Biology subjects

Lewandowska, M.

Publications and source records attributed to Lewandowska, M..

11 recordsLinked to original sources

bioRxiv2025

An ancient anthozoan protein reveals an alternative evolutionary path of antiviral signaling

How antiviral immunity first arose in animals is a central question in evolutionary biology. Using the sea anemone Nematostella vectensis, we identify CARDIB, a previously uncharacterized gene located next to RLRb, a cnidarian homolog of the vertebrate RIG-I-like receptor family. This conserved genomic linkage across Anthozoa reveals an ancient coupling between immune sensing and regulation. Despite sequence similarity to vertebrate MAVS, CARDIB performs an opposing function: it represses immune genes under basal conditions yet is essential for activation upon viral challenge. CARDIB binds RLRb via a single CARD domain, forming a repressive complex. Loss of either gene abolishes antiviral transcription, disrupts apoptosis, and elevates viral load under lab conditions. Both genes as well as the RLRb paralog, RLRa, are essential for antiviral defense under native conditions. Phylogeny places the cnidarian CARDs distinctly from the vertebrate RLR-MAVS families, revealing an ancient antiviral system regulating antiviral response through CARD-based signaling.

evolutionary biology↗

bioRxiv2025

Multi-Source Neural Activity Indices and Spatial Filters for EEG/MEG Inverse Problem: An Extension to MNE-Python

Accurate electroencephalography (EEG) and magnetoencephalography (MEG) source localization and reconstruction are essential for understanding brain function, yet remain challenging because the underlying EEG/MEG inverse problem is inherently ill-posed. Spatial filtering (beamforming) approaches, such as linearly constrained minimum variance (LCMV) spatial filters, are widely used and well supported by existing analysis software. In this work, we extend this framework by deriving a novel family of unbiased multi-source neural activity indices that form the localization stage of a two-stage spatial-filtering-based localization-reconstruction framework for the EEG/MEG inverse problem. In contrast to existing formulations, the proposed indices do not require knowledge of the target source covariance matrix, making them directly applicable in practical experimental settings. Their compact algebraic forms enable straightforward and numerically efficient implementation. The framework is validated on simulated EEG data and its applicability is illustrated through an example involving experimental EEG data from an oddball paradigm. To facilitate adoption, we provide a full open-source implementation extending MNE-Python, accompanied by a practical tutorial.

neuroscience↗

bioRxiv2025

Characterization of RNA interference in the model cnidarian Nematostella vectensis reveals partial target silencing but lack of small RNA amplification

RNA interference (RNAi) is a sequence-specific mRNA degradation mechanism, which serves as an antiviral pathway by processing viral double-stranded RNA (dsRNA) into short interfering RNAs (siRNAs), leading to virus destruction. It is considered as an ancestral mechanism which invertebrates rely on for defense against viruses, whereas vertebrates have evolved instead the interferon pathway. Recent studies suggest that sea anemones, members of the basally-branching phylum Cnidaria, might possess an immune response with more vertebrate characteristics than previously thought; however, it is unknown whether cnidarians also employ RNAi as an antiviral response similarly to nematodes and insects. Here, we characterize the response of the model cnidarian Nematostella vectensis to simulated viral infection. We injected dsRNA with eGFP sequence into eGFP-expressing transgenic zygotes and show that siRNAs mapping to the eGFP sequence are generated and induce a moderate but significant knockdown of eGFP expression. Interestingly, we detected no evidence for secondary siRNA production, despite their crucial role in the amplification of antiviral response in other organisms. Notably, siRNA pathway components are specifically upregulated upon dsRNA injection, while microRNA pathway components are downregulated. Furthermore, injection of mRNA coding for self-replicating viral gene fused to eGFP, also induced upregulation of siRNA-related genes and a mild decrease in transgene expression. Overall, we propose that N. vectensis possesses an siRNA-mediated antiviral response that lacks secondary amplification and functions as a short-term antiviral mechanism.

evolutionary biology↗

bioRxiv2024

Heat stress drives rapid viral and antiviral innate immunity activation in Hexacorallia

The cnidarian class Hexacorallia, encompassing stony corals and sea anemones, plays a critical role in marine ecosystems. Coral bleaching, the disruption of the symbiosis between stony corals and zooxanthellate algae, is driven by climate change-induced seawater warming and further exacerbated by pathogenic microbes. However, how pathogens, especially viruses, contribute to accelerated bleaching remains poorly understood. The present study utilizes the model sea anemone Nematostella vectensis to explore these dynamics by creating a transgenic line with a reporter gene regulated by sequences from two RIG-I-like receptor (RLR) genes involved in antiviral responses. Under heat stress, the reporter gene showed significant upregulation, indicating that these regulatory sequences are indeed responsive to thermal stress. Analyses of transcriptome data of N. vectensis, Exaiptasia diaphana (another sea anemone), and the stony coral Stylophora pistillata revealed stress-induced activation of a set of bona fide immune-related genes conserved between the three species. Population-specific differences in stress-induced transcriptional responses of immune-related genes were evident in both Nematostella and Stylophora, depending on geographic origin. In Exaiptasia, the presence or absence of zooxanthellae also influenced stress-induced immune gene expression. To test whether the viruses themselves may contribute to this immune response under stress, we subjected Nematostella polyps to variable periods of heat stress and measured the transcript levels of resident viruses as well as selected antiviral genes. While the antiviral genes responded within 1-3 hours of heat stress, viral gene expression was already upregulated within 30 minutes, suggesting that their increase might be contributing to the elevated immune response under stress, and consequentially, the further demise of organismal homeostasis. These findings highlight the complex interplay between environmental stress, viruses, immune responses, and symbiotic states in Hexacorallia. Better understanding of these mechanisms could provide insights into the role of immune pathways in coral resilience and bleaching in a changing climate.

evolutionary biology↗

bioRxiv2024

Fitness adaptations of Japanese encephalitis virus in pigs following vector-free serial passaging

Japanese encephalitis virus (JEV) is a zoonotic mosquito-transmitted Flavivirus circulating in birds and pigs. In humans, JEV can cause severe viral encephalitis with high mortality. Considering that vector-free direct virus transmission was observed in pigs, JEV introduction into an immunologically naive pig population could result in a series of direct transmissions disrupting the alternating host cycling between vertebrates and mosquitoes. To assess the potential consequences of such a realistic scenario, we passaged JEV ten times in pigs. This resulted in higher in vivo viral replication, increased shedding, and stronger innate immune responses in pigs. Nevertheless, the viral tissue tropism remained similar and frequency of direct transmission was not enhanced. Next generation sequencing showed single nucleotide deviations in 10% of the genome during passaging. In total, 25 point mutations were selected to reach a frequency of at least 35% in one of the passages. From these, six mutations resulted in amino acid changes located in the precursor of membrane, the envelope, the non-structural 3 and the non-structural 5 proteins. In a competition experiment with two lines of passaging, the mutation M374L in the envelope protein and N275D in the non-structural protein 5 showed a fitness advantage in pigs. Altogether, the interruption of the alternating host cycle of JEV caused a prominent selection of viral quasispecies as well as selection of de novo mutations associated with fitness gains in pigs, albeit without enhancing direct transmission frequency. Author summaryJapanese encephalitis virus (JEV) represents a major health threat in parts of Asia and Oceania. Primary vertebrate hosts are birds and pigs, but human infection also occurs and can cause severe encephalitis with high mortality. Like other Flaviviruses transmitted by insect bites, JEV requires replication in alternating cycles between mosquitoes on one side and birds or pigs on the other side. However, we previously reported that direct transmissions between pigs in absence of mosquitos can occur. Considering the increased risks for such events after the spread of JEV to a new region with immunologically naive pigs, the present study was performed to understand if and how a series of direct transmissions would promote JEV adaptations to pigs and change virus-host interactions. Pigs infected with JEV passaged ten times showed enhanced clinical symptoms and stronger antiviral immune response, but luckily no increase in direct transmission was observed. Nevertheless, genomic analysis demonstrated a complete change in dominant virus variants, as well as selection of six viral amino acid changes. This indicates that interruptions of the alternating lifestyle of JEV causes a strong evolutionary pressure, which through fitness adaptations can change the viral characteristics.

microbiology↗

bioRxiv2023

Induction of apoptosis by double-stranded RNA was present in the last common ancestor of cnidarian and bilaterian animals

Apoptosis, a major form of programmed cell death, is an essential component of host defense against invading intracellular pathogens. Viruses encode inhibitors of apoptosis to evade host responses during infection, and to support their own replication and survival. Therefore, hosts and their viruses are entangled in a constant evolutionary arms race to control apoptosis. Until now, apoptosis in the context of the antiviral immune system has been almost exclusively studied in vertebrates. This limited phyletic sampling makes it impossible to determine whether a similar mechanism existed in the last common ancestor of animals. Here, we established assays to probe apoptosis in the sea anemone Nematostella vectensis, a model species of Cnidaria, a phylum that diverged approximately 600 million years ago from the rest of animals. We show that polyinosinic:polycytidylic acid (poly I:C), a synthetic long double-stranded RNA mimicking viral RNA and a primary ligand for the vertebrate RLR melanoma differentiation-associated protein 5 (MDA5), is sufficient to induce apoptosis in N. vectensis. Furthermore, at the transcriptomic level, apoptosis related genes are significantly enriched upon poly(I:C) exposure in N. vectensis as well as bilaterian invertebrates. Our phylogenetic analysis of caspase family genes in N. vectensis reveals conservation of all four caspase genes involved in apoptosis in mammals and revealed a cnidarian-specific caspase gene which was strongly upregulated. Altogether, our findings suggest that apoptosis in response to a viral challenge is a functionally conserved mechanism that can be traced back to the last common ancestor of Bilateria and Cnidaria.

evolutionary biology↗

bioRxiv2022

Dominant toxin hypothesis: unravelling the venom phenotype across micro and macroevolution

Venom is a complex trait with substantial inter- and intraspecific variability resulting from strong selective pressures acting on the expression of many toxic proteins. However, understanding the processes underlying the toxin expression dynamics that determine the venom phenotype remains unresolved. Here, we use comparative genomics and transcriptomics to reveal that toxin expression in sea anemones evolves rapidly with little constraint and that a single toxin family dictates the venom phenotype in each species. This dominant toxin family is characterized by massive gene duplication events. In-depth analysis of the sea anemone, Nematostella vectensis, revealed significant variation in the number of copies of the dominant toxin (Nv1) across populations, corresponding to significant differences in Nv1 expression at both the transcript and protein levels. These differences in Nv1 copies are driven by independent expansion events, resulting in distinct haplotypes that have a restricted geographical distribution. Strikingly, one population has undergone a severe contraction event, causing a near-complete loss of Nv1 production. Our findings across micro- and macroevolutionary scales in sea anemones complement observations of single dominant toxin family present in other venomous organisms and establishes the dominant toxin hypothesis whereby venomous animals have convergently evolved a similar strategy in shaping the venom phenotype.

evolutionary biology↗

bioRxiv2020

Functional characterization of the cnidarian antiviral immune response reveals ancestral complexity

Animals developed a broad repertoire of innate immune sensors and downstream effector cascades for defense against RNA viruses. Yet, this system highly varies between different bilaterian animals, masking its ancestral state. In this study we aimed to characterize the antiviral immune response of the cnidarian Nematostella vectensis and decipher the function of the retinoic acid-inducible gene I-like receptors (RLRs) known to detect viral double-stranded RNA (dsRNA) in bilaterians, but activate different antiviral pathways in vertebrates and nematodes. We show that a mimic of long viral dsRNA triggers a complex antiviral immune response bearing features distinctive for both vertebrate and invertebrate systems. Furthermore, the results of affinity assays and knockdown experiments provide functional evidence for the conserved role of RLRs in initiating immune response to dsRNA that originated before the cnidarian-bilaterian split and lay a strong foundation for future research on the evolution of the immune responses to RNA viruses.

evolutionary biology↗

bioRxiv2020

Functional characterization of a "plant-like" HYL1 homolog in the cnidarian Nematostella vectensis indicates a conserved involvement in microRNA biogenesis

While the biogenesis of microRNAs (miRNAs) in both animals and plants depends on the RNase III Dicer, its partner proteins are considered distinct for each kingdom. Nevertheless, recent discovery of homologs of Hyponastic Leaves1 (HYL1), a "plant-specific" Dicer partner, in the metazoan phylum Cnidaria, challenges the view that miRNAs evolved convergently in animals and plants. Here we show that the HYL1 homolog Hyl1-like a (Hyl1La) is crucial for development and miRNA biogenesis in the cnidarian model Nematostella vectensis. Inhibition of Hyl1La by morpholinos resulted in metamorphosis arrest in Nematostella embryos and a significant reduction in levels of most miRNAs. Further, meta-analysis of morphants of miRNA biogenesis components, like Dicer1, shows clustering of their miRNA profiles with Hyl1La morphants. Strikingly, immunoprecipitation of Hyl1La followed by quantitative PCR revealed that in contrast to the plant HYL1, Hyl1La interacts only with precursor miRNAs and not with primary miRNAs. This was complemented by an in vitro binding assay of Hyl1La to synthetic precursor miRNA. Altogether, these results suggest that the last common ancestor of animals and plants carried a HYL1 homolog that took essential part in miRNA biogenesis and indicate early emergence of the miRNA system before plants and animals separated. Impact statementPresence of a functional homolog of HYL1 in Nematostella vectensis, a basal animal model, indicates divergent evolution of miRNA biogenesis pathway in plants and animals from an ancestral miRNA system

evolutionary biology↗

bioRxiv2020

Unravelling the developmental and functional significance of an ancient Argonaute duplication

microRNAs (miRNAs), base-pair to messenger RNA targets and guide Argonaute proteins to mediate their silencing. This target regulation is considered crucial for animal physiology and development. However, this notion is based exclusively on studies in bilaterians, which comprise almost all lab model animals. To fill this glaring phylogenetic gap, we characterized the functions of two Argonaute paralogs in the sea anemone Nematostella vectensis of the phylum Cnidaria, which is separated from bilaterians by [~]600 million years. Using genetic manipulation, Argonaute-immunoprecipitations and high-throughput sequencing we provide experimental evidence for the developmental importance of miRNAs in a non-bilaterian animal. Additionally, we uncover unexpected differential distribution of distinct miRNAs between the two Argonautes and the ability of one of them to load additional types of small RNAs. This enables us to postulate a novel model for evolution of miRNA precursors in sea anemones and their relatives, revealing alternative trajectories for metazoan miRNA evolution.

evolutionary biology↗

bioRxiv2020

Initial virome characterization of the common cnidarian lab model Nematostella vectensis

The role of viruses in forming a stable holobiont has been a subject of extensive research in the recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based virus identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed almost complete lack of viruses in the samples from the early developmental stages which together with the identification of the viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for functional studies of viruses and antiviral systems in this lab model cnidarian.

evolutionary biology↗