Biology subjects

Shaw, T.

Publications and source records attributed to Shaw, T..

11 recordsLinked to original sources

bioRxiv2026

iPSC-Derived Chondroprogenitors as a Promising Cell Source for Cartilage Engineering: A Comparison with MSCs in Unmodified and Peptide-Functionalized Alginate Hydrogels

Articular cartilage degeneration is a hallmark of degenerative joint diseases, yet its limited regenerative capacity poses significant challenges for tissue engineering. While mesenchymal stem cells (MSCs) are the most commonly employed cell type in cartilage tissue engineering, they exhibit donor variability, restricted expansion capacity, and tendencies toward fibrocartilage formation and hypertrophic differentiation. Human induced pluripotent stem cell-derived chondroprogenitors (iCPs) represent a promising alternative, offering scalable production of developmentally relevant cells with intrinsic chondrogenic commitment. However, their performance within three-dimensional biomaterial scaffolds remains largely unexplored. Here, we compared chondrogenic differentiation of iCPs and MSCs within alginate hydrogels of varying stiffness (0.37 - 4.55 kPa) exhibiting physiologically relevant stress relaxation properties. Intermediate stiffness (2% alginate, ~2.17 kPa) optimally supported chondrogenesis for both cell types. While MSCs differentiated as single cells, iCPs spontaneously self-organized into cartilaginous aggregates without requiring a separate pellet pre-culture step, showing significantly higher hyaline indices and reduced COL10 expression, despite initial low viability in hydrogels. To further enhance chondrogenesis, we functionalized 2% alginate gels with RGD and HAVDI peptides mimicking integrin- and cadherin-mediated signaling. HAVDI/RGD functionalization significantly enhanced hyaline cartilage marker expression in both cell types, with iCPs exhibiting superior matrix composition characterized by elevated aggrecan and SOX9 expression and reduced COL10 and MMP13 compared to MSCs. These findings establish iCPs as a promising cell source for cartilage tissue engineering and disease modeling, particularly within biomaterials integrating mechanical and bioactive cues that recapitulate the native cartilage microenvironment.

cell biology↗

bioRxiv2025

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cellular trajectory regionalises tumours into distinct tissue niches and manifests in a molecularly conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to map cancer cell states jointly with clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

cancer biology↗

bioRxiv2024

Modelling inflammation-induced peripheral sensitization in a dish - more complex than expected?

Peripheral sensitization of nociceptors is believed to be a key driver of chronic pain states. Here, we sought to study the effects of a modified version of inflammatory soup on the excitability of human stem-cell derived sensory neurons. For this, we used a pre-existing and a novel stem cell line, modified to stably express the calcium sensor GCamP6f. Upon treatment with inflammatory soup, we observed no changes in neuronal transcription or functional responses upon calcium imaging, and only a very minor increase in resting membrane potential via whole cell patch clamping. Similarly small changes were observed when treating mouse primary sensory neurons with inflammatory soup. A semi-systematic re-examination of past literature further indicated that observed effects of inflammatory mediators on dissociated sensory neuron cultures are generally very small. We conclude that modelling inflammation-induced peripheral sensitization in vitro is non-trivial and will require careful selection of mediators and/or more complex, longitudinal multi-cellular setups. Especially in the latter, our novel GCamP6f induced-pluripotent stem cell line may be of value.

neuroscience↗

bioRxiv2024

Perceived biodiversity: is what we measure also what we see and hear?

1. Biodiversity is crucial for human health and well-being. Perceived biodiversity - peoples subjective experience of biodiversity - seems to be particularly relevant for mental well-being. 2. Using photographs and audio recordings of forests that varied in levels of species richness, we conducted two sorting studies to assess how people perceive visual and acoustic diversity and whether their perceptions align with measured tree and bird species richness ( actual diversity). Per study, 48 participants were asked to sort the stimuli according to any similarity-based sorting criteria they liked ( open sorts) and perceived diversity ( closed sorts). 3. The main perceived visual forest characteristics identified by participants in the open visual sorts were vegetation density, light conditions, forest structural attributes and colours. The main perceived acoustic forest characteristics identified in the open acoustic sorts comprised bird song characteristics, physical properties such as volume, references to the time of day or seasonality and evoked emotions. 4. Perceived visual and acoustic diversity were significantly correlated with actual tree and bird species richness, respectively. Notably, the relationship was twice as strong for the acoustic sense. The acoustic sense may thus be crucial to obtain a more thorough understanding of perceived biodiversity. 5. We further computed several visual and acoustic diversity indices from the photos and audio recordings, e.g. colourfulness or acoustic complexity, and assessed their relevance for perceived and actual diversity. While all acoustic diversity indices were significantly associated with perceived acoustic diversity and bird richness, we could not identify a visual diversity index that captured perceived visual diversity and tree richness. 6. Our results suggest that people can perceive species richness. Our identified visual and acoustic forest characteristics may help to better understand perceived diversity and how it differs from actual diversity. We present acoustic diversity indices that quantify aspects of perceived and actual acoustic diversity. These indices may serve as cost-efficient tools to manage and plan greenspaces to promote biodiversity and mental well-being.

ecology↗

bioRxiv2024

Immune determinants of pegivirus persistence, control, and cross-species infection in the laboratory mouse

Approximately 15% of the global human population is viremic with human pegivirus (HPgV), a +ssRNA virus in the Flaviviridae family. An unusual feature of HPgV is its ability to persistently infect individuals without causing overt disease or evoking robust immune responses, but this phenomenon is poorly understood due to a dearth of systems for studying HPgV. In this study, we create the first mouse model of PgV infection by adapting a PgV discovered in a wild rat (RPgV) to infect the standard laboratory mouse. Adaptation to the mouse initially required defective innate immunity and the accumulation of a single mutation in the E2 envelope glycoprotein, but passage into wild-type (WT) mice resulted in twelve additional mutations that enable persistent high-titer viremia, closely recapitulating the course of HPgV in humans. Mouse-adapted (ma)PgV infection of various knockout mice showed that lymphocytes exert a significant antiviral effect in the chronic phase of infection, but that this effect is also unable to fully control viremia in most individuals. Chronic type-I interferon signaling appears to paradoxically enable maPgV persistence, likely via T cell dysfunction that has been demonstrated in other chronic viral infections. However, unlike many persistent viruses, maPgV does not depend upon the induction of PD-1-mediated immune tolerance to maintain persistence. In-depth analysis of rare WT mice that achieved sterilizing maPgV immunity suggests that multiple possible paths to achieving PgV immunity exist and may include a combination of cellular, humoral, and non-canonical mechanisms. Altogether, our creation of maPgV opens up the vast murine toolkit for understanding the enigmatic biology of PgVs. In addition to novel insights into multiple aspects of PgV immunity, the lack of PD-1-mediated immune tolerance induced by PgV infection is unique among persistent viruses and suggests a highly novel mechanism of immune evasion. AUTHOR SUMMARYViruses capable of persistently infecting an individual host have developed sophisticated mechanisms for evading host immunity, and understanding these mechanisms can reveal novel features of the host immune system. One such virus, human pegivirus (HPgV), infects [~]15% of the global human population, but little is known about its biology beyond the fact that it does not cause overt disease. We created the first mouse model of PgV infection by adapting a rat pegivirus to infect laboratory mice. This mouse-adapted virus (maPgV) caused infection that was detectable in the blood of mice for >300 days without causing signs of disease, closely recapitulating the course of HPgV in humans. This enabled unprecedented exploration of PgV immunity, revealing a pro-viral role for type-I interferon in chronic infection; a lack of PD-1-mediated tolerance to PgV infection; and multiple mechanisms by which PgV immunity can be achieved by an immunocompetent host. These data indicate that the PgV immune evasion strategy has aspects that are both common and unique among persistent viral infections. The creation of maPgV represents the first PgV infection model in wild-type mice, thus opening the entire toolkit of the mouse host to enable further investigation of persistent RNA infections.

microbiology↗

bioRxiv2024

Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment

Collective alignment of cell populations is a commonly observed phenomena in biology. An important example are aligning fibroblasts in healthy or scar tissue. In this work we derive and simulate a mechanistic agent-based model of the collective behaviour of actively moving and interacting cells, with a focus on understanding collective alignment. The derivation strategy is based on energy minimisation. The model ingredients are motivated by data on the behaviour of different populations of aligning fibroblasts and include: Self-propulsion, overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces. We find that there is an optimal ratio of self-propulsion speed and overlap avoidance that maximises collective alignment. Further we find that deformability aids alignment, and that cell-cell junctions by themselves hinder alignment. However, if cytoskeletal forces are transmitted via cell-cell junctions we observe strong collective alignment over large spatial scales.

cell biology↗

bioRxiv2023

A (Sub)field Guide to Quality Control in Hippocampal Subfield Segmentation on High-resolution T2-weighted MRI

Inquiries into properties of brain structure and function have progressed due to developments in magnetic resonance imaging (MRI). To sustain progress in investigating and quantifying neuroanatomical details in vivo, the reliability and validity of brain measurements are paramount. Quality control (QC) is a set of procedures for mitigating errors and ensuring the validity and reliability of brain measurements. Despite its importance, there is little guidance on best QC practices and reporting procedures. The study of hippocampal subfields in vivo is a critical case for QC because of their small size, inter-dependent boundary definitions, and common artifacts in the MRI data used for subfield measurements. We addressed this gap by surveying the broader scientific community studying hippocampal subfields on their views and approaches to QC. We received responses from 37 investigators spanning 10 countries, covering different career stages, and studying both healthy and pathological development and aging. In this sample, 81% of researchers considered QC to be very important or important, and 19% viewed it as fairly important. Despite this, only 46% of researchers reported on their QC processes in prior publications. In many instances, lack of reporting appeared due to ambiguous guidance on relevant details and guidance for reporting, rather than absence of QC. Here, we provide recommendations for correcting errors to maximize reliability and minimize bias. We also summarize threats to segmentation accuracy, review common QC methods, and make recommendations for best practices and reporting in publications. Implementing the recommended QC practices will collectively improve inferences to the larger population, as well as have implications for clinical practice and public health.

neuroscience↗

bioRxiv2021

Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers

Super enhancers (SEs) are broad enhancer domains usually containing multiple constituent enhancers that hold elevated activities in gene regulation. Disruption in one or more constituent enhancers causes aberrant SE activities that lead to gene dysregulation in diseases. To quantify SE aberrations, differential analysis is performed to compare SE activities between cell conditions. The state-of-art strategy in estimating differential SEs relies on overall activities and neglect the changes in length and structure of SEs. Here, we propose a novel computational method to identify differential SEs by weighting the combinatorial effects of constituent-enhancer activities and locations (i.e., internal dynamics). In addition to overall activity changes, our method identified four novel classes of differential SEs with distinct enhancer structural alterations. We demonstrate that these structure alterations hold distinct regulatory impact, such as regulating different number of genes and modulating gene expression with different strengths, highlighting the differentiated regulatory roles of these unexplored SE features. When compared to the existing method, our method showed improved identification of differential SEs that were linked to better discernment of cell-type-specific SE activity and functional interpretation. We implement an R package, DASE, to facilitate the use of our method.

bioinformatics↗

bioRxiv2018

Unraveling the implications of environmental, host and pathogen-specific determinants on clinical presentations and disease progression among Indian melioidosis patients.

BackgroundMelioidosis is gaining recognition as an emerging infectious disease with diverse clinical manifestations and high-case fatality rates,worldwide. However, the molecular epidemiology of the disease outside the endemic regions such as,Thailand and Northern Australia remains unclear.\n\nMethodsClinical data and B. pseudomallei (Bps) isolates obtained from 199 culture-confirmed cases of melioidosis, diagnosed during 2006-2016 inSouth India were used to elucidate the host and pathogen-specific variable virulence determinants associated with clinical presentations and disease progression. Further, we determined the temporal variations and the influence of ecological factors on Bps Lipopolysaccharide (LPS) genotypes causing infections.\n\nResultSevere forms of the disease were observed amongst 169 (85%) patients. Renal dysfunction and infection due to Bps harboring Bim-ABm variant had significant associations with severe forms of the disease. Diabetes mellitus, septicemic melioidosis and infection due to LPS-B genotype were independent risk factors for mortality. LPS-B (74%) and LPS-A (20.6%) were the prevalent genotypes causing infections. Both genotypes demonstrated temporal variations and had significant correlations with rainfall and humidity.\n\nConclusionOur study findings suggest that the pathogen-specific virulence traits, under the influence of ecological factors are the key drivers for geographical variations in the molecular epidemiology of melioidosis.

microbiology↗

bioRxiv2017

More Highly Myelinated White Matter Tracts are Associated with Faster Processing Speed in Healthy Adults

The objective of this study was to investigate whether the myelin content of white matter tracts is predictive of cogni-tive processing speed and whether such associations are modulated by age. Associations between myelin content and processing speed was assessed in 570 community-living individuals (277 middle-age, 293 older-age). Myelin content was measured using the mean T1w/T2w magnetic resonance ratio, in six white matter tracts (anterior corona radiata, superior corona radiata, pontine crossing tract, anterior limb of the internal capsule, genu of the corpus callosum, and splenium of the corpus callosum). Processing speed was estimated by extracting a principal component from 5 sep-arate tests of processing speed. It was found that myelin content of the bilateral anterior limb of the internal capsule and left splenium of the corpus callosum were significant predictors of processing speed, even after controlling for socio-demographic, health and genetic variables and correcting for multiple comparisons. A 1 SD increase in the myelin content of the anterior limb of the internal capsule was associated with 2.53% increase in processing speed and within the left splenium of the corpus callosum with a 2.20% increase in processing speed. In addition, significant differences in myelin content between middle-age and older participants were found in all six white matter tracts. The present results indicate that myelin content, estimated in vivo using a neuroimaging approach in healthy older adults is sufficiently precise to predict variability in processing speed in behavioural measures.

neuroscience↗

bioRxiv2016

Metabolome Identification by Systematic Stable Isotope Labeling Experiments and False Discovery Analysis with a Target-Decoy Strategy

We introduce a formula-based strategy and algorithm (JUMPm) for global metabolite identification and false discovery analysis in untargeted mass spectrometry-based metabolomics. JUMPm determines the chemical formulas of metabolites from unlabeled and stable-isotope labeled metabolome data, and derives the most likely metabolite identity by searching structure databases. JUMPm also estimates the false discovery rate (FDR) with a target-decoy strategy based on the octet rule of chemistry. With systematic stable isotope labeling of yeast, we identified 2,085 chemical formulas (10% FDR), 892 of which were assigned with metabolite structures. We evaluated JUMPm with a library of synthetic standards, and found that 96% of the formulas were correctly identified. We extended the method to mammalian cells with direct isotope labeling and by heavy yeast spike-in. This strategy and algorithm provide a powerful a practical solution for global identification of metabolites with a critical measure of confidence.

biochemistry↗