ORCID Profile
0000-0002-3703-4111
Current Organisations
Universidade de Lisboa
,
University of Western Australia
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Publisher: The Royal Society
Date: 25-02-2009
Abstract: It is generally accepted that mutation rates of RNA viruses are inherently high due to the lack of proofreading mechanisms. However, direct estimates of mutation rate are surprisingly scarce, in particular for plant viruses. Here, based on the analysis of in vivo mutation frequencies in tobacco etch virus , we calculate an upper-bound mutation rate estimation of 3×10 −5 per site and per round of replication a value which turns out to be undistinguishable from the methodological error. Nonetheless, the value is barely on the lower side of the range accepted for RNA viruses, although in good agreement with the only direct estimate obtained for other plant viruses. These observations suggest that, perhaps, differences in the selective pressures operating during plant virus evolution may have driven their mutation rates towards values lower than those characteristic of other RNA viruses infecting bacteria or animals.
Publisher: Elsevier BV
Date: 12-2008
DOI: 10.1016/J.MEEGID.2008.07.010
Abstract: Host-range expansion is thought to allow viruses to broaden their ecological niches by allowing access to new resources. However, traits governing the infection of multiple hosts may decrease fitness in the original one due to the pleiotropic effect of adaptive mutations that may give rise to fitness tradeoffs across hosts. Here, we have experimentally examined the consequences of host-specialization in the plant pathogen Tobacco etch potyvirus (TEV). Replicate populations of TEV were allowed to evolve for 15 serial undiluted passages on the original tobacco host or on pepper, a novel host. Virulence and biologically active viral load were evaluated during the course of the experiment for each lineage on both potential hosts. In agreement with the tradeoff hypothesis, lineages evolved in the novel host experienced substantial increases in virulence and virus accumulation in its own host, but suffered reduced virulence and accumulation on the original host. By contrast, lineages evolved on the ancestral host did not increase virulence or viral load on either host. Genomic consensus sequences were obtained for each lineage at the end time point. The potential relevance for the evolution of virulence and virus fitness of the characterized mutations is discussed.
Publisher: Wiley
Date: 30-08-2012
Publisher: Springer Science and Business Media LLC
Date: 07-08-2008
Abstract: Tobacco etch potyvirus (TEV) has been extensively used as model system for the study of positive-sense RNA virus infecting plants. TEV ability to infect Arabidopsis thaliana varies among ecotypes. In this study, changes in gene expression of A. thaliana ecotype L er infected with TEV have been explored using long-oligonucleotide arrays. A. thaliana L er is a susceptible host that allows systemic movement, although the viral load is low and syndrome induced ranges from asymptomatic to mild. Gene expression profiles were monitored in whole plants 21 days post-inoculation (dpi). Microarrays contained 26,173 protein-coding genes and 87 miRNAs. Expression analysis identified 1727 genes that displayed significant and consistent changes in expression levels either up or down, in infected plants. Identified TEV-responsive genes encode a erse array of functional categories that include responses to biotic (such as the systemic acquired resistance pathway and hypersensitive responses) and abiotic stresses (droughtness, salinity, temperature, and wounding). The expression of many different transcription factors was also significantly affected, including members of the R2R3-MYB family and ABA-inducible TFs. In concordance with several other plant and animal viruses, the expression of heat-shock proteins (HSP) was also increased. Finally, we have associated functional GO categories with KEGG biochemical pathways, and found that many of the altered biological functions are controlled by changes in basal metabolism. TEV infection significantly impacts a wide array of cellular processes, in particular, stress-response pathways, including the systemic acquired resistance and hypersensitive responses. However, many of the observed alterations may represent a global response to viral infection rather than being specific of TEV.
Publisher: Wiley
Date: 28-02-2018
DOI: 10.1111/PCE.13141
Abstract: Dormant or quiescent buds of woody perennials are often dense and in the case of grapevine (Vitis vinifera L.) have a low tissue oxygen status. The precise timing of the decision to resume growth is difficult to predict, but once committed, the increase in tissue oxygen status is rapid and developmentally regulated. Here, we show that more than a third of the grapevine homologues of widely conserved hypoxia-responsive genes and nearly a fifth of all grapevine genes possessing a plant hypoxia-responsive promoter element were differentially regulated during bud burst, in apparent harmony with resumption of meristem identity and cell-cycle gene regulation. We then investigated the molecular and biochemical properties of the grapevine ERF-VII homologues, which in other species are oxygen labile and function in transcriptional regulation of hypoxia-responsive genes. Each of the 3 VvERF-VIIs were substrates for oxygen-dependent proteolysis in vitro, as a function of the N-terminal cysteine. Collectively, these data support an important developmental function of oxygen-dependent signalling in determining the timing and effective coordination bud burst in grapevine. In addition, novel regulators, including GASA-, TCP-, MYB3R-, PLT-, and WUS-like transcription factors, were identified as hallmarks of the orderly and functional resumption of growth following quiescence in buds.
Publisher: Oxford University Press (OUP)
Date: 11-02-2015
DOI: 10.1093/JXB/ERU517
Publisher: MDPI AG
Date: 21-05-2015
Publisher: Cold Spring Harbor Laboratory
Date: 03-05-2023
DOI: 10.1101/2023.04.29.23289314
Abstract: Recurrent wheezing disorders including asthma are complex and heterogeneous diseases that affect up to 30% of all children, contributing to a major burden on children, their families, and global healthcare systems. It is now recognized that a dysfunctional airway epithelium plays a central role in the pathogenesis of recurrent wheeze, although the underlying mechanisms are still not fully understood. This prospective birth cohort aims to bridge this knowledge gap by investigating the influence of intrinsic epithelial dysfunction on the risk for developing respiratory disorders and the modulation of this risk by maternal morbidities, in utero exposures, and respiratory exposures in the first year of life. The Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) study is nested within the ORIGINS Project and will monitor 400 infants from birth to five years. The primary outcome of the AERIAL study will be the identification of epithelial endotypes and exposure variables that influence the development of recurrent wheezing, asthma, and allergic sensitisation. Nasal respiratory epithelium at birth to six weeks, one, three, and five years will be analysed by bulk RNA-seq and DNA methylation sequencing. Maternal morbidities and in utero exposures will be identified on maternal history and their effects measured through transcriptomic and epigenetic analyses of the amnion and newborn epithelium. Exposures within the first year of life will be identified based on infant medical history as well as on background and symptomatic nasal s ling for viral PCR and microbiome analysis. Daily temperatures and symptoms recorded in a study-specific Smartphone App will be used to identify symptomatic respiratory illnesses. Ethical approval has been obtained from Ramsey Health Care HREC WA-SA (#1908). Results will be disseminated through open-access peer-reviewed manuscripts, conference presentations, and through different media channels to consumers, ORIGINS families, and the wider community.
Publisher: Bentham Science Publishers Ltd.
Date: 02-04-2009
Publisher: MDPI AG
Date: 07-12-2021
DOI: 10.3390/JPM11121323
Abstract: The airway epithelium of children with wheeze is characterized by defective repair that contributes to disease pathobiology. Dysregulation of developmental processes controlled by Notch has been identified in chronic asthma. However, its role in airway epithelial cells of young children with wheeze, particularly during repair, is yet to be determined. We hypothesized that Notch is dysregulated in primary airway epithelial cells (pAEC) of children with wheeze contributing to defective repair. This study investigated transcriptional and protein expression and function of Notch in pAEC isolated from children with and without wheeze. Primary AEC of children with and without wheeze were found to express all known Notch receptors and ligands, although pAEC from children with wheeze expressed significantly lower NOTCH2 (10-fold, p = 0.004) and higher JAG1 (3.5-fold, p = 0.002) mRNA levels. These dysregulations were maintained in vitro and cultures from children with wheeze displayed altered kinetics of both NOTCH2 and JAG1 expression during repair. Following Notch signaling inhibition, pAEC from children without wheeze failed to repair (wound closure rate of 76.9 ± 3.2%). Overexpression of NOTCH2 in pAEC from children with wheeze failed to rescue epithelial repair following wounding. This study illustrates the involvement of the Notch pathway in airway epithelial wound repair in health and disease, where its dysregulation may contribute to asthma development.
Publisher: Elsevier BV
Date: 06-2013
DOI: 10.1016/J.PLAPHY.2013.02.024
Abstract: Grapevine (Vitis species) is the most economically important fruit crop worldwide. Ripening of non-climacteric fruits such as grapes has been the subject of intense research. Despite this interest, little is known on the role played by polyamines in the onset of ripening of non-climacteric fruits. These growth regulators have been involved in plant development and stress responses. Molecular and biochemical studies were developed in three important Portuguese cultivars (Trincadeira, Touriga Nacional and Aragonês) during the year 2008 and in Trincadeira during 2007 in order to gather insights on the role of polyamines in grape ripening. Microarray and real-time qPCR studies revealed up-regulation of a gene coding for arginine decarboxylase (ADC) during grape ripening in all the varieties. This increase was not accompanied by an increase in free and conjugated polyamines that presented a strong decrease. Putrescine and Spermidine levels were higher at earlier stages of development, while Spermine level remained constant. Berries of Trincadeira cultivar presented the highest content in total free and conjugated polyamines at earlier stages of fruit development in particular in the year 2007. The decrease in polyamines content during grape ripening was accompanied by up-regulation of genes coding for diamine oxidase (CuAO) and polyamine oxidase (PAO), together with a significant increase in their enzymatic activity and in the hydrogen peroxide content. These results provide, for the first time, strong evidence of a role of polyamine catabolism in grape ripening possibly through interaction with other growth regulators.
Publisher: Cold Spring Harbor Laboratory
Date: 05-06-2023
DOI: 10.1101/2023.06.04.23290702
Abstract: Chronic obstructive pulmonary disease (COPD) is a complex disorder with a high degree of interin idual variability. Gastrointestinal dysfunction is common in COPD patients and has been proposed to influence the clinical progression of the disease. Using the presence of bile acid(s) (BA) in bronchoalveolar lavage fluid (BAL) as a marker of gastric aspiration, we evaluated the relationships between BAs, clinical outcomes, and bacterial lung colonisation. We used BAL specimens from a cohort of COPD patients and healthy controls. Bile acids were profiled and quantified in BAL supernatants using mass spectrometry. Microbial DNA was extracted from BAL cell pellets and quantified using qPCR. We profiled the BAL microbiota using an licon sequencing approach targeting the V3-V4 region of the 16S rRNA gene. Detection of BAs in BAL was more likely at earliest clinical stages of COPD and was independent of the degree of airway obstruction. BAL specimens with BAs demonstrated higher bacterial biomass and lower ersity. Likewise, the odds of recovering bacterial cultures from BAL were higher if BAs were also detected. Detection of BAs in BAL was not associated with either inflammatory markers or clinical outcomes. We also observed different bacterial community types in BAL, which were associated with different clinical groups, levels of inflammatory markers, and the degree of airway obstruction. Detection of BAs in BAL was associated with different parameters of airway ecology. Further studies are needed to evaluate whether BAs in BAL can be used to stratify patients and for predicting disease progression trajectories.
Publisher: MDPI AG
Date: 12-07-2022
DOI: 10.3390/V14071522
Abstract: Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing “Big Data” offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
Publisher: Frontiers Media SA
Date: 16-07-2020
Publisher: Cold Spring Harbor Laboratory
Date: 11-09-2019
DOI: 10.1101/765594
Abstract: Phosphatidylinositol 3-phosphate (PtdIns3 P ) is one of the five different phosphoinositides (PPIs) species in plant cells, which regulate several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3 P mode of action, specifically through PtdIns3 P -binding effectors such as FYVE and PHOX proteins have been partially explored in plants with main focus on Arabidopsis thaliana. Additionally, they have been underexplored in other plant organisms such as bryophytes, the earliest erging group of terrestrial flora. In this study, we searched for genes coding for FYVE and PHOX domains containing sequences from different photosynthetic organisms in order to gather evolutionary insights on these PPI binding domains, followed by an in silico characterization of the FYVE and PHOX gene family in the moss Physcomitrella patens . Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis -acting regulatory elements and transcription factor binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens . The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2D to 3D growth, which could provide ancestral regulatory players undertaken during plant evolution.
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.PLAPHY.2013.11.002
Abstract: Grapes are economically the most important fruit worldwide. However, the complexity of biological events that lead to ripening of nonclimacteric fruits is not fully understood, particularly the role of polyamines' catabolism. The transcriptional and metabolic profilings complemented with biochemical data were studied during ripening of Trincadeira grapes submitted to guazatine treatment, a potent inhibitor of polyamine oxidase activity. The mRNA expression profiles of one time point (EL 38) corresponding to harvest stage was compared between mock and guazatine treatments using Affymetrix GrapeGen(®) genome array. A total of 2113 probesets (1880 unigenes) were differentially expressed between these s les. Quantitative RT-PCR validated microarrays results being carried out for EL 35 (véraison berries), EL 36 (ripe berries) and EL 38 (harvest stage berries). Metabolic profiling using HPLC and (1)H NMR spectroscopy showed increase of putrescine, proline, threonine and 1-O-ethyl-β-glucoside in guazatine treated s les. Genes involved in amino acid, carbohydrate and water transport were down-regulated in guazatine treated s les suggesting that the strong dehydrated phenotype obtained in guazatine treated s les may be due to impaired transport mechanisms. Genes involved in terpenes' metabolism were differentially expressed between guazatine and mock treated s les. Altogether, results support an important role of polyamine catabolism in grape ripening namely in cell expansion and aroma development.
Publisher: MDPI AG
Date: 06-05-2020
DOI: 10.3390/DIAGNOSTICS10050282
Abstract: Background: Cystic fibrosis (CF) is a hereditary disorder in which persistent unresolved inflammation and recurrent airway infections play major roles in the initiation and progression of the disease. Little is known about triggering factors modulating the transition to chronic microbial infection and inflammation particularly in young children. Cystic fibrosis respiratory disease starts early in life, with the detection of inflammatory markers and infection evident even before respiratory symptoms arise. Thus, identifying factors that dysregulate immune responsiveness at the earliest stages of the disease will provide novel targets for early therapeutic intervention. Methods: We evaluated the clinical significance of bile acid detection in the bronchoalveolar lavage fluid of clinically stable preschool-aged children diagnosed with CF. Results: We applied an unbiased classification strategy to categorize these specimens based on bile acid profiles. We provide clear associations linking the presence of bile acids in the lungs with alterations in the expression of inflammatory markers. Using multiple regression analysis, we also demonstrate that clustering based on bile acid profiles is a meaningful predictor of the progression of structural lung disease. Conclusions: Altogether, our work has identified a clinically relevant host-derived factor that may participate in shaping early events in the aetiology of CF respiratory disease.
Publisher: Oxford University Press (OUP)
Date: 04-12-2017
DOI: 10.1104/PP.17.01479
Publisher: Public Library of Science (PLoS)
Date: 11-06-2008
Publisher: Cold Spring Harbor Laboratory
Date: 19-04-2022
DOI: 10.1101/2022.04.19.488653
Abstract: Different to root hairs and pollen tubes, Physcomitrium patens apical growing protonemal cells have the singularity that they continue to undergo cell isions as the plant develops, allowing to study autophagy in the context of a multicellular apical growing tissue coupled to development. Herein, we showed that the core autophagy machinery is present in the moss P. patens , and deeply characterized the growth and development of wild-type, atg5 and atg7 loss-of-function mutants under optimal and nutrient-deprived conditions. Our results showed that the growth of the different morphological and functional protonemata apical growing cells, chloronema and caulonema, is differentially modulated by this process. These differences depend on the protonema cell type and position along the protonemal filament, and growth condition. As a global plant response, the absence of autophagy triggers the spread of the colony through protonemata growth at the expense of a reduction in buds and gametophore development, and thus the adult gametophytic and reproductive phases. Altogether this study provides valuable information indicating that autophagy has roles during apical growth with differential responses within the cell types of the same tissue and contributes to life cycle progression and thus the development of the 2D and 3D tissues of P. patens . Autophagy is differentially induced in protonemal cells, and contributes to apical growth, life cycle progression, and thus the development of the 2D and 3D tissues of P. patens .
Publisher: Elsevier BV
Date: 02-2017
DOI: 10.1016/J.TPLANTS.2016.11.013
Abstract: Plants are developmentally disposed to significant changes in oxygen availability, but our understanding of the importance of hypoxia is almost entirely limited to stress biology. Differential patterns of the abundance of oxygen, nitric oxide (
Publisher: Frontiers Media SA
Date: 06-10-2020
Publisher: Springer Science and Business Media LLC
Date: 2011
Publisher: Cold Spring Harbor Laboratory
Date: 03-04-2023
DOI: 10.1101/2023.04.03.23288063
Abstract: Long term outcomes of allograft recipients are compromised by the development of chronic lung allograft dysfunction (CLAD) promoting bronchiolitis obliterans syndrome (BOS). We established baseline transcriptomic profiles of both the large and small airway epithelial cells (referred as LAEC and SAEC, respectively) to identify regional differences irrespective of initiating disease. We obtained matched primary LAEC and SAEC from lung allograft recipients (n=4, 42.5 ± 4.2 years) and established primary cultures. Bulk RNA sequencing was performed to determine differentially expressed genes. We observed differences in the transcriptional program between LAEC and SAEC Transcription factors (TF) were ranked within the top ten differentially regulated genes. The most abundant TF families included C2H2-ZF, homeobox and bHLH. Upstream regulator analyses identified homeobox genes being significantly in LAEC. Protein-protein interaction network analysis emphasised the role of TFs ( ISL1, MSX1, HOXA1, GATA6, ZNF423 ) in airway modulation. Additionally, functional enrichment analysis revealed the activation of chemotaxis, metalloendipeptidase/metallopeptidase activity and pro-inflammatory signatures (IL17 signalling and RAGE), in LAEC, while SAEC were characterised by elevated expression of surfactant metabolism related genes. Moreover, alveolar and club cells-related genes were expressed in SAEC, suggesting a lower airway-specific signature. Our analysis shows robust transcriptional differences between LAEC and SAEC. We suggest a potential role for homeobox TF family as well as the activation of the immune system in the biology of LAEC. Conversely, we observed an alveoli-like transcriptional signature in SAEC, including gas-exchange signals and surfactant metabolism pathways involved in lung homeostasis.
Publisher: Elsevier BV
Date: 11-2021
DOI: 10.1016/J.MIMET.2021.106346
Abstract: Antimicrobial resistance is a current global health crisis, and the increasing emergence of multidrug resistant infections has led to the resurgent interest in bacteriophages as an alternative treatment. Prior to clinical application, phage suitability is assessed, via susceptibility testing and breadth of host range to bacteriophage, however, these are both large-scale manual processes and labor-intensive. The aim of the study was to establish and validate a scaled down methodology for high-throughput screening to reduce procedural footprint. In this paper, we describe a scaled-down adapted methodology that can successfully screen bacteriophages, isolated and purified from wastewater s les. Furthermore, we describe a miniaturized host range assay against clinical Pseudomonas aeruginosa isolates using a spot test (2 μL/ drop) that was found to be both sensitive (94.6%) and specific (94.7%). It also demonstrated a positive predictive value (PPV) of 86.4% and negative predictive value (NPV) of 98%. The breadth of host range of bacteriophages that exhibited lytic activity on P. aeruginosa isolates was corroborated using the scaled down assay. The high correlation achieved in this study confirms miniaturization as the first step in future automation that could test phage ersity and efficacy as antimicrobials.
Publisher: Public Library of Science (PLoS)
Date: 02-04-2013
Publisher: Wiley
Date: 11-04-2022
DOI: 10.1111/IMCB.12547
Abstract: A population of neutrophils recruited into cystic fibrosis (CF) airways is associated with proteolytic lung damage, exhibiting high expression of primary granule exocytosis marker CD63 and reduced phagocytic receptor CD16. Causative factors for this population are unknown, limiting intervention. Here we present a laboratory model to characterize responses of differentiated airway epithelium and neutrophils following respiratory infection. Pediatric primary airway epithelial cells were cultured at the air–liquid interface, challenged in idually or in combination with rhinovirus (RV) and Pseudomonas aeruginosa , then apically washed with medical saline to s le epithelial infection milieus. Cytokine multiplex analysis revealed epithelial antiviral signals, including IP‐10 and RANTES, increased with exclusive RV infection but were diminished if P. aeruginosa was also present. Proinflammatory signals interleukin‐1α and β were dominant in P. aeruginosa infection milieus. Infection washes were also applied to a published model of neutrophil transmigration into the airways. Neutrophils migrating into bacterial and viral–bacterial co‐infection milieus exhibited the in vivo CF phenotype of increased CD63 expression and reduced CD16 expression, while neutrophils migrating into milieus of RV‐infected or uninfected cultures did not. In idually, bacterial products lipopolysaccharide and N ‐formylmethionyl‐leucyl‐phenylalanine and isolated cytokine signals only partially activated this phenotype, suggesting that additional soluble factors in the infection microenvironment trigger primary granule release. Findings identify P. aeruginosa as a trigger of acute airway inflammation and neutrophil primary granule exocytosis, underscoring potential roles of airway microbes in prompting this neutrophil subset. Further studies are required to characterize microbes implicated in primary granule release, and identify potential therapeutic targets.
Publisher: Springer New York
Date: 28-10-2017
DOI: 10.1007/978-1-4939-7398-9_36
Abstract: Polyamines are small aliphatic amines that are found in both prokaryotic and eukaryotic organisms. These growth regulators have been implicated in abiotic and biotic stresses as well as plant development and morphogenesis. Several studies have also suggested a key role of polyamines during fruit set and early development. Polyamines have also been linked to fruit ripening and in the regulation of fruit quality-related traits.Recent studies indicate that during ripening of both climacteric and non-climacteric fruits, a decline in total polyamine contents is observed together with an increased catabolism of these growth regulators.In this review, we explore the current knowledge on polyamine biosynthesis and catabolism during fruit set and ripening. The study of the role of polyamine metabolism in fruit ripening indicates the possible application of these natural polycations to control ripening and postharvest decay as well as to improve fruit quality traits.
No related grants have been discovered for Patricia Agudelo.