Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair

Recurrent submicroscopic genomic copy number changes are the result of nonallelic homologous recombination (NAHR). Nonrecurrent aberrations, however, can result from different nonexclusive recombination-repair mechanisms. We previously described small microduplications at Xq28 containing MECP2 in four male patients with a severe neurological phenotype. Here, we report on the fine-mapping and breakpoint analysis of 16 unique microduplications. The size of the overlapping copy number changes varies between 0.3 and 2.3 Mb, and FISH analysis on three patients demonstrated a tandem orientation. Although eight of the 32 breakpoint regions coincide with low-copy repeats, none of the duplications are the result of NAHR. Bioinformatics analysis of the breakpoint regions demonstrated a 2.5-fold higher frequency of Alu interspersed repeats as compared with control regions, as well as a very high GC content (53%). Unexpectedly, we obtained the junction in only one patient by long-range PCR, which revealed nonhomologous end joining as the mechanism. Breakpoint analysis in two other patients by inverse PCR and subsequent array comparative genomic hybridization analysis demonstrated the presence of a second duplicated region more telomeric at Xq28, of which one copy was inserted in between the duplicated MECP2 regions. These data suggest a two-step mechanism in which part of Xq28 is first inserted near the MECP2 locus, followed by breakage-induced replication with strand invasion of the normal sister chromatid. Our results indicate that the mechanism by which copy number changes occur in regions with a complex genomic architecture can yield complex rearrangements.

Retinoic acid inhibits dendritic cell differentiation driven by interleukin-4

All-trans-retinoic acid (atRA) appears to affect Th1-Th2 differentiation and its effects on immune responses might also be mediated by dendritic cell (DC). Nonetheless, studies have been showing contradictory results since was observed either induction or inhibition of DC differentiation. Our aim was to investigate atRA action on human monocyte derived DC differentiation. For this purpose we tested pharmacological and physiological doses of atRA with or without cytokines. Cell phenotypes were analyzed by flow cytometry and function was investigated by phagocytosis and respiratory burst. DC, positive control group, was differentiated with GM-CSF and IL-4 and maturated with TNF-alpha. We demonstrated that atRA effects depend on the dose used as pharmacological doses inhibited expression of all phenotypic markers tested while a physiological dose caused cell differentiation. However, atRA combined or not with cytokines did not promote DC differentiation. In fact, atRA was detrimental on IL-4 property as a DC inductor. (C) 2009 Elsevier Inc. All rights reserved.

Development of an adenoviral vector with robust expression driven by p53

Here we introduce a new adenoviral vector where transgene expression is driven by p53. We first developed a synthetic promoter, referred to as PGTx beta containing a p53-responsive element, a minimal promoter and the first intron of the rabbit P-globin gene. Initial assays using plasmid-based vectors indicated that expression was tightly controlled by p53 and was 5-fold stronger than the constitutive CMV immediate early promoter/enhancer. The adenoviral vector, AdPG, was also shown to offer p53-responsive expression in prostate carcinoma cells LNCaP (wt p53), DU-145 (temperature sensitive mutant of p53) and PC3 (p53-null, but engineered to express temperature-sensitive p53 mutants). AdPG served as a sensor of p53 activity in LNCaP cells treated with chemotherapeutic agents. Since p53 can be induced by radiotherapy and chemotherapy, this new vector could be further developed for use in combination with conventional therapies to bring about cooperation between the genetic and pharmacologic treatment modalities. (c) 2007 Elsevier Inc. All rights reserved.

Preventive and curative glycoside kaempferol treatments attenuate the TH2-driven allergic airway disease

Asthma is a chronic respiratory disease characterized by airway inflammation and airway hyperresponsiveness (AHR). One strategy to treat allergic diseases is the development of new drugs. Flavonoids are compounds derived from plants and are known to have antiallergic, anti-inflammatory, and antioxidant properties. To investigate whether the flavonoid kaempferol glycoside 3-O-[beta-D-glycopiranosil-(1 -> 6)-alpha-L-ramnopiranosil]-7-O-alpha-L-ramnopiranosil-kaempferol (GRRK) would be capable of modulating allergic airway disease (AAD) either as a preventive (GRRK P) or curative (GRRK C) treatment in an experimental model of asthma. At weekly intervals, BALB/c mice were subcutaneously (sc) sensitized twice with ovalbumin (OVA)/alum and challenged twice with OVA administered intranasally. To evaluate any preventive effects GRRK was administered 1 h (hour) before each OVA-sensitization and challenge, while to analyze the curative effects mice were first sensitized with OVA, followed by GRRK given at day 18 through 21. The onset: of AAD was evaluated 24 h after the last OVA challenge. Both treatments resulted in a dose-dependent reduction in total leukocyte and eosinophil counts in the bronchoalveolar lavage fluid (BAL). GRRK also decreased CD4(+), B220(+), MHC class II and CD40 molecule expressions in BAL cells. Histology and lung mechanic showed that GRRK suppressed mucus production and ameliorated the AHR induced by OVA challenge. Furthermore, GRRK impaired Th2 cytokine production (IL-5 and IL-13) and did not induce a Th1 pattern of inflammation. These findings demonstrate that GRRK treatment before or after established allergic lung disease down-regulates key asthmatic features. Therefore. GRRK has a potential clinical use for the treatment of allergic asthma. (C) 2009 Elsevier B.V. All rights reserved.

An approach for solving the lot-sizing problem of a market-driven foundry

Foundries can be found all over Brazil and they are very important to its economy. In 2008, a mixed integer-programming model for small market-driven foundries was published, attempting to minimize delivery delays. We undertook a study of that model. Here, we present a new approach based on the decomposition of the problem into two sub-problems: production planning of alloys and production planning of items. Both sub-problems are solved using a Lagrangian heuristic based on transferences. An important aspect of the proposed heuristic is its ability to take into account a secondary practice objective solution: the furnace waste. Computational tests show that the approach proposed here is able to generate good quality solutions that outperform prior results. Journal of the Operational Research Society (2010) 61, 108-114. doi:10.1057/jors.2008.151

Fault Coverage-Driven Incremental Test Generation

In this paper, we consider a classical problem of complete test generation for deterministic finite-state machines (FSMs) in a more general setting. The first generalization is that the number of states in implementation FSMs can even be smaller than that of the specification FSM. Previous work deals only with the case when the implementation FSMs are allowed to have the same number of states as the specification FSM. This generalization provides more options to the test designer: when traditional methods trigger a test explosion for large specification machines, tests with a lower, but yet guaranteed, fault coverage can still be generated. The second generalization is that tests can be generated starting with a user-defined test suite, by incrementally extending it until the desired fault coverage is achieved. Solving the generalized test derivation problem, we formulate sufficient conditions for test suite completeness weaker than the existing ones and use them to elaborate an algorithm that can be used both for extending user-defined test suites to achieve the desired fault coverage and for test generation. We present the experimental results that indicate that the proposed algorithm allows obtaining a trade-off between the length and fault coverage of test suites.

Spallation product distributions and neutron multiplicities for accelerator-driven system using the CRISP code

Neutron multiplicities for several targets and spallation products of proton-induced reactions in thin targets of interest to an accelerator-driven system obtained with the CRISP code have been reported. This code is a Monte Carlo calculation that simulates the intranuclear cascade and evaporationl fission competition processes. Results are compared with experimental data, and agreement between each other can be considered quite satisfactory in a very broad energy range of incitant particles and different targets.

The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes

We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of ail asymmetric simple exclusion process (ASEP). The model is formulated to account for (i) excluded-volume interactions, (ii) the observed asymmetry of the stochastic movement of individual motors and (iii) interactions between motors and cargo. Items (i) and (ii) form the basis of ASEP models and have already been considered to study the behavior of motor density profile [A. Parmeggiani. T. Franosch, E. Frey, Phase Coexistence in driven one-dimensional transport, Phys. Rev. Lett. 90 (2003) 086601-1-086601-4]. Item (iii) is new. It is introduced here as an attempt to describe explicitly the dependence of cargo movement on the dynamics of motors in this context. The steady-state Solutions Of the model indicate that the system undergoes a phase transition of condensation type as the motor density varies. We study the consequences of this transition to the behavior of the average cargo velocity. (C) 2009 Elsevier B.V. All rights reserved.

Fock space for fermion-like lattices and the linear Glauber model

The concept of Fock space representation is developed to deal with stochastic spin lattices written in terms of fermion operators. A density operator is introduced in order to follow in parallel the developments of the case of bosons in the literature. Some general conceptual quantities for spin lattices are then derived, including the notion of generating function and path integral via Grassmann variables. The formalism is used to derive the Liouvillian of the d-dimensional Linear Glauber dynamics in the Fock-space representation. Then the time evolution equations for the magnetization and the two-point correlation function are derived in terms of the number operator. (C) 2008 Elsevier B.V. All rights reserved.

Exact vortex solutions in an extended Skyrme-Faddeev model

We construct exact vortex solutions in 3+1 dimensions to a theory which is an extension, due to Gies, of the Skyrme-Faddeev model, and that is believed to describe some aspects of the low energy limit of the pure SU(2) Yang-Mills theory. Despite the efforts in the last decades those are the first exact analytical solutions to be constructed for such type of theory. The exact vortices appear in a very particular sector of the theory characterized by special values of the coupling constants, and by a constraint that leads to an infinite number of conserved charges. The theory is scale invariant in that sector, and the solutions satisfy Bogomolny type equations. The energy of the static vortex is proportional to its topological charge, and waves can travel with the speed of light along them, adding to the energy a term proportional to a U(1) No ether charge they create. We believe such vortices may play a role in the strong coupling regime of the pure SU(2) Yang-Mills theory.

Transition to quantum turbulence in finite-size superfluids

A novel concept of quantum turbulence in finite size superfluids, such as trapped bosonic atoms, is discussed. We have used an atomic (87)Rb Bose-Einstein condensate (BEC) to study the emergence of this phenomenon. In our experiment, the transition to the quantum turbulent regime is characterized by a tangled vortex lines formation, controlled by the amplitude and time duration of the excitation produced by an external oscillating field. A simple model is suggested to account for the experimental observations. The transition from the non-turbulent to the turbulent regime is a rather gradual crossover. But it takes place in a sharp enough way, allowing for the definition of an effective critical line separating the regimes. Quantum turbulence emerging in a finite-size superfluid may be a new idea helpful for revealing important features associated to turbulence, a more general and broad phenomenon. [GRAPHICS] Amplitude versus elapsed time diagram of magnetically excited BEC superfluid, presenting the evolution from the non-turbulent regime, with well separated vortices, to the turbulent regimes, with tangled vortices (C) 2011 by Astro Ltd. Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA

Exact vortex solutions in a CP(N) Skyrme-Faddeev type model

We consider a four dimensional field theory with target space being CP(N) which constitutes a generalization of the usual Skyrme-Faddeev model defined on CP(1). We show that it possesses an integrable sector presenting an infinite number of local conservation laws, which are associated to the hidden symmetries of the zero curvature representation of the theory in loop space. We construct an infinite class of exact solutions for that integrable submodel where the fields are meromorphic functions of the combinations (x(1) + i x(2)) and (x(3) + x(0)) of the Cartesian coordinates of four dimensional Minkowski space-time. Among those solutions we have static vortices and also vortices with waves traveling along them with the speed of light. The energy per unity of length of the vortices show an interesting and intricate interaction among the vortices and waves.

Orbitally driven east-west antiphasing of South American precipitation

The variations of tropical precipitation are antiphased between the hemispheres on orbital timescales. This antiphasing arises through the alternating strength of incoming solar radiation in the two hemispheres, which affects monsoon intensity and hence the position of the meridional atmospheric circulation of the Hadley cells(1-4). Here we compare an oxygen isotopic record recovered from a speleothem from northeast Brazil for the past 26,000 years with existing reconstructions of precipitation in tropical South America(5-8). During the Holocene, we identify a similar, but zonally oriented, antiphasing of precipitation within the same hemisphere: northeast Brazil experiences humid conditions during low summer insolation and aridity when summer insolation is high, whereas the rest of southern tropical South America shows opposite characteristics. Simulations with a general circulation model that incorporates isotopic variations support this pattern as well as the link to insolation-driven monsoon activity. Our results suggest that convective heating over tropical South America and associated adjustments in large-scale subsidence over northeast Brazil lead to a remote forcing of the South American monsoon, which determines most of the precipitation changes in the region on orbital timescales.

U-curve: A branch-and-bound optimization algorithm for U-shaped cost functions on Boolean lattices applied to the feature selection problem

This paper presents the formulation of a combinatorial optimization problem with the following characteristics: (i) the search space is the power set of a finite set structured as a Boolean lattice; (ii) the cost function forms a U-shaped curve when applied to any lattice chain. This formulation applies for feature selection in the context of pattern recognition. The known approaches for this problem are branch-and-bound algorithms and heuristics that explore partially the search space. Branch-and-bound algorithms are equivalent to the full search, while heuristics are not. This paper presents a branch-and-bound algorithm that differs from the others known by exploring the lattice structure and the U-shaped chain curves of the search space. The main contribution of this paper is the architecture of this algorithm that is based on the representation and exploration of the search space by new lattice properties proven here. Several experiments, with well known public data, indicate the superiority of the proposed method to the sequential floating forward selection (SFFS), which is a popular heuristic that gives good results in very short computational time. In all experiments, the proposed method got better or equal results in similar or even smaller computational time. (C) 2009 Elsevier Ltd. All rights reserved.

Fibroblast growth factor 2 restrains ras-driven proliferation of malignant cells by triggering RhoA-mediated senescence

Fibroblast growth factor 2 (FGF2) is considered to be a bona fide oncogenic factor, although results from our group and others call this into question. Here, we report that exogenous recombinant FGF2 irreversibly inhibits proliferation by inducing senescence in Ras-dependent malignant mouse cells, but not in immortalized nontumorigenic cell lines. We report the following findings in K-Ras-dependent malignant YI adrenocortical cells and H-Ras V12-transformed BALB-3T3 fibroblasts: (a) FGF2 inhibits clonal growth and tumor onset in nude and immunocompetent BALB/c mice, (b) FGF2 irreversibly blocks the cell cycle, and (c) FGF2 induces the senescence-associated -galactosidase with no accompanying signs of apoptosis or necrosis. The tyrosine kinase inhibitor PD173074 completely protected malignant cells from FGF2. In Yl adrenal cells, reducing the constitutively high levels of K-Ras-GTP using the dominant-negative RasN17 mutant made cells resistant to FGF2 cytotoxicity. In addition, transfection of the dominant-negative RhoA-N19 into either YI or 3T3-B61 malignant cell lines yielded stable clonal transfectants that were unable to activate RhoA and were resistant to the FGF2 stress response. We conclude that in Rasdependent malignant cells, FGF2 interacts with its cognate receptors to trigger a senescence-like process involving RboAGTP. Surprisingly, attempts to select FGF2-resistant cells from the Yl and 3T3-B61 cell lines yielded only rare clones that (a) had lost the overexpressed ras oncogene, (b) were dependent on FGF2 for proliferation, and (c) were poorly tumorigenic. Thus, FGF2 exerted a strong negative selection that Rasdependent malignant cells could rarely overcome.