Biology subjects

Penzes, J.

Publications and source records attributed to Penzes, J..

5 recordsLinked to original sources

bioRxiv2026

First community challenge for automated virus taxonomy

The rapid rate of virus discovery renders manual curation by taxonomy experts increasingly impractical, creating a need for reliable software that can reproducibly assign viral contigs to taxa at all fifteen ranks of the virus taxonomy. We led an open community challenge for the computational taxonomic classification of viruses and assembled a dataset of virus sequences combining expert-curated and metagenomic sequences. Seventeen teams contributed a total of thirty-four automated, fully reproducible classification pipelines. Most tools correctly assigned viruses belonging to established species, genera, or families, but viruses that are unclassified at those lower ranks remain challenging. This study provides datasets, open-source software, novel approaches, and recommendations to benchmark computational taxonomic classification of viruses, and support organizing the many viruses discovered in big omics data.

microbiology↗

bioRxiv2023

Birds escape the oxidative stress costs of high blood glucose levels

Chronically high blood glucose levels (hyperglycaemia) can compromise healthy ageing and lifespan at the individual level. Elevated oxidative stress can play a central role in hyperglycaemia-induced pathologies. Nevertheless, the lifespan of birds shows no species-level association with blood glucose. This suggests that the potential pathologies of high blood glucose levels can be avoided by adaptations in oxidative physiology at the macroevolutionary scale. However, this hypothesis remains unexplored. Here, we examined this hypothesis using comparative analyses controlled for phylogeny, allometry and fecundity based on data from 51 songbird species (681 individuals with blood glucose and 1021 individuals with oxidative state data). We measured blood glucose at baseline and after stress stimulus and computed glucose stress reactivity as the magnitude of change between the two time points. We also measured three parameters of non-enzymatic antioxidants (uric acid, total antioxidants and glutathione) and a marker of oxidative lipid damage (malondialdehyde). We found no clear evidence for blood glucose concentration being correlated with either antioxidant or lipid damage levels at the macroevolutionary scale, as opposed to the hypothesis postulating that high blood glucose levels entail oxidative costs. The only exception was the moderate evidence for species with a stronger stress-induced increase in blood glucose concentration evolving moderately lower investment into antioxidant defence (uric acid and glutathione). Neither baseline nor stress-induced glucose levels were associated with oxidative physiology. Our findings support the hypothesis that birds evolved adaptations preventing the (glyc)oxidative costs of high blood glucose observed at the within-species level. Such adaptations may explain the decoupled evolution of glycaemia and lifespan in birds and possibly the paradoxical combination of long lifespan and high blood glucose levels relative to mammals. Summary statementHigh blood glucose levels can harm organisms by causing oxidative stress. We show that, at the macroevolutionary level, songbirds defy this expectation, as their glucose levels and oxidative physiology are uncoupled.

evolutionary biology↗

bioRxiv2020

Varietas delectat: groups with diverse personalities mitigate physiological stress in a songbird

Social groups often consist of diverse phenotypes, including personality types, and this diversity is known to affect the functioning of the group as a whole. Social selection theory proposes that group composition (i.e. social environment) also influences the performance of individual group members. However, the effect of group behavioural composition on group members remains largely unexplored, and it is still contentious whether individuals benefit more in a social environment with homogeneous or diverse behavioural composition. We experimentally formed groups of house sparrows Passer domesticus with high and low diversity of personality (exploratory behaviour), and found that their physiological state (body condition, physiological stress and oxidative damage) improved with increasing group-level diversity of personality. These findings demonstrate that group personality composition affects the condition of group members and individuals benefit from social heterosis (i.e. associating with a diverse set of behavioural types). This aspect of the social life can play a key role in affiliation rules of social animals and might explain the evolutionary coexistence of different personalities in nature.

ecology↗

bioRxiv2020

Insulin-like growth factor 1 induces oxidative damage, but does not affect survival in a songbird

Lifespan evolves as a compromise between antagonistic selection forces. Insulin-like growth factor 1 (IGF-1) is a pleiotropic hormone that regulates several life-history traits. High levels of IGF-1 have been linked to increased mortality, partly by causing oxidative stress. However, these effects have no experimental evidence in wild animals. We implanted microspheres loaded with exogenous IGF-1 into bearded reedlings, a common short-lived Eurasian songbird. The treatment elevated plasma IGF-1 levels for at least 24 h. Oxidative damage to lipids significantly increased the day after the manipulation in treated birds, but returned to baseline levels four days post-treatment. The treatment had no effect on survival over 16 months; however, birds with higher pre-treatment (baseline) IGF-1 levels had better survival prospects. These results suggest that, although high IGF-1 levels may induce oxidative damage, natural variation in this hormones level may reflect the outcome of individual optimization.

evolutionary biology↗

bioRxiv2019

An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts.

Chapparvoviruses are a highly divergent group of parvoviruses (family Parvoviridae) first identified in 2013. Interest in these poorly characterized viruses has been raised by recent studies indicating that they are the cause of chronic kidney disease that arises spontaneously in laboratory mice. In this study, we investigate the biological and evolutionary characteristics of chapparvoviruses via comparative analysis of genome sequence data. Our analysis, which incorporates sequences derived from endogenous viral elements (EVEs) as well as exogenous viruses, reveals that chapparvoviruses are an ancient lineage within the family Parvoviridae, clustering separately from members of both currently established parvoviral subfamilies. Consistent with this, they exhibit a number of characteristic genomic and structural features, i.e. a large number of putative auxiliary protein-encoding genes, capsid protein genes non-homologous to any hitherto parvoviral cap, as well as a putative capsid structure lacking the canonical fifth strand of the ABIDG sheet comprising the luminal side of the jelly roll. Our findings demonstrate that the chapparvovirus lineage infects an exceptionally broad range of host species, including both vertebrates and invertebrates. Furthermore, we observe that chapparvoviruses found in fish are more closely related to those from invertebrates than they are to those that infect amniote vertebrates. This suggests that transmission between distantly related host species may have occurred in the past. Our study provides the first integrated overview of the chapparvovirus group, and revises current views of parvovirus evolution\n\nAUTHOR SUMMARYChapparvoviruses are a recently identified group of viruses about which relatively little is known. However, recent studies have shown that these viruses cause disease in laboratory mice and are prevalent in the fecal virome of pigs and poultry, raising interest in their potential impact as pathogens, and utility as experimental tools. We examined the genomes of chapparvoviruses and endogenous viral elements ( fossilized virus sequences derived from ancestral viruses) using a variety of bioinformatics-based approaches. We show that the chapparvoviruses have an ancient origin and are evolutionarily distinct from all other related viruses. Accordingly, their genomes and virions exhibit a range of distinct characteristic features. We examine the distribution of these features in the light of chapparvovirus evolutionary history (which we can also infer from genomic data), revealing new insights into chapparvovirus biology.

evolutionary biology↗