Biology subjects

Reid, B.

Publications and source records attributed to Reid, B..

7 recordsLinked to original sources

bioRxiv2026

Biochar suppression of antibiotic resistance genes in the soil microbiome

Antimicrobial resistance (AMR) in soils frequently arises from low-level antibiotic presence in agriculture systems where livestock receive antibiotics for disease prevention. Here we assess the influence of oak (Quercus robur) wood biochar (pyrolysis at 7600C) on the microbiome of a parkland soil, after 300 days of incubation, in the presence and absence of the antibiotic sulphamethazine (SMZ). Stable isotope probing coupled to metagenomics was carried out to identify metabolically active microorganisms and quantify antimicrobial resistance gene (ARG) prevalence. Across all treatments, Pseudomonadota and Actinobacteriota dominated (63-78%), with Pseudomonadota enriched in the biologically active heavy water fraction. Gemmatimonadota increased, and Bacillota decreased in heavy fractions, while minor phyla displayed variable shifts. Biochar significantly reduced ARG prevalence in the active heavy water metagenome from 23,485 ARGs in control soils to 10,002 ARGs in biochar-amended soils, while SMZ alone increased to 26,193 ARGs found in their metagenome. Combined biochar and SMZ treatment resulted in lower ARGs (16,890 ARGs) than both control and SMZ-only soils, likely due to a combination of ARG adsorption, antibiotic immobilisation, and microbial community restructuring. These results highlight the potential of biochar as a soil amendment for mitigating the proliferation of AMR in agriculture environments.

microbiology↗

bioRxiv2026

Dimensionally traceable 3D microstructures for multimodal microscope calibration

High-resolution microscopy techniques are used across research and industry to analyse biological systems, from biomolecules to subcellular organelles, multicellular models and tissues. As multimodal imaging workflows and quantitative analysis of bioimaging data become increasingly widespread, there is a growing need for materials and methods to calibrate imaging systems and evaluate the fidelity of generated image data. Here, we present three-dimensional microscopy phantoms fabricated using two-photon photolithography from transparent resins that exhibit both broadband visible autofluorescence and Raman scattering across the fingerprint and C-H stretching regions. Suitable for analysis using optical profilometry, the phantoms were dimensionally calibrated with SI traceability using a metrological confocal microscope. Immersible in air and common aqueous imaging media, the phantoms are compatible with a wide variety of optical microscopy techniques, including one and two-photon excited fluorescence and coherent Raman scattering microscopy. We employed a forked wedge design to validate image deconvolution results and a stacked lattice phantom to recover image distortion matrices under realistic biological imaging conditions. We demonstrate the impact of correcting chromatic offsets and axial scaling errors for a representative application: analysis of a cell seeded scaffold using confocal laser scanning fluorescence microscopy. These phantoms provide a versatile platform for calibration, quality control and validation of multimodal imaging pipelines and improved quantitative optical microscopy.

bioengineering↗

bioRxiv2025

Oxygen uptake in human donor corneas: the centripetal gradient and its changes in culture and correlation with wounds and aminophylline treatment

Oxygen is a diatomic element abundant in the atmosphere and is essential for homeostatic and metabolic processes within the cornea. The avascular cornea uptakes oxygen from the atmosphere and performs refractory and protective functions that are essential for eyesight. However, the spatial-temporal profile of oxygen uptake (O2U) in human corneas remains uncharacterized in literature. Utilizing the micro optrode technique and donor corneas, we demonstrated that the limbus has a significantly higher O2U than the cornea center, exhibiting a pattern of centripetal gradient of O2U. This pattern is thus conserved in the corneas of mice, rats, non-human primates, and humans, representing a metabolic feature of physiological significance, which may have diagnostic and prognostic value. Being cultured at 37{degrees}C and 5% CO2, this centripetal pattern became more prominent in the first three days, and less so on day 4. The pattern remained in the corneas with injury, increased O2U appears to correlate with wound healing, similar to patterns observed in animal models with a dynamic increase of metabolism in the periphery, followed by the limbus, and subsequent return to baseline. Administration of the drug aminophylline prevented a decrease of O2U at day 4. We conclude that the centripetal pattern of O2U is conserved across species and in the human cornea. Combined, our results suggest the functional and clinical significance of the mesoscopic metabolism pattern for further study and the use of aminophylline as a therapeutic agent to increase O2U and enhance corneal wound healing.

cell biology↗

bioRxiv2024

Galvanotactic directionality of cell groups depends on group size

Motile cells migrate directionally in the electric field in a process known as galvanotaxis, important and under-investigated phenomenon in wound healing and development. We previously reported that individual fish keratocyte cells migrate to the cathode in electric fields, that inhibition of PI3 kinase reverses single cells to the anode, and that large cohesive groups of either unperturbed or PI3K-inhibited cells migrate to the cathode. Here we find that small uninhibited cell groups move to the cathode, while small groups of PI3K-inhibited cells move to the anode. Small groups move faster than large groups, and groups of unperturbed cells move faster than PI3K-inhibited cell groups of comparable sizes. Shapes and sizes of large groups change little when they start migrating, while size and shapes of small groups change significantly, lamellipodia disappear from the rear edges of these groups, and their shapes start to resemble giant single cells. Our results are consistent with the computational model, according to which cells inside and at the edge of the groups pool their propulsive forces to move but interpret directional signals differently. Namely, cells in the group interior are directed to the cathode independently of their chemical state. Meanwhile, the edge cells behave like individual cells: they are directed to the cathode/anode in uninhibited/PI3K-inhibited groups, respectively. As a result, all cells drive uninhibited groups to the cathode, while larger PI3K-inhibited groups are directed by cell majority in the group interior to the cathode, while majority of the edge cells in small groups win the tug-of-war driving these groups to the anode. Significance statementMotile cells migrate directionally in electric fields. This behavior - galvanotaxis - is important in many physiological phenomena. Individual fish keratocytes migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Uninhibited cell groups move to the cathode. Surprisingly, groups of PI3K-inhibited cells exhibit bidirectional behavior: larger/smaller groups move to the cathode/anode, respectively. A mechanical model suggests that inner and outer cells interpret directional signals differently, and that a tug-of-war between the outer and inner cells directs the cell groups. These results shed light on general principles of collective cell migration.

cell biology↗

bioRxiv2024

Quantifiable Blood TCR Repertoire Components Associated with Immune Aging

T cell senescence results in decayed adaptive immune protection in older individuals, with decreased or increased abundance of certain T cell phenotypic subpopulations. However, no study has linked aging to the dynamic changes of T cell clones. Through a newly develop computational framework, Repertoire Functional Units (RFU), we investigated over 6,500 TCR repertoire sequencing samples from multiple human cohorts. Our analysis identified age-associated RFUs repeatedly and consistently across different cohorts. Quantification of RFU decreases with aging revealed accelerated loss under immunosuppressive conditions. Systematic analysis of age-associated RFUs in clinical samples manifested a potential link between these RFUs and improved clinical outcomes during acute viral infections, such as lower ICU admission and reduced risk of developing complications. Finally, our investigation of bone-marrow transplantation patients indicated a secondary expansion of the age-associated clones upon receiving stem cells from younger donors. Together, our results suggest the existence of certain clones or a TCR clock that could reflect the immune functions in aging populations.

immunology↗

bioRxiv2020

PI3K inhibition reverses migratory direction of single cells but not cell groups in electric field

Motile cells migrate directionally in the electric field in a process known as galvanotaxis. Galvanotaxis is important in wound healing, development, cell division, and nerve growth. Different cell types migrate in opposite directions in electric fields, to either cathode, or anode, and the same cell can switch the directionality depending on chemical conditions. We previously reported that individual fish keratocyte cells sense electric fields and migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Many physiological processes rely on collective, not individual, cell migration, so here we report on directional migration of cohesive cell groups in electric fields. Uninhibited cell groups of any size move to the cathode, with speed decreasing and directionality increasing with the group size. Surprisingly, large groups of PI3K-inhibited cells move to the cathode, in the direction opposite to that of individual cells, which move to the anode, while such small groups are not persistently directional. In the large groups, cells velocities are distributed unevenly: the fastest cells are at the front of the uninhibited groups, but at the middle and rear of the PI3K-inhibited groups. Our results are most consistent with the hypothesis, supported by the computational model, that cells inside and at the edge of the groups interpret directional signals differently. Namely, cells in the group interior are directed to the cathode independently of their chemical state. Meanwhile, edge cells behave like the individual cells: they are directed to the cathode/anode in uninhibited/PI3K-inhibited groups, respectively. As a result, all cells drive uninhibited groups to the cathode, but a mechanical tug-of-war between the inner and edge cells directs large PI3K-inhibited groups with cell majority in the interior to the cathode, while rendering small groups non-directional. Significance statementMotile cells migrate directionally in electric fields. This behavior - galvanotaxis - is important in many physiological phenomena. Individual fish keratocytes migrate to the cathode, while inhibition of PI3K reverses single cells to the anode. Uninhibited cell groups move to the cathode. Surprisingly, large groups of PI3K-inhibited cells also move to the cathode, in the direction opposite to that of individual cells. The fastest cells are at the front of the uninhibited groups, but at the middle and rear of the PI3K-inhibited groups. We posit that inner and edge cells interpret directional signals differently, and that a tug-of-war between the edge and inner cells directs the cell groups. These results shed light on general principles of collective cell migration.

biophysics↗

bioRxiv2018

Infection-generated electric field in gut epithelium drives bidirectional migration of macrophages

Many bacterial pathogens hijack macrophages to egress from the port of entry to the lymphatic/blood-stream, causing dissemination of life-threatening infections. However, the underlying mechanisms are not well understood. Here, we report that Salmonella infection generates directional electric fields (EF) in the follicle-associated epithelium of mouse cecum. In vitro application of an EF, mimicking the infection-generated electric field (IGEF), induces directional migration of primary mouse macrophages to the anode, which is reversed to the cathode upon Salmonella infection. This infection-dependent directional switch is independent of the Salmonella pathogenicity island 1 (SPI-1) type III secretion system. The switch is accompanied by a reduction of sialic acids on glycosylated surface components during phagocytosis of bacteria, which is absent in macrophages challenged by microspheres. Moreover, enzymatic cleavage of terminally exposed sialic acids reduces macrophage surface negativity and severely impairs directional migration of macrophages in response to EF. Based on these findings, we propose that macrophages are attracted to the site of infection by a combination of chemotaxis and galvanotaxis; after phagocytosis of bacteria, surface electrical properties of the macrophage change, and galvanotaxis directs the cells away from the site of infection.\n\nAbbreviationsCFU, colony-forming unit; Con A, Concanavalin A; EF, electric field; FAE, follicle-associated epithelium; GNL, Galanthus Nivalis lectin; IGEF, infection-generated electric field; Ji, electric current density; MAL-2, Maackia Amurensis lectin II; MLN, mesenteric lymph node; MOI, multiplicity of infection; nMFI, normalized mean fluorescence intensity; RCA-1, Ricinus Communis Agglutinin I; SNA, Sambucus Nigra lectin; S. Typhimurium, Salmonella enterica serotype Typhimurium; SPI-1, Salmonella pathogenicity island 1; PDMS, polydimethylsiloxane; TEP, trans-epithelial potential difference; TLR, Toll-like receptors; WGEF, wound-generated electric field

cell biology↗