Biology subjects

Pereira, A.

Publications and source records attributed to Pereira, A..

33 records · Page 2Linked to original sources

bioRxiv2021

Neurotoxic astrocytic glypican-4 drives APOE4-dependent tau pathology

The aggregation of tau proteins into insoluble filaments and the spread of these filaments across brain regions are the major drivers of neurodegeneration in tauopathies, including in Alzheimers disease (AD). Apolipoprotein E4 (APOE4), a crucial genetic risk factor for late-onset AD, has been shown to exacerbate tau pathology in mouse models. However, the exact mechanisms through which APOE4 induces tau pathology remains unknown. Here, we report that the astrocyte-secreted protein glypican-4 (GPC-4), which we identify as a novel binding partner of APOE4, drives tau pathology. We discovered that GPC-4 preferentially interacts with APOE4 in comparison to APOE2, considered to be a protective allele to AD, and post-mortem APOE4-carrying AD brains highly express GPC-4 in neurotoxic astrocytes. The astrocyte-secreted GPC-4 induced both tau accumulation and propagation in vitro. CRISPR/dCas9 mediated activation of GPC-4 in a tauopathy mouse model robustly induced tau pathology. Using in vitro Tau FRET-biosensor cells, human iPSCs-derived astrocytes and an in vivo mouse model, we found that APOE4-induced tau pathology was greatly diminished in the absence of GPC-4. We further show that APOE4-mediated surface trafficking of APOE receptor low-density lipoprotein receptor-related protein 1 (LRP1) through GPC-4 can be a gateway to tau spreading. Together, our data comprehensively demonstrate that APOE4-induced tau pathologies are directly mediated by GPC-4.

neuroscience↗

bioRxiv2021

Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients

Risk factors for COVID-19 disease severity are still poorly understood. Considering the pivotal role of gut microbiota on host immune and inflammatory functions, we investigated the association between changes in gut microbiota composition and the clinical severity of COVID-19. We conducted a multicentre cross-sectional study prospectively enrolling 115 COVID-19 patients categorized according to: 1) WHO Clinical Progression Scale - mild 19 (16.5%), moderate 37 (32.2%) or severe 59 (51.3%); and 2) location of recovery from COVID-19 - ambulatory 14 (household isolation; 12.2%), hospitalized in ward 40 (34.8%) or intensive care unit 61 (53.0%). Gut microbiota analysis was performed through 16S rRNA gene sequencing and data obtained was further related with clinical parameters of COVID-19 patients. Risk factors for COVID-19 severity were identified by univariate and multivariable logistic regression models. In comparison with mild COVID-19 patients, the gut microbiota of moderate and severe patients has: a) lower Firmicutes/Bacteroidetes ratio, b) higher abundance of Proteobacteria; and c) lower abundance of beneficial butyrate-producing bacteria such as Roseburia and Lachnospira genera. Multivariable regression analysis showed that Shannon index diversity (odds ratio [OR] 2.85 [95% CI 1.09-7.41]; p=0.032) and C-Reactive Protein (OR 3.45 [95% CI 1.33-8.91]; p=0.011) were risk factors for COVID-19 severe disease (a score of 6 or higher in WHO clinical progression scale). In conclusion, our results demonstrated that hospitalised moderate and severe COVID-19 patients have microbial signatures of gut dysbiosis and for the first time, the gut microbiota diversity is pointed out as a prognostic biomarker for COVID-19 disease severity.

microbiology↗

bioRxiv2021

In vitro neuronal networks show bidirectional axonal conduction with antidromic action potentials effectively depolarizing the soma

Recent technological advances are revealing the complex physiology of the axon and challenging long-standing assumptions. Namely, while most action potential (AP) initiation occurs at the axon initial segment in central nervous system neurons, initiation in distal parts of the axon has been shown to occur in both physiological and pathological conditions. However, such ectopic action potential (EAP) activity has not been reported yet in studies using neuronal cultures and its functional role, if exists, is still not clear. Here, we show the spontaneous occurrence of EAPs and effective antidromic conduction in hippocampal neuronal cultures. We also observe a significant fraction of bidirectional axonal conduction in dorsal root ganglia neuronal cultures. We investigate and characterize this antidromic propagation via a combination of microfluidics, microelectrode arrays, advanced data analysis and in silico studies. We show that EAPs and antidromic conduction can occur spontaneously, and after distal axotomy or physiological changes in the axon biochemical environment. Conduction velocity is asymmetrical, with antidromic conduction being slower than orthodromic. Importantly, EAPs may carry information and can have a functional impact on the neuron, as they consistently depolarize the soma. Thus, plasticity or gene transduction mechanisms triggered by soma depolarization can also be affected by these antidromic APs. Altogether these findings have important implications for the study of neuronal function in vitro, reshaping our understanding on how information flows in neuronal cultures.

neuroscience↗

bioRxiv2021

Modulation of early level EEG signatures by distributed facial emotion cues

Face perception plays an important role in our daily social interactions, as it is essential to recognize emotions. The N170 Event Related Potential (ERP) component has been widely identified as a major face-sensitive neuronal marker. However, despite extensive investigations conducted to examine this electroencephalographic pattern, there is yet no agreement regarding its sensitivity to the content of facial expressions. Here, we aim to clarify the EEG signatures of the recognition of facial expressions by investigating ERP components that we hypothesize to be associated with this cognitive process. We asked the question whether the recognition of facial expressions is encoded by the N170 as weel as at the level of P100 and P250. In order to test this hypothesis, we analysed differences in amplitudes and latencies for the three ERPs, in a sample of 20 participants. A visual paradigm requiring explicit recognition of happy, sad and neutral faces was used. The facial cues were explicitly controlled to vary only regarding mouth and eye components. We found that non neutral emotion expressions elicit a response difference in the amplitude of N170 and P250. In contrast with the P100, there by excluding a role for low level factors. Our study brings new light to the controversy whether emotional face expressions modulate early visual response components, which have been often analysed apart. The results support the tenet that neutral and emotional faces evoke distinct N170 patterns, but go further by revealing that this is also true for P250, unlike the P100.

neuroscience↗

bioRxiv2021

Ribosomal DNA revealed an extensive role of allopolyploidy in the radiation of Ulex L.

We studied the phylogeny of Ulex L., a genus of spiny legumes, which its center of diversity in the Iberian Peninsula, using ribosomal DNA markers (rDNA), namely ETS, 5.8S and ITS (45S), and 5S intergenic spacer regions. One of the main findings was the presence of very different haplotypes in 5S-IGS genes and, to a less extent, in ETS and ITS, in seven polyploid taxa. We interpreted these results as an indication of hybrid origins and proposed allopolyploidy for U. argenteus ssp. subsericeus, U. australis ssp. australis, U. australis ssp. welwitschianus, U. densus, U. europaeus ssp. europaeus, U. europaeus ssp. latebracteatus, and U. jussiaei. These results reinforce an early hypothesis which stated that the radiation of Ulex occurred mainly by polyplodization. Phylograms showed two main clades, one grouping the hydrophilic U. gallii, U. breoganii and U. minor, and the other grouping the southern, xerophytic, taxa. The putative allopolyploids showed haplotypes, which grouped in both clades, indicating that allopolyploidy, occurred through hybridization from these hydrophilic and xerophytic lineages. The phylogenetic position of U. micranthus is not certain and it is discussed. The 5S-IGS showed to retain more polymorphisms than ETS gene or ITS markers. This result is compatible with the hypothesis that 5S rDNA region is less vulnerable to inter-loci concerted evolution than 45S, providing a more suitable marker for reconstructing histories of allopolyploid species. We discuss the taxonomic consequences of these results.

molecular biology↗

bioRxiv2020

Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation.

PurposeVariants in MYBPC3 causing loss-of-function are the most common cause of HCM. However, a substantial number of patients carry missense variants of uncertain significance (VUS) in MYBPC3. We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on protein folding, will improve clinical risk stratification of patients with HCM and a MYBPC3 VUS. MethodsAmong 7,963 patients in the multi-center Sarcomeric Human Cardiomyopathy Registry, 120 unique missense VUSs in MYBPC3 were identified. Variants were evaluated for their effect on subdomain folding and a stratified time-to-event analysis for an overall composite endpoint (first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation, and stroke) was performed for patients with HCM and a MYBPC3 missense VUS. ResultsWe demonstrated that patients carrying a MYBPC3 VUS predicted to cause subdomain misfolding (STRUM +, {Delta}{Delta}G [≤]-1.2 kcal/mol) exhibited a higher rate of adverse events compared to those with a STRUM-VUS (Hazard Ratio=2.29, P=0.0282). In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants that were predicted to cause subdomain misfolding. ConclusionsSTRUM enables clinical risk stratification of patients with HCM and a MYBPC3 VUS and has the capacity to improve prognostic predictions and clinical decision making.

genetics↗

bioRxiv2020

Prediction and characterization of transcription factors involved in drought stress response

Transcription factors (TFs) play a central role in regulating molecular level responses of plants to external stresses such as water limiting conditions, but identification of such TFs in the genome remains a challenge. Here, we describe a network-based supervised machine learning framework that accurately predicts and ranks all TFs in the genome according to their potential association with drought tolerance. We show that top ranked regulators fall mainly into two age groups; genes that appeared first in land plants and genes that emerged later in the Oryza clade. TFs predicted to be high in the ranking belong to specific gene families, have relatively simple intron/exon and protein structures, and functionally converge to regulate primary and secondary metabolism pathways. Repeated trials of nested cross-validation tests showed that models trained only on regulatory network patterns, inferred from large transcriptome datasets, outperform models trained on heterogenous genomic features in the prediction of known drought response regulators. A new R/Shiny based web application, called the DroughtApp, provides a primer for generation of new testable hypotheses related to regulation of drought stress response. Furthermore, to test the system we experimentally validated predictions on the functional role of the rice transcription factor OsbHLH148, using RNA sequencing of knockout mutants in response to drought stress and protein-DNA interaction assays. Our study exemplifies the integration of domain knowledge for prioritization of regulatory genes in biological pathways of well-studied agricultural traits. One Sentence SummaryNetwork-based supervised machine learning accurately predicts transcription factors involved in drought tolerance.

systems biology↗

bioRxiv2020

C. elegans aversive olfactory learning generates diverse intergenerational effects

Parental experience can modulate the behavior of the progeny through the inheritance of phenotypic traits acquired by the progenitors. While the molecular mechanisms for behavioral inheritance are studied under several environmental conditions, it remains largely unexplored how the nature of the parental experience affects the information transferred to the next generation. To address this question we used C. elegans, a nematode that feeds on bacteria in its habitat. Some of these bacteria are pathogenic and the worm learns to avoid them after a brief exposure. We found, unexpectedly, that a short parental experience increased the preference for the pathogen in the progeny. Furthermore, increasing the time of parental exposure switched the response of the progeny from attraction to avoidance. To characterize the underlying molecular mechanisms, we found that the RNA-dependent RNA Polymerase (RdRP) RRF-3, required for the biogenesis of 26G endo-siRNAs, regulated both types of intergenerational effects. Together, we show that different parental experiences with the same environmental stimulus generate diverse effects on the behavior of the progeny through small RNA-mediated regulation of gene expression.

neuroscience↗

bioRxiv2019

The evolution of competitive ability for essential resources

Competition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species minimum resource requirements, their R*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered - to what extent are species competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposed Chlamydomonas reinhardtii for approximately 285 generations to seven environments in chemostats which differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients.

evolutionary biology↗

bioRxiv2019

Long-term single-cell passaging of human iPSCs fully supports pluripotency and high-efficient trilineage differentiation capacity

ObjectivesTo validate a straightforward single-cell passaging cultivation method that enables high-quality maintenance of hiPSC without the appearance of karyotypic abnormalities or loss of pluripotency. MethodsCells were kept in culture for over 50 passages, following a structured chronogram of passage and monitoring cell growth by population doubling time (PDT) calculation and cell confluence. Standard procedures for iPSC monitoring as embryonic body (EB) formation, karyotyping and pluripotency markers expression were evaluated in order to monitor the cellular state in the long-term culture. Cells that underwent these tests were then subjected to differentiation into keratinocytes and cardiomyocytes to evaluate its differentiation capacity. ResultshiPSC clones maintained its pluripotent capability as well as chromosomal integrity and were able to generate derivatives from the three germ layers at high passages by embryoid body formation and high-efficient direct differentiation into keratinocytes and cardiomyocytes. ConclusionOur findings support the routine of hiPSC single-cell passaging as a reliable procedure even after long-term cultivation, providing healthy PSCs to be used in drugs discovery, toxicity and disease modeling as well as for therapeutic approaches.

cell biology↗

bioRxiv2019

B-1 cell-mediated modulation of M1-macrophage profile can ameliorate microbicidal functions and disrupt the evasion mechanisms of Encephalitozoon cuniculi

Here, we have investigated the possible effect of B-1 cells on the activity of peritoneal macrophages in E. cuniculi infection. In the presence of B-1 cells, peritoneal macrophages had an M1 profile with showed increased phagocytic capacity and index, associated with the intense microbicidal activity, increased proinflammatory cytokines production and a higher percentage of apoptotic death. The absence of B-1 cells was associated with a predominance of the M2 macrophages, indicating reduced phagocytic capacity and index, microbicidal activity, proinflammatory cytokine production, and apoptotic death, but equal death rate. In addition, in the M2 macrophages, spores of phagocytic E. cuniculi with polar tubular extrusion were observed, which is an important mechanism of evasion of the immune response. The results showed the importance of B-1 cells in the modulation of macrophage function against E. cuniculi infection, increasing microbicidal activity, and reducing the fungal mechanisms involved in the evasion of the immune response.\n\nHighlightsO_LIE. cuniculi phagocytosis and microbicidal activity by macrophages increases in the presence of B-1 cells\nC_LIO_LIM1 macrophage profiles were predominant in the presence of B-1 cells\nC_LIO_LIExtrusion of the polar tubule of E. cuniculi occur inside M2 macrophages in cultures without B-1 cells\nC_LIO_LIB-1 cells derived phagocytes (B-1CDP) identified with microbicidal activity against spores of E. cuniculi\nC_LI\n\nAuthor SummaryThe adaptive immune response plays a key role against Encephalitozoon cuniculi, an opportunistic fungus for T cells immunodeficient patients. The role of B cells and antibody play in natural resistance to Encephalitozoon cuniculi remains unresolved. Previously, we demonstrated that B-1 deficient mice (XID), an important component of innate immunity, were more susceptible to encephalitozoonosis, despite the increase in the number of CD4+ and CD8+ T lymphocytes. Here we observed that the absence of B-1 cells was associated with a larger population of M2 macrophages, an anti-inflammatory profile, which had lower microbicidal activity and phagocytic E. cuniculi spores were seen with the extrusion of the polar tubule, which is an important mechanism of evasion of the immune response. The results showed the importance of B-1 cells in the modulation of macrophage function against E. cuniculi infection, increasing microbicidal activity, and reducing the fungal mechanisms involved in the evasion of the immune response.

microbiology↗

bioRxiv2019

Postnatal development of skeletal muscle in IUGR pigs: morphofunctional phenotype and molecular mechanisms

Intrauterine growth restriction (IUGR) is a serious condition which impairs the achievement of the fetus full growth potential and occurs in a natural and severe manner in pigs. Knowledge on skeletal muscle morphofunctional phenotype and its molecular regulation in IUGR pigs is important to understand postnatal muscle development and may help the establishment of therapies to improve skeletal muscle growth in those individuals. To investigate the impairment of skeletal muscle postnatal development due to IUGR, we evaluated the histomorphometrical pattern of the semitendinosus muscle, the Myosin Heavy Chain (embryonic, I, IIa, IIb and IIx MyHC) fiber composition and the relative expression of genes related to myogenesis, adipogenesis and growth during three specific periods: postnatal myogenesis (newborn to 100 days of age), postnatal development (newborn to 150 days of age), and hypertrophy (100 days to 150 days of age), comparing IUGR and normal birth weight (NW) pigs. Growth restriction in utero affected muscle fiber diameter, total fiber number and muscle cross sectional area which were smaller in IUGR pigs at birth (P < 0.05). Even though the percentage of MyHC-I myofibers was higher in IUGR females at birth (P < 0.05), in older gilts, a lower percentage of MyHC-IIx isoform (P < 0.05) and the presence of emb-MyHC were also observed in that experimental group. Regarding the pattern of gene expression in the postnatal myogenesis period, growth restriction in utero led to a down regulation of myogenic factors, which delayed the expression of signals that induces skeletal muscle myogenesis (PAX7, MYOD, MYOG, MYF5 and DES). Taken together, the muscle morphofunctional aspects described and their ontogenetic regulation define the possible molecular origins of the notorious damage to the postnatal musculature development in IUGR pigs.

cell biology↗

bioRxiv2018

Learning of pathogenic bacteria in adult C. elegans bidirectionally regulates pathogen response in the progeny

Parental experience can generate adaptive changes in the behavioral and physiological traits of the offspring1-3. However, the biological properties of this intergenerational regulation and the underlying molecular and cellular mechanism are not well understood. Here, we show that the experience of learning to avoid pathogenic bacteria in C. elegans alters the behavioral response to the pathogen in the progeny through the endogenous RNA interference (RNAi) pathway. We previously show that the adult C. elegans learns to avoid the smell of pathogenic bacteria, such as the Pseudomonas aeruginosa strain PA14, after feeding on the pathogen for a few hours4,5. Here, we report that this learning experience can bidirectionally regulate the olfactory response to PA14 in the progeny that are never directly exposed to the pathogen. The olfactory preference for PA14 in these progeny is linearly correlated with the learned avoidance of PA14 in their mothers. If the mothers show strong learning of PA14, their progeny avoid PA14; intriguingly, if the mothers show weak learning of PA14, the progeny prefer PA14, suggesting that the PA14-trained mothers transmit both the negative and positive information of PA14 to their progeny. The intergenerational behavioral effect results from an altered behavioral decision regulated by an olfactory sensorimotor neural circuit. Learning to avoid the pathogen also influences the development of the progeny, which is regulated independently from the behavioral change. Animals mutated for the RRF-3/RNA-directed RNA polymerase, a master regulator for the synthesis of the small interfering RNAs that are maternally inherited or in the soma6,7, display the normal naive and learned response to PA14 but are defective in regulating the olfactory response to PA14 in their progeny. Our results characterize an intergenerational effect that allows the progeny to rapidly adapt to an environmental condition that is critical for survival.

neuroscience↗

bioRxiv2017

RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response

Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g. response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice stress transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 stress-specific gene modules covering 28,421 rice genes (>72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.

systems biology↗

bioRxiv2017

SANe: The Seed Active Network For Mining Transcriptional Regulatory Programs of Seed Development

Developing seeds undergo coordinated physiological and morphological changes crucial for development of the embryo, dormancy and germination. The metabolic changes that occur during seed development are regulated by interconnected network of Transcription Factors (TFs) that regulate gene expression in a spatiotemporal manner. The complexity of these networks is such that the TFs that play key regulatory roles during seed development are largely unknown. In this study, we created a genome-scale regulatory network dedicated to describing regulation of biological processes within various compartments and developmental stages of Arabidopsis seeds. Differential network analysis revealed key TFs that rewire their targeting patterns specifically during seed development, many of which were already known, and a few novel ones that we verified experimentally. Our method shows that a high-resolution tissue-specific transcriptome dataset can be accurately modeled as a functional regulatory network predictive of related TFs. We provide an easy to use webtool using which researchers can upload a newly generated transcriptome and identify key TFs important to their dataset as well as gauge their regulatory effect on phenotypes observed in the experiment. We refer to this network as Seed Active Network (SANe) and made it accessible at https://plantstress-pereira.uark.edu/SANe/. We anticipate SANe will facilitate the discovery of TFs yet unknown for their involvement in seed related metabolic pathways and provide an interface to generate new hypothesis for experimentation.

bioinformatics↗