Biology subjects

Delgado, A.

Publications and source records attributed to Delgado, A..

16 recordsLinked to original sources

bioRxiv2026

The brain-meningeal interface functions as a reservoir and entry site for brain parenchymal macrophages

Microglia are regarded as self-maintaining brain parenchymal macrophages without contribution from adult hematopoiesis. Nevertheless, peripheral macrophage engraftment into the brain has been reported, but the biological variables governing central nervous system (CNS) macrophage niche access remain unclear. We show that CNS macrophage engraftment is determined by the balance between tissue-resident macrophage (TRM) self-renewal and the temporal alignment of niche opening with the availability of engraftment-competent cells and proximity to the vacated niche, rather than prolonged niche vacancy. Fate mapping revealed that monocytes entering the subdural space undergo border-associated macrophage (BAM)-like differentiation, clonal expansion, and transpial migration into the parenchyma, whereas mature BAMs directly repopulate selectively vacated parenchymal niches. We further identify a parenchymal macrophage population with a peripheral BAM-like transcriptional program in aged and neurodegenerative human brains, challenging the dogma of MG-exclusivity. Together, these findings establish a predictive framework for interpreting macrophage maintenance and replacement and for developing macrophage-based therapies.

neuroscience↗

bioRxiv2025

Altered NPTX2 dynamics associated with impaired cognitive aging

Changes in synaptic integrity and neural activity homeostasis are hallmarks of brain aging and are closely tied to cognitive outcomes. Yet, defining their relationship across the continuum from normal aging to neurodegenerative disease has proven challenging. Recent research investigating the dynamic changes of neuronal pentraxin 2 (NPTX2, or Narp, neuronal activity-related pentraxin) in cerebrospinal fluid (CSF) of Alzheimers disease (AD) subjects supports its promise as a prognostic marker of disease progression, possibly as an expression of synaptic damage related to cognitive impairment. However, studies in human subjects are unable to clearly differentiate age-related and disease-related processes. Here we took advantage of a well-characterized rat model that displays substantial individual differences in hippocampal memory during aging, uncontaminated by slowly progressive, spontaneous neurodegenerative disease. Through this approach, we aimed to interrogate the underlying neural substrates that mediate aging as a uniquely permissive condition and the primary risk for neurodegeneration. We found that successful cognitive aging is associated with an elevation of NPTX2 levels above that found in young or cognitively impaired subjects. Pharmacological engagement of neural activity was sufficient to increase NPTX2 levels in all subjects, but cognitively-impaired aged subjects failed to recruit NPTX2 in response to a hippocampus-dependent memory task. Together the findings demonstrate that changes in NPTX2 are coupled to differential cognitive outcomes of aging, and that successful neurocognitive aging is associated with adaptive upregulation of NPTX2, not simply the persistence of youthful synaptic dynamics. Significance StatementAlthough aging is the most prominent risk factor for Alzheimer Disease (AD), the age-dependent processes that disrupt neurophysiological homeostasis leading to neurodegenerative disease remain poorly defined. Alterations in NPTX2, a synaptic protein biomarker for AD, may elucidate aging processes underlying pathological trajectories. We examined NPTX2 in an aging context and identified circuit specific alterations of NPTX2 that are coupled with distinct memory outcomes in aging in the absence of potential confounds of neurodegenerative disease. Greater NPTX2, associated with successful cognitive aging, may reflect coordinated molecular and circuit-level adaptations that sustain memory-relevant hippocampal activity. Development of targets and interventions that promote neuroadaptive network homeostasis, bending the trajectory of aging away from neurodegeneration, are a potentially valuable alternative to current therapeutic strategies.

neuroscience↗

bioRxiv2025

Long-Term Organ Culture Reveals Differential Stem Cell-Driven Remodelling in Myometrium and MED12-Mutant Uterine Leiomyoma

Uterine leiomyomas or fibroids are highly prevalent benign tumors of the female reproductive tract, often causing significant symptoms and requiring surgical intervention, leading to substantial healthcare costs worldwide. Their molecular pathogenesis remains incompletely understood, but evidence suggests that somatic stem cells play a pivotal role in myometrial growth, whereas a genetic alteration, particularly mutations in MED12, may transform a myometrial stem cell into a tumor-initiating cell, promoting fibroid growth. In organ cultures of fibroids and myometrium, most differentiated cells degenerated by day 7, whereas stem cells remained quiescent and viable within their native niches. Notably, between days 15 and 29, hypoxia-induced activation triggered stem cell proliferation and differentiation within the ex vivo slices. Transcriptomic profiling revealed statistically significant upregulation of stemness-associated genes, including HMGA, ITG, KLF, HOX, and SOX family members, in long-term cultured slices compared with baseline tissue, and between normal and tumor cultures. Reactome pathway enrichment analysis further identified distinct metabolic, extracellular matrix remodeling, immune surveillance, angiogenic, and cell death- related programs distinguishing myometrial from leiomyoma cultures. Furthermore, previously reported gene and pathway differences between healthy and fibroid tissues were robustly confirmed, validating the culture model. In conclusion, our findings establish long-term organ culture as a powerful, physiologically relevant platform for investigating stem cell dynamics in myometrium and uterine leiomyoma. They also provide proof of concept for extending this approach to other tissue types, enabling the discovery of mechanisms underlying stem cell activation, differentiation, and death, with broad translational potential in regenerative medicine and cancer biology.

molecular biology↗

bioRxiv2024

A novel class of allosteric glucosylceramidase beta 1 correctors that reduce cellular stress and enhance lysosomal function

Mutations in glucosylceramidase beta 1 (GCase) disrupt the proteins conformational maturation in the endoplasmic reticulum (ER) and hinder its transport to the lysosome. The intralysosomal accumulation of glucocerebrosides, which are substrates of the GCase enzyme, impairs lysosomal function and is linked to Gaucher disease (GD). GCase mutations also increase the risk of Parkinsons disease (PD) and Dementia with Lewy Bodies. We used Site-directed Enzyme Enhancement Therapy (SEE-Tx(R)) technology to design two structurally targeted allosteric regulators (STARs) of GCase. Administration of GT-02287 and GT-02329 to cultured GD patient-derived primary human fibroblasts enhances folding and protects the two most common disease-causing GCase variants, GCaseAsn370Ser and GCaseLeu444Pro, from proteasomal degradation. Mechanistically, these treatments facilitate the lysosomal delivery of enzymatically active forms of mutant GCase, leading to improved lysosomal function and reduced cellular stress in GD patient-derived fibroblasts. The findings suggest that the allosteric pharmacologic regulators GT-02287 and GT-02329 hold promise for further development as potential therapeutic agents for GCase-related disorders, including GD, PD and Dementia with Lewy Bodies.

cell biology↗

bioRxiv2024

Pharmacological GCase Activity Enhancement Inhibits Tau Accumulation

A slow decline in the autophagy-lysosomal pathway is a hallmark of the normal aging brain. Yet, an acceleration of this cellular function may propel neurodegenerative events. In fact, mutations in genes associated with the autophagy-lysosomal pathway can lead to Parkinsons disease. Also, amyloidogenic protein deposition is observed in lysosomal storage disorders, which are caused by genetic mutations representing risk factors for Parkinsons disease. For example, Gauchers disease GBA1 mutations leading to defects in lysosomal sphingolipid metabolism cause -synuclein accumulation. We observed that increased lysosomal Tau accumulation is found in human dermal fibroblasts engineered for inducible Tau expression. Inhibition of the GBA1 product GCase augmented Tau-dependent lysosomal stress and Tau accumulation. Here, we show increased Tau seed-induced Tau accumulation in Gauchers fibroblasts carrying GBA1 mutations when compared to normal fibroblasts. Pharmacological enhancement of GCase reversed this effect, notably, also in normal fibroblasts. This suggests that boosting GCase activity may represent a therapeutic strategy to slow down aging-dependent lysosomal deficits and brain protein deposition.

cell biology↗

bioRxiv2024

Virus propagation linked to exceedingly rare gene-expression errors

Viruses are obligate parasites that establish extensive interactions with proteins and other biomolecules of their hosts. About 20% of protein molecules bear phenotypic mutations due to errors during gene expression. Phenotypic mutations are not inherited and are not purged/amplified by natural selection. Therefore, protein variants harboring phenotypic mutations remain at very low levels. Here, we show that proteins at exceedingly low levels may enable virus propagation. Bacteriophage T7 recruits the host thioredoxin as an essential processivity factor for its replisome. Thioredoxin constitutive expression yields 10000-20000 molecules per E. coli cell. We inserted early stop codons in the thioredoxin gene and appended to its end the sequence encoding for a photoconvertible fluorescent protein. Virus propagation was not abolished, indicating that some thioredoxin molecules were produced through mistranscription or mistranslation. Single-molecule localization microscopy detected 12{+/-}5 molecules per cell when an ochre codon was inserted. This work demonstrates that crucial virus-host biomolecular interactions may need occur only a few times to trigger virus propagation and supports that viruses may exploit the wide diversity of host and viral protein variants arising from gene-expression errors to establish such interactions. Immediate implications of this notion for the mechanisms of cross-species transmission and antibody evasion are discussed.

microbiology↗

bioRxiv2024

The psychedelic, DOI, increases dopamine release in nucleus accumbens to predictable rewards and reward cues

Psychedelics produce lasting therapeutic responses in neuropsychiatric diseases suggesting they may disrupt entrenched associations and catalyze learning. Here, we examine psychedelic effects on dopamine signaling in the nucleus accumbens (NAc) core, a region extensively linked to reward learning, motivation, and drug-seeking. We measure phasic dopamine transients following acute psychedelic administration during well learned Pavlovian tasks in which sequential cues predict rewards. We find that the psychedelic 5-HT2A/2C agonist, DOI, increases dopamine signaling to rewards and proximal reward cues but not to the distal cues that predict these events. We determine that the elevated dopamine produced by psychedelics to reward cues occurs independently of psychedelic-induced changes in reward value. The increased dopamine associated with predictable reward cues supports psychedelic-induced increases in prediction error signaling. These findings lay a foundation for developing psychedelic strategies aimed at engaging error-driven learning mechanisms to disrupt entrenched associations or produce new associations.

neuroscience↗

bioRxiv2023

Sleep and circadian rhythm disruption by NPTX2 loss of function

Sleep and circadian rhythm disruption (SCRD) is commonly observed in aging, especially in individuals who experience progressive cognitive decline to mild cognitive impairment (MCI) and Alzheimers disease (AD). However, precise molecular mechanisms underlying the association between SCRD and aging are not fully understood. Orexin A is a well-characterized "sleep neuropeptide" that is expressed in hypothalamic neurons and evokes wake behavior. The importance of Orexin is exemplified in narcolepsy where it is profoundly down-regulated. Interestingly, the synaptic immediate early gene NPTX2 is co-expressed in Orexin neurons and is similarly reduced in narcolepsy. NPTX2 is also down-regulated in CSF of some cognitively normal older individuals and predicts the time of transition from normal cognition to MCI. The association between Orexin and NPTX2 is further evinced here where we observe that Orexin A and NPTX2 are highly correlated in CSF of cognitively normal aged individuals and raises the question of whether SCRD that are typically attributed to Orexin A loss of function may be modified by concomitant NPTX2 down-regulation. Is NPTX2 an effector of sleep or simply a reporter of orexin-dependent SCRD? To address this question, we examined NPTX2 KO mice and found they retain Orexin expression in the brain and so provide an opportunity to examine the specific contribution of NPTX2 to SCRD. Our results reveal that NPTX2 KO mice exhibit a disrupted circadian onset time, coupled with increased activity during the sleep phase, suggesting difficulties in maintaining states. Sleep EEG indicates distinct temporal allocation shifts across vigilance states, characterized by reduced wake and increased NREM time. Evident sleep fragmentation manifests through alterations of event occurrences during Wake and NREM, notably during light transition periods, in conjunction with an increased frequency of sleep transitions in NPTX2 KO mice, particularly between Wake and NREM. EEG spectral analysis indicated significant shifts in power across various frequency bands in the wake, NREM, and REM states, suggestive of disrupted neuronal synchronicity. An intriguing observation is the diminished occurrence of sleep spindles, one of the earliest measures of human sleep disruption, in NPTX2 KO mice. These findings highlight the effector role of NPTX2 loss of function as an instigator of SCRD and a potential mediator of sleep disruption in aging.

neuroscience↗

bioRxiv2023

Stratigraphic distribution of ammonoids and other macrofossils from the upper Albian-lower Cenomanian interval in Putumayo, Colombia, northern South America: new data for mid-Cretaceous basin correlation

Despite the rich paleontological heritage of Colombia, in the equatorial Neotropics, one of the least explored regions in terms of its fossil record is the Putumayo region near Ecuador, largely due to its considerable ground cover, thick vegetation, rock weathering, geographic remoteness, and overall inaccessibility to well-exposed outcrops. This precludes detailed comparisons with neighboring basins, and thus the generation of more comprehensive biostratigraphic correlations for western northern South America and other paleobiogeographic regions, e.g., Mediterranean Tethys, northern Africa, Western Interior Basin. Here, we report 67 occurrences of mid- Cretaceous ammonoids and other macrofossils (e.g., bivalves, decapod crustaceans, fish remains, plant remains), from the middle Albian of the uppermost Caballos Formation and the upper Albian-lower Cenomanian of the lower Villeta Formation, collected in-situ from a stratigraphic section cropping out on the Mocoa-San Francisco road in the Department of Putumayo, Colombia. Among the ammonoid taxa recovered are several morphotypes assignable to ?Schloenbachia sp., cf. Engonoceras sp., Oxytropidoceras (Venezoliceras) sp., Oxytropidoceras (Laraiceras) sp., cf. Oxytropidoceras sp., Mortoniceras (Mortoniceras) cf. vespertinum, Mortoniceras (Mortoniceras) sp., Algericeras sp., Hysteroceras sp. 1, Hysteroceras sp. 2, cf, Hysteroceras sp., cf. Forbesiceras sp., Graysonites sp., Hamites sp., and two isolated aptychi. The occurrence of the ammonoid genera Oxytropidoceras, Mortoniceras, and Schloenbachia, suggest interconnection of the Putumayo Basin during the mid-Cretaceous with the Upper Magdalena Valley in Colombia and the Oriente Basin in Ecuador, which, together with the rest of the ammonoid assemblage, provide biostratigraphic data to define the upper Albian-lower Cenomanian in the basin and thus in northwestern South America.

paleontology↗

bioRxiv2023

Molecular and organizational diversity intersect to generate functional synaptic heterogeneity within and between excitatory neuronal subtypes

Synaptic heterogeneity is a hallmark of nervous systems that enables complex and adaptable communication in neural circuits. To understand circuit function, it is thus critical to determine the factors that contribute to the functional diversity of synapses. We investigated the contributions of voltage-gated calcium channel (VGCC) abundance, spatial organization, and subunit composition to synapse diversity among and between synapses formed by two closely related Drosophila glutamatergic motor neurons with distinct neurotransmitter release probabilities (Pr). Surprisingly, VGCC levels are highly predictive of heterogeneous Pr among individual synapses of either low- or high-Pr inputs, but not between inputs. We find that the same number of VGCCs are more densely organized at high-Pr synapses, consistent with tighter VGCC-synaptic vesicle coupling. We generated endogenously tagged lines to investigate VGCC subunits in vivo and found that the 2{delta}-3 subunit Straightjacket along with the CAST/ELKS active zone (AZ) protein Bruchpilot, both key regulators of VGCCs, are less abundant at high-Pr inputs, yet positively correlate with Pr among synapses formed by either input. Consistently, both Straightjacket and Bruchpilot levels are dynamically increased across AZs of both inputs when neurotransmitter release is potentiated to maintain stable communication following glutamate receptor inhibition. Together, these findings suggest a model in which VGCC and AZ protein abundance intersects with input-specific spatial and molecular organization to shape the functional diversity of synapses.

neuroscience↗

bioRxiv2022

Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function

Nervous system function relies on the formation and function of synaptic connections between neurons. Through a genetic screen in Drosophila for new conserved synaptic genes, we identified CG42261/Fid/ TRMT9B as a negative regulator of synaptogenesis. TRMT9B has been studied for its role as a tumor suppressor in multiple carcinomas and is one of two metazoan homologs of yeast tRNA methyltransferase 9 (Trm9), which methylates tRNA wobble uridines. Members of the expanded family of tRNA methyltransferases are increasingly being associated with neurological disorders and new biochemical functions. Interestingly, whereas Trm9 homolog ALKBH8/CG17807 is ubiquitously expressed, we find that TRMT9B is enriched in the nervous system, including at synapses. However, in the absence of animal models the role of TRMT9B in the nervous system has remained unknown. Here, we generated null alleles of TRMT9B and ALKBH8, and through liquid chromatography-mass spectrometry find that ALKBH8 is responsible for canonical tRNA wobble uridine methylation under basal conditions. In the nervous system, we find that TRMT9B negatively regulates synaptogenesis through a methyltransferase-dependent mechanism in agreement with our modeling studies. Finally, we find that neurotransmitter release is impaired in TRMT9B mutants. Our findings reveal a role for TRMT9B in regulating synapse formation and function, and highlight the importance of the expanded family of tRNA methyltransferases in the nervous system.

neuroscience↗

bioRxiv2022

Metadata preservation and stewardship for genomic data is possible, but must happen now

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species and population resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies of evolutionary biology, molecular ecology and conservation genetics produce large amounts of genome-scale genetic diversity data for wild populations. While open data policies have ensured an abundance of freely available genomic data stored in the databases of the International Nucleotide Sequence Database Collaboration (INSDC), only about 13% of current accessions have the associated spatial and temporal metadata in INSDC necessary to be reused in monitoring programs, macrogenetic studies, or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata in sources external to the INSDC and to test the hypothesis that these metadata decay with time. We also worked to remediate these missing metadata by extracting them, when present, from associated published papers, online repositories, and/or from direct communication with authors. Starting with 848 programmatically identified candidate datasets (INSDC BioProjects), we manually determined that 561 contained samples from wild populations. We successfully restored spatiotemporal metadata (locality name and/or geospatial coordinates and collection year) for 78% of these 561 datasets (N = 440 BioProjects comprising 45,105 individuals or BioSamples from 762 species in 17 phyla). We also quantified the availability of 33 additional categories of metadata in sources external to the INSDC. Information about associated publications and the type of habitat from which the samples were taken was the most easily found; information about sampling permits was the most challenging to locate. Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors discovered useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declines significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This observable metadata decay, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost forever.

bioinformatics↗

bioRxiv2021

miR-17~92 exerts stage-specific effects in adult V-SVZ neural stem cell lineages

In the adult mouse brain, neural stem cells (NSCs) in the ventricular-subventricular zone (V-SVZ) generate neurons and glia throughout life. microRNAs are important regulators of cell states, frequently acting in a stage- or context-dependent manner. Here, miRNA profiling of FACS-purified populations identified miR-17[~]92 as highly upregulated in activated NSCs and transit amplifying cells (TACs) in comparison to quiescent NSCs. Conditional deletion of miR-17[~]92 in NSCs reduced stem cell proliferation both in vitro and in vivo. In contrast, in TACs, miR-17[~]92 deletion caused a selective shift from neurogenic DLX2+ TACs towards oligodendrogenic OLIG2+ TACs, resulting in increased oligodendrogenesis to the corpus callosum. miR-17[~]92 deletion also decreased proliferation and maturation of intraventricular oligodendrocyte progenitor cells. Together, these findings reveal stage- and cell-type-specific functions of the miR-17[~]92 cluster within adult V-SVZ neural stem cell lineages.

neuroscience↗

bioRxiv2020

Evidence for a role of phenotypic mutations in virus adaptation

Viruses interact extensively with the host molecular machinery, but the underlying mechanisms are poorly understood. Bacteriophage T7 recruits the small protein thioredoxin of the E. coli host as an essential processivity factor for the viral DNA polymerase. We challenged the phage to propagate in a host in which thioredoxin had been extensively modified to hamper its recruitment. The virus adapted to the engineered host without losing the capability to propagate in the original host, but no genetic mutations were fixed in the thioredoxin binding domain of the viral DNA polymerase. Virus adaptation correlated with mutations in the viral RNA polymerase, supporting that promiscuous thioredoxin recruitment was enabled by phenotypic mutations caused by transcription errors. These results point to a hitherto unknown mechanism of virus adaptation that may play a role in crossspecies transmission. We propose that phenotypic mutations may generally contribute to the capability of viruses to evade antiviral strategies.

evolutionary biology↗

bioRxiv2019

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF phenotype

Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, we developed a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and derived a new standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. The GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers new opportunities for research focused on how the microbiota shapes host physiology in health and disease.

microbiology↗

bioRxiv2019

Release of stem cells from quiescence reveals multiple gliogenic domains in the adult brain

Quiescent neural stem cells (NSCs) in the adult ventricular-subventricular zone (V-SVZ) have a regional identity and undergo activation to generate neurons. The domains for gliogenesis are less explored. Here we show that Platelet-Derived Growth Factor Receptor beta (PDGFR{beta}) is expressed by adult V-SVZ NSCs that generate olfactory bulb interneurons and glia with slow baseline kinetics. Selective deletion of PDGFR{beta} in adult V-SVZ NSCs leads to their release from quiescence uncovering multiple domains in the septal wall for oligodendrocyte and astrocyte formation. Unexpectedly, we identify a novel intraventricular oligodendrocyte progenitor inside the brain ventricles. Together our findings reveal different NSC spatial domains for gliogenesis in the adult V-SVZ that are largely quiescent under homeostasis and may have key functions for brain plasticity.

neuroscience↗