Biology subjects

Taylor, K. A.

Publications and source records attributed to Taylor, K. A..

6 recordsLinked to original sources

bioRxiv2026

STILL-13C: Spatial tracing of isotopically labelled lipids with 13C reveals metabolic heterogeneity in intact tissues

Lipid metabolism is dynamically rewired across tissues in response to developmental, environmental and therapeutic cues. This adaptation drives treatment resistance in a range of human pathologies, but current lipidomic techniques fail to capture the underlying mechanisms, relying on steady-state measurements from homogenised samples that obscure spatial heterogeneity and pathway flux. Here we introduce spatial tracing of isotopically labelled lipids (STILL-13C), a workflow that uses stable isotope tracing and high-resolution mass spectrometry imaging (MSI) to map lipid metabolic flux directly in intact human tissues with unprecedented pathway coverage. STILL-13C overcomes longstanding limitations of bulk and MSI-based analyses by spatially resolving isotopologue labelling of simple and complex lipids, enabling simultaneous tracing of fatty acid synthesis, remodelling and multiple convergent pathways required for phospholipid assembly, while preserving tissue architecture and regional metabolic context. Applied to patient-derived prostate cancer explants cultured ex vivo, STILL-13C revealed heterogeneity in lipid pathway activity between neighbouring epithelial regions and spatially resolved responses to pathway inhibition. This work establishes a broadly applicable platform for investigating spatial heterogeneity in lipid metabolic flux and its perturbation in intact tissues.

molecular biology↗

bioRxiv2023

A Method for Optimizing Imaging Parameters to Record Neuronal and Cellular Activity at Depth with Bioluminescence

Optical imaging of activity has provided valuable insight into brain function and accelerated the field of neuroscience in recent years. Genetically encoded fluorescent activity sensors of calcium, neurotransmitters and voltage have been tools of choice for optical recording of neuronal activity. However, photon scattering and absorbance limits fluorescence imaging to superficial regions for in vivo activity imaging. This limitation prevents recording of population level activity in lower brain regions of experimental animals without implanted hardware. Single and multiphoton methods find maximal use in the cortex and experience loss of signal at greater depths. Successful efforts have been made to increase the depth of fluorescence imaging using fiber photometry and gradient reflective index lenses. However, these methods are highly invasive, requiring an implant within the brain. Bioluminescence imaging offers a promising alternative to achieve activity imaging in deeper brain regions without hardware implanted within the brain. Bioluminescent reporters can be genetically encoded and produce photons without external excitation. The use of enzymatic photon production also enables prolonged imaging sessions without the risk of photobleaching or phototoxicity. These characteristics render bioluminescence suitable to non-invasive imaging of deep neuronal populations. To facilitate the adoption of bioluminescent activity imaging, we sought to develop a low cost, simple in vitro method to optimize imaging parameters for determining optimal exposure times and optical hardware configurations to determine what frame rates can be captured with an individual labs imaging hardware with sufficient signal-to-noise ratios without the use of animals prior to starting an in vivo experiment. To achieve this, we developed an assay for modeling in vivo optical conditions with a brain tissue phantom paired with engineered cells that produce bioluminescence. We then used this assay to limit-test the detection depth vs maximum frame rate for bioluminescence imaging at experimentally relevant tissue depths using off the shelf imaging hardware. With this method, we demonstrate an effective means for increasing the utility of bioluminescent tools and lowering the barrier to adoption of bioluminescence activity imaging with bioluminescent sensors.

neuroscience↗

bioRxiv2021

Untwisted α-synuclein Filaments formed in the Presence of Lipid Vesicles

Accumulation of filamentous aggregates of -synuclein is a pathological hallmark of several neurodegenerative diseases including Parkinsons disease (PD). Interaction between -synuclein and lipids has been shown to play a critical role in aggregation of -synuclein. Most structural studies have, however, been focused on -synuclein filaments formed in the absence of lipids. Here, we report structural investigation of -synuclein filaments assembled under the quiescent conditions in the presence of anionic lipid vesicles using electron microscopy (EM) including cryo-EM. Our transmission electron microscopy (TEM) analyses reveal that -synuclein forms curly protofilaments at an early stage of aggregation. The flexible protofilaments were then converted to long filaments after a longer incubation of 30 days. More detailed structural analyses using cryo-EM reveal that the long filaments adopt untwisted structures with different diameters, which have not been observed in previous -synuclein filaments formed in vitro. The untwisted filaments are rather similar to straight filaments with no observable twist that are extracted from patients with dementia with Lewy bodies. Our structural studies highlight the conformational diversity of -synuclein filaments, requiring additional structural investigation of not only more ex vivo -synuclein filaments, but also in vitro -synuclein filaments formed in the presence of diverse co-factors to better understand the molecular basis of diverse molecular conformations of -synuclein filaments.

biochemistry↗

bioRxiv2021

metaboprep: an R package for pre-analysis data description and processing.

MotivationMetabolomics is an increasingly common part of health research and there is need for pre-analytical data processing. Researchers typically need to characterize the data and to exclude errors within the context of the intended analysis. While some pre-processing steps are common, there is currently a lack of standardization and reporting transparency for these procedures. ResultsHere we introduce metaboprep, a standardized data processing workflow to extract and characterize high quality metabolomics data sets. The package extracts data from pre-formed worksheets, provides summary statistics and enables the user to select samples and metabolites for their analysis based on a set of quality metrics. A report summarizing quality metrics and the influence of available batch variables on the data is generated for the purpose of open disclosure. Where possible, we provide users flexibility in defining their own selection thresholds. Availability and implementationmetaboprep is an open-source R package available at https://github.com/MRCIEU/metaboprep Contactd.a.hughes@bristol.ac.uk or laura.corbin@bristol.ac.uk

bioinformatics↗

bioRxiv2021

Distinct cryo-EM Structure of α-synuclein Filaments derived by Tau

Recent structural studies of ex vivo amyloid filaments extracted from human patients demonstrated that the ex vivo filaments associated with different disease phenotypes adopt diverse molecular conformations distinct from those in vitro amyloid filaments. A very recent cryo-EM structural study also revealed that ex vivo -synuclein filaments extracted from multiple system atrophy (MSA) patients adopt quite distinct molecular structures from those of in vitro -synuclein filaments, suggesting the presence of co-factors for -synuclein aggregation in vivo. Here, we report structural characterizations of -synuclein filaments derived by a potential co-factor, tau, using cryo-EM and solid-state NMR. Our cryo-EM structure of the tau-promoted -synuclein filament at 4.0 [A] resolution is somewhat similar to one of the polymorphs of in vitro -synuclein filaments. However, the N- and C-terminal regions of the tau-promoted -synuclein filament have different molecular conformations. Our structural studies highlight the conformational plasticity of -synuclein filaments, requiring additional structural investigation of not only more ex vivo -synuclein filaments, but also in vitro -synuclein filaments formed in the presence of diverse co-factors to better understand molecular basis of diverse molecular conformations of -synuclein filaments.

biochemistry↗

bioRxiv2020

CryoEM Structure of Drosophila Flight Muscle Thick Filaments at 7A Resolution

Striated muscle thick filaments are composed of myosin II and several non-myosin proteins. Myosin IIs long -helical coiled-coil tail forms the dense protein backbone of filaments while its N-terminal globular head containing the catalytic and actin binding activities extends outward from the backbone. Here we report the structure of thick filaments of the flight muscle of the fruit fly Drosophila melanogaster at 7 [A] resolution. Its myosin tails are arranged in curved molecular crystalline layers identical to flight muscles of the giant waterbug Lethocerus indicus. Four non-myosin densities are observed, three of which correspond to ones found in Lethocerus; one new density, possibly stretchin-Mlck, is found on the backbone outer surface. Surprisingly, the myosin heads are disordered rather than ordered along the filament backbone. Our results show striking myosin tail similarity within flight muscle filaments of two insect orders separated by several hundred million years of evolution. Significance StatementMyosin thick filaments are one of striated muscles key structures, but also one of its least understood. A key question is how the myosin a-helical coiled-coil tail is arranged in the backbone. At 7[A] resolution, sufficient to resolve individual a-helices, the myosin tail arrangement in thick filaments from the flight muscle of the fruit fly Drosophila melanogaster is strikingly similar to the myosin tail arrangement in flight muscles of the giant waterbug Lethocerus indicus. Nearly every other thick filament feature is different. Drosophila and Lethocerus evolved separately >245 million years ago suggesting myosin tail packing into curved molecular crystalline layers forms a highly conserved thick filament building block and different properties are obtained by alterations in non-myosin proteins.

biophysics↗