Biology subjects

De Palma, A.

Publications and source records attributed to De Palma, A..

9 recordsLinked to original sources

bioRxiv2024

microRNA-544a as a new modulator of the Wnt-signalling network in the articular cartilage and osteoarthritis

ObjectiveDetermining the effect of microRNA-544a (miR-544a) in articular chondrocytes isolated from patients affected by osteoarthritis (OA) and its role in the modulation of the Wnt signalling. MethodsArticular chondrocytes were isolated from patients undergoing joint replacement because of OA. Expression levels of miR-544a were measured by PCR and by in situ hybridization. Putative targets of miR-544a were confirmed by reporter assay and by qPCR in cells stimulated with a miR-544a mimic. The effect of miR-544a on chondrocyte metabolism was monitored by qPCR for phenotypic markers, protein expression levels of aggrecan neoepitopes/MMP-13 and modulation of alcian blue content in micromass cultures, upon stimulation with a miR-544a mimic. The expression levels of MMP-13 and Aggrecan neoepitopes in response to miR-544a stimulation was also measured in co-stimulation with Xav-939 and KN93, which are respectively {beta}-catenin and CaMKII inhibitors. ResultsOur results suggest that miR-544a enhances the activation of the Wnt-signalling in the articular chondrocytes, by downregulating the expression of components of the Wnt/{beta}-catenin destruction complex. The expression of miR-544a is higher in chondrocytes isolated from damaged areas of the articular cartilage removed from OA patients, and can be upregulated by pro-inflammatory and pro-fibrotic cytokines. miR-544a exerts a pro-catabolic effect of articular chondrocytes, which is rescued both by the inhibition of the Wnt/{beta}-catenin and Wnt/CaMKII signalling pathways. Conclusionour results point to miR-544a as a new, important modulator of the Wnt signalling network within the articular cartilage suggesting a key role for microRNAs in regulating how the multiple branches of the network and their interaction modulate cartilage homeostasis.

pharmacology and toxicology↗

bioRxiv2020

The impacts of biofuel crops on local biodiversity: a global synthesis

Concerns about the environmental impacts of climate change have led to increased targets for biofuel in the global energy market. First-generation biofuel crops contain oil, sugar or starch and are usually also grown for food, whereas second-generation biofuel is derived from non-food sources, including lignocellulosic crops, fast-growing trees, crop residues and waste. Increasing biofuel production drives land-use change, a major cause of biodiversity loss, but there is limited knowledge of how different first- and second-generation biofuel crops affect local biodiversity. A more detailed understanding could support better decisions about the net environmental impacts of biofuels. We synthesised data from 116 sources where a potential biofuel crop was grown and estimated how two measures of local biodiversity, species richness and total abundance, responded to different crops. Local species richness and abundance were 37% and 49% lower at sites planted with first-generation biofuel crops than in sites with primary vegetation. Soybean, wheat, maize and oil palm had the worst effects; the worst affected regions were Asia and Central and South America; and plant species richness and vertebrate abundance were the worst affected biodiversity measures. Second-generation biofuels had significantly smaller effects: species richness and abundance were 19% and 25%, respectively, lower in such sites than in primary vegetation. Our models suggest that land clearance to generate biofuel results in negative impacts on local biodiversity. However, the geographic and taxonomic variation in effects, and the variation in yields among different crops, are all relevant for making the most sustainable land-use decisions.

ecology↗

bioRxiv2019

Effects of land-use change and related pressures on alien and native subsets of island communities

Island species and habitats are particularly vulnerable to human disturbances, and anthropogenic changes are increasingly overwriting natural island biogeographic patterns. However, quantitative comparisons of how native and alien assemblages respond to human disturbances are scarce. Using data from 6,242 species of vertebrates, invertebrates and plants, from 7,718 sites on 81 islands, we model how land-use change, human population density and distance to the nearest road affect local assemblages of alien and native species on islands. We found that land-use change reduces both richness and abundance of native species, whereas the number and abundance of alien species are high in plantation forests and agricultural or urban sites. In contrast to the long-established pattern for native species (i.e., decline in species number with island isolation), more isolated islands have more alien species across most land uses than do less isolated islands. We show that alien species play a major role in the turnover of island assemblages: our models show that aliens outnumber natives among the species present at disturbed sites but absent from minimally-disturbed primary vegetation. Finally, we found a homogenization pattern for both native and alien assemblages across sites within most land uses. The declines of native species on islands in the face of human pressures, and the particular proneness to invasions of the more remote islands, highlight the need to reduce the intensity of human pressures on islands and to prevent the introduction and establishment of alien species.

ecology↗

bioRxiv2019

Gcn5 and Ubp8 dependent ubiquitylation affects glycolysis in yeast

Many of the molecular mechanisms affected by ubiquitylation are highly conserved from yeast to humans and are associated to a plethora of diseases including cancers. To elucidate the regulatory role of epigenetic factors such as the catalytic subunits of SAGA complex, KAT-Gcn5 and Ub-protease Ubp8, on ubiquitylation of non-histone proteins we have performed a comprehensive analysis of the Ub-proteome in yeast Saccharomyces cerevisiae in strains disrupted in Gcn5, Ubp8 or both respect to wild type. We found significative alteration of ubiquitylation in proteins belonging to different functional categories with a recurrence of identical proteins in absence of Gcn5 or Ubp8 indicating shared targets and their interlaced function. Among the processes involved we noteworthy identified all major enzymes engaged in energy metabolism and glycolysis such as PFK1, PFK2 and others showing increased ubiquitylation respect to WT. We showed that the higher degree of ubiquitylation found is at post-translational level and does not depend on transcription. Noteworthy, we found in vivo severe defects of growth in poor sugar medium and inability to adaptive switch from fermentative to respiratory growth in strains lacking Gcn5 and Ubp8. Our findings data provide a novel, direct link, between metabolism and epigenetic control with a novel role of DUB-Ubp8 and KAT-Gcn5 on the ubiquitylation marking all the main glycolytic enzymes required for an effective execution of the glycolytic flux. Collectively our experimental results and the proposed model can lead to future research and innovative strategies that by targeting epigenetic modulators might be able to lower sugar utilization also in human cells.\n\nAuthor SummaryMolecular mechanisms dissected in simple yeast might be translated to similar circuitries in human cells for new discoveries in human diseases including cancer. Ubiquitylation of proteins is an evolutionary conserved mechanism required for many biological processes. Different post-translational modifications (PTMs) such as ubiquitylation, acetylation, methylation etc. are reciprocally regulated for deposition or removal. Epigenetic factors writing the PTMs code are often components of multiproteic complexes such as SAGA complex that holds the K-acetyltransferase (KAT) Gcn5 and the Ubiquitin-protease (DUB) Ubp8 highly conserved in Evolution. Cells respond to environment and nutrients by changing metabolism and group of enzymes involved in specific pathways are often coregulated by the deposition of selected PTMs. This study analyses the composition and quantitation of Ub-proteins differentially modified in absence of KAT-Gcn5 and DUB-Ubp8 in yeast. Interstingly, we highlighted the role of Gcn5/Ubp8 dependent ubiquitylation in marking major glycolytic enzymes necessary for glucose utilization. Our study suggests a novel regulatory pathway and, considering that lowering glycolysis is a promising strategy to target tumor metabolism, we propose this study as an interesting perspective to lower enhanced glycolysis in tumors.

molecular biology↗

bioRxiv2019

Land-use and related pressures have reduced biotic integrity more on islands than on mainlands

Tracking progress towards biodiversity targets requires indicators that are sensitive to changes at policy-relevant scales, can easily be aggregated to any spatial scale and are simple to understand. The Biodiversity Intactness Index (BII), which estimates the average abundance of a diverse set of organisms in a given area relative to their reference populations, was proposed in 2005 in response to this need. A new implementation of BII was developed as part of the PREDICTS project in 2016 and has been adopted by GEO BON, IPBES and CBD. The previous global models for BII estimation could not account for pressures having different effects in different settings. Islands are a setting of particular interest: many are home to a disproportionate number of endemic species; oceanic islands may have relatively low overall species diversity because of their isolation; and the pattern and timing of human pressures can be very different from that seen on mainlands. Here, we test whether biotic integrity - as estimated by BII - has decreased more severely on islands than mainlands. We update methods previously used to estimate BII globally (Newbold et al., 2016) to allow pressure effects to differ between islands and mainlands, while also implementing some other recent improvements in modelling. We estimate BII for islands and mainlands by combining global models of how two aspects of biodiversity - overall abundance, and compositional similarity to minimally-impacted sites - have been affected by human pressures. We use these models to project high-resolution ([~]1km2) global maps of BII for the year 2005. We calculate average BII for island and mainland biomes, countries, IPBES regions and biodiversity hotspots; and repeat our analyses using a richness-based version of BII. BII on both islands and mainlands has fallen below the values proposed as safe limits across most regions, biomes and biodiversity hotspots. Our BII estimates are lower than those published in 2016, globally, within all biodiversity hotspots and within most biomes, and show greater spatial heterogeneity; detailed analysis of these differences shows that they arise mostly from a combination of improvements to the modelling framework. Average BII does not strongly differ between islands and mainlands, but richness-based BII has fallen by more on islands. It seems native species are more negatively affected by rising human population density and road development on islands than mainlands, and islands have seen more land conversion. Our results highlight the parlous state of biodiversity native to islands.

ecology↗

bioRxiv2019

Risks to pollinators from different land-use transitions: bee species’ responses to agricultural expansion show strong phylogenetic signal

Bee species worldwide are facing a future of further land-use change and intensification. Populations of closely-related species with similar ecological characteristics are likely to respond similarly to such pressures. Such phylogenetic signal in species responses could undermine the stability of pollination services in agricultural and natural systems. We use abundance data from a global compilation of bee assemblages in different land uses to assess the sensitivity of 573 bee species to agricultural expansion, intensification and urbanization; and combine the results with the Bee Tree of Life to assess phylogenetic signal. In addition, we assess whether variation in species sensitivity to land-use change is better explained by phylogenetic or available functional trait differences. Bee species show strong phylogenetic signal in sensitivity to agricultural land expansion but only a weak signal in sensitivity to agricultural intensification and urbanisation. Sensitivities were usually best explained by a combination of functional and phylogenetic distances. This finding suggests that the commonly-recorded traits, despite being meaningful as functional response traits, do not capture all important determinants of bee species vulnerability or resistance. However, it also suggests that model-based predictions of the sensitivity of poorly known species may be sufficient to help guide conservation efforts.

ecology↗

bioRxiv2018

Worldwide impacts of past and projected future land-use change on local species richness and the Biodiversity Intactness Index

Although people have modified the world around us throughout human history, the Great Acceleration has seen drivers such as land conversion, exploitation of natural populations, species introductions, pollution and human-induced climate change placing biodiversity under increasing pressure. In this paper we examine 1) how terrestrial species communities have been impacted over the last thousand years of human development and 2) how plausible futures defined by alternative socio-economic scenarios are expected to impact species communities in the future. We use the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) database to model impacts of land-use change and human population on local species richness, community abundance, and biodiversity intactness using a mixed-effects modelling structure. Historical impacts are inferred through projection of model results onto maps of historical land use, provided by the land-use harmonization project, and gridded human population density (HYDE 3.1). Future impacts are explored using the Shared Socio-economic Pathway (SSP) scenarios. These scenarios detail five plausible global futures based upon socio-economic factors such as wealth, population, education, technology, and reliance on fossil fuels, and can be combined with Representative Concentration Pathway (RCP) scenarios to consider climate mitigation strategies. We project model results onto the gridded outputs of six SSP/RCP scenario combinations: SSP1/RCP2.6, SSP2/RCP4.5, SSP3/RCP7.0, SSP4/RCP3.4, SSP4/RCP6.0, and SSP5/RCP8.5. Historical trend lines show that most losses in local biodiversity are relatively recent, with 75% of all loss in both abundance-based Biodiversity Intactness Index and species richness occurring post-1800. Stark regional differences emerge in all future scenarios, with biodiversity in African regions undergoing greater losses than Oceania, North America and the European regions. Although climate change is expected to have severe detrimental impacts to biodiversity - which are not quantified in these results - it is important to consider how the climate change mitigation itself may also impact biodiversity. Our results suggest that strong climate change mitigation through biofuel production will detrimentally impact biodiversity: SSP4/RCP3.4 (with high biofuel mitigation) is predicted to see two times the decrease in abundance-based biodiversity intactness and three times the decrease in local species richness between 2015-2100 as is predicted for SSP4/RCP6.0 (with lower levels of mitigation). SSP4/RCP3.4 forecasts the greatest impact to average local species richness of all the SSP/RCP combinations with an average loss of 13% of local species richness projected to have occurred by 2100. SSP3/RCP7.0 - a scenario describing a globally segregated, and economically protectionist future with low climate change mitigation - has the worst impacts on abundance-based biodiversity intactness with an average loss of 26% of intactness by 2100. However, a brighter future is possible; SSP1/RCP2.6 describes a more sustainable future, where human populations are provided for without further jeopardising environmental integrity - in this scenario we project that biodiversity will recover somewhat, with gains in biodiversity intactness and species richness in many regions of the world by 2100.

ecology↗

bioRxiv2018

Changes in the Biodiversity Intactness Index in tropical and subtropical forest biomes, 2001-2012.

Few biodiversity indicators are available that reflect broad-sense biodiversity - rather than particular taxa - at fine spatial and temporal resolution. The Biodiversity Intactness Index (BII) reports how the average abundance of native terrestrial species in a region compares with their abundances before pronounced human impacts. BII is designed for use with data from a wide range of taxa and functional groups and for estimation at any resolution for which data on land use and related pressures are available. For each year from 2001 to 2012 we combined models of how land use and related pressures in tropical and subtropical forested biomes affect overall abundance and compositional similarity with data on anthropogenic pressures. We used these data to produce annual maps of modelled BII at a spatial resolution of 30 arc seconds (roughly 1km at the equator) across tropical and subtropical forested biomes. This is the first time temporal change in BII has been estimated across such a large region. The modelling approach used for compositional similarity is an improvement over that used previously when estimating BII, using data more efficiently. Overall, BII fell by an average of 2.4 percentage points between 2001 and 2012, with 83 countries seeing an average reduction and 45 an average increase, and the extent of primary forest fell by 3.9% over the same period. Changes are not strongly related to countries rates of economic growth over the same period.

ecology↗

bioRxiv2018

A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios

Abstract.To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land use and climate change on biodiversity and ecosystem services (i.e. natures contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs) to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenarios selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem service models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modelling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modelling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

ecology↗