atoms with disequality constraints, the formalisms used in the non-redundant clause learning calculus (NRCL), and to atoms with membership constraints, a formalism used for example in decision procedures for algebraic data types. Although these formalisms cannot represent models of clause sets with inherently infinite models, through an additional approximation step they can. This is our second main result. For clause sets including the definition of an equivalence relation with the help of an additional, novel approximation, called reflexive relation splitting, the approximation refinement calculus can automatically show satisfiability through the MSLH clause set formalism.Comment: 15 page

Breakdown rates and macroinvertebrate colonisation of alder (Alnus glutinosa) leaves in an acid lake (Lake Orta, N Italy), before, during and after a liming intervention

To test the effectiveness of the liming intervention on Lake Orta, the speed of leaves decay and of colonisation processes by macrobenthonic fauna were studied on alder leaves (Alnus glutinosa) placed on the bottom of the lake and recovered after appropriate time intervals. Experiments were performed at two sites (North and South) and two depths (-3 and –18 m), during three successive winters: 1988-1989 (pre-liming), 1989-1990 (liming), 1990-1991 (post-liming). Two main results emerged: 1) alder leaves, which are known to have a medium to high decaying speed in a number of aquatic environments, behave in Lake Orta as a low speed species. Decaying processes in the three years are significantly different only in station N3, where the mean breakdown rate in 1988- 1989 is more than twice that measured in the two subsequent winters. 2) The species richness of colonising benthic fauna is low: the community is made up almost exclusively of Chironomidae, which form 70 to 100% of the whole population; among them, the genus Phenopsectra is always present, while Tanytarsus was collected only during the first year and in the less deep sampling sites. The mean population abundances were higher before liming

Scavenger 0.1: A Theorem Prover Based on Conflict Resolution

This paper introduces Scavenger, the first theorem prover for pure first-order logic without equality based on the new conflict resolution calculus. Conflict resolution has a restricted resolution inference rule that resembles (a first-order generalization of) unit propagation as well as a rule for assuming decision literals and a rule for deriving new clauses by (a first-order generalization of) conflict-driven clause learning.Comment: Published at CADE 201

Splitting Proofs for Interpolation

We study interpolant extraction from local first-order refutations. We present a new theoretical perspective on interpolation based on clearly separating the condition on logical strength of the formula from the requirement on the com- mon signature. This allows us to highlight the space of all interpolants that can be extracted from a refutation as a space of simple choices on how to split the refuta- tion into two parts. We use this new insight to develop an algorithm for extracting interpolants which are linear in the size of the input refutation and can be further optimized using metrics such as number of non-logical symbols or quantifiers. We implemented the new algorithm in first-order theorem prover VAMPIRE and evaluated it on a large number of examples coming from the first-order proving community. Our experiments give practical evidence that our work improves the state-of-the-art in first-order interpolation.Comment: 26th Conference on Automated Deduction, 201

Thermo-mechanical behavior of surface acoustic waves in ordered arrays of nanodisks studied by near infrared pump-probe diffraction experiments

The ultrafast thermal and mechanical dynamics of a two-dimensional lattice of metallic nano-disks has been studied by near infrared pump-probe diffraction measurements, over a temporal range spanning from 100 fs to several nanoseconds. The experiments demonstrate that, in these systems, a two-dimensional surface acoustic wave (2DSAW), with a wavevector given by the reciprocal periodicity of the array, can be excited by ~120 fs Ti:sapphire laser pulses. In order to clarify the interaction between the nanodisks and the substrate, numerical calculations of the elastic eigenmodes and simulations of the thermodynamics of the system are developed through finite-element analysis. At this light, we unambiguously show that the observed 2DSAW velocity shift originates from the mechanical interaction between the 2DSAWs and the nano-disks, while the correlated 2DSAW damping is due to the energy radiation into the substrate.Comment: 13 pages, 10 figure

Comparative chondrogenesis of human cells in a 3D integrated experimental/computational mechanobiology model

We present an integrated experimental–computational mechanobiology model of chondrogenesis. The response of human articular chondrocytes to culture medium perfusion, versus perfusion associated with cyclic pressurisation, versus non-perfused culture, was compared in a pellet culture model, and multiphysic computation was used to quantify oxygen transport and flow dynamics in the various culture conditions. At 2 weeks of culture, the measured cell metabolic activity and the matrix content in collagen type II and aggrecan were greatest in the perfused+ pressurised pellets. The main effects of perfusion alone, relative to static controls, were to suppress collagen type I and GAG contents, which were greatest in the non-perfused pellets. All pellets showed a peripheral layer of proliferating cells, which was thickest in the perfused pellets, and most pellets showed internal gradients in cell density and matrix composition. In perfused pellets, the computed lowest oxygen concentration was 0.075mM (7.5% tension), the maximal oxygen flux was 477.5 nmol/m2/s and the maximal fluid shear stress, acting on the pellet surface, was 1.8mPa (0.018 dyn/cm2). In the non-perfused pellets, the lowest oxygen concentration was 0.003mM (0.3% tension) and the maximal oxygen flux was 102.4nmol/m2/s.Alocal correlationwas observed, between the gradients in pellet properties obtained from histology, and the oxygen fields calculated with multiphysic simulation. Our results showup-regulation of hyalinematrix protein production by human chondrocytes in response to perfusion associated with cyclic pressurisation. These results could be favourably exploited in tissue engineering applications

New results on rewrite-based satisfiability procedures

Program analysis and verification require decision procedures to reason on theories of data structures. Many problems can be reduced to the satisfiability of sets of ground literals in theory T. If a sound and complete inference system for first-order logic is guaranteed to terminate on T-satisfiability problems, any theorem-proving strategy with that system and a fair search plan is a T-satisfiability procedure. We prove termination of a rewrite-based first-order engine on the theories of records, integer offsets, integer offsets modulo and lists. We give a modularity theorem stating sufficient conditions for termination on a combinations of theories, given termination on each. The above theories, as well as others, satisfy these conditions. We introduce several sets of benchmarks on these theories and their combinations, including both parametric synthetic benchmarks to test scalability, and real-world problems to test performances on huge sets of literals. We compare the rewrite-based theorem prover E with the validity checkers CVC and CVC Lite. Contrary to the folklore that a general-purpose prover cannot compete with reasoners with built-in theories, the experiments are overall favorable to the theorem prover, showing that not only the rewriting approach is elegant and conceptually simple, but has important practical implications.Comment: To appear in the ACM Transactions on Computational Logic, 49 page