Biology subjects

Valdes, J.

Publications and source records attributed to Valdes, J..

8 recordsLinked to original sources

bioRxiv2026

Hunger and sleep recruit distinct brain systems to form spatial memory

By demonstrating that hunger consolidates spatial memory via a non-hippocampal mechanism that critically involves the retrosplenial cortex, we identify a mode of memory formation that is distinct from well-known hippocampus-dependent memory formation during sleep. Food-deprived rats encoded object locations and, during a subsequent 2-h consolidation phase, either received food and slept (Sleep-Fed) or stayed awake (Wake-Fed), or remained hungry and stayed awake (Wake-Hungry). At later retrieval testing, both Wake-Hungry and Sleep-Fed rats exhibited robust spatial memory, whereas Wake-Fed rats did not. Blocking neuropeptide-Y (NPY) signaling during the consolidation phase abolished hunger-consolidated memory. Unlike sleep-dependent consolidation, hunger-consolidated memory did not require the hippocampus during consolidation or retrieval, and not even during encoding. In contrast, inhibiting retrosplenial cortex during retrieval abolished hunger-consolidated memory but spared memory formed during sleep. Thus, recruitment of brain systems to form spatial memory is tuned to specific brain states, and fundamentally differs between sleep and hunger.

neuroscience↗

bioRxiv2025

Seeing the forest and the trees: a workflow for automatic acquisition of ultra-high resolution drone photos of tropical forest canopies to support botanical and ecological studies

Tropical forest canopies contain many tree and liana species, and foliar and reproductive characteristics useful for taxonomic identification are often difficult to see from the forest floor. As such, taxonomic identification often becomes a bottleneck in tropical forest inventories. Here we present a drone-based workflow to automatically acquire large volumes of close-up, ultra-high resolution photos of selected tree crowns (or specific locations over the canopy) to support tropical botanical and ecological studies (https://youtu.be/80goMEifpc4). Our workflow is built around the small, easy-to-use DJI Mavic 3 Enterprise (M3E) drone, which is equipped with a wide-angle and a telephoto camera. On day one, the pilot maps a forest area of up to [~]200 ha with the wide-angle camera to generate a high-resolution digital surface model (DSM) and orthomosaic using structure-from-motion (SfM) photogrammetry. On subsequent days, the pilot acquires close-up photos with the telephoto camera from up to 300 selected canopy trees per day. These close-up photos are acquired from 6 m above the canopy and contain a high level of visual detail that allows botanists to reliably identify many tree and liana species. The photos are geolocated with survey-grade accuracy using RTK GNSS, thus facilitating spatial co-registration with other data sources, including the photogrammetry products. The primary operational challenge of our workflow is the need to maintain RTK corrections with the drone to ensure that close-up photos are acquired exactly at the predefined locations. The maximum operational range we achieved was 3 km, which would allow the pilot to reach any tree within a [~]2800 ha area from the take-off point. Although our workflow was developed to support taxonomic identification of tropical trees and lianas, it could be extended to any other forest or vegetation type to support botanical, phenological, and ecological studies. We provide harpia, an open-source Python library to program these automatic close-up photo missions with the M3E drone (https://github.com/traitlab/harpia). Data/code for peer review statementWe provide harpia, an open-source Python library to program these automatic close-up photo missions (https://github.com/traitlab/harpia). Drone imagery and labelled close-up photo data are not yet publicly available because they were acquired with the goal of publishing benchmark machine learning datasets and models for tree and liana species classification and prior publication of the data would jeopardize this future publication.

ecology↗

bioRxiv2025

Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of de novo Polycomb recruitment

Polycomb domains safeguard cell identity by maintaining lineage-specific chromatin states enriched in repressive histone modifications, preserving the epigenetic memory of cell lineages. While Polycomb Repressive Complex 2 (PRC2) can re-establish its occupancy after perturbation, the mechanisms that guide de novo Polycomb recruitment remain unclear. To address this, we engineered an auxin-inducible degradation system to reversibly deplete and reintroduce the endogenous PRC2 core subunit Suz12 in mouse embryonic stem cells (mESCs). Genome-wide profiling at an early recovery time point revealed [~]1,100 PRC2 nucleation sites, characterized by rapid Suz12 and histone H3K27me3 re-accumulation with strong signal, with minimal impact on gene expression. These sites were significantly enriched at bivalent promoters, coinciding with unmethylated CpG islands and chromatin states associated with developmental regulation, and were largely conserved in differentiated cells. Motif analysis identified G/C-rich DNA sequences associated with E2F and zinc-finger proteins, alongside strong co-occupancy with MTF2 and JARID2, two PRC2 cofactors previously implicated in Polycomb targeting. Notably, a subset of nucleation sites overlapped with long-range chromatin interaction anchors in histone H3K27me3 HiChIP datasets. These findings reveal that PRC2 de novo nucleation sites are associated with a combination of chromatin states, DNA sequence features, cofactor co-occupancy and spatial genome organization, suggesting that epigenetic memory can be re-established through defined genomic and chromatin features. Author summaryPolycomb group proteins are key epigenetic regulators that silence gene expression by establishing and dispersing repressive chromatin domains marked by histone modifications such as histone H3K27me3 and H2AK119ub1 and are critical for defining cell identity. During differentiation, Polycomb domains are dynamically redistributed, implying a mechanism for de novo targeting to specific loci. How the Polycomb Repressive Complex 2 (PRC2) is initially recruited to these nucleation sites and which features stabilize its binding remain poorly understood. To explore this, we studied the characteristics of the de novo recruitment sites of PRC2 in mouse embryonic stem cells (mESCs) using an auxin-inducible degradation (AID) system targeting PRC2 to deplete and reintroduce the core subunit Suz12. We identified recruitment sites after complete clearance of the histone H3K27me3 through ChIP-seq at a very early time point after Suz12 reintroduction. Most nucleation sites were located at bivalent promoters of developmental genes and correlated with unmethylated CpG islands. Motif analysis revealed over-represented sequences and accessory partners such as MTF2 and JARID2, along with long-range chromatin interactions. These nucleation sites were also conserved in differentiated cells, highlighting their potential role in developmental regulation. Our study provides insight into how Polycomb domains are established and how epigenetic memory is maintained in stem cells.

molecular biology↗

bioRxiv2025

Phenotypic and transcriptomic similarity between the N2 Ancestral and a Tropical wild isolate of C. elegans reveals divergence from the reference Bristol strain

In recent years, the scientific community has increasingly recognized the importance of incorporating ecologically relevant perspectives into laboratory research. In the case of the free-living nematode Caenorhabditis elegans, numerous studies have documented the domestication of the N2 Bristol strain (isolated in 1951). This has led to a growing interest in recently isolated wild strains from diverse latitudes, which offer insights into natural variation evolution and life-history traits. Here, we compared a recently isolated tropical strain from Mexico City to the N2 Bristol strain. To contextualize laboratory adaptation, we also included the N2 Ancestral strain, a cryopreserved lineage from 1969 with minimal generational drift. Phenotypic assays revealed that, under standard laboratory conditions, the Mexican strain exhibited reduced lifespan and fertility, but enhanced resistance to Pseudomonas aeruginosa, whereas the Ancestral strain showed higher oxidative stress tolerance but reduced thermotolerance. RNA-seq analyses showed that transcriptomic profiles of the Mexican and Ancestral strains were more similar to each other than to the N2 Bristol, suggesting that long-term domestication has driven regulatory divergence. Differential gene expression analyses identified strain-specific signatures in stress, immune and collagen-related pathways. Under heat stress, transcriptional profiling revealed that only a small set of canonical heat shock genes was commonly upregulated across the three strains, yet wild strains showed more dynamic regulation, while N2 Bristol exhibited a distinct, possible preconditioned response. These findings reveal phenotypic trade-offs and regulatory divergence shaped by natural versus laboratory environments, and underscore evolutionary dynamics and adaptive potential of C. elegans in response to distinct ecological histories.

evolutionary biology↗

bioRxiv2024

Origin, Trophic Transfer And Recycling Of Particulate Organic Matter In The Waters Of Two Upwelling Bays Of Humboldt Current System: Insights From Compound-Specific Isotopic Compositions Of Amino Acids

Particulate organic matter (POM) is considered the primary source of N and C in the ocean. In pelagic marine environments, POM consists of algae and detrital nitrogen, with amino acids representing the largest chemical fraction. Currently, measurements of the isotopic distributions of N atoms in amino acids are considered powerful tools for exploring and determining the metabolic sources involved in the synthesis and degradation of organic matter. In this study, we measured the {delta}15N of amino acid signatures ({delta}15N-AA) in suspended and sinking POM collected from two upwelling bays in northern Chile, to examine isotopic enrichment patterns and gain insights into the origins, trophic transfer, and heterotrophic reworking of this organic fraction. At Mejillones Bay, the {delta}15N-AA values of suspended POM ranged from 5 {per thousand} to 27 {per thousand}, while at Antofagasta Bay, these values oscillated between 9 {per thousand} and 24 {per thousand}. The sinking POM collected from sediment traps exhibited values and isotopic fractionation patterns similar to those observed in the deeper layers of the water columns in both bays. The enrichment patterns of {delta}15N-phenylalanine and {delta}15N-NO - demonstrated the autochthonous character of the POM and its predominantly marine origin at both bays. The parameters trophic transfer ({Delta}Tr) and heterotrophic reworking ({Sigma}V) indicated that the heterotrophic recycling of POM occurs more intensively at through the oxyclines. Furthermore, these parameters revealed an enhanced trophic transfer magnitude and higher heterotrophic re-synthesis of POM in the waters of Mejillones Bay, resulting in a lower flux of exported POM than that observed in Antofagasta Bay. These differences highlight the spatial heterogeneous nature of organic matter transfer and reworking processes in this upwelling system.

ecology↗

bioRxiv2019

In your phase! Neural phase synchronization underlies visual imagery of faces

Mental imagery is the process through which we retrieve and recombine information from our memory to elicit the subjective impression of "seeing with the minds eye". In the social domain, we imagine other individuals while recalling our encounters with them or modelling alternative social interactions in future. Many studies using imaging and neurophysiological techniques have shown several similarities in brain activity between visual imagery and visual perception, and have identified frontoparietal, occipital and temporal neural components of visual imagery. However, the neural connectivity between these regions during visual imagery of socially relevant stimuli have not been studied. Here we used electroencephalography to investigate neural connectivity and its dynamics between frontal, parietal, occipital and temporal electrodes during visual imagery of faces. We found that voluntary visual imagery of faces is associated with long-range phase synchronisation in the gamma frequency range between frontoparietal electrode pairs and between occipitoparietal electrode pairs. In contrast, no effect of imagery was observed in the connectivity between occipitotemporal electrode pairs. Gamma range synchronisation between occipitoparietal electrode pairs predicted subjective ratings of the contour definition of imagined faces. Furthermore, we found that visual imagery of faces is associated with an increase of short-range frontal synchronisation in the theta frequency range, which temporally preceded the long-range increase in the gamma synchronisation. We speculate that the local frontal synchrony in the theta frequency range might be associated with an effortful top-down mnemonic reactivation of faces. In contrast, the long-range connectivity in the gamma frequency range along the fronto-parieto-occipital axis might be related to the endogenous binding and subjective clarity of facial visual features.

neuroscience↗

bioRxiv2019

Effects of Topical Antimicrobial Formulations on Pseudomonas aeruginosa Biofilm in an In vivo Porcine Burn Wound Model

Silver has been incorporated into a variety of wound dressings and topical agents to prevent and combat wound infections. Pseudomonas aeruginosa is a common cause of burn wound infections and well-known biofilm producer. The objective of this study was to evaluate the effects of a panel of wound dressings containing different silver formulations on P. aeruginosa biofilms using an in vivo porcine burn wound model. Second-degree burns were created on the skin of specific pathogen-free pigs (n = 3) and inoculated with 2.14 x 105 cfu P. aeruginosa per wound. Biofilms were allowed to develop for 24 h, and then each wound was treated with one of 6 treatments: silver oxynitrate dressing (OXY), silver oxynitrate powder (POWD), nanocrystalline silver dressing (NANO), silver chloride dressing (AGCL), silver sulfadiazine (SSD), or a negative control polyurethane film with no silver-based formulation (NEG). Wounds were cultured at D3 post-infection (n = 3 per pig per treatment) and at D6 post-infection (n = 3 per pig per treatment) for quantification of bacteria. On D6, biopsies (n = 3 per treatment) were taken from POWD, SSD, and NEG wounds and wound healing progress was evaluated histologically. At the time of treatment initiation, 24 h post-infection, 8.71 log cfu P. aeruginosa were present in burn wounds. On D3 and D6, all treatments significantly reduced bacterial counts in wounds as compared to NEG, but POWD caused an approximately 7-log reduction in bacterial counts on both days and was the only treatment to reduce the bacterial counts to below the threshold for detecting bacteria. The OXY, NANO, and SSD treatments had similar reductions in bacterial recovery on D3 and D6 of approximately 2.5-4 log. The histological healing metrics of reepithelialization percentage, epithelial thickness, white cell infiltration, angiogenesis, and granulation tissue formation were similar among wounds from POWD, SSD, and NEG groups at 6 days post-infection. Silver oxynitrate powder reduced P. aeruginosa growth in burn wounds more effectively than other silver-based dressings but did not impact wound healing.

microbiology↗

bioRxiv2019

FRONTAL MIDLINE THETA REFLECTS COGNITIVE CONTROL DURING PLANNING.

Neural correlates of cognitive planning are not understood well at present. Behavioral paradigms targeting this function are a current challenge in cognitive neuroscience. We recorded EEG activity while subjects were performing a novel behavioral paradigm that evaluates cognitive planning function. Participants showed longer reaction times and decreased accuracy during the planning condition compared to the control condition, suggesting that the planning condition is more time consuming, therefore reflecting higher cognitive demand. Moreover, cognitive planning induced a frontal midline theta (FM{theta}) frequency band originating in prefrontal cortex (PFC) as shown in previous cognitive control studies. When subjects began planning, there was a progressive and sustained increase in FM{theta} starting after 500 milliseconds (ms) of planning. Hence, we characterized for first time, both spatial and temporal FM{theta} dynamics of cognitive planning as a marker of cognitive control function.

neuroscience↗