Biology subjects

Jennings, P. A.

Publications and source records attributed to Jennings, P. A..

3 recordsLinked to original sources

bioRxiv2026

AberTrap: an open-source, lightweight, programmable sampler of airborne biological particles

1. Context. Capturing and identifying airborne biological matter (bioaerosols) enables detailed characterisation of ecological communities, but the cost and weight of existing commercially available active air samplers limits the deployment of multiple devices needed to realise this potential. 2. Method. We present the AberTrap, a lightweight (~50g), open-source (CC-BY-SA), programmable rotating-arm bioaerosol sampler that can be self-built from common laboratory components and makerspace equipment at low cost (ca {pound}20 per unit, exc. power supply). To characterise the device's performance, we first explored the influence of rotational speed and paddle design on aerosol capture under controlled conditions, using fluorescein and a range of biological aerosols (4.5-33 m). To demonstrate its utility for ecological applications, we then validated field performance in a species-rich broadleaf woodland (England, UK), deploying eight samplers over five days and identifying captured fungal aerosols by ITS2 metabarcoding. 3. Key results. Modifying paddle design allowed us to influence particle selection and capture efficiency. Slotted paddles captured significantly more aerosols than plain paddles despite sampling less air, which we traced to the concentration of aerosols at the paddle leading edges. This effect was most pronounced for the smallest particles and outweighs the influence of rotational speed. In the field, 20 daily samples (four samplers over five days) detected 2,431 fungal taxa, 78.9% of the Chao2-estimated total fungal richness. A single sampler captured only 59% of this richness. Continuous 5-day sampling recovered 78% of the taxa detected by daily sampling, indicating only modest paddle saturation over this period. Our time segregated design allowed us to infer dispersal dynamics; 35% of taxa were recorded only on one day, and 19% recorded across all five days. Overall, replicate AberTraps provided high sampling completeness. 4. Implications. The AberTrap provides a low-cost, lightweight and programmable alternative to commercial rotating-arm samplers, enabling levels of spatial and temporal replication impractical with existing devices. Low cost and portability facilitate deployment in remote or resource-limited contexts. Its open-source, adaptable design allows the device to be tailored for applications in biodiversity assessment, pathogen surveillance and ecological monitoring.

ecology↗

bioRxiv2026

Disordered N-terminal region of CLK1 oligomerizes for recruitment to nuclear substructures and splicing function

Cdc2-like kinase 1 (CLK1) phosphorylates the serine-arginine (SR) proteins, a family of nuclear factors essential for mRNA splicing. The ability of CLK1 to recognize and efficiently modify SR proteins is strictly dependent on a lengthy, disordered N-terminus flanking its kinase domain. In addition to stimulating phosphorylation, this 150-residue extension also induces large oligomer formation in CLK1 but it is unclear whether said structure is important for catalytic or cellular function. We identified a subset of N-terminal residues that, upon removal, impairs oligomerization of CLK1 but does not abolish phosphorylation of the SR protein SRSF1. Despite robust phosphorylation, CLK1 lacking these high-order oligomerization sequences cannot effectively enter nuclear speckles and release SRSF1. This inability to mobilize CLK1 has detrimental effects on the alternative splicing of the CLK1 gene, severing an important, autoregulatory mechanism that controls active cellular levels of the kinase. Such findings indicate that whereas a limited group of residues in the N-terminus activates the kinase domain for SR protein phosphorylation, sequences that induce oligomerization direct CLK1 to the proper subnuclear structures for splicing function.

biochemistry↗

bioRxiv2017

Guiding the design of bacterial signaling interactions using a coevolutionary landscape

The selection of amino acid identities that encode new interactions between two-component signaling (TCS) proteins remains a significant challenge. Recent work constructed a co-evolutionary landscape that can be used to select mutations to maintain signal transfer interactions between partner TCS proteins without introducing signal transfer between non-partners (crosstalk). A bigger challenge is to introduce mutations between non-natural partner TCS proteins using the landscape to enhance, suppress, or have a neutral effect on their basal signal transfer rates. This study focuses on the selection of mutations to a response regulator (RR) from Bacilus subtilis and its effect on phosphotransfer with a histidine kinase (HK) from Escherichia Coli. Twelve single-point mutations of the RR protein are selected from the landscape and experimentally expressed to directly test the theoretical predictions on the effect of signal transfer. Differential Scanning Calorimetry is used to monitor any protein stability effects caused by the mutations, which could be detrimental to proper protein function. Of these proteins, seven mutants successfully perturb phosphoryl transfer activity in the computationally predicted manner between the TCS proteins. Furthermore, brute-force exhaustive mutagenesis approaches indicate that only 1% of mutations result in enhanced activity. In comparison, of the six mutations predicted to enhance phosphotransfer, two mutations exhibit a significant enhancement while two mutations are comparable to the wild-type. Thus co-evolutionary landscape theory offers significant improvement over traditional large-scale mutational studies in the efficiency of selecting mutations for protein engineering and design.

bioinformatics↗