Kirsty Jane Shaw

The scaly-sided merganser, Mergus squamatus, is a threatened piscivorous duck which has been declining since the late 1900s due to habitat loss, over-hunting, and climate change. Despite being a species of global conservation concern and subject to ex situ and in situ conservation efforts, genomic research has been limited, hindering our understanding of its population genetic status and evolutionary history. In this study, we present the first fully annotated, chromosome-level genome for the scaly-sided merganser, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C sequencing. The final assembly spans 1.1 Gb across 308 scaffolds, 64 of which are anchored into 35 chromosomes, plus the mitogenome, covering 99.5% of the genome. The assembly shows high contiguity (N50 = 84.3 Mb) and completeness, with a Benchmarking Universal Single-Copy Ortholog score of 98%. Repeat sequences comprise 9.55% of the genome. Homology-based gene annotation identified ∼15,200 protein-coding genes. A complete 16,624 bp mitochondrial genome was also assembled and annotated. Synteny analysis revealed strong chromosomal conservation across the wider Anatidae family, with evidence of lineage-specific rearrangements. Pairwise Sequential Markovian Coalescence modeling indicates recent stability in the effective population size of the species, with past declines coinciding with Pleistocene glacial cycles. Our high-quality genome provides an essential resource for conservation genomic and evolutionary studies of the scaly-sided merganser, supporting ongoing efforts to manage and protect this globally threatened species.

Harbour (Phoca vitulina) and grey (Halichoerus grypus) seal pups are commonly admitted to wildlife rehabilitation centres with infection by parasitic lungworm (Otostrongylus circumlitus). Infection can result in bronchopneumonia, pulmonary haemorrhage and secondary bacterial infections, which can lead to death. Therefore, early and accurate diagnosis is critical to ensure timely administration of anthelmintics, antibiotics, anti-inflammatories, mucolytics and oral fluids. However, current detection methods available to rehabilitators are slow, labour-intensive, have low sensitivity and require specialist expertise for accurate lungworm identification. To provide a rapid and cost-effective diagnostic tool with high accuracy and sensitivity, a polydimethylsiloxane (PDMS) lab on a chip (LOC) device was developed for O. circumlitus DNA detection. A DNA extraction protocol, incorporating superparamagnetic particles (SPMPs), was developed for use on parasite tissue and seal faecal samples. A loop-mediated isothermal amplification (LAMP) reaction, specific to O. circumlitus, was optimised to enable species-specific DNA amplification and consequent colourimetric detection. The LAMP displayed sufficient specificity to differentiate O. circumlitus from other seal parasites, such as tapeworm, ascarids and Corynosoma. The LAMP reaction was integrated onto the PDMS device along with an immiscible filtration assisted by surface tension (IFAST) method, enabling rapid cell lysis, DNA extraction and O. circumlitus detection. Overall, O. circumlitus positive samples, as indicated by a colour change from pink to yellow, could be detected within 60 minutes from sample collection with as little as 100 pg of DNA. The LOC device was trialled at a rehabilitation centre where it successfully distinguished between O. circumlitus positive and negative seal faecal samples, enabling accurate and fast diagnosis by non-specialist users. Integration of this device in triage and health monitoring protocols could optimise diagnostic efficiency, treatment, and in turn reduce mortality of seal pups.

Aubregrinia taiensis is a rare and critically endangered tree species with a highly restricted native range distribution in Ghana, Côte d’Ivoire, and Liberia. In this study, we present a detailed spatial analysis of the distributions of A. taiensis across range countries in West Africa. Habitat Suitability Models (HSMs) for the species were developed using the machine-learning maximum entropy (Maxent) method. Bioclimatic environmental variables from the WorldClim database were used to simulate the future distribution of the species based on two greenhouse gas emission scenarios (RCP 4.5 and RCP 8.5) for 2050 and 2070. Our results confirm the species' narrow and highly fragmented population. The current range of A. taiensis in Ghana is estimated as 65,123.78 km2, spanning the upper limits of the south-western wet-evergreen forest, to the lower portions of the forest-savannah transition zone. Four main bioclimatic variables, Bio 10 (mean temperature of warmest quarter), Bio 1 (annual mean precipitation), Bio 5 (maximum temperature of the warmest month), and elevation, were found to influence the occurrence and suitability of A. taiensis. Further, our models indicated significant range contractions of 76.4% and 89.6% under both emission scenarios. By 2070, climatic changes could push the species to the brink of extinction. Specific conservation interventions are proposed. Keywords: biodiversity hotspots; endangered flora; climate change impacts; habitat modeling; Maxent.

Atmospheric ice-nucleating particles (INPs) make up a vanishingly small proportion of atmospheric aerosol but are key to triggering the freezing of supercooled liquid water droplets, altering the lifetime and radiative properties of clouds and having a substantial impact on weather and climate. However, INPs are notoriously difficult to model due to a lack of information on their global sources, sinks, concentrations, and activity, necessitating the development of new instrumentation for quantifying and characterizing INPs in a rapid and automated manner. Microfluidic technology has been increasingly adopted by ice nucleation research groups in recent years as a means of performing droplet freezing analysis of INPs, enabling the measurement of hundreds or thousands of droplets per experiment at temperatures down to the homogeneous freezing of water. The potential for microfluidics extends far beyond this, with an entire toolbox of bioanalytical separation and detection techniques developed over 30 years for medical applications. Such methods could easily be adapted to biological and biogenic INP analysis to revolutionize the field, for example, in the identification and quantification of ice-nucleating bacteria and fungi. Combined with miniaturized sampling techniques, we can envisage the development and deployment of microfluidic sample-to-answer platforms for automated, user-friendly sampling and analysis of biological INPs in the field that would enable a greater understanding of their global and seasonal activity. Here, we review the various components that such a platform would incorporate to highlight the feasibility, and the challenges, of such an endeavor, from sampling and droplet freezing assays to separations and bioanalysis.

Urinary tract infections (UTIs) represent the most prevalent type of outpatient infection, with significant adverse health and economic burdens. Current culture-based antibiotic susceptibility testing can take up to 72 h resulting in ineffective prescription of broad-spectrum antibiotics, poor clinical outcomes and development of further antibiotic resistance. We report an electrochemical lab-on-a-chip (LOC) for testing samples against seven clinically-relevant antibiotics. The LOC contained eight chambers, each housing an antibiotic-loaded hydrogel (cephalexin, ceftriaxone, colistin, gentamicin, piperacillin, trimethoprim, vancomycin) or antibiotic-free control, alongside a resazurin bulk-modified screen-printed electrode for electrochemical detection of metabolically active bacteria using differential pulse voltammetry. Antibiotic susceptibility in simulated UTI samples or donated human urine with either Escherichia coli or Klebsiella pneumoniae could be established within 85 min. Incorporating electrochemical detection onto a LOC provides an inexpensive, simple method for the sensitive determination of antibiotic susceptibility that is significantly faster than using a culture-based approach.

Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple “yes” or “no” result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.

The UK shores are home to approximately 40% of the world's population of gray seals (Halichoerus grypus) and 40% of Europe's harbor seals (Phoca vitulina). Stranded juvenile seals of both species are frequently rescued and admitted for rehabilitation. This study investigates the causes of P. vitulina and H. grypus admittance to rehabilitation centers in the UK and Ireland and identifies factors that can affect juvenile seal survival. Rehabilitation records for 1,435 P. vitulina and 2,691 H. grypus were used from five rehabilitation centers from 1988 through 2020. The most common nonexclusive reasons for seal admission to rehabilitation centers included malnourishment (37%), injuries (37%), maternal abandonment (15%), lethargy (12%), and parasite infections (8%). A mixed effects logistic regression model showed that H. grypus had 4.55 times higher survival odds than P. vitulina and that the odds of survival to release multiplied by 1.07 for every kilogram over their age‐predicted weight. This weight‐dependent survival could be attributed to the importance of fat in thermoregulation, hydration, and buoyancy during foraging. We recommend that seal rehabilitators pay special attention to the weight of admitted juvenile seals during triage and treatment to enhance their odds of survival and consequent release to the wild.