We analyse fruit feeding ecology of Mediterranean passerines in a regional, trait-based framework, with emphasis on their role as seed dispersers in Iberian scrub and woodland habitats. We compiled ecomorphological traits for 146 species (N> 6000 individuals), including body mass, gape width, and gut morphology and transit rates, from mist-netted birds, museum specimens, and published […]
Stress-responsive enhancer RNAs couple chromatin reprogramming to post-transcriptional control of senescence
Background: Cellular senescence is accompanied by extensive epigenomic reprogramming leading to changes in enhancer RNA levels, yet how enhancer activity is translated into functional RNA-level regulation remains unclear. Here we investigate how enhancer reprogramming during senescence impacts functional RNA-level regulation by eRNAs. Results: By integrating time-resolved transcriptomic analyses across multiple primary human cell types, we […]
Additive Channels in Curved Fitness Landscapes
Additive genetic models often predict evolutionary change reasonably well, even though fitness landscapes can be curved and gene interactions are common. This paper explores one possible explanation: populations may frequently reside in regions of genetic space where local curvature contributes relatively little to fitness variation, so that linear predictions remain adequate. We call such regions […]
Diatom Endosymbionts have Shrinking but Stable Genomes Despite Low Coding Density
Successful establishment of long-term, obligate endosymbiotic relationships requires integration of hosts and endosymbionts across multiple levels. For example, highly integrated, host-beneficial endosymbionts typically have extremely reduced genomes and metabolisms. However, we do not yet fully understand the specific mechanisms that drive this integration or if there is a specific order in which these changes must […]
Adaptive receptor expression and the emergence of disease as loss of signaling homeostasis
Our bodies have evolved to maintain homeostasis through regulatory systems that continuously adapt to keep physiological processes within a normal range. From this perspective, complex chronic disease can be understood as a breakdown of compensatory mechanisms, resulting in loss of homeostasis. Here we propose that adaptive receptor expression dynamics may serve as one such compensatory […]
Dissociable contributions of cortical thickness and surface area to cognitive ageing: evidence from multiple longitudinal cohorts.
Cortical volume, a widely-used marker of brain ageing, is the product of two genetically and developmentally dissociable morphometric features: thickness and area. However, it remains unclear whether these two features have dissociable consequences for cognitive ageing. To address this, we analyse cross-sectional and longitudinal neuroimaging and cognitive data from one discovery cohort (Cam-CAN) and two […]
LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads
Long-read sequencing is a powerful technique capturing multiple variants within single continuous reads. This length allows individual reads to bridge small and structural variants while carrying crucial phasing information. However, current computational tools treat small variant calling, structural variant (SV) detection and phasing as largely disconnected problems, failing to unleash the full potential of long […]
TEsingle enables locus-specific transposable element expression analysis at single-cell resolution
Transposable elements (TEs) are mobile genetic sequences that can generate new copies of themselves via insertional mutations. These viral-like sequences comprise nearly half the human genome and are present in most genome wide sequencing assays. While only a small fraction of genomic TEs have retained their ability to transpose, TE sequences are often transcribed from […]
ATHILAfinder: a tool to detect ATHILA LTR retrotransposons in plant genomes
Motivation The ATHILA lineage of LTR retrotransposons has colonised all branches of the plant tree of life. In Arabidopsis thaliana and A. lyrata, ATHILA elements have invaded centromeres, influencing the genetic and epigenetic organisation, and driving satellite evolution. To assess the broader significance of ATHILA across plants, a computational pipeline is needed to identify ATHILA […]
Microfluidic low-input profiling reveals lncRNA roles in disease
Long noncoding RNAs (lncRNAs) regulate gene expression through binding to DNA, various RNAs, and proteins, playing potentially important but poorly understood roles in diseases. Existing approaches for profiling lncRNA-chromatin interactions at the genome scale require large quantities of input material (e.g., 100 million cells per assay). Applying these technologies to tissue samples has been challenging […]
DNA Traces on the Shroud of Turin: Metagenomics of the 1978 Official Sample Collection
This research provides original insights into the diversity of DNA extracted from samples collected in 1978 from the Turin Shroud, revealing its biological complexity through rigorous DNA and metagenomic analyses. Our findings highlight its preservation conditions and environmental interactions, offering valuable perspectives into the identified genetic variants, which originated from multiple biological sources. Several human […]
TEsingle enables locus-specific transposable element expression analysis at single-cell resolution
Transposable elements (TEs) are mobile genetic sequences that can generate new copies of themselves via insertional mutations. These viral-like sequences comprise nearly half the human genome and are present in most genome wide sequencing assays. While only a small fraction of genomic TEs have retained their ability to transpose, TE sequences are often transcribed from […]