Biology subjects

Ferreira, P.

Publications and source records attributed to Ferreira, P..

10 recordsLinked to original sources

bioRxiv2026

Cldn18 evolution reveals pleiotropic constraints in vertebrate stomach loss

Understanding the origins of anatomical innovations is central to elucidate the evolution of phenotypic diversity, as novel body plans often underpin the colonization of new ecological niches. The stomach, with its acid-secreting glands, evolved in the gnathostome ancestor and has been lost repeatedly. Claudin 18 (CLDN18) is a tight-junction protein that preserves gastric epithelial integrity against extreme H gradients and, in mammals, also acts in the lung through alternative first-exon isoforms. This dual role suggests that pleiotropy may shape the fate of CLDN18 after stomach loss. Here, we provide a detailed analysis of CLDN18 evolution across jawed vertebrates. CLDN18 originated in the gnathostome ancestor and is expressed in the stomach of elasmobranchs. We found no evidence of the gene in chimaeras or lungfishes, two additional agastric lineages, extending the loss of cldn18a previously described in agastric teleosts. Exon 1 architecture indicates a tandem duplication in the Euteleostomi ancestor, whereas stomach- and lung-associated isoforms are partitioned in most tetrapods examined. Monotremes, although agastric, retain only the lung-associated exon 1, consistent with lung function sustaining selection on the locus. Together, these findings reveal a complex evolutionary history involving gene loss, alternative splicing, tissue-specific regulation, and secondary exon loss, highlighting how pleiotropy and regulatory partitioning shaped the evolution of epithelia in jawed vertebrates.

evolutionary biology↗

bioRxiv2025

Cell lineage inference from mitochondrial mutations

Tracing genealogical relationships between cells and their molecular states is essential for understanding tissue development, maintenance and disease. We present mt-SCITE, a computational method that reconstructs cell division histories from mitochondrial mutations in single cells. On simulated and experimental benchmarks, mt-SCITE outperformed existing methods in terms of cell lineage reconstruction, and scaled to thousands of cells. Applied to expanded CD8+ T cells following vaccination, mt-SCITE resolved subclonal relationships and revealed clones with predominantly memory-like, effector-like, or mixed states. mt-SCITE robustly identifies clonally related populations and resolves substructure within them, providing a broadly applicable approach to study cell lineage development.

bioinformatics↗

bioRxiv2025

Platelet mitochondrial transfer via extracellular vesicles modulates neutrophil phenotype and function

Platelet activation causes the release of extracellular vesicles, of which a small proportion contain respiratory competent mitochondria. Mitochondria are integral for energy production and in the regulation of apoptotic pathways. However, the existence of extracellular mitochondria highlights a potential new role in intercellular communication. We hypothesised that platelet extracellular vesicles could be taken up by circulatory cells and alter their function. In this work we demonstrate that platelet extracellular vesicles containing mitochondria interact with and are internalised by neutrophils. Flow cytometry revealed that this interaction promotes neutrophil surface receptor changes, indicative of enhanced neutrophil activation, adhesion and migration pathways. The internalisation of platelet mitochondria renders neutrophils unable to subsequently engulf bacteria, demonstrating reduced phagocytic capacity, but enhances the formation of neutrophil extracellular traps, both alone and in the presence of additional stimuli. Our findings show that platelet mitochondria released in extracellular vesicles can alter neutrophil activity and so may be important intercellular communicators and modulators of inflammatory and immune responses.

cell biology↗

bioRxiv2024

Discovery, Characterization and Synthetic Potential of Two Novel Bacterial Alcohol Oxidases

The search for novel synthetic tools to prepare industrial chemicals in a safer and greener manner is a continuing challenge in synthetic chemistry. In this manuscript, we report the discovery, characterization, and synthetic potential of two novel aryl-alcohol oxidases from bacteria which are able to oxidize a variety of aliphatic and aromatic alcohols in high efficiencies (up to 4970 min-1mM-1). Crystal structures revealed unusually wide-open entrance to the active-site pockets compared to that previously described for traditional fungal aryl-alcohol oxidases, which could correlate with differences in substrate scope, catalytic efficiency, and other functional properties. Preparative-scale reactions and ability to operate at high substrate loadings also demonstrate the potential of these enzymes in synthetic chemistry with turnover numbers > 30000. Moreover, their availability as soluble and active recombinant proteins enabled their use as cell-free extracts which further highlights their potential for the large-scale production of carbonyl compounds.

biochemistry↗

bioRxiv2021

Refining the domain architecture model of the replication origin firing factor Treslin/TICRR

Faithful genome duplication requires appropriately controlled replication origin firing. The metazoan Treslin/TICRR origin firing factor and its yeast orthologue Sld3 are regulation hubs of origin firing. They share the Sld3-Treslin domain (STD) and the adjacent TopBP1/Dpb11 interaction domain (TDIN). We report a revised domain architecture model of Treslin/TICRR. Complementary protein sequence analyses uncovered Ku70-homologous {beta}-barrel folds in the Treslin/TICRR middle domain (M domain) and in Sld3. Thus, the Sld3-homologous Treslin/TICRR core comprises its three central domains, M domain, STD and TDIN. This Sld3-core is flanked by non-conserved terminal domains, the CIT (conserved in Treslins) and the C-terminus. We also identified Ku70-like {beta}-barrels in MTBP and Sld7. Our binding experiments showed that the Treslin {beta}-barrel mediates interaction with the MTBP {beta}-barrel, reminiscent of the homotypic Ku70-Ku80 dimerization. This binding mode is conserved in the Sld3-Sld7 dimer. We used Treslin/TICRR domain mutants to show that all Sld3-core domains and the non-conserved terminal domains fulfil important functions during origin firing in human cells. Thus, metazoa-specific and widely conserved molecular processes cooperate during origin firing in metazoa.

molecular biology↗

bioRxiv2020

Within-patient genetic diversity of SARS-CoV-2

SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viruses can also display genetic diversity within individual hosts, and co-existing viral variants may affect disease progression and the success of medical interventions. To systematically examine the intra-patient genetic diversity of SARS-CoV-2, we processed a large cohort of 3939 publicly-available deeply sequenced genomes with specialised bioinformatics software, along with 749 recently sequenced samples from Switzerland. We found that the distribution of diversity across patients and across genomic loci is very unbalanced with a minority of hosts and positions accounting for much of the diversity. For example, the D614G variant in the Spike gene, which is present in the consensus sequences of 67.4% of patients, is also highly diverse within hosts, with 29.7% of the public cohort being affected by this coexistence and exhibiting different variants. We also investigated the impact of several technical and epidemiological parameters on genetic heterogeneity and found that age, which is known to be correlated with poor disease outcomes, is a significant predictor of viral genetic diversity. Author SummarySince it arose in late 2019, the new coronavirus (SARS-CoV-2) behind the COVID-19 pandemic has mutated and evolved during its global spread. Individual patients may host different versions, or variants, of the virus, hallmarked by different mutations. We examine the diversity of genetic variants coexisting within patients across a cohort of 3939 publicly accessible samples and 749 recently sequenced samples from Switzerland. We find that a small number of patients carry most of the diversity, and that patients with more diversity tend to be older. We also find that most of the diversity is concentrated in certain regions and positions of the virus genome. In particular, we find that a variant reported to increase infectivity is among the most diverse positions. Our study provides a large-scale survey of within-patient diversity of the SARS-CoV-2 genome.

genomics↗

bioRxiv2020

Single-cell copy number calling and event history reconstruction

Copy number alterations are driving forces of tumour development and the emergence of intra-tumour heterogeneity. A comprehensive picture of these genomic aberrations is therefore essential for the development of personalised and precise cancer diagnostics and therapies. Single-cell sequencing offers the highest resolution for copy number profiling down to the level of individual cells. Recent high-throughput protocols allow for the processing of hundreds of cells through shallow whole-genome DNA sequencing. The resulting low read-depth data poses substantial statistical and computational challenges to the identification of copy number alterations. We developed SCICoNE, a statistical model and MCMC algorithm tailored to single-cell copy number profiling from shallow whole-genome DNA sequencing data. SCICoNE reconstructs the history of copy number events in the tumour and uses these evolutionary relationships to identify the copy number profiles of the individual cells. We show the accuracy of this approach in evaluations on simulated data and demonstrate its practicability in applications to two breast cancer samples from different sequencing protocols.

cancer biology↗

bioRxiv2019

Temperature Dramatically Shapes Mosquito Gene Expression with Consequences for Mosquito-Zika Virus Interactions

Vector-borne flaviviruses are emerging threats to human health. For successful transmission, the virus needs to efficiently enter mosquito cells, replicate within, and escape several tissue barriers while mosquitoes elicit major transcriptional responses to flavivirus infection. This process will not only be affected by the specific mosquito-pathogen pairing, but also variation in key environmental variables such as temperature. Thus far, few studies have examined the molecular responses triggered by temperature and how these responses modify infection outcomes despite substantial evidence showing strong relationships between temperature and transmission in a diversity of systems. To define the host transcriptional changes associated with temperature variation during the early infection process, we compared the transcriptome of mosquito midgut samples from mosquitoes exposed to Zika virus (ZIKV) and non-exposed mosquitoes housed at three different temperatures (20, 28, and 36{degrees}C). While the high temperature samples did not have significant changes from standard rearing conditions (28{degrees}C) 48 hr post-exposure, the transcriptome profile of mosquitoes housed at 20{degrees}C was dramatically different. The expression of genes most altered by the cooler temperature involved aspects of blood-meal digestion, ROS metabolism, and mosquito innate immunity. Further, we did not find significant differences in the viral RNA copy number between 24 and 48 hr post-exposure at 20{degrees}C, suggesting ZIKV replication is limited by cold-induced changes to the mosquito midgut environment. In ZIKV-exposed mosquitoes, vitellogenin, a lipid carrier protein, was the most up-regulated at 20{degrees}C. Our results provide a deeper understanding of the temperature-triggered transcriptional changes in Aedes aegypti and can be used to further define the molecular mechanisms driven by environmental temperature variation.\n\nContribution to the Field StatementA variety of methods for engineering refractory mosquitoes are currently being studied and show promise for disease control. Although considerable effort has been put into understanding the immune system of mosquitoes in response to infections, almost nothing is understood about environmental influences in regulating these responses. Here, we used RNA sequencing to study the effect of temperature on the mosquito transcriptome profile, as well as assess the changes in the immune response to ZIKV infection at three different temperatures. We found a remarkable effect of temperature on the transcriptome profile of mosquitoes exposed to cool conditions (20{degrees}C) after imbibing a blood meal, as well as accumulation of transcripts involved with different mechanisms associated with blood meal digestion, metabolism, and some components of the immune response in mosquitoes. Our results provide new insights in potential mechanisms that limit temperature-driven pathogen establishment and replication within the mosquito vector.

molecular biology↗

bioRxiv2018

Comparative Proteomics Reveals Characteristic Proteins on Praziquantel-resistance in Schistosoma mansoni

The extensive use of Praziquantel (PZQ), the only drug available to treat schistosomiasis, has brought concern about the emergence of PZQ-resistance/tolerance by Schistosoma spp., thus reaffirming an urge for the development of new treatment alternatives. Therefore, it is imperative and urgent to study this phenomenon trying to understand what is involved in its occurrence. Studies of Schistosoma spp. genome, transcriptome and proteome are crucial to better understand this situation. By stepwise drug pressure from a fully susceptible parasite strain, our group selected a S. mansoni variant strain stably resistant to PZQ and isogenic to its fully susceptible parental counterpart, except for the genetic determinants of PZQ-resistance phenotype. Based on this, the objective of this study was to compare the proteomes of both strains, identifying proteins from male and female adult worms of PZQ-resistant and PZQ-susceptible strains, exposed and not exposed to PZQ, which were separated by high-resolution two-dimensional electrophoresis and sequenced by high throughput LC-MS/MS. Likewise, this work is extremely relevant since for the first time the proteome of a S. mansoni PZQ-resistant strain is studied and compared to the proteome of the respective S. mansoni PZQ-susceptible strain. This study identified 60 S. mansoni proteins, some of which differentially expressed in either strain, which may putatively be involved in the PZQ-resistance phenomenon. This information represents substantial progress towards deciphering the worm proteome. Furthermore, these data may constitute an informative source for further investigations into PZQ-resistance and increase the possibility of identifying proteins related to this condition, possibly contributing to avoid or decrease the likelihood of development and spread of PZQ-resistance. This is an innovative study that opens doors to PZQ-resistance surveys, contributing to discover a solution to PZQ-resistance problem, as suggests new potential targets for study.

pharmacology and toxicology↗

bioRxiv2018

FALCON: a method to infer metagenomic composition of ancient DNA

The general approaches to detect and quantify metagenomic sample composition are based on the alignment of the reads, according to an existing database containing reference microbial sequences. However, without proper parameterization, these methods are not suitable for ancient DNA. Quantifying somewhat dissimilar sequences by alignment methods is problematic, due to the need of fine-tuned thresholds, considering relaxed edit distances and the consequent increase of computational cost. Additionally, the choice of the thresholds poses the problem of how to quantify similarity without producing overestimated measures. We propose FALCON-meta, a compression-based method to infer metagenomic composition of next-generation sequencing samples. This unsupervised alignment-free method runs efficiently on FASTQ samples. FALCON-meta quickly learns how to give importance to the models that cooperate to predict similarity, incorporating parallelism and flexibility for multiple hardware characteristics. It shows substantial identification capabilities in ancient DNA without overestimation. In one of the examples, we found and authenticated an ancient Pseudomonas bacteria in a Mammoth mitogenome.\n\nFALCON-meta can be accessed at https://github.com/pratas/falcon.

bioinformatics↗