Institution
Fundación Instituto Leloir
Facility•Buenos Aires, Argentina•
About: Fundación Instituto Leloir is a facility organization based out in Buenos Aires, Argentina. It is known for research contribution in the topics: Dentate gyrus & Neurogenesis. The organization has 702 authors who have published 1052 publications receiving 39299 citations.
Topics: Dentate gyrus, Neurogenesis, RNA, Arabidopsis, Gene
Papers published on a yearly basis
Papers
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TL;DR: A model was used to simulate phytochrome B activity under a range of field conditions and provided values of phyB activity that predicted hypocotyl growth in the field with reasonable accuracy, and defined two scenarios, one is under shade, in cloudy weather, at the extremes of the photoperiod or in the presence of rapid fluctuations of the light environment caused by wind-induced movements of the foliage.
Abstract: Vegetation shade is characterized by marked decreases in the red/far-red ratio and photosynthetic irradiance. The activity of phytochrome in the field has typically been described by its photoequilibrium, defined by the photochemical properties of the pigment in combination with the spectral distribution of the light. This approach represents an oversimplification because phytochrome B (phyB) activity depends not only on its photochemical reactions but also on its rates of synthesis, degradation, translocation to the nucleus, and thermal reversion. To account for these complex cellular reactions, we used a model to simulate phyB activity under a range of field conditions. The model provided values of phyB activity that in turn predicted hypocotyl growth in the field with reasonable accuracy. On the basis of these observations, we define two scenarios, one is under shade, in cloudy weather, at the extremes of the photoperiod or in the presence of rapid fluctuations of the light environment caused by wind-induced movements of the foliage, where phyB activity departs from photoequilibrium and becomes affected by irradiance and temperature in addition to the spectral distribution. The other scenario is under full sunlight, where phyB activity responds mainly to the spectral distribution of the light.
27 citations
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TL;DR: The TDR Targets database now facilitates the investigation of drug repurposing against pathogen targets, which can potentially help in identifying candidate targets for bioactive compounds with previously unknown targets.
Abstract: The volume of biological, chemical and functional data deposited in the public domain is growing rapidly, thanks to next generation sequencing and highly-automated screening technologies. These datasets represent invaluable resources for drug discovery, particularly for less studied neglected disease pathogens. To leverage these datasets, smart and intensive data integration is required to guide computational inferences across diverse organisms. The TDR Targets chemogenomics resource integrates genomic data from human pathogens and model organisms along with information on bioactive compounds and their annotated activities. This report highlights the latest updates on the available data and functionality in TDR Targets 6. Based on chemogenomic network models providing links between inhibitors and targets, the database now incorporates network-driven target prioritizations, and novel visualizations of network subgraphs displaying chemical- and target-similarity neighborhoods along with associated target-compound bioactivity links. Available data can be browsed and queried through a new user interface, that allow users to perform prioritizations of protein targets and chemical inhibitors. As such, TDR Targets now facilitates the investigation of drug repurposing against pathogen targets, which can potentially help in identifying candidate targets for bioactive compounds with previously unknown targets. TDR Targets is available at https://tdrtargets.org.
27 citations
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TL;DR: It is found that activating mutations of PKs constitute a distinct group of drivers and that specific bioinformatics tools are needed to identify them in the numerous cancer sequencing projects currently underway.
Abstract: Mutations leading to activation of proto-oncogenic protein kinases (PKs) are a type of drivers crucial for understanding tumorogenesis and as targets for antitumor drugs. However, bioinformatics tools so far developed to differentiate driver mutations, typically based on conservation considerations, systematically fail to recognize activating mutations in PKs. Here, we present the first comprehensive analysis of the 407 activating mutations described in the literature, which affect 41 PKs. Unexpectedly, we found that these mutations do not associate with conserved positions and do not directly affect ATP binding or catalytic residues. Instead, they cluster around three segments that have been demonstrated to act, in some PKs, as "molecular brakes" of the kinase activity. This finding led us to hypothesize that an auto inhibitory mechanism mediated by such "brakes" is present in all PKs and that the majority of activating mutations act by releasing it. Our results also demonstrate that activating mutations of PKs constitute a distinct group of drivers and that specific bioinformatics tools are needed to identify them in the numerous cancer sequencing projects currently underway. The clustering in three segments should represent the starting point of such tools, a hypothesis that we tested by identifying two somatic mutations in EPHA7 that might be functionally relevant.
27 citations
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TL;DR: In this paper, the authors evaluated transcriptome-wide changes in stratified seeds irradiated with a pulse of red (Rp) or far-red (FRp) by RNA sequencing (RNA-seq).
Abstract: Seed dormancy and germination are relevant processes for a successful seedling establishment in the field. Light is one of the most important environmental factors involved in the relief of dormancy to promote seed germination. In Arabidopsis thaliana seeds, phytochrome photoreceptors tightly regulate gene expression at different levels. The contribution of alternative splicing (AS) regulation in the photocontrol of seed germination is still unknown. The aim of this work is to study gene expression modulated by light during germination of A. thaliana seeds, with focus on AS changes. Hence, we evaluated transcriptome-wide changes in stratified seeds irradiated with a pulse of red (Rp) or far-red (FRp) by RNA sequencing (RNA-seq). Our results show that the Rp changes the expression of ∼20% of the transcriptome and modifies the AS pattern of 226 genes associated with mRNA processing, RNA splicing, and mRNA metabolic processes. We further confirmed these effects for some of the affected AS events. Interestingly, the reverse transcriptase-polymerase chain reaction (RT-PCR) analyses show that the Rp modulates the AS of splicing-related factors (At-SR30, At-RS31a, At-RS31, and At-U2AF65A), a light-signaling component (At-PIF6), and a dormancy-related gene (At-DRM1). Furthermore, while the phytochrome B (phyB) is responsible for the AS pattern changes of At-U2AF65A and At-PIF6, the regulation of the other AS events is independent of this photoreceptor. We conclude that (i) Rp triggers AS changes in some splicing factors, light-signaling components, and dormancy/germination regulators; (ii) phyB modulates only some of these AS events; and (iii) AS events are regulated by R and FR light, but this regulation is not directly associated with the intensity of germination response. These data will help in boosting research in the splicing field and our understanding about the role of this mechanism during the photocontrol of seed germination.
27 citations
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TL;DR: The purpose of this chapter is to discuss the circadian control of clock outputs, spanning the most immediate ones within pacemaker neurons to the circadian modulation of different behaviors, with a focus on the examples that shed light on the surprising degree of plasticity that characterizes the underlying circuits.
Abstract: Over the years it has become clear that the biological clock acts at different levels, ranging from the control of gene expression, protein stability, or subcellular localization of key proteins, to the fine tuning of network properties and modulation of input signals, ultimately ensuring that the organism will be best synchronized to a changing environment at the physiological and behavioral levels. The purpose of this chapter is to discuss the circadian control of clock outputs, spanning the most immediate ones within pacemaker neurons (i.e., membrane excitability, release of neurotransmitters, structural changes) to the circadian modulation of different behaviors (locomotor activity, learning and memory, social interaction), with a focus on the examples that shed light on the surprising degree of plasticity that characterizes the underlying circuits.
27 citations
Authors
Showing all 707 results
Name | H-index | Papers | Citations |
---|---|---|---|
Jorge J. Casal | 61 | 182 | 10814 |
Silvia N.J. Moreno | 61 | 225 | 10585 |
Won Sang Park | 58 | 227 | 10501 |
Su Young Kim | 51 | 198 | 8829 |
Marcelo J. Yanovsky | 44 | 93 | 7949 |
Mario D. Galigniana | 40 | 99 | 5257 |
Eduardo M. Castaño | 40 | 89 | 7125 |
Andrea V. Gamarnik | 38 | 82 | 5896 |
Osvaldo L. Podhajcer | 35 | 122 | 4996 |
Alejandro F. Schinder | 34 | 64 | 10256 |
Juliana Idoyaga | 32 | 63 | 5326 |
Fernando Alberto Goldbaum | 32 | 103 | 3385 |
Fernando Juan Pitossi | 31 | 65 | 4489 |
Kevin Gaston | 29 | 78 | 2725 |
Jong Woo Lee | 29 | 77 | 3453 |