Modelling mucociliary clearance

Mathematical modelling of the fluid mechanics of mucociliary clearance (MCC) is reviewed and future challenges for researchers are discussed. The morphology of the bronchial and tracheal airway surface liquid (ASL) and ciliated epithelium are briefly introduced. The cilia beat cycle, beat frequency and metachronal coordination are described, along with the rheology of the mucous layer. Theoretical modelling of MCC from the late 1960s onwards is reviewed, and distinctions between ‘phenomenological’, ‘slender body theory’ and recent ‘fluid–structure interaction’ models are explained.\ud \ud The ASL consists of two layers, an overlying mucous layer and underlying watery periciliary layer (PCL) which bathes the cilia. Previous models have predicted very little transport of fluid in the PCL compared with the mucous layer. Fluorescent tracer transport experiments on human airway cultures conducted by Matsui et al. [Matsui, H., Randell, S.H., Peretti, S.W., Davis, C.W., Boucher, R.C., 1998. Coordinated clearance of periciliary liquid and mucus from airway surfaces. J. Clin. Invest. 102 (6), 1125–1131] apparently showed equal transport in both the PCL and mucous layer. Recent attempts to resolve this discrepancy by the present authors are reviewed, along with associated modelling findings. These findings have suggested new insights into the interaction of cilia with mucus due to pressure gradients associated with the flat PCL/mucus interface. This phenomenon complements previously known mechanisms for ciliary propulsion. Modelling results are related to clinical findings, in particular the increased MCC observed in patients with pseudohypoaldosteronism. Recent important advances by several groups in modelling the fluid–structure interaction by which the cilia movement and fluid transport emerge from specification of internal mechanics, viscous and elastic forces are reviewed. Finally, we discuss the limitations of existing work, and the challenges for the next generation of models, which may provide further insight into this complex and vital system

Identification of gene expression logical invariants in Arabidopsis.

Numerous gene expression datasets from diverse tissue samples from the plant variety Arabidopsis thaliana have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of the publicly available Arabidopsis datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated. We pointed out serious issues in the data normalization steps widely accepted and published recently in this context. We put together a web resource where gene expression relationships can be explored online which helps visualize the logical relationships between genes. We believe that this website will be useful in identifying important genes in different biological context. The web link is http://hegemon.ucsd.edu/plant/

Limitations in Predicting the Space Radiation Health Risk for Exploration Astronauts

Despite years of research, understanding of the space radiation environment and the risk it poses to long-duration astronauts remains limited. There is a disparity between research results and observed empirical effects seen in human astronaut crews, likely due to the numerous factors that limit terrestrial simulation of the complex space environment and extrapolation of human clinical consequences from varied animal models. Given the intended future of human spaceflight, with efforts now to rapidly expand capabilities for human missions to the moon and Mars, there is a pressing need to improve upon the understanding of the space radiation risk, predict likely clinical outcomes of interplanetary radiation exposure, and develop appropriate and effective mitigation strategies for future missions. To achieve this goal, the space radiation and aerospace community must recognize the historical limitations of radiation research and how such limitations could be addressed in future research endeavors. We have sought to highlight the numerous factors that limit understanding of the risk of space radiation for human crews and to identify ways in which these limitations could be addressed for improved understanding and appropriate risk posture regarding future human spaceflight.Comment: Accepted for publication by Nature Microgravity (2018

Visualization of Inflammation in Experimental Colitis by Magnetic Resonance Imaging Using Very Small Superparamagnetic Iron Oxide Particles

Inflammatory bowel diseases (IBD) comprise mainly ulcerative colitis (UC) and Crohn´s disease (CD). Both forms present with a chronic inflammation of the (gastro) intestinal tract, which induces excessive changes in the composition of the associated extracellular matrix (ECM). In UC, the inflammation is limited to the colon, whereas it can occur throughout the entire gastrointestinal tract in CD. Tools for early diagnosis of IBD are still very limited and highly invasive and measures for standardized evaluation of structural changes are scarce. To investigate an efficient non-invasive way of diagnosing intestinal inflammation and early changes of the ECM, very small superparamagnetic iron oxide nanoparticles (VSOPs) in magnetic resonance imaging (MRI) were applied in two mouse models of experimental colitis: the dextran sulfate sodium (DSS)-induced colitis and the transfer model of colitis. For further validation of ECM changes and inflammation, tissue sections were analyzed by immunohistochemistry. For in depth ex-vivo investigation of VSOPs localization within the tissue, Europium-doped VSOPs served to visualize the contrast agent by imaging mass cytometry (IMC). VSOPs accumulation in the inflamed colon wall of DSS-induced colitis mice was visualized in T2* weighted MRI scans. Components of the ECM, especially the hyaluronic acid content, were found to influence VSOPs binding. Using IMC, co-localization of VSOPs with macrophages and endothelial cells in colon tissue was shown. In contrast to the DSS model, colonic inflammation could not be visualized with VSOP-enhanced MRI in transfer colitis. VSOPs present a potential contrast agent for contrast-enhanced MRI to detect intestinal inflammation in mice at an early stage and in a less invasive manner depending on hyaluronic acid content

The Emerging Role of Ten-Eleven Translocation 1 in Epigenetic Responses to Environmental Exposures.

Mounting evidence from epidemiological studies and animal models has linked exposures to environmental factors to changes in epigenetic markers, especially in DNA methylation. These epigenetic changes may lead to dysregulation of molecular processes and functions and mediate the impact of environmental exposures in complex diseases. However, detailed molecular events that result in epigenetic changes following exposures remain unclear. Here, we review the emerging evidence supporting a critical role of ten-eleven translocation 1 (TET1) in mediating these processes. Targeting TET1 and its associated pathways may have therapeutic potential in alleviating negative impacts of environmental exposures, preventing and treating exposure-related diseases

Human Health in Space Travel: Limitations and Opportunities

Space travel presents unique environmental challenges that enact molecular, cellular, and physiological changes across many regions within the human body. Specifically, the high energy and variable mass of the particles from space radiation present new and unexplored consequences in which astronauts will be at greater risk of deleterious health effects beyond Earth's protective magnetosphere. Longer missions beyond low Earth orbit will result in greater doses of space radiation, increasing the risk of developing degenerative tissue diseases from the accumulation of genetic mutations and high oxidative stress. This thesis maps the findings of space-related biological research on humans and animals exposed to spaceflight effects –to present the risks associated with spaceflight, health responses to these risks, and the mitigative strategies that can be applied to counteract deleterious health effects and ensure successful spaceflight missions in the future.Polymathic Scholar

Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress

Reactive oxygen species (ROS) are increasingly recognised as important signalling molecules through oxidation of protein cysteine residues. Comprehensive identification of redox-regulated proteins and pathways is crucial to understand ROS-mediated events. Here, we present stable isotope cysteine labelling with iodoacetamide (SICyLIA), a mass spectrometry-based workflow to assess proteome-scale cysteine oxidation. SICyLIA does not require enrichment steps and achieves unbiased proteome-wide sensitivity. Applying SICyLIA to diverse cellular models and primary tissues provides detailed insights into thiol oxidation proteomes. Our results demonstrate that acute and chronic oxidative stress causes oxidation of distinct metabolic proteins, indicating that cysteine oxidation plays a key role in the metabolic adaptation to redox stress. Analysis of mouse kidneys identifies oxidation of proteins circulating in biofluids, through which cellular redox stress can affect whole-body physiology. Obtaining accurate peptide oxidation profiles from complex organs using SICyLIA holds promise for future analysis of patient-derived samples to study human pathologies

Theoretical and experimental considerations of selective vulnerability In Parkinson's disease

Les maladies neurodégénératives sont typiquement caractérisées en fonction de leurs symptômes et des observations pathologiques effectuées après le décès. Les symptômes spécifiques à la maladie sont également normalement associés aux dysfonctionnements et à la dégénérescence de certaines sous- populations spécifiques de neurones dans le système nerveux. La maladie de Parkinson (MP) est une maladie neurodégénérative principalement caractérisée par des symptômes moteurs dus à la dégénérescence spécifique des neurones dopaminergiques (DA) de la substantia nigra pars compacta (SNpc/SNc). Il semble cependant que les neurones DA de la SNc ne soient pas la seule population de neurones qui dégénère dans la MP. L'analyse post-mortem, l'imagerie in vivo et les symptômes cliniques démontrent que le dysfonctionnement et la dégénérescence se produisent dans plusieurs autres régions du système nerveux, incluant par exemple des neurones noradrénergiques (NA) du locus coeruleus (LC), des neurones sérotoninergiques des noyaux du raphé et des neurones cholinergiques du noyau moteur dorsal du nerf vague (DMV) et du noyau pédonculopontin. Comme d'autres maladies neurodégénératives, la MP est causée par plusieurs facteurs, tant génétiques qu'environnementaux. De nombreuses observations suggèrent que ces facteurs soient associés au dysfonctionnement de plusieurs systèmes ou fonctions cellulaires incluant la production d’énergie par la mitochondrie, l’élimination de protéines dysfonctionnelles par le protéasome et le lysosome, la régulation de l’équilibre entre la production d'espèces oxydatives réactives et les mécanismes antioxydants, la régulation des niveaux de calcium intracellulaire et l’inflammation. Il semble donc que le dysfonctionnement de ces facteurs converge pour provoquer la dégénérescence neuronale dans le contexte du vieillissement. Ce qui rend les neurones de certaines régions du système nerveux intrinsèquement plus vulnérables aux facteurs associés à la MP est une question fondamentale qui n’est pas résolue pour le moment. Les travaux de cette thèse sont basés sur l’hypothèse proposant que cette vulnérabilité sélective découle de propriétés communes retrouvées chez les neurones vulnérables. En particulier, les neurones vulnérables auraient en commun d’être des neurones de projections dotés d’un axone complexe qui projette sur de longues distances, formant un nombre très élevé de terminaisons axonales sur de vastes territoires du système nerveux. De plus, ces neurones présenteraient des propriétés physiologiques distinctives, incluant notamment une décharge autonome (pacemaker). Ensemble, ces caractéristiques pourraient contribuer à placer ces neurones dans des conditions de fonctionnement aux limites de leur capacités bioénergétiques et homéostatiques, rendant difficile toute adaptation aux dysfonctionnements cellulaires associés au vieillissement et causés par les facteurs de risques de la MP. Dans cette thèse, je présenterai une revue systématique de la littérature sur la perte de neurones dans le cerveau des personnes atteintes de la maladie de Parkinson, montrant que l'identité neurochimique précise des neurones qui dégénèrent dans la maladie de Parkinson, et l'ordre temporel dans lequel cela se produit, n’est pas clair. Cependant, en analysant les points de vue présentés dans les publications citant cette revue, nous avons remarqué que la majorité de ceux-ci ne reflètent pas le message central de notre publication. Puisque l’identification de l’identité des neurones vulnérables et non vulnérables à la MP est fondamentale pour le développement de théories et hypothèses sur les causes de la MP, nous suivons cette première publication avec une lettre réaffirmant l'importance de faire face aux problèmes identifiés dans notre revue. Nous présentons ensuite des données in vitro montrant que les neurones vulnérables à la MP, comparés à ceux qui sont moins vulnérables, ont une capacité intrinsèque à développer des champs axonaux plus importants et plus complexes, avec un nombre plus élevé de sites actifs de libération de neurotransmetteurs. De plus, nous constatons que ces observations sont corrélées à une vulnérabilité plus élevée face à un stress oxydatif pertinent pour la MP. Ces données sont en accord avec l'hypothèse selon laquelle le domaine axonal, et en particulier le nombre de sites de libération de neurotransmetteurs par neurone, est un facteur important qui contribue à rendre un neurone sélectivement vulnérable dans le contexte de la MP. Enfin, nous présentons une méthode d’analyse d’image open-source visant à aider les biologistes et les neuroscientifiques à automatiser la quantification du nombre de neurones dans des cultures primaires de neurones, telle qu’utilisée dans les travaux de cette thèse. Nous proposons que cet algorithme simple — mais robuste — permettra aux biologistes d'automatiser le comptage des neurones avec une grande précision, quelque chose de difficile à effectuer avec les autres approches open-source disponibles présentement. Nous espérons que les travaux présentés dans cette thèse permettront de contribuer à raffiner les théories visant à expliquer l’origine de la MP et à terme, de développer de nouvelles approches thérapeutiques.Neurodegenerative diseases are typically characterized based on their symptoms, and pathological factors identified after death. The disease-specific symptoms are due to the dysfunction and degeneration of specific subpopulations of neurons, which cause dysfunction in particular brain functions. Parkinson's disease (PD) is a neurodegenerative disease primarily characterized by motor symptoms due to the specific degeneration of dopamine (DA) neurons of the substantia nigra pars compacta (SNpc/SNc): a population of neurons essential for motor control. SNc DA neurons are, however, not the only population of neurons that degenerate in PD. Post-mortem analysis, in vivo imaging, and clinical symptoms demonstrate that dysfunction and degeneration occur in several other neuronal nuclei. These include, but are not limited to, noradrenergic (NA) locus coeruleus (LC) neurons, serotonin neurons of the raphe nuclei, and cholinergic neurons of the dorsal motor nucleus of the vagus (DMV) and pedunculopontine nucleus. Like other neurodegenerative diseases, PD is linked to several risk factors, both genetic and environmental. The evidence suggests that these risk factors are associated with the dysfunction in systems of cellular bioenergetics (including mitochondrial function); proteostatic homeostasis; endolysosomal function; an imbalance between the production of reactive oxidative species (ROS), and antioxidant mechanisms; calcium homeostasis; alpha-synuclein misfolding; and neuroinflammation. Consequently, together with aging, these risk factors converge on causing the selective degeneration of "PD-vulnerable" nuclei. What makes these neurons intrinsically vulnerable to PD-associated risk factors is a fundamental question — and understanding these neurons will reveal biological mechanisms that we can target to protect these cells from degeneration. Our best hypotheses to explain why these neurons are based on the observations that most PD- vulnerable neurons are long-range projection neuromodulatory neurons sharing common characteristics: projecting to voluminous territories, having very long and highly branched unmyelinated axonal domains with vast numbers of neurotransmitter release sites, and exhibiting a unique physiology such as pacemaker firing. Taken together, this suggests that these neurons function at the tail-end of their bioenergetic and homeostatic capacity, unable to tolerate any further demands, such as those incurred in the presence of risk factors associated with PD. In this thesis, I will present a systematic review on the literature on purported cell loss in PD brains, showing that — given the actual primary evidence — the precise neurochemical identity of neurons that degenerate in PD, and the temporal order of this degeneration, is far less clear than described by most publications. This review — at the time of writing — has gone on to be highly cited. However, analyzing the claims made in publications citing this review, we discover that the majority of claims do not reflect the core message of our publication. Since the identity of PD-vulnerable and non-PD-vulnerable neurons is fundamental to theory and hypotheses when trying to understand PD, we follow this first publication with a letter restating the importance to address our observations. We then present in vitro data showing that classically PD-vulnerable neurons, when compared to non-PD vulnerable neurons, have an intrinsic capacity to develop larger and more complex axonal domains, with higher numbers of active neurotransmitter release sites. Moreover, we find that these observations correlate to elevated vulnerability to PD-relevant stress assays. These data provide additional support for the hypothesis that the axonal domain — and in particular — the number of active neurotransmitter sites per neuron, is a cell-autonomous factor rendering a neuron selectively vulnerable in the context of PD. Finally, we present an open-source tool to support biologists and neuroscientists in automating the quantification of neuron numbers in medium-throughput primary cell cultures. Where the application of other open-source solutions is either too simplistic for the use-case or technically challenging to implement, this simple — yet robust algorithm — allows biologists with limited computational nous to automate neuron counting with high precision. We hope that the work presented in this thesis will contribute to the refinement of theories aimed at explaining the origin of PD and, ultimately, to the development of new therapeutic approaches