A 43-nucleotide U-rich element in 3′-untranslated region of large number of Trypanosoma cruzi transcripts is important for mRNA Abundance in intracellular amastigotes

Trypanosoma cruzi, the agent of Chagas disease, does not seem to control gene expression through regulation of transcription initiation and makes use of post-transcriptional mechanisms. We report here a 43-nt U-rich RNA element located in the 3′-untranslated region (3′-UTR) of a large number of T. cruzi mRNAs that is important for mRNA abundance in the intracellular amastigote stage of the parasite. Whole genome scan analysis, differential display RT-PCR, Northern blot, and RT-PCR analyses were used to determine the transcript levels of more than 900 U-rich-containing mRNAs of large gene families as well as single and low copy number genes. Our results indicate that the 43-nt U-richmRNAelement is preferentially present in amastigotes. The cis-element of a protein kinase 3′-UTR but not its mutated version promoted the expression of the green fluorescent protein reporter gene in amastigotes. The regulatory ciselement, but not its mutated version, was also shown to interact with the trypanosome-specific RNA-binding protein (RBP) TcUBP1 but not with other related RBPs. Co-immunoprecipitation experiments of TcUBP1-containing ribonucleoprotein complexes formed in vivo validated the interaction with representative endogenous RNAs having the element. These results suggest that this 43-nt U-rich element together with other yet unidentified sequences might be involved in the modulation of abundance and/or translation of subsets of transcripts in the amastigote stage.Fil: Li, Zhu Hong. University of Georgia; Estados UnidosFil: de Gaudenzi, Javier Gerardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Alvarez, Vanina Eder. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Mendiondo, Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Wang, Haiming. University of Georgia; Estados UnidosFil: Kissinger, Jessica C.. University of Georgia; Estados UnidosFil: Frasch, Alberto Carlos C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Docampo, Roberto. University of Georgia; Estados Unido

Sources and sinks separating domains of left- and right-traveling waves: Experiment versus amplitude equations

In many pattern forming systems that exhibit traveling waves, sources and sinks occur which separate patches of oppositely traveling waves. We show that simple qualitative features of their dynamics can be compared to predictions from coupled amplitude equations. In heated wire convection experiments, we find a discrepancy between the observed multiplicity of sources and theoretical predictions. The expression for the observed motion of sinks is incompatible with any amplitude equation description.Comment: 4 pages, RevTeX, 3 figur

Deletion of low molecular weight protein tyrosine phosphatase (Acp1) protects against stress-induced cardiomyopathy.

The low molecular weight protein tyrosine phosphatase (LMPTP), encoded by the ACP1 gene, is a ubiquitously expressed phosphatase whose in vivo function in the heart and in cardiac diseases remains unknown. To investigate the in vivo role of LMPTP in cardiac function, we generated mice with genetic inactivation of the Acp1 locus and studied their response to long-term pressure overload. Acp1(-/-) mice develop normally and ageing mice do not show pathology in major tissues under basal conditions. However, Acp1(-/-) mice are strikingly resistant to pressure overload hypertrophy and heart failure. Lmptp expression is high in the embryonic mouse heart, decreased in the postnatal stage, and increased in the adult mouse failing heart. We also show that LMPTP expression increases in end-stage heart failure in humans. Consistent with their protected phenotype, Acp1(-/-) mice subjected to pressure overload hypertrophy have attenuated fibrosis and decreased expression of fibrotic genes. Transcriptional profiling and analysis of molecular signalling show that the resistance of Acp1(-/-) mice to pathological cardiac stress correlates with marginal re-expression of fetal cardiac genes, increased insulin receptor beta phosphorylation, as well as PKA and ephrin receptor expression, and inactivation of the CaMKIIδ pathway. Our data show that ablation of Lmptp inhibits pathological cardiac remodelling and suggest that inhibition of LMPTP may be of therapeutic relevance for the treatment of human heart failure

Filamin a expression negatively regulates Sphingosine-1-phosphate-induced NF-κB activation in melanoma cells by inhibition o Akt signaling

Sphingosine-1-phosphate (S1P) is a bioactive lipid mediator that regulates many processes in inflammation and cancer. S1P is a ligand for five G-protein-coupled receptors, S1PR1 to -5, and also has important intracellular actions. Previously, we showed that intracellular S1P is involved in tumor necrosis factor alpha (TNF)-induced NF-κB activation in melanoma cell lines that express filamin A (FLNA). Here, we show that extracellular S1P activates NF-κB only in melanoma cells that lack FLNA. In these cells, S1P, but not TNF, promotes IκB kinase (IKK) and p65 phosphorylation, IκBα degradation, p65 nuclear translocation, and NF-κB reporter activity. NF-κB activation induced by S1P was mediated via S1PR1 and S1PR2. Exogenous S1P enhanced the phosphorylation of protein kinase Cδ (PKCδ), and its downregulation reduced S1P-induced the phosphorylation of IKK and p65. In addition, silencing of Bcl10 also inhibited S1P-induced IKK phosphorylation. Surprisingly, S1P reduced Akt activation in melanoma cells that express FLNA, whereas in the absence of FLNA, high phosphorylation levels of Akt were maintained, enabling S1P-mediated NF-κB signaling. In accord, inhibition of Akt suppressed S1P-mediated IKK and p65 phosphorylation and degradation of IκBα. Hence, these results support a negative role of FLNA in S1P-mediated NF-κB activation in melanoma cells through modulation of Akt.Fil: Campos, Ludmila Estefanía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Rodriguez, Yamila Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Machado Leopoldino, Andreia. Virginia Commonwealth University. School of Medicine; Estados Unidos. Universidade de Sao Paulo; BrasilFil: Hait, Nitai C.. Virginia Commonwealth University. School of Medicine; Estados UnidosFil: Lopez Bergami, Pablo Roberto. Universidad Maimonides; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Castro, Melina Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Sanchez, Emilse Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Maceyka, Michael. Virginia Commonwealth University. School of Medicine; Estados UnidosFil: Spiegel, Sarah. Virginia Commonwealth University School Of Medicine;Fil: Alvarez, Sergio Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; Argentin

Functional Approach to Quantum Decoherence and the Classical Final Limit

For a wide set of quantum systems it is demonstrated that the quantum regime can be considered as the transient phase while the final classical statistical regime is a permanent state. A basis where exact matrix decoherence appears for these final states is found. The relation with the decoherence of histories formalism is studied. A set of final intrinsically consistent histories is found.Comment: 20 pages. Phys. Rev A in press 200

Experimental realisation of Shor's quantum factoring algorithm using qubit recycling

Quantum computational algorithms exploit quantum mechanics to solve problems exponentially faster than the best classical algorithms. Shor's quantum algorithm for fast number factoring is a key example and the prime motivator in the international effort to realise a quantum computer. However, due to the substantial resource requirement, to date, there have been only four small-scale demonstrations. Here we address this resource demand and demonstrate a scalable version of Shor's algorithm in which the n qubit control register is replaced by a single qubit that is recycled n times: the total number of qubits is one third of that required in the standard protocol. Encoding the work register in higher-dimensional states, we implement a two-photon compiled algorithm to factor N=21. The algorithmic output is distinguishable from noise, in contrast to previous demonstrations. These results point to larger-scale implementations of Shor's algorithm by harnessing scalable resource reductions applicable to all physical architectures.Comment: 7 pages, 3 figure

Symbolic dynamics to enhance diagnostic ability of portable oximetry from the Phone Oximeter in the detection of paediatric sleep apnoea

Objective: This study is aimed at assessing symbolic dynamics as a reliable technique to characterize complex fluctuations of portable oximetry in the context of automated detection of childhood obstructive sleep apnoea-hypopnoea syndrome (OSAHS). Approach: Nocturnal oximetry signals from 142 children with suspected OSAHS were acquired using the Phone Oximeter: a portable device that integrates a pulse oximeter with a smartphone. An apnoea-hypopnoea index (AHI) ⩾ 5 events h−1 from simultaneous in-lab polysomnography was used to confirm moderate-to-severe childhood OSAHS. Symbolic dynamics was used to parameterise non-linear changes in the overnight oximetry profile. Conventional indices, anthropometric measures, and time-domain linear statistics were also considered. Forward stepwise logistic regression was used to obtain an optimum feature subset. Logistic regression (LR) was used to identify children with moderate-to-severe OSAHS. Main results: The histogram of 3-symbol words from symbolic dynamics showed significant differences (p < 0.01) between children with AHI < 5 events h−1 and moderate-to-severe patients (AHI ⩾ 5 events h−1). Words representing increasing oximetry values after apnoeic events (re-saturations) showed relevant diagnostic information. Regarding the performance of individual characterization approaches, the LR model composed of features from symbolic dynamics alone reached a maximum performance of 78.4% accuracy (65.2% sensitivity; 86.8% specificity) and 0.83 area under the ROC curve (AUC). The classification performance improved combining all features. The optimum model from feature selection achieved 83.3% accuracy (73.5% sensitivity; 89.5% specificity) and 0.89 AUC, significantly (p <0.01) outperforming the other models. Significance: Symbolic dynamics provides complementary information to conventional oximetry analysis enabling reliable detection of moderate-to-severe paediatric OSAHS from portable oximetry

Left ventricular thrombus mimicking primary cardiac tumor in a patient with primary antiphospholipid syndrome and recurrent systemic embolism

Primary antiphospholipid syndrome (APS) is a well-defined entity characterized by spontaneous and recurrent abortion, thrombocytopenia and recurrent vascular thromboses (arterial and venous). Left ventricular thrombus mimicking primary cardiac tumor with recurrent systemic embolism has not been previously reported. In this report we describe a 39 year-old man admitted to hospital presenting with left hemiparesis and a peripheral embolism. He had no history of thrombotic events. Transthoracic echocardiography showed a large, polypoid and mobile mass (4.0 × 1.2 cm) attached to the apex of the left ventricle, highly suggestive of primary cardiac tumor. The patient subsequently underwent open heart surgery. The histological examination showed an older thrombus and a fresh thrombus. Post-operative laboratory tests showed lupus anticoagulant activity, confirming the primary APS diagnosis. The patient initiated treatment with oral anticoagulation (INR levels between 2 and 3) and was discharged 29 days after surgery. At ten month follow-up, he was symptom-free with long-term anticoagulation therapy. No evidence of intracardiac mass recurrence on two-dimensional echocardiography was seen. Intracardiac thrombus has been rarely reported as a complication of primary APS. Left ventricular mass mimicking primary cardiac tumor with recurrent systemic embolism has not been previously reported. Pre-operative investigations could not distinguish such a thrombus from a cardiac tumor and the diagnosis was made post-operatively

Reverse Engineering Gene Networks with ANN: Variability in Network Inference Algorithms

Motivation :Reconstructing the topology of a gene regulatory network is one of the key tasks in systems biology. Despite of the wide variety of proposed methods, very little work has been dedicated to the assessment of their stability properties. Here we present a methodical comparison of the performance of a novel method (RegnANN) for gene network inference based on multilayer perceptrons with three reference algorithms (ARACNE, CLR, KELLER), focussing our analysis on the prediction variability induced by both the network intrinsic structure and the available data. Results: The extensive evaluation on both synthetic data and a selection of gene modules of "Escherichia coli" indicates that all the algorithms suffer of instability and variability issues with regards to the reconstruction of the topology of the network. This instability makes objectively very hard the task of establishing which method performs best. Nevertheless, RegnANN shows MCC scores that compare very favorably with all the other inference methods tested. Availability: The software for the RegnANN inference algorithm is distributed under GPL3 and it is available at the corresponding author home page (http://mpba.fbk.eu/grimaldi/regnann-supmat