ALBERT

Description: Background: Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information. Results: The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening. Conclusions: A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process.

Description: Author(s): Moisés Bravo-Gaete, Sebastián Gómez, and Mokhtar Hassaïne The aim of this paper is to propose a generalized Cardy formula for three-dimensional hyperscaling violation black holes. We first note that for the hyperscaling violation metrics, the scaling of the entropy in terms of the temperature (defined as the effective spatial dimensionality divided by the ... [Phys. Rev. D 91, 124038] Published Thu Jun 11, 2015

Description: Background: Understanding the mechanisms by which hundreds of diverse cell types develop from a single mammalian zygote has been a central challenge of developmental biology. Conrad H. Waddington, in his metaphoric “epigenetic landscape” visualized the early embryogenesis as a hierarchy of lineage bifurcations. In each bifurcation, a single progenitor cell type produces two different cell lineages. The tristable dynamical systems are used to model the lineage bifurcations. It is also shown that a genetic circuit consisting of two auto-activating transcription factors (TFs) with cross inhibitions can form a tristable dynamical system. Results: We used gene expression profiles of pre-implantation mouse embryos at the single cell resolution to visualize the Waddington landscape of the early embryogenesis. For each lineage bifurcation we identified two clusters of TFs – rather than two single TFs as previously proposed – that had opposite expression patterns between the pair of bifurcated cell types. The regulatory circuitry among each pair of TF clusters resembled a genetic circuit of a pair of single TFs; it consisted of positive feedbacks among the TFs of the same cluster, and negative interactions among the members of the opposite clusters. Our analyses indicated that the tristable dynamical system of the two-cluster regulatory circuitry is more robust than the genetic circuit of two single TFs. Conclusions: We propose that a modular hierarchy of regulatory circuits, each consisting of two mutually inhibiting and auto-activating TF clusters, can form hierarchical lineage bifurcations with improved safeguarding of critical early embryogenesis against biological perturbations. Furthermore, our computationally fast framework for modeling and visualizing the epigenetic landscape can be used to obtain insights from experimental data of development at the single cell resolution.

Description: Author(s): J. Cuerda, F. Rüting, F. J. García-Vidal, and J. Bravo-Abad In the context of plasmonic nanolasers, it has been previously recognized that systems with physically extended modes (as opposed to isolated cavity modes) can support lasing, and plasmonic crystals are a platform for such effects. In the present paper the authors present a general study that explores, from a unified perspective, the lasing properties of plasmonic crystals incorporating optically pumped four-level gain media. [Phys. Rev. B 91, 041118] Published Mon Jan 26, 2015

Description: Background: Poly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that have important functions in the regulation of translation and the control of mRNA stability in eukaryotes. Most PABPs encode a C-terminal domain known as the MLLE domain (previously PABC or CTC), which can mediate protein interactions. In earlier work we identified and predicted that four classes of MLLE-interacting proteins were present in Arabidopsis thaliana, which we named CID A, B, C, and D. These proteins encode transcription-activating domains (CID A), the Lsm and LsmAD domains of ataxin-2 (CID B), the CUE and small MutS-related domains (CID C), and two RNA recognition domains (CID D). We recently found that a novel class that lacks the LsmAD domain is present in CID B proteins. Results: We extended our analysis to other classes of CIDs present in the viridiplantae. We found that novel variants also evolved in classes CID A and CID C. A specific transcription factor domain is present in a distinct lineage in class A, and a variant that lacks at least two distinct domains was also identified in a divergent lineage in class C. We did not detect any variants in Class D CIDs. This class often consists of four to six highly conserved RNA-binding proteins, which suggests that major redundancy is present in this class. Conclusions: CIDs are likely to operate as components of posttranscriptional regulatory assemblies. The evident diversification of CIDs may be neutral or may be important for plant adaptation to the environment and for acquisition of specific traits during evolution. The fact that CIDs subclasses are maintained in early lineages suggest that a presumed interference between duplicates was resolved, and a defined function for each subclass was achieved.

Description: Author(s): Moisés Bravo-Gaete, Sebastián Gómez, and Mokhtar Hassaïne We first observe that for Lifshitz black holes of which the only charge is the mass, the resulting Smarr relation is a direct consequence of the Lifshitz Cardy formula. From this observation, we propose to extend the Cardy formula to the case of electrically charged Lifshitz black holes satisfying a… [Phys. Rev. D 92, 124002] Published Tue Dec 01, 2015

Description: Background: Current biomedical research needs to leverage and exploit the large amount of information reported in scientific publications. Automated text mining approaches, in particular those aimed at finding relationships between entities, are key for identification of actionable knowledge from free text repositories. We present the BeFree system aimed at identifying relationships between biomedical entities with a special focus on genes and their associated diseases. Results: By exploiting morpho-syntactic information of the text, BeFree is able to identify gene-disease, drug-disease and drug-target associations with state-of-the-art performance. The application of BeFree to real-case scenarios shows its effectiveness in extracting information relevant for translational research. We show the value of the gene-disease associations extracted by BeFree through a number of analyses and integration with other data sources. BeFree succeeds in identifying genes associated to a major cause of morbidity worldwide, depression, which are not present in other public resources. Moreover, large-scale extraction and analysis of gene-disease associations, and integration with current biomedical knowledge, provided interesting insights on the kind of information that can be found in the literature, and raised challenges regarding data prioritization and curation. We found that only a small proportion of the gene-disease associations discovered by using BeFree is collected in expert-curated databases. Thus, there is a pressing need to find alternative strategies to manual curation, in order to review, prioritize and curate text-mining data and incorporate it into domain-specific databases. We present our strategy for data prioritization and discuss its implications for supporting biomedical research and applications. Conclusions: BeFree is a novel text mining system that performs competitively for the identification of gene-disease, drug-disease and drug-target associations. Our analyses show that mining only a small fraction of MEDLINE results in a large dataset of gene-disease associations, and only a small proportion of this dataset is actually recorded in curated resources (2%), raising several issues on data prioritization and curation. We propose that joint analysis of text mined data with data curated by experts appears as a suitable approach to both assess data quality and highlight novel and interesting information.

Description: Author(s): Moisés Bravo-Gaete and Mokhtar Hassaïne In arbitrary dimension, we consider the Einstein-Maxwell Lagrangian supplemented by the more general quadratic-curvature corrections. For this model, we derive four classes of charged Lifshitz black hole solutions for which the metric function is shown to depend on a unique integration constant. The... [Phys. Rev. D 91, 064038] Published Mon Mar 16, 2015

Description: Author(s): Eloy Ayón-Beato, Moisés Bravo-Gaete, Francisco Correa, Mokhtar Hassaïne, María Montserrat Juárez-Aubry, and Julio Oliva The aim of this paper is to confirm in new concrete examples that the semiclassical entropy of a three-dimensional Lifshitz black hole can be recovered through an anisotropic generalization of the Cardy formula derived from the growth of the number of states of a boundary nonrelativistic field theor... [Phys. Rev. D 91, 064006] Published Mon Mar 02, 2015