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NeuroImage Dec 2022In primates, faces and bodies activate distinct regions in the inferior temporal (IT) cortex and are typically studied separately. Yet, primates interact with whole...
In primates, faces and bodies activate distinct regions in the inferior temporal (IT) cortex and are typically studied separately. Yet, primates interact with whole agents and not with random concatenations of faces and bodies. Despite its social importance, it is still poorly understood how faces and bodies interact in IT. Here, we addressed this gap by measuring fMRI activations to whole agents and to unnatural face-body configurations in which the head was mislocated with respect to the body, and examined how these relate to the sum of the activations to their corresponding faces and bodies. First, we mapped patches in the IT of awake macaques that were activated more by images of whole monkeys compared to objects and found that these mostly overlapped with body and face patches. In a second fMRI experiment, we obtained no evidence for superadditive responses in these "monkey patches", with the activation to the monkeys being less or equal to the summed face-body activations. However, monkey patches in the anterior IT were activated more by natural compared to unnatural configurations. The stronger activations to natural configurations could not be explained by the summed face-body activations. These univariate results were supported by regression analyses in which we modeled the activations to both configurations as a weighted linear combination of the activations to the faces and bodies, showing higher regression coefficients for the natural compared to the unnatural configurations. Deeper layers of trained convolutional neural networks also contained units that responded more to natural compared to unnatural monkey configurations. Unlike the monkey fMRI patches, these units showed substantial superadditive responses to the natural configurations. Our monkey fMRI data suggest configuration-sensitive face-body interactions in anterior IT, adding to the evidence for an integrated face-body processing in the primate ventral visual stream, and open the way for mechanistic studies using single unit recordings in these patches.
Topics: Animals; Brain Mapping; Pattern Recognition, Visual; Photic Stimulation; Temporal Lobe; Magnetic Resonance Imaging; Macaca
PubMed: 36216293
DOI: 10.1016/j.neuroimage.2022.119676 -
The Science of the Total Environment Feb 2023Nitrogen (N) is a macronutrient that, together with P and K, is vital for improving agricultural yields, but its excessive use in crop fertilisation and presence in...
Nitrogen (N) is a macronutrient that, together with P and K, is vital for improving agricultural yields, but its excessive use in crop fertilisation and presence in treated wastewater and sludge are generating emissions both into the atmosphere and into natural water bodies, which leads to eutrophication events. The Haber-Bosch process is energy-intensive and it is the main chemical route to produce reactive nitrogen for the production of fertilisers. Furthermore, there is a strong dependence on imports of reactive nitrogen in Spain and Europe. For these reasons, it is necessary to propose sustainable alternatives that allow solving environmental and supply problems, in addition to proposing efficient management schemes that fit into the circular economy approach. In this context, a nitrogen flow analysis (NFA) was carried out for Spain with the year 2016 as reference. To assess some interactions and flows of N, specific sub-models were also considered for the agriculture and waste management systems. For the food and non-food flow systems, country-specific data were considered. The sectors covered were crop production (CP), animal production (AP), food processing (FP), non-food production (NF) and human consumption (HC). The results reveal a total annual import of 2142 kt N/y, of which 43 % accumulated in stocks of soils and water bodies (913 kt N/y). The largest proportion of losses was associated with emissions from agriculture (724 kt N/y to water bodies and 132 kt N/y accumulated in soils), followed by industry emissions to the atmosphere (122 kt N/y). Wastewater treatment plants (WWTPs) received around 67 kt N/y, of which 26 % was removed as biosolids and 20 % of these biosolids were recovered to be used for fertilising applications. The 49 kt N/y discharged in the final treated effluent represented 79 % of the total loss of reactive nitrogen to water bodies. In addition, an analysis of N-use efficiency and the actions required for its improvement in Spain, as well as the impact of the current diet on the N cycle, was carried out.
Topics: Humans; Nitrogen; Spain; Europe; Water
PubMed: 36372164
DOI: 10.1016/j.scitotenv.2022.160117 -
Frontiers in Cellular Neuroscience 2019Circadian rhythms are biological variables that oscillate with periods close to 24 h that are generated internally by biological clocks. Depending on the tissue/cell...
Circadian rhythms are biological variables that oscillate with periods close to 24 h that are generated internally by biological clocks. Depending on the tissue/cell type, about 5-20% of genes are expressed rhythmically. Unexpectedly, the correlation between the oscillations of messengers and the proteins they encode is low. We hypothesize that these discrepancies could be because in certain phases of the circadian cycle some messengers could be translationally silenced and stored. Processing bodies (PBs) are membraneless organelles formed by ribonucleoprotein aggregates located in the cytoplasm. They contain silenced messengers and factors involved in mRNA processing. A previous work showed that the number of cells containing these mRNA granules varies when comparing two time-points in U2OS cell cultures and that these differences disappear when an essential clock gene is silenced. Here we evaluate whether PBs oscillate in Neuro2A cells. We analyzed in cell cultures synchronized with dexamethasone the variations in the number, the signal intensity of the markers used (GE-1/HEDLS and DDX6), and the area of PBs between 8 and 68 h post-synchronization. All three parameters oscillated with periods compatible with a circadian regulated process. The most robust rhythm was the number of PBs. These rhythms could be generated by oscillations in proteins that have been involved in the nucleation of these foci such as LSM1, TTP, and BRF1. The described phenomenon would allow to explain the differences observed in the temporal profiles of some messengers and their proteins and to understand how circadian clocks can control post-transcriptionally cellular functions.
PubMed: 31736713
DOI: 10.3389/fncel.2019.00487 -
Folia Morphologica 2020Nuclear bodies (NB) are membrane-less subnuclear organelles that perform important functions in the cell, such as transcription, RNA splicing, processing and transport...
BACKGROUND
Nuclear bodies (NB) are membrane-less subnuclear organelles that perform important functions in the cell, such as transcription, RNA splicing, processing and transport of ribosomal pre-RNA, epigenetic regulation, and others. The aim of the work was to analyse the classification of NB in the Terminologia Histologica (TH) and biological and bibliographical databases.
MATERIALS AND METHODS
The semantic structure of the Nucleoplasm section in the TH was analysed and unsystematic bibliographical search was made in the PubMed, SciELO, EMBASE databases and European Bioinformatics Institute (EMBL-EBI) biology database to identify which structures are classified as NB.
RESULTS
It was found that the terms Corpusculum convolutum, Macula interchromatinea and Corpusculum PML are not correctly classified in the TH, since they are subordinated under the term Chromatinum and not under Corpusculum nucleare. The bibliography consulted showed that 100%, 92.6% and 81.5% of articles mentioned Corpusculum convolutum, Macula interchromatinea and Corpusculum PML, respectively as nuclear bodies.
CONCLUSIONS
It is suggested to relocate the terms Corpusculum convolutum, Macula interchromatinea and Corpusculum PML with the name of Corpusculum nucleare and the incorporation of two new entities to the Histological Terminology according to the information collected: paraspeckles and histone locus body.
Topics: Cell Nucleus; Humans; Terminology as Topic
PubMed: 31448403
DOI: 10.5603/FM.a2019.0091 -
Virology Aug 2022In the adenovirus-infected cells, virus mRNAs are selectively exported to the cytoplasm by virus early gene products to facilitate virus replication. We previously...
In the adenovirus-infected cells, virus mRNAs are selectively exported to the cytoplasm by virus early gene products to facilitate virus replication. We previously showed AU-rich elements (AREs) containing mRNAs are exported to the cytoplasm and stabilized in infected cells. Here, we analyzed ribonucleoprotein (RNP) granules in the cytoplasm that are involved in mRNA degradation to elucidate the mechanism of ARE-mRNA stabilization in adenovirus infected cells. Our findings showed that processing bodies (PBs) aggregate, then almost all PBs are translocated to aggresomes formed by adenoviral gene products during the late phase of infection. Furthermore, E4orf3 was required for the PBs translocation, and the same domains of E4orf3-mutants required to change the form of promyelocytic leukemia bodies were also needed for PBs translocation. Luciferase activity showed that these domains were critical for miRNA- and ARE-mediated mRNA decay. These findings suggest that adenovirus changes the behavior of PBs to prevent ARE-mRNA downregulation.
Topics: Adenoviridae; Adenoviridae Infections; Cytoplasm; Humans; Processing Bodies; RNA, Messenger; Viral Proteins; Virus Replication
PubMed: 35779334
DOI: 10.1016/j.virol.2022.06.009 -
Molecular Horticulture Aug 2023The CCCH proteins play important roles in plant growth and development, hormone response, pathogen defense and abiotic stress tolerance. However, the knowledge of their...
The CCCH proteins play important roles in plant growth and development, hormone response, pathogen defense and abiotic stress tolerance. However, the knowledge of their roles in thermotolerance are scarce. Here, we identified a heat-inducible CCCH gene LlC3H18 from lily. LlC3H18 was localized in the cytoplasm and nucleus under normal conditions, while it translocated in the cytoplasmic foci and co-located with the markers of two messenger ribonucleoprotein (mRNP) granules, processing bodies (PBs) and stress granules (SGs) under heat stress conditions, and it also exhibited RNA-binding ability. In addition, LlC3H18 exhibited transactivation activity in both yeast and plant cells. In lily and Arabidopsis, overexpression of LlC3H18 damaged their thermotolerances, and silencing of LlC3H18 in lily also impaired its thermotolerance. Similarly, Arabidopsis atc3h18 mutant also showed decreased thermotolerance. These results indicated that the appropriate expression of C3H18 was crucial for establishing thermotolerance. Further analysis found that LlC3H18 directly bound to the promoter of LlWRKY33 and activated its expression. Besides, it was found that LlMYB305 acted as an upstream factor of LlC3H18 and activated its expression. In conclusion, we demonstrated that there may be a LlMYB305-LlC3H18-LlWRKY33 regulatory module in lily that is involved in the establishment of thermotolerance and finely regulates heat stress response.
PubMed: 37789438
DOI: 10.1186/s43897-023-00064-1 -
NMR in Biomedicine Jul 2023In recent years, MRS has benefited from increased MRI field strengths, new acquisition protocols and new processing techniques. This review aims to determine how this... (Review)
Review
BACKGROUND
In recent years, MRS has benefited from increased MRI field strengths, new acquisition protocols and new processing techniques. This review aims to determine how this has altered our understanding of MRS neurometabolic markers in neurodegenerative dementias.
METHODS
Our systematic review of human in vivo MRS literature since 2002 pertains to Alzheimer's disease (AD), dementia with Lewy bodies (DLB), Parkinson's disease dementia, frontotemporal dementia (FTD), prodromal and 'at-risk' states. Studies using field strengths of 3 T or more were included.
RESULTS
Of 85 studies, AD and/or mild cognitive impairment (MCI) were the most common conditions of interest (58 papers, 68%). Only 14 (16%) studies included other dementia syndromes and 13 (15%) investigated 'at-risk' cohorts. Earlier findings of lower N-acetylaspartate and higher myo-inositol were confirmed. Additionally, lower choline and creatine in AD and MCI were reported, though inconsistently. Previously challenging-to-measure metabolites (glutathione, glutamate and gamma-aminobutyric acid) were reportedly lower in AD, FTD and DLB compared with controls.
DISCUSSION
Increasing field strength alongside targeted acquisition protocols has revealed additional metabolite changes. Most studies were small and regional metabolite differences between dementia types may not have been captured due to the predominant placement of voxels in the posterior cingulate cortex. The standard of data collection, quality control and analysis is improving due to greater consensus regarding acquisition and processing techniques. Ongoing harmonization of techniques, creation of larger and longitudinal cohorts, and placement of MRS voxels in more diverse regions will strengthen future research.
Topics: Humans; Frontotemporal Dementia; Prodromal Symptoms; Parkinson Disease; Alzheimer Disease; Magnetic Resonance Imaging
PubMed: 36624067
DOI: 10.1002/nbm.4896 -
Journal of Molecular Biology Mar 2023Eukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism. Drosophila melanogaster genome encodes eight eIF4E...
Eukaryotic translation initiation factor 4E (eIF4E) is a key factor involved in different aspects of mRNA metabolism. Drosophila melanogaster genome encodes eight eIF4E isoforms, and the canonical isoform eIF4E-1 is a ubiquitous protein that plays a key role in mRNA translation. eIF4E-3 is specifically expressed in testis and controls translation during spermatogenesis. In eukaryotic cells, translational control and mRNA decay is highly regulated in different cytoplasmic ribonucleoprotein foci, which include the processing bodies (PBs). In this study, we show that Drosophila eIF4E-1 and eIF4E-3 occur in PBs along the DEAD-box RNA helicase Me31B. We show that Me31B interacts with eIF4E-1 and eIF4E-3 by means of yeast two-hybrid system, FRET in D. melanogaster S2 cells and coimmunoprecipitation in testis. Truncation and point mutations of Me31B proteins show two eIF4E-binding sites located in different protein domains. Residues Y401-L407 (at the carboxy-terminus) are essential for interaction with eIF4E-1, whereas residues F63-L70 (at the amino-terminus) are critical for interaction with eIF4E-3. The residue W117 in eIF4E-1 and the homolog position F103 in eIF4E-3 are necessary for Me31B-eIF4E interaction suggesting that the change of tryptophan to phenylalanine provides specificity. Me31B represents a novel type of eIF4E-interacting protein with dual and specific interaction domains that might be recognized by different eIF4E isoforms in different tissues, adding complexity to the control of gene expression in eukaryotes.
Topics: Animals; Male; Drosophila melanogaster; Drosophila Proteins; Eukaryotic Initiation Factor-4E; Protein Binding; Protein Biosynthesis; Protein Isoforms; Protein Interaction Domains and Motifs
PubMed: 36638908
DOI: 10.1016/j.jmb.2023.167949 -
Journal of Virology Sep 2021Several viruses have been proven to inhibit the formation of RNA processing bodies (P-bodies); however, knowledge regarding whether enterovirus blocks P-body formation...
Several viruses have been proven to inhibit the formation of RNA processing bodies (P-bodies); however, knowledge regarding whether enterovirus blocks P-body formation remains unclear, and the detailed molecular mechanisms and functions of picornavirus regulation of P-bodies are limited. Here, we show the crucial role of 2A protease in inhibiting P-bodies to promote viral replication during enterovirus 71 infection. Moreover, we found that the activity of 2A protease is essential to inhibit P-body formation, which was proven by the result that infection with EV71-2A, a 2A protease activity-inactivated recombinant virus, failed to block the formation of P-bodies. Furthermore, we show that DDX6, a scaffolding protein of P-bodies, interacted with viral RNA to facilitate viral replication rather than viral translation, by using a luciferase mRNA reporter system and nascent RNA capture assay. Altogether, our data first demonstrate that the 2A protease of enterovirus inhibits P-body formation to facilitate viral RNA synthesis by recruiting the P-body components to viral RNA. Processing bodies (P-bodies) are constitutively present in eukaryotic cells and play an important role in the mRNA cycle, including regulation of gene expression and mRNA degradation. The P-body is the structure that viruses manipulate to facilitate their survival. Here, we show that the 2A protease alone was efficient to block P-body formation during enterovirus 71 infection, and its activity is essential. When the assembly of P-bodies was blocked by 2A protease, DDX6 and 4E-T, which were required for P-body formation, bound to viral RNA to facilitate viral RNA synthesis. We propose a model revealing that EV71 manipulates P-body formation to generate an environment that is conducive to viral replication by facilitating viral RNA synthesis: 2A protease blocked P-body assembly to make it possible for virus to take advantage of P-body components.
Topics: Cell Line, Tumor; Cytoplasmic Granules; DEAD-box RNA Helicases; Enterovirus A, Human; HeLa Cells; Humans; Nucleocytoplasmic Transport Proteins; Peptide Hydrolases; Proto-Oncogene Proteins; RNA, Viral; Ribonucleoproteins; Virus Replication
PubMed: 34287048
DOI: 10.1128/JVI.00922-21 -
PloS One 2022Across three experiments (N = 302), we explored whether people cognitively elaborate humanoid robots as human- or object-like. In doing so, we relied on the inversion...
Across three experiments (N = 302), we explored whether people cognitively elaborate humanoid robots as human- or object-like. In doing so, we relied on the inversion paradigm, which is an experimental procedure extensively used by cognitive research to investigate the elaboration of social (vs. non-social) stimuli. Overall, mixed-model analyses revealed that full-bodies of humanoid robots were subjected to the inversion effect (body-inversion effect) and, thus, followed a configural processing similar to that activated for human beings. Such a pattern of finding emerged regardless of the similarity of the considered humanoid robots to human beings. That is, it occurred when considering bodies of humanoid robots with medium (Experiment 1), high and low (Experiment 2) levels of human likeness. Instead, Experiment 3 revealed that only faces of humanoid robots with high (vs. low) levels of human likeness were subjected to the inversion effects and, thus, cognitively anthropomorphized. Theoretical and practical implications of these findings for robotic and psychological research are discussed.
Topics: Cognition; Humans; Robotics
PubMed: 35881625
DOI: 10.1371/journal.pone.0270787