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Byrne, H.

Publications and source records attributed to Byrne, H..

25 records · Page 2Linked to original sources

Signatures of adaptive evolution in platyrrhine primate genomes

The family Cebidae (capuchin and squirrel monkeys) form a remarkable platyrrhine clade exhibiting among the largest primate encephalisation quotients. Each cebid lineage is characterised by notable lineage-specific traits, with capuchins showing striking similarities to Hominidae including high sensorimotor intelligence with tool use, advanced cognitive abilities, and behavioural flexibility. Here, we take a comparative genomics approach, analysing five cebid branches including successive lineages, to infer a stepwise timeline for cebid adaptive evolution. We uncover candidate targets of selection across various periods of cebid evolution that may underlie the emergence of lineage-specific traits. Our analyses highlight shifting and sustained selective pressures on genes related to brain development, longevity, reproduction, and morphology, including evidence for cumulative and diversifying neurobiological adaptations over cebid evolutionary history. In addition to generating a new, high-quality reference genome assembly for robust capuchins, our results lend to a better understanding of the adaptive diversification of this distinctive primate clade.

genomics↗

An Age-Specific Atlas for Delineation of White Matter Pathways in Children Aged 6-8 Years

Diffusion MRI allows non-invasive assessment of white matter maturation in typical development and of white matter damage due to brain injury or pathology. Probabilistic white matter atlases provide delineation of white matter tracts, allowing diffusion metrics to be measured in specific white matter pathways. However, given the known age-dependency of developmental change in white matter it may not be optimal to use an adult template when assessing data acquired from children. This study develops an age-specific probabilistic white matter atlas for delineation of 12 major white matter tracts in children aged 6-8 years. By comparing to subject-specific tract tracing in two validation cohorts, we demonstrate that this age-specific atlas gives better overall performance than simply registering to the Johns Hopkins University adult white matter template. Specifically, when normalising diffusion data acquired from children to an adult template, estimates of fractional anisotropy (FA) values for corticospinal tract, uncinate fasciculus, forceps minor, cingulate gyrus part of the cingulum and anterior thalamic radiation were all less accurate than those obtained when using an age-specific atlas, potentially leading to false negatives when performing group comparisons. We then applied the newly developed atlas to compare FA between children treated with therapeutic hypothermia for neonatal encephalopathy and age-matched controls, which revealed significant reductions in the fornix, the left superior longitudinal fasciculus, and both the hippocampal and cingulum parts of the left cingulate gyrus. To our knowledge, this is the first publicly available probabilistic atlas of white matter tracts for this age group.

neuroscience↗

A multiscale model of complex endothelial cell dynamics in early angiogenesis

We introduce a hybrid two-dimensional multiscale model of angiogenesis, the process by which endothelial cells (ECs) migrate from a pre-existing vascular bed in response to local environmental cues and cell-cell interactions, to create a new vascular network. Recent experimental studies have highlighted a central role of cell rearrangements in the formation of angiogenic networks. Our model accounts for this phenomenon via the heterogeneous response of ECs to their microenvironment. These cell rearrangements, in turn, dynamically remodel the local environment. The model reproduces characteristic features of angiogenic sprouting that include branching, chemotactic sensitivity, the brush border effect, and cell mixing. These properties, rather than being hardwired into the model, emerge naturally from the gene expression patterns of individual cells. After calibrating and validating our model against experimental data, we use it to predict how the structure of the vascular network changes as the baseline gene expression levels of the VEGF-Delta-Notch pathway, and the composition of the extracellular environment, vary. In order to investigate the impact of cell rearrangements on the vascular network structure, we introduce the mixing measure, a scalar metric that quantifies cell mixing as the vascular network grows. We calculate the mixing measure for the simulated vascular networks generated by ECs of different lineages (wild type cells and mutant cells with impaired expression of a specific receptor). Our results show that the time evolution of the mixing measure is directly correlated to the generic features of the vascular branching pattern, thus, supporting the hypothesis that cell rearrangements play an essential role in sprouting angiogenesis. Furthermore, we predict that lower cell rearrangement leads to an imbalance between branching and sprout elongation. Since the computation of this statistic requires only individual cell trajectories, it can be computed for networks generated in biological experiments, making it a potential biomarker for pathological angiogenesis. Author summaryAngiogenesis, the process by which new blood vessels are formed by sprouting from the pre-existing vascular bed, plays a key role in both physiological and pathological processes, including tumour growth. The structure of a growing vascular network is determined by the coordinated behaviour of endothelial cells in response to various signalling cues. Recent experimental studies have highlighted the importance of cell rearrangements as a driver for sprout elongation. However, the functional role of this phenomenon remains unclear. We formulate a new multiscale model of angiogenesis which, by accounting explicitly for the complex dynamics of endothelial cells within growing angiogenic sprouts, is able to produce generic features of angiogenic structures (branching, chemotactic sensitivity, cell mixing, etc.) as emergent properties of its dynamics. We validate our model against experimental data and then use it to quantify the phenomenon of cell mixing in vascular networks generated by endothelial cells of different lineages. Our results show that there is a direct correlation between the time evolution of cell mixing in a growing vascular network and its branching structure, thus paving the way for understanding the functional role of cell rearrangements in angiogenesis.

systems biology↗

Radiation resistant cancer cells enhance the survival and resistance of sensitive cells in prostate spheroids

Intratumoural heterogeneity contributes to local tumour recurrence and variable responses to radiotherapy in prostate cancer. Despite the multiclonal nature of the disease, tumour control probability for conventional treatment plans is modelled on the assumption that tumour cells in the target region respond identically and independently. Here, using tumour cell subpopulations with different radiation sensitivities from prostate tumour cell lines, we show that radiation resistant cells enhance the survival and radiation resistance of radio-sensitive cells in spheroids but not in monolayer culture. Mathematical modelling indicates that these phenotypic changes result from both competitive and antagonistic cellular interactions in spheroids. Interactions mediated by oxygen constraints define the spatial localisation of the cell populations in spheroids and in xenografts, while those mediated by paracrine signals further modify the microenvironment. Our results show new mechanisms of radiotherapy resistance mediated by cellular interactions and by the microenvironment.

cancer biology↗

A Biomechanical Model of Tumor-induced Intracranial Pressure and Edema in Brain Tissue

Brain tumor growth and tumor-induced edema result in increased intracranial pressure (ICP), which, in turn, is responsible for conditions as benign as headaches and vomiting, or as severe as seizures, neurological damage, or even death. Therefore, it has been hypothesized that tracking ICP dynamics may offer improved prognostic potential in terms of early detection of brain cancer and better delimitation of the tumor boundary. However, translating such theory into clinical practice remains a challenge, in part, due to an incomplete understanding of how ICP correlates with tumor grade. Here, we propose a multiphase mixture model that describes the biomechanical response of healthy brain tissue - in terms of changes in ICP and edema - to a growing tumor. The model captures ICP dynamics within the diseased brain and accounts for the ability/inability of healthy tissue to compensate for this pressure. We propose parameter regimes that distinguish brain tumors by grade thereby providing critical insight into how ICP dynamics vary by severity of disease. In particular, we offer an explanation for clinically observed phenomena such as lack of symptoms in low grade glioma patients versus a rapid onset of symptoms in those with malignant tumors. Our model also takes into account the effects tumor-derived proteases may have on ICP levels and extent of tumor invasion. This work represents an important first step towards understanding the mechanisms that underlie the onset of edema and ICP in cancer-afflicted brains. Continued modeling effort in this direction has the potential to make an impact in the field of brain cancer diagnostics.

cancer biology↗

Chronic inflammation delays cell migration to villi in the intestinal epithelium

The intestinal epithelium is a single layer of cells which provides the first line of defence of the intestinal mucosa to bacterial infection. Cohesion of this physical barrier is supported by renewal of epithelial stem cells, residing in invaginations called crypts, and by crypt cell migration onto protrusions called villi; dysregulation of such mechanism may render the gut susceptible to chronic inflammation. The impact that excessive or misplaced epithelial cell death may have on villus cell migration is currently unknown. We integrated cell-tracking methods with computational models to determine how epithelial homeostasis is affected by acute and chronic inflammatory cell death. Parameter inference reveals that acute inflammatory cell death has a transient effect on epithelial cell dynamics, whereas cell death caused by chronic inflammation causes a delay in the accumulation of labelled cells onto the villus compared to control. Such a delay may be reproduced by using a cell-based model to simulate the dynamics of each cell in a crypt-villus geometry, showing that a prolonged increase in cell death slows the migration of cells from the crypt to the villus. This investigation highlights which injuries (acute or chronic) may be regenerated and which cause disruption of healthy epithelial homeostasis.

systems biology↗

Inducing Chondrogenesis In MSC/Chondrocyte Co-Cultures Using Exogenous TGF-β: A Mathematical Model

The differentiation of mesenchymal stem cells (MSCs) into chondrocytes (native cartilage cells), or chondrogenesis, is a key step in the tissue engineering of articular cartilage, where the motility and high proliferation rate of MSCs used as seed cells are exploited. Chondrogenesis is regulated by transforming growth factor-beta (TGF-{beta}), a short-lived cytokine whose effect is prolonged by storage in the extracellular matrix. Tissue engineering applications require the complete differentiation of an initial population of MSCs, and two common strategies used to achieve this in vitro are (1) co-culture the MSCs with chondrocytes, which constitutively produce TGF-{beta}; or (2) add exogenous TGF-{beta}. To investigate these strategies we develop an ordinary differential equation model of the interactions between TGF-{beta}, MSCs and chondrocyte. Here the dynamics of TGF-{beta} are much faster than those of the cell processes; this difference in time-scales is exploited to simplify subsequent model analysis. Using our model we demonstrate that under strategy 1 complete chondrogenesis will be induced if the initial proportion of chondrocytes exceeds a critical value. Similarly, under strategy 2 we find that there is a critical concentration of exogenous TGF-{beta} above which all MSCs will ultimately differentiate. Finally, we use the model to demonstrate the potential advantages of adopting a hybrid strategy where exogenous TGF-{beta} is added to a co-culture of MSCs and chondrocytes, as compared to using either strategy 1 or 2 in isolation.

bioengineering↗