Biology subjects

Carvalho, T.

Publications and source records attributed to Carvalho, T..

18 recordsLinked to original sources

bioRxiv2026

A shared extracellular plasticity program drives brain repair and tumor progression

Injury induces complex multicellular repair responses that restore tissue integrity and replenish lost cells. In the brain, regeneration is limited and depends on the proliferation of neural and glial progenitors. But how these cells remodel the microenvironment to support repair remains poorly understood. Here, we profile dividing cells in the injured fruit fly brain revealing signatures of neural stem cell activation and ECM remodeling. We find that rapid activation of a Heparan Sulfate-binding factor (Hpsl) and changes in glypicans condition the extracellular space for proliferation. Hpsl promotes signalling of scarce Dpp/BMP ligands in brain cells with latent proliferative capacity and regulates organismal resilience to brain injury. We further show that malignant cells in fly and mouse brains promote similar HS-interactions to support tumor progression. Together, our findings identify extracellular proteoglycan remodeling as a key regulator of brain repair and uncover a common plasticity program engaged by brain damage and tumorigenesis.

cell biology↗

bioRxiv2026

Fungal hydrophobins unleashed from food waste: production, rodlet assembly, and functional properties in Ganoderma adspersum

Ganoderma adspersum is a white-rot fungus (WRF) that produces amphipathic, surface-active proteins, known as hydrophobins. To explore sustainable routes for protein production and waste valorization, G. adspersum was cultivated under defined shaking conditions using different carbon and nitrogen sources, including apple skin food waste. From these cultures, we report for the first time the isolation and characterization of a novel class I hydrophobin, designated as Gad1. Atomic force microscopy revealed abundant rodlet-like nanostructures consistent with class I hydrophobin assemblies, and Raman spectroscopy confirmed {beta}-sheet enrichment typical of amyloid-like organization. MALDI-TOF mass spectrometry further identified Gad1 along with additional hydrophobin-like proteins in the foam. Hydrophobin-enriched foam extracts were used to form stable oil-in-water emulsions that could be converted into porous, freezedried composite aerogels. These findings expand the known diversity of hydrophobins in whiterot fungi and demonstrate that food-waste-derived substrates can support hydrophobin production and functional biomaterial formation.

biophysics↗

bioRxiv2025

Increased striatal coupling one week after ischemic stroke revealed by ultrafast functional MRI

BackgroundNetwork reorganization following ischemic stroke is thought to play a role in recovery. Although cortico-cortical reorganization is widely established, changes in interhemispheric striatal connections following ischemia remain poorly understood, even when stroke occurs in motor areas. Given the importance of the striatum to motor function, we investigated network-level striatal coupling in stroke using ultrafast resting-state fMRI, which has recently been shown to facilitate the dissection of synchronous oscillatory activity better than its conventional [~]1 sec time-resolution counterparts. MethodsA cohort of (N=18) sedated rats were randomized and N=9 rats underwent unilateral photothrombotic ischemic lesioning in motor cortex. One week after the lesion, when plasticity and recovery are well established, all animals were scanned on a 9.4T MRI scanner using a cryogenic coil using an ultrafast resting-state functional MRI sequence with temporal resolution of 90 ms. Data were collected for 24 minutes, and spectral power, phase locking, and functional connectivity were quantified. Histology was performed to confirm lesion extent. ResultsWhile cortico-cortical power, connectivity and synchrony were diminished one week post-stroke as expected, we surprisingly found increased striato-striatal power, synchrony and functional connectivity in the stroked group compared with the control group. In stroked animals, the spectral power in the ultraslow oscillation frequency band (0.02-0.4 Hz) significantly increased in the striatum while decreasing in the cortex. When data were undersampled to "conventional" fMRI temporal resolution (900 ms), the striatal effects were lost, revealing the power of ultrafast fMRI approaches in unveiling such phenomena. ConclusionsIncreased striato-striatal coupling, in the form of increased synchrony, spectral power, and functional connectivity, was revealed by ultrafast resting-state fMRI, but not conventional temporal resolution resting-state fMRI. Our findings suggest more involvement of subcortical areas in network reorganization than previously thought.

neuroscience↗

bioRxiv2025

Homology-mediated transformation of frog-killing fungus Batrachochytrium dendrobatidis illuminates chytrid development and pathogenesis

The chytrid fungus Batrachochytrium dendrobatidis (Bd) infects amphibians and causes chytridiomycosis, a disease linked to global amphibian decline. Despite its ecological importance, Bd has lacked robust tools for genetic manipulation, limiting molecular insights into its development and pathogenicity. Here, we establish homologous recombination as a system for stable transformation of Bd, enabling targeted chromosomal integration of exogenous DNA, endogenous protein tagging, and targeted gene deletion. We use this system to visualize Bd infection in live amphibians to enhance understanding of host invasion and pathogenesis. We also use this system to test a previous hypothesis regarding the role of chitin synthases in Bd development by tagging the endogenous chitin synthase Myo17D and observing its rapid relocalization to the plasma membrane during de novo cell wall assembly. Finally, we use our homologous recombination approach for targeted gene deletion by knocking out the URA3 locus, and confirm the resulting genotype and phenotype via sequencing and drug resistance assays. This genetic transformation system offers a foundational tool for molecular studies of Bd, advancing our capacity to dissect molecular mechanisms of chytrid pathogenesis.

cell biology↗

bioRxiv2025

The small GTPase Rab5 inhibits actin polymerization mediated by the Legionella pneumophila effector VipA

Legionella pneumophila is a facultative intracellular Gram-negative bacterium that causes Legionnaires disease, one of the most severe manifestations of atypical pneumonia. L. pneumophila naturally thrives within protozoan hosts in aquatic environments, which serve as reservoirs for bacterial replication and transmission. Inhalation of contaminated aerosols delivers L. pneumophila to the lungs where it is able to infect human alveolar macrophages and multiply intracellularly inside a membrane-bound compartment, the Legionella-containing vacuole (LCV). The main virulence factor of the bacteria is the Icm/Dot type IVb secretion system, responsible for the translocation of over 300 bacterial effector proteins into host cells. These effectors allow the remodelation of the LCV into a replication-competent compartment that seggregates from the phagolysosomal pathway. After being translocated into host cells, L. pneumophila effector VipA associates with early endosomes and F-actin. VipA increases the polymerization of actin filaments in vitro by promoting the nucleation step without the requirement of additional partners, and impairs vesicle trafficking in Saccharomyces cerevisiae. In this work, we sought the interacting partners of VipA in early endosomes and explored the effects of this association. We found that VipA interacts directly to two key components of these organelles, the membrane lipid PI3P and the small GTPase Rab5. Binding to Rab5 requires the N-terminal region of VipA but not the C-terminal/actin-binding region. Furthermore, binding to Rab5 inhibits VipA-mediated actin polymerization by preventing de novo actin filament formation. These findings offer new insights into VipAs mode of action and underscore the intricate interactions between L. pneumophila effectors and their host cell targets, namely the endocytic pathway.

microbiology↗

bioRxiv2024

Deuterium Metabolic Imaging Phenotypes Mouse Glioblastoma Heterogeneity Through Glucose Turnover Kinetics

Glioblastomas are aggressive brain tumors with dismal prognosis. One of the main bottlenecks for developing more effective therapies for glioblastoma stems from their histologic and molecular heterogeneity, leading to distinct tumor microenvironments and disease phenotypes. Effectively characterizing these features would improve the clinical management of glioblastoma. Glucose flux rates through glycolysis and mitochondrial oxidation have been recently shown to quantitatively depict glioblastoma proliferation in mouse models (GL261 and CT2A tumors) using dynamic glucose-enhanced (DGE) deuterium spectroscopy. However, the spatial features of tumor microenvironment phenotypes remain hitherto unresolved. Here, we develop a DGE Deuterium Metabolic Imaging (DMI) approach for profiling tumor microenvironments through glucose conversion kinetics. Using a multimodal combination of tumor mouse models, novel strategies for spectroscopic imaging and noise attenuation, and histopathological correlations, we show that tumor lactate turnover mirrors phenotype differences between GL261 and CT2A mouse glioblastoma, whereas recycling of the peritumoral glutamate-glutamine pool is a potential marker of invasion capacity in pooled cohorts, linked to secondary brain lesions. These findings were validated by histopathological characterization of each tumor, including cell density and proliferation, peritumoral invasion and distant migration, and immune cell infiltration. Our study bodes well for precision neuro-oncology, highlighting the importance of mapping glucose flux rates to better understand the metabolic heterogeneity of glioblastoma and its links to disease phenotypes.

cancer biology↗

bioRxiv2024

Heterotypic competition between cancer cells and hepatocytes generates heterogeneous context-dependent phenotypes

Competitive interactions between tumor cells and surrounding healthy cells are constantly present during the progression of a solid tumor, and their outcome has been proposed to affect the clinical behavior. Previous studies have described various mechanistic and molecular aspects that characterize this process, overall indicating that cancer cells behave as supercompetitors, which eliminate neighboring healthy cells to gain vital space for growth and infiltration of the tissue. Nevertheless, there is a lack of systematic characterization of these competitive interactions, particularly in the context of cancer in mammals. Furthermore, previous studies in the field of cell competition have primarily focused on homotypic cell competition, involving different clones of the same cell or cells deriving from the same tissue. Data are scarce regarding heterotypic cell competition between two unrelated cell types, which is particularly critical for the understanding of metastatic tumors. In this research, we study cell competition in the context of liver metastases, providing a broad characterization of this process in different relevant scenarios, including cells growing in vitro in 2D and 3D, and in vivo. Results show that in vitro, only a subset of cancer cell lines are coherently strong or moderate competitors against hepatocytes, while the remaining demonstrate poor competitiveness. The competitive proficiency can vary depending on the experimental growth system that is employed, and often predicts the phenotype of liver metastases in terms of aggressiveness and morphology. Finally, our data point towards an involvement of mechanical competition in determining the supercompetitor trait of cancer cells. Altogether, our research provides the first comprehensive characterization of heterotypic cell competition, and indicates that cancer cells possess heterogeneous competitive proficiency towards hepatocytes which can be affected by the growth conditions.

cancer biology↗

bioRxiv2024

Non-invasive MRI of Blood-Cerebrospinal Fluid-Barrier Function: a Functional Biomarker of Early Alzheimer's Disease Pathology

INTRODUCTIONChoroid plexus (CP) dysfunction is thought to contribute to toxic protein build-up in neurodegenerative disorders, including Alzheimers disease (AD). However, the dynamics of this process remain unknown, mainly due to the paucity of in-vivo methods capable of assessing CP function. METHODSHere, we harness recent developments in Arterial Spin Labelling MRI to measure water delivery across the blood cerebrospinal fluid barrier (BCSFB) as a proxy for CP function, as well as cerebral blood flow (CBF), at different stages of AD progression in the widely used triple transgenic mouse model (3Tg), which recapitulates aspects of disease pathology. RESULTSTotal BCSFB-mediated water delivery is significantly higher in 3Tg mice (>50%) from 8 weeks (preclinical stage), while tissue parameters such as CBF and T1 are not different between groups at all ages. DISCUSSIONOur work shows changes in BCSFB function in the early stages of AD, providing a novel biomarker of pathology.

neuroscience↗

bioRxiv2023

Byproducts of inflammatory radical metabolism provide transient nutrient niches for microbes in the inflamed gut

Louis Pasteurs experiments on tartaric acid laid the foundation for our understanding of molecular chirality, but major questions remain. By comparing the optical activity of naturally-occurring tartaric acid with chemically-synthesized paratartaric acid, Pasteur realized that naturally-occurring tartaric acid contained only L-tartaric acid while paratartaric acid consisted of a racemic mixture of D- and L-tartaric acid. Curiously, D-tartaric acid has no known natural source, yet several gut bacteria specifically degrade D-tartaric acid. Here, we investigated the oxidation of monosaccharides by inflammatory reactive oxygen and nitrogen species. We found that this reaction yields an array of alpha hydroxy carboxylic acids, including tartaric acid isomers. Utilization of inflammation- derived D- and L-tartaric acid enhanced colonization by Salmonella Typhimurium and E. coli in murine models of gut inflammation. Our findings suggest that byproducts of inflammatory radical metabolism, such as tartrate and other alpha hydroxy carboxylic acids, create transient nutrient niches for enteric pathogens and other potentially harmful bacteria. Furthermore, this work illustrates that inflammatory radicals generate a zoo of molecules, some of which may erroneously presumed to be xenobiotics.

microbiology↗

bioRxiv2023

Global trends in antimicrobial resistance on organic and conventional farms

Various stewardship policies, regulations, and voluntary bans have focused on protecting antimicrobials by limiting their use in livestock. These efforts ignited management shifts ranging from largely nominal (e.g., drugs banned for use as growth promoters were reclassified as prophylactic drugs) to organic farming, which drastically reduces or eliminates use of antimicrobials. Understanding how these farming practices influence the prevalence of antimicrobial resistance in livestock carries important implications for policy makers, public health officials, and farm managers. Here, we reviewed studies spanning the last 20 years to ask if the most stringent effort to reduce antimicrobial use in livestock -- organic farming -- results in notable reductions in the prevalence of antimicrobial resistance across broad scale geographic ranges, pathogens, and livestock hosts. Our results validate organic farming in reducing the prevalence of antimicrobial resistance (AMR) by [~]31.2%,[~]26.9%, [~]28.2%,[~]42.9 and [~]36.2% in cattle, chicken, environment, pigs and turkey respectively while also revealing significant variation in the strength of this reduction across contexts. Given that our results join others indicating that AMR is increasing across all types of farms, our results highlight areas where organic farming has been most effective and may provide economical and scalable solutions for farmers.

microbiology↗

bioRxiv2023

Absence of Telomerase Leads to Immune Response and Tumor Regression in Zebrafish Melanoma

Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types, including melanoma. However, it is unclear when and if telomerase is strictly required during tumorigenesis. Here, we show that melanoma can occur in the absence of telomerase but is required to sustain later growth and to avoid tumor regression. We combined telomerase mutant zebrafish (tert-/-) with two established melanoma models and found equal melanoma incidence and invasiveness as tumors became visible. Later, however, while tert+/+ fish develop increasing larger tumors, tert-/- tumors stagnate growth and regress. tert-/- tumors showed lower cell proliferation, higher apoptosis and melanocyte differentiation. We also detected an immune response directed at tert-/- tumors. tert-/- tumors exhibited increased immune cell infiltrates and resume growth when transplanted into immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish, albeit at later stages of progression, to sustain growth while avoiding immune rejection and regression. Thus, absence of telomerase restricts melanoma through tumor-autonomous mechanisms (cell cycle arrest, apoptosis and melanocyte differentiation) and a non-tumor-autonomous mechanisms (immune rejection).

cancer biology↗

bioRxiv2022

UBE2C promotes leptomeningeal dissemination and is a therapeutic target in brain metastatic disease

Despite current improvements in systemic cancer treatment, brain metastases (BM) remain incurable, and there is an unmet clinical need for effective targeted therapies. Here, we sought common molecular events in brain metastatic disease. RNA sequencing of thirty human BM identified the upregulation of UBE2C, a gene that ensures the correct transition from metaphase to anaphase, across different primary tumor origins. Tissue microarray analysis of an independent BM patient cohort revealed that high expression of UBE2C was associated with decreased survival. UBE2C-driven orthotopic mouse models developed extensive leptomeningeal dissemination, likely due to increased migration and invasion. Early cancer treatment with dactolisib (dual PI3K/mTOR inhibitor) prevented the development of UBE2C-induced leptomeningeal metastases. Our findings reveal UBE2C as a key player in the development of metastatic brain disease and highlight PI3K/mTOR inhibition as a promising anticancer therapy to prevent late-stage metastatic brain cancer.

cancer biology↗

bioRxiv2022

Coinfection with chytrid genotypes drives divergent infection dynamics reflecting broad epidemiological patterns

By altering the abundance, diversity, and distribution of species -- and their pathogens -- globalization may inadvertently select for more virulent pathogens. In Brazils Atlantic Forest, a hotspot of amphibian biodiversity, the pet trade has facilitated the co-occurrence of previously isolated enzootic and panzootic lineages of the pathogenic amphibian-chytrid ( Bd) and generated new virulent recombinant genotypes ( hybrid). Epidemiological data indicate that amphibian declines are most severe in hybrid zones, suggesting that coinfections are causing more severe infections or selecting for higher virulence. We investigated how coinfections involving these genotypes shaped virulence and transmission. Overall, coinfection favored the more virulent and competitively superior panzootic genotype, despite dampening its virulence and transmission. However, for the least virulent and least competitive genotype, coinfection increased both pathogen virulence and transmission. Thus, by integrating experimental and epidemiological data, our results provide mechanistic insight into how globalization can select for, and propel, the emergence of introduced hypervirulent lineages, such as the globally distributed panzootic lineage of Bd.

ecology↗

bioRxiv2021

Maternal γδ T Cells Shape Offspring Pulmonary Type-2 Immunity In A Microbiota-Dependent Manner

Immune system development is greatly influenced by vertically transferred cues. However, beyond antibody-producing B cells, little is known about the role of other cell subsets of the maternal immune system in regulating offspring immunity. We reasoned {gamma}{delta} T cells to be attractive candidates based on their tissue distribution pattern: abundant in the skin, mammary glands and female reproductive tract. Here we found that mice born from {gamma}{delta} T cell-deficient (TCR{delta}-/-) dams display, early after birth, a pulmonary milieu selectively enriched in type-2 cytokines such as IL-33, IL-4, IL-5, and IL-13, and type-2-polarized immune cells, when compared to the progeny of {gamma}{delta} T cell-sufficient dams. In addition, upon helminth infection, mice born from TCR{delta}-/- dams sustained an increased type-2 inflammatory response. Critically, this was independent of the genotype of the pups. Despite similar levels of circulating antibodies in mothers and progeny, the intestinal microbiota in the offspring of TCR{delta}-/- and TCR{delta}+/- dams harbored distinct bacterial communities acquired during birth and fostering. These differences were accompanied by changes in the intestinal short-chain fatty acids (SCFA) profile. Importantly, antibiotic treatment abrogated the differences observed in the pulmonary milieu, and exogenous SCFA supplementation suppressed first-breath- and infection-induced inflammation. In summary, maternal {gamma}{delta} T cells control the establishment of a neonatal gut-lung axis by conditioning the postnatal microbial colonization of the off-spring and bacterial-derived metabolite availability; ultimately impacting on the development of pulmonary type-2 immunity in the offspring.

immunology↗

bioRxiv2020

Patient-derived models of brain metastases recapitulate the histopathology and biology of human metastatic cancers

PurposeDissemination of cancer cells from primary tumors to the brain is observed in the great majority of cancer patients, contributing to increased morbidity and being the main cause of death. Most mechanistic and preclinical studies have relied on aggressive cancer cell lines, which fail to represent tumor heterogeneity and are unsuitable to validate therapies due to fast cancer progression in vivo. Experimental designWe established a unique library of subcutaneous and intracardiac patient-derived xenografts (PDXs) of brain metastases (BMs) from eight distinct primary tumor origins. Cancer progression in mice was compared to the matched patient clinical outcome, metastatic dissemination pattern and histopathological features. Preclinical studies with FDA approved drugs were performed. ResultsIn vivo tumor formation of flank-implanted BMs correlated with patients poor survival and serial passaging increased tumor aggressiveness. Subcutaneous xenografts originated spontaneous metastases in 61% of the cases, including in the leptomeningeal space (21%). The intracardiac model increased the tropism to the brain and leptomeninges (46%). Strikingly, 62% of intracardiac PDXs shared metastatic sites with the donor patients, including the primary cancer organ and the central nervous system (CNS). Of therapeutic relevance, PDX-derived cultures and corresponding mouse xenografts can be effectively treated with targeted anticancer drugs. ConclusionsPatient-derived models of BMs recapitulate the biology of human metastatic disease and can be a valuable translational platform for precision medicine. TRANSLATIONAL RELEVANCESubcutaneous and intracardiac mouse xenografts of human brain metastases exhibit a spontaneous dissemination pattern that resembles patients metastatic disease. The preclinical testing of targeted anticancer drugs using patient-derived cultures and patient-derived xenografts of brain metastasis showed an effective therapeutic response. These translational models represent an outstanding tool to advance the understanding of the biology of brain metastases and to foster the rapid discovery of novel therapeutics.

cancer biology↗

bioRxiv2020

IDseq - An Open Source Cloud-based Pipeline and Analysis Service for Metagenomic Pathogen Detection and Monitoring

BackgroundMetagenomic next generation sequencing (mNGS) has enabled the rapid, unbiased detection and identification of microbes without pathogen-specific reagents, culturing, or a priori knowledge of the microbial landscape. mNGS data analysis requires a series of computationally intensive processing steps to accurately determine the microbial composition of a sample. Existing mNGS data analysis tools typically require bioinformatics expertise and access to local server-class hardware resources. For many research laboratories, this presents an obstacle, especially in resource limited environments. FindingsWe present IDseq, an open source cloud-based metagenomics pipeline and service for global pathogen detection and monitoring (https://idseq.net). The IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes an assembly-based alignment pipeline which results in the assignment of reads and contigs to taxonomic categories. The taxonomic relative abundances are reported and visualized in an easy-to-use web application to facilitate data interpretation and hypothesis generation. Furthermore, IDseq supports environmental background model generation and automatic internal spike-in control recognition, providing statistics which are critical for data interpretation. IDseq was designed with the specific intent of detecting novel pathogens. Here, we benchmark novel virus detection capability using both synthetically evolved viral sequences, and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist from Wuhan, China, infected with the recently emergent SARS-CoV-2. ConclusionThe IDseq Portal reduces the barrier to entry for mNGS data analysis and enables bench scientists, clinicians, and bioinformaticians to gain insight from mNGS datasets for both known and novel pathogens.

bioinformatics↗

bioRxiv2020

First description of a herpesvirus infection in genus Lepus

During the necropsies of Iberian hares obtained in 2018/2019, along with signs of the nodular form of myxomatosis, other unexpected external lesions were also observed. Histopathology revealed nuclear inclusion bodies in stromal cells suggesting the additional presence of a nuclear replicating virus. Transmission electron microscopy further demonstrated the presence of herpesvirus particles in the tissues of affected hares. We confirmed the presence of herpesvirus in 13 MYXV-positive hares by PCR and sequencing analysis. Herpesvirus-DNA was also detected in seven healthy hares, suggesting its asymptomatic circulation. Phylogenetic analysis based on DNA polymerase gene, grouped this virus within the gammaherpesviruses, close to herpesviruses from bats and rodents. We propose to name this new virus Leporid gammaherpesvirus 5 (LeHV-5), according to the International Committee on Taxonomy of Viruses standards. The impact of herpesvirus infection on the reproduction and mortality of the Iberian hare is yet unknown but may aggravate the decline of wild populations caused by the recently emerged natural recombinant myxoma virus.

microbiology↗

bioRxiv2019

Light-entrained and brain-tuned circadian circuits regulate ILC3 and gut homeostasis

Group 3 innate lymphoid cells (ILC3) are major regulators of inflammation, infection, microbiota composition and metabolism1. ILC3 and neuronal cells were shown to interact at discrete mucosal locations to steer mucosal defence2,3. Nevertheless, whether neuroimmune circuits operate at an organismal level, integrating extrinsic environmental signals to orchestrate ILC3 responses remains elusive. Here we show that light-entrained and brain-tuned circadian circuits regulate enteric ILC3, intestinal homeostasis, gut defence and the host lipid metabolism. We found that enteric ILC3 display circadian expression of clock genes and ILC3-related transcription factors. ILC3-autonomous ablation of the circadian regulator Arntl led to disrupted gut ILC3 homeostasis, impaired epithelial reactivity, deregulated microbiome, increased susceptibility to bowel infection and disrupted lipid metabolism. Loss of ILC3-intrinsic Arntl shaped the gut postcode receptors of ILC3. Strikingly, light-dark cycles, feeding rhythms and microbial cues differentially regulated ILC3 clocks, with light signals as major entraining cues of ILC3. Accordingly, surgical- and genetically-induced deregulation of brain rhythmicity led to disrupted circadian ILC3 oscillations, deregulated microbiome and altered lipid metabolism. Our work reveals a circadian circuitry that translates environmental light cues into enteric ILC3, shaping intestinal health, metabolism and organismal homeostasis.

immunology↗