Biology subjects

Prado, J.

Publications and source records attributed to Prado, J..

8 recordsLinked to original sources

bioRxiv2026

The Effects of Phosphorylation on the Structure and Function of Motif A, an Intrinsically Disordered Region within SIRT1

The NAD+ dependent deacetylase sirtuin-1 (SIRT1) is known to elicit cellular defenses against aging, cancer, and other aberrant pathologies. Previous studies have identified an intrinsically disordered region of SIRT1 comprised of N-terminal residues 1-52, herein referred to as motif A, which activates SIRT1 activity, likely through intramolecular interactions. Additionally, phosphorylation of N-terminal residues Ser27 and Ser47 has been shown to be important for regulating SIRT1 activity and stability. The lack of in vitro characterization of these effects hampers our further understanding of the role of motif A in SIRT1 regulation. In this study, we elucidate the role phosphorylation plays in motif As structure as well as its regulatory effects on SIRT1 activity against Ac-p65. We find that phosphomimetic mutation at Ser27 significantly increases the activation effect of motif A towards SIRT1. This result is supported by molecular dynamics simulations of the phosphomimetics, which reveal stabilization of different transient structures for motif A depending on whether Ser27 and Ser47 have been modified. A key finding suggested by this study is that phosphorylation of S27 appears to activate SIRT1 by causing motif A, which is intrinsically disordered in the WT, to fold into an ordered structure. This conclusion is based on both the experimental findings and simulation results. These findings contribute to our understanding of SIRT1 regulation, specifically the role played by phosphorylation within the N-terminal disordered region.

biochemistry↗

bioRxiv2025

A developmentally regulated long-range enhancer-promoter contact mediates human neural development

SOX2 is a core pluripotency factor in human embryonic stem cells (hESCs), but upon differentiation to the three germ layers, its expression is preserved selectively in neuroectoderm. The mechanisms regulating SOX2 transcription in distinct developmental stages remain incompletely understood. Here, we demonstrate that a distant enhancer 550 kb from the human SOX2 locus is selectively activated in neural stem cells (NSCs) and establishes long-range contact with the SOX2 gene. CRISPR-Cas9 excision of the enhancer has no effect in hESCs but reduces SOX2 transcription in NSCs and impairs neuroectodermal differentiation and forebrain specification in teratomas and cerebral organoids. CRISPR excision of a CTCF recognition motif adjacent to the enhancer does not affect enhancer activation in neuroectoderm but reduces chromatin looping and SOX2 transcription to partially reproduce phenotypes seen with enhancer deletion. Our findings indicate that the development of the human nervous system depends on a developmentally regulated long-range contact between a distant enhancer and the SOX2 locus.

developmental biology↗

bioRxiv2025

Arithmetic learning is associated with developmental increases in similarity between brain activity and artificial neural networks

The ability to learn simple arithmetic is often thought to rely on the associative nature of human memory, where repeated exposure to arithmetic problems strengthens the relations between operands and outcomes. This view is reminiscent of learning in large language artificial neural networks (ANNs), where training involves statistical associations between symbolic inputs and outputs. Based on this parallel, we hypothesized that brain activity during arithmetic problem-solving should be increasingly similar to ANN-derived representations with learning and development. We used fMRI to investigate the relation between brain activity during single-digit addition problem-solving and ANN features in 104 participants across four age groups (8-, 11-, 14-year-olds, and adults). Vertex-wise encoding models were used to predict brain activity using latent features extracted from pre-trained ANNs. Results revealed that the ANN-based model better predicted arithmetic-related activity in older than younger participants in a specific region of the left precentral sulcus. Prediction accuracy was higher for smaller than larger problems, consistent with the idea that associations between problems may decrease in strength with problem size. Furthermore, ANN prediction patterns aligned with a model in which each addition problem was increasingly represented separately with age. On the one hand, these findings may support the idea that, with learning and development, some neural representations of arithmetic problems become discretely organized in memory and increasingly resemble ANN-like processing. On the other hand, the lack of relation between the ANN-based model and activity in other brain regions suggests some degree of dissimilarity between arithmetic processing in humans and ANNs, suggesting the existence of additional mechanisms for simple arithmetic learning in humans.

neuroscience↗

bioRxiv2024

Transfer of IgG from Long COVID patients induces symptomology in mice

SARS-CoV-2 infections worldwide led to a surge in cases of Long COVID, a post-infectious syndrome. It has been hypothesized that autoantibodies play a crucial role in the development of Long COVID and other syndromes, such as fibromyalgia and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). In this study, we tested this hypothesis by passively transferring total IgG from Long COVID patients to mice. Using Glial Fibrillary Acidic Protein (GFAP) and type-I interferon expression, we stratified patients into three Long COVID subgroups, each with unique plasma proteome signatures. Remarkably, IgG transfer from the two subgroups, which are characterized by higher plasma levels of neuronal proteins and leukocyte activation markers, induced pronounced and persistent sensory hypersensitivity with distinct kinetics. Conversely, IgG transfer from the third subgroup, which are characterized by enriched skeletal and cardiac muscle proteome profiles, reduced locomotor activity in mice without affecting their motor coordination. These findings demonstrate that transfer of IgG from Long COVID patients to mice replicates disease symptoms, underscoring IgGs causative role in Long COVID pathogenesis. This work proposes a murine model that mirrors Long COVIDs pathophysiological mechanisms, which may be used as a tool for screening and developing targeted therapeutics.

immunology↗

bioRxiv2022

Chromatin Remodeling in Patient-Derived Colorectal Cancer Models

Patient-Derived Organoids (PDO) and Xenografts (PDX) are the current gold standards for patient derived models of cancer (PDMC). Nevertheless, how patient tumor cells evolve in these models and the impact on drug response remains unclear. Herein, we compared the transcriptomic and chromatin accessibility landscapes of six matched sets of colorectal cancer (CRC) PDO, PDX, PDO-derived PDX (PDOX), and original patient tumors (PT) and discovered two major remodeling axes. The first axis delineates PDX and PDO from PT, and the second axis distinguishes PDX and PDO. PDOX were more similar to PDX than they were to PDO, indicating that the growth environment is a driving force for chromatin adaptation. Using bivariate genomic footprinting analysis, we identified transcription factors (TF) that differentially bind to open chromatins between matched PDO and PDOX. Among them, KLF14 and EGR2 footprints were enriched in all six PDOX relative to matched PDO, and silencing of KLF14 or EGR2 promoted tumor growth. Furthermore, EPHA4, a shared downstream target gene of KLF14 and EGR2, altered tumor sensitivity to MEK inhibitor treatment. Altogether, patient-derived CRC cells undergo both common and distinct chromatin remodeling in PDO and PDX/PDOX, driven largely by their respective microenvironments, which results in differences in growth and drug sensitivity and needs to be taken into consideration when interpreting their ability to predict clinical outcome.

cancer biology↗

bioRxiv2022

Peer presence elicits task-independent changes within and beyond the mentalizing network across children and adults

There is ample behavioral evidence that others mere presence can affect any behavior in human and non-human animals, generally facilitating the expression of mastered responses while impairing the acquisition of novel ones. Much less is known about i) how the brain orchestrates the modulation of such a wide array of behaviors by others presence and ii) when these neural underpinnings mature during development. To address these issues, fMRI data were collected in children and adults alternately observed and unobserved by a familiar peer. Subjects performed two tasks. One, numerosity comparison, depends on number-processing brain areas, the other, phonological comparison, on language-processing areas. Consistently with previous behavioral findings, peer observation facilitated both tasks, and childrens improvement was comparable to adults. Regarding brain activation, we found virtually no evidence of observation-driven changes within the number- or language-related areas specific to each task. Rather, we observed the same task-independent changes for both numerosity and phonological comparisons. This unique neural signature encompassed a large brain network of domain-general areas involved in social cognition, especially mentalizing, attention, and reward. It was also largely shared by children and adults. The one exception was childrens right temporoparietal junction, which failed to show the observation- driven lesser deactivation seen in adults. These findings indicate that social facilitation of some human education-related skills is i) primarily orchestrated by domain-general brain networks, rather than by task-selective substrates, and ii) relatively mature early in the course of education, thus having a protracted impact on academic achievements that may have heretofore been underestimated. HighlightO_LIBasic math and reading skills were measured in children and adults. C_LIO_LIParticipants were alternately observed and unobserved by a familiar peer. C_LIO_LIBehavior showed that children were as facilitated by peer observation as adults. C_LIO_LIfMRI data showed task-independent, observation-driven changes in mentalizing, attention, and reward brain regions. C_LIO_LIAll adults neural changes were also found in children, except one located in right temporo- parietal junction. C_LI

neuroscience↗

bioRxiv2020

Macrophages transfer mitochondria to neurons to resolve inflammatory pain

The current paradigm is that inflammatory pain passively resolves following the cessation of inflammation. Yet, in a substantial proportion of patients with inflammatory diseases, resolution of inflammation is not sufficient to resolve pain, resulting in chronic pain. Mechanistic insight how inflammatory pain is resolved is lacking. Here we show that macrophages actively control resolution of inflammatory pain remotely from the site of inflammation by transferring mitochondria to sensory neurons. During resolution of inflammatory pain in mice, M2-like macrophages infiltrate the dorsal root ganglia that contain the somata of sensory neurons, concurrent with the recovery of oxidative phosphorylation in sensory neurons. The resolution of pain and the transfer of mitochondria requires expression of CD200 Receptor (CD200R) on macrophages and the non-canonical CD200R-ligand iSec1 on sensory neurons. Our data reveal a novel mechanism for active resolution of inflammatory pain. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/940445v3_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1048f6org.highwire.dtl.DTLVardef@1262306org.highwire.dtl.DTLVardef@c58261org.highwire.dtl.DTLVardef@f2d4a0_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2019

Looking for a reference for large datasets: relative reliability of visual and automatic sleep scoring

Study ObjectivesNew challenges in sleep science require to describe fine grain phenomena or to deal with large datasets. Beside the human resource challenge of scoring huge datasets, the inter- and intra-expert variability may also reduce the sensitivity of such studies. Searching for a way to disentangle the variability induced by the scoring method from the actual variability in the data, visual and automatic sleep scorings of healthy individuals were examined.\n\nMethodsA first dataset (DS1, 4 recordings) scored by 6 experts plus an autoscoring algorithm was used to characterize inter-scoring variability. A second dataset (DS2, 88 recordings) scored a few weeks later was used to investigate intra-expert variability. Percentage agreements and Congers kappa were derived from epoch-by-epoch comparisons on pairwise, consensus and majority scorings.\n\nResultsOn DS1 the number of epochs of agreement decreased when the number of expert increased, in both majority and consensus scoring, where agreement ranged from 86% (pairwise) to 69% (all experts). Adding autoscoring to visual scorings changed the kappa value from 0.81 to 0.79. Agreement between expert consensus and autoscoring was 93%. On DS2 intra-expert variability was evidenced by the kappa systematic decrease between autoscoring and each single expert between datasets (0.75 to 0.70).\n\nConclusionsVisual scoring induces inter- and intra-expert variability, which is difficult to address especially in big data studies. When proven to be reliable and if perfectly reproducible, autoscoring methods can cope with intra-scorer variability making them a sensible option when dealing with large datasets.\n\nStatement of SignificanceWe confirmed and extended previous findings highlighting the intra- and inter-expert variability in visual sleep scoring. On large datasets those variability issues cannot be completely addressed by neither practical nor statistical solutions such as group training, majority or consensus scoring.\n\nWhen an automated scoring method can be proven to be as reasonably imperfect as visual scoring but perfectly reproducible, it can serve as a reliable scoring reference for sleep studies.

neuroscience↗