Biology subjects

Papakostas, S.

Publications and source records attributed to Papakostas, S..

3 recordsLinked to original sources

bioRxiv2025

MeRIP-seq detects temperature related variation in methylated environmental RNA in fish

Environmental RNA (eRNA) enables non-invasive, near-real-time and potentially functional insight into aquatic communities by capturing RNA molecules released by living organisms. While most eRNA studies focus solely on transcript abundance, this overlooks other regulatory layers that shape how organisms respond to stress. RNA modifications, particularly N6-methyladenosine (m6A), influence RNA stability, processing, and translation and are known to change under temperature challenges. These properties make m6A a compelling target for eRNA-based biomonitoring. We investigated whether m6A marks can be recovered from waterborne eRNA released by an African cichlid fish during elevated temperature exposure. eRNA was collected from tank water under control and thermal treatments, enriched for methylated RNA fragments by immunoprecipitation, and sequenced using immunoprecipitation-based MeRIP-Sequencing. Using this approach, we achieved remarkably high read mapping rates to the target fish species, compared to previous studies focusing solely on mRNA sequencing. Moreover, we detect 412 eRNAs having differing abundances between the elevated temperature and control group. Gene ontology analysis reveals that these are enriched in functional categories related to thermal physiology, suggesting a role in the organisms response to temperature stress. These results indicate an enormous potential of this approach to effectively and non-invasively capture signals of temperature stress response of fish via eRNA. While the current modest replicate depth constrained robust assessment of heat-associated changes in m6A, to our knowledge, this is the first attempt to assess m6A RNA modification in the context of eRNA research and the first evidence indicating that extra-organismal eRNA can retain epitranscriptomic information.

molecular biology↗

bioRxiv2020

The Growth Rate Hypothesis as a predictive framework for microevolutionary adaptation to selection for high population growth: an experimental test under phosphorus rich and phosphorus poor conditions

The growth rate hypothesis, a central concept of Ecological Stoichiometry, explains the frequently observed positive association between somatic growth rate and somatic phosphorus content (Psom) in organisms across a broad range of taxa. Here, we explore its potential in predicting intraspecific microevolutionary adaptation. For this, we subjected zooplankton populations to selection for fast population growth (PGR) in either a P-rich (HP) or P-poor (LP) food environment. With common garden transplant experiments we demonstrate evolution in HP populations towards increased PGR concomitant with an increase in Psom. In contrast we show that LP populations evolved higher PGR independently of Psom. We conclude that the GRH hypothesis has considerable value for predicting microevolutionary change, but that its application may be contingent on stoichiometric context. Our results highlight the potential of cryptic evolution in determining the performance response of field populations to elemental limitation of their food resources.

ecology↗

bioRxiv2017

Modularity Facilitates Flexible Tuning Of Plastic And Evolutionary Gene Expression Responses During Early Divergence

Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying co-expressed modules now enable systems genetics approaches also in non-model species for better understanding of gene expression responses during early divergence. Here, we combined gene co-expression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that co-expression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.

evolutionary biology↗