Biology subjects

Hunt, D.

Publications and source records attributed to Hunt, D..

15 recordsLinked to original sources

bioRxiv2026

Acute Temporal Dynamics of Brain Injury Plasma Biomarkers following Controlled Football Heading

Footballers are routinely exposed to repeated non-concussive head impacts with (soccer) heading, the acute neurobiological consequences of which remain poorly characterised. Current evidence for acute changes in biofluid markers following heading is tempered by design limitations including inadequate impact exposure monitoring, uncontrolled confounders (e.g. exercise), the lack of a control group and heterogeneity in sampling times. This study attempts to address these limitations with a novel combination of serial sampling measuring biomarkers across five timepoints (pre and 0.5, 2, 4 and 24 h post heading), a within-subject, time-matched resting control condition and participant-level finite element modelling used for impact quantification. In a counter-balanced crossover design, twelve male football players aged 18-31 completed a heading session with 10 verified rotational headers delivered from a ball launcher at 10 m and a control condition. Impact kinematics were captured with instrumented mouthguards and modelled using the Edinburgh finite element head model (EdiFEHM). Additional monitoring measures included near point convergence (NPC) at each timepoint and the sport concussion assessment tool (SCAT6) at the pre, 0.5 and 24 h timepoints. The Quanterix Simoa N4PD Advantage Plus assay was used to quantify plasma concentration of neurofilament light (NfL), glial fibrillary acidic protein (GFAP), ubiquitin carboxy-terminal hydrolase L1 (UCH-L1) and brain-derived tau (BD-tau) measured for the first time in this context. GFAP and BD-tau showed significant main effects of time (both P < 0.005) but no effect of heading. UCH-L1 was excluded and NfL restricted to descriptive analysis as both fell near or below the minimum assay quantification level. NPC alongside SCAT6 symptom and cognitive scores remained unaffected by heading. Tissue strain modelling showed a mean peak MPS95 of 0.099 (range: 0.074-0.144) consistent with low magnitude non-concussive impact exposure across participants. These findings provide a methodological framework and anchor point for non-concussive impact research employing biofluid sampling while highlighting sensitivity limitations of current multiplex Simoa assays in certain biomarkers for healthy young-adult populations. Design elements including time-matched controls, serial sampling and individualised mechanical exposure outcomes are essential for characterising exposure and avoiding spurious findings. The study was preregistered with the ISRCTN registry (ISRCTN44241334).

neuroscience↗

bioRxiv2026

CDK8 phosphorylation of DELLA limits Mediator recruitment in gibberellin signaling

Gibberellin (GA) promotes plant growth primarily by triggering degradation of DELLA transcription regulators, yet how DELLA activity is fine-tuned dynamically by phosphorylation independently of proteolysis remains poorly understood. Here we show that the CDK8 kinase module of the Mediator complex attenuates activity of the Arabidopsis DELLA protein RGA by modulating coactivator recruitment. Using TurboID-based proximity labeling, biochemical and genetic analyses, we identify CDK8 as an in-planta kinase that phosphorylates RGA at Ser170 within its disordered PolyS/T region. This phosphorylation does not affect RGA stability, localization or interactions with transcription factors or histone H2A, but selectively weakens RGA association with the Mediator subunit MED15, thereby reducing DELLA-dependent transcription activation. Consistently, cdk8 mutants show impaired GA-responses and delayed developmental phase transitions that are partially rescued by loss of DELLA function. Our findings uncover a phosphorylation-dependent mechanism by which the Mediator kinase module fine-tunes hormone-responsive transcription through selective control of DELLA-coactivator interactions.

plant biology↗

bioRxiv2026

QNPtoVox: A methods pipeline for mapping 2D quantitative neuropathology to 3D MNI voxel space.

1.Quantitative neuropathology has advanced through whole-slide imaging and digital histology platforms. Yet, these measurements rarely align with neuroimaging coordinate frameworks that may be useful for spatial modeling and other applications. QNPtoVox, short for quantitative neuropathology to voxels, is a reproducible, modular pipeline that transforms quantitative metrics generated by digital pathology software (HALO) into voxel-based maps registered to a standard common coordinate (MNI) template. The workflow integrates digital histopathology, gross tissue photography, ex-vivo MRI, and nonlinear registration to generate spatially standardized 3D pathology representations. This Methods article provides a complete procedural description, including required materials, step-wise instructions, operator-dependent checkpoints, expected outputs, reproducibility evaluation, and troubleshooting. QNPtoVox enables voxel-level integration of neuropathology with neuroimaging tools, unlocking existing histopathology datasets for computational modeling and cross-cohort harmonization.

neuroscience↗

bioRxiv2025

Fiber Type and Stimulus Determine Progression of Skeletal Muscle Atrophy

BackgroundSkeletal muscle atrophy is prevalent worldwide and is a major detractor from length and quality of life. It is often diagnosed and treated as a single disorder, but the causal stimuli and progression of atrophy vary widely. Malnutrition and disuse are two common causes of muscle atrophy, and despite their prevalence and extensive characterization, there have been no direct comparisons of how these two types of atrophy progress and whether they differentially affect skeletal muscle fiber types. The purpose of this study is to directly compare atrophy from fasting and disuse and provide a transcriptomic resource for future research on both conditions. MethodsWe fasted or hindlimb suspended (HS) two cohorts of 12-week-old female C57/bl6 mice. Mice were fasted for up to 72 hours to induce malnutrition atrophy or were hindlimb suspended for 0, 3, 7, 14, or 28 days to induce disuse atrophy. At each timepoint, mice were euthanized and three muscles (tibialis anterior (TA), extensor digitorum longus (EDL), and soleus) were weighed and collected for RNA sequencing. Atrophy progression and gene expression changes were compared across muscle fiber types and atrophy stimuli. ResultsWe found differences in atrophy progression between muscle fiber types based on fiber twitch speed and atrophy stimulus. Fasted mice lost 25% of their body weight and 23% of fast-twitch TA mass with little change in soleus. In contrast, HS mice lost 40% of the slower-twitch soleus but the effect on the TA was negligible. Gene expression varied in response to both atrophy stimuli, but a greater number of genes changed with fasting compared to HS in the EDL and soleus. By muscle type, a greater transcriptional shift occurred in the EDL with fasting while the soleus showed more gene changes during HS. Enrichment analysis of transcriptional changes showed similarities (downregulation in muscle growth pathways) and differences (increased fatty acid metabolism in fasting and increased neuronal activity in HS) between atrophy stimuli. ConclusionsAtrophy progression varies based on stimuli and muscle fiber type. This study provides a large, matched data set where the effects of different atrophic stimuli can be easily and directly compared in multiple fiber types. To our knowledge, this is the first study to closely compare these two atrophy stimuli in a muscle type-specific context. This work demonstrates that atrophy is not a single disorder and that the development of therapies may need to be tailored to the atrophic stimulus.

molecular biology↗

bioRxiv2025

Decades-long elevation of interferon-alpha drives a Sjogren disease endotype: an interdisciplinary study

BACKGROUNDMechanistic heterogeneity is a major obstacle to the development of effective treatment for Sjogren disease (SjD) and there is a pressing need to stratify SjD according to precision medicine principles. Aberrant activation of the type I interferon (IFN) pathway represents a leading candidate pathway, but a causal role of elevated IFN- in driving a Sjogren disease endotype remains to be established. METHODSWe used ultrasensitive single molecule ELISA, and an oligoprotein interferon signature score (derived from broad capture proteomics), to study the role of IFN- in Sjogren disease. We analysed samples from the UK Primary Sjogren Syndrome Registry (UKPSSR, n=177) and UK Biobank Plasma Proteomics Project (n=47606 without Sjogren, n=257 with Sjogren, including 137 individuals sampled prior to diagnosis) to determine the timecourse and immune endotype associated with elevated IFN-. To address causality we created a new transgenic mouse model of IFN- overexpression to establish whether chronically elevated IFN- drives this immune endotype. FINDINGSOligoprotein interferon signatures can be detected at least 14 years prior to diagnosis of Sjogren disease in the UK Biobank-PPP. IFN- concentrations are elevated in 60% of Sjogren disease patients in the UKPSSR. Individuals with elevated IFN- display a distinct immunological endotype characterised by cytopenias, hypergammaglobulinaemia, multiple autoantibodies and autoimmunity against the Sjogren autoantigen TRIM21/Ro52. To address the key question of causal direction, we created a new mouse model of systemic chronic IFN- elevation, in which Ifn4 is overexpressed by conventional dendritic cells. This model recapitulates key features of the endotype and can be partially reversed by IFNAR1 blockade. INTERPRETATIONElevation of IFN- drives an immune endotype of Sjogren disease, originating over a decade prior to diagnosis. SjD patients with elevated IFN- concentrations are broadly clinically similar to those with normal IFN- concentrations, yet are immunologically distinct. This highlights the mechanistic heterogeneity of SjD and the need for immunological stratification along precision medicine principles, using high resolution biomarkers. As well as demonstrating causal direction, biological modelling shows that chronic IFN- elevation over the lifecourse has the potential to establish persistent immune dysregulation which responds only partially to interferon receptor blockade. These findings provide insights into SjD and other "interferonopathic" rheumatological disorders. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE for "Sjogrens Syndrome/Disease" and "interferon", including the terms "subsets", "sub-groups", "phenotypes", and "endotypes", filtering by "clinical trial", "stratification", and "immune-mediated inflammatory". We also included major review articles from noted experts. We identified reports of associations between IFN- and SjD, usually using indirect or imprecise measures of IFN-. None of these studies included prediagnostic samples and causal inference was limited. Added value of this studyThis study shows that IFN-, when measured directly using ultrasensitive single molecule ELISA approaches (uniquely optimised to determine healthy control concentrations), is elevated in a subset of people with SjD with a specific immunological endotype. Analysis of prediagnostic proteomics shows this elevation can be detected up to 14 years before diagnosis. We show that IFN- drives this endotype (as opposed to vice versa) by recapitulating key endotype features in a novel and unambiguous experimental mouse model of chronic IFN- elevation. We also show that the pathogenic consequences of IFN- elevation over long periods of time can only be partially reversed using IFNAR blockade. Implications of all the available evidenceThese data have important implications for future research, clinical practice, trial design, and therapeutic development. First, our findings provide clinical evidence, supported by unambiguous preclinical evidence, that decades-long elevated IFN can cause and drive a SjD endotype - and accurately defines the level of heterogeneity. Secondly, we provide biomarkers which may be of use in stratifying clinical trial design and also for early identification of at-risk individuals. Thirdly we provide biological proof of principle that longstanding and potentially undiagnosed elevation of IFN- can establish persistent immune dysregulation which may respond only partially to IFNAR blockade. Together these findings inform precision medicine approaches and future trial design.

immunology↗

bioRxiv2025

TTLL4 glutamyltransferase is a therapeutic target for NPM1-mutated acute myeloid leukemia

NPM1-mutated acute myeloid leukemia (AML) is defined by aberrant cytoplasmic localization of the mutant NPM1c protein, and therapeutic strategies targeting this specific disease remain limited. Here, we identify TTLL4, a mono-glutamate glutamyltransferase, as a selective vulnerability in NPM1c AML. TTLL4 catalyzes post-translational hyper-glutamylation of NPM1c at E126, stabilizes its cytoplasmic localization and promotes a differentiation block in leukemic cells. Multiple genetic TTLL4 inactivation approaches in human NPM1c-mutant cell lines reduce NPM1c glutamylation, trigger myeloid differentiation, and impair proliferation. Transcriptomic analyses show that TTLL4 knockdown pheno-copies NPM1c degradation and aligns with KMT2A and XPO1-targeted gene expression programs. Furthermore, Ttll4 knockout significantly prolonged survival in an NPM1c/NRAS-driven mouse AML model and promoted differentiation. We identify a small molecule, EN7, that selectively inhibits TTLL4 and recapitulates these phenotypes in NPM1c+ cells. These findings identify glutamylation as a new axis of leukemic regulation and highlight TTLL4 as a druggable epigenetic regulator in NPM1c AML.

cancer biology↗

bioRxiv2024

Free water elimination tractometry for aging brains

Tractometry of diffusion-weighted magnetic resonance imaging (dMRI) non-invasively quantifies tissue properties of brain connections. It is widely used in aging studies but could be less reliable in aging brains due to increased white matter free water. We demonstrate that computational free water elimination (FWE) increases reliability and accuracy of tractometry in a large (n = 339) cohort of older adults (66 - 103 y.o.). We found substantial (up to [~]37%) improvements in reliability in a split-half comparison at every stage of the pipeline: estimation of voxel-level fiber orientation distribution functions, delineation of major pathway trajectories, and assessment of tissue properties along the pathways. FWE also improves inferences from tractometry, producing more accurate cross-validated predictions of clinician Fazekas scores. By sub-sampling a multi-b-value dataset, we demonstrated that these findings generalize to both single-b-value data, which is important for many datasets where only one b-value may be available. Overall, the results highlight the importance of accounting for free water in tractometry studies, especially in aging brains. We provide opensource software for free-water elimination that can be applied to a wide range of clinical and research datasets (https://github.com/nrdg/fwe).

neuroscience↗

bioRxiv2024

The O-Fucosyltransferase SPINDLY Attenuates Auxin-Induced Fruit Growth by Inhibiting ARF6 and ARF8 binding to Coactivator Mediator Complex in Arabidopsis

The phytohormone auxin plays a pivotal role in promoting fruit initiation and growth upon fertilization in flowering plants. Upregulation of auxin signaling by genetic mutations or exogenous auxin treatment can induce seedless fruit formation from unpollinated ovaries, termed parthenocarpy. Recent studies suggested that the class A AUXIN RESPONSE FACTOR6 (ARF6) and ARF8 in Arabidopsis play dual functions by first inhibiting fruit initiation when complexed with unidentified corepressor IAA protein(s) before pollination, and later promoting fruit growth after fertilization as ARF dimers. However, whether and how posttranslational modification(s) regulate ARF6- and ARF8-mediated fruit growth were unknown. In this study, we reveal that both ARF6 and ARF8 are O-fucosylated in their middle region (MR) by SPINDLY (SPY), a novel nucleocytoplasmic protein O-fucosyltransferase, which catalyzes the addition of a fucose moiety to specific Ser/Thr residues of target proteins. Epistasis, biochemical and transcriptome analyses indicated that ARF6 and ARF8 are downstream of SPY, but ARF8 plays a more predominant role in parthenocarpic fruit growth. Intriguingly, two ARF6/8-interacting proteins, the co-repressor IAA9 and MED8, a subunit of the coactivator Mediator complex, were also O-fucosylated by SPY. Biochemical assays demonstrated that SPY-mediated O-fucosylation of these proteins reduced ARF-MED8 interaction, which led to enhanced transcription repression activity of the ARF6/8-IAA9 complex but impaired transactivation activities of ARF6/8. Our study unveils the role of protein O-fucosylation by SPY in attenuating auxin-triggered fruit growth through modulation of activities of key transcription factors, a co-repressor and the coactivator MED complex.

plant biology↗

bioRxiv2023

Phosphorylation Promotes DELLA Activity by Enhancing Its Binding to Histone H2A at Target Chromatin in Arabidopsis

DELLA proteins are conserved master growth regulators that play a central role in controlling plant development in response to internal and environmental cues. DELLAs function as transcription regulators, which are recruited to target promoters by binding to transcription factors (TFs) and histone H2A via its GRAS domain. Recent studies showed that DELLA stability is regulated post-translationally via two mechanisms, phytohormone gibberellin-induced polyubiquitination for its rapid degradation, and Small Ubiquitin-like Modifier (SUMO)- conjugation to alter its accumulation. Moreover, DELLA activity is dynamically modulated by two distinct glycosylations: DELLA-TF interactions are enhanced by O-fucosylation, but inhibited by O-linked N-acetylglucosamine (O-GlcNAc) modification. However, the role of DELLA phosphorylation remains unclear. Here, we identified phosphorylation sites in REPRESSOR OF ga1-3 (RGA, an AtDELLA) purified from Arabidopsis by tandem mass spectrometry analysis, and showed that phosphorylation of the RGA LKS-peptide in the poly- S/T region enhances RGA-H2A interaction and RGA association with target promoters. Interestingly, phosphorylation does not affect RGA-TF interactions. Our study has uncovered that phosphorylation is a new regulatory mechanism of DELLA activity.

plant biology↗

bioRxiv2023

Evidence for kilometer-scale biophysical features at the Gulf Stream front

Understanding the interplay of ocean physics and biology, particularly at the submesoscale and below (<30km), is an ongoing challenge in oceanography. While poorly constrained, these scales may be of critical importance for understanding how changing ocean dynamics will impact marine ecosystems. Fronts in the ocean, regions where two disparate water masses meet and isopycnals become tilted towards vertical, are considered hotspots for biophysical interaction, but there is limited observational evidence at the appropriate scales to assess their importance. Western boundary currents like the Gulf Stream are of particular interest as these dynamic physical regions are thought to influence both productivity and composition of primary producers; however, how exactly this plays out, and at what scales, is not well known. Using satellite data and two years of detailed in situ observations across the Gulf Stream front near Cape Hatteras, North Carolina, U.S.A., we investigate how submesoscale frontal dynamics could affect biological communities associated with frontal regions and generate hotspots of productivity and export. In this analysis we assess the seasonality and phenology of the region, generalize the kilometer-scale structure of the front, and analyze 69 transects to assess two physical processes of potential biogeochemical importance: cold shelf filament subduction and high salinity Sargasso Sea obduction. We link these processes observationally to the meander phase of the Gulf Stream and discuss how cold filament subduction could be exporting carbon and how obduction of high salinity water from depth often leads to high chlorophyll-a. Finally, we report on phytoplankton community composition in each of these features and integrate these new observations into our understanding of frontal submesoscale dynamics. Plain Language SummaryPhytoplankton move with large currents and are stirred by eddies with diameters ranging from 100s of kilometers down to the meter scale. Their growth is impacted by physical factors like light and temperature and also chemical and biological factors like nutrient availability, and their accumulation is also impacted by top down controls (zooplankton grazing, viral lysis) and competition with other phytoplankton. This interplay of physics and biology in determining the biomass and composition of phytoplankton communities is poorly understood and is key to understanding marine ecosystem resilience and structure in a changing ocean. In this work we investigated the impact of physics and biology on phytoplankton across scales focusing on the Gulf Stream front. Fronts in the ocean are where lines of equal density go from being horizontal to having a vertical tile, and because of this can enable nutrients and plankton to move from depth to the surface and vice versa. The objective of this work is to understand how physics might drive important changes in phytoplankton biomass and composition in the Gulf Stream front, which is amongst the sharpest gradients in temperature, density, and current speed in the global ocean. We find two frequent processes at the front, the apparent subduction of cold filaments down along the edge of the Gulf Stream, associated with meander troughs, and obduction of high salinity Sargasso Sea water into the front linked to meander crests. While ephemeral, these processes are frequent and could have a large impact on local phytoplankton biomass, phytoplankton composition, and the export of organic matter to depth. Key PointsO_LIThe frontal zone between the Gulf Stream and the shelf has an interface water mass which appears to have different origins with a range of biogeochemical impacts. C_LIO_LIMeanders appear to largely control the frontal interface: troughs lead to subduction of shelf filaments and crests lead to obduction of high salinity water. C_LIO_LIThese two processes are common at the front and could lead to ephemeral kilometer- scale export and productivity. C_LI

ecology↗

bioRxiv2023

Glutamylation of Npm2 and Nap1 acidic disordered regions increases DNA charge mimicry to enhance chaperone efficiency

Histone chaperones-structurally diverse, non-catalytic proteins enriched with acidic intrinsically disordered regions (IDRs)-protect histones from spurious nucleic acid interactions and guide their deposition into and out of nucleosomes. Despite their conservation and ubiquity, the function of the chaperone acidic IDRs remains unclear. Here, we show that the Xenopus laevis Npm2 and Nap1 acidic IDRs are substrates for TTLL4 (Tubulin Tyrosine Ligase Like 4)-catalyzed post-translational glutamate-glutamylation. We demonstrate that, to bind, stabilize, and deposit histones into nucleosomes, chaperone acidic IDRs function as DNA mimetics. Our biochemical, computational, and biophysical studies reveal that glutamylation of these chaperone polyelectrolyte acidic stretches functions to enhance DNA electrostatic mimicry, promoting the binding and stabilization of H2A/H2B heterodimers and facilitating nucleosome assembly. This discovery provides insights into both the previously unclear function of the acidic IDRs and the regulatory role of post-translational modifications in chromatin dynamics.

biochemistry↗

bioRxiv2023

A Gulf Stream cold-core eddy harbors a distinct microbiome compared to environmentally-similar adjacent waters

AbstractMesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental parameters compared to surrounding waters, in order to better understand the processes dominating microbial community assembly in the dynamic coastal ocean. Our microbiome-based approach identified the eddy as distinct from the surround Gulf Stream waters. The eddy-associated microbial community occupied a larger area than identified by temperature and salinity alone, increasing the predicted extent of eddy-associated biogeochemical processes. While the eddy formed on the continental shelf, after two weeks both environmental parameters and microbiome composition of the eddy were most similar to the Gulf Stream, suggesting the effect of environmental filtering on community assembly or physical mixing with adjacent Gulf Stream waters. In spite of the potential for eddy-driven upwelling to introduce nutrients and stimulate primary production, eddy surface waters exhibit lower chlorophyll a along with a distinct and less even microbial community, compared to the Gulf Stream. At the population level, the eddy microbiome exhibited differences among the cyanobacteria (e.g. lower Trichodesmium and higher Prochlorococcus) and in the heterotrophic alpha Proteobacteria (e.g. lower relative abundances of specific SAR11 clades) versus the Gulf Stream. However, better delineation of the relative roles of processes driving eddy community assembly will likely require following the eddy and surrounding waters since inception; additionally, sampling throughout the water column could better clarify the contribution of these mesoscale features to primary production and carbon export in the oceans.

ecology↗

bioRxiv2021

Differential levels of IFNα subtypes in autoimmunity and viral infection

Type I interferons are essential for host response to viral infections, while dysregulation of their response can result in autoinflammation or autoimmunity. Among IFN (alpha) responses, 13 subtypes exist that signal through the same receptor, but have been reported to have different effector functions. However, the lack of available tools for discriminating these closely related subtypes, in particular at the protein level, has restricted the study of their differential roles in disease. We developed a digital ELISA with specificity and high sensitivity for the IFN2 subtype. Application of this assay, in parallel with our previously described pan-IFN assay, allowed us to study different IFN protein responses following cellular stimulation and in diverse patient cohorts. We observed different ratios of IFN protein responses between viral infection and autoimmune patients. This analysis also revealed a small percentage of autoimmune patients with high IFN2 protein measurements but low pan-IFN measurements. Correlation with an ISG score and functional activity showed that in this small sub group of patients, IFN2 protein measurements did not reflect its biological activity. This unusual phenotype was partly explained by the presence of anti-IFN auto-antibodies in a subset of autoimmune patients. This study reports ultrasensitive assays for the study of IFN proteins in patient samples and highlights the insights that can be obtained from the use of multiple phenotypic readouts in translational and clinical studies.

immunology↗

bioRxiv2018

Live imaging of Aiptasia larvae, a model system for studying coral bleaching, using a simple microfluidic device

Coral reefs, and their associated diverse ecosystems, are of enormous ecological importance. In recent years, coral health has been severely impacted by environmental stressors brought on by human activity and climate change, threatening the extinction of several major reef ecosystems. Reef damage is mediated by a process called coral bleaching where corals, sea anemones, and other cnidarians lose their photosynthetic algal symbionts (genus Symbiodinium) upon stress induction, resulting in drastically decreased host energy harvest and, ultimately, coral death. The mechanism by which this critical cnidarian-algal symbiosis is lost remains poorly understood. Here, we report Traptasia, a simple microfluidic device with multiple traps designed to isolate and image individual live larvae of Aiptasia, a sea anemone model organism, and their algal symbionts over extended time courses. Aiptasia larvae are ~100 m in length, deformable, and highly motile, posing particular challenges for long-term imaging. Using a trap design optimized via fluid flow simulations and polymer bead loading tests, we trapped Aiptasia larvae containing algal symbionts and demonstrated stable imaging for >10 hours. We visualized algal migration within Aiptasia larvae and observed algal expulsion under an environmental stressor. To our knowledge, this device is the first to enable live imaging of cnidarian larvae and their algal symbionts and, in further implementation, could provide important insights into the cellular mechanisms of coral bleaching under different environmental stressors. The device is simple to use, requires minimal external equipment and no specialized training to operate, and can easily be adapted to study a variety of large, motile organisms.

ecology↗

bioRxiv2017

ShuTu: Open-Source Software for Efficient and Accurate Reconstruction of Dendritic Morphology

Neurons perform computations by integrating inputs from thousands of synapses - mostly in the dendritic tree - to drive action potential firing in the axon. One fruitful approach to understanding this process is to record from neurons using patch-clamp electrodes, fill the recorded neuron with a substance that allows subsequent staining, reconstruct the three-dimensional architecture of the dendrites, and use the resulting functional and structural data to develop computer models of dendritic integration. Accurately producing quantitative reconstructions of dendrites is typically a tedious process taking many hours of manual inspection and measurement. Here we present ShuTu, a new software package that facilitates accurate and efficient reconstruction of dendrites imaged using bright-field microscopy. The program operates in two steps: (1) automated identification of dendritic process, and (2) manual correction of errors in the automated reconstruction. This approach allows neurons with complex dendritic morphologies to be reconstructed rapidly and efficiently, thus facilitating the use of computer models to study dendritic structure-function relationships and the computations performed by single neurons.\n\nSignificance StatementWe developed a software package - ShuTu - that integrates automated reconstruction of stained neurons with manual error correction. This package facilitates rapid reconstruction of the three-dimensional geometry of neuronal dendritic trees, often needed for computational simulations of the functional properties of these structures.

neuroscience↗