Biology subjects

Castillo, E.

Publications and source records attributed to Castillo, E..

12 recordsLinked to original sources

bioRxiv2026

Advanced Maternal Age Impairs Decidual Angiogenesis and Spiral Artery Remodelling

Pregnancy presents an extreme physiological challenge that relies on rapid angiogenic vascular expansion and remodelling to establish the maternal-fetal vascular unit at the uteroplacental interface. These adaptations to the pregnancy-specific decidual vasculature are necessary for pregnancy progression. Advanced age pregnancies (AAP; pregnant person >35 years old) are associated with increased risk of poor pregnancy outcomes. Despite increasing evidence of the centrality of vascular aging in mediating organotypic dysfunction, whether vascular aging in the decidua occurs in the context of AAP is unknown. Using a murine model of AAP, we find that alongside embryonic developmental delay and deficient placental vascularization, AAP dams had impaired decidual angiogenesis and spiral artery remodeling with imbalances in both systemic and local uterine angiogenic factor expression in the VEGF and angiopoietin signalling families. These findings reveal that pregnancy may expose vascular aging mechanisms that contribute to declining reproductive success and increased cardiovascular risk later in life.

developmental biology↗

bioRxiv2026

MRI-Based Blood Clot Phenotyping: An In Vitro Study

Background and PurposeNeurointerventional outcomes depend on clot composition and may be influenced by clot contraction. Thus, a priori identification of clot composition and contraction could inform procedural strategies and improve outcomes. The goal of our work is to conduct an in vitro test to determine whether MRI can reliably predict both clot composition and contractile state. Materials and MethodsTo this end, we prepared blood clots spanning clinically observed compositions (0-80% red blood cells (RBCs)) in both contracted and uncontracted states. Contraction was controlled by coagulating blood with or without thrombin. We imaged these clots using quantitative, clinical, and investigational MRI sequences. Using these data, we then determined whether MRI signal intensities, quantitative parameters, and radiomic features capturing intensity and texture patterns can (i) predict clot hematocrit and (ii) classify clots by composition (RBC-rich vs. fibrin-rich) and contraction state. ResultsQuantitative MRI parameters (T1, T2, ADC) decreased with increasing hematocrit (R2 = 0.56-0.85, p < 0.001), while signal intensities from clinical sequences showed weaker correlations (R2 = 0.46-0.62, p < 0.001). Radiomic models predicted hematocrit with performance comparable to MRI parameters. When applied to classification, radiomic features accurately discriminated RBC-versus fibrin-rich clots, with AUCs exceeding 0.90 across nearly all sequences. In contrast, classification of contraction state showed greater variability in AUCs across sequences but remained high for quantitative T1 and T2 values (AUCs up to 0.88). Trends were consistent across clots coagulated with and without thrombin. Pooling features across sequences did not outperform the best individual sequence for either regression or classification. ConclusionsWe demonstrate that MRI-based radiomic analysis quantitatively characterizes clot composition and contraction in vitro. These findings support the feasibility of using MRI for pre-interventional clot phenotyping, with potential to inform thrombolytic and mechanical thrombectomy strategies. Thus, in vivo studies validating these results are warranted.

bioengineering↗

bioRxiv2025

Distinct Metabolic Signatures Linked to High-Resolution Computed Tomography Radiographic Phenotypes in Stable and Progressive Fibrotic Lung Disease

Rationale and ObjectivesThis study aimed to identify distinct metabolic signatures associated with disease progression by integrating high-resolution computed tomography (HRCT) visual scoring with comprehensive metabolomic profiling. Materials and MethodsThis single-center, cross-sectional study enrolled 60 idiopathic pulmonary fibrosis/interstitial lung disease (IPF/ILD) patients from December 2021 to October 2022. Participants underwent standardized pulmonary function testing, HRCT imaging, and peripheral blood collection for metabolomic analysis using one-dimensional hydrogen nuclear magnetic resonance (1H NMR) spectroscopy and ultra-high-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS). A comprehensive HRCT scoring system quantified total HRCT composite scores. Linear regression analysis integrated radiographic scores with metabolomic profiles, adjusted for multiple covariates ResultsStable IPF/ILD exhibited moderate negative correlations between the six most significant metabolites and HRCT scores (r = -0.27 to -0.51), along with a high abundance of specific phospholipids (triacylglycerol, monoacylglycerol, phosphatidylglycerol, phosphatidylethanolamine, diacylglycerol), sphingomyelin, ceramide, and acylcarnitine. In contrast, progressive disease showed weak positive correlations between the six most significant metabolites and HRCT scores (r = 0.19-0.26), and moderate negative correlation between specific triacylglycerol species and HRCT scores (r = -0.37-0.4). Furthermore, metabolomic analysis in individuals with progressive disease revealed both high and low abundances of specific phospholipid species (including high and low triacylglycerol species, as well as low levels of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and phosphatidylinositol), along with high levels of certain sphingomyelin, ceramide, taurine, and purine bases, and low levels of xanthine and lactic acid observed. ConclusionIntegration of systematic HRCT visual scoring with metabolomic profiling successfully differentiated stable from progressive IPF/ILD through distinct molecular-radiographic signatures. FundingSupporting Effective Educator Development (SEED) grant

cell biology↗

bioRxiv2025

Context-dependent response of endothelial cells to PIK3CA mutation

Cancer mutations in the PIK3CA gene cause congenital disorders. The endothelium is among the most frequently affected tissues in these disorders, displaying aberrant vascular overgrowth in the form of malformations. Pathological PIK3CA vascular phenotypes are found in veins and capillaries but rarely in arteries for reasons that are unclear at present. Here, using lineage tracing, we show that expression of mutated PIK3CAH1047R in endothelial cells leads to marked clonal expansions in capillary and venous endothelial cells. In contrast, mature arterial endothelial cells are refractory to PIK3CA mutation under these conditions and never display pathological phenotypes. Moreover, PIK3CAH1047Rexpression in arterial precursors interrupts arterial differentiation, thereby driving fate switch towards venous identity. This fate rewiring offers an additional layer of protection to prevent arterial damage in response to PIK3CA genetic perturbation. Molecularly, the PIK3CAH1047R-driven arterial-to-venous fate switch is orchestrated by upregulation of the vein-specifying transcription factor Nr2f2/COUP-TFII. Our findings reveal that pathogenic responses to PIK3CAH1047Rgreatly depend on the diferentation stage and fate trajectory of the targeted cell. Arteries are thus shielded against PIK3CA mutation, solving the long-standing question on the rarity of PIK3CA-related arterial malformations observed in patients.

developmental biology↗

bioRxiv2024

Identification of Recurrent Dynamics in Distributed Neural Populations

Large-scale recordings of neural activity over broad anatomical areas with high spatial and temporal resolution are increasingly common in modern experimental neuroscience. Recently, recurrent switching dynamical systems have been used to tackle the scale and complexity of these data. However, an important challenge remains in providing insights into the existence and structure of recurrent linear dynamics in neural time series data. Here we test a scalable approach to time-varying autoregression with low-rank tensors to recover the recurrent dynamics in stochastic neural mass models with multiple stable attractors. We demonstrate that the sparse representation of time-varying system matrices in terms of temporal modes can recover the attractor structure of simple systems via clustering. We then consider simulations based on a human brain connectivity matrix in high and low global connection strength regimes, and reveal the hierarchical clustering structure of the dynamics. Finally, we explain the impact of the forecast time delay on the estimation of the underlying rank and temporal variability of the time series dynamics. This study illustrates that prediction error minimization is not sufficient to recover meaningful dynamic structure and that it is crucial to account for the three key timescales arising from dynamics, noise processes, and attractor switching.

neuroscience↗

bioRxiv2024

Evolutionary analysis of genome-specific duplications in flatworm genomes

Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., genome-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are assumed to be key players in the adaptation process of species to each particular niche. Our results showed that genes associated with specific functions, such as response to stress, ion binding, oxidoreductase activity, and peptidase, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of the expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our results support the critical role of gene duplication in the evolution of flatworms.

evolutionary biology↗

bioRxiv2023

Single-cell transcriptional landscapes of bovine peri-implantation development

Supporting healthy pregnancy outcomes requires a comprehensive understanding of the cellular hierarchy and underlying molecular mechanisms during peri-implantation development. Here, we present a single-cell transcriptome-wide view of the bovine peri-implantation embryo development at day 12, 14, 16 and 18, when most of the pregnancy failure occurs in cattle. We defined the development and dynamic progression of cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages during bovine peri-implantation development. Notably, the comprehensive transcriptomic mapping of trophoblast development revealed a previously unrecognized primitive trophoblast cell lineage that is responsible for pregnancy maintenance in bovine prior to the time when binucleate cells emerge. We analyzed novel markers for the cell lineage development during bovine early development. We also identified cell-cell communication signaling underling embryonic and extraembryonic cell interaction to ensure proper early development. Collectively, our work provides foundational information to discover essential biological pathways underpinning bovine peri-implantation development and the molecular causes of the early pregnancy failure during this critical period. Significance StatementPeri-implantation development is essential for successful reproduction in mammalian species, and cattle have a unique process of elongation that proceeds for two weeks prior to implantation and represents a period when many pregnancies fail. Although the bovine embryo elongation has been studied histologically, the essential cellular and molecular factors governing lineage differentiation remain unexplored. This study profiled the transcriptome of single cells in the bovine peri-implantation development throughout day 12, 14, 16, and 18, and identified peri-implantation stage-related features of cell lineages. The candidate regulatory genes, factors, pathways and embryonic and extraembryonic cell interactions were also prioritized to ensure proper embryo elongation in cattle.

developmental biology↗

bioRxiv2023

Total Chemical Synthesis of Glycosylated TREM2 Ectodomain

Mutations in a microglia-associated gene TREM2 increase the risk of Alzheimers disease. Currently, structural and functional studies of TREM2 mainly rely on recombinant TREM2 proteins expressed from mammalian cells. However, using this method, it is difficult to achieve site-specific labeling. Here we present the total chemical synthesis of the 116 amino-acid TREM2 ectodomain. Rigorous structural analysis ensured correct structural fold after refolding. Treating microglial cells with refolded synthetic TREM2 enhanced microglial phagocytosis, proliferation, and survival. We also prepared TREM2 constructs with defined glycosylation patterns and found that glycosylation at N79 is critical to the thermal stability of TREM2. This method will provide access to TREM2 constructs with site-specific labeling, such as fluorescent labeling, reactive chemical handles, and enrichment handles, to further advance our understanding of TREM2 in Alzheimers disease.

biochemistry↗

bioRxiv2021

Cofilin pathology is a new player on α-synuclein-induced spine impairment in models of hippocampal synucleinopathy

Cognitive dysfunction and dementia are presently recognized as major complications in -synucleinopathies, namely in Dementia with Lewy Bodies (DLB) and Parkinsons disease with dementia (PDD). In these disorders, -Synuclein (Syn) accumulation affects severely the hippocampus by inducing synaptic dysfunction which culminates in cognitive impairment. To characterize the mechanisms underlying Syn-induced neuronal dysfunction we analysed the effect of overexpression or extracellular administration of Syn on hippocampal neurons. We observed that Syn induces the dysregulation of the actin-binding protein cofilin and its assembly into rod structures in a mechanism mediated by the cellular prion protein (PrPC). Moreover, we unraveled cofilin pathology as mediator of Syn-induced dendritic spine impairment in hippocampal neurons. Importantly, in a synucleinopathy mouse model with cognitive impairment we validated cofilin dysregulation and synaptic dysfunction at the same age when cognitive deficits were observed. Our data supports cofilin as a novel player on hippocampal synaptic dysfunction triggered by Syn on Lewy Body dementias.

neuroscience↗

bioRxiv2021

Parallel functional testing identifies enhancers active in early postnatal mouse brain

Enhancers are cis-regulatory elements that play critical regulatory roles in modulating developmental transcription programs and driving cell-type specific and context-dependent gene expression in the brain. The development of massively parallel reporter assays (MPRAs) has enabled high-throughput functional screening of candidate DNA sequences for enhancer activity. Tissue-specific screening of in vivo enhancer function at scale has the potential to greatly expand our understanding of the role of non-coding sequences in development, evolution, and disease. Here, we adapted a self-transcribing regulatory element MPRA strategy for delivery to early postnatal mouse brain via recombinant adeno-associated virus (rAAV). We identified and validated putative enhancers capable of driving reporter gene expression in mouse forebrain, including regulatory elements within an intronic CACNA1C linkage disequilibrium block associated with risk in neuropsychiatric disorder genetic studies. Paired screening and single enhancer in vivo functional testing, as we show here, represents a powerful approach towards characterizing regulatory activity of enhancers and understanding how enhancer sequences organize gene expression in normal and pathogenic brain development.

neuroscience↗

bioRxiv2019

Ventral Pallidum is Essential for Cocaine Reinstatement After Voluntary Abstinence

Addiction is a chronic relapsing disorder, and during recovery many people experience several relapse events as they attempt to voluntarily abstain from drug. New preclinical relapse models have emerged which capture this common human experience of relapse after voluntary abstinence, and mounting evidence indicates that reinstatement of drug seeking after voluntary abstinence recruits neural circuits distinct from reinstatement following experimenter-imposed abstinence, or abstinence due to extinction training. Ventral pallidum (VP), a key limbic node involved in drug seeking, has well-established roles in conventional reinstatement models tested following extinction training, but it is unclear whether this region also participates in more translationally-relevant models of relapse. Here we show that chemogenetic inhibition of VP neurons strongly attenuates cocaine-, context-, and cue-induced reinstatement tested after voluntary, punishment-induced abstinence. This effect was strongest in the most compulsive, punishment-resistant rats, and reinstatement was associated with neural activity in anatomically-defined VP subregions. VP inhibition also attenuated the propensity of rats to display hesitations, a risk assessment behavior seen during punished drug taking that is likely due to concurrent approach and avoidance motivations. These results indicate that VP, unlike other connected limbic brain regions, is essential for reinstatement of drug seeking after voluntary abstinence. Since VP inhibition effects were strongest in the most compulsively cocaine-seeking individuals, this could indicate that VP plays a particularly important role in the most pathological, addiction-like behavior, making it an attractive target for future therapeutic interventions.

neuroscience↗

bioRxiv2017

Raspberry Pi Powered Imaging for Plant Phenotyping

O_LIPremise of the study: Image-based phenomics is a powerful approach to capture and quantify plant diversity. However, commercial platforms that make consistent image acquisition easy are often cost-prohibitive. To make high-throughput phenotyping methods more accessible, low-cost microcomputers and cameras can be used to acquire plant image data.\nC_LIO_LIMethods and Results: We used low-cost Raspberry Pi computers and cameras to manage and capture plant image data. Detailed here are three different applications of Raspberry Pi controlled imaging platforms for seed and shoot imaging. Images obtained from each platform were suitable for extracting quantifiable plant traits (shape, area, height, color) en masse using open-source image processing software such as PlantCV.\nC_LIO_LIConclusion: This protocol describes three low-cost platforms for image acquisition that are useful for quantifying plant diversity. When coupled with open-source image processing tools, these imaging platforms provide viable low-cost solutions for incorporating high-throughput phenomics into a wide range of research programs.\nC_LI

plant biology↗