Biology subjects

Aanstad, P.

Publications and source records attributed to Aanstad, P..

3 recordsLinked to original sources

bioRxiv2026

City life: airborne DNA metagenomic biodiversity monitoring reveals dynamic changes across time and space

Airborne environmental DNA can capture biodiversity across the tree of life, but low sample biomass makes rapid, untargeted detection technically challenging. We combined 45-min air collection, nanopore sequencing and real-time taxonomic analysis in a shotgun metagenomic workflow capable of producing results within 3 hours. Across 77 samples from 13 London sites, including a year of weekly sampling at the Natural History Museum Wildlife Garden, we detected 1,916 species spanning bacteria, fungi, plants and animals. Communities varied spatially and seasonally, shifting from plant dominance in spring to ascomycete dominance in summer and basidiomycete dominance in late autumn and winter. Plant read abundance increased with upwind vegetation, linking airborne signals to surrounding habitat. Detection of catalogued garden plants depended on reference availability, dispersal biology, plant size and proximity to the collector. Together, these findings establish airborne shotgun metagenomics as a platform for rapid, repeated and scalable biodiversity assessment across space and time.

ecology↗

bioRxiv2021

How low can you go? Driving down the DNA input requirements for nanopore sequencing

The requirement for large amounts of purified DNA limits many sequencing experiments, especially when seeking to avoid pre-amplification or when using third generation technology to sequence molecules directly. We wanted to test the limits of current nanopore sequencing input requirements and devised a set of experiments to evaluate extraction and library preparation approaches for low inputs. We found an optimised bead beating approach combined with a magnetic bead protocol, rather than traditional spin columns for DNA extraction, improved both molecule length, integrity score and DNA yield. Through reducing the DNA input to as little as 6.25 % of recommended (25 ng versus 400 ng) and reaction volumes in half, library construction can be completed, and sequencing begun within 20 minutes of sample collection. Applying these approaches, we demonstrated that our pipeline can be used as a cheap and effective method to de novo assemble a genome and identify genes from low quantities and quality of DNA. With our rapid extraction protocol using transportable equipment and low input library construction we were able to generate a de novo assembly from a single insect (Drosophila melanogaster) spanning 125 Mbp / 85 % of the reference genome, over 96.9% complete BUSCO genes, with a contig N50 over 1.2 Mbp, including chromosome arm sized contigs, for a modest consumable cost under {pound}600.

genomics↗

bioRxiv2019

Zebrafish Gpr161 contributes to basal hedgehog repression in a tissue-specific manner

Hedgehog (Hh) ligands act as morphogens to direct patterning and proliferation during embryonic development. Protein kinase A (PKA) is a central negative regulator of Hh signalling, and in the absence of Hh ligands, PKA activity prevents inappropriate expression of Hh target genes. The Gs- coupled receptor Gpr161 contributes to the basal Hh repression machinery by activating PKA, although the extent of this contribution is unclear. Here we show that loss of Gpr161 in zebrafish leads to constitutive activation of low-, but not high-level Hh target gene expression in the neural tube. In contrast, in the myotome, both high- and low-level Hh signalling is constitutively activated in the absence of Gpr161 function. Our results suggest that the relative contribution of Gpr161 to basal repression of Hh signalling is tissue-specific. Distinct combinations of G-protein-coupled receptors may allow the fine-tuning of PKA activity to ensure the appropriate sensitivity to Hh across different tissues.

cell biology↗