Biology subjects

Oliveira, A.

Publications and source records attributed to Oliveira, A..

15 recordsLinked to original sources

bioRxiv2026

A Weight Loss Fibrotic Response in Visceral Fat Is Driven by Defective Lysosome-Dependent Collagenolysis

Obesity induces pathological remodeling of white adipose tissue (WAT), including chronic inflammation and fibrosis, which drive metabolic dysfunction. Although weight loss (WL) is the cornerstone of obesity treatment and improves systemic metabolic health, its impact on WAT remodeling remains incompletely understood. Using a mouse model of diet-induced obesity followed by nutritional weight loss, we show that visceral WAT (vWAT) fails to fully recover despite normalization of body weight and marked metabolic improvment. Notably, vWAT fibrosis persists and continues to progress after WL. This occurs while extracellular matrix (ECM) production by adipose progenitor cells is markedly reduced following WL, explaining why pharmacological inhibition of ECM synthesis fails to prevent fibrosis during WL. Instead, we observed impaired collagen degradation by both progenitor cells and macrophages, along with lysosomal dysfunction, during WL. This suggests that defective ECM degradation, rather than continued ECM production, underlies fibrosis persistence and aggravation during WL. Together, these findings identify impaired collagenolysis as a critical barrier to adipose tissue recovery after WL and suggest that enhancing ECM clearance, rather than inhibiting ECM synthesis, may represent a more effective therapeutic strategy to restore adipose tissue function.

pathology↗

bioRxiv2026

Elevated MPS1 converts the fibrous corona into a source of chromosomal instability in colon cancer

Chromosomal instability (CIN), characterised by recurrent chromosome mis-segregation, fuels intratumour heterogeneity and tumour evolution. Yet, its proximal molecular causes remain ill-defined. Tumour-scale genomic and transcriptomic analyses associate MPS1 overexpression with CIN in colon carcinomas. Consistently, CIN+ patient-derived colon cancer cells (PCCCs) display elevated MPS1, frequent merotelic kinetochore-microtubule attachments and lagging chromosomes that are suppressed by partial MPS1 inhibition. Conversely, ectopic MPS1 overexpression in otherwise stable near-diploid cells phenocopies these defects, inducing micronuclei formation and karyotypic divergence. Mechanistically, MPS1 overactivity maintains ROD phosphorylation at Thr13/Ser15, continuously sustaining fibrous corona assembly despite mature end-on attachments. 3D-STED microscopy reveals split-interface configurations in which microtubules from opposing poles engage the canonical outer-kinetochore surface and a spatially distinct corona domain, explaining how merotely forms and persists into anaphase. Disrupting corona assembly restores chromosome segregation fidelity in MPS1-overexpressing RPE-1 cells and in CIN+ PCCCs. Together, our findings establish MPS1 overexpression as a driver of CIN and uncover how oncogenic transcriptional rewiring of mitotic signalling converts a transient microtubule-capture structure into a pathological source of merotely and chromosome mis-segregation in colon cancer.

cell biology↗

bioRxiv2026

Beyond signaling activation: Phosphorylation modulates Grb2 phase separation to create multivalent scaffolds

The Growth Factor Receptor-Bound Protein 2 (Grb2) is a central adaptor protein in signal transduction pathways, yet how its monomer-dimer equilibrium governs its supramolecular organization remains elusive. Here, we demonstrate that the oligomeric state of Grb2 acts as a binary switch for Liquid-Liquid Phase Separation (LLPS). While the auto-inhibited homodimer forms only transient, thermodynamically unstable assemblies in crowding conditions, the phosphorylation-mimetic monomer (Y160E) drives the formation of robust, gel-like condensates. Integrating turbidity assays, temperature-controlled dynamic light scattering, fluorescence recovery after photobleaching (FRAP), hyperspectral imaging analyses, and coarse-grained molecular dynamics simulations, we reveal that this phase transition is enthalpy-driven and reliant on a specific electrostatic network between the SH2 domain residue R142 and a C-terminal SH3 acidic cluster (Q170-D172). Crucially, we show that these monomeric condensates function as "scaffolds" that efficiently recruit and sequester cytosolic wild-type dimers ("clients") into the dense phase. This recruitment mechanism resolves the paradox of how non-condensing wild-type proteins participate in phase separation. Our findings propose a novel regulatory model where phosphorylation nucleates the formation of high-density signaling hubs, redefining Grb2 from a passive adaptor to a dynamic spatial organizer of the Ras/MAPK pathway.

biophysics↗

bioRxiv2026

Decellularized Small Intestine for Full Thickness Burn Wound Treatment

Treating extensive full-thickness burn wounds remains difficult in clinical practice because available donor skin is often limited, the risk of infection is high, and many standard dressings do not perform well when defects are large or structurally complex. These limitations have shifted attention to decellularized extracellular matrix (dECM) scaffolds, which can provide physical coverage while preserving biochemical cues that may support tissue repair. Based on this rationale, we designed a decellularization method that improves reagent penetration to produce a full-thickness porcine decellularized small intestine (dSI) scaffold for use in burn wound coverage. The protocol removed most cellular material while leaving low levels of detergent residue, and it maintained the native three-layer structure of the intestinal wall. Most key ECM components, such as collagen and glycosaminoglycans, were also retained. In this study, the dSI showed several properties relevant to burn care, capacity to absorb large amounts of fluid, water vapor transmission rates similar to those reported for skin, and resisted microbial penetration in vitro. From a mechanical standpoint, the scaffold retained anisotropic behaviour and remained stable under cyclic loading. This pattern indicates that it could withstand repeated deformation instead of acting like a fragile membrane. Degradation tests under enzymatic and oxidative conditions indicate that the material breaks down in a controlled way over a period that appears consistent with typical wound-healing timelines. In vitro assays indicated that the scaffold was cytocompatible, as human dermal fibroblasts and keratinocytes both attached to its surface and continued to proliferate. Cell responses differed depending on surface orientation, suggesting that preserved intestinal layers may shape cell behaviour in ways that are often missing in thinner or more uniform matrices. Overall, full-thickness dSI appears to act as a biologically active scaffold and shows mechanical properties that exceed those of many currently used burn dressings.

bioengineering↗

bioRxiv2026

Inhibition of the mitochondrial pyruvate carrier attenuates the integrated stress response activation in a cellular model of Huntington's disease

Mitochondrial pyruvate carrier (MPC) inhibition was found protective in models of neurodegenerative diseases, such as Alzheimers and Parkinsons. However, little is known about MPC as a potential therapeutic target in Huntingtons disease (HD), a neurodegenerative disorder with dysregulation of the pro-survival pathway integrated stress response (ISR). Here, we investigate if MPC inhibition modulates the ISR and mitigates mutant huntingtin (mut-Htt) proteotoxicity in a cellular HD model. We treated cells expressing N-terminal fragments of wild-type- (wt-) or mut-Htt with two MPC inhibitors (mitoglitazone and UK5099) or solvent control. Metabolism was assessed analysing resazurin reduction, oxygen consumption, extracellular acidification, and ATP levels. ISR activation and huntingtin proteostasis were assessed using western-blot and filter-trap assays. Mut-Htt-expressing cells showed decreased resazurin reduction and ATP levels, and increased eIF2 phosphorylation, indicating metabolic stress and ISR activation. MPC inhibitors (100 {micro}M) increased resazurin reduction and decreased respiration. The latter was rescued by the membrane-permeant methyl pyruvate, which bypasses MPC inhibition. In wt-Htt-expressing cells, MPC inhibitors increased levels of ATP and ISR markers, suggesting metabolic adaptation and ISR activation. In mut-Htt-expressing cells, MPC inhibitors preserved ATP levels and attenuated mut-Htt-induced eIF2 phosphorylation but without changing soluble or aggregated mut-Htt levels. This work showed that MPC inhibition differentially modulates the ISR: it activates ISR in control cells and attenuates overactive ISR in mut-Htt-expressing cells. However, MPC inhibition did not impact the proteostasis of N-terminal fragment mut-Htt. Further studies are essential to explore MPC inhibition in less severe full-length mut-Htt-expressing models to better understand its therapeutic potential in HD.

pharmacology and toxicology↗

bioRxiv2024

POLO kinase inhibits Protein Phosphatase 1 to promote the Spindle Assembly Checkpoint and prevent aneuploidy

Protein phosphatase 1 (PP1) is essential for spindle assembly checkpoint (SAC) silencing and mitotic exit, but its regulation during mitosis remains ill-defined. Here, we demonstrate in vitro and in Drosophila cells that the mitotic kinase POLO phosphorylates PP187B at a conserved residue (T286) within a pocket implicated in the recognition of RVxF-containing target proteins. Phosphorylation of T286 inhibits PP187B binding to the RVxF motif of the SAC kinase MPS1, dampening the dephosphorylation of MPS1 T-loop. Phosphorylation of T286 is dynamically regulated during mitosis. It occurs at unattached/tensionless kinetochores and decreases as chromosomes congress. Expression of phosphomimetic PP187BT286D prevents MPS1 inactivation in metaphase and causes a SAC-dependent delay of anaphase onset. Conversely, an unphosphorylatable PP187BT286A mutant impairs MPS1 activation at unattached kinetochores and weakens the SAC. In vivo, larval neuroblasts expressing PP187BT286 phosphomutants exhibit frequent chromosome mis-segregation and aneuploidy. Thus, our findings identify POLO-mediated phosphorylation of PP187B as a critical regulatory strategy that fine-tunes phosphatase activity to ensure a robust and timely SAC and prevent genome instability.

cell biology↗

bioRxiv2024

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting and inadequate model documentation of model results. Addressing this gap, we introduce FROG analysis, a community-driven initiative aimed at standardizing reproducibility assessments of CBMs and GEMs. The FROG framework encompasses four key analyses--Flux variability, Reaction deletion, Objective function, and Gene deletion--to produce standardized, numerically reproducible FROG reports. These reports serve as reference datasets, enabling model evaluators, curators, and independent researchers to verify the reproducibility of GEMs systematically. BioModels, a leading repository of systems biology models, has integrated FROG analysis into its curation workflow, enhancing the reproducibility and reusability of submitted GEMs. In our study evaluating 65 GEM submissions from the community, approximately 40% reproduced without intervention, 28% requiring minor adjustments, and 32% needing input from authors. The standardization introduced by FROG analysis facilitated the detection and resolution of issues, ultimately leading to the successful reproduction of all models. By establishing a standardized and comprehensive approach to evaluating GEM reproducibility, FROG analysis significantly contributes to making CBMs and GEMs more transparent, reusable, and reliable for the broader scientific community.

systems biology↗

bioRxiv2024

MAC: An Artifact Correction Framework for Brain MRI based on Deep Neural Networks

The correction of artifacts in Magnetic Resonance Imaging (MRI) is increasingly relevant as voluntary and involuntary artifacts can hinder data acquisition. Reverting from corrupted to artifact-free images is a complex task. Deep Learning (DL) models have been employed to preserve data characteristics and to identify and correct those artifacts. We propose MOANA, a novel DL-based solution to correct artifacts in multi-contrast brain MRI scans. MOANA offers two models: the simulation and the correction models. The simulation model introduces perturbations similar to those occurring in an exam while preserving the original image as ground truth; this is required as publicly available datasets rarely have motion-corrupted images. It allows the addition of three types of artifacts with different degrees of severity. The DL-based correction model adds a fourth contrast to state-of-the-art solutions while im-proving the overall performance of the models. MOANA achieved the highest results in the FLAIR contrast, with a Structural Similarity Index Measure (SSIM) of 0.9803 and a Normalized Mutual Information (NMI) of 0.8030. With this, the MOANA model can correct large volumes of images in less time and adapt to different levels of artifact severity, allowing for better diagnosis.

bioinformatics↗

bioRxiv2023

Obesity-elicited macrophages shape CD9hi progenitor fate to promote adipose tissue fibrosis and dysfunction

Obesity is a life-threatening condition characterized by a maladaptive remodeling of the visceral white adipose tissue (vWAT), including fibrosis, that drives vWAT metabolic alterations. We previously identified CD9hi adipose tissue progenitors as the main drivers of vWAT fibrosis in mice and humans. However, how their functions are controlled, especially by macrophages, remains largely unknown. We found that obesity-elicited monocyte-derived macrophages (obeMac) accumulation was considerably elevated in mice prone to obesity-induced vWAT fibrosis. Limiting obeMac build-up decreased the numbers and fibrogenic activation of CD9hi progenitors, leading to decreased vWAT fibrosis and improved glucose homeostasis. In patients with obesity, we identified macrophages similar to mouse obeMacs that were associated with accumulation of CD9hi progenitors in the vWAT and loss of glycemic control. Finally, intercellular communication analysis identified mediators produced by obeMacs that control the fibrogenic potential of CD9hi progenitors. Together, we uncovered an obeMac-CD9hi progenitors axis controlling vWAT fibrosis and dysfunction.

pathology↗

bioRxiv2022

Exploring Xylella fastidiosa's metabolic traits using a GSM model of the phytopathogenic bacterium

Xylella fastidiosa is a gram-negative phytopathogenic bacterium that caused a significant economic impact around the world. In the last decade, genome-scale metabolic models have become important systems biology tools for studying the metabolic behaviour of different pathogens and driving the discovery of novel drug targets. This work is a second iteration of the iMS508 model for X. fastidiosa subsp. pauca De Donno. The model comprises 1138 reactions, 1234 metabolites, and 509 genes. in silico validation of the metabolic model was achieved through the comparison of simulations with available experimental data. Aerobic metabolism was simulated properly and fastidian gum production rates predicted accurately.

bioinformatics↗

bioRxiv2022

Studies on the interaction of three lytic bacteriophages with a wide collection of Escherichia coli strains implicated in swine enteric colibacillosis

AO_SCPLOWBSTRACTC_SCPLOWThe misuse of antibiotics in the swine industry and their on-going restriction requires alternatives to control enterotoxigenic and shiga toxin-producing Escherichia coli (ETEC and STEC, respectively). This study evaluates the potential of three coliphages, vB_EcoM_FJ1, vB_EcoM_FN and vB_EcoM_SP1 against 104 ETEC, STEC and ETEC/STEC strains isolated from pig colibacillosis in Portuguese (2018-2020) and Spanish farms (2006-2016), encompassing 71.2% mcr-positive strains (33.7% with mcr-1, 1.9% mcr-2, 35.6% mcr-4 and 2.9% mcr-5) and 18.3% positive strains for TEM (1%), SHV (6.7%), and CTX-M (11.5%) extended-spectrum beta-lactamase-encoding genes. In general, all bacteriophages presented a narrow lytic spectrum (up to 2.9%) against the 104 ETEC, STEC and ETEC/STEC. Bacteriophages shared >80% overall nucleotide identity with E. coli phage T4 (Tevenvirinae subfamily), but a particular look at the distal part of the long tail fiber (gp38) revealed no homology. All bacteriophages recognize lipopolysaccharides as receptors, and additionally, FN binds to an outer membrane protein A. Bacteriophage-insensitive mutants of vB_EcoM_FJ1 (90%) and vB_EcoM_FN (100%) were shown to be more susceptible to pig serum inactivation comparatively to the parental strain and furthermore, their adhesion capacity to porcine intestinal cells was diminished by, approximately, 90%. Contrariwise, vB_EcoM_SP1 insensitive variants did not display phenotypic differences comparing to the wild-type strain. This study demonstrates that besides being T4-like, these bacteriophages revealed a narrow lytic spectrum against diarrhoeagenic E. coli strains and that the acquisition of novel bacteriophage-encoded adhesins (gp38) seems to be determinant for such results.

microbiology↗

bioRxiv2021

Mechanosensitive control of mitotic entry

As cells prepare to divide, they must ensure that enough space is available to assemble the mitotic machinery without perturbing tissue homeostasis1. To do so, cells undergo a series of biochemical reactions regulated by cyclin B1-CDK1 that trigger the reorganization of the actomyosin cytoskeleton2 and ensure the coordination of cytoplasmic and nuclear events3. Along with the biochemical events that control mitotic entry, mechanical forces have recently emerged as important players in the regulation of cell cycle events4-6. However, the exact link between mechanical forces and the biochemical pathways that control mitotic progression remains to be established. Here, we identify a mechanical signal on the nucleus that helps set the time for nuclear envelope permeabilization (NEP) and mitotic entry. This signal relies on actomyosin contractility, which leads to nuclear unfolding during the G2-M transition, activating the stretch-sensitive cPLA2 on the nuclear envelope. This contributes to the spatiotemporal translocation of cyclin B1 to the nucleus. Our data demonstrate how nuclear mechanics during the G2-M transition contribute to timely and efficient mitotic spindle assembly and prevents chromosomal instability.

cell biology↗

bioRxiv2021

Targeting activated macrophages intracellular milieu to augment anti-inflammatory drug potency

We present pH-responsive phosphorylcholine polymersomes ability to target activated macrophages via scavenger receptors, enter them via endocytosis, and escape from early endosomes enabling the intra-cellular drug delivery. Using an arthritis experimental model and the gold standard disease modifying anti-rheumatic drug, methotrexate, we prove that polymersomes augments therapeutic efficacy, while minimizing the off-target effect. First, we demonstrate the selective accumulation of polymersomes within the inflamed synovial tissues and cells, including macrophages. Second, we show the beneficial therapeutic effect of methotrexate loaded polymersomes in preventing both joint inflammation and further damage. Hence, we prove the therapeutic potential of polymersomes in enhancing the complete prevention of arthritis progression, which makes it a promising nanotherapy for arthritis treatment as well as other inflammatory disorders. TeaserWe show that the effective targeting and delivery of drugs to the main inflammation actors, the macrophages, enhances arthritis therapy.

immunology↗

bioRxiv2020

A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coil

Acrylic acid is a value-added chemical used in industry to produce diapers, coatings, paints, and adhesives, among many others. Due to its economic importance, there is currently a need for new and sustainable ways to synthesise it. Recently, the focus has been laid in the use of Escherichia coli to express the full bio-based pathway using 3-hydroxypropionate as an intermediary through three distinct pathways (glycerol, malonyl-CoA, and {beta}-alanine). Hence, the goals of this work were to use COPASI software to assess which of the three pathways has a higher potential for industrial-scale production, from either glucose or glycerol, and identify potential targets to improve the biosynthetic pathways yields. When compared to the available literature, the models developed during this work successfully predict the production of 3-hydroxypropionate, using glycerol as carbon source in the glycerol pathway, and using glucose as a carbon source in the malonyl-CoA and {beta}-alanine pathways. Finally, this work allowed to identify four potential over-expression targets (glycerol-3-phosphate dehydrogenase (G3pD), acetyl-CoA carboxylase (AccC), aspartate aminotransferase (AspAT), and aspartate carboxylase (AspC)) that should, theoretically, result in higher AA yields. Author summaryAcrylic acid is an economically important chemical compound due to its high market value. Nevertheless, the majority of acrylic acid consumed worldwide its produced from petroleum derivatives by a purely chemical process, which is not only expensive, but it also contributes towards environment deterioration. Hence, justifying the current need for sustainable novel production methods that allow higher profit margins. Ideally, to minimise production cust, the pathway should consist in the direct bio-based production from microbial feedstocks, such as Escherichia coli, but the current yields achieved are still to low to compete with conventional method. In this work, even though the glycerol pathway presented higher yields, we identified the malonyl-CoA route, when using glucose as carbon source, as having the most potential for industrial-scale production, since it is cheaper to implement. Furthermore, we also identified potential optimisation targets for all the tested pathways, that can help the bio-based method to compete with the conventional process.

bioengineering↗

bioRxiv2018

Unveiling Leishmania invasion of fibroblasts: calcium signaling, lysosome recruitment and exocytosis culminate with actin-independent invasion.

Intracellular parasites of the genus Leishmania are the causative agents of human leishmaniasis, a widespread emergent tropical disease. The parasite is transmitted by the bite of a hematophagous sandfly vector that inoculates motile flagellated promastigote forms into the dermis of the mammalian host. After inoculation, parasites are ultimately captured by macrophages and multiply as round-shaped amastigote forms. Macrophages seem not to be the first infected cells since parasites were observed invading neutrophils first whose leishmania-containing apoptotic bodies were latter captured by macrophages, thereby becoming infected. The fact that Leishmania spp are able to live and replicate inside immune phagocytic cells and that macrophages are the main cell type found infected in chronicity created the perception that Leishmania spp are passive players waiting to be captured by phagocytes. However, several groups have described the infection of non-phagocytic cells in vivo and in vitro. The objective of this work was to study the cellular mechanisms involved in the invasion of non-professional phagocytes by Leishmania. We show that promastigotes of L.amazonensis actively induces invasion in fibroblasts without cytoskeleton activity, thus by a mechanism that is distinct from phagocytosis. Inside fibroblasts parasites transformed in amastigotes, remained viable for at least two weeks and re-transformed in promastigotes when returned to insect vector conditions. Similarly to what was observed for T. cruzi, infection involves calcium signaling, recruitment and exocytosis of lysosomes involved in plasma membrane repair and lysosome-triggered endocytosis. Conditions that alter lysosomal function such as cytochalasin-D and brefeldin-A treatment or the knockout of host cell lysosomal proteins LAMP-1 and 2 dramatically affected invasion. Likewise, triggering of lysosomal exocytosis and lysosome-dependent plasma membrane repair by low doses of streptolysin-O dramatically increased parasite entry. Together our results show that L.amazonensis promastigotes are able to take advantage of calcium-dependent lysosomal exocytosis and lysosome-induced endocytosis to invade and persist in non-phagocytic cells.\n\nAUTHOR SUMMARYIntracellular parasites of the genus Leishmania are the causative agents of leishmaniasis. The disease is transmitted by the bite of a sand fly vector which inoculates the parasite into the skin of mammalian hosts, including humans. During chronic infection the parasite lives and replicates inside phagocytic cells, notably the macrophages. An interesting but overlooked finding on Leishmania infection is that non-phagocytic cells have also been found infected by amastigotes. Nevertheless, the mechanisms by which Leishmania invades non-phagocytic cells were not studied to date. Here we show that L. amazonensis can actively induce their own entry into fibroblasts independently of actin cytoskeleton activity, thus by a mechanism that is distinct from phagocytosis. Invasion involves subversion of host cell functions such as calcium signaling and recruitment and exocytosis of host cell lysosomes involved in plasma membrane repair and whose positioning and content interfere in invasion. Parasites were able to replicate and remained viable in fibroblasts, suggesting that cell invasion trough the mechanism demonstrated here could serve as a parasite hideout and reservoir, facilitating infection amplification and persistence.

cell biology↗