Biology subjects

Swift, S.

Publications and source records attributed to Swift, S..

8 recordsLinked to original sources

bioRxiv2025

Terrigenous inputs link nutrient dynamics to microbial communities in a tropical lagoon

Nutrient availability drives community structure and ecosystem processes, especially in tropical lagoons that are typically oligotrophic but often receive allochthonous inputs from land. Terrestrially-derived nutrients are introduced to tropical lagoons by surface runoff and submarine groundwater discharge, which are influenced by seasonal precipitation. Lagoon habitats are distributed along an onshore-offshore gradient; terrigenous inputs presumably diminish along the same continuum. We characterized nutrient enrichment in the lagoons of a tropical high island, Moorea, French Polynesia, using spatially distributed measurements of nitrogen content in the tissues of a widespread macroalga during the rainy season over four years. We used synoptic water column sampling to identify associations among macroalgal nutrient content and the composition of inorganic macronutrients, dissolved organic matter, and microbial communities. We paired these data with quantifications of land use in nearby watersheds to uncover links between terrestrial factors, aquatic chemistry, and microbial communities. Algal N content was highest near shore and near large, human-impacted watersheds, and lower at offshore sites. Sites with high algal N had water columns with high nitrite + nitrate, silicate, and increased humic organic matter (based on a fluorescence humification index), especially following rain. Microbial communities were differentiated among nearshore habitats and covaried with algal N and water chemistry, supporting the hypothesis that terrigenous nutrient enrichment shapes microbial dynamics in otherwise oligotrophic tropical lagoons. This study reveals that land-sea connections create nutrient subsidies that are important for lagoon biogeochemistry and microbiology, indicating that changes in land use or precipitation will modify ecosystem processes in tropical lagoons.

ecology↗

bioRxiv2025

Computational design of dynamic biosensors for emerging synthetic opioids

Nitazenes are an emergent class of synthetic opioids that rival or exceed fentanyl in their potency. These compounds have been detected internationally in illicit drugs and are the cause of increasing numbers of hospitalizations and overdoses. New analogs are consistently released, making detection challenging - new ways of testing a wide range of nitazenes and their metabolic products are urgently needed. Here, we developed a computational protocol to redesign the plant abscisic acid receptor PYR1 to bind diverse nitazenes and maintain its dynamic transduction mechanism. The best design has a low nanomolar limit of detection in vitro against nitazene and menitazene. Deep mutational scanning yielded sensors able to recognize a range of clinically relevant nitazenes and the common metabolic byproduct in complex biological matrices with limited cross-specificity against unrelated opioids. Application of protein design tools on privileged receptors like PYR1 may yield general sensors for a wide range of applications in vitro and in vivo.

biochemistry↗

bioRxiv2025

Real-world testing of the durability claims of a commercially available spray-on surface biocide

Self-disinfecting biocidal surfaces have been proposed as a solution to prevent infections caused by the transmission of microorganisms from frequently touched surfaces in hospitals and other settings. For example, surface anchoring quaternary ammonium salt (SAQAS)-based biocides are purported to maintain their antimicrobial potency for up to 30 days and are available as spray-on formulations. We tested the 30-day potency claim of a commercially available spray-on SAQAS-based biocide ("SAQAS-A") under "real-world" conditions in a microbiology laboratory where regular cleaning is routine. To do this, we determined the background microbial burden on high-traffic floor areas, routinely used bench areas, frequently touched handles, and glass surfaces for 30 days before and after applying SAQAS-A. Experiments were repeated three times, and data was analysed using two Generalised Linear Mixed Models. We observed that for >80% of bench samples, the number of viable bacteria recovered was below the highest acceptable level of 2.5 CFU/cm2, with minimal reduction in CFU recovery observed after SAQAS-A treatment. In contrast, the number of floor and glass samples in which the microbial burden exceeded 2.5 CFU/cm2 was greater after biocide application (12.7 and 73%, respectively) than before (4.8 and 37%, respectively). Analysis of all data using two statistical models confirmed that the application of SAQAS-A had no antimicrobial effect. In conclusion, our results indicate that SAQAS-A was ineffective in preventing surface contamination over 30 days in a real-world scenario where routine cleaning occurs. ImportanceWe tested the claim that a commercially available spray-on biocide could protect surfaces from microbial contamination for 30 days. In the presence of routine disinfection, we found that spray-on applications of the surface anchoring quaternary ammonium salt-based biocide did not protect frequently touched surfaces in a working microbiology research lab for up to 30 days. Our data show that users of this type of product should be aware of the limitations of manufacturers claims of "continued protection", and manufacturers should consider formulations that more reliably attach to surfaces. Similarly, regulatory and consumer protection agencies should provide clear guidance for companies wishing to make durability and longevity claims for biocidal surface applications.

microbiology↗

bioRxiv2022

Transcriptomic profiling reveals distinct subsets of immune checkpoint inhibitor-induced myositis

ObjectivesInflammatory myopathy or myositis is a heterogeneous family of immune-mediated diseases including dermatomyositis (DM), antisynthetase syndrome (AS), immune-mediated necrotizing myopathy (IMNM), and inclusion body myositis (IBM). Immune checkpoint inhibitors (ICI) can also cause myositis (ICI-myositis). This study was designed to define gene expression patterns in muscle biopsies from patients with ICI-myositis. MethodsBulk RNA sequencing was performed on 200 muscle biopsies (35 ICI-myositis, 44 DM, 18 AS, 54 IMNM, 16 IBM, and 33 normal muscle biopsies) and single nuclei RNA sequencing was performed on 22 muscle biopsies (7 ICI-myositis, 4 DM, 3 AS, 6 IMNM, and 2 IBM). ResultsUnsupervised clustering defined three distinct transcriptomic subsets of ICI-myositis: ICI-DM, ICI-MYO1, and ICI-MYO2. ICI-DM included patients with DM and anti-TIF1{gamma} autoantibodies who, like DM patients, overexpressed type 1 interferon-inducible genes. ICI-MYO1 patients had highly inflammatory muscle biopsies and included all patients that developed co-existing myocarditis. ICI-MYO2 was composed of patients with predominant necrotizing pathology and low levels of muscle inflammation. The type 2 interferon pathway was activated both in ICI-DM and ICI-MYO1. Unlike the other types of myositis, all three subsets of ICI-myositis patients overexpressed genes involved in the IL6 pathway. ConclusionsWe identified three distinct types of ICI-myositis based on transcriptomic analyses. The IL6 pathway was overexpressed in all groups, the type I interferon pathway activation was specific for ICI-DM, the type 2 IFN pathway was overexpressed in both ICIDM and ICI-MYO1, and only ICI-MYO1 patients developed myocarditis.

immunology↗

bioRxiv2022

The efficacy of commercial decontamination agents differs between standardised test settings and real-world usage for a variety of bacterial species

Decontamination of surfaces and items plays an important role in reducing the spread of infectious microorganisms in many settings including hospitals and research institutes. Regardless of the location, appropriate decontamination procedures are required for maintaining biosafety and biosecurity. For example, effective decontamination of microbial cultures is essential to ensure proper biocontainment and safety within microbiological laboratories. To this end, many commercial decontamination agents are available which have been tested to a prescribed standard to substantiate their efficacy. However, these standardised tests are unlikely to accurately reflect all conditions encountered in medical and biomedical research. Despite this, laboratory workers and other users of decontamination agents may assume that all decontamination agents will work in all situations. We tested commonly used commercial decontamination agents against a range of bacterial species to determine their efficacy under real-world laboratory conditions. As each decontamination agent has a different recommended dilution for use, to compare their efficacy we calculated their effective ratio which reflects the difference between the manufacturer-recommended dilution and the dilution needed to achieve decontamination under real-world laboratory conditions. Effective ratios above 1 indicate that the agent was active at a dilution more dilute than recommended whereas effective ratios lower than 1 indicate that the agent required a higher concentration than recommended. Our results show that the quaternary ammonium agents TriGene Advance and Chemgene HLD4L were the most active out of the agents tested, with biocidal activity measured at up to 64 times the recommended dilution. In contrast, hypochlorite (bleach) and Prevail (stabilised hydrogen peroxide) had the lowest effective ratios amongst the tested agents. In conclusion, our data suggest that not all decontamination agents will work at the recommended dilutions under real-world laboratory conditions. We recommend that the protocols for the use of decontamination agents are verified under the specific conditions required to ensure they are fit for purpose.

microbiology↗

bioRxiv2019

Induction of microbial oxidative stress as a new strategy to enhance the enzymatic degradation of organic micropollutants in wastewater

Organic micropollutants (OMPs) are pervasive anthropogenic contaminants of fresh and marine waters with known potential to adversely affect aquatic life (e.g. endocrine disruption). Their ubiquitous environmental occurrence is primarily attributed to wastewater treatment plant discharges following their incomplete removal by common biological treatment processes. This study assesses a new strategy for promoting the degradation of six model OMPs (i.e. sulfamethoxazole, carbamazepine, tylosin, atrazine, naproxen and ibuprofen) by stimulating microbial oxidoreductase production to counter the effects of oxidative stress caused by oxygen perturbation. Microbial cultures from dairy farm wastewater were exposed to a cyclical ON-OFF perturbations of oxygen supply, ranging from 0.16 to 2 cycles per hour (i.e. 2, 1, 0.5, 0.25 and 0.16 cycles/hour), in laboratory bioreactors. The activity and relative abundances of microbial oxidoreductases (such as peroxidases, cytochromes P450) were upregulated by oxygen perturbation. In comparison to controls subjected to constant oxygen levels, OMP concentrations in perturbed cultures decreased by 70{+/-}9% (mean {+/-} SD). A distance-based linear model confirmed strong positive correlations between the relative abundance of the bacterial families, Rhodocyclaceae, Syntrophaceae and Syntrophobacteraceae, and oxygen perturbations. Our results confirm that intentional perturbation of oxygen supply to induce microbial oxidative stress can improve OMP removal efficiencies in wastewater treatment bioreactors.

bioengineering↗

bioRxiv2016

A novel restraint device for injection of Galleria mellonella larvae that minimises the risk of accidental operator needle stick injury

Larvae of the insect Galleria mellonella are increasingly being used for studying pathogenic microbes and their virulence mechanisms, and as a rapid model for screening novel antimicrobial agents. The larvae (waxworms) are most frequently infected by injection of pathogenic organisms into the haemocoel through the insects prolegs. The mostly widely used method for restraining the waxworms for injection is by grasping them between the operators fingers, which puts the operator at risk of needle stick injury, an important consideration when working with highly pathogenic and/or drug-resistant microorganisms. While use of a stab proof glove can reduce this risk of injury, it does so at the loss of manual dexterity and speed, resulting in a more labour-intensive and cumbersome assay. We describe a simple cost effective device (the so-called Galleria Grabber) for restraining waxworms for injection that keeps the operators fingers clear of the needle thus reducing the risk of injury.

microbiology↗

bioRxiv2016

Effect of common and experimental anti-tuberculosis treatments on Mycobacterium tuberculosis growing as biofilms

Much is known regarding the antibiotic susceptibility of planktonic cultures of Mycobacterium tuberculosis, the bacterium responsible for the lung disease tuberculosis (TB). As planktonically-grown M. tuberculosis are unlikely to be entirely representative of the bacterium during infection, we set out to determine how effective a range of anti-mycobacterial treatments were against M. tuberculosis growing as a biofilm, a bacterial phenotype known to be more resistant to antibiotic treatment. Light levels from bioluminescently-labelled M. tuberculosis H37Rv (strain BSG001) were used as a surrogate for bacterial viability, and were monitored before and after 1 week of treatment. After treatment, biofilms were disrupted, washed and inoculated into fresh broth and plated onto solid media to rescue any surviving bacteria. We found that in this phenotypic state M. tuberculosis was resistant to the majority of the compounds tested. Minimum inhibitory concentrations (MICs) increased by 20-fold to greater than 1000-fold, underlying the potential of this phenotype to cause significant problems during treatment.

microbiology↗