Biology subjects

Duarte, I.

Publications and source records attributed to Duarte, I..

9 recordsLinked to original sources

bioRxiv2025

Physiological and Metabolic Responses of Chickpea to Post-Flowering High Temperatures and Limited Water Availability

Post-flowering elevated temperatures are increasingly frequent and strongly affect crop yield and seed nutritional quality. This study examined the impact of elevated post-flowering temperatures (32{degrees}C/25{degrees}C, day/night) combined with two watering regimes (40% and 10% field capacity) on chickpea genotypes. Elvar and Electra, top-yielding Portuguese genotypes well adapted to southern Portugals dry climate were evaluated. Under controlled high-temperature conditions (Phenolab), reproductive cycle was shortened to 30-35 days, compared with 65 days under greenhouse conditions (24{degrees}C/18{degrees}C). Water use peaked soon after flowering and declined after 19 days, regardless of genotype or watering regime, suggesting a physiological limitation on water use. Elevated temperature strongly reduced seed number and weight while altering composition. Nutrient density improved, with higher protein and mineral levels (P, Mg, S, Mo, Fe, Zn) and lower starch content, highlighting a consistent protein-starch trade-off unaffected by water availability. While growth environment largely determined composition, enzymatic activity patterns revealed genotype-specific differences in carbon metabolism (e.g. sucrose synthase, cell wall invertase, aldolase and phosphoglucose isomerase). Overall, these findings suggest genotype-specific responses driven by carbon metabolism and emphasize integrating metabolic, physiological and composition traits in breeding for yield stability and nutritional value. HighlightPost-flowering temperature dictates reproductive duration and seed composition, enhancing nutritional density but lowering yield. Protein-starch trade-off was consistent across genotypes, while enzymatic activity profiles enabled genotype discrimination under contrasting environments.

plant biology↗

bioRxiv2025

Aging: an inevitable road toward gut microbiota pathoadaptation

Laboratory-raised mice live approximately seven times longer and healthier lives compared to their wild counterparts, due to a standardized healthy diet and limited exposure to environmental stressors1. Aging is associated with increased inflammation and microbial dysbiosis2-4. Collectively, these influence microbiota evolution and may contribute to the enrichment in pathobiont frequency observed in old age4. Alternatively, this increase could stem from a decline in colonization resistance5,6, creating favorable conditions for pathobiont invasion. Here, we sought to test whether aging in healthy, controlled conditions, could prevent the selection of age-associated pathobionts. We have followed the adaptive evolution of a commensal strain of Escherichia coli in the guts of mice of advanced age and found that it acquired several mutations common to bacteria colonizing young mice, which were absent in old animals. This, together with the increase in Akkermansia muciniphila in mice of advanced age, suggest healthy aging7,8. However, mutations acquired exclusively in the older were mainly pathoadaptive, tuning the metabolism to oxygen and iron availability, hypermotility, and biofilm formation. In summary, while the evolutionary signature in the guts of very old mice shows youth-like features that may be associated with longevity, the selection of pathoadaptive traits is magnified in very old age. While suggesting that a breach in colonization resistance is not needed to justify the abundance of age-associated pathobionts, our findings raise the question whether specialized bacteria, as opposing to generalists such as E. coli, will display the same ability to evolve pathoadaptive traits. HighlightsO_LIGut commensals face increasingly personalized selective pressures in the aging gut C_LIO_LIEven healthy aging selects for pathoadaptive traits in the gut microbiota C_LIO_LIE. coli s adaptive pattern better reflects the metabolome than microbiota composition C_LI In BriefPathobionts are often enriched in the microbiota of the elderly. Melo-Miranda et al. showed that irrespectively of limiting the opportunity for gut invasion, the strength of selection for pathoadaptation increases with aging. Yet, the gut environment of extreme ages seems to converge, highlighting the discontinuity of the aging process.

evolutionary biology↗

bioRxiv2024

An ancient lysozyme in placozoans

Lysozymes are an essential part of immunity and nutrition in metazoans, degrading bacterial cell walls via the hydrolysis of peptidoglycan. Although various lysozymes have been reported for higher animals, the origin of animal lysozymes remains elusive as they seem to be lacking in all early branching phyla. In this study, we investigated a putative goose-type lysozyme (PLys, glycoside hydrolase family 23, GH23) of the placozoan Trichoplax sp. H2. We show that PLys is highly active and produced in gland cells of the ventral epithelium. PLys contains a protective and non-conserved cysteine-rich domain N-terminal of the conserved GH23 lysozyme domain. A truncation of this N-terminal domain in the maturation process of PLys leads to a drastic increase in enzymatic activity at the cost of stability. As the lysozyme is most active under acidic conditions, we investigated the pH trajectories during extracellular digestion in situ. Using a pH-senstive fluorescence reporter, we show that Trichoplax sp. H2 acidifies its temporary feeding grooves pulsatively during digestive events close to the optimum pH for PLys activity. To elucidate the evolutionary origin of the metazoan GH23 lysozyme family, we applied a structure-based phylogenetics approach to show that the metazoan g-type GH23 lysozymes originated from a horizontal gene transfer event from bacteria to an early pre-bilaterian ancestor. GH23 lysozymes have then been retained and expanded in many phyla, including Porifera, Cnidaria, Placozoa and chordates, acting as first animal lysozyme and a key component in the antibacterial arsenal since early animal evolution.

evolutionary biology↗

bioRxiv2023

SPATIO-TEMPORAL DYNAMICS OF EARLY SOMITE SEGMENTATION IN THE CHICKEN EMBRYO

During vertebrate embryo development, the body is progressively segmented along the anterior-posterior (A-P) axis early in development. The rate of somite formation is controlled by the somitogenesis embryo clock (EC), which was first described as gene expression oscillations of hairy1 (hes4) in the presomitic mesoderm of chick embryos with 15-20 somites. Here, the EC displays the same periodicity as somite formation, 90 min, whereas the posterior-most somites (44-52) only arise every 150 minutes, matched by a corresponding slower pace of the EC. Evidence suggests that the rostral-most somites are formed faster, however, their periodicity and the EC expression dynamics in these early stages are unknown. In this study, we used time-lapse imaging of chicken embryos from primitive streak to somitogenesis stages with high temporal resolution (3-minute intervals). We measured the length between the anterior-most and the last formed somitic clefts in each captured frame and developed a simple algorithm to automatically infer both the length and time of formation of each somite. We found that the occipital somites (up to somite 5) form at an average rate of 75 minutes, while somites 6 onwards are formed approximately every 90 minutes. We also assessed the expression dynamics of hairy1 using half-embryo explants cultured for different periods of time. This showed that EC hairy1 expression is highly dynamic prior to somitogenesis and assumes a clear oscillatory behaviour as the first somites are formed. Importantly, using ex ovo culture and live-imaging techniques, we showed that the hairy1 expression pattern recapitulates with the formation of each new pair of somites, indicating that somite segmentation is coupled with EC oscillations since the onset of somitogenesis. HighlightsO_LITime of early somite formation can be inferred from sequential length measurements C_LIO_LIThe cranial-most somites are formed faster than trunk somites C_LIO_LIOscillations of hairy1 expression are temporally coupled with early somite formation C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC="FIGDIR/small/535703v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@f643aborg.highwire.dtl.DTLVardef@1d4a9b0org.highwire.dtl.DTLVardef@d085a1org.highwire.dtl.DTLVardef@1f51399_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2021

Preferential allelic expression of PIK3CA mutations is frequent in breast cancer and is prognostically significant

PIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor positive cohort, but the benefit of PI3K inhibitors has had limited success compared with approaches targeting other less common mutations. We found allelic imbalances in the expression of PIK3CA in normal breast tissue and mapped a germline candidate regulatory variant. An imbalance was also frequently observed in the expression of the missense mutant and wild-type PIK3CA alleles in breast tumors from METABRIC and TCGA projects. Moreover, although 60% of tumors preferentially expressed the mutant allele, 10% did preferentially express the wild-type allele. Mechanistically, we show that these imbalances are more frequently due to regulatory variants in cis than altered copy-number and predict that somatic variants have a more significant role than germline ones. We further found that imbalanced allelic expression between mutant and wild-type alleles due to cis-regulatory variants associated with poor prognosis (p=0.0081). Interestingly, ER+, PR+, and Her2- tumors expressing very low levels of the mutant allele had the poorest prognosis (DSS <7.5yrs for ER+ and PR+ tumors and <5yrs for Her2- tumors). Hence, our work provides compelling evidence to support the clinical utility of PIK3CA allelic expression in breast cancer in identifying this cohort of low mutant allele expressing patients of poorer prognosis, who will unlikely benefit from PI3K inhibitors. Furthermore, our work establishes a new model of differential regulation of critical cancer-promoting genes.

cancer biology↗

bioRxiv2021

FrozenChicken: Promoting the meta-analysis of chicken microarray data

The FrozenChicken RData package, contains the frozen vectors for the commercially available (in situ oligonucleotide) Affymetrix Chicken Genome Array (GEO platform id GPL3213). This package will promote, simplify, and ease the meta-analysis of chicken microarray data by the research community studying vertebrate development using the chick model organism. The package is freely available in https://github.com/iduarte/FrozenChicken. (*Equal contribution.)

bioinformatics↗

bioRxiv2021

quincunx: an R package to query, download and wrangle PGS Catalog data

MotivationThe Polygenic Score (PGS) Catalog is a recently established open database of published polygenic scores that, to date, has collected, curated, and made available 721 polygenic scores from over 133 publications. The PGS Catalog REST API is the only method allowing programmatic access to this resource. ResultsHere, we describe quincunx, an R package that provides the first client interface to the PGS Catalog REST API. quincunx enables users to query and quickly retrieve, filter and integrate metadata associated with polygenic scores, as well as polygenic scoring files in tidy table format. Availabilityquincunx is freely available under an MIT License, and can be accessed from https://github.com/maialab/quincunx.

bioinformatics↗

bioRxiv2019

How to make methodological decisions when inferring social networks

Constructing and analysing social networks data can be challenging. When designing new studies, researchers are confronted with having to make decisions about how data are collected and networks are constructed, and the answers are not always straightforward. The current lack of guidance on building a social network for a new study system might lead researchers to try several different methods, and risk generating false results arising from multiple hypotheses testing. We suggest an approach for making decisions when developing a network without jeopardising the validity of future hypothesis tests. We argue that choosing the best edge definition for a network can be made using a priori knowledge of the species, and testing hypotheses that are known and independent from those that the network will ultimately be used to evaluate. We illustrate this approach by conducting a pilot study with the aim of identifying how to construct a social network for colonies of cooperatively breeding sociable weavers. We first identified two ways of collecting data using different numbers of feeders and three ways to define associations among birds. We then identified which combination of data collection and association definition maximised (i) the assortment of individuals into breeding groups (birds that contribute towards the same nest and maintain cohesion when foraging), and (ii) socially differentiated relationships (more strong and weak relationships than expected by chance). Our approach highlights how existing knowledge about a system can be used to help navigate the myriad of methodological decisions about data collection and network inference.\n\nSIGNIFICANCE STATEMENTGeneral guidance on how to analyse social networks has been provided in recent papers. However less attention has been given to system-specific methodological decisions when designing new studies, specifically on how data are collected, and how edge weights are defined from the collected data. This lack of guidance can lead researchers into being less critical about their study design and making arbitrary decisions or trying several different methods driven by a given preferred hypothesis of interest without realising the consequences of such approaches. Here we show that pilot studies combined with a priori knowledge of the study species social behaviour can greatly facilitate making methodological decisions. Furthermore, we empirically show that different decisions, even if data are collected under the same context (e.g. foraging), can affect the quality of a network.

animal behavior and cognition↗

bioRxiv2019

Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. E2: Massive bacterial transfer of genes involved in carbohydrate metabolism

Lateral gene transfer (also known as Horizontal Gene Transfer) is the transmission of genetic material between phylogenetically unrelated organisms. Previous studies have been showing the importance of this process for the evolution of unicellular eukaryotes, particularly those living in highly competitive niches such as the herbivore gut.\n\nPyromices sp. is an obligate anaerobic chytrid fungus that grows as a commensal organism in the gut of mammalian herbivores, possessing hydrogenosomes instead of mitochondria, producing hydrogen, and playing a key role in the digestion of plant cell wall material. These particular features make its genome particularly valuable for the study of the evolution and adaptation of unicellular eukaryotes to the cellulose-rich and anaerobic environment of the herbivore gut.\n\nHere we performed a detailed large-scale lateral gene transfer (LGT) analysis of the genome from the chytrid fungus Piromyces sp. strain E2. For this we set out to elucidate (i) which proteins were likely transferred to its genome, (ii) from which bacterial donor species, and (iii) which functions were laterally acquired. Using sequence comparison and phylogenetic analyses, we have found 704 LGT candidates, representing nearly 5% of the Piromyces sp. orfeome (i.e. the complete set of open reading frames), mostly transferred from Firmicutes, Fibrobacteres, Bacteroidetes and Proteobacteria, closely following the microbial abundance reported for the herbivore gut. With respect to the functional analysis, the LGT candidate set includes proteins from 250 different orthologous groups, with a clear over-representation of genes belonging to the Carbohydrate Transport and Metabolism functional class. Finally, we performed a graph density analysis on the metabolic pathways formed by the LGT candidate proteins, showing that the acquired functions fit cohesively within Piromyces metabolic network, and are not randomly distributed within the global KEGG metabolic map. Overall, our study suggests that Piromyces adaptation to living anaerobically and in the a cellulose-rich environment has been undoubtedly fostered by the acquisition of foreign genes from bacterial neighbors, showing the global importance of such evolutionary mechanisms for successful eukaryotic thriving in such competitive environments.

evolutionary biology↗