Biology subjects

Ferreira, J.

Publications and source records attributed to Ferreira, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Anthropogenic disturbance inverts microclimate stratification in tropical forests

Tropical rainforests generate and maintain their own microclimate regimes and the resultant cooler, more humid and stable environments foster the hyperdiversity typical of these ecosystems. Although the temporal and spatial (horizontal) distributions of microclimates have been relatively well studied, the vertical dimension has received less attention, and little is known about how forest disturbance affects the vertical stratification of microclimates in tropical forests. In this study, we examine how the vertical distribution of temperatures varies between undisturbed and burned Amazonian forests. We installed five vertical transects with temperature dataloggers distributed at 7 different heights to collect data over multiple days during the end of the dry season. We investigated how anthropogenic disturbance (fire) mediates the vertical stratification of microclimate and whether microclimate buffering (i.e, the difference between understorey and canopy temperatures) varies according to the forest structure. We showed that anthropogenic disturbance can cause an inversion in the vertical stratification of microclimates, with burned forests having hotter temperatures (up to 2 {degrees}C) in the understorey than in the canopy during the day - the opposite of what is found in undisturbed forests (typically 3 {degrees}C cooler). During the night, while understorey and canopy temperatures are similar in undisturbed forests, we found that, in burned forests, understorey temperatures were up to 2 {degrees}C cooler than in the canopy. Microclimate buffering by day was best explained by aboveground carbon stocks, with higher temperature buffering in more carbon rich forests. Our study shows that anthropogenic disturbance alters the vertical stratification of temperatures in Amazonian forests, leading to significant temporal changes along the diel cycle. Future research should focus on understanding these changes across a wider range of disturbance regimes, and explore the consequences for biodiversity and ecosystem functions from the canopy to the forest floor.

ecology↗

bioRxiv2026

Macroevolutionary dynamics of beetles reveal long-term coupling with vascular plant diversification

Beetles (Coleoptera) represent the most species-rich group of organisms, yet the macroevolutionary processes underlying their exceptional diversification remain unresolved. Here, we estimated their origination and extinction dynamics as well as the potential drivers shaping these patterns, using Bayesian birth-death models applied to a comprehensive fossil occurrence dataset. We find that beetles have experienced low extinction rates and exhibited high resilience through major extinction events. Vascular plant diversities emerge as a key driver of beetle diversification, with origination rates positively correlated with angiosperms, and extinction rates negatively correlated, especially for Polyphaga, the most diverse beetle clade. Together, our results provide quantitative evidence that the angiosperm radiation not only promoted beetle origination, but also buffered them against extinction, illustrating how ecological interactions can shape macroevolution.

evolutionary biology↗

bioRxiv2026

Structural Insights into the Integration of Temperature and pH by Sperm Calcium Channel CatSper

The cation channel of sperm (CatSper) is a sperm-specific calcium channel essential for male fertility across metazoans. Its activation is tightly restricted to defined physiological contexts, including intracellular alkalinization, membrane depolarization, and elevated temperature. The structural and evolutionary mechanisms underlying this polymodal integration remain poorly understood, in part due to the architectural complexity of CatSper, a [~]15-subunit assembly organized in zigzag arrays along the sperm flagellum. Here we combine comparative genomics across 47 species with AlphaFold3-based modeling and evolutionary sequence-structure analyses to uncover a mechanism for temperature and pH integration. We identify the pore-forming subunit CatSper1 as an evolutionary hotspot exhibiting exceptional divergence in its N-terminal domain. Phylogenetic analysis shows that N-terminal length and histidine enrichment scale with species-specific fertilization temperatures, suggesting adaptive tuning of physicochemical sensitivity. Structural modeling indicates that conserved surface-exposed histidine clusters form inter-complex coupling interfaces between adjacent CatSper assemblies positioned near the dominant voltage-sensing module. Functional validation using electrophysiology and calcium imaging in mouse sperm shows that capacitation-associated partial removal of the CatSper1 N-terminus selectively impairs temperature-dependent activation. Together, these findings support a model in which temperature-dependent histidine deprotonation modulates supramolecular CatSper assembly to coordinate channel activation.

physiology↗

bioRxiv2025

Hyperdominance and rarity in Amazonian secondary forests

Recent studies have shown that a few tree species dominate abundance and carbon storage in undisturbed Amazonian forests. However, this pattern remains poorly understood in forests regrowing after deforestation. Understanding dominance patterns in secondary forests is important as it could improve insights into their functioning and guide management and restoration efforts. We used unweighted and novel plot-weighted approaches to assess hyperdominance in abundance and carbon storage of trees and palms during secondary forest recovery, using data from 102 plots across four regions in the eastern Amazon, separated by an average distance of 600 km (range: 150-1,000 km). Secondary forests show extreme hyperdominance in all approaches, with just 16-25 species ([~]3.6-5.6%) accounting for over 50% of abundance and carbon storage. A small subset of species ([~]9%) were found across all regions and successional stages, highlighting their key role in ecosystem structure and function during forest regrowth. Annona exsucca, Cecropia palmata, Tapirira guianensis, Inga alba, Attalea maripa, Amphiodon effusus, Banara guianensis, and Vismia guianensis consistently emerged as hyperdominant across stem size classes, approaches, and metrics, jointly accounting for roughly 16-27% of total abundance and carbon in Amazonian secondary forests. For larger stems >10cm DBH, hyperdominant species exhibited lower wood density compared to non-hyperdominant species across all successional stages, suggesting these specialist pioneers have distinct ecological strategies from the rest of the community. Our findings indicate that secondary forest functioning can be largely predicted by a relatively limited set of species, providing a framework for future research ranging from ecophysiology to remote sensing of canopy traits and restoration planning.

ecology↗

bioRxiv2025

Combined interventions are required to reverse biodiversity and carbon losses in tropical forest frontiers

Halting deforestation and promoting restoration are at the core of biodiversity and climate strategies in tropical forest regions. Avoiding forest disturbances is also critically important but has received far less attention, and there is a lack of clarity about the cost-effectiveness of these three different interventions. We provide the first comparison of the biodiversity and carbon benefits and costs associated with each intervention, comparing observed and counterfactual outcomes based on in-depth field assessments and high-resolution remote sensing in Amazonian Brazil. Avoiding forest disturbances delivered the greatest benefits and was more cost-effective than either avoiding deforestation or restoration, with results being robust to a range of benefit and cost assumptions. However, combined interventions delivered the greatest gains and were essential to reverse biodiversity and carbon losses.

ecology↗

bioRxiv2025

MCUR1-CCDC90B complex is a conserved regulator of metabolic homeostasis

The mitochondrial calcium uniporter regulator 1 (MCUR1) is an evolutionarily conserved protein of the inner mitochondrial membrane1, yet its physiological role has remained elusive. Although initially proposed to function as a subunit of the mitochondrial calcium uniporter complex (MCUC)2-4, emerging evidence suggests that MCUR1 has a broader functional spectrum5-7. Here, we identify a biallelic loss-of-function MCUR1 variant (c.802C>T; p.R268X) in a patient with a progressive neurological phenotype. This mutation leads to loss of MCUR1 protein and exerts a dominant-negative effect on its paralog, CCDC90B. We show that MCUR1 and CCDC90B form a hetero-oligomeric complex whose stability depends on MCUR1. Deletion of MCUR1 and CCDC90B in the fission yeast Schizosaccharomyces pombe, which lacks the MCUC, impairs lipid and amino acid metabolism and causes nitrogen source-dependent growth defects that are rescued by expression of human MCUR1. Patient serum metabolomics confirms an imbalance in the amino acid pool, while MCUR1 deficiency in patient-derived skin fibroblasts upregulates autophagy, perturbs non-essential amino acid metabolism, and limits biosynthetic capacity, resulting in delayed proliferation and migration. These findings redefine the MCUR1-CCDC90B coiled-coil complex as a transmembrane scaffold critical for the integrity of mitochondrial protein complexes and the maintenance of metabolic homeostasis, suggesting a potential link between MCUR1 deficiency and human neurometabolic disease.

cell biology↗

bioRxiv2025

Multilayered Defense Responses in Sugarcane Against Pratylenchus zeae Revealed by Comparative Transcriptomics

1.The root-lesion nematode Pratylenchus zeae ranks among the most pervasive soilborne threats to global sugarcane (Saccharum spp.) production, however, the molecular basis of host resistance to this pathogen remains largely unexplored. Using comparative transcriptomics 15 days after inoculation, we profiled root response patterns of a resistant cultivar (RB966982) and a susceptible cultivar (CTC9001). Differential gene expression analysis identified 3,385 DEGs (1,426 up, 1,959 down) in the susceptible CTC9001 and 8,689 DEGs (5,334 up, 3,355 down) in the resistant RB966982 when comparing control and inoculated plants, revealing distinct genotype-specific defense strategies. The resistant genotype mounted a coordinated, multilayered defense marked by dramatic transcriptional reprogramming, including intensified glycolysis and fatty-acid biosynthesis, elevated oxidoreductase/ROS activity, and concurrent activation of jasmonic and salicylic acid associated pathways, with strong induction of multiple PR1 homologs. RB966982 also showed pre-primed and inducible resistance gene analogs and targeted cell-wall reinforcement through xyloglucan fucosylation. By contrast, CTC9001 displayed a delayed or attenuated response characterized by cell-proliferation signatures and broad activation of callose-related defenses (1,3-{beta}-D-glucan synthesis) that appear insufficient to limit nematode progression. GO enrichment analysis revealed that the resistant response was dominated by biological processes linked to carbohydrate and lipid metabolism, oxidoreductase activity, hormone signaling, and cell-wall organization, while the susceptible response was enriched in stress-related pathways lacking coordinated metabolic and structural reinforcement. Collectively, these findings indicate that durable resistance to P. zeae is unlikely to arise from a single mechanism, effective protection will require stacking complementary defense layers, including early metabolic reprogramming, robust hormone-mediated signaling, and reinforced cell-wall barriers. The candidate RGAs, PR1 homologs, and cell-wall remodeling enzymes identified here, together with the GO-enriched pathways, provide concrete targets for marker-assisted breeding and gene editing strategies aimed at developing sugarcane cultivars with durable nematode resistance.

bioinformatics↗

bioRxiv2025

Depth-resolved fiber photometry of amyloid plaque signals in freely behaving Alzheimer's disease mice

Alzheimers disease pathology typically manifests itself across multiple brain regions yet assessment at this scale in mouse models remains a challenge. This hinders the development of novel therapeutic approaches. Here we introduce a novel fiber photometry approach to monitor amyloid pathology in freely behaving mice. We first demonstrated that flat fiber-based photometry can detect amyloid signals across multiple brain regions under anesthesia after injecting a blood-brain barrier permeable tracer, Methoxy-X04. The depth profile of in vivo fluorescent signals was correlated with postmortem histological plaque signals. After confirming its feasibility ex vivo, we chronically implanted a tapered fiber for depth-resolved fiber photometry in freely behaving mice. After injecting Methoxy-X04, fluorescent signals increased in a depth-specific manner in Alzheimers mice, but not in wild-type littermates. While fiber photometry has been widely adopted to monitor neuronal and non-neuronal activity, our approach expands the capabilities to monitor molecular pathologies such as amyloid plaques, even in a freely behaving condition.

neuroscience↗

bioRxiv2025

Bacterial Vaginosis Toxins Impair Sperm Capacitation and Fertilization

Study questionWhat effect do toxins produced by bacterial vaginosis (BV) bacteria have on sperm function? Summary answerBacterial vaginosis toxins dysregulate sperm capacitation and intracellular calcium homeostasis and impair the ability of sperm to fertilize oocytes. What is known alreadyIn bacterial vaginosis, which is linked to infertility, overgrowth of Prevotella and Gardnerella in the vagina is accompanied by elevated concentrations of the toxins lipopolysaccharide (LPS) and vaginolysin (VLY). Study design, size, durationThis was a laboratory study in which human semen samples were collected from consenting healthy donors with normal semen parameters. Mouse sperm samples were obtained from the caudal epididymis. Participants/materials, setting, methodsMotile mouse and human sperm were isolated via swim-up and treated under non-capacitating or capacitating conditions. LPS from Escherichia coli was commercially available. VLY was produced by cloning the Gardnerella VLY protein in the ClearColi expression system. Mouse sperm were pre-incubated in in vitro fertilization medium with LPS or VLY and then co-cultured with ovulated cumulus-oocyte complexes. The effects of LPS and VLY on sperm motility and hyperactivation were assessed with computer-assisted sperm analysis. Effects on viability were assessed by Hoechst staining. Acrosomal exocytosis was assessed in sperm from transgenic Acr-eGFP mice and in human sperm stained with Pisum sativum agglutinin FITC. Intracellular calcium dynamics were assessed by staining sperm with the calcium-sensitive dye Fluo-4 AM and fluorescent imaging several sperm at the single-cell level. The effects of LPS on sperm from CatSper knock-out mice were assessed. Additionally, sperm were treated with a toll-like receptor 4 antagonist and further exposed to LPS. Main results and the role of chanceExposure of mouse sperm to LPS or VLY significantly decreased in vitro fertilization (P < 0.05). Under capacitating conditions, both toxins initially increased mouse and human sperm hyperactivation, then significantly decreased sperm motility (P < 0.05), hyperactivation (P < 0.05), and acrosomal exocytosis (P < 0.01). These changes were accompanied by a rapid and irreversible increase in intracellular calcium concentration. Effects of LPS, but not VLY, were prevented by polymyxin-B, which aggregates LPS. The LPS-induced intracellular calcium increase required external calcium but not the calcium channel CatSper and was inhibited by the Toll-like receptor 4 antagonist. Limitations, reasons for cautionFirst, the commercially available LPS we used was isolated from Escherichia coli, rather than from the BV-associated bacteria Prevotella bivia. Second, we did not quantify the absolute sperm intracellular calcium concentration before or after LPS or VLY treatment. Third, all of our experiments were in vitro. Wider implications of the findingsThese studies suggest that BV-associated toxins contribute to infertility by, in part, impairing sperm capacitation and reducing their fertilizing ability. Study funding/competing interest(s)This work was supported by the National Institutes of Health (grant #R01 HD069631). The authors declare that they have no conflict of interest.

physiology↗

bioRxiv2025

Pex30-dependent membrane contacts sites maintain ER lipid homeostasis

In eukaryotic cells, communication between organelles and the coordination of their activities depend on membrane contact sites (MCS). How MCS are regulated under the dynamic cellular environment remains poorly understood. Here, we investigate how Pex30, a membrane protein localized to the endoplasmic reticulum (ER), regulates multiple MCS in budding yeast. We show that Pex30 is critical for the integrity of ER MCS with peroxisomes and vacuoles. This requires the Dysferlin domain (DysF) on Pex30 cytosolic tail. This domain binds to phosphatidic acid (PA) both in vitro and in silico, and it is important for normal PA metabolism in vivo . The DysF domain is evolutionarily conserved and may play a general role in PA homeostasis across eukaryotes. We further show that ER-Vacuole MCS requires Pex30 C-terminal Domain of Unknown Function and that its activity is controlled by phosphorylation in response to metabolic cues. These findings provide new insights into the dynamic nature of MCS and their coordination with cellular metabolism.

cell biology↗

bioRxiv2023

Software Package for Transcranial Magnetic Stimulation Coil and Coil Array Analysis and Design

ObjectiveThis study aims to describe a MATLAB software package for transcranial magnetic stimulation (TMS) coil analysis and design. ApproachElectric and magnetic fields of the coils as well as their self- and mutual (for coil arrays) inductances are computed, with or without a magnetic core. Solid and stranded (Litz wire) conductors are also taken into consideration. The starting point is the centerline of a coil conductor(s), which is a 3D curve defined by the user. Then, a wire mesh and a computer aided design (CAD) mesh for the volume conductor of a given cross-section (circular, elliptical, or rectangular) are automatically generated. Self- and mutual inductances of the coil(s) are computed. Given the conductor current and its time derivative, electric and magnetic fields of the coil(s) are determined anywhere in space. Computations are performed with the fast multipole method (FMM), which is the most efficient way to evaluate the fields of many elementary current elements (current dipoles) comprising the current carrying conductor at a large number of observation points. This is the major underlying mathematical operation behind both inductance and field calculations. Main ResultsThe wire-based approach enables precise replication of even the most complex physical conductor geometries, while the FMM acceleration quickly evaluates large quantities of elementary current filaments. Agreement to within 0.74% was obtained between the inductances computed by the FMM method and ANSYS Maxwell 3D for the same coil model. Although not provided in this study, it is possible to evaluate non-linear magnetic cores in addition to the linear core exemplified. An experimental comparison was carried out against a physical MagVenture C-B60 coil; the measured and simulated inductances differed by only 1.25%, and nearly perfect correlation was found between the measured and computed E-field values at each observation point. SignificanceThe developed software package is applicable to any quasistatic inductor design, not necessarily to the TMS coils only.

neuroscience↗

bioRxiv2023

Cholesteryl hemiazelate Identified in Cardiovascular Disease Patients Causes in vitro and in vivo Inflammation

Oxidation of polyunsaturated fatty acids (PUFA) in low-density lipoproteins (LDL) trapped in the arterial intima plays a critical role in atherosclerosis. Though there have been many studies on the atherogenicity of oxidized derivatives of unsaturated fatty acid esters of cholesterol, the effects of the oxidation end-products of these esters has been ignored in the literature. Through lipidomics analyses of the plasma of cardiovascular disease patients and human endarterectomy specimens we identified and quantified cholesteryl hemiesters (ChE), end-products of oxidation of polyunsaturated-fatty acid esters of cholesterol. Cholesteryl hemiazelate (ChA) was the most prevalent ChE identified. Importantly human monocytes, monocyte-derived macrophages (MDM) and neutrophils exhibit inflammatory features when exposed to sub-toxic concentrations of ChA in vitro. ChA increases the secretion of proinflammatory cytokines such as IL-1{beta} and IL-6 and modulates the surface markers profile of monocytes and MDM. In vivo, when zebrafish larvae were fed with a ChA-enriched diet they exhibited neutrophil and macrophage accumulation in the vasculature in a caspase 1- and cathepsin B-dependent manner. ChA also triggered lipid accumulation at the bifurcation sites of the vasculature of the zebrafish larvae and negatively impacted their life expectancy. We conclude that ChA has pro-atherogenic properties and can be considered part of a damage-associated molecular pattern (DAMP) in the development of atherosclerosis.

pathology↗

bioRxiv2021

A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale

Constraint-based (CB) metabolic models provide a mathematical framework and scaffold for in silico cell metabolism analysis and manipulation. In the past decade, significant efforts have been done to model human metabolism, enabled by the increased availability of multi-omics datasets and curated genome-scale reconstructions, as well as the development of several algorithms for context-specific model (CSM) reconstruction. Although CSM reconstruction has revealed insights on the deregulated metabolism of several pathologies, the process of reconstructing representative models of human tissues still lacks benchmarks and appropriate integrated software frameworks, since many tools required for this process are still disperse across various software platforms, some of which are proprietary. In this work, we address this challenge by assembling a scalable CSM reconstruction pipeline capable of integrating transcriptomics data in CB models. We combined omics preprocessing methods inspired by previous efforts with in-house implementations of existing CSM algorithms and new model refinement and validation routines, all implemented in the Troppo Python-based open-source framework. The pipeline was validated with multi-omics datasets from the Cancer Cell Line Encyclopedia (CCLE), also including reference fluxomics measurements for the MCF7 cell line. We reconstructed over 6000 models based on the Human-GEM template model for 733 cell lines featured in the CCLE, using MCF7 models as reference to find the best parameter combinations. These reference models outperform earlier studies using the same template by comparing gene essentiality and fluxomics experiments. We also analysed the heterogeneity of breast cancer cell lines, identifying key changes in metabolism related to cancer aggressiveness. Despite the many challenges in CB modelling, we demonstrate using our pipeline that combining transcriptomics data in metabolic models can be used to investigate key metabolic shifts. Significant limitations were found on these models ability for reliable quantitative flux prediction, thus motivating further work in genome-wide phenotype prediction. Author summaryGenome-scale models of human metabolism are promising tools capable of contextualising large omics datasets within a framework that enables analysis and manipulation of metabolic phenotypes. Despite various successes in applying these methods to provide mechanistic hypotheses for deregulated metabolism in disease, there is no standardized workflow to extract these models using existing methods and the tools required to do so are mostly implemented using proprietary software. We have assembled a generic pipeline to extract and validate context-specific metabolic models using multi-omics datasets and implemented it using the troppo framework. We first validate our pipeline using MCF7 cell line models and assess their ability to predict lethal gene knockouts as well as flux activity using multi-omics data. We also demonstrate how this approach can be generalized for large-scale transcriptomics datasets and used to generate insights on the metabolic heterogeneity of cancer and relevant features for other data mining approaches. The pipeline is available as part of an open-source framework that is generic for a variety of applications.

systems biology↗

bioRxiv2021

Soluble adenylyl cyclase inhibition prevents human sperm functions essential for fertilization

Soluble adenylyl cyclase (sAC: ADCY10) is essential for activating dormant sperm. Studies of freshly dissected mouse sperm identified sAC as needed for initiating capacitation and activating motility. We now use an improved sAC inhibitor, TDI-10229, for a comprehensive analysis of sAC function in human sperm. Unlike dissected mouse sperm, human sperm are collected post-ejaculation, after sAC activity has already been stimulated. Even in ejaculated human sperm, TDI-10229 interrupts stimulated motility and capacitation, and it prevents acrosome reaction in capacitated sperm. At present, there are no non-hormonal, pharmacological methods for contraception. Because sAC activity is required post-ejaculation at multiple points during the sperms journey to fertilize the oocyte, sAC inhibitors define candidates for non-hormonal, on-demand contraceptives suitable for delivery via intravaginal devices in females.

pharmacology and toxicology↗

bioRxiv2021

Mild impairment of mitochondrial function increases longevity and pathogen resistance through ATFS-1-driven activation of p38-regulated innate immunity

While mitochondrial function is essential for life in all multicellular organisms, a mild impairment of mitochondrial function can extend longevity. By understanding the molecular mechanisms involved, these pathways might be targeted to promote healthy aging. In studying two long-lived mitochondrial mutants in C. elegans, we found that disrupting subunits of the mitochondrial electron transport chain resulted in upregulation of genes involved in innate immunity, which we found to be dependent on not only the canonical p38-mediated innate immune signaling pathway but also on the mitochondrial unfolded protein response. Both of these pathways are absolutely required for the increased resistance to bacterial pathogens and extended longevity of the long-lived mitochondrial mutants, as is the FOXO transcription factor DAF-16. This work demonstrates that both the p38-mediated innate immune signaling pathway and the mitochondrial unfolded protein response can act on the same innate immunity genes to promote resistance to bacterial pathogens, and that input from the mitochondria can extend longevity by signaling through these two pathways. Combined, this indicates that multiple evolutionarily conserved genetic pathways controlling innate immunity also function to modulate lifespan. Significance StatementIn this work, we explore the relationship between mitochondrial function, aging and innate immunity. We find that mild impairment of mitochondrial function results in upregulation of genes involved in innate immunity, increased resistance to bacterial pathogens and lifespan extension, all of which are dependent on two evolutionarily conserved signaling pathways. This work demonstrates how changes in functional status of the mitochondria can trigger activation of innate immunity, and that the underlying mechanisms are important for the longevity of the organism. This work advances our understanding of connections between metabolism and immunity. As the pathways studied here are conserved up to mammals, these insights may help us to understand the role of mitochondrial health, innate immunity and lifespan in humans.

cell biology↗

bioRxiv2021

Adult zebrafish anaesthesia: a study of efficacy and behavioural recovery of different anaesthetics

The use of proper anaesthesia in zebrafish research is essential to ensure fish welfare and data reliability. However, anaesthesia long-term side effects remain poorly understood. The purpose of this study was to assess anaesthesia quality and recovery in adult zebrafish using different anaesthetic protocols and to determine possible long-term effects on the fish activity and anxiety-like behaviours after anaesthesia. Mixed sex adult AB zebrafish were randomly assigned to 5 different groups (control, 175mg/L MS222, 45 mg/L clove oil, 2 mg/L etomidate and 5mg/L propofol combined with 150mg/L lidocaine) and placed in the respective anaesthetic bath. Time to lose the equilibrium, response to touch and to tail pinch stimuli, and recovery after anaesthesia administration were evaluated. In addition, after stopping anaesthesia, respiratory rate, activity and anxiety-like behaviours in the novel tank test were studied. Overall, all protocols proved to be adequate for zebrafish anaesthesia research as they showed full recovery at 1h, and only etomidate had minor effects on fish behaviour in the novel tank, a validated test for anxiety.

animal behavior and cognition↗

bioRxiv2021

Cholesteryl Hemiazelate Induces Lysosome Dysfunction and Exocytosis in Macrophages

OBJECTIVEA key event in atherogenesis is the formation of lipid-loaded macrophages, lipidotic cells, which exhibit irreversible accumulation of undigested modified low-density lipoproteins in lysosomes. This event culminates with the loss of cell homeostasis, inflammation and cell death. In this study we propose to identify the chemical etiological factors and understanding the molecular and cellular mechanisms responsible for the impairment of lysosome function in macrophages. APPROACH AND RESULTSUsing shotgun lipidomics we have discovered that a family of oxidized lipids (cholesteryl hemiesters, ChE), end products of oxidation of polyunsaturated cholesteryl esters, occurs at higher concentrations in the plasma of two cohorts of cardiovascular disease patients than in the plasma of a control cohort. Macrophages exposed to the most prevalent ChE, cholesteryl hemiazelate (ChA) exhibit lysosome enlargement, peripheral lysosomal positioning, lysosome dysfunction and lipidosis which are irreversible. The transcriptomic profile of macrophages exposed to ChA indicates that the lysosome pathway is deeply affected and is well correlated with lysosome phenotypic and functional changes. Interestingly, the dysfunctional peripheral lysosomes are more prone to fuse with the plasma membrane, secreting their undigested luminal content into the extracellular milieu with potential consequences to the pathology. CONCLUSIONWe identify ChA not only as one of the molecules involved in the etiology of irreversible lysosome dysfunction culminating with lipidosis but also as a promoter of exocytosis of the dysfunctional lysosomes. The latter event is a new mechanism that may be important in the pathogenesis of atherosclerosis.

cell biology↗

bioRxiv2020

Optimizing the molecular diagnosis of Covid-19 by combining RT-PCR and a pseudo-convolutional machine learning approach to characterize virus DNA sequences

The proliferation of the SARS-Cov-2 virus to the whole world caused more than 250,000 deaths worldwide and over 4 million confirmed cases. The severity of Covid-19, the exponential rate at which the virus proliferates, and the rapid exhaustion of the public health resources are critical factors. The RT-PCR with virus DNA identification is still the benchmark Covid-19 diagnosis method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach, and represented by co-occurrence matrices. This technique analyzes the DNA sequences obtained by the RT-PCR method, eliminating sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-Cov-2. Experiments with all 24 virus families and SARS-Cov-2 (multi-class scenario) resulted 0.822222 {+/-} 0.05613 for sensitivity and 0.99974 {+/-} 0.00001 for specificity using Random Forests with 100 trees and 30% overlap. When we compared SARS-Cov-2 with similar-symptoms virus families, we got 0.97059 {+/-} 0.03387 for sensitivity, and 0.99187 {+/-} 0.00046 for specificity with MLP classifier and 30% overlap. In the real test scenario, in which SARS-Cov-2 is compared to Coronaviridae and healthy human DNA sequences, we got 0.98824 {+/-} 001198 for sensitivity and 0.99860 {+/-} 0.00020 for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify SARS-Cov-2 DNA sequences faster with higher specificity and sensitivity.

bioinformatics↗