Biology subjects

Pereira, H.

Publications and source records attributed to Pereira, H..

11 recordsLinked to original sources

bioRxiv2025

Greener, Wilder, Better: Valuing Complexity and Diversity in Urban Riparian Areas

(1) Riparian areas are among the most valuable ecosystems on earth due to their high biodiversity and contributions to human well-being, yet urban riparian areas face significant threats from urbanization and associated expansion. Current management strategies do not consider all the contributions of urban green spaces to human well-being. Over the last decade stated preference studies have been widely used to gain insights into public attitudes towards urban green spaces. However, whether and to what extent the public values urban biodiversity in urban riparian areas remains unclear. (2) We used a discrete choice experiment approach to determine public preference for urban biodiversity and management interventions in urban riparian areas through a discrete choice experiment conducted in Poland. (3) We found strong positive preferences for highly complex and dense vegetation along urban riparian areas, indicating a public inclination towards enhancing natural biodiversity in public spaces. Additionally, respondents expressed a preference for reducing impermeable surfaces, such as concrete pathways, highlighting the value placed on minimizing urban encroachment. (4) Willingness-to-pay (WTP) results suggested that the public in Poland is prepared to financially support certain biodiversity conservation measures and land-conversion interventions in urban green spaces. (5) These results underscore the importance of integrating ecological research and public preferences into urban riparian management strategies, emphasizing the need for policy approaches that prioritize biodiversity conservation while balancing urban development.

ecology↗

bioRxiv2025

TOWARDS CLIMATE-SMART REWILDING: AN INTEGRATED FRAMEWORK FOR BIODIVERSITY, CLIMATE CHANGE, AND SOCIETY

The UN Decade on Ecosystem Restoration and the Kunming-Montreal Global Biodiversity Framework aim to restore 30% of degraded ecosystems. Both the IPCC and IPBES highlight the crucial role of ecosystem restoration in addressing the interconnected crises of climate change and biodiversity loss. One key restoration strategy is rewilding, which enhances ecosystem complexity with minimal human intervention. While traditional rewilding strategies often focus on benefits for biodiversity, we propose a climate-smart rewilding framework as a new approach designed to deliver climate benefits alongside biodiversity restoration. This framework seeks to integrate biodiversity, climate change adaptation and mitigation, as well as socio-economic benefits and trade-offs. We illustrate how this framework can be utilized to identify areas across Europe where rewilding could increase carbon sequestration, enhance species abilities to adapt to the velocity of climate change, and maximize wildlife-watching benefits while minimizing the costs associated with livestock-wildlife conflict. Finally, we acknowledge some limitations of climate-smart rewilding, but we argue that its adaptability and low cost render it a promising solution to the challenges facing Europe and beyond.

ecology↗

bioRxiv2025

Finding space for rewilding: participatory scenarios reveal ecological opportunities based on plural values of nature

O_LIRewilding aims to restore degraded ecosystems in human-dominated areas by promoting self-sustained ecosystems and reducing human control over ecological processes. However, co-benefits and trade-offs between rewilding actions and the interests of local societies must be thoroughly considered. IPBES proposed the Nature Futures framework, a scenario tool to engage society in conservation planning. However, its potential for co-designing ecological restoration remains to be explored. C_LIO_LIThis paper presents a novel methodology that utilises the Nature Futures Framework to address opportunities, co-benefits and trade-offs using rewilding. The study aims to investigate the Nature futures Framework effectiveness in rewilding by involving stakeholders in participatory scenario development. To accomplish this, we conducted stakeholder interviews to co-design three distinct scenarios that reflect diverse values of nature and rewilding strategies for the German Oder Delta. C_LIO_LIThe scenario development process identified spatial priorities for three scenarios: Nature for Nature, Nature for Society (NfS) and Nature as Culture. (NaC). The first, focused on rewilding and increasing forest and river connectivity across 65.8% of the study area. NfS narratives covering 14.4% of the area emphasised de-intensification of forestry and reflooding of peatlands, while NaC prioritised transformation towards extensive agriculture and reflooding for paludiculture across 8.6%. C_LIO_LIThe study identified regions with single and multiple values of nature. Further, there were regions of overlap between scenarios, highlighting the interconnectedness of different rewilding actions and priorities. By pinpointing corresponding values, the research highlighted actions that could result in co-benefits. The findings emphasise the importance of considering pluralistic values when designing rewilding actions, which encourages stakeholders to highlight areas of less resistance to rewilding and co-adapt to the changes in the landscape. C_LIO_LIThis study presents a methodological framework for participatory scenario development for rewilding initiatives. By combining participatory processes with the Nature Futures Framework, our structured approach helps identify priority areas and navigate socio-ecological challenges in landscape restoration. It employs participatory mapping to aid the visualization of land-use changes and aligning rewilding actions with ecological and societal needs. This approach enhances governance frameworks and promotes inclusive rewilding efforts, creating a replicable model for landscape restoration that connects rewilding with sustainability and societal well-being goals. C_LI

ecology↗

bioRxiv2025

Harnessing the immune system to treat bone loss: The immunomodulatory and osteoprotective effects of the microalga Skeletonema costatum

The emerging field of osteoimmunology provides compelling evidence for the pivotal role of the immune system in the development of bone erosive pathologies such as osteoporosis. However, no immunomodulatory drug has yet been integrated into the therapeutic management of bone loss. Recently, driven by the demand for next-generation treatments for these conditions, natural compounds are gaining renewed attention as promising candidates for drug discovery. In this study, we explored the anti-osteoclastogenic effects of an emerging extract from the marine microalga Skeletonema costatum. Using a zebrafish model of bone regeneration, we demonstrated the extracts ability to inhibit the recruitment of osteoclast progenitors and block their differentiation into mature osteoclasts in vivo. Bulk RNA sequencing of early-stage fin blastemas revealed the downregulation of genes involved in inflammation, T-cell activation, and antigen presentation, suggesting that the extract exerts its effects primarily through immunomodulatory mechanisms. To further assess its therapeutic potential, we tested the extract in a medaka model of RANKL-induced osteoporosis and on a murine macrophage cell line. The extract effectively prevented bone loss in fish and inhibited osteoclastic differentiation in murine macrophages in vitro. Collectively, our findings provide mechanistic insights into a novel, therapeutically relevant natural extract, offering proof of concept for its osteoprotective potential through immune system modulation. SignificanceRecent findings in the field of osteoimmunology reveal the potential of targeting immune cells to regulate bone homeostasis. However, this approach has yet to be applied to therapies for bone erosive conditions. This study explores the potential of an immunomodulatory strategy using an emerging natural extract, which prevent osteoclast differentiation by modulating inflammation, T-cell activation, and macrophage fate determination in zebrafish and medaka models of bone regeneration and osteoporosis. The extract also inhibits osteoclastic differentiation in a murine macrophage line, suggesting its translatability to mammalian systems. By focusing on immune pathways, this research provides a proof of concept for developing immunomodulatory treatments for osteoporosis and similar conditions, addressing a critical need in bone health management.

immunology↗

bioRxiv2024

Narratives for positive nature futures in Europe

O_LIThe Nature Futures Framework (NFF) is a novel tool for the development of positive scenarios centred on the relationship of nature and people, emphasising biodiversity as part of the solution to environmental challenges across various spatial and temporal scales, explicitly addressing a plurality of values for nature. C_LIO_LIIn this work, we describe the process that has led to the formulation of continental-scale positive narratives for conservation in Europe based on the NFF and its value perspectives (Nature for Nature; Nature for Society; Nature as Culture), through a stakeholder group elicitation. We focused on 6 topics in the narratives: Nature Protection and Restoration; Forestry; Freshwater Ecosystems; Urban Systems; Agriculture, and Energy. We analyse differences and similarities among the narratives across these topics. C_LIO_LIWe develop three novel Nature Futures narratives for Europe with contrasting perspectives and priorities for the six topics. Within the EU socioeconomic trends and policy framework, common solutions that simultaneously tackle biodiversity conservation and instrumental and cultural Natures Contributions to People (NCP) provision emerged. C_LIO_LIThis set of narratives may integrate preferences concerning EU-level conservation targets and plausible socio-ecological development pathways, supporting the modelling of positive scenarios for nature that can be crucial in guiding policy decisions towards recovery of nature. C_LI

ecology↗

bioRxiv2024

The gut microbiota-immune-brain axis in a wild vertebrate: dynamic interactions and health impacts

The gut microbiota-immune-brain axis is a feedback network which influences diverse physiological processes and plays a pivotal role in overall health and well-being. Although research in humans and laboratory mice has shed light into the associations and mechanisms governing this communication network, evidence of such interactions in wild, especially in young animals, is lacking. We therefore investigated these interactions during early development in a population of common buzzards (Buteo buteo) and their effects on individual condition. In a longitudinal study, we used a multi-marker approach to establish potential links between the bacterial and eukaryotic gut microbiota, a panel of immune assays and feather corticosterone measurements as a proxy for long-term stress. Using Bayesian structural equation modelling, we found no support for feedback between gut microbial diversity and immune or stress parameters. However, we did find strong relationships in the feedback network. Immunity was negatively correlated with corticosterone levels, and microbial diversity was positively associated with nestling body condition. Furthermore, corticosterone levels and eukaryotic microbiota diversity decreased with age while immune activity increased. The absence of conclusive support for the microbiota-immune-brain axis in common buzzard nestlings, coupled with the evidence for stress mediated immunosuppression, suggests a dominating role of stress-dominated maturation of the immune system during early development. Confounding factors inherent to wild systems and developing animals might override associations known from adult laboratory model subjects. The positive association between microbial diversity and body condition indicates the potential health benefits of possessing a diverse and stable microbiota.

microbiology↗

bioRxiv2024

SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences

BackgroundSynthetic biology involves combining different DNA fragments, each containing functional biological parts, to address specific problems. Fundamental gene-function research often requires cloning and propagating DNA fragments, such as those from the iGEM Parts Registry or Addgene, typically distributed as circular plasmids. Addgenes repository alone offers around 150,000 plasmids. To ensure data integrity, cryptographic checksums can be calculated for the sequences. Each sequence has a unique checksum, making checksums useful for validation and quick lookups of associated annotations. For example, the SEGUID checksum uniquely identifies protein sequences with a 27-character string. ObjectivesThe original SEGUID, while effective for protein sequences and single-stranded DNA (ssDNA), is not suitable for circular DNA since there is no natural starting position nor for double-stranded DNA (dsDNA) since two separate sequences are present. Challenges include how to uniquely represent linear dsDNA, circular ssDNA, and circular dsDNA. To meet these needs, we propose SEGUID v2, which extends the original SEGUID to handle additional types of sequences. ConclusionsSEGUID v2 produces orientation and rotation in-variant checksums for single-stranded, double-stranded, possibly staggered, linear, and circular DNA and RNA sequences. Customizable alphabets allow for other types of sequences. In contrast to the original SEGUID, which uses Base64, SEGUID v2 uses Base64url to encode the SHA-1 hash. This ensures SEGUID v2 checksums can be used as-is in filenames, regardless of platform, and in URLs, with minimal friction. AvailabilitySEGUID v2 is readily available for major program-ming languages, distributed under the MIT license. JavaScript package seguid is available on npm, Python package seguid on PyPi, R package seguid on CRAN, and a Tcl script on GitHub. These tools, along with documentation, examples, and an online SEGUID Calculator, can be found at https://www.seguid.org.

bioinformatics↗

bioRxiv2022

Road encroachment mediates species occupancy, trait filtering and dissimilarity of songbird communities

Assessing the road effects on biodiversity is challenging because impacts may depend on both wildlife responses to roads and on the spatial arrangement of roads. We questioned whether an increase in road encroachment i.e., the advancement of roads into non-urban areas, leads to significant changes (positive and negative) in species occurrence, and if so, whether those changes are linked to specific traits related to perturbation sensitiveness, therefore acting as filters that increase the community compositional dissimilarity. Using a large citizen-science dataset of point-counts performed throughout Iberian Peninsula (4,459 unique survey sites), we modelled the effect of road density on the occurrence of common songbirds (n=58), while accounting for potential confounding effects of environment and survey effort. We then tested if species occurrence patterns would be linked to specific traits related to the ability to cope with human presence. Finally, we assessed how road density affect the community compositional dissimilarity. We estimated 24 (41%) and 12 (21%) species to be negatively and positively affected by roads, respectively. Increased road encroachment was positively related with a higher prevalence of urban dwellers and negatively related with the occurrence of species nesting and foraging on the ground. Furthermore, increasing road density translated into an increasing community compositional dissimilarity, mostly due to species turnover. Our study support previous research showing that roads have different effects on the occurrence of different species, but we revealed that at least three species' traits have a clear relation with such road responses. Such trait filtering is probably causing a high species turnover between songbird communities occurring in roaded and nearby roadless areas. Overall, we found that different species-specific responses to roads translates into changes at the community level. Landscape and road-network management should be conceived acknowledging that roads are contributing to biodiversity changes. As so, building upon the concepts of Land Sharing / Land Sparing, conservation actions should be tailored according to the different species responses e.g., road verge management targeting species having a positive relation with road density; and compensation actions targeting species showing a negative response toward roads.

ecology↗

bioRxiv2020

A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process

SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral main protease is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. Although several mechanisms of self-cleavage had been proposed for SARS-CoV, the lack of structural information for each step is a setback to the understanding of this process. Herein, we used X-ray crystallography to characterize an immature form of the main protease, which revealed major conformational changes in the positioning of domain-three over the active site, hampering the dimerization and diminishing its activity. We propose that this form preludes the cis-cleavage of N-terminal residues within the dimer, leading to the mature active site. Using fragment screening, we probe new cavities in this form which can be used to guide therapeutic development. Furthermore, we characterized a serine site-directed mutant of the main protease bound to its endogenous N and C-terminal residues during the formation of the tetramer. This quaternary form is also present in solution, suggesting a transitional state during the C-terminal trans-cleavage. This data sheds light in the structural modifications of the SARS-CoV-2 main protease during maturation, which can guide the development of new inhibitors targeting its intermediary states.

biochemistry↗

bioRxiv2019

Linkage disequilibrium and haplotype block patterns in popcorn populations

Linkage disequilibrium (LD) analysis provides information on evolutionary aspects of the populations and allows selecting populations and single nucleotide polymorphisms (SNPs) for association studies. Recently, haplotype blocks have been used to increase the power of quantitative trait loci detection in genome-wide association studies and the prediction accuracy with genomic selection. The objectives of this study were to compare the degree of LD, the LD decay, the LD decay extent, and the number and length of haplotype blocks in the populations and to elaborate the first LD map for maize, for elucidating if the maize chromosomes also had a pattern of interspaced regions of high and low rates of recombination. We used a biparental temperate population, a tropical synthetic, and a tropical breeding population, genotyped for approximately 75,000 SNPs. The level of LD expressed by the r2 values is surprisingly low (0.02, 0.04, and 0.04), but comparable to some non-isolated human populations. The general evidence is that the synthetic is the population with higher LD. It is not expected a significant advantage of haplotype-based association study and along generations genomic selection due to the reduced number of SNPs in the haplotype blocks (2 to 3). The results concerning LD decay (rapid decay after 5-10 kb) and LD decay extent (along up to 300 kb) are in the range observed with maize inbred line panels. Our most important result is that maize chromosomes had a pattern of regions of extensive LD interspaced with regions of low LD. However, our simple simulated LD map provides evidence that this pattern can reflect regions with differences of allele frequencies and LD level (expressed by D) and not regions with high and low rates of recombination.

genetics↗

bioRxiv2018

The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleotide selectivity of PNPs

Purine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, named as SmPNP2. Screening of different ligands using a thermofluorescence approach indicated cytidine and cytosine as potential ligands. The binding of cytosine was confirmed by isothermal titration calorimetry, with a KD of 27 M, and kinetic parameters for cytidine catalysis were obtained by ITC resulting in a KM of 76.3 M. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystallographic structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capability of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site allowing an alternative binding mode for nucleosides, with a 180{degrees} rotation from the canonical binding mode. The remarkable plasticity of this binding site deepens the understanding of the correlation between structure and nucleotide selectivity, offering new ways to analyses PNP activity.\n\nAuthor SummarySchistosoma mansoni is a human parasite dependent on purine salvage for purine bases supply. Purine nucleoside phosphorylase (PNP) is a key enzyme in this pathway. It carries two PNP isoforms, one previously characterized (SmPNP1) and one unknown (SmPNP2). Here we present the crystallographic structure of SmPNP2 and its complex with cytosine, cytidine, ribose-l-phosphate, adenine, hypoxanthine, and tubercidin. Cytidine and cytosine were identified as ligands of SmPNP2 using a thermofluorescence approach. Binding of cytosine was proven by Isothermal Titration Calorimetry (ITC) and cytidine, inosine, and adenosine kinetic parameters were also obtained. Purine bases showed different binding in the active site, rotated 180{degrees} from the canonical binding mode. Its the first report showing a Low Molecular Mass PNP capable of catalyzing both types of nucleotide bases. The SmPNP2 odd behavior sheds a new light on the Schistosoma mansonis life cycle metabolic adaptation.

biochemistry↗