Biology subjects

Burke, M. J.

Publications and source records attributed to Burke, M. J..

3 recordsLinked to original sources

bioRxiv2026

Chronic Stress Exacerbates Long-term Microvascular Network Dysfunction Following Brain Trauma

BackgroundPreexisting factors are among the strongest predictors of recovery following traumatic brain injury (TBI), with chronic stress closely associated with permanent disability and worse long-term outcomes. While chronic cerebrovascular dysfunction is linked to these poor trajectories, as impaired blood flow regulation drives secondary disease progression, the mechanisms regulating this vascular failure remain incompletely understood. Crucially, how premorbid chronic stress and TBI disrupt the fundamental coordination of the cerebrovascular network post-injury remains unknown. MethodsTo elucidate this coordination at rest and in response to increased neuronal activity, we used a model of three repeated moderate closed cortical impacts comorbid with chronic stress induced by social isolation (SI) post-weaning. Our previously developed vascular analysis pipeline (NOVAS3D) was employed to estimate changes in vascular radii across cerebrovasculature proximal to neuronal activation. Arteries and veins were annotated in the imaged volumes to allow for blood flow simulations. ResultsUsing graph-based network analysis, we demonstrate that TBI, when compounded with chronic stress, critically disrupts the long-range coordination of the capillary network. Specifically, the functional coordination of radius changes between nearby, non-adjacent capillaries was reduced by 40{+/-}20% in TBI+SI mice relative to controls. Consequently, simulations estimated that the vascular networks in TBI+SI mice experienced a 68{+/-}7% reduction in arterial red blood cell velocity (VRBC) responses to neuronal activation. These network-wide impairments were fundamentally driven by severely blunted vessel reactivity, including a 28{+/-}7% decrease in the magnitude of arteriolar dilations and a 47{+/-}7% decrease in the magnitude of arteriolar constrictions. ConclusionThese findings provide a mechanistic foundation for worse clinical outcomes seen in TBI patients with comorbid chronic stress, identifying arteriolar reactivity and long-range capillary coordination as critical therapeutic targets to mitigate secondary injury and improve long-term recovery.

neuroscience↗

bioRxiv2026

Label-Free AI-Classification of Subcellular Organelles Based on Optical Photothermal Infrared Images

Cells maintain homeostasis by dynamically reorganizing their organelles to tune metabolism in response to stress. Fluorescence microscopy maps organelle locations with subcellular resolution but provides limited information on their chemical composition. Infrared (IR) imaging offers a label-free alternative for probing intrinsic molecular vibrations that report on lipids, carbohydrates, and nucleic acids. However, its broader application to subcellular biology has been limited by spatial resolution and hyperspectral data complexity. Here, we combine submicron optical photothermal IR imaging with machine learning to classify subcellular structures in fixed U-2 OS cells. Using fluorescent-labeled organelles as ground truth, we trained and evaluated random forest (RF) classifiers and U-Net convolutional neural networks to identify organelles from IR spectra. The RF model converged rapidly, requiring fewer than 75 spectra per class per cell and fewer than 25 cells, indicating that models trained on small cellular regions can be extended to classify whole-cell images. The resulting classifiers accurately identified multiple organelles, including the endoplasmic reticulum, Golgi apparatus, mitochondria, nucleus, nucleolus, and stress granules. In contrast, classification was unsuccessful for nuclear speckles, actin, and microtubules, suggesting that some structures lack sufficiently distinct IR signatures under these conditions. Classifiers trained in U-2 OS cells generalized to HEK 293 cells, consistent with conserved organelle biochemical composition across cell types. However, the classifiers failed under cellular stress, indicating sensitivity to stress-induced changes in organelle state. Together, these results establish a scalable, label-free strategy for high-resolution mapping of organelle biochemical composition and provide a foundation for subcellular biomarker discovery and disease-state diagnostics.

biophysics↗

bioRxiv2022

An Ultralong Bovine CDRH3 that Targets a Conserved, Cryptic Epitope on SARS-CoV and SARS-CoV-2

The ability of broadly neutralising antibodies to target conserved epitopes gives them huge potential as antibody-based therapeutics, particularly in the face of constant viral antigen evolution. Certain bovine antibodies are highly adept at binding conserved, glycosylated epitopes, courtesy of their ultralong complementarity determining region (CDR)H3. Here, we used a SARS-naive, bovine ultralong CDRH3 library and mammalian cell display, to isolate a bovine paratope that engages the SARS-CoV and SARS-CoV-2 receptor-binding domain (RBD). This neutralises viruses pseudo-typed with SARS-CoV Spike protein but not by competition with RBD binding to ACE2. Instead, using differential hydrogen-deuterium exchange mass spectrometry and site-directed mutagenesis, we demonstrate that this ultralong CDRH3 recognises a rarely identified, conserved, cryptic epitope that overlaps the target of pan-sarbecovirus antibodies (7D6/6D6). The epitope is glycan-shielded and becomes accessible only transiently via inter-domain movements. This represents the first bovine anti-sarbecovirus paratope and highlights the power of this approach in identifying novel tools to combat emerging pathogens.

molecular biology↗