Biology subjects

Hidalgo, M.

Publications and source records attributed to Hidalgo, M..

14 recordsLinked to original sources

bioRxiv2025

A survey of bacterial and fungal communities of table olives.

Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures. HighlightsO_LIWe report a metataxonomic survey of microbial communities in 363 table olive samples C_LIO_LIAlkali treatment and natural fermentation drive distinct microbial community structures C_LIO_LIHouse microbiota and stochastic colonization generate high within-variety variability C_LIO_LIMicrobiome data provide ecological foundations for olive microbiome-based starters C_LI

microbiology↗

bioRxiv2025

Distinct dynamic stability patterns among three Atlantic cod subpopulations in the North Sea

Atlantic cod (Gadus morhua) in the North Sea and adjacent waters has been extensively studied due to its continued population decline despite reduced fishing pressure. Recent evidence reveals that it forms a metapopulation consisting of three subpopulations-- Northwestern, Southern, and Viking--highlighting the need to understand their distinct dynamics to support spatially targeted fisheries management. We applied a dynamical systems approach to quantify two key properties for each subpopulation from 1983 to 2023: dynamic stability, indicating whether subpopulations tend to return to or move away from their state each year, and the relative sensitivity of age groups, reflecting the magnitude of change in each groups abundance in response to perturbations in the age-structured interaction network. We found distinct dynamic stability patterns among the three subpopulations. The Northwestern subpopulation fluctuated between stable and unstable states before stabilizing at low abundance. The Southern subpopulation shifted from high-abundance, stable states toward low abundance at a transient with an uncertain future. The Viking subpopulation remained stable with relatively constant abundance over time. Throughout the study period, the age-1 group remained highly sensitive to perturbations in both the Southern and Viking subpopulations, whereas no single age group showed dominant sensitivity in the Northwestern subpopulation. Fishing mortality causally influenced the abundance and/or stability of the Northwestern and Southern subpopulations, but not the Viking subpopulation. In contrast, sea bottom temperature did not affect the abundance or stability of any of the subpopulations. Our findings reveal distinct patterns in abundance, dynamic stability, relative sensitivity of age groups, and responses to external drivers across the three subpopulations, highlighting the importance of accounting for the complex population structure of Atlantic cod in future research, assessments, and management efforts.

ecology↗

bioRxiv2025

Tracking changes in stability of North Sea Atlantic cod in 40 years

Tracking changes in the stability of low-abundance populations is vital for conservation. While the stability of natural populations is often assessed based on linear dynamics, many exhibit state-dependent dynamics, such as the iconic Atlantic cod in the North Sea (Gadus morhua). This fish population experienced an abrupt decline in the year 2000 and has not shown a clear sign of recovery despite relaxed fishing pressure. To understand the mechanisms behind the recovery dynamics, we used a dynamical systems approach to reconstruct the state space of the population from yearly abundance data of age groups between 1982-2021. Specifically, we estimated yearly interaction matrices of age groups and derived yearly population stability, defined as the rate of recovery to or departure from the current state after a small perturbation to the matrix. We found that since the abrupt decline in abundance of North Sea cod in the year 2000, the population continued to fluctuate closer to the transition threshold; some age groups experienced weaker self-regulation; and age-1 group became more sensitive to perturbations than older groups. These results provide important information on North Sea cods resilience and capacity to buffer natural and anthropogenic impacts.

ecology↗

bioRxiv2021

Drivers of phylogenetic structure in Amazonian freshwater fish assemblages

AimCommunity phylogenetics provides important information about the evolutionary and ecological factors help structure regional species assemblages. Here, we analyze phylogenetic diversity (phylodiversity) patterns among fish species in 97 sub-drainages of the Amazon basin, to evaluate the roles of historical and contemporary processes in generating and maintaining the exceptional richness and endemism of Amazonian fish species assemblages. LocationAmazon River basin TaxonFreshwater fishes MethodsUsing a large comprehensive database of freshwater fish species distributions, and a well-sampled molecular phylogeny of ray-finned (actinopterygian) fishes, we develop of multivariate statistical model to correlate estimated historical and contemporary environmental parameters with sub-drainage phylodiversity patterns. The model employs three phylogenetic metrics: i.e.: phylogenetic diversity (PD) sensu stricto, mean pairwise phylogenetic distance (MPD) between species capturing phylodiversity variation at older evolutionary timescales), and mean nearest taxon distance (MNTD) capturing variation in phylodiversity at younger evolutionary timescales. ResultsThe model recovered significant effects of elevation gradients, contemporary climate, habitat fragmentation, water types, and past marine incursions on assemblage phylodiversity patterns. The model also found significantly negative relationships among the three phylogenetic metrics, and between these metrics and distance to mouth of the Amazon, representing a West-East longitudinal gradient. Main conclusionsOur study revealed a highly non-random spatial and environmental distribution of our three phylogenetic diversity metrics across the 97 sub-drainages of the Amazon basin. Beyond significant regional effects of several environmental and historical drivers, we also found a significant West-East gradient of increasing phylogenetic diversity and phylogenetic relatedness, both patterns suggesting deeper evolutionary divergences among taxa located to the east, and more diverse, more recent radiations in the western sub-drainages. We conclude that western Amazonia can be seen as an evolutionary "cradle" of biodiversity for freshwater fishes in the Amazon basin as a whole. Significance StatementThis manuscript reveals spatial patterns of freshwater fish phylogenetic diversity and relatedness and explains its major contemporary and historical drivers in the Amazon basin. Amazon basin contains the highest freshwater biodiversity on Earth, as so investigate phylogenetic dimension of diversity is extremally relevant from the perspective of understanding the information on the evolutionary processes that had shaped Amazonian contemporary fish assemblages.

ecology↗

bioRxiv2021

A conserved paint box underlies color pattern diversity in Estrildid finches

Many animals exhibit typical color patterns that have been linked to key adaptive functions, yet the developmental mechanisms establishing these crucial designs remain unclear. Here, we surveyed color distribution in the plumage across a large number of passerine finches. Despite extreme apparent pattern diversity, we identified a small set of conserved color regions whose combinatory association can explain all observed patterns. We found these domains are instructed by early embryonic landmarks, and through profiling and comparative analyses produced a molecular map marking putative color domains in the developing skin. This revealed cryptic pre-patterning common to differently colored species, uncovering a simple molecular landscape underlying extensive color pattern variation.

developmental biology↗

bioRxiv2020

Amblyomma mixtum free-living stages: Summer and winter use, preference, and niche width in an agroecosystem (Yopal, Casanare, Colombia)

Studying a species tolerance to an ecosystems environmental conditions and its selection of available resources is relevant in ecological and evolutionary terms. Moreover, formulation of effective control strategies implicitly includes the study of habitat use and preference and niche width in anthropogenically transformed natural landscapes. Here, we evaluated whether the use, habitat preference, and niche range of the Amblyomma mixtum tick changed between stages, habitats, and seasons (summer-winter 2019) on a farm in Yopal (Casanare, Colombia). To this end, the presence and relative abundance of larvae, nymphs, and free-living adults was quantified in four different habitats according to the type of vegetation cover (Riparian Forest, Cocoa Crop, King Grass Crop, and Star Grass Paddock). Habitat availability was calculated, environmental variables were analyzed, and various indices of habitat use and preference and niche width were calculated. A. mixtums habitat use and preference and niche width changed between stages, habitat types, and time of the year. The total abundance of A. mixtum was an order of magnitude greater in summer than winter. Nymphs and larvae dominated it in the summer and adults in the winter. In summer, all the stages used the four habitats. In winter, the larvae did not use two habitats (Riparian Forest and Cocoa Crop); nymphs did not use the cocoa crop. A. mixtum adults used all the habitats in both seasons. In summer, the nymphs and larvae preferred three of the four habitats (King Grass Crop, Star Grass Paddock, and Cocoa Crops), while adults preferred the King Grass Crop. In winter, the nymphs and larvae preferred the King Grass Crop and Star Grass Paddock, while the adults preferred the King Grass Crop. The value of the niche width index was high for larvae, nymphs, and adults in summer, while it was high only for adults in winter. A. mixtum is exposed to significant daily, seasonal, and multiannual variations in relative humidity (minimum 30%), ambient temperature (minimum 18{degrees}C), solar radiation (maximum 800 W/m2), and precipitation (maximum 481 mm/month). Thus, the local A. mixtum population could rapidly acclimatize to changing habitats (unstable or temporary) under fluctuating environmental conditions (e.g., King Grass Crop). However, the winter flood season in Yopal could exceed A. mixtums adaptive capacity during its most vulnerable stages. Mathematically, a low number of female A. mixtum, surviving the most demanding environmental conditions, could sufficiently ensure the populations persistence, which, coupled with the vast host range, could facilitate the ticks stages dispersal among habitats to complete their life cycle. A. mixtums population control should be carried out during its season of greater vulnerability (winter), when the population is low, particularly the females.

ecology↗

bioRxiv2020

Clonal expansion of personalized anti-tumor T cells from circulation using tumor organoid-immune co-cultures

Tumor-specific cytotoxic T cells are effective tools for cancer immunotherapy, but the ability to generate them continues to be a challenge. Furthermore, there are no compelling approaches to empirically identify tumor-targeting T cells and T cell receptors by exploiting the multitude of antigens on tumor cell surfaces. Here, we use patients peripheral blood and autologous tumor organoids to enrich tumor-specific cytotoxic T cells with patient-specific killing mechanisms and a tissue-resident memory phenotype. We further demonstrate that these organoid-primed T (opT) cells undergo several orders of magnitude of clonal expansion and express T cells receptors and check-point proteins unique to each patient. Importantly, transferring the TCRs to heterologous T cells was sufficient to confer tumor recognition in a patient-specific manner. Thus, we report a patient-specific and antigen-agnostic platform for expansion of tumor-targeting T cells and identification of cancer-targeting TCRs from the peripheral blood of pancreatic cancer patients that can be exploited for immunotherapy applications.

cancer biology↗

bioRxiv2020

Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data

Marine biota is redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. We further found that single surveys do not cover the full range of the main commercial demersal fish species and that an average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with vector autoregressive spatio-temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate-driven ocean changes.

ecology↗

bioRxiv2020

Fatal toxicity of chloroquine or hydroxychloroquine with metformin in mice

Guided by the principle of primum non nocere (first do no harm), we report a cautionary note on the potential fatal toxicity of chloroquine (CQ) or hydroxychloroquine (HCQ) in combination with anti-diabetic drug metformin. We observed that the combination of CQ or HCQ and metformin, which were used in our studies as potential anti-cancer drugs, killed 30-40% of mice. While our observations in mice may not translate to toxicity in humans, the reports that CQ or HCQ has anti-COVID-19 activity, the use of CQ resulting in toxicity and at least one death, and the recent Emergency Use Authorization (EUA) for CQ and HCQ by the US Food and Drug Administration (FDA) prompted our report. Here we report the lethality of CQ or HCQ in combination with metformin as a warning of its potential serious clinical toxicity. We hope that our report will be helpful to stimulate pharmacovigilance and monitoring of adverse drug reactions with the use of CQ or HCQ, particularly in combination with metformin.

pharmacology and toxicology↗

bioRxiv2020

A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer

Pancreatic cancer (PC) is a complex disease in which both non-genetic and genetic factors interplay. To-date, 40 GWAS hits have been associated with PC risk in individuals of European descent, explaining 4.1% of the phenotypic variance. Here, we complemented a classical new PC GWAS (1D) with spatial autocorrelation analysis (2D) and Hi-C maps (3D) to gain additional insight into the inherited basis of PC. In-silico functional analysis of public genomic information allowed prioritization of potentially relevant candidate variants. We replicated 17/40 previous PC-GWAS hits and identified novel variants with potential biological functions. The spatial autocorrelation approach prioritized low MAF variants not detected by GWAS. These were further expanded via 3D interactions to 54 target regions with high functional relevance. This multi-step strategy, combined with an in-depth in-silico functional analysis, offers a comprehensive approach to advance the study of PC genetic susceptibility and could be applied to other diseases.

genetics↗

bioRxiv2019

Guillain-Barre syndrome outbreak in Peru: Association with polymorphisms in IL-17, ICAM-1 and CD1

Guillain-Barre Syndrome (GBS) is considered a complex disorder with significant environmental effect and genetic susceptibility. Genetic polymorphisms in CD1E, CD1A, IL-17 and/or ICAM-1 genes had been proposed as susceptibility genetic variants for GBS mainly in Caucasian population. This study explores the association between selected polymorphisms in these genes and GBS susceptibility in confirmed GBS cases reported in mestizo population from northern Peru during the most recent GBS outbreak of May 2018. A total of 9 non-related cases and 11 controls were sequenced for the polymorphic regions of CD1A, CD1E, IL-17 and ICAM-1 genes. We found a significant protective association between heterozygous GA genotype in ICAM-1 gene (241Gly / Arg) and GBS (p <0.047). IL-17 was monomorphic in both controls and patients. No significant differences were found in the frequency of SNPs in CD1A and CD1E between the group with GBS patients and healthy controls. Further studies with larger sample size will be required to validate these findings.

molecular biology↗

bioRxiv2019

Pancreatic tumor organoids for modeling in vivo drug response and discovering clinically-actionable biomarkers

Patient-derived models are transforming translational cancer research. It is not clear if the emergence of patient-derived organoid (PDO) models can extend the utility of the widely used patient-derived xenograft (PDX). In addition, the utility of PDO models for serum biomarker discovery is not known. Here, we demonstrate that PDO models recapitulate the genomics, cell biology, glycomics and drug responses observed in PDX models. Furthermore, we demonstrate the applicability of PDO models for identification of N-glycans that are enriched in the glycome of pancreatic ductal adenocarcinoma (PDAC). Surprisingly, among all the glycans observed in PDX and PDOs, a core set of 57 N-glycans represent 50-94% of the relative abundance of all N-glycans detected, suggesting that only a subset of glycans dominate the cell surface landscape in PDAC. In addition, we outline a tumor organoid-based pipeline to identify surface proteins in extracellular vesicles (EV) from media supernatant of PDO cultures. When combined with the affinity-based validation platform, the EV surface proteins discovered in PDOs are effective in differentiating patients with PDAC from those with benign pancreatitis in the clinic, identifying PDO as powerful discovery platform for serum biomarkers. Thus, PDOs extend the utility of the archival collections of PDX models for translational research and function as a powerful platform for identification of clinically-actionable biomarkers in patients blood. Significance statementTumor organoids extend the utility of PDX models as platforms for investigating drug response, glycosylation changes and function as new platforms for discovering blood-based biomarkers

cancer biology↗

bioRxiv2018

Symmetry breaking in the embryonic skin triggers a directional and sequential front of competence during plumage patterning

The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns1-4 yet drawing testable hypotheses from those often remains difficult4,5. Consequently, little is known on pattern-forming events. Here, we extend modeling to reproduce not only the final plumage pattern of birds, but also the observed natural variation in its dynamics of emergence in five species. We built a unified model intrinsically generating the directionality, sequence, and duration of patterning, and used in vivo experiments to test its parameter-based predictions. We showed that while patterning duration is controlled by overall cell proliferation, its directional and sequential progression result from a pre-pattern: an initial break in surface symmetry launches a traveling front of increased cell density that defines domains with self-organizing capacity. These results show that universal mechanisms combining pre-patterning and self-organization govern the timely emergence of the plumage pattern in birds.

developmental biology↗

bioRxiv2017

Whole-exome sequencing of plasma cell-free DNA portrays the somatic mutation landscape of refractory metastatic colorectal cancer and enables the discovery of mutated KDR/VEGFR2 receptors as modulators of anti-angiogenic therapies.

The non-invasive detection of cancer mutations is a breakthrough in oncology. Here, we applied whole-exome sequencing of matched germline and basal plasma cell-free DNA samples (WES-cfDNA) on a RAS/BRAF/PIK3CA wild-type metastatic colorectal cancer patient with primary resistance to standard treatment regimens including VEGFR inhibitors. Using WES-cfDNA, we could detect 73% (54/74) of the somatic mutations uncovered by WES-tumor including a variety of mutation types: frameshift (indels), missense, noncoding (splicing), and nonsense mutations. Additionally, WES-cfDNA discovered 14 high-confidence somatic mutations not identified by WES-tumor. Importantly, in the absence of the tumor specimen, WES-cfDNA could identify 68 of the 88 (77.3%) total mutations that could be identified by both techniques. Of tumor biology relevance, we identified the novel KDR/VEGFR2 L840F somatic mutation, which we showed was a clonal mutation event in this tumor. Comprehensive in vitro and in vivo functional assays confirmed that L840F causes strong resistance to anti-angiogenic drugs, whereas the KDR/VEGFR2 hot-spot mutant R1032Q confers sensitivity to cabozantinib. Moreover, we found a 1-3% of recurrent KDR somatic mutations across large and non-overlapping cancer sequencing projects, and the majority of these mutations were located in protein residues frequently mutated in other cancer-relevant kinases, such as EGFR, ABL1, and ALK, suggesting a functional role.\n\nIn summary, the current study highlights the capability of exomic sequencing of cfDNA from plasma of cancer patients as a powerful platform for somatic landscape analysis and discovery of resistance-associated cancer mutations. Because of its advantage to generate results highly concordant to those of tumor sequencing without the hurdle of conventional tumor biopsies, we anticipate that WES-cfDNA will become frequently used in oncology. Moreover, our study identified for the first-time KDR/VEGFR2 somatic mutations as potential genetic biomarkers of response to anti-angiogenic cancer therapies and will serve as reference for further studies on the topic.

cancer biology↗