Biology subjects

Turner, R. J.

Publications and source records attributed to Turner, R. J..

7 recordsLinked to original sources

bioRxiv2025

Contrasts and similarities in the transcriptomic response to antimicrobial coinage metals in Escherichia coli

With the rise of resistance to last resort antibiotics, metal-based antimicrobials have re-emerged as an alternative to prevent and manage infections. The group 11 metals (copper, silver, gold), historically known for their usage in coins and similar chemical properties, have demonstrated promising bactericidal activity. Despite their efficiency, we do not have a complete understanding for how bacteria are eradicated by metal ions and how they respond to metal-induced stress. One understudied aspect of these metal-bacteria interactions are prolonged exposure models, as other studies tend to focus on the acute toxic response of antimicrobial metals. We used RNA-seq profiling to understand the Escherichia coli physiological response to sublethal inhibitory antimicrobial coinage metal stress after 10 hours of incubation. Gene expression patterns of the adaptive and intrinsic response elicited by each metal were identified, including increased essential metal uptake (Ag, Cu, Au), cysteine biosynthesis (Cu, Au), change of the metal ion oxidation state (Cu, Au), efflux of metal stressor (Cu), protein translation and ribosome biogenesis (Au), and cell envelope stress response (Ag). In this paper, we highlight the remarkable differences and similarities in the transcriptomic response profile of E. coli to these antimicrobial metal elements. IMPORTANCEDogma has existed that all antimicrobial metals kill bacteria the same way, leading to the assumption that bacteria respond the same way to metal toxicity. Nowadays, we have a better understanding why some metal elements are more toxic than others, but questions remain in relation to how bacteria adapt to survive and thrive when challenged by different metal-based antimicrobials. Our study advances the field by characterizing the type of bacterial response(s) to acclimate and grow during a prolonged exposure of silver, copper and gold - metallic elements that are known for their antimicrobial activity. Taking advantage of well-characterized Escherichia coli, we propose a model that summarizes our findings after comparing the shared and unique responses to each of these metals. This information enhances our understanding of bacterial tolerance to metal-based antimicrobials, which can lead to improved drug development strategies as society continues to search for alternatives against antibiotic-resistant pathogens.

microbiology↗

bioRxiv2025

Optical Brain Pulse Monitoring for Detection of Large Vessel Occlusion Stroke in a Sheep Model

Early stroke detection and treatment are critical for improving patient outcomes. Optical brain pulse monitoring (OBPM) uses red and infrared light to capture brain pulse waveforms reflecting arteriole-to-venous pressure levels driving microvascular blood flow. This study assessed OBPMs potential to detect middle cerebral artery occlusion (MCAo) and reperfusion in a clinically relevant sheep model. Stroke was induced in 11 Merino wethers via 4-hour occlusion of the right MCA, followed by 6 hours of reperfusion. OBPM recordings were taken at baseline, MCAo, early and late reperfusion. The OBPM brain pulse waveform classes were classified based on the presence of arterial or central venous circulation wave features. Magnetic resonance imaging assessed infarct volume at 2 hours post-reperfusion. Invasive brain tissue oxygen and intracranial pressures were also monitored. The OBPM brain pulse waveform classes changed during MCAo and reperfusion (p <0.0001). MCAo was associated brain pulses with venous circulation features (p = 0.0007). Reperfusion was associated with the return of arterial circulation features (p = 0.001). Early reperfusion was also associated with an increase in the brain pulse amplitude (p < 0.05) and the respiratory wave amplitude (p < 0.05). OBPM may aid in early stroke detection and reperfusion assessment following intervention.

physiology↗

bioRxiv2024

Novel Pentafluorosulfanyl-containing Triclocarban Analogs selectively kill Gram-positive bacteria.

The antibacterial and antibiofilm efficacy of our novel pentafluorosulfanyl-containing triclocarban analogs was explored against seven different Gram-positive and Gram-negative indicator strains. After initial screening, they had bactericidal and bacteriostatic activity against Gram-positive bacteria, especially Staphylococcus aureus and MRSA (methicillin-resistant staphylococcus aureus) in a very low concentration. Our results were compared with the most common antibiotic being used (Ciprofloxacin and Gentamycin); the novel components had significantly better antibacterial and antibiofilm activity in lower concentrations in comparison to the antibiotics. For instance, EBP-59 minimum inhibitory concentration was < 0.0003 mM, while ciprofloxacin 0.08 mM. Further antibacterial activity of novel components was surveyed against 10 clinical antibiotic resistance MRSA isolates. Again, novel components had significantly better antibacterial and antibiofilm activity in comparison with antibiotics. Mechanistic studies have revealed that none of these novel compounds exhibit any effect on the reduced thiol, disrupting iron sulfur clusters, or hydrogen peroxide pathways. Instead, their impact is attributed to the disruption of the Gram-positive bacterial cell membrane. Toxicity and safety testing on tissue cell culture showed promising results for the safety of components to the host.

microbiology↗

bioRxiv2023

Leakage beyond the primary infarction: A temporal analysis of cerebrovascular dysregulation at sites of hippocampal secondary neurodegeneration following cortical photothrombotic stroke

We have previously demonstrated that a cortical stroke causes persistent impairment of hippocampal-dependent cognitive tasks concomitant with secondary neurodegenerative processes such as amyloid-{beta} accumulation in the hippocampus, a region remote from the primary infarct. Interestingly, there is emerging evidence suggesting that deposition of amyloid-{beta} around cerebral vessels may lead to cerebrovascular structural changes, neurovascular dysfunction, and disruption of blood-brain barrier integrity. However, there is limited knowledge about the temporal changes of hippocampal cerebrovasculature after cortical stroke. In the current study, we aimed to characterise the spatiotemporal cerebrovascular changes after cortical stroke. This was done using the photothrombotic stroke model targeting the motor and somatosensory cortices of mice. Cerebrovascular morphology as well as the colocalization of amyloid-{beta} with vasculature and blood-brain-barrier integrity were assessed in the cortex and hippocampal regions at 7, 28 and 84 days post-stroke. Our findings showed transient cerebrovascular remodelling in the peri-infarct area up to 28 days post-stroke. Importantly, the cerebrovascular changes were extended beyond the peri-infarct region to the ipsilateral hippocampus and were sustained out to 84 days post-stroke. When investigating vessel diameter, we showed a decrease at 84 days in the peri-infarct and CA1 regions that was exacerbated in vessels with amyloid-{beta} deposition. Lastly, we showed sustained vascular leakage in the peri-infarct and ipsilateral hippocampus, indicative of a compromised blood-brain-barrier. Our findings indicate that hippocampal vasculature may represent an important therapeutic target to mitigate the progression of post-stroke cognitive impairment.

neuroscience↗

bioRxiv2021

Assessing microbial growth of six pure cultures grown anaerobically using optical density, ATP measurements, DNA concentrations and 16S rRNA targeted qPCR to compare commonly used techniques in lab and industry settings

This is a paper focusing on the comparison of growth curves using field relevant testing methods and moving away from colony counts. Challenges exist to explore antimicrobial growth of fastidious strains, poorly culturable bacterial and bacterial communities of environmental interest. Thus, various approaches have been explored to follow bacteria growth that can be an efficient surrogate for classical optical density or colony forming unit measurements. Here we tested optical density, ATP assays, DNA concentrations and 16S rRNA qPCR as means to monitor pure culture growth of six different species including Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica. Optical density is and excellent, rapid monitoring method of pure culture planktonic cells but cannot be applied to environmental or complex samples. ATP assays provide rapid results but conversions to cell counts may be misleading for different species. DNA concentration is a very reliable technique which can be used for any sample type and provides genetic materials for downstream applications. qPCR of the 16S rRNA gene is a widely applicable technique for monitoring microbial cell concentrations but is susceptible to variation between replicates. DNA concentrations were found to correlate the best with the other three assays and provides the advantages of rapid extraction, consistency between replicates and potential for downstream analysis, DNA concentrations is determined to be the best universal monitoring method for complex environmental samples.

microbiology↗

bioRxiv2020

Lessons and considerations for the creation of universal primers targeting non-conserved, horizontally mobile genes

Effective and accurate primer design is an increasingly important skill as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such as dsrAB and dnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a model community of six members (Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica). Using sequence alignments and in silico PCR analyses, a new approach for creating universal primers sets targeting mobile, non-conserved genes has been developed and compared to more traditional approaches used for highly conserved genes. A discussion of the potential shortfalls of the primer sets designed this way are described. The approach described here can be adapted to any unique gene set and aid in creating a wider, more robust library of primer sets to detect less conserved genes and improve the field of PCR-based screening research. ImportanceIncreasing use of molecular detection methods, specifically PCR and qPCR, requires utmost confidence in the results while minimizing false positives and negatives due to poor primer designs. Frequently, these detection methods are focused on conserved, core genes which limits their applications. These screening methods are being used in various industries for specific genetic targets or key organisms such as viral or infectious strains, or characteristic genes indicating the presence of key metabolic processes. The significance of this work is to improve primer design approaches to broaden the scope of detectable genes. The use of the techniques explored here will improve detection of non-conserved genes through unique primer design approaches. Additionally, the approaches here highlight additional, important information which can be gleaned during the in silico phase of primer design which will improve our gene annotations based on sequence homologies.

genetics↗

bioRxiv2016

Aer is a family of Energy-Taxis Receptors in Pseudomonas which also involves Aer-2 and CttP

Chemotaxis allows bacteria to sense gradients in their environment and respond by directing their swimming. Aer is a receptor that, instead of responding to a specific chemoattractant, allows bacteria to sense cellular energy levels and move towards favourable environments. In Pseudomonas, the number of apparent Aer homologs differs between the only two species it had been characterized in, P. aeruginosa and P. putida. Here we combined bioinformatic approaches with deletional mutagenesis in P. pseudoalcaligenes KF707 to further characterize Aer. It was determined that the number of Aer homologs varies between 0-4 throughout the Pseudomonas genus, and they were phylogenetically classified into 5 subgroups. We also used sequence analysis to show that these homologous receptors differ in their HAMP signal transduction domains. Genetic analysis also indicated that some Aer homologs have likely been subject to horizontal transfer. P. pseudoalcaligenes KF707 was unique among species for having three Aer homologs as well as the receptors CttP and McpB. Phenotypic characterization in this species showed the most prevalent homolog of Aer was key, but not essential for energy-taxis. This study demonstrates that energy-taxis in Pseudomonas varies between species and provides a new naming convention and associated phylogenetic details for Aer chemoreceptors.

microbiology↗