MicroRNA Profiling and Bioinformatics Target Analysis in Dorsal Hippocampus of Chronically Stressed Rats: Relevance to Depression Pathophysiology

Indexación: Scopus.1Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Santiago, Chile, 2National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC, United States, 3Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile, 4Millennium Institute for Integrative Biology (iBio), FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile, 5Department of Kinesiology, Faculty of Health Sciences, Universidad Católica del Maule, Talca, Chile, 6Escuela de Química y Farmacia, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile.This study was supported by the following grants: FONDECYT 1120528 (JLF), Fondo Central de Investigación, Universidad de Chile ENL025/16 (JLF), ES090079 (JAC). Research in RG and EV laboratories is funded by Instituto Milenio iBio – Iniciativa Científica Milenio MINECON.Studies conducted in rodents subjected to chronic stress and some observations in humans after psychosocial stress, have allowed to establish a link between stress and the susceptibility to many complex diseases, including mood disorders. The studies in rodents have revealed that chronic exposure to stress negatively affects synaptic plasticity by triggering changes in the production of trophic factors, subunit levels of glutamate ionotropic receptors, neuron morphology, and neurogenesis in the adult hippocampus. These modifications may account for the impairment in learning and memory processes observed in chronically stressed animals. It is plausible then, that stress modifies the interplay between signal transduction cascades and gene expression regulation in the hippocampus, therefore leading to altered neuroplasticity and functioning of neural circuits. Considering that miRNAs play an important role in post-transcriptional-regulation of gene expression and participate in several hippocampus-dependent functions; we evaluated the consequences of chronic stress on the expression of miRNAs in dorsal (anterior) portion of the hippocampus, which participates in memory formation in rodents. Here, we show that male rats exposed to daily restraint stress (2.5 h/day) during 7 and 14 days display a differential profile of miRNA levels in dorsal hippocampus and remarkably, we found that some of these miRNAs belong to the miR-379-410 cluster. We confirmed a rise in miR-92a and miR-485 levels after 14 days of stress by qPCR, an effect that was not mimicked by chronic administration of corticosterone (14 days). Our in silico study identified the top-10 biological functions influenced by miR-92a, nine of which were shared with miR-485: Nervous system development and function, Tissue development, Behavior, Embryonic development, Organ development, Organismal development, Organismal survival, Tissue morphology, and Organ morphology. Furthermore, our in silico study provided a landscape of potential miRNA-92a and miR-485 targets, along with relevant canonical pathways related to axonal guidance signaling and cAMP signaling, which may influence the functioning of several neuroplastic substrates in dorsal hippocampus. Additionally, the combined effect of miR-92a and miR-485 on transcription factors, along with histone-modifying enzymes, may have a functional relevance by producing changes in gene regulatory networks that modify the neuroplastic capacity of the adult dorsal hippocampus under stress. © 2018 Muñoz-Llanos, García-Pérez, Xu, Tejos-Bravo, Vidal, Moyano, Gutiérrez, Aguayo, Pacheco, García-Rojo, Aliaga, Rojas, Cidlowski and Fiedler.https://www.frontiersin.org/articles/10.3389/fnmol.2018.00251/ful

Bayesian Inference in MANTID - An Update

In the context of neutron science, Bayesian inference methods have been recently implemented within the MANTID framework [Monserrat D et al. 2015 J. Phys. Conf. Ser. 663 012009 (2015)]. In this contribution, we highlight the advantages of this software package for robust data analysis and subsequent model selection. To this end, we use the celebrated Rosenbrock function to illustrate its merits and strengths relative to classical fitting algorithms. We also introduce the latest additions implemented in MANTID, with a view to increasing its user friendliness as well as stimulating wider use. These include simulated-annealing schemes to reduce the need for initial guesses, as well as new options for multidimensional fitting. © Published under licence by IOP Publishing Ltd.Peer ReviewedPostprint (published version

A Discriminative Model of Stochastic Edit Distance in the form of a Conditional Transducer

pages 240-252International audienceMany real-world applications such as spell-checking or DNA analysis use the Levenshtein edit-distance to compute similarities between strings. In practice, the costs of the primitive edit operations (insertion, deletion and substitution of symbols) are generally hand-tuned. In this paper, we propose an algorithm to learn these costs. The underlying model is a probabilitic transducer, computed by using grammatical inference techniques, that allows us to learn both the structure and the probabilities of the model. Beyond the fact that the learned transducers are neither deterministic nor stochastic in the standard terminology, they are conditional, thus independant from the distributions of the input strings. Finally, we show through experiments that our method allows us to design cost functions that depend on the string context where the edit operations are used. In other words, we get kinds of \textit{context-sensitive} edit distances

Non-ohmic critical fluctuation conductivity of layered superconductors in magnetic field

Thermal fluctuation conductivity for a layered superconductor in perpendicular magnetic field is treated in the frame of the self-consistent Hartree approximation for an arbitrarily strong in-plane electric field. The simultaneous application of the two fields results in a slightly stronger suppression of the superconducting fluctuations, compared to the case when the fields are applied individually.Comment: 4 pages, 1 figure, to be published in Phys. Rev.

High prevalence and diversity of extended-spectrum β-lactamase and emergence of OXA-48 producing Enterobacterales in wildlife in Catalonia

The contract of LMG was supported by the Instituto Nacional de Investigaci?n y Tecnolog?a Agraria y Alimentaria (INIA) and the European Social Fund. AV was supported by a PIF grant from the Universitat Aut?noma de Barcelona. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Our grateful thanks to the Torreferrussa WRC staff. A.C. was student of the Master?s Degree in Zoonosis and One Health (UAB). The authors are also grateful to the Centres de Recerca de Catalunya (CERCA) Programme.Most of the studies focused on antimicrobial resistance (AMR) performed in wildlife describe Escherichia coli as the principal indicator of the selective pressure. In the present study, several species of Enterobacterales with a large panel of cephalosporin resistant (CR) genes have been isolated from wildlife in Catalonia. A total of 307 wild animals were examined to determine the prevalence of CR enterobacteria, AMR phenotypes and the presence of common carbapenem and CR genes. The overall prevalence of CR-phenotype was 13% (40/ 307): 17.3% in wild mammals (18/104) and 11.5% in wild birds (22/191) (p<0.01). Hedgehogs showed the highest prevalence (13.5% of 104) of the mammal specimens, and raptors the highest in bird specimen (7.3% of 191). Although CR E. coli was the most frequently isolated (45%), other CR- Enterobacterales like Klebsiella pneumoniae (20%), Citrobacter freundii (15%), Enterobacter cloacae (5%), Proteus mirabilis (5%), Providencia spp (5%) and Serratia marcescens (2.5%) were also isolated. A high diversity of CR genes was identified among the isolates, with 50% yielding blaCMY-2, 23% blaSHV-12, 20% blaCMY-1 and 18% blaCTX-M-15. Additionally, resistance to carbapenems associated to OXA-48 gene was found. Most of the CR isolates, principally K. pneumoniae and C. freundii, were multiresistant with co-resistance to fluoroquinolones, tetracycline, sulphonamides and aminoglycosides. This study reports high prevalence of Enterobacterales harbouring a variety of CR genes and OXA-48 mediated-carbapenem resistance, all of them frequently associated to nosocomial human infections, for the first time in wild mammals and wild birds. Implementation of control measures to reduce the impact of anthropogenic pressure in the environment is urgently needed

Unital Quantum Channels - Convex Structure and Revivals of Birkhoff's Theorem

The set of doubly-stochastic quantum channels and its subset of mixtures of unitaries are investigated. We provide a detailed analysis of their structure together with computable criteria for the separation of the two sets. When applied to O(d)-covariant channels this leads to a complete characterization and reveals a remarkable feature: instances of channels which are not in the convex hull of unitaries can return to it when either taking finitely many copies of them or supplementing with a completely depolarizing channel. In these scenarios this implies that a channel whose noise initially resists any environment-assisted attempt of correction can become perfectly correctable.Comment: 31 page

Non-zero entropy density in the XY chain out of equilibrium

The von Neumann entropy density of a block of n spins is proved to be non-zero for large n in the non-equilibrium steady state of the XY chain constructed by coupling a finite cutout of the chain to the two infinite parts to its left and right which act as thermal reservoirs at different temperatures. Moreover, the non-equilibrium density is shown to be strictly greater than the density in thermal equilibrium

Critical fluctuation conductivity in layered superconductors in strong electric field

The paraconductivity, originating from critical superconducting order-parameter fluctuations in the vicinity of the critical temperature in a layered superconductor is calculated in the frame of the self-consistent Hartree approximation, for an arbitrarily strong electric field and zero magnetic field. The paraconductivity diverges less steep towards the critical temperature in the Hartree approximation than in the Gaussian one and it shows a distinctly enhanced variation with the electric field. Our results indicate that high electric fields can be effectively used to suppress order-parameter fluctuations in high-temperature superconductors.Comment: 11 pages, 2 figures, to be published in Phys. Rev.

New Insights into White-Light Flare Emission from Radiative-Hydrodynamic Modeling of a Chromospheric Condensation

(abridged) The heating mechanism at high densities during M dwarf flares is poorly understood. Spectra of M dwarf flares in the optical and near-ultraviolet wavelength regimes have revealed three continuum components during the impulsive phase: 1) an energetically dominant blackbody component with a color temperature of T $\sim$ 10,000 K in the blue-optical, 2) a smaller amount of Balmer continuum emission in the near-ultraviolet at lambda $<$ 3646 Angstroms and 3) an apparent pseudo-continuum of blended high-order Balmer lines. These properties are not reproduced by models that employ a typical "solar-type" flare heating level in nonthermal electrons, and therefore our understanding of these spectra is limited to a phenomenological interpretation. We present a new 1D radiative-hydrodynamic model of an M dwarf flare from precipitating nonthermal electrons with a large energy flux of $10^{13}$ erg cm$^{-2}$ s$^{-1}$. The simulation produces bright continuum emission from a dense, hot chromospheric condensation. For the first time, the observed color temperature and Balmer jump ratio are produced self-consistently in a radiative-hydrodynamic flare model. We find that a T $\sim$ 10,000 K blackbody-like continuum component and a small Balmer jump ratio result from optically thick Balmer and Paschen recombination radiation, and thus the properties of the flux spectrum are caused by blue light escaping over a larger physical depth range compared to red and near-ultraviolet light. To model the near-ultraviolet pseudo-continuum previously attributed to overlapping Balmer lines, we include the extra Balmer continuum opacity from Landau-Zener transitions that result from merged, high order energy levels of hydrogen in a dense, partially ionized atmosphere. This reveals a new diagnostic of ambient charge density in the densest regions of the atmosphere that are heated during dMe and solar flares.Comment: 50 pages, 2 tables, 13 figures. Accepted for publication in the Solar Physics Topical Issue, "Solar and Stellar Flares". Version 2 (June 22, 2015): updated to include comments by Guest Editor. The final publication is available at Springer via http://dx.doi.org/10.1007/s11207-015-0708-

Study of Loschmidt Echo for a qubit coupled to an XY-spin chain environment

We study the temporal evolution of a central spin-1/2 (qubit) coupled to the environment which is chosen to be a spin-1/2 transverse XY spin chain. We explore the entire phase diagram of the spin-Hamiltonian and investigate the behavior of Loschmidt echo(LE) close to critical and multicritical point(MCP). To achieve this, the qubit is coupled to the spin chain through the anisotropy term as well as one of the interaction terms. Our study reveals that the echo has a faster decay with the system size (in the short time limit) close to a MCP and also the scaling obeyed by the quasiperiod of the collapse and revival of the LE is different in comparison to that close to a QCP. We also show that even when approached along the gapless critical line, the scaling of the LE is determined by the MCP where the energy gap shows a faster decay with the system size. This claim is verified by studying the short-time and also the collapse and revival behavior of the LE at a quasicritical point on the ferromagnetic side of the MCP. We also connect our observation to the decoherence of the central spin.Comment: Accepted for publication in EPJ