Biology subjects

Fuentes, A.

Publications and source records attributed to Fuentes, A..

12 recordsLinked to original sources

bioRxiv2026

Subacute and Chronic Cognitive and Cerebrovascular Functional Consequences of Mild Traumatic Brain Injury in Rats

Traumatic brain injury (TBI) is the main cause of death and disability in the United States in people younger than 35 years old and is a common cause of wartime injuries. Mild TBI (mTBI) is a predisposing factor for later development of dementia and cerebrovascular disease. Aerobic exercise was reported to improve cognitive function in chronic TBI through improved vascular function. The aims of the study are to characterize and correlate the subacute (10 weeks) and chronic (12 months) cognitive and cerebrovascular functional impairment following mTBI and evaluate the modulating effect of exercise early or late following mTBI on these changes. Sprague-Dawley rats received midline fluid percussion injury or sham procedure and followed for 10 weeks or 12 months with a subgroup of mTBI rats undergoing 5-week treadmill aerobic exercise 2 weeks (early) or 10 months (late) post-injury for 6 weeks. Cognitive function was assessed using novel object recognition (NOR) and novel object location (NOL) tests. Regional cerebral blood volume (CBV) and cerebrovascular reactivity following hypercapneic stimulation (CVR) using contrast magnetic resonance imaging (MRI) and ex vivo pial artery vasoreactivity to intraluminal pressure, angiotensin II and diethylenetriamine NONOate (DETA NONOate) were measured. There was no difference in NOR or NOL at 10 weeks between mTBI and sham. NOR, but not NOL, was reduced in mTBI rats at 12 months. CBV at 10 weeks was higher in the primary somatosensory trunk cortex (trunk) and dentate gyrus regions in mTBI, but not at 12 months. CVR was lower in the trunk region of mTBI rats at 12 months. Compared to sham response at 10 weeks, there was impaired arterial constriction response to 90 mm Hg intraluminal pressure in mTBI rats at 10 weeks and in sham and mTBI rats at 12 months, with no difference seen in response to angiotensin II or DETA-NONOate exposure. There was no correlation between cognitive and vascular outcomes at 10 weeks or 12 months. Early or late exercise did not affect 12-month cognitive or vascular function following mTBI. The study showed chronic impairment in short-term memory cognitive function, regional cerebrovascular reactivity and early onset of impaired cerebrovascular myogenic response in rats subjected to mTBI. The findings of persistent cognitive and cerebrovascular impairment in this animal model enhance our understanding of the long-term consequence of mTBI.

neuroscience↗

bioRxiv2026

Life-cycle trajectory inference links temperature-gated progenitors to reproductive fate

Temperature shapes reproductive strategies across animals, yet how individuals switch between sexual and asexual reproduction remains unknown. We establish the planarian Phagocata morgani as a model for temperature-dependent reproductive plasticity and adapt multiplexed single-cell transcriptomics to profile >1 million nuclei from >300 animals across body sizes and temperatures. Leveraging individual variation in cell composition, we reconstruct an organism-wide trajectory that bifurcates toward alternative reproductive fates. Temperature extremes constrain worms to one fate, whereas intermediate conditions permit probabilistic commitment to either. At the bifurcation, temperature gates a stem cell pool: warmth suppresses differentiation and promotes progenitor accumulation, whereas cold transcriptionally activates this pool for de novo sexual organogenesis. These findings reveal how environmental inputs act on stem cells to couple body size, temperature, and reproductive fate.

Developmental Biology↗

bioRxiv2025

Setting priorities for the acquisition of primary plant occurrence data

AimEffective implementation of the Global Biodiversity Framework and Global Strategy for Plant Conservation depends on accurate species distribution data. Current vascular plant distribution data, while crucial for understanding terrestrial ecosystems, is often sparse and biased and requires significant expansion. This study developed a scalable approach to prioritize areas for plant occurrence data acquisition, adaptable to national priorities and providing a framework for botanical institutions to coordinate efforts and allocate resources. LocationGlobal. MethodsUsing a Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) analysis, we prioritized areas based on: (a) ecosystem service value; (b) floristic value threatened by climate or land-use change; and (c) uncertainty in species richness estimates, stratified by biome and region. Regional prioritization maps for Africa & Madagascar; East, South and Southeast Asia; Siberia and the Russian Far East; South America; and North & Central America were reviewed by botanical experts for validation. Scalability was assessed by comparing regional and global analyses. ResultsData-driven priority maps, divided into tree-dominated and grassland/deforested areas, largely received expert support. High similarity between global and regional maps demonstrated scalability. Main conclusionsOur approach provides a framework for supporting national implementation of the Global Biodiversity Framework. Variables and their weights can be tailored to national or local needs. The methods flexibility and adaptability extend to other taxonomic groups and objectives, such as protected area selection By prioritizing data acquisition, whether field-based or digital, this research promotes the efficient use of resources. A key advantage of this approach is its capacity to systematically translate expert opinion into explicit and quantitative criteria, which in turn facilitates clear communication with policymakers and funders.

plant biology↗

bioRxiv2025

Phage intervention improves colitis and response to corticosteroids by attenuating virulence of Crohn's disease-associated bacteria

Adherent-invasive Escherichia coli (AIEC) exhibit proinflammatory properties and have been implicated in the pathogenesis of Crohns disease (CD), a form of inflammatory bowel disease (IBD). Antibiotic use in CD lacks specificity and may worsen microbiome disruption, prompting interest in bacteriophages (phages) for targeted microbiome editing. Here, we identified HER259, a phage active against the clinical AIEC strain NRG857c. Using gnotobiotic models of AIEC-driven colitis, we show that HER259 attenuates AIEC virulence, including suppression of the FimH adhesin through inversion of the fimS promoter to its off orientation. Withdrawal of HER259 treatment leads to reversion of the fimS promoter and reactivated colitis in mice. HER259 phage also enhances the therapeutic effect of sub-therapeutic budesonide, independent of microbial drug metabolism. These findings support targeted phage therapy as an adjunct treatment approach in IBD, demonstrating modulation of bacterial virulence and improved response to conventional treatments which may reduce drug-related side effects. One Sentence SummaryBacteriophage HER259 improves colitis severity mediated by Crohns disease Escherichia coli NRG857c, and increases efficacy of budesonide.

microbiology↗

bioRxiv2024

Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing

Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor the incorporation of non-canonical bases in genome-resolved metagenomic datasets and elucidate the replication patterns of both bacteria and phages. This technology enables the simultaneous reconstruction of both prokaryotic and viral genomes (alongside genomics downstream analyses like metabolic predictions), in addition to providing information regarding their replication in enrichment cultures. By spiking the base analog 5-bromo-2-deoxyuridine (BrdU) into activated sludge microcosms, we determined that 114 of the 118 high-quality genomes recovered were actively replicating in enrichment cultures from activated sludge and identified both slow (low BrdU incorporation and change in abundance) and rapidly replicating organisms (high BrdU incorporation and change in abundance). Some of the genomes detected exhibited regions rich in BrdU that were predicted to represent prophages in their lytic cycle. Ultimately, this novel means of monitoring the replication responses of microbes, and deciphering their genomes and active mobile genetic elements will advance and empower strategies aimed at isolating previously uncultivated microbes in pure culture.

microbiology↗

bioRxiv2023

Molecular and phylogenetic characterization of the monkeypox outbreak in the South of Spain

Until the May 2022 Monkeypox outbreak, which spread rapidly to many non-endemic countries, the virus was considered a viral zoonosis limited to some African countries. The Andalusian circuit of genomic surveillance was rapidly applied to characterize the Monkeypox outbreak in the South of Spain. Whole genome sequencing was used to obtain the genomic profiles of samples collected across the south of Spain, representative of all the provinces of Andalusia. Phylogenetic analysis was used to study the relationship of the isolates and the available sequences of the 2022 outbreak. Whole genome sequencing of a total of 160 monkeypox viruses from the different provinces that reported cases were obtained. Interestingly, we report the sequences of monkeypox viruses obtained from two patients who died. While one of the isolates bore no noteworthy mutations that explain a potential heightened virulence, in another patient the second consecutive genome sequence, performed after the administration of tecovirimat, uncovered a mutation within the A0A7H0DN30 gene, known to be a prime target for tecovirimat in its Vaccinia counterpart. In general, a low number of mutations were observed in the sequences reported, which were very similar to the reference of the 2022 outbreak (OX044336), as expected from a DNA virus. The samples likely correspond to several introductions of the circulating monkeypox viruses from the last outbreak. The virus sequenced from one of the two patients that died presented a mutation in a gene that bears potential connections to drug resistance. This mutation was absent in the initial sequencing prior to treatment.

microbiology↗

bioRxiv2023

Evidence for deliberate burial of the dead by Homo naledi

In this study we describe new results of excavations in the Dinaledi Subsystem of the Rising Star cave system, South Africa. In two areas within the Hill Antechamber and the Dinaledi Chamber this work uncovered concentrations of abundant Homo naledi fossils including articulated, matrix-supported skeletal regions consistent with rapid covering by sediment prior to the decomposition of soft tissue. We additionally re-examine the spatial positioning of skeletal material and associated sediments within the Puzzle Box area, from which abundant H. naledi remains representing a minimum of six individuals were recovered in 2013 and 2014. Multiple lines of evidence exclude the hypothesis that skeletal remains from these three areas come from bodies that decomposed on the floor of the chamber or within a shallow depression prior to burial by sediments. The spatial positioning of skeletal material, the topography of the subsystem, and observations on sediments within and surrounding features exclude the hypothesis that rapid burial by sediment was a result of gravity-driven slumping or spontaneous movement of sediments. We present a minimal hypothesis of hominin cultural burial and test the evidence from all three areas, finding that this hypothesis is most compatible with the pattern of evidence. These results suggest that mortuary behavior including cultural burial was part of the repertoire of Homo naledi.

paleontology↗

bioRxiv2023

241,000 to 335,000 Years Old Rock Engravings Made by Homo naledi in the Rising Star Cave system, South Africa.

The production of painted, etched or engraved designs on cave walls or other surfaces is recognized as a major cognitive step in human evolution. Such intentional designs, which are widely interpreted as signifying, recording, and transmitting information in a durable manner were once considered exclusive to Late Pleistocene Homo sapiens. Here we present observations of what appear to be engraved abstract patterns and shapes within the Dinaledi Subsystem of the Rising Star cave system in South Africa, incised into the dolomitic limestone walls of the cave. The markings described here are found on a pillar in the Hill Antechamber that extends into the natural fissure corridor that links the two chambers and we associate them with H. naledi. They include deeply impressed lines, cross-hatchings, percussion marks, and other geometric shapes on flat wall surfaces and in and around existing cracks and grooves in the dolomitic limestone walls, found in one specific location of the Dinaledi Subsystem. Remains of multiple Homo naledi are found in this part of the cave system and evidence mortuary behaviour appears in both the Dinaledi Chamber and adjacent Hill Antechamber dated to between 241 and 335 ka (Dirks et al., 2017; Robbins et al., 2021, Berger et al, 2025).

evolutionary biology↗

bioRxiv2023

Burials and engravings in a small-brained hominin, Homo naledi, from the late Pleistocene: contexts and evolutionary implications

Explorations in the Dinaledi Subsystem of the Rising Star cave system have yielded some of the earliest evidence of a mortuary practice in hominins. Because the evidence is attributable to the small-brained Homo naledi, these analyses call into question several assumptions about behavioral and cognitive evolution in Pleistocene hominins. The evidence from the Dinaledi Subsystem, and at other locations across the Rising Star cave system may widen the phylogenetic breadth of mortuary, and possibly funerary, behaviors. These discoveries may also associate the creation of meaning making and increased behavioral complexity with a small-brained hominin species, challenging certain assertions about the role of encephalization and cognition in hominin and human evolution. We suggest that the hominin socio-cognitive niche is more diverse than previously thought. If true, technological, meaning-making activities, and cognitive advances in human evolution are not associated solely with the evolution of larger brained members of the genus Homo. One-Sentence SummaryEvidence for complex behaviors associated with a small-brained hominin suggest that large brains are not solely responsible for the manifestation of human-like behavioral complexity.

evolutionary biology↗

bioRxiv2022

Chronic Cognitive and Cerebrovascular Function Following Mild Traumatic Brain Injury in Rats

Severe traumatic brain injury results in cognitive dysfunction in part due to vascular perturbations. In contrast, the long-term vasculo-cognitive pathophysiology of mild TBI (mTBI) remains unknown. We evaluated mTBI effects on chronic cognitive and cerebrovascular function and assessed their interrelationships. Sprague-Dawley rats received midline fluid percussion injury (N=20) or sham (N=21). Cognitive function was assessed (3- and 6-month novel object recognition (NOR), novel object location (NOL) and temporal order object recognition (TOR)). 6-month cerebral blood flow (CBF) and blood volume (CBV) using contrast MRI and ex vivo pial artery endothelial and smooth muscle-dependent function were measured. mTBI rats showed impaired NOR, with similar (non-significant) trends in NOL/TOR. Regional CBF and CBV were similar in sham and mTBI. NOR correlated with CBF in lateral hippocampus, medial hippocampus and primary somatosensory barrel cortex while inversely correlating with arterial smooth muscle-dependent dilation. 6-month baseline endothelial and smooth muscle-dependent arterial function were similar among mTBI and sham, but post-angiotensin II stimulation, mTBI showed no change in smooth muscle-dependent dilation from baseline response, unlike the reduction in sham. mTBI led to chronic cognitive dysfunction and altered angiotensin II-stimulated smooth muscle-dependent vasoreactivity, a paradigm that could advance understanding of the long-term sequelae of human mild TBI.

neuroscience↗

bioRxiv2019

Bacterially produced GABA protects neurons from degeneration

Caenorhabditis elegans and its cognate bacterial diet comprise a reliable, widespread model to study diet and microbiota effects on host physiology. Nonetheless, how diet influences the rate at which neurons die remains largely unknown. A number of models have been used in C. elegans as surrogates for neurodegeneration. One of these is a C. elegans strain expressing a neurotoxic allele of the MEC-4(d) DEG/ENaC channel which causes the progressive degeneration of the touch receptor neurons (TRNs). Using such model, this study evaluated the effect of various dietary bacteria on neurodegeneration dynamics. While degeneration of TRNs was steadily carried and completed at adulthood in the strain routinely used for C. elegans maintenance Escherichia coli OP50, it was significantly reduced in environmental and other laboratory bacterial strains. Strikingly, neuroprotection reached more than 40% in the E. coli HT115 strain. HT115 protection was long lasting well into old age of animals and not restricted to the TRNs. Small amounts of HT115 on OP50 bacteria as well as UV-killed HT115 were still sufficient to produce neuroprotection. Early growth of worms in HT115 protected neurons from degeneration during later growth in OP50. HT115 diet promoted the nuclear translocation of the DAF-16/FOXO transcription factor, a phenomenon previously reported to underlie neuroprotection caused by downregulation of the insulin receptor in this system. Moreover, a daf-16 loss of function mutation abolishes HT115-driven neuroprotection. Comparative genomics, transcriptomics and metabolomics approaches pinpointed the neurotransmitter {gamma}-aminobutyric acid (GABA) as a metabolite differentially produced between E. coli HT115 and OP50. HT115 mutant lacking glutamate decarboxylase enzyme genes (gad), which catalyze the conversion of GABA from glutamate, lost the ability to produce GABA and also to stop neurodegeneration. Moreover, in situ GABA supplementation or heterologous expression of glutamate decarboxylase in E. coli OP50 conferred neuroprotective activity to this strain. Specific C. elegans GABA transporters and receptors were required for full HT115-mediated neuroprotection. Together, these results demonstrate that bacterially produced GABA exerts an effect of neuroprotection in the host, highlighting the role of neuroactive compounds of the diet in nervous system homeostasis.

microbiology↗

bioRxiv2019

High density of white-faced capuchins (Cebus capucinus) and habitat quality in the Taboga Forest of Costa Rica

Across the globe, primate species and habitats are threatened by human activity. This is especially true for species found in tropical dry forests, which are widely distributed and comprise diverse habitats that remain largely unprotected. Evidence suggests that some primate species endemic to tropical dry forests may be more sensitive to anthropogenic disturbance than others, but our ability to predict primate abundance in the face of disturbance also depends on the specific variables for each site. Here, we consider the factors that explain the high density of white-faced capuchins (Cebus capucinus) found in the Taboga Forest, Costa Rica, a relatively small fragment of tropical dry forest surrounded by agricultural fields. Our analyses suggest that, for capuchins (and potentially for mantled howler monkeys, Alouatta palliata), the size and disturbance of a forest fragment may matter less than the composition and availability of key resources, like above-ground water. Group sightings for both species were higher near permanent water sources, but group sightings did not vary between edge and interior forest. These findings help explain why some primate species can flourish even alongside anthropogenic disturbance and thus carry important implications for conservation efforts. Smaller forest fragments, like Taboga, may be able to support high densities of some species because they provide a mosaic of habitats and key resources that buffer adverse ecological conditions. Future studies will assess the extent to which primates in the Taboga Forest rely on the canals versus the river and will consider how the high density of capuchins in Taboga influences ranging patterns, home range overlap, and the frequency and intensity of intergroup encounters.\n\nRESEARCH HIGHLIGHTSO_LIHere we introduce a new white-faced capuchin study site in the Taboga Forest, Costa Rica, a fragmented tropical dry forest.\nC_LIO_LIForest fragments like Taboga may support high primate densities because they provide a mosaic of habitats and key resources.\nC_LI

animal behavior and cognition↗