Biology subjects

Castillo, A.

Publications and source records attributed to Castillo, A..

17 recordsLinked to original sources

bioRxiv2026

Selective Packaging of Rotavirus Double-Layered Particles into Host Microvesicles

Rotavirus is a non-enveloped RNA virus traditionally thought to exit host cells through lytic or conventional vesicular pathways, but recent evidence shows that it also exploits host microvesicles for non-lytic transmission. To characterize this transmission pathway, we combined high-resolution microscopy (TEM, confocal microscopy, immunogold labeling) with biochemical and infectivity assays. Our work revealed that rotavirus infection robustly increased microvesicle production, and individual vesicles frequently contained multiple viral particles. Quantitative analysis revealed striking differential partitioning of particle types. Mature triple-layered particles predominated within infected cells, whereas extracellular microvesicles were strongly enriched for immature double-layered particles. Although free double-layered particles lack the outer capsid required for classical receptor-mediated entry, microvesicle-associated particles initiated productive infections, whereas disruption of the vesicular membrane abolished infectivity. These findings suggest an evolutionarily advantageous dual transmission strategy. By using host-derived membranes to transmit otherwise non-infectious intermediates, rotavirus can bypass outer-capsid-dependent entry, potentially reducing the energetic cost of producing fully mature infectious particles while enabling collective transmission. Maintaining a free-virus pathway may nevertheless be important because transmission by individual mature virions imposes population bottlenecks that limit the propagation of defective or cheating genomes and preserve high-fitness genotypes. Thus, partitioning viral progeny between vesicle-associated double-layered particles and free triple-layered particles may balance the immediate benefits of collective spread with long-term genetic quality control. Whether double-layered particle enrichment arises from active sorting or spatial coupling between viral assembly and microvesicle biogenesis remains unresolved.

microbiology↗

bioRxiv2026

Recovery of an 18th Century Rhinovirus Genome through Ancient RNA Isolation of Human Lungs

RNA viruses cause substantial global morbidity, yet their impact prior to the twentieth century remains obscured. While ancient DNA studies have transformed our understanding of past pathogens, ancient RNA (aRNA) isolation is largely restricted to exceptionally preserved samples. Here, we simultaneously recover aDNA and aRNA from non-formalin-fixed human lung specimens and reconstructed an 18th-century Human Rhinovirus (HRV) A genome--the oldest human RNA virus identified to date. The RNA is highly fragmented, with distinctive terminal misincorporations and coverage patterns consistent with double-stranded RNA. Phylogenetic analyses indicate that this historical HRV genome is an extinct lineage related to contemporary genotypes, providing a unique perspective on rhinovirus evolution. These findings demonstrate that centuries-old medical specimens can retain informative aRNA, expanding the temporal scope of paleovirology.

genomics↗

bioRxiv2025

Rats Exposed to a Low Resource Environment in Early Life Display Sex Differences in Blood Pressure, Autonomic Activity, and Brain and Kidney Pro-inflammatory Markers During Adulthood

Introduction: Poverty, a low resource state, is a common adverse childhood experience (ACE) and early life stress (ELS). People who experienced childhood poverty are at greater risk for developing hypertension during adulthood, with sex differences. To determine the possible mechanisms of these sex differences, we investigated the alterations in blood pressure (BP), autonomic activity, and inflammation in the brain and kidneys of rats exposed to an impoverished environment during the early postnatal period, by using the limited bedding and nesting (LBN) model. Methods: The LBN model mimics childhood poverty by creating a low resource environment on postnatal days 2-9. After weaning, offspring were separated by sex and LBN exposure and were evaluated at 16-18 weeks of age (Adulthood). Results: LBN males displayed an increase in BP compared to the control (CON), whereas LBN females showed no changes. Sympathetic nerve activity (SNA) was increased in LBN males and females compared to the CON, while only parasympathetic nerve activity (PNA) was increased in LBN vs. CON females. Pro-inflammatory cytokines, IL-17 and TNF-, were decreased in the brains of LBN vs. CON males, with no alterations in females. Conclusion: Adult LBN males have elevated BP, due to increased SNA, while LBN females may be protected from increased BP due to a simultaneous increase in SNA and PNA. The reduction in IL-17 and TNF- in LBN males may serve as a compensatory mechanism to lower BP. This study provides insights into sex differences in BP for adults who experienced childhood poverty.

physiology↗

bioRxiv2025

Clonal memory of colitis accumulates and promotes tumor growth

Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

cancer biology↗

bioRxiv2024

Intrauterine Growth-Restricted Pregnant Rats, from Hypertensive Placental Ischemic Dams Display Preeclamptic-like Symptoms: A New Rodent Model of Preeclampsia

Preeclampsia (PE) is characterized by de novo hypertension (HTN) and is one of the primary causes of intrauterine growth restriction (IUGR). PE is associated with placental ischemia, decreased nitric oxide (NO) bioavailability, oxidative stress (OS), and organ damage in the kidneys and brain. This study aims to characterize a new model of PE using IUGR rats from hypertensive placental ischemic dams. It is hypothesized that pregnant IUGR rats from hypertensive placental ischemic dams will have elevated blood pressure (BP), OS, and organ damage. MethodsPregnant Sprague Dawley rats are divided into 2 groups: normal pregnant (NP) and reduced uterine perfusion pressure (RUPP) hypertensive placental ischemic dams. Offspring from NP and RUPP dams were mated at 10 weeks of age to generate pregnant IUGR (IUGR Preg; n=3-8) and pregnant CON (CON Preg; n=3-6) rats. BP and other markers of PE were evaluated during late gestation. ResultsPregnant IUGR rats had elevated BP and systemic OS, as demonstrated by higher trending 8-isoprostanes and lower circulating antioxidant capacity. Maternal body weight of pregnant IUGR rats and their pups weights were decreased, while the brains were enlarged. Brain OS was elevated, with a rise in hydrogen peroxide (H2O2) and heat shock protein 1 (HSP- 1), along with lower Manganese Superoxide Dismutase (MnSOD) and antioxidant capacity. ConclusionPregnant IUGR rats, born from hypertensive placental ischemic dams, have HTN and increased systemic and brain OS, with larger brain sizes and smaller pups. Pregnant IUGR rats exhibit an preeclamptic-like phenotype, which suggests a new epigenetic model of PE.

physiology↗

bioRxiv2023

Yeast diversity in open agave fermentations across Mexico

Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX.1.0 culture collection by isolating 4,524 strains from 68 sites in diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and a subset of the strains was verified by ITS and D1/D2 sequencing. The most abundant species isolated from all producing regions were Saccharomyces cerevisiae, Pichia kudriavzevii, Pichia manshurica, and Kluyveromyces marxianus. Despite the great diversity of environmental conditions and production practices the composition of yeast communities remained largely homogeneous throughout locations and fermentation stages, even if less abundant but commonly occurring yeasts were considered. Furthermore, ITS and D1/D2 sequencing revealed two candidate new species of Saccharomycetales. To explore the intraspecific variation of the yeasts from agave fermentations, we conducted genome sequencing on four isolates of the non-conventional yeast Kazachstania humilis. The genomes of these four strains were considerably distinct from other genomes of the same species, suggesting that they belong to a different population. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments. TAKE AWAYO_LIWe isolated and identified 4,524 yeast strains from open agave fermentations in Mexico. C_LIO_LIYeast communities remained largely homogeneous throughout diverse locations. C_LIO_LIKazachstania humilis genomes differed significantly from isolates in other regions of the world. C_LIO_LIWe report two candidate new species related to the Pichia clade. C_LI

microbiology↗

bioRxiv2023

Longitudinal analysis of a dietary mouse model of non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH)

Non-alcoholic fatty liver disease (NAFLD), and resultant non-alcoholic steatohepatitis (NASH), incidence and prevalence are rising globally due to increasing rates of obesity and diabetes. Currently, there are no approved pharmacological treatments for NAFLD, highlighting a need for additional mechanistic studies to develop prevention and/or therapeutic strategies. Diet-induced preclinical models of NAFLD can be used to examine the dynamic changes that occur during NAFLD development and progression throughout the lifespan. To date, most studies utilizing such models have focused exclusively on terminal time points and have likely missed critical early and late changes that are important for NAFLD progression (i.e, worsening). We performed a longitudinal analysis of histopathological, biochemical, transcriptomic, and microbiome changes that occurred in adult male mice fed either a control diet or a NASH-promoting diet (high in fat, fructose, and cholesterol) for up to 30 weeks. We observed progressive development of NAFLD in mice fed the NASH diet compared to the control diet. Differential expression of immune-related genes was observed at an early stage of diet-induced NAFLD development (10 weeks) and persisted into the later stages of the disease (20 and 30 weeks). Differential expression of xenobiotic metabolism related genes was observed at the late stage of diet-induced NAFLD development (30 weeks). Microbiome analysis revealed an increased abundance of Bacteroides at an early stage (10 weeks) that persisted into the later stages of the disease (20 and 30 weeks). These data provide insight into the progressive changes that occur during NAFLD/NASH development and progression in the context of a typical Western diet. Furthermore, these data are consistent with what has been reported in patients with NAFLD/NASH, supporting the preclinical use of this diet-induced model for development of strategies to prevent or treat the disease.

physiology↗

bioRxiv2023

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements

Cis-regulatory elements control gene expression and are dynamic in their structure, reflecting changes to the composition of diverse effector proteins over time1-3. Here we sought to connect the structural changes at cis-regulatory elements to alterations in cellular fate and function. To do this we developed PRINT, a computational method that uses deep learning to correct sequence bias in chromatin accessibility data and identifies multi-scale footprints of DNA-protein interactions. We find that multi-scale footprints enable more accurate inference of TF and nucleosome binding. Using PRINT with single-cell multi-omics, we discover wide-spread changes to the structure and function of candidate cis-regulatory elements (cCREs) across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Activity segmentation using the co-variance across cell states identifies "sub-cCREs" as modular cCRE subunits of regulatory DNA. We apply this single-cell and PRINT approach to characterize the age-associated alterations to cCREs within hematopoietic stem cells (HSCs). Remarkably, we find a spectrum of aging alterations among HSCs corresponding to a global gain of sub-cCRE activity while preserving cCRE accessibility. Collectively, we reveal the functional importance of cCRE structure across cell states, highlighting changes to gene regulation at single-cell and single-base-pair resolution.

genomics↗

bioRxiv2023

Spatial and temporal representation of marine fish occurrences available online

Despite the 243,000 species of marine species described by 2022, our knowledge about the biodiversity in the oceans is still incomplete. This may have dreaded and detrimental effect for the conservation of marine ecosystems under the current anthropization of our biota and the fast pacing climate and global change scenario. However, a large number of online repositories cataloging, storing and distributing biodiversity information hosting taxonomic information and species occurrence data have emerged recently. FishBase, the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS) are part of these publicly available repositories representing a variety of sources that have exploded in number. However, despite the incredible accumulation of biodiversity records, not all the information is really useful, nor does it represent any new knowledge regarding global species richness patterns. In this study we evaluated the spatial and temporal representativeness of the records of marine fishes (order Actinopterygii) available in the GBIF and OBIS global repositories. We provide a methodological framework based on a set of non-parametric estimators to calculate species richness from incidence data, using hexagonal grids as sampling units overlapped on the marine bioregions worldwide. Using standard ecological and spatial analysis tools, we identify regions that are adequately represented in terms of available records and therefore have more reliable data, as well as regions with few records that do not represent current species richness. We overlap these results with the location of marine protected areas and fishing exploitation zones to understand the anthropogenic effect on marine ichthyofauna. We additionally evaluate hypotheses regarding the taxonomic, geographic, and temporal distribution of information biases to deepen our current understanding of public records of species occurrences worldwide. Considering that more than 40 years of information was analyzed, the results showed that on a global scale, the primary data on marine fish available on GBIF and OBIS platforms are still far from being representative and complete. Only 1.14% of the records were useful for our analyses. In addition, we found that the information seems to be biased towards coastal areas, regions close to developed countries and areas where there is a large fishing activity. Finally, the best represented species and families are those with a small body size, which use shallow habitats and have commercial cultural value.

ecology↗

bioRxiv2023

Acute effects of subanesthetic ketamine on cerebrovascular hemodynamics in humans: A TD-fNIRS neuroimaging study

Quantifying neural activity in natural conditions (i.e. conditions comparable to the standard clinical patient experience) during the administration of psychedelics may further our scientific understanding of the effects and mechanisms of action. This data may facilitate the discovery of novel biomarkers enabling more personalized treatments and improved patient outcomes. In this single-blind, placebo-controlled study with a non-randomized design, we use time-domain functional near-infrared spectroscopy (TD-fNIRS) to measure acute brain dynamics after intramuscular subanesthetic ketamine (0.75 mg/kg) and placebo (saline) administration in healthy participants (n = 15, 8 females, 7 males, age 32.4 {+/-} 7.5 years) in a clinical setting. We found that the ketamine administration caused an altered state of consciousness and changes in systemic physiology (e.g. increase in pulse rate and electrodermal activity). Furthermore, ketamine led to a brain-wide reduction in the fractional amplitude of low frequency fluctuations (fALFF), and a decrease in the global brain connectivity of the prefrontal region. Lastly, we provide preliminary evidence that a combination of neural and physiological metrics may serve as predictors of subjective mystical experiences and reductions in depressive symptomatology. Overall, our studies demonstrated the successful application of fNIRS neuroimaging to study the physiological effects of the psychoactive substance ketamine and can be regarded as an important step toward larger scale clinical fNIRS studies that can quantify the impact of psychedelics on the brain in standard clinical settings.

neuroscience↗

bioRxiv2022

ARHGAP17 regulates the spatiotemporal activity of Cdc42 at invadopodia

Invadopodia formation is regulated by Rho GTPases. However, the molecular mechanisms that control Rho GTPase signaling at invadopodia remain poorly understood. Here, we have identified ARHGAP17, a Cdc42-specific RhoGAP, as a key regulator of invadopodia in breast cancer cells and by RhoGAPs characterized a novel ARHGAP17-mediated signaling pathway that controls the spatiotemporal activity of Cdc42 during invadopodia turnover. Our results show that during invadopodia assembly, ARHGAP17 localizes to the invadopodia ring and restricts the activity of Cdc42 to the invadopodia core, where it promotes invadopodia growth. Invadopodia disassembly starts when ARHGAP17 translocates from the invadopodia ring to the core, in a process that is mediated by its interaction with the Cdc42 effector CIP4. Once at the core, ARHGAP17 inactivates Cdc42 to promote invadopodia disassembly. Our results in invadopodia provide new insights on the coordinated transition between the activation and inactivation of Rho GTPases.

cell biology↗

bioRxiv2021

Expression and novel alternative purification of the recombinant nucleocapsid (N) protein of SARS-CoV-2 in Escherichia coli for the serodiagnosis of COVID-19

The SARS-CoV-2 coronavirus causes severe acute respiratory syndrome and has caused a global pandemic by causing the COVID-19 disease. To monitor and control it, diagnostic methods such as molecular and serological tests are necessary. The serological approach uses SARS-CoV-2 antigens to detect the antibodies present in patients using quantitative techniques such as enzyme-linked immunosorbent assay (ELISA) or qualitative rapid tests such as lateral flow chromatography (RDTs). The main antigens used are the spike protein (S) and the nucleocapsid protein (N). Both proteins are obtained in different expression systems, in eukaryotic cells, their production is expensive, so in this work we chose a simpler and cheaper system such as prokaryotic to express and purify the N protein. Thereore, the nucleotide sequence had to being optimized to be expressed in Escherichia coli. The protein N is sensitive to E.coli proteases and also has the ability to self-proteolyze under native conditions, degrading into different fragments. However, under denaturing conditions, using urea and at pH 5.3 it is stable and efficiently purified using metal exchange chromatography (IMAC). In our purification strategy, we surprisingly found that by not using a sonicator, a homogeneous and time-stable preparation of the recombinant antigen is obtained. An approximate yield of 200 mg / L was obtained. It was then tested with healthy sera and sera from COVID-19 convalescent patients in Wester-blot tests that were able to recognize it. Our work provides a novel strategy to produce the SARS-CoV-2 protein N so that it can be used as an input in the development and innovation of serological tests in the diagnosis of COVID-19.

cell biology↗

bioRxiv2020

Atlas and developmental dynamics of mouse DNase I hypersensitive sites

Early mammalian development is orchestrated by genome-encoded regulatory elements populated by a changing complement of regulatory factors, creating a dynamic chromatin landscape. To define the spatiotemporal organization of regulatory DNA landscapes during mouse development and maturation, we generated nucleotide-resolution DNA accessibility maps from 15 tissues sampled at 9 intervals spanning post-conception day 9.5 through early adult, and integrated these with 41 adult-stage DNase-seq profiles to create a global atlas of mouse regulatory DNA. Collectively, we delineated >1.8 million DNase I hypersensitive sites (DHSs), with the vast majority displaying temporal and tissue-selective patterning. Here we show that tissue regulatory DNA compartments show sharp embryonic-to-fetal transitions characterized by wholesale turnover of DHSs and progressive domination by a diminishing number of transcription factors. We show further that aligning mouse and human fetal development on a regulatory axis exposes disease-associated variation enriched in early intervals lacking human samples. Our results provide an expansive new resource for decoding mammalian developmental regulatory programs.

genomics↗

bioRxiv2020

The visual ecology of a color polymorphic reef fish: the role of aggressive mimicry.

Since all forms of mimicry are based on perceptual deception, the sensory ecology of the intended receiver is of paramount importance to test the necessary precondition for mimicry to occur, i.e. model-mimic misidentification, and to gain insight in the origin and evolutionary trajectory of the signals. Here we test the potential for aggressive mimicry by a group of coral reef fishes, the color polymorphic Hypoplectrus hamlets, from the point of view of their most common prey, small epibenthic gobies and mysid shrimp. We build visual models based on the visual pigments and spatial resolution of the prey, the underwater light spectrum and color reflectances of putative models and their hamlet mimics. Our results are consistent with one mimic-model relationship between the butter hamlet H. unicolor and its model the butterflyfish Chaetodon capistratus but do not support a second proposed mimic-model pair between the black hamlet H. nigricans and the dusky damselfish Stegastes adustus. We discuss our results in the context of color morphs divergence in the Hypoplectrus species radiation and suggest that aggressive mimicry in H. unicolor might have originated in the context of protective (Batesian) mimicry by the hamlet from its fish predators.

evolutionary biology↗

bioRxiv2019

Genetic variation of Aedes aegypti populations from Ecuador

This is the first genetic analysis in Ecuador of Aedes aegypti using fragments of mitochondrial genes, NADH dehydrogenase subunit 4 (ND4) and cytochrome oxidase subunit I (COI). A total of 154 mosquitoes from 23 localities were collected in the Pacific coastal lowlands, Amazon basin lowlands, and the Galapagos Islands from 2012 to 2019. The analysis of fragments of the genes COI (672 bp) and ND4 (262 bp) and concatenated analysis of both COI and ND4 showed two haplotypes (H1, H2) present in Ecuador mainland and the Galapagos Islands. The phylogenetic analysis identified two well-supported clades. Combined analysis of both genes from ten localities also resulted in two haplotypes. Nucleotide diversity, neutrality tests (Tajimas test D, Fu and Lis F*and D*) and AMOVA analysis of the entire data set suggest balancing selection for both genes. The results indicate genetic variation without geographical restriction. COI-H1 grouped with sequences from the Americas, West and Central Africa, East Africa, Asia, and Australia. ND4-H1 grouped with similar sequences from the Americas, Asia and West Africa. COI-H2 grouped with sequences from Asia and the Americas. ND4-H2 grouped with sequences from the Americas. We report overlapping peaks in four sequences that suggest heteroplasmy in the individuals. The origin of the populations of Aedes aegypti in Ecuador show African genetic origin and are widely present in several countries in the Americas. One of the genetic variants is more common in all the localities and the two haplotypes are distributed indistinctly in the three geographical sampled areas in Ecuador.

genetics↗

bioRxiv2018

Maintaining trunk neural crest cells as crestospheres

Neural crest cells have broad migratory and differentiative ability that differs according to their axial level of origin. However, their transient nature has limited understanding of their stem cell and self-renewal properties. While an in vitro culture method has made it possible to maintain cranial neural crest cells as self-renewing multipotent crestospheres (Kerosuo et al., 2015), these same conditions failed to preserve trunk neural crest in a stem-like state. Here we optimize culture conditions for maintenance of trunk crestospheres, comprised of both neural crest stem and progenitor cells. Trunk crestospheres display elevated expression of neural crest cell markers as compared to those characteristic of neural tube or mesodermal fates. Moreover, trunk crestospheres have increased expression of trunk-related markers as compared to cranial genes. Finally, we use lentiviral transduction as a tool to manipulate gene expression in trunk crestospheres. Taken together, this method enables long-term in vitro maintenance and manipulation of trunk neural crest cells in a premigratory stem or early progenitor state to probe the mechanisms underlying their stemness and lineage decisions.\n\nHighlightsO_LITrunk-derived multipotent neural crest stem cells can be cultured as crestospheres\nC_LIO_LITrunk-derived crestospheres require different conditions than cranial\nC_LIO_LITrunk crestospheres consist of neural crest stem and progenitor cells\nC_LIO_LITrunk crestospheres can be efficiently transduced using lentiviral vectors\nC_LI

developmental biology↗

bioRxiv2018

Gut microbiota density influences host physiology and is shaped by host and microbial factors

To identify factors that regulate gut microbiota density and the impact of varied microbiota density on health, we assayed this fundamental ecosystem property in fecal samples across mammals, human disease, and therapeutic interventions. Physiologic features of the host (carrying capacity) and the fitness of the gut microbiota shape microbiota density. Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohns disease, ulcerative colitis, and ileal pouch-anal anastomosis. The gut microbiota in recurrent Clostridium difficile infection had lower density and reduced fitness that were restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease in terms of microbiota density, host carrying capacity, and microbiota fitness provide new insights into microbiome structure and microbiome targeted therapeutics.

microbiology↗