Biology subjects

Pinheiro, A.

Publications and source records attributed to Pinheiro, A..

9 recordsLinked to original sources

bioRxiv2024

Not enough pleasure? Influence of hallucination proneness on sensory feedback processing of positive self-voice

Ample research explored changes in sensory feedback processing of the self-voice as well as the control of attention allocation in voice hearers, including both non-clinical voice hearers and voice hearers with a psychotic disorder. While the attentional bias toward negative emotional information in voice hearers with a psychotic disorder due to heightened sensitivity towards threat/danger is well established, it remains unclear how positive emotion captures or controls attention. Manipulating the certainty of sensory feedback to the self-voice, transitioning from fully neutral to entirely positive (100% neutral, 60-40% neutral-pleasure, 50-50% neutral-pleasure, 40-60% neutral-pleasure, 100% pleasure), provides an opportunity to investigate attentional control and sensory feedback processing in positive self-voice as a function of hallucination proneness (HP). Participants with different HP scores self-generated and passively listened to their own voices during EEG recordings. N100 or P200 responses to self-generated and externally-generated self-voices did not differ. Further, HP did not modulate N100/P200 responses. These null findings might result from the minimal perceptual discriminability among the five types of voices varying in pleasure content. This might have led to less variation in certainty regarding the sensory feedback to self-voice, and consequently a lack of differential engagement of attentional resources. The lack of a global N100 suppression effect prompts inquiry into the association of sense of ownership/agency and pleasure.

neuroscience↗

bioRxiv2024

The Dlk1-Dio3 noncoding RNA cluster coordinately regulates mitochondrial respiration and chromatin structure to establish proper cell state for muscle differentiation

The coordinate regulation of metabolism and epigenetics to establish cell state-specific gene expression patterns during lineage progression is a central aspect of cell differentiation, but the factors that regulate this elaborate interplay are not well-defined. The imprinted Dlk1-Dio3 noncoding RNA (ncRNA) cluster has been associated with metabolism in various progenitor cells, suggesting it functions as a regulator of metabolism and cell state. Here, we directly demonstrate that the Dlk1-Dio3 ncRNA cluster coordinates mitochondrial respiration and chromatin structure to maintain proper cell state. Stable muscle cell lines were generated harboring two distinct deletions in the proximal promoter region resulting in either greatly upregulated or downregulated expression of the entire Dlk1-Dio3 ncRNA cluster. Both mutant lines displayed impaired muscle differentiation along with altered mitochondrial respiration and genome-wide changes in chromatin accessibility and histone methylation. Global gene expression patterns and pathway analyses indicated a reprogramming of myogenic cell state creating a differentiated-like phenotype in proliferating myoblasts. Our results strongly suggest the Dlk1-Dio3 ncRNA locus is a nodal regulator coordinating metabolic activity and the epigenome to maintain proper cell state in the myogenic lineage. Summary statementMuscle cell state is regulated by the imprinted Dlk1-Dio3 noncoding RNA locus through its coordinate control of mitochondrial activity and histone modifications.

developmental biology↗

bioRxiv2023

Exploring Neural Dynamics in Self-Voice Processing and Perception: Implications for Hallucination Proneness.

Altered sensory feedback processing and attention control are assumed to contribute to auditory verbal hallucinations, which are experienced by the general population and patients with psychosis, implying a continuum of hallucination proneness (HP). However, the interaction of altered sensory feedback processing and attention control along this HP continuum remains unclear. Manipulating the level of certainty of sensory feedback by changing self-voice quality (100% neutral, 60-40% neutral-angry, 50-50% neutral-angry, 40-60% neutral-angry, 100% angry) in individuals varying in HP, we tested this interaction using electroencephalography while participants self-generated or passively listened to their voices. Regardless of voice quality, HP modulated the N100 and P200 suppression effects. High HP individuals showed an increased N100 response to the self-generated voices and an increased P200 response for externally-generated voices. This may indicate increased error awareness and attention allocation in high HP individuals for self-voice generation stemming from altered sensory feedback processing, and/or attentional control. The current findings suggest that alterations of the sensory feedback processing in self-voice production are a fundamental characteristic of the continuum of HP, regardless of the clinical status of voice hearers. HighlightsO_LIAltered N100 voice suppression in high HP, regardless of the clinical status. C_LIO_LIHigh HP associated with altered sensory feedback processing and attentional control. C_LIO_LICurrent findings support a neurophysiological continuum of HP. C_LI

neuroscience↗

bioRxiv2023

Hallucination proneness alters sensory feedback processing in self-voice production

BackgroundSensory suppression occurs when hearing ones self-generated voice, as opposed to passively listening to ones own voice. Quality changes of sensory feedback to the self-generated voice can increase attentional control. These changes affect the self-other voice distinction and might lead to hearing non-existent voices in the absence of an external source (i.e., auditory verbal hallucinations (AVH)). However, it is unclear how changes in sensory feedback processing and attention allocation interact and how this interaction might relate to hallucination proneness (HP). Study DesignParticipants varying in HP self-generated and passively listened to their voice that varied in emotional quality and certainty of recognition -- 100% neutral, 60-40% neutral-angry, 50-50% neutral-angry, 40-60% neutral-angry, 100% angry, during EEG recordings. Study ResultsThe N1 auditory evoked potential was more suppressed for the self-generated than externally generated voices. Increased HP was associated with (i) an increased N1 response to the self-compared to externally generated voices, (ii) a reduced N1 response for angry compared to neutral voices, and (iii) a reduced N2 response to unexpected voice quality in sensory feedback (60-40% neutral-angry) compared to neutral voices. ConclusionsThe current study highlights an association between increased HP and systematic changes of the emotional quality and certainty in sensory feedback processing (N1) and attentional control (N2) in self-voice production in a non-clinical population. Considering that voice hearers also display these changes, these findings support the continuum hypothesis. However, additional research is needed to validate this conclusion.

neuroscience↗

bioRxiv2021

Establishment of the family Zarkiaceae (Oscillatoriales, Cyanobacteria) and description of the new marine genera Zarkia (Zarkiaceae, Oscillatoriales) and Romeriopsis (Leptolyngbyaceae, Synechococcales), from northern Portugal

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/439031v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1ed7edaorg.highwire.dtl.DTLVardef@1234542org.highwire.dtl.DTLVardef@97f6cborg.highwire.dtl.DTLVardef@cb8cce_HPS_FORMAT_FIGEXP M_FIG C_FIG The morphology, 16S rRNA gene phylogeny and the 16S-23S rRNA gene ITS secondary structures of three strains of marine Cyanobacteria, isolated from inter- and subtidal environments from north Portugal were studied, resulting in the description of Zarkia subtidalensis gen. et. sp. nov. (Zarkiaceae fam. nov.) and Romeriopsis marina gen. et. sp. nov (Leptolyngbyaceae). No diacritical morphological characters were found either for the new family or for the new genera. The 16S rRNA gene Maximum Likelihood and Bayesian phylogenies supported that Zarkia and Zarkiaceae are members of the Oscillatoriales, positioned close to Microcoleaceae genera, but distant from Microcoleus. Romeriopsis is positioned within the Leptolyngbyaceae and is closely related to Alkalinema. The secondary structures of the D1-D1, Box B, V2 and V3 helices corroborate with the phylogenetic results. Furthermore, our study supports previous observations of polyphyletic Oscillatoriales families and reinforces the need for their taxonomical revision.

microbiology↗

bioRxiv2020

Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism

The N protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. Its N-terminal domain (NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRS), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. N-NTD dsRNA destabilizing activity was more efficient for dsTRS than dsNS. N-NTD dynamics, especially a tweezer-like motion of {beta}2-{beta}3 and 2-{beta}5 loops, played a key role in WC base-pairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event. IMPORTANCECoronaviruses are among the largest positive-sense RNA viruses. They display a unique discontinous transcription mechanism, involving N protein as a major player. The N-NTD promote the dsRNA melting releasing the nascent sense negative strand via a poorly known mechanism of action. It specifically recognizes the body TRS conserved RNA motif located at the 5 end of each ORF. N protein has the ability to transfer the nascent RNA strand to the leader TRS. The mechanism is essential and one single mutation at the RNA binding site of the N-NTD impairs the viral replication. Here, we describe a counterintuitive mechanism of action of N-NTD based on molecular dynamics simulation and kinetic modelling of the experimental melting activity of N-NTD. This data impacts directly in the understanding of the way N protein acts in the cell and will guide future experiments.

biophysics↗

bioRxiv2020

Novel ionic liquids-based extraction method that preserves molecular structure from cutin

The biopolyester cutin is ubiquitous in land plants, building the polymeric matrix of the plants outermost defensive barrier - the cuticle. Cutin influences many biological processes in planta however due to its complexity and highly branched nature, the native structure remains partially unresolved. Our aim was to define an original workflow for the purification and systematic characterisation of the molecular structure of cutin. To purify cutin we tested the ionic liquids cholinium hexanoate and 1-butyl-3-methyl-imidazolium acetate. The ensuing polymers are highly esterified, amorphous and have the typical monomeric composition as demonstrated by solid state NMR, complemented by spectroscopic (GC-MS), thermal (DSC) and x-ray scattering (WAXS) analyses. A systematic study by solution-state NMR of cryogenically milled cutins extracted from Micro-Tom tomatoes (the wild type and the gpat6 and cus1 mutants) was undertaken. Their molecular structures, relative distribution of ester aliphatics, free acid end-groups and free hydroxyl groups, differentiating between those derived from primary and secondary esters, were solved. The acquired data demonstrate the existence of free hydroxyl groups in cutin and reveal novel insights on how the mutations impact the esterification arrangement of cutin. Compared to conventional approaches, the usage of ionic liquids for the study of plant polyesters opens new avenues since simple modifications can be applied to recover a biopolymer carrying distinct types/degrees of modifications (e.g. preservation of esters or cuticular polysaccharides), which in combination with the solution NMR methodologies developed here, constitutes now essential tools to fingerprint the multi-functionality and the structure of cutin in planta.

plant biology↗

bioRxiv2019

Biophysical properties of intermediate states of EMT outperform both epithelial and mesenchymal states.

Potential metastatic cells can dissociate from a primary breast tumor by undergoing an epithelial-to-mesenchymal transmission (EMT). Recent work has revealed that cells in intermediate states of EMT acquire an augmented capacity for tumor-cell dissemination. These states have been characterized by molecular markers, but the structural features and the cellular mechanisms that underlie the acquisition of their invasive properties are still unknown. Using human mammary epithelial cells, we generated cells in intermediate states of EMT through the induction of a single EMT-inducing transcription factor, ZEB1, and cells in a mesenchymal state by stimulation with TGF{beta}. In stereotypic and spatially-defined culture conditions, the architecture, internal organization and mechanical properties of cells in the epithelial, intermediate and mesenchymal state were measured and compared. We found that the lack of intercellular cohesiveness in epithelial and mesenchymal cells can be detected early by microtubule destabilization and the repositioning of the centrosome from the cell-cell junction to the cell center. Consistent with their high migration velocities, cells in intermediate states produced low contractile forces compared with epithelial and mesenchymal cells. The high contractile forces in mesenchymal cells powered a retrograde flow pushing the nucleus away from cell adhesion to the extracellular matrix. Therefore, cells in intermediate state had structural and mechanical properties that were distinct but not necessarily intermediate between epithelial and mesenchymal cells. Based on these observations, we found that a panel of triple-negative breast cancer lines had intermediate rather than mesenchymal characteristics suggesting that the structural and mechanical properties of the intermediate state are important for understanding tumor-cell dissemination.

cell biology↗

bioRxiv2019

Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen

High Content Screening is an important tool in drug discovery and characterisation. Often, high content drug screens are performed on one single cell line. Yet, a single cell line cannot be thought of as a perfect disease model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterise drugs with respect to their effect not only on one cell line but on a panel of cell lines is therefore a promising strategy to streamline the drug discovery process. The contribution of this paper is twofold. First, we investigate whether we can predict drug mechanism of action (MOA) at the molecular level without optimisation of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each manifesting potentially different morphological baselines. For this, we propose multitask autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease.

bioinformatics↗