Biology subjects

Gibson, A.

Publications and source records attributed to Gibson, A..

16 recordsLinked to original sources

bioRxiv2025

Comparative Analysis of Denitrification and Other Nitrogen Cycle Genes in Diverse Environmental Microbiomes

The nitrogen cycle includes the microbial transformation of reactive nitrogenous molecules within a given ecosystem. Shotgun metagenomics, the unbiased sequencing of a microbial community, can reveal the unique gene profile and community composition of diverse microbiomes. We used NCycDB, an assembly-free, alignment-based pipeline, to determine and compare the potential nitrogen cycle processes in seven distinct microbiomes: wetland soils, agricultural soils, forest soils, compost, river water, and pond water from Knox County, Ohio, and lake water from the McMurdo Dry Valley Region in Antarctica. Soil metagenomes showed high levels of bacterial denitrifier genes, whereas freshwater metagenomes showed fewer denitrifiers. In wetland and agricultural soil cores, the relative abundance of norB, the marker gene for nitric oxide reductase, was a predictor of ambient N2O flux as measured by gas chromatography. Denitrifiers were predicted using the Kraken2/Bracken pipeline. In Ohio wetland soils, the relative abundance of Bradyrhizobium species were strongly associated with denitrification genes. We also explored how freshwater environmental factors select for or against nitrogen cycle genes. Denitrifier genes were positively correlated with phosphate concentration. Denitrifiers and denitrification genes were detected under microaerobic conditions, demonstrating that denitrification activity diminishes proportionally to oxygen concentration. An improved understanding of the denitrifier community in diverse microbiomes is necessary to mitigate excess N2O emissions from anthropogenic activities such as wetland drainage and crop production. IMPORTANCETerrestrial nitrogen limitations have historically reduced crop output. To fertilize crops, humans have developed synthetic N fixation methods, such as the Haber-Bosch process, which now account for half of global nitrogen uptake in biomass. The resulting nitrogen surplus in soils leads to eutrophication, harmful algal blooms in lakes and other aquatic ecosystems, and increased N2O emissions from denitrification via anaerobic respiration by soil bacteria. Considering that the nitrogen cycle is controlled by microbial communities, we need a better understanding of how nitrogen-cycling microbes control N runoff and N2O flux in each unique microbiome.

microbiology↗

bioRxiv2025

Female assortment in Gouldian Finch (Chloebia gouldiae) Flocks: A case of female-driven social niche construction?

The organization of animal groups is both a cause of and a consequence of patterns of interactions among individuals. The stability of social organization reflects how individuals construct and maintain resilient patterns of interactions across changes in group size and membership. Who you choose to associate with may have numerous advantages, primarily through avoiding potentially costly interactions with others. In this study, we describe patterns of social interactions in multiple flocks of Gouldian finches that were exposed to changing social conditions. In the first condition, flocks experienced repeated introductions of juveniles into the group. In a second condition, an adult flock was exposed to changing conditions where males were swapped between the flocks. In almost all flocks, we found significant levels of female-driven sex assortment. Further analysis shows that females were more likely to "leave" interactions after being approached by males than males, thus constituting a social decision to avoid male interactions. These findings highlight how the stable interactive decisions made by individuals contribute to higher-order patterns of organization in bird flocks.

animal behavior and cognition↗

bioRxiv2025

Acetaminophen inhibits diacylglycerol lipase synthesis of 2-arachidonoyl glycerol: implications for nociception

SUMMARYThough acetaminophen is a ubiquitous analgesic, its mechanism of action remains unknown. Thus, even though acetaminophen causes ∼500 deaths each year in the US it has not been possible to design safer alternatives. Because endocannabinoids may have a role in acetaminophen action, we examined interactions between the two. We now report that acetaminophen inhibits the activity of diacylglycerol lipase α (DAGLα), but not DAGLβ, decreasing production of the endocannabinoid 2-arachidonoyl glycerol. This gave rise to the counterintuitive hypothesis that decreasing endocannabinoid production by DAGLαinhibitionmay be antinociceptive in certain settings. Supporting this hypothesis, we find that DAGL inhibition by RHC80267 is antinociceptive in wildtype but not CB1 knockout mice in the hotplate test. We propose 1) that activation of DAGLα may exacerbate some forms of nociception and 2) a novel mechanism for the antinociceptive actions of acetaminophen whereby acetaminophen inhibits a DAGLα/CB1-based circuit that plays a permissive role in at least one form of nociception.

neuroscience↗

bioRxiv2024

Isotonic medium treatment limits burn wound microbial colonization and improves tissue repair

Burn injuries undergo a complex healing process in which progressive spreading of epithelial damage can lead to secondary complications such as wound infection, which is a major driver of mortality among burn patients. We recently reported that burning larval zebrafish triggers dysregulated keratinocyte dynamics compared to mechanical injury. Here, we investigate keratinocyte behavior following burn injury and the subsequent potential for microbial colonization of burn wounds over time. Real-time imaging, coupled with tracking of photoconverted cells, revealed that early keratinocyte motility contributes to the spread of epithelial damage beyond the initial site of burn injury and that increased epithelial damage was associated with wound colonization by the fungal pathogen Candida albicans. Modulating osmotic balance by treating larval zebrafish with isotonic medium limited the spread of epithelial damage and reduced microbial colonization of burn wounds. Using cultured human skin, we found that topical treatment with isotonic solution (saline) similarly prevented the spread of epithelial damage over time. These findings indicate that keratinocyte behavior contribute to burn wound progression in larval zebrafish and link keratinocyte dynamics to microbial colonization of burn wounded tissue.

cell biology↗

bioRxiv2024

Still Not Sterile: Chlorhexidine gluconate treatment does not completely reduce skin microbial bioburden and promotes pathogen overabundance in patients undergoing elective surgeries.

Surgical site infections (SSI) continue to occur despite widespread adoption of surgical antiseptics. The effects of chlorhexidine gluconate (CHG)-based antiseptics on the skin microbiome also remains undefined due to confounding effects of CHG persistence on skin. Patients undergoing elective surgery were enrolled to characterize the immediate and long-term impact of pre-surgical preparation with CHG antiseptic on skin microbial communities. Due to the broad-spectrum antimicrobial activity of CHG and its propensity to bind extracellular DNA, methods to selectively identify live microorganisms are critical to this process and to fully elucidate the effectiveness of pre-surgical protocols and potential disruptions to the healthy skin microbiome. Swabs of the surgical site skin microbiome were collected at multiple timepoints before and after surgery. Microbial bioburden and community compositions were evaluated with viability qPCR and 16S ribosomal RNA gene profiling. Pre-operative CHG induced a measurable reduction in the viable microbial bioburden at the surgical site. On the day of surgery, surgical sites displayed a significant increase in the relative abundance of several SSI associated bacterial genera, including, Acinetobacter, Bacillus, Escherichia-Shigella, and Pseudomonas, compared to baseline. Bacillus species isolated from subjects at baseline showed resistance to CHG with MICs exceeding 1000 {micro}g/ml. Despite major shifts in the skin microbiome upon exposure to CHG, they were transient in the majority of individuals. Skin microbial community structure recovered by the post-surgical follow-up. In short, this study shows that pre-surgical application of CHG can significantly reduce viable skin microbial bioburden, however, complete sterility is not achieved. While CHG induces temporary shifts in the skin microbiome, including enrichment for potentially pathogenic taxa, the skin microbiome recovers back to near baseline. Collectively, these findings identify tangible avenues for improving antiseptic formulations and offer further support that the skin microbiome is viable, stable, and resilient to chemical perturbation.

microbiology↗

bioRxiv2024

Pond Water Microbiome Taxa Profiles and Antibiotic Resistance Genes Associated with Acidity and Tannins

Microbial communities of small freshwater bodies are poorly understood. Four ponds in Knox County, Ohio, were sampled over two years to investigate the relationship between the microbial taxa profiles, antibiotic resistance genes (ARGs), and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration and metagenomes were analyzed by short-read sequencing. Taxa profiles were predicted by the Kraken2/Bracken pipelines. Bacterial taxa with high abundance in these ponds included Betaproteobacteria (Polynucleobacter and Methylopumilus) and Actinobacteria (Planktophila, Nanopelagicus, and Mycolicibacterium). One pond, a former quarry with elevated pH, showed high prevalence of Cyanobacteria with a seasonal shift from Synechococcus to Planktothrix in the fall. Planktothrix increase was associated with acidification. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database (CARD). The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and other cell defenses (mtrA). Pump function and global activation of transcription incur large energy expenditures, whose fitness cost may increase at high external pH where the cells proton-motive force is diminished. The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannins) which contribute a large transmembrane pH difference to the proton-motive force, thus increasing the cells energy available for pump function and global gene expression. IMPORTANCECompared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes. Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity for freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes the bacterial taxa composition and ARG prevalence including possible influence of factors such as pH and tannic acid levels.

microbiology↗

bioRxiv2024

Single-cell transcriptional landscape of temporal neutrophil response to burn wound in larval zebrafish

Neutrophils accumulate early in tissue injury. However, the cellular and functional heterogeneity of neutrophils during homeostasis and in response to tissue damage remains unclear. Here, we use larval zebrafish to understand neutrophil responses to thermal injury. Single-cell transcriptional mapping of myeloid cells during a 3-day time course in burn and control larvae revealed distinct neutrophil subsets and their cell-cell interactions with macrophages across time and conditions. The trajectory formed by three zebrafish neutrophil subsets resembles human neutrophil maturation, with varying transition patterns between conditions. Through ligand-receptor cell-cell interaction analysis, we found neutrophils communicate more in burns in a pathway and temporal manner. Finally, we identified the correlation between zebrafish myeloid signatures and human burn severity, establishing GPR84+ neutrophils as a potential marker of early innate immune response in burns. This work builds the molecular foundation and a comparative single-cell genomic framework to identify neutrophil markers of tissue damage using model organisms.

immunology↗

bioRxiv2024

Transcriptome-wide quantitative profiling of PUS7-dependent pseudouridylation by nanopore direct long read RNA sequencing

Understanding the interactions between different RNA modifications is essential for unraveling their biological functions. Here, we report NanoPsiPy, a computational pipeline that employs nanopore direct RNA sequencing to identify pseudouridine ({Psi}) sites and quantify their levels at single-nucleotide resolution. We validated NanoPsiPy by transcriptome-wide profiling of PUS7-dependent {Psi} sites in poly-A RNA and rRNA. NanoPsiPy leverages {Psi}-induced U-to-C basecalling errors in nanopore sequencing data, allowing detection of both low and high stoichiometric {Psi} sites. We identified 8,624 PUS7-dependent {Psi} sites in 1,246 mRNAs encoding proteins associated with ribosome biogenesis, translation, and energy metabolism. Importantly, integrative analysis revealed that PUS7 knockdown increases global mRNA N6-methyladenosine (m6A) and 5-methylcytosine (m5C) levels, suggesting an antagonistic relationship between {Psi} and these modifications. Our study underscores the potential of nanopore direct RNA sequencing in revealing the co-regulation of RNA modifications and the capacity of NanoPsiPy in analyzing pseudouridylation and its impact on other RNA modifications.

cancer biology↗

bioRxiv2023

Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis.

Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCR{beta} clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.

immunology↗

bioRxiv2023

What is Slough?A pilot study to define the proteomic and microbial composition of wound slough and its implications for wound healing.

Slough is a well-known feature of non-healing wounds. This study aims to determine the proteomic and microbiologic components of slough as well as interrogate the associations between wound slough components and wound healing. Twenty-three subjects with slow-to-heal wounds and visible slough were enrolled. Etiologies included venous stasis ulcers, post-surgical site infections, and pressure ulcers. Patient co-morbidities and wound healing outcome at 3-months post-sample collection was recorded. Debrided slough was analyzed microscopically, through untargeted proteomics, and high-throughput bacterial 16S-ribosomal gene sequencing. Microscopic imaging revealed wound slough to be amorphous in structure and highly variable. 16S-profiling found slough microbial communities to associate with wound etiology and location on the body. Across all subjects, slough largely consisted of proteins involved in skin structure and formation, blood-clot formation, and immune processes. To predict variables associated with wound healing, protein, microbial, and clinical datasets were integrated into a supervised discriminant analysis. This analysis revealed that healing wounds were enriched for proteins involved in skin barrier development and negative regulation of immune responses. While wounds that deteriorated over time started off with a higher baseline Bates-Jensen Wound Assessment Score and were enriched for anerobic bacterial taxa and chronic inflammatory proteins. To our knowledge, this is the first study to integrate clinical, microbiome, and proteomic data to systematically characterize wound slough and integrate it into a single assessment to predict wound healing outcome. Collectively, our findings underscore how slough components can help identify wounds at risk of continued impaired healing and serves as an underutilized biomarker.

microbiology↗

bioRxiv2021

Single Nucleotide Polymorphisms in the Bovine TLR2 Extracellular Domain Contribute to Breed and Species-Specific Innate Immune Functionality

Recent evidence suggests that several cattle breeds may be more resistant to infection with the zoonotic pathogen Mycobacterium bovis than others. Our data presented here suggests that the response to mycobacterial antigens varies in macrophages generated from Brown Swiss (BS) and Holstein Frisian (HF) cattle, two breeds belonging to the Bos taurus family. Whole genome sequencing of the Brown Swiss genome identified several potential candidate genes, in particular Toll-like Receptor-2 (TLR2) a pattern recognition receptor (PRR) that has previously been described to be involved in mycobacterial recognition. Further investigation revealed single nucleotide polymorphisms (SNP) in TLR2 that were identified between DNA isolated from cells of BS and HF cows. Interestingly, one specific SNP, H326Q, showed a different genotype frequency in two cattle subspecies, Bos taurus and Bos indicus. Cloning of the TLR2 gene and subsequent gene-reporter and chemokine assays revealed that this SNP, present in BS and Bos indicus breeds, resulted in a significantly higher response to mycobacterial antigens as well as tri-acylated lipopeptide ligands in general. Comparing wild-type and H326Q containing TLR2 responses, wild-type bovine TLR2 response showed clear, diminished mycobacterial antigen responses compared to human TLR2, however bovine TLR2 responses containing H326Q were found to be partially recovered compared to human TLR2. The creation of human:bovine TLR2 chimeras increased the response to mycobacterial antigens compared to the full-length bovine TLR2, but significantly reduced the response compared to the full-length human TLR2. Thus, our data, not only present evidence that TLR2 is a major PRR in the mammalian species-specific response to mycobacterial antigens, but furthermore, that there are clear differences between the response seen in different cattle breeds, which may contribute to their enhanced or reduced susceptibility to mycobacterial infection.

immunology↗

bioRxiv2021

Hypoxia induced carbonic anhydrase mediated dorsal horn sensory neuron activation and induction ofneuropathic pain

Neuropathic pain such as that seen in diabetes mellitus, results in part from central sensitisation in the spinal cord dorsal horn. However, the mechanisms responsible for such sensitisation remain unclear. There is evidence that disturbances in the integrity of the spinal vascular network can be a causative factor in the development of neuropathic pain. Here we show that reduced blood flow and vascularity of the dorsal horn leads to the onset of neuropathic pain. Using rodent models (type 1 diabetes and an inducible endothelial specific vascular endothelial growth factor receptor 2 knockout mouse) that result in degeneration of the endothelium in the dorsal horn we show that spinal cord vasculopathy results in nociceptive behavioural hypersensitivity. This also results in increased hypoxia in dorsal horn sensory neurons, depicted by increased expression of hypoxia markers hypoxia inducible factor 1, glucose transporter 3 and carbonic anhydrase 7. Furthermore, inducing hypoxia via intrathecal delivery of dimethyloxalylglycine leads to the activation of dorsal horn sensory neurons as well as mechanical and thermal hypersensitivity. This shows that hypoxic signalling induced by reduced vascularity results in increased hypersensitivity and pain. Inhibition of carbonic anhydrase activity, through intraperitoneal injection of acetazolamide, inhibited hypoxia induced pain behaviours. This investigation demonstrates that induction of a hypoxic microenvironment in the dorsal horn, as occurs in diabetes, is an integral process by which sensory neurons are activated to initiate neuropathic pain states. This leads to the conjecture that reversing hypoxia by improving spinal cord microvascular blood flow could reverse or prevent neuropathic pain.

neuroscience↗

bioRxiv2021

Crosstalk between enterocytes and innate lymphoid cells drives early IFN-g-mediated control of Cryptosporidium

The intestinal parasite, Cryptosporidium, is a major contributor to global child mortality and causes opportunistic infection in immune deficient individuals. Innate resistance to Cryptosporidium, which specifically invades enterocytes, is dependent on the production of IFN-{gamma}, yet whether enterocytes contribute to parasite control is poorly understood. In this study, utilizing the natural mouse pathogen, Cryptosporidium tyzzeri, we show that epithelial-derived IL-18 synergized with IL-12 to stimulate innate lymphoid cell (ILC) production of IFN-{gamma}. This innate IFN-{gamma} was required for early parasite control. Loss of STAT1 in enterocytes, but not dendritic cells or macrophages, antagonized early parasite control. Transcriptional profiling of enterocytes from infected mice identified an IFN-{gamma} signature and enrichment of anti-microbial effectors like IDO, GBP and IRG. Deletion experiments identified a role for Irgm1/m3 in parasite control. Thus, enterocytes promote ILC production of IFN-{gamma} that acts on enterocytes to restrict the growth of C. tyzzeri.

immunology↗

bioRxiv2021

Trade-offs between antiseptic cytotoxicity and efficacy in a human ex vivo wound contamination model

Wound cleansing agents are routine in wound care, even in the absence of signs of infection. Antiseptic activity prevents contaminating microbes from establishing an infection while also raising concerns of cytotoxicity and delayed wound healing. Here, we used an ex vivo human skin excisional wound model to evaluate the cytotoxicity of five clinically-used wound cleaning agents (saline, povidone iodine, Dove(R) soap, Dial(R) soap, and chlorhexidine gluconate). We established a wound contamination model using [~]100 cells of Pseudomonas aeruginosa per wound to evaluate antiseptic efficacy and microbial biofilm spatial organization. We found that Dial(R) soap and chlorhexidine gluconate significantly reduced metabolic activity of the biopsies, while all treatments except saline affected local cellular viability. Within the contamination model, only chlorhexidine gluconate treatment resulted in significantly lower P. aeruginosa counts at 24 hours post-treatment, driven by sub-limit-of-detection counts immediately post-treatment. Later applications of chlorhexidine gluconate had no effects on microbial growth, with microscopy showing extensive surface colonization of the wound bed. We present a clinically-relevant model for evaluating antiseptic cytotoxicity and efficacy, with the ability to resolve spatial localization and temporal dynamics of tissue viability and microbial growth.

microbiology↗

bioRxiv2020

Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms

A hallmark of chronic infections are polymicrobial biofilms. The forces governing assembly and maturation of these microbial ecosystems are largely unexplored but the consequences on host response and clinical outcome can be significant. In the context of wound healing, formation of a biofilm and a stable microbial community structure is associated with impaired tissue repair resulting in a non-healing chronic wound. These types of wounds can persist for years simmering below the threshold of classical clinical infection or cycling through phases of recurrent infection. In the most severe outcome amputation of lower extremities may occur if spreading infection ensues. Here we take an ecological perspective to study priority effects and competitive exclusion on overall biofilm community structure in a three-membered community of microbes derived from a chronic wound. We find that priority effects occur across both biotic and abiotic substrates, and ecological interactions can alter both fungal physiology and host inflammatory response. We show that bacterial-competition occurs for binding to fungal structures, and some species trigger the yeast-hyphae switch, resulting in enhanced neutrophil killing and inflammation. Collectively, the results presented here facilitate our understanding of fungal-bacterial microbial community dynamics and their effects on, host-microbe interactions, pathogenesis, and ultimately, wound healing.

microbiology↗

bioRxiv2020

Modelling early thermal injury using an ex vivo human skin model of contact burns

BackgroundEarly mechanisms underlying the progressive tissue death and the regenerative capability of burn wounds are understudied in human skin. A clinically relevant, reproducible model for human burn wound healing is needed to elucidate the early changes in the human burn wound environment. This study reports a reproducible contact burn model on human skin that explores the extent of tissue injury and healing over time, and defines the inter-individual variability in human skin to enable use in mechanistic studies on burn wound progression and healing. MethodsUsing a customized burn device, contact burns of various depths were created on human skin by two operators and were evaluated for histologic depth by three raters to determine reproducibility. Early burn wound progression and wound healing were also evaluated histologically after the thermally injured human skin was cultured ex vivo for up to 14 days. ResultsBurn depths were reproducibly generated on human skin in a temperature- or time-dependent manner. No significant difference in operator-created or rater-determined depth was observed within each patient sample. However, significant inter-individual variation was identified in burn depth in ten patient samples. Burn-injured ex vivo human skin placed into culture demonstrated differential progression of cell death and collagen denaturation for high and low temperature contact burns, while re-epithelialization was observed in superficial burn wounds over a period of 14 days. ConclusionThis model represents an invaluable tool to evaluate the inter-individual variability in early burn wound progression and wound healing to complement current animal models and enhance the translation of preclinical research to improvements in patient care.

cell biology↗