Biology subjects

Paraskevopoulou, S.

Publications and source records attributed to Paraskevopoulou, S..

11 recordsLinked to original sources

bioRxiv2026

Lateral gene transfer introduced the microbial anaerobiosis-related gene rquA into early animals

Lateral gene transfer (LGT) enables rapid metabolic innovation in microbes, but its evolutionary importance in animals remains debated. Among metabolic traits with major ecological consequences, adaptations to low-oxygen conditions often involve modifications of mitochondrial electron transport and the quinones that mediate electron flow. Rhodoquinone-based anaerobic metabolism occurs in several eukaryotic lineages, yet the evolutionary routes by which animals acquired this capability are poorly understood. Here we show that freshwater sponges possess a rhodoquinone biosynthesis gene, rquA, previously restricted to microbial lineages, which was acquired by lateral gene transfer and functionally integrated into sponge metabolism. Heterologous expression of rquA from the model freshwater sponge Ephydatia muelleri enables rhodoquinone production in yeast, consistent with functional conservation. In E. muelleri, the rquA gene is upregulated under hypoxia and rhodoquinone is detectable across all lifestages, however, it is most abundant in early development in the pluiripotent gemmules. Using comparative genomics, we find that the presence of rquA in freshwater sponges correlates with loss of key genes of the ubiquinone biosynthesis pathway, suggesting these animals cannot synthesize ubiquinone de novo and we show that E. muelleri can convert exogenous ubiquinone to rhodoquinone. Rhodoquinone levels were significantly higher in rquA-encoding freshwater sponges compared to marine sponges that were sampled from natural environments. This study reveals that an early animal lineage acquired a microbial metabolism-related gene via lateral gene transfer during or before the transition to freshwater environments, enabling rhodoquinone utilization and potentially enhancing tolerance to oxygen fluctuations. Thereby, demonstrating how LGT shapes energy metabolism even in multicellular organisms.

evolutionary biology↗

bioRxiv2026

Semi-permeable capsules enable parallel cultivation and live microscopic observations of microbial eukaryotes

Semi-permeable capsules (SPCs) create enclosed porous microenvironments, diffusible to only small proteins and macromolecules. This presents a powerful tool for single cell observation, isolation, and sequencing. However, their range of use for sustaining viable microbial eukaryotes is largely unexplored. Single-cell eukaryotes are often understudied, with a wealth of unknown lifecycles, culturing methods and inter-microbial interactions, which are difficult to visualize. Here, we show that eukaryotes from eight different supergroups can be captured and propagated in SPCs. Encapsulation allowed observations of cell stages, motility and growth in a traceable and parallelized manner.

microbiology↗

bioRxiv2025

Light pollution affects the behavior and life history traits of aquatic invertebrates

Circadian rhythms regulate essential biological processes, including behavior, reproduction and survival, across diverse organisms. Disruptions to this cycle, whether through artificial light at night (ALAN) or reduced exposure to full-spectrum daylight, can interfere with biological processes and ultimately threaten biodiversity. This concern is growing as ALAN spreads beyond urban areas through streetlights and skyglow. Aquatic ecosystems, in which zooplankton play a key role as primary consumers as well as prey for higher trophic levels, are particularly vulnerable. Despite growing research on the impact of ALAN on some zooplankton, rotifers remain largely understudied. Here, we conducted two experiments to assess the effects of light on Brachionus species. The first experiment examined how different ALAN wavelengths influenced life history traits in three Brachionus species, while the second one investigated the attachment behavior of B. rubens on a Daphnia host under four light conditions. Our findings reveal that ALAN has strong but species-specific effects on rotifers. Green light enhanced survival and reproductive output in B. calyciflorus sensu stricto, while suppressed reproduction in B. fernandoi. In B. rubens, white light particularly altered reproductive patterns and attachment behavior. These results highlight the complex and species-specific impacts that ALAN has on rotifers, emphasizing the need for further research to fully understand its broader ecological consequences.

ecology↗

bioRxiv2025

Transcriptomic landscape reveals immunity related trade-offs in an invertebrate-fungal host-parasite system

O_LIBy exploiting host resources, parasites impose significant fitness costs onto their hosts, thereby affecting their population dynamics. Hosts, in turn, employ a series of mechanism to resist or tolerate parasitic infections. Unlike vertebrates, which possess a sophisticated immune system, invertebrates rely solely on innate immunity to combat pathogens. Despite over 50 years of research, the molecular basis of innate immunity in non-insect invertebrates remains limited. C_LIO_LIWe used the Daphnia magna - Metschnikowia bicuspidata host-parasite system to shed light on conserved immune responses among Daphnia species and parasite-driven immunological shifts. We examined the transcriptomic landscape across infected, exposed-uninfected and unexposed individuals and identified candidate genes that might be involved in the haemocyte recruitment. Additionally, we identified genes that might encode for reinforcement of the gut epithelium, and thus confer resistance to the parasite. C_LIO_LIWe measured life-history traits and observed that shifts correlated with immune activation. Specifically, exposed-uninfected individuals exhibited a delay in reproductive maturation, likely a direct effect of immune activation. However, these shifts appeared temporal, as animals compensated in total reproductive output over time. C_LIO_LIUnlike exposed-uninfected animals, infected individuals exhibited metabolic shifts that are indicative of host metabolic exhaustion. This metabolic reallocation aligns with the terminal investment hypothesis, where hosts facing high mortality risk divert resources from somatic maintenance to immediate reproduction in order to maximize fitness before death. C_LIO_LIOur findings provide novel insights into the molecular and physiological mechanisms underlying invertebrate immune responses and life-history trade-offs in the context of parasitic infections. C_LI

evolutionary biology↗

bioRxiv2025

Decoding host responses: How a freshwater invertebrate defends against a parasitic bacterium

Host-parasite interactions drive coevolutionary dynamics, often leading to reciprocal adaptations between hosts and parasites, a process known as the Red Queen arms race. While the molecular mechanisms underlying vertebrate and insect immune responses have been studied extensively, those of aquatic invertebrates remain unexplored, despite their critical role in ecosystem stability and aquaculture. Here, we use the Daphnia magna-Pasteuria ramosa system to investigate the hosts immune response and the molecular mechanisms underlying host-parasite interactions. We inoculated 800 D. magna hosts with 20,000 mature spores of P. ramosa and tracked the progression of infection by measuring the proportion of infected individuals and the developmental stages of the parasite at multiple time points post-inoculation (hereafter p.i.). RNA sequencing was performed at key infection phases, early (Cauliflower stage), mid (Cauliflower and Grape stages), and terminal (Cauliflower, Grape, and Mature spore stages), to capture gene expression changes linked to infection dynamics. Our transcriptomic analyses revealed key immune genes involved in host defense, including genes involved in Toll signaling pathways, thereby revealing significant changes in pathways related to immune function, host metabolism, and resource allocation. Our findings suggest that iron sequestration may serve as a host defense strategy to restrict parasite growth, representing a form of nutritional immunity. Furthermore, pathways associated with infection-induced phenotypic traits, such as somatic growth, red coloration, and castration, were significantly upregulated, underscoring the impact of the infection on host physiology. Taken together, these findings provide new insights into the interplay between hosts and parasites at a molecular level in an ecologically relevant system, advancing our understanding of infection strategies in aquatic invertebrates.

evolutionary biology↗

bioRxiv2024

CIEVaD: a lightweight workflow collection for rapid and on demand deployment of end-to-end testing of genomic variant detection

The identification of genomic variants has become a routine task in the thriving age of genome sequencing. Particularly small genomic variants of single or few nucleotides are routinely investigated for their impact on an organisms phenotype. Hence, precise and robust detection of the variants exact genomic location and change in nucleotide composition is vital in many biological applications. Although a plethora of methods exist for the many key steps of variant detection, thoroughly testing the detection process and evaluating its results is still a cumbersome procedure. In this work, we present a collection of trivial to apply and highly modifiable workflows to facilitate the generation of synthetic test data as well as to evaluate the accordance of a user-provided set of variants with the test data. AvailabilityThe workflows are implemented in Nextflow and are freely available and open-source at https://github.com/rki-mf1/cievad under the GPL-3.0 license.

bioinformatics↗

bioRxiv2023

The gems of the Middle-East: Unveiling the biodiversity of Monogonont rotifers in temporary waterbodies of Israel

Temporary ponds represent ecologically important habitats that support high species diversity and provide essential ecosystem services, particularly in certain countries surrounding the Mediterranean Sea, where natural lakes are scarce. Israel is located along the southeastern Mediterranean coast and features Mediterranean and arid climatic zones that vary in a variety of meteorological parameters. Temporary ponds are prevalent throughout Israel, including the Mediterranean coast, Mediterranean mountain (i.e., Galilee region), and arid climatic zones. These temporal ponds harbor diverse invertebrate communities that exhibit significant spatial and temporal variations. Among these communities, Monogonont rotifers are notably one of the most diverse and abundant groups. Despite their significant role in aquatic food webs, rotifers are often overlooked in environmental studies, likely due to their small size and difficulties associated with their taxonomy. Resilient resting eggs produced by Monogonont rotifers during periods of unsuitable environmental conditions serve as significant source of propagules that drive the recolonization of temporary ponds upon rehydration, thereby influencing the dynamics of the pond community and metacommunity organization. Here, we examined the diversity of Monogonont rotifers by rehydrating sediment from 30 temporary ponds across Israel. Our analysis identified 39 species, with 25 (64%) of them being reported for the first time in Israel. We found the highest diversity of Monogonont rotifers in the Mediterranean coast region, which is characterized by low altitude, long hydroperiod, and relatively low mean summer daily maximum temperature, while the lowest diversity was found in the Arid region which is characterized by high altitude, short hydroperiod, and high mean summer daily maximum temperature. Our findings suggest that altitude, hydroperiod and mean summer daily maximum temperature are important parameters associated with the observed biodiversity patterns. Our metacommunity analysis further revealed a small contribution of geographic distance (2%) and environmental factors (1%) in shaping rotifer metacommunities. We also found a significant positive correlation among community composition, environmental distance (i.e., Gowers distance) and geographic distance, possibly due to a linearity in the sampling set-up. Overall, our study highlights the importance of temporary ponds as significant habitats for diverse rotifer communities and emphasizes the need to further study "micro" invertebrate diversity in these unique ecosystems.

ecology↗

bioRxiv2021

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains

We examined the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 that arose in the United Kingdom and spread globally. Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa B.1.351 variant, than of the infecting variant. The drop in cross-reactivity was more pronounced following B.1.1.7 than parental strain infection, indicating asymmetric heterotypic immunity induced by SARS-CoV-2 variants.

immunology↗

bioRxiv2021

Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases

Differences in humoral immunity to coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), between children and adults remain unexplained and the impact of underlying immune dysfunction or suppression unknown. Here, we examined the antibody immune competence of children and adolescents with prevalent inflammatory rheumatic diseases, juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM) and juvenile systemic lupus erythematosus (JSLE), against the seasonal human coronavirus (HCoV)-OC43 that frequently infects this age group. Despite immune dysfunction and immunosuppressive treatment, JIA, JDM and JSLE patients mounted comparable or stronger responses than healthier peers, dominated by IgG antibodies to HCoV-OC43 spike, and harboured IgG antibodies that cross-reacted with SARS-CoV-2 spike. In contrast, responses to HCoV-OC43 and SARS-CoV-2 nucleoproteins exhibited delayed age-dependent class-switching and were not elevated in JIA, JDM and JSLE patients, arguing against increased exposure. Consequently, autoimmune rheumatic diseases and their treatment were associated with a favourable ratio of spike to nucleoprotein antibodies.

immunology↗

bioRxiv2020

Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans

Several related human coronaviruses (HCoVs) are endemic in the human population, causing mild respiratory infections1. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent of Coronavirus disease 2019 (COVID-19), is a recent zoonotic infection that has quickly reached pandemic proportions2,3. Zoonotic introduction of novel coronaviruses is thought to occur in the absence of pre-existing immunity in the target human population. Using diverse assays for detection of antibodies reactive with the SARS-CoV-2 spike (S) glycoprotein, we demonstrate the presence of pre-existing humoral immunity in uninfected and unexposed humans to the new coronavirus. SARS-CoV-2 S-reactive antibodies were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents. These were predominantly of the IgG class and targeted the S2 subunit. In contrast, SARS-CoV-2 infection induced higher titres of SARS-CoV-2 S-reactive IgG antibodies, targeting both the S1 and S2 subunits, as well as concomitant IgM and IgA antibodies, lasting throughout the observation period of 6 weeks since symptoms onset. SARS-CoV-2-uninfected donor sera also variably reacted with SARS-CoV-2 S and nucleoprotein (N), but not with the S1 subunit or the receptor binding domain (RBD) of S on standard enzyme immunoassays. Notably, SARS-CoV-2-uninfected donor sera exhibited specific neutralising activity against SARS-CoV-2 and SARS-CoV-2 S pseudotypes, according to levels of SARS-CoV-2 S-binding IgG and with efficiencies comparable to those of COVID-19 patient sera. Distinguishing pre-existing and de novo antibody responses to SARS-CoV-2 will be critical for our understanding of susceptibility to and the natural course of SARS-CoV-2 infection.

immunology↗

bioRxiv2019

Introgression of Austrian fire-bellied toads (Bombina bombina) into northern German populations confirmed by complete mitochondrial genomes and transcriptome-wide Single Nucleotide Polymorphisms (SNPs)

The fire-bellied toad (Bombina bombina) is a small amphibian species inhabiting the lowlands of Central and Eastern Europe. Continual population fragmentation has caused a decrease in genetic diversity and gene flow in margin populations in Northern Germany. Previous research using mitochondrial control region data uncovered a translocation of allochthonous toads from Austria into a single northern German population, Hogsdorf. Microsatellite and MHC data also confirmed this introgression, but were limited in revealing the true extent of this translocation for all investigated populations. Here, we utilize complete mitochondrial genomes and nuclear data, in the form of transcriptomes, to unravel the full extent of admixture from this translocation. The increased number of loci enabled us to uncover signs of introgression in four out of the five northern populations investigated. Moreover, as hybrids between B. bombina and its sister species, B. variegata, have been reported in Austria, we also investigated whether B. variegata alleles were translocated into the northern gene pool. We found evidence for hybridization between Austrian B. bombina and B. variegata, as well as traces of B. variegata alleles in one of the five German populations included in this study. These findings present the first reported case of introgressed relict B. variegata alleles from the Southern lineage being detected in Northern Germany.

evolutionary biology↗