Biology subjects

Coll, M.

Publications and source records attributed to Coll, M..

14 recordsLinked to original sources

bioRxiv2026

Does herbivore diversity increase induced phytochemical diversity? Testing the pathway co-activation hypothesis

The mechanistic link between multiple herbivory and phytochemical diversity as an emergent plant trait is poorly understood. Because alternative, interacting biosynthetic pathways enable high specificity of induced plant responses to different herbivores, we hypothesized that multi-species herbivory increases phytochemical diversity by simultaneously activating mutually-antagonistic response pathways. We tested this hypothesis using a dual-herbivory experiment with phloem-feeding aphids and leaf-chewing caterpillars on cabbage seedlings, combined with untargeted metabolomics. To isolate plant responses to herbivore identities from responses to damage levels, we equalized herbivory pressures across treatments. The underlying mechanism was tested using similar applications of the respective defense phytohormones. Phytochemical richness increased under dual-herbivory relative to single-species herbivory. Phytochemical evenness (2D diversity) increased from caterpillar-only to dual-herbivory. Phytohormone applications produced similar effects, supporting the hypothesized mechanism. Analyses of glucosinolate levels and whole-metabolome shifts were consistent with prevalent, but not exclusive, antagonistic JA-SA crosstalk, explaining the increased phytochemical evenness under combined exposures. The demonstrated general mechanistic basis suggests a broad positive relationship between phytochemical and herbivore diversity across plant-herbivore systems. Using a theoretical simulation model, we extend our two-species hypothesis to the community level. The ecological effects of herbivore-induced plasticity in phytochemical diversity may ultimately cascade through communities and food web interactions.

plant biology↗

bioRxiv2025

Patient-derived liver biopsy organoids enable precision alcohol-associated liver disease modeling

Background & AimsAlcohol-associated liver disease (ALD) is a major cause of liver disease worldwide with scarce therapeutic options. Animal models poorly recapitulate advanced ALD precluding the development of new treatments. Organoids have emerged as a powerful human-based preclinical tool. However, current patient-derived liver organoids fail to recapitulate the epithelial heterogeneity and its generation requires liver surgical resections, thus limiting personalized disease modeling. Here, we report the development of organoids from liver needle biopsies (b-Orgs) from patients with ALD. Methodsb-Orgs were generated from tru-cut biopsies from patients at early (n=28) and advanced (n=34) stages of ALD. b-Orgs were characterized by immunofluorescence, bulk and single cell RNA-sequencing and compared to parental tissues. b-Orgs were used to model ALD progression, identify pathogenic drivers, induce alcohol-associated hepatitis (AH) and evaluate response to prednisolone. ResultsPhenotypic and functional analysis of b-Orgs showed hepatocyte- enriched features. Single-cell RNA-sequencing revealed a heterogeneous cell composition comprising hepatocyte, biliary and progenitor populations, mirroring the epithelial landscape found in patients with advanced ALD. Moreover, b-Orgs preserved disease-stage features and allowed to identify the association of ELF3 with cell plasticity and disease progression. Finally, stimulation of b-Orgs with drivers of ALD induced pathophysiological features of alcohol-associated hepatitis, including ROS production, lipid accumulation, inflammation and decreased cell proliferation, which were mitigated in response to prednisolone. Conclusions Overall, we provide a human-based model that recapitulates epithelial complexity and patient specific features, allowing to identify drivers of cell plasticity and expanding organoid-based liver disease modeling for personalized medicine. Impact and implications Here, we describe the generation of biopsy-derived organoids (b-Orgs) from patients with liver disease. b-Orgs reproduce the liver epithelial cell composition found in patients liver tissue and are efficiently generated from different stages of the disease, providing a platform for patient- tailored disease modeling and drug testing.

cell biology↗

bioRxiv2024

Use of the non-paretic arm reflects a habitual behaviour in chronic stroke

BackgroundA proportion of stroke survivors use their affected arm less than might be expected based on their level of impairment. The resulting non-use of the affected arm has a negative impact on participation in neurorehabilitation and functional independence. However, non-use remains poorly understood. One possibility is that prioritising the non-paretic arm reflects a habit, despite residual functional capacity in the paretic arm. Methods30 chronic stroke survivors (Mean FM: 28.9 {+/-} 11.3) participated in a simplified version of the forced response paradigm, which reliably identifies the presence of a habit. Participants were asked to choose which arm to use to maximise points scored during a reaching task. During half of the trials, the presumed habit of using the non-paretic arm yielded more points, whereas in the other half using the non-paretic arm incurred a loss of points. Participants completed two versions of this task, once with unlimited response time available and once without. ResultsParticipants scored fewer points in the limited response condition compared to the unlimited response conditions. This difference was driven by a selective increase in the use of the non-paretic arm in trials where the paretic arm yielded more points. The results were not mediated by former hand dominance. ConclusionsOur results demonstrate that not using the non-paretic arm may reflect a habit response that is more readily triggered in demanding (e.g. time-limited) situations. This may explain why successful neurorehabilitation does not always result in a more functionally useful arm. Our results pave the way for targeted interventions such as habit breaking techniques to be included in clinical practise.

neuroscience↗

bioRxiv2024

Late Miocene transformation of Mediterranean Sea biodiversity

Understanding deep-time marine biodiversity change under the combined effects of climate and connectivity changes is fundamental for predicting the impacts of modern climate change in semi-enclosed seas. We quantify the Late Miocene-Early Pliocene (11.63-3.6 Ma) taxonomic diversity of the Mediterranean Sea for calcareous nannoplankton, dinocysts, foraminifera, ostracods, corals, molluscs, bryozoans, echinoids, fishes, and marine mammals. During this time, marine biota was affected by global climate cooling and the restriction of the Mediterraneans connection to the Atlantic Ocean that peaked with the Messinian Salinity Crisis. Although the net change in species richness from the Tortonian to the Zanclean varies by group, species turnover is greater than 30% in all cases. The results show clear perturbation already in the pre-evaporitic Messinian (7.25-5.97 Ma), with patterns differing among groups and sub-basins.

paleontology↗

bioRxiv2024

Trajectory analysis of hepatic stellate cell differentiation reveals metabolic regulation of cell commitment and fibrosis

Defining the trajectory of cells during differentiation and disease offers the possibility to understand the mechanisms driving cell fate and identity. However, trajectories of human cells are largely unexplored. By investigating the proteome trajectory of iPSCs differentiation to hepatic stellate cells (dHSCs), we identified RORA as a key transcription factor governing the metabolic reprogramming of HSCs necessary for HSCs commitment, identity, and activation. Using RORA deficient iPSCs and pharmacologic interventions, we showed that RORA is required for mesoderm differentiation and prevents dHSCs activation by reducing the high energetic state of the cells. While RORA knockout mice had enhanced fibrosis, RORA agonists rescued multi- organ fibrosis in in vivo models. RORA expression was consistently found to be negatively correlated with liver fibrosis and HSCs activation markers in patients with liver disease. This study reveals that RORA regulates cell metabolic plasticity, crucial for mesoderm differentiation, pericyte quiescence, and fibrosis, influencing cell commitment and disease mechanisms. SummaryThis study describes the trajectory of induced pluripotent stem cells (iPSCs) differentiation to hepatic stellate cells (dHSCs). We identify RAR-related orphan receptor alpha (RORA) as a transcription factor essential for mesoderm commitment and dHSCs identity and fibrogenic activation by regulating metabolic plasticity.

cell biology↗

bioRxiv2023

Hepatocyte Dedifferentiation Profiling In Alcohol-Related Liver Disease Identifies CXCR4 As A Driver Of Cell Reprogramming

Background and AimsLoss of hepatocyte identity is associated with impaired liver function in alcohol-related hepatitis (AH). In this context, hepatocyte dedifferentiation gives rise to cells with a hepatobiliary (HB) phenotype expressing biliary and hepatocytes markers and showing immature features. However, the mechanisms and the impact of hepatocyte dedifferentiation in liver disease are poorly understood. MethodsHB cells and ductular reaction (DR) cells were quantified and microdissected from liver biopsies from patients with alcohol-related liver disease (ALD). Hepatocyte- specific overexpression or deletion of CXCR4, and CXCR4 pharmacological inhibition were assessed in mouse liver injury. Patient-derived and mouse organoids were generated to assess plasticity. ResultsHere we show that HB and DR cells are increased in patients with decompensated cirrhosis and AH, but only HB cells correlate with poor liver function and patients outcome. Transcriptomic profiling of HB cells revealed the expression of biliary-specific genes and a mild reduction of hepatocyte metabolism. Functional analysis identified pathways involved in hepatocyte reprogramming, inflammation, stemness and cancer gene programs. CXCR4 pathway was highly enriched in HB cells, and correlated with disease severity and hepatocyte dedifferentiation. In vitro, CXCR4 was associated with biliary phenotype and loss of hepatocyte features. Liver overexpression of CXCR4 in chronic liver injury decreased hepatocyte specific gene expression profile and promoted liver injury. CXCR4 deletion or its pharmacological inhibition ameliorated hepatocyte dedifferentiation and reduced DR and fibrosis progression. ConclusionsThis study shows the association of hepatocyte dedifferentiation with disease progression and poor outcome in AH. Moreover, the transcriptomic profiling of HB cells revealed CXCR4 as a new driver of hepatocyte-to-biliary reprogramming and as a potential therapeutic target to halt hepatocyte dedifferentiation in AH. Lay summaryHere we describe that hepatocyte dedifferentiation is associated with disease severity and a reduced synthetic capacity of the liver. Moreover, we identify the CXCR4 pathway as a driver of hepatocyte dedifferentiation and as a therapeutic target in alcohol-related hepatitis.

cell biology↗

bioRxiv2023

Identifying and prioritizing demersal fisheries restricted areas based on combined ecological and fisheries criteria: the western Mediterranean

The western Mediterranean basin is a high marine biodiversity area under severe pressure by changing climate and intense human activities. Beyond national jurisdictions, international institutions such as the General Fisheries Commission for the Mediterranean (GFCM) work towards canalizing a regional consensus that fishing practices should evolve to better support the 2030 Agenda for Sustainable Development. In this context, Fisheries Restricted Areas (FRA) are proposed as effective management measures to contribute towards increasing fisheries sustainability in the region that can be considered, under some conditions, as Nature-based Solutions (NbS); however, how to operationalize their framework remains unclear. In this study, based on combined ecological and fisheries criteria, we identify and prioritize six potential priority areas for management (PAMs) in the western Mediterranean Sea. They are specifically aimed at the protection and recovery of Essential Fish Habitats and the conservation of Vulnerable Marine Ecosystems, whilst requiring limited adaptation of fisheries practices due to their relative low fishing pressure. We compare the identified areas to those that are currently under protection, and to areas that have been proposed for protection at the GFCM. Our results show that the FRAs and other spatial management measures introduced in the last years marginally contribute to the protection PAMs in the western Mediterranean region. However, the adoption of FRAs that are currently under discussion at the GFCM could contribute significantly to improve the situation. FRAs could also contribute to operationalize NbS in the western Mediterranean Sea when properly designed and implemented. HighlightsO_LIBased on combined ecological and fisheries criteria, six priority areas for management (PAMs) in the western Mediterranean Sea have being identified, with multiple ecological values and relative low trawling. C_LIO_LICurrent spatial management measures implemented have little contribution on PAMs protection. C_LIO_LIFisheries Restricted Areas currently under discussion at the GFCM can significantly increase the protection level of high priority PAMs. C_LI

ecology↗

bioRxiv2022

Costs and economic impacts of expanding marine protected area systems to 30% coverage

International proposals for marine biodiversity seek to expand marine protected area (MPA) coverage from 8% to 30%, known as 30x30. Quadrupling MPA coverage implies considerably higher MPA system costs and governments need early knowledge of these to inform debate. Ambitious MPA expansion also implies large potential losses or "opportunity costs" for fishers, putting pressure on governments to compromise and permit some fishing inside protected areas (a mixed high/low protection system). Crafting a balanced compromise needs to be informed by model projections of future fisheries outcomes under different protection regimes, climate change scenarios and behavioural adaptations. Here, we develop the first models for management costs at national MPA-system scale. We create scenarios of 30x30 at different compromises around protection strictness. We then examine how both MPA costs and opportunity costs vary with strictness, by simultaneously applying our management cost models and two Marine Ecosystem Models. We find that a no-take (high protection) MPA system could cost just $2 billion/year for the developing world and ~$8 billion overall, but would also create opportunity costs several times larger. A compromise mix of high and medium protection would have much higher MPA costs (e.g. $4.5 billion for the developing world) but much lower opportunity costs, to the point of fisheries actually benefiting in the future. Since lower protection also compromises on biodiversity goals, our results show the trade-offs that political decisions need to consider beyond COP15. More generally, the unusually large opportunity costs show how marine contexts generate very different economic issues from terrestrial ones, by attempting to protect a common pool resource area that envisages no automatic market compensation for income lost to conservation.

ecology↗

bioRxiv2022

Three decades of increasing fish biodiversity across the north-east Atlantic and the Arctic Ocean

Observed range shifts of numerous species support predictions of climate change models that species will shift their distribution northwards into the Arctic and sub-Arctic seas due to ocean warming. However, how this is affecting overall species richness is unclear. Here we analyse scientific research trawl surveys from the North Sea to the Arctic Ocean collected from 1994 to 2020, including 193 fish species. We found that demersal fish species richness at the local scale has doubled in some Arctic regions, including the Barents Sea, and increased at a lower rate at adjacent regions in the last three decades, followed by an increase in species richness and turnover at a regional scale. These changes in biodiversity paralleled an increase in sea bottom temperature. Within the study area, Arctic species probability of occurrence generally declined over time. However, the increase of species from southern latitudes, together with an increase of some Arctic species, ultimately led to an enrichment of the Arctic and sub-Arctic marine fauna due to increasing water temperature consistent with climate change. Significance StatementGlobal modelling studies suggest increased species arrivals from lower latitudes and local expirations at high latitudes due to global warming. Our analysis of 20,670 standardized scientific trawl surveys with 193 fish species from the north-east Atlantic and Arctic Oceans found an increase in species richness in the region parallel to an increase in sea bottom temperature. Some Arctic species declined in probability of occurrence over time, but some increased. This, together with the increase of southern-latitude species led to an enrichment of the Arctic and sub-Arctic marine fauna attributed to climate change.

ecology↗

bioRxiv2022

Palaeontological evidence for community-level decrease in mesopelagic fish size during Pleistocene climate warming in the eastern Mediterranean

Mesopelagic fishes are an important element of marine food webs, a huge, still mostly untapped food resource, and great contributors to the biological carbon pump, whose future under climate change scenarios are unknown. The shrinking of commercial fishes within decades has been an alarming observation, but its causes remain contended. Here, we investigate the effect of warming climate on mesopelagic fish size in the eastern Mediterranean Sea during a glacial-interglacial-glacial transition of the Middle Pleistocene (marine isotope stages 20-18; 814-712 Kyr B.P.), which included a 4 {degrees}C increase of global seawater temperature. Our results based on fossil otoliths show that the median size of lanternfishes, one of the most abundant groups of mesopelagic fishes in fossil and modern assemblages, declined by ~35% with climate warming at the community level. However, individual mesopelagic species showed different and often opposing trends in size across the studied time interval, suggesting that climate warming in the interglacial resulted in an ecological shift toward increased relative abundance of smaller-sized mesopelagic fishes due to geographic and/or bathymetric distribution range shifts, and the size-dependent effects of warming.

paleontology↗

bioRxiv2021

Skillful prediction of tropical Pacific fisheries provided by Atlantic Ninos

Tropical Pacific upwelling-dependent ecosystems are the most productive and variable worldwide, mainly due to the influence of El Nino Southern Oscillation (ENSO). ENSO can be forecasted seasons ahead thanks to assorted climate precursors (local-Pacific processes, pantropical interactions). However, owing to observational data scarcity and bias-related issues in earth system models, little is known about the importance of these precursors for marine ecosystem prediction. With recently released reanalysis-nudged global marine ecosystem simulations, these constraints can be sidestepped, allowing full examination of tropical Pacific ecosystem predictability. By complementing historical fishing records with marine ecosystem model data, we show herein that equatorial Atlantic Sea Surface Temperatures (SSTs) constitute a superlative predictability source for tropical Pacific marine yields, which can be forecasted over large-scale areas up to 2 years in advance. A detailed physical-biological mechanism is proposed whereby Atlantic SSTs modulate upwelling of nutrient-rich waters in the tropical Pacific, leading to a bottom-up propagation of the climate-related signal across the marine food web. Our results represent historical and near-future climate conditions and provide a useful springboard for implementing a marine ecosystem prediction system in the tropical Pacific.

ecology↗

bioRxiv2021

Energy content of anchovy and sardine using surrogate calorimetry methods

European anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) are crucial species for the marine ecosystem of the Northwestern Mediterranean Sea. They account for a high percentage of fish landings and they represent an important economic income. Concerns over their stock status are rising in recent years as biomass, growth, reproductive capacity and body condition of both species are declining. Therefore, there is an urgent need for a continuous and fast body condition monitoring scheme. Energy storage variability has important implications for both fish recruitment and population structure. Direct condition indices, such as bomb calorimetry, are highly reliable for measuring the energy content, but extremely time-consuming. Alternatively, fatmeter analysis and relative condition index (Kn) have been proposed as effective indirect methods. The aim of this study is to test the application of fatmeter as a surrogate of bomb calorimetry to infer the energy content of both small pelagic fishes. For the validation, fatmeter values were compared with both energy density (ED; via bomb calorimetry) and Kn values. Individuals of both species were sampled monthly in Barcelona harbor for a year in order to assess seasonal variations in energy content. Our results highlight that fatmeter measurements are strongly correlated with calorimetry for sardine, while a weaker but significant correlation was found for anchovy. The observed differences between the two species are related to their breeding strategies. Based on this study, fatmeter analysis appears to be a faster and suitable method to evaluate the energy content of both species routinely., In addition, we provide a linear model to infer ED from fatmeter values of both small pelagic fish. Eventually, these findings could allow for the avoidance of bomb calorimetry and could be used to implement body condition monitoring protocols, and to boost continuous large-scale monitoring.

physiology↗

bioRxiv2020

Current and potential contributions of the Gulf of Lion Fisheries Restricted Area to fisheries sustainability in the NW Mediterranean Sea

Many commercial species of the world are overexploited resulting in substantial reductions of biomass and ecological changes. Spatial-temporal restrictions of fishing activities are important measures used for the management of marine stocks. However, evidence of whether fishing bans benefit whole ecosystems is still scant. Here, we developed a food-web model approach using the Ecopath with Ecosim (EwE) model representing the Fisheries Restricted Area (FRA) of the Gulf of Lion ecosystem (CoSEGoL model) prior to the establishment of the fisheries restrictions (2006-2008) to characterize the structure and functioning of the ecosystem before and after its establishment. The constructed food-web model was, then, fitted to available time series of data from 2008 to 2016 to verify whether this FRA has contributed to recovery of target demersal species and the demersal community. The fitted model was used to explore alternative future management scenarios to explore feasible management options in order to ensure a full ecosystem recovery under climate change conditions. Both small positive and negative ecosystem changes occurred between prior and after the establishment of the FRA, potentially revealing a lack of protection efficiency and/or enforcement. Scenarios of management options under plausible climate futures revealed possible recovery of targeted species, especially European hake. The study highlighted the importance of considering trophic interactions between predators and prey to identify trade-offs and synergies in fisheries management outcomes and the need to consider both fishing and climate dynamics.

ecology↗

bioRxiv2018

Ensemble projections of global ocean animal biomass with climate change

Climate change is shifting the abundance and distribution of marine species with consequences for ecosystem functioning, seafood supply, management and conservation. Several approaches for future projection exist but these have never been compared systematically to assess their variability. We conducted standardized ensemble projections including 6 global fisheries and marine ecosystem models, forced with 2 Earth-system models and 4 emission scenarios in a fished and unfished ocean, to derive average trends and associated uncertainties. Without fishing, mean global animal biomass decreased by 5% ({+/-}4%) under low and 17% ({+/-}11%) under high emissions by 2100, primarily driven by increasing temperature and decreasing primary production. These climate-change effects were slightly weaker for larger animals and in a fished ocean. Considerable regional variation ranged from strong biomass increases in high latitudes to strong decreases in mid-low latitudes, with good model agreement on the direction of change but variable magnitude. Uncertainties due to differences among ecosystem or Earth-system models were similar, suggesting equal need for model improvement. Our ensemble projections provide the most comprehensive outlook on potential climate-driven ecological changes in the ocean to date. Realized future trends will largely depend on how fisheries and management adapt to these changes in a changing climate.

ecology↗