Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

Yeast glycolysis is considered the prototype of dissipative biochemical oscillators. In cellular conditions, under sinusoidal source of glucose, the activity of glycolytic enzymes can display either periodic, quasiperiodic or chaotic behavior. In order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the non-linear statistical tool of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic speed functions of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. In agreement with experimental conditions, the studied time series corresponded to a quasi-periodic route to chaos. The results of the analysis are three-fold: first, in addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. Second, the dynamical structure exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis.Comment: Biologically improve

Translation And Interpreting: Volunteer Work And Social Commitment

This article is a presentation of ECOS, Traductores e Intérpretes por la Solidaridad (ECOS, Translators and Interpreters for Solidarity), an association based in the Faculty of Translation and Interpreting at the University of Granada. It reviews the history of the association, its philosophy and current lines of work. After a brief explanation of what we at ECOS understand by social commitment in translation and interpreting, it proceeds to an outline of the boundaries of this concept: who the volunteers are; how, when and where they do their work. It explains, too, that community interpreting is not the same as volunteer work, and reviews volunteer organizations in translation and interpreting, both in Spain and at the international level. Then it discusses the relation between social commitment and training in translation and interpreting, defending the view that translators and interpreters must be trained for society and not just for the market. Finally, the authors conclude with a call to create networks of volunteer translators and interpreters, to supply a consistent standard of work at the local and world level, in the framework of international social forums

Polyglutamine-expanded androgen receptor interferes with TFEB to elicit autophagy defects in SBMA.

Macroautophagy (hereafter autophagy) is a key pathway in neurodegeneration. Despite protective actions, autophagy may contribute to neuron demise when dysregulated. Here we consider X-linked spinal and bulbar muscular atrophy (SBMA), a repeat disorder caused by polyglutamine-expanded androgen receptor (polyQ-AR). We found that polyQ-AR reduced long-term protein turnover and impaired autophagic flux in motor neuron-like cells. Ultrastructural analysis of SBMA mice revealed a block in autophagy pathway progression. We examined the transcriptional regulation of autophagy and observed a functionally significant physical interaction between transcription factor EB (TFEB) and AR. Normal AR promoted, but polyQ-AR interfered with, TFEB transactivation. To evaluate physiological relevance, we reprogrammed patient fibroblasts to induced pluripotent stem cells and then to neuronal precursor cells (NPCs). We compared multiple SBMA NPC lines and documented the metabolic and autophagic flux defects that could be rescued by TFEB. Our results indicate that polyQ-AR diminishes TFEB function to impair autophagy and promote SBMA pathogenesis

A method for synthetic LiDAR generation to create annotated datasets for autonomous vehicles perception

Proceedings of: 2019 IEEE Intelligent Transportation Systems Conference (ITSC)LiDAR devices have become a key sensor for autonomous vehicles perception due to their ability to capture reliable geometry information. Indeed, approaches processing LiDAR data have shown an impressive accuracy for 3D object detection tasks, outperforming methods solely based on image inputs. However, the wide diversity of on-board sensor configurations makes the deployment of published algorithms into real platforms a hard task, due to the scarcity of annotated datasets containing laser scans. We present a method to generate new point clouds datasets as captured by a real LiDAR device. The proposed pipeline makes use of multiple frames to perform an accurate 3D reconstruction of the scene in the spherical coordinates system that enables the simulation of the sweeps of a virtual LiDAR sensor, configurable both in location and inner specifications. The similarity between real data and the generated synthetic clouds is assessed through a set of experiments performed using KITTI Depth and Object Benchmarks.Research supported by the Spanish Government through the CICYT projects (TRA2016-78886-C3-1-R and RTI2018-096036-B-C21), and the Comunidad de Madrid through SEGVAUTO-4.0-CM (P2018/EMT-4362). We gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research

Assessing the role of high-frequency winds and sea ice loss on arctic phytoplankton blooms in an ice-ocean-biogeochemical model

Identificadors digitals: Digital object identifier for the 'European Research Council' (http://dx.doi.org/10.13039/501100000781) and Digital object identifier for 'Horizon 2020' (http://dx.doi.org/10.13039/501100007601)Unidad de excelencia María de Maeztu MdM-2015-0552The long-term trend of increasing phytoplankton net primary production (NPP) in the Arctic correlates with increasing light penetration due to sea ice loss. However, recent studies suggest that enhanced stormy wind mixing may also play a significant role enhancing NPP. Here, we isolate the role of sea ice and stormy winds (hereafter high-frequency winds) using an eddy-permitting ice-ocean-biogeochemical model configured for the North Atlantic and the Arctic. In the model, the presence of high-frequency winds stimulates nutrient upwelling by producing an earlier and longer autumn-winter mixing period with deeper mixing layer. The early onset of autumn mixing results in nutrients being brought-up to near-surface waters before the light becomes the dominant limiting factor, which leads to the autumn bloom. The enhanced mixing results in higher nutrient concentrations in spring and thus a large spring bloom. The model also shows significant iron limitation in the Labrador Sea, which is intensified by high-frequency winds. The effect of sea ice loss on NPP was found to be regionally dependent on the presence of high-frequency winds. This numerical study suggests high-frequency winds play significant role increasing NPP in the Arctic and sub-Arctic by alleviating phytoplankton nutrient limitation and that the isolated effect of sea ice loss on light plays a comparatively minor role

Estructuras anulares en la cordillera oriental de colombia y su relación a fenómenos diapíricos

There is a wide area, in the Cordillera Oriental of Colombia, which presents very specialgeographic and geologic characteristics. In the same zone there are some very well defined types of mineralization, which do not appear in the rest of the country.  The tectonics of the zone presents not well explained particularities. The zone extends from Villarrica (Tolima) (southern part) to Mesa de Los Santos and Sierra del Cocuy piedmont (north); and from the Borde Llanero fault to the east, to Bituima and Salina faults to the west

The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

[Background] Experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a metabolic core formed by a set of enzymatic reactions which are always active under all environmental conditions, while the rest of catalytic processes are only intermittently active. The reactions of the metabolic core are essential for biomass formation and to assure optimal metabolic performance. The on-off catalytic reactions and the metabolic core are essential elements of a Systemic Metabolic Structure which seems to be a key feature common to all cellular organisms. [Methodology/Principal Findings] In order to investigate the functional importance of the metabolic core we have studied different catalytic patterns of a dissipative metabolic network under different external conditions. The emerging biochemical data have been analysed using information-based dynamic tools, such as Pearson's correlation and Transfer Entropy (which measures effective functionality). Our results show that a functional structure of effective connectivity emerges which is dynamical and characterized by significant variations of bio-molecular information flows. [Conclusions/Significance] We have quantified essential aspects of the metabolic core functionality. The always active enzymatic reactions form a hub –with a high degree of effective connectivity- exhibiting a wide range of functional information values being able to act either as a source or as a sink of bio-molecular causal interactions. Likewise, we have found that the metabolic core is an essential part of an emergent functional structure characterized by catalytic modules and metabolic switches which allow critical transitions in enzymatic activity. Both, the metabolic core and the catalytic switches in which also intermittently-active enzymes are involved seem to be fundamental elements in the self-regulation of the Systemic Metabolic Structure.Consejo Superior de Investigaciones Cientificas (CSIC),grant 201020I026. Ministerio de Ciencia e Innovacion (MICINN). Programa Ramon y Cajal. Campus de Excelencia Internacional CEI BioTIC GENIL, grant PYR-2010-14. Junta de Andalucia, grant P09-FQM-4682

Antibody Mediated Rejection and T-cell Mediated Rejection Molecular Signatures Using Next-Generation Sequencing in Kidney Transplant Biopsies

Kidney biopsies; Kidney transplantation; Next generation sequencingBiopsias de riñón; Trasplante de riñón; Secuenciación de nueva generaciónBiòpsies de ronyó; Trasplantament de ronyó; Seqüenciació de nova generacióRecently, interest in transcriptomic assessment of kidney biopsies has been growing. This study investigates the use of NGS to identify gene expression changes and analyse the pathways involved in rejection. An Illumina bulk RNA sequencing on the polyadenylated RNA of 770 kidney biopsies was conducted. Differentially-expressed genes (DEGs) were determined for AMR and TCMR using DESeq2. Genes were segregated according to their previous descriptions in known panels (microarray or the Banff Human Organ Transplant (B-HOT) panel) to obtain NGS-specific genes. Pathway enrichment analysis was performed using the Reactome and Kyoto Encyclopaedia of Genes and Genomes (KEGG) public repositories. The differential gene expression using NGS analysis identified 6,141 and 8,478 transcripts associated with AMR and TCMR. While most of the genes identified were included in the microarray and the B-HOT panels, NGS analysis identified 603 (9.8%) and 1,186 (14%) new specific genes. Pathways analysis showed that the B-HOT panel was associated with the main immunological processes involved during AMR and TCMR. The microarrays specifically integrated metabolic functions and cell cycle progression processes. Novel NGS-specific based transcripts associated with AMR and TCMR were discovered, which might represent a novel source of targets for drug designing and repurposing.The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. The EU-TRAIN study was funded by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 754995. The KTD-Innov study was funded by the French government, with financial support managed by the National Research Agency (ANR) under the program “Investissements d’avenir,” with the grant agreement no. ANR-17-RHUS-0010. INSERM-Action thématique incitative sur programme Avenir (ATIP-Avenir) provided financial support